Introduction – Exploring life : The Science of Biology
I.
Biology is Studied Using the Scientific Method
A. Science is based on a systematic thought process.
1. Deductive reasoning - Summarize the information at hand and draw conclusions from that information; proceeds from
the general to the specific.
2. Inductive reasoning - Drawing a generalization from several specific observations; proceeds from the specific to the
general. Must be careful, because it is impossible to prove the accuracy of the generalization.
B. Observations, testable models, and experiments
1. The scientific method is a recursive process for discovering knowledge that involves making observations, making
testable models, and conducting experiments.
2. First step involves collecting information and/or summarizing existing observations about the phenomenon under
study.
3. This permits the formulation of a hypothesis, a testable model that explains the existing observations and makes
predictions that can be tested.
4. An experiment is conducted to test the correctness of the hypothesis
 Experimental or treatment group - the individuals given the specific treatment or condition being tested
 Control group - the individuals not given the specific treatment
5. Observation and measurement of the experimental and control groups and comparison of the data obtained provides
evidence to either support or reject the hypothesis.
6. Care must be taken that the experimental and control groups receive the same treatments except for the specific effect
being tested. Example: the placebo effect.
7. The recursive nature of the process: experiments provide more observations, and at any time more observations may be
added in and more testable models may be produced; this may in turn lead to more experiments, and the process
continues. This generally leads to progress towards more and more reliable models of how nature works. Creative
thinking often plays a major role when rapid progress occurs.
C. Hypothesis, theory, and law
1. A well supported hypothesis that links together a large body of observations is considered a theory.
2. A theory that links together significant bodies of thought and yields unvarying and uniform predictions over a long
period of time becomes considered a principle or law.
D. The supernatural, by definition, is outside the bounds of science. Supernatural causes and effects cannot be proved or
disproved.
E. science and technology – the goal of science is to understand nature; the goal of technology is to apply scientific knowledge
for a specific purpose
II. Characteristics of Living Matter
A. Living things are composed of cells.
1. Cell - The basic structural and functional unit of life consisting of living material bounded by a membrane. The smallest
unit of living things capable of growth and development.
2. Unicellular - An organism consisting of a single cell.
3. Multicellular - An organism consisting of more than one cell.
B. Living things grow and develop.
1. Growth-increase in size because number of cells or size of cells increases.
2. Development-changes in roles of cells during the life cycle of an organism.
C. Metabolism includes the chemical processes essential to growth and repair.
1. Metabolism - the sum of the chemical reactions and energy transformations that take place within a cell.
2. Homeostasis - the tendency of an organism to maintain a relatively constant internal environment.
D. Living things respond to stimuli (stimulus - physical or chemical changes in the internal or external environment of an
organism)
E. Living things reproduce.
1. Asexual reproduction – copying; reproduction not involving sex (genetic recombination); resulting from only cell
division.
2. Sexual reproduction – reproduction involving sex; typically involves the formation of specialized egg and sperm cells
and their fusion to produce a zygote which grows and develops into a new organism.
III. Information Transfer in Living Systems
A. Information must be transferred from one generation to the next.
1. DNA (deoxyribonucleic acid) is responsible for information transfer from one generation to the next.
2. DNA is the chemical substance that makes up genes, the units of heredity.
B. Information must be transferred from one cell generation to the next.
C. Information is exchanged between cells.
1. Hormones are chemical signals used for intercellular signaling.
2.
Physical signals also lead to intercellular communication, e.g. nerve cells.
IV. Biological Organisms Show Great Diversity
A. Biologists use a binomial system for classifying organisms.
1. Taxonomy - the science of classifying and naming organisms.
2. Carolus Linnaeus (18th century Swedish botanist) developed a system of classification that is the basis of what is used
today
3. Species - basic unit of classification or taxonomy
 if sexual, a group of organisms that can interbreed and produce fertile offspring
 if asexual, grouped based on similarities (DNA sequence is best)
 about 1.8 million living species have been described, likely millions more
4. Genus - a group of closely related species.
5. Together the genus and specific epithet names make up the binomial name used to name a species
 The Genus name is always capitalized, and the specific epithet is never capitalized.
 The Genus and specific epithet are always together, and italicized (or underlined).
 Example: Homo sapiens or Homo sapiens
B. Taxonomic classification is hierarchical.
1. A group of related genera make up a Family.
2. Related families make up an Order.
3. Related orders are grouped into a Class.
4. Related classes are grouped into a Phylum or Division.
5. Related phyla or divisions are grouped into a Kingdom.
6. Related kingdoms are grouped into a Domain, the highest level of classification in the modern system.
7. The gold standard for “related” is based on DNA sequence similarities, but other criteria are used as well (we don’t have
the complete DNA sequence of all known species)
C. The most widely accepted classification system today includes three domains and six kingdoms
1. Two domains consist of prokaryotes, organisms with no true cellular nucleus
 Domain Archaea – Kingdom Archaebacteria – bacteria typically found in extreme environments; distinguished
from other bacteria mainly by ribosomal RNA sequence; include methanogens, extreme halophiles, and extreme
thermophiles
 Domain Bacteria – Kingdom Eubacteria – very diverse group of bacteria; examples: blue-green algae, Escherichia
coli
2. One domain, Eukarya, consists of eukaryotes, organisms with a discrete cellular nucleus; it is divided into four
kingdoms:
 Kingdom Protista – Single celled and simple multicellular organisms having nuclei, and not fitting into the other
three eukaryotic kingdoms. Includes protozoa, algae, water molds, and slime molds.
 Kingdom Plantae – Plants are complex multicellular organisms having tissues and organs. Plant cells have walls
containing cellulose as the main structural component. Most are photosynthetic, and those that are have
chlorophyll in chloroplasts.
 Kingdom Fungi – Organisms with cell walls containing chitin as the main structural component. Most are
multicellular. Most are decomposers. Includes molds and yeasts as well as mushrooms, etc.
 Kingdom Animalia – Complex multicellular organisms that must eat other organisms for nourishment. No cells
walls. Typically have organs and organ systems. Most forms are motile.
V. Life Depends on a Continuous Input of Energy
A. At the cellular level part of the energy that is obtained from nutrients is utilized to synthesize new cellular components.
1. Used for maintenance of existing cellular structures and components (replacement of damaged or worn out materials
within the cell)
2. Used to produce materials to support growth, development, and reproduction
B. Part of the energy obtained from nutrients is used to support:
1. Movement, either of cell itself or of materials into and out of the cell
2. Signaling responses, such as hormone production and perception, nerve impulses, etc.
3. Other forms of cell work, such as symbiotic relationships with other organisms, defense against pathogens
C. Energy flows through ecosystems (the concept of a food chain or food web).
1. Producers (autotrophs) manufacture their own food from simple materials
 usually produce food by the process of photosynthesis:
Carbon dioxide + Water + light energy ───> Carbohydrate (food) + Oxygen
 use such food by oxidative respiration
Carbohydrate (food) + Oxygen ───> Carbon dioxide + Water + energy
 overall, producers use carbon dioxide and water and release food and oxygen
2.
3.
Consumers (heterotrophs) obtain energy by eating other organisms (ultimate source of food is producers); use food and
oxygen, and release carbon dioxide and water
Decomposers obtain energy by breaking down the waste products, by products, and dead bodies of producers and
consumers. Usually bacteria and fungi.
VI. Themes that pervade biology
A. The cell
B. Information management
C. Energy management
D. Structure and function
E. Unity and diversity
F. Emergent properties
G. Evolution – the core unifying theme
Chapter 1: Introduction – The Science of Biology
1. Discuss in your group how the scientific method works, and the difference
between inductive and deductive reasoning. Come up with examples of
inductive and deductive reasoning. Do NOT worry about learning the
scientific method as “step one – step two – etc.”
2. Discuss testable models, including terms for them and why “testable”
matters. How does this relate to the supernatural?
3. Explain the characteristics of living matter to each other.
“Fido” question (will be given in class).
Answer the
4. Discuss the role of information in life, and how it is dealt with (on the
molecular level).
5. Explain to each other the binomial system and taxonomic hierarchy. What
is a species name? What do the two words in a species name represent, and
how do you write them? How will you memorize the hierarchy?
6. What are the three domains and six kingdoms? How do you decide which
kingdom to put a eukaryote into?
7. What is the importance of energy in living systems? What are autotrophs
and heterotrophs?
VII. Biology is Studied Using the Scientific Method
A. Science is based on a systematic thought process.
1.
Deductive reasoning - Summarize the information at hand and draw conclusions from that information; proceeds from
the general to the specific.
2.
Inductive reasoning - Drawing a generalization from several specific observations; proceeds from the specific to the
general. Must be careful, because it is impossible to prove the accuracy of the generalization.
B. Observations, testable models, and experiments
1.
The scientific method is a recursive process for discovering knowledge that involves making observations, making
testable models, and conducting experiments.
2.
First step involves collecting information and/or summarizing existing observations about the phenomenon under
study.
3.
This permits the formulation of a hypothesis, a testable model that explains the existing observations and makes
predictions that can be tested.
4.
5.
An experiment is conducted to test the correctness of the hypothesis

Experimental or treatment group - the individuals given the specific treatment or condition being tested

Control group - the individuals not given the specific treatment
Observation and measurement of the experimental and control groups and comparison of the data obtained provides
evidence to either support or reject the hypothesis.
6.
Care must be taken that the experimental and control groups receive the same treatments except for the specific effect
being tested. Example: the placebo effect.
7.
The recursive nature of the process: experiments provide more observations, and at any time more observations may be
added in and more testable models may be produced; this may in turn lead to more experiments, and the process
continues. This generally leads to progress towards more and more reliable models of how nature works. Creative
thinking often plays a major role when rapid progress occurs.
C. Hypothesis, theory, and law
1.
A well supported hypothesis that links together a large body of observations is considered a theory.
2.
A theory that links together significant bodies of thought and yields unvarying and uniform predictions over a long
period of time becomes considered a principle or law.
D. The supernatural, by definition, is outside the bounds of science. Supernatural causes and effects cannot be proved or
disproved.
E. science and technology – the goal of science is to understand nature; the goal of technology is to apply scientific knowledge
for a specific purpose
VIII.
Characteristics of Living Matter
A. Living things are composed of cells.
1.
Cell - The basic structural and functional unit of life consisting of living material bounded by a membrane. The smallest
unit of living things capable of growth and development.
2.
Unicellular - An organism consisting of a single cell.
3.
Multicellular - An organism consisting of more than one cell.
B. Living things grow and develop.
1.
Growth-increase in size because number of cells or size of cells increases.
2.
Development-changes in roles of cells during the life cycle of an organism.
C. Metabolism includes the chemical processes essential to growth and repair.
1.
Metabolism - the sum of the chemical reactions and energy transformations that take place within a cell.
2.
Homeostasis - the tendency of an organism to maintain a relatively constant internal environment.
D. Living things respond to stimuli (stimulus - physical or chemical changes in the internal or external environment of an
organism)
E. Living things reproduce.
1.
Asexual reproduction – copying; reproduction not involving sex (genetic recombination); resulting from only cell
division.
2.
Sexual reproduction – reproduction involving sex; typically involves the formation of specialized egg and sperm cells
and their fusion to produce a zygote which grows and develops into a new organism.
IX. Information Transfer in Living Systems
A. Information must be transferred from one generation to the next.
1.
DNA (deoxyribonucleic acid) is responsible for information transfer from one generation to the next.
2.
DNA is the chemical substance that makes up genes, the units of heredity.
B. Information must be transferred from one cell generation to the next.
C. Information is exchanged between cells.
1.
Hormones are chemical signals used for intercellular signaling.
2.
Physical signals also lead to intercellular communication, e.g. nerve cells.
X. Biological Organisms Show Great Diversity
A. Biologists use a binomial system for classifying organisms.
1.
Taxonomy - the science of classifying and naming organisms.
2.
Carolus Linnaeus (18th century Swedish botanist) developed a system of classification that is the basis of what is used
today
3.
Species - basic unit of classification or taxonomy

if sexual, a group of organisms that can interbreed and produce fertile offspring

if asexual, grouped based on similarities (DNA sequence is best)

about 1.8 million living species have been described, likely millions more
4.
Genus - a group of closely related species.
5.
Together the genus and specific epithet names make up the binomial name used to name a species

The Genus name is always capitalized, and the specific epithet is never capitalized.

The Genus and specific epithet are always together, and italicized (or underlined).

Example: Homo sapiens or Homo sapiens
B. Taxonomic classification is hierarchical.
1.
A group of related genera make up a Family.
2.
Related families make up an Order.
3.
Related orders are grouped into a Class.
4.
Related classes are grouped into a Phylum or Division.
5.
Related phyla or divisions are grouped into a Kingdom.
6.
Related kingdoms are grouped into a Domain, the highest level of classification in the modern system.
7.
The gold standard for “related” is based on DNA sequence similarities, but other criteria are used as well (we don’t have
the complete DNA sequence of all known species)
C. The most widely accepted classification system today includes three domains and six kingdoms
1.
Two domains consist of prokaryotes, organisms with no true cellular nucleus

Domain Archaea – Kingdom Archaebacteria – bacteria typically found in extreme environments; distinguished
from other bacteria mainly by ribosomal RNA sequence; include methanogens, extreme halophiles, and extreme
thermophiles

Domain Bacteria – Kingdom Eubacteria – very diverse group of bacteria; examples: blue-green algae, Escherichia
coli
2.
One domain, Eukarya, consists of eukaryotes, organisms with a discrete cellular nucleus; it is divided into four
kingdoms:

Kingdom Protista – Single celled and simple multicellular organisms having nuclei, and not fitting into the other
three eukaryotic kingdoms. Includes protozoa, algae, water molds, and slime molds.

Kingdom Plantae – Plants are complex multicellular organisms having tissues and organs. Plant cells have walls
containing cellulose as the main structural component. Most are photosynthetic, and those that are have
chlorophyll in chloroplasts.

Kingdom Fungi – Organisms with cell walls containing chitin as the main structural component. Most are
multicellular. Most are decomposers. Includes molds and yeasts as well as mushrooms, etc.

Kingdom Animalia – Complex multicellular organisms that must eat other organisms for nourishment. No cells
walls. Typically have organs and organ systems. Most forms are motile.
XI. Life Depends on a Continuous Input of Energy
A. At the cellular level part of the energy that is obtained from nutrients is utilized to synthesize new cellular components.
1.
Used for maintenance of existing cellular structures and components (replacement of damaged or worn out materials
within the cell)
2.
Used to produce materials to support growth, development, and reproduction
B. Part of the energy obtained from nutrients is used to support:
1.
Movement, either of cell itself or of materials into and out of the cell
2.
Signaling responses, such as hormone production and perception, nerve impulses, etc.
3.
Other forms of cell work, such as symbiotic relationships with other organisms, defense against pathogens
C. Energy flows through ecosystems (the concept of a food chain or food web).
1.
Producers (autotrophs) manufacture their own food from simple materials

usually produce food by the process of photosynthesis:
Carbon dioxide + Water + light energy ───> Carbohydrate (food) + Oxygen

use such food by oxidative respiration
Carbohydrate (food) + Oxygen ───> Carbon dioxide + Water + energy

2.
overall, producers use carbon dioxide and water and release food and oxygen
Consumers (heterotrophs) obtain energy by eating other organisms (ultimate source of food is producers); use food and
oxygen, and release carbon dioxide and water
3.
Decomposers obtain energy by breaking down the waste products, by products, and dead bodies of producers and
consumers. Usually bacteria and fungi.
XII. Themes that pervade biology
A. The cell
B. Information management (heritable information, regulation, and interaction with the environment)
C. Energy management
D. Structure and function
E. Unity and diversity
F.
Emergent properties
G. Evolution – the core unifying theme that explains much of the observations connected with the other themes
H. In addition, an awareness of the process scientific inquiry and the application of science (technology) are important aspects of
any study of biology.
Chapter 2: The chemical context of life
You must understand chemistry to understand life (and to pass this course)!
Overview: In many ways, life can be viewed as a complicated chemical reaction. Modern models of how life works at all levels
typically have at least some aspect of chemistry as a major component or underpinning.
I.
Elements and Atoms
A. elements – substances that cannot be further broken down into other substances (at least by ordinary chemical reactions)
1. every element has a chemical symbol (H for hydrogen, O for oxygen, etc.); this is most familiar from the periodic table
2. there are 92 naturally occurring elements, from hydrogen up to uranium
 4 elements (oxygen, carbon, hydrogen, and nitrogen = O, C, H, N) make about 96% of the mass of most living
things
 8 others are consistently present in small amounts in living things (Ca, P, K, S, Na, Mg, Cl, Fe)
 several others are typically found only in trace amounts (trace elements); these tend to vary considerably in amount
and even presence depending on the type of organism
B. an atom is the smallest unit of an element that still retains the properties of that element
C. atoms consist of subatomic particles
1. electron - contributes no significant mass to the atom, but carries a (-1) electrical charge
2. proton - contributes a mass of approximately 1 mass unit, and carries a (+1) electrical charge
3. neutron - contributes a mass of approximately 1 mass unit, and carries no net electrical charge
4. protons and neutrons are found in the nucleus (center) of an atom
5. elements differ from each other because they contain different numbers of protons (all hydrogen atoms contain 1 proton,
all carbon atoms contain 6 protons, all oxygen atoms contain 8 protons, etc.)
 atomic number = number of protons in the nucleus
 the periodic table has elements arranged largely according to atomic number
6. protons + neutrons determine atomic mass
 each contribute ~1 atomic mass unit (amu, or Dalton)
 atoms that have the same number of protons but have different numbers of neutrons (therefore different masses) are
referred to as isotopes
D. atomic nuclei can undergo changes (decay)
1. some elements are more stable than others
2. some isotopes are more stable than others (most unstable = radioisotopes)
3. decay rates are statistical averages, and are used for measuring time passage in many areas of science (carbon dating,
etc.)
4. the radiation emitted upon decay (alpha, beta, and/or gamma) can be used as a tool for experiments; can also be used
medically; has other uses and dangers (nuclear power, nuclear bombs, radiation poisoning, etc.)
5. radiation can cause mutations in DNA, can interfere with cell division
E. electrons occupy orbitals surrounding the nucleus and move at the speed of light
1. because ATOMS are electrically neutral the number of electrons an atom has always equals the number of protons
2. electrons can exist at different energy levels, which correspond to orbitals
 the further away an orbital carries an electron from the nucleus, the higher the energy level of the electron
 electrons with similar energies make up an electron shell
3. the outer electron(s) are known as the valence electron(s); collectively, they occupy the valence shell
F.
4. the chemical properties of an atom are largely determined by the valence electrons
the science of chemistry mostly involves study of how electrons move about the nucleus, store energy, and determine
chemical properties of substances as a result
II. Describing Atomic Combinations
A. atoms combine to form molecules and compounds
1. molecule – two or more atoms held together by covalent bonds (defined later)
 may be composed of one or more elements (examples: O2, H2O)
 not all substances are molecular (NaCl, table salt, isn’t)
 if a substance is molecular, then an individual molecule is the smallest unit of the substance that exhibits the
properties of the substance
 thus, a molecule differs in its physical and chemical properties from the elements that make it up
2. compound - a specific combination of two or more different elements chemically combined in a fixed ratio
 compounds have unique physical and chemical properties that differ from those of the elements used to make it
 some compounds are held together by covalent bonds and are therefore molecular; some are held together by ionic
bonds (defined later)
B. chemists use two types of formulas to describe substances
1. chemical formula - a shorthand formula showing the number of atoms of each element present in a molecule
 often called molecular formula if a molecule is involved; examples: H 2O, CO2, O2, C6H12O6
 follows simplest ratio for ionic substances (NaCl, etc.)
2. structural formula - shows the arrangement of atoms in a molecule
 examples:
 water
H─O─H
 carbon dioxide
O═C═O
 molecular oxygen
O═O
C. the number of units of a substance are described using the mole
1. molecular mass is the sum of the atomic masses of the atoms in the molecule
2. since the actual mass of an atom is extremely small, it is convenient in the real world to work with a large number of
atoms at the same time
3. The amount of a substance that in grams has the same number as the atomic mass is a mole
4. Thus, water has molecular mass 1+1+16 = 18; a mole of water has a mass of 18 g
5. The mole is simply a conversion factor from the small scale of atomic mass units to the more familiar gram scale
 the factor represents the number of units (molecules or atoms) in a mole
 this factor, called Avogadro’s number, is 6.02 x 1023 atoms or molecules
III. Chemical Bonds Hold Molecules Together and Store Energy
A. recall that electrons in the outermost shell of an atom (valence electrons) determine the chemical behavior of the atom, i.e.
what type and how many chemical bonds it can readily form
B. most atoms in biological systems seek to have 8 electrons in their outermost shell (hydrogen seeks to have 0 or 2 electrons in
its outermost shell)
C. since atoms have the same number of electrons as protons, they meet this need to have a full valence shell by sharing, giving
up, or acquiring electrons from other atoms; this forms chemical bonds
1. a chemical bond is a reduced energy state
2. bond energy is the amount of energy required to break a particular chemical bond
D. there are two principle types of strong chemical bonds
1. covalent bonds - electrons are shared between two atoms
2. ionic bonds - one atom completely gives up an electron to another atom
E. covalent bonds
1. result in filled valence shells
2. electrons are shared in pairs
3. a single electron pair shared = a single covalent bond
4. double and triple covalent bonds are also possible
5. carbon forms 4 covalent bonds
6. covalent bonds give molecules definite shapes
 the shared atomic orbitals require definite spatial arrangements that depend on the atoms involved in the bond
7. covalent bonds can be nonpolar (equal sharing of electrons) or polar (unequal sharing of electrons)
 polar bonds result if one nucleus holds a stronger attraction on the electron pair
 molecules with polar bonds (polar molecules) have regions with partial charges
F. ionic bonds
1. when an atom gains or gives up one or more electrons, it is called an ion
 cations - ions that have lost one or more electrons; have a positive charge

anions - ions that have gained one or more electrons; have a negative charge
 the suffix –ide indicates an anion
2. polyatomic ions can also form
 covalently bound atoms that lose or gain electrons or protons
 only polyatomic ions can lose or gain protons
 polyatomic cations = positive charge; polyatomic anions = negative charge
3. an ionic bond is formed by the attraction between a cation and an anion
4. an ionic compound is a substance held together by ionic bonds
 ionic compounds dissociate into individual ions when dissolved in a polar substance, such as water
 hydration – surrounding the ions with the ends water molecules with the opposite (partial) charge
G. hydrogen bonds
1. weak interactions involving partially (+) charged hydrogen atoms
2. the interaction is with another atom with a partial (-) charge
3. can be within the same (large) molecule, or between molecules
4. hydrogen bonds are common and important in living things
 water forms hydrogen bonds
 because they are weak, hydrogen bonds are relatively easy to manipulate
 collectively, hydrogen bonds can be very strong – they hold together the two strands of DNA, for example
H. In aqueous systems (such as living organisms), the effective relative bond strengths are:
covalent bond > ionic bond > hydrogen bond
IV. Chemical Equations Describe Chemical Reactions
A. Reactants are written on the left
B. Products are written on the right
C. an arrow (
) is used to show the direction the reaction proceeds
C6H12O6 + 6 O2
6 CO2 + 6 H2O + Energy
D. double arrows of equal lengths (
rates in both directions)
N2 + 3 H 2
) indicate equilibrium reactions (reactions proceeding simultaneously at equal
2 NH3
E. Sometimes, different lengths of double arrows are used to indicate which direction is favored
CO2 + H2O
H2CO3
V. Oxidation-Reduction Reactions (redox reactions) Are Common in Biological Systems
A. oxidation is a chemical process in which an atom, molecule, or ion loses an electron(s)
B. reduction is the opposite – an electron is gained (charge is reduced)
C. oxidation and reduction are always paired (hence redox reactions)
D. example: rusting
1. when iron rusts, iron oxide is formed by the oxidation of iron; this can be described by a chemical reaction as shown
below:

2.
2 Fe2O3
during the process iron atoms (Fe) become iron ions (Fe 3+):

3.
4.
4 Fe + 3 O2
4 Fe
4 Fe3+ + 12 e-
therefore, we can say that iron atoms were oxidized to produce iron ions above
on the flip side, the oxygen atoms gain electrons; we can say that the oxygen is reduced in the reaction:

3 O2 + 12 e-
6 O2-
E. oxygen is the most common oxidizing agent (hence the general term oxidation)
F. in biological systems, typically molecules are oxidized and reduced
1. very important in many processes such as photosynthesis, respiration
2. electrons are less easily lost from molecules than from atoms


molecules typically will lose the equivalent of a complete hydrogen atom when oxidized
this means that both a proton and an electron are removed from the oxidized molecule and may be added to the
reduced molecule
Chapter 2: You must understand chemistry to understand life
8. Describe the difference between the terms “element” and “atom”. What are
chemical symbols, and what is the periodic table?
9. Draw a model of a neutral atom with atomic number 6 and atomic mass 12,
and compare with your groupmates.
10. Draw a model of a neutral atom with atomic number 6 and atomic mass
14, and compare with your groupmates. Then compare with the previous
atom that you drew and discuss isotopes.
11. What are electron orbitals? What is the valence shell? How does the
valence shell relate to chemical reactivity of an atom?
12. As a group, draw a Venn diagram for the following terms: molecule,
compound. Then place the following in the diagram: O2, NaCl, H2O
13. Discuss moles, atomic mass units, and Avogadro’s number. Why use
moles instead of just mass? Discuss the water and glucose problem.
14. What is a covalent bond? What do polar and nonpolar mean for covalent
bonds? Give an example of each.
15. What are ions? What are cations and anions? What is an ionic bond?
Give an example.
16. What are hydrogen bonds? Draw an example.
17. Discuss the chemical equations in the notes and the terms there (reactant,
product, equilibrium).
18. What is a redox reaction, and how does it relate to movement of electrons
and movement of energy? What gets oxidized/reduced in the following:
making NaCl; rusting iron What gains/loses energy in each case?
Overview: In many ways, life can be viewed as a complicated chemical reaction. Modern models of how life works at all levels
typically have at least some aspect of chemistry as a major component or underpinning.
VI. Elements and Atoms
A. elements – substances that cannot be further broken down into other substances (at least by ordinary chemical reactions)
1.
every element has a chemical symbol (H for hydrogen, O for oxygen, etc.); this is most familiar from the periodic table
2.
there are 92 naturally occurring elements, from hydrogen up to uranium

4 elements (O, C, H, N) make about 96% of the mass of most living things

8 others are consistently present in small amounts in living things (Ca, P, K, S, Na, Mg, Cl, Fe)

several others are typically found only in trace amounts (trace elements); these tend to vary considerably in amount
and even presence depending on the type of organism
B. an atom is the smallest unit of an element that still retains the properties of that element
C. atoms consist of subatomic particles
1.
electron - contributes no significant mass to the atom, but carries a (-1) electrical charge
2.
proton - contributes a mass of approximately 1 mass unit, and carries a (+1) electrical charge
3.
neutron - contributes a mass of approximately 1 mass unit, and carries no net electrical charge
4.
protons and neutrons are found in the nucleus (center) of an atom
5.
elements differ from each other because they contain different numbers of protons (all hydrogen atoms contain 1 proton,
all carbon atoms contain 6 protons, all oxygen atoms contain 8 protons, etc.)
6.

atomic number = number of protons in the nucleus

the periodic table has elements arranged largely according to atomic number
protons + neutrons determine atomic mass

each contribute ~1 atomic mass unit (amu, or Dalton)

atoms that have the same number of protons but have different numbers of neutrons (therefore different masses) are
referred to as isotopes
D. atomic nuclei can undergo changes (decay)
1.
some elements are more stable than others
2.
some isotopes are more stable than others (most unstable = radioisotopes)
3.
decay rates are statistical averages; used for measuring time passage in many areas of science (carbon dating, etc.)
4.
the radiation emitted upon decay (alpha, beta, and/or gamma) can be used as a tool for experiments; can also be used
medically; has other uses and dangers (nuclear power, nuclear bombs, radiation poisoning, etc.)
5.
radiation can cause mutations in DNA, can interfere with cell division
E. electrons occupy orbitals surrounding the nucleus and move at the speed of light
F.
1.
because ATOMS are electrically neutral the number of electrons an atom has always equals the number of protons
2.
electrons can exist at different energy levels, which correspond to orbitals

the further away an orbital carries an electron from the nucleus, the higher the energy level of the electron

electrons with similar energies make up an electron shell
3.
the outer electron(s) are known as the valence electron(s); collectively, they occupy the valence shell
4.
the chemical properties of an atom are largely determined by the valence electrons
the science of chemistry mostly involves study of how electrons move about the nucleus, store energy, and determine
chemical properties of substances as a result
VII. Describing Atomic Combinations
A. atoms combine to form molecules and compounds
1.
molecule – two or more atoms held together by covalent bonds (defined later)

may be composed of one or more elements (examples: O2, H2O)

not all substances are molecular (NaCl, table salt, isn’t)

if a substance is molecular, then an individual molecule is the smallest unit of the substance that exhibits the
properties of the substance

2.
thus, a molecule differs in its physical and chemical properties from the elements that make it up
compound - a specific combination of two or more different elements chemically combined in a fixed ratio

compounds have unique physical and chemical properties that differ from those of the elements used to make it

some compounds are held together by covalent bonds and are therefore molecular; some are held together by ionic
bonds (defined later)
B. chemists use two types of formulas to describe substances
1.
2.
chemical formula - a shorthand formula showing the number of atoms of each element present in a molecule

often called molecular formula if a molecule is involved; examples: H 2O, CO2, O2, C6H12O6

follows simplest ratio for ionic substances (NaCl, etc.)
structural formula - shows the arrangement of atoms in a molecule

examples:

water
H─O─H

carbon dioxide
O═C═O

molecular oxygen
O═O
C. the number of units of a substance are described using the mole
1.
molecular mass is the sum of the atomic masses of the atoms in the molecule
2.
since the actual mass of an atom is extremely small, it is convenient in the real world to work with a large number of
atoms at the same time
VIII.
3.
The amount of a substance that in grams has the same number as the atomic mass is a mole
4.
Thus, water has molecular mass 1+1+16 = 18; a mole of water has a mass of 18 g
5.
The mole is simply a conversion factor from the small scale of atomic mass units to the more familiar gram scale

the factor represents the number of units (molecules or atoms) in a mole

this factor, called Avogadro’s number, is 6.02 x 1023 atoms or molecules
Chemical Bonds Hold Molecules Together and Store Energy
A. recall that electrons in the outermost shell of an atom (valence electrons) determine the chemical behavior of the atom, i.e.
what type and how many chemical bonds it can readily form
B. most atoms in biological systems seek to have 8 electrons in their outermost shell (hydrogen seeks to have 0 or 2 electrons in
its outermost shell)
C. since atoms have the same number of electrons as protons, they meet this need to have a full valence shell by sharing, giving
up, or acquiring electrons from other atoms; this forms chemical bonds
1.
a chemical bond is a reduced energy state
2.
bond energy is the amount of energy required to break a particular chemical bond
D. there are two principle types of strong chemical bonds
1.
covalent bonds - electrons are shared between two atoms
2.
ionic bonds - one atom completely gives up an electron to another atom
E. covalent bonds
1.
result in filled valence shells
2.
electrons are shared in pairs
3.
a single electron pair shared = a single covalent bond
4.
double and triple covalent bonds are also possible
5.
carbon forms 4 covalent bonds
6.
covalent bonds give molecules definite shapes

7.
F.
the shared atomic orbitals require definite spatial arrangements that depend on the atoms involved in the bond
covalent bonds can be nonpolar (equal sharing of electrons) or polar (unequal sharing of electrons)

polar bonds result if one nucleus holds a stronger attraction on the electron pair

molecules with polar bonds (polar molecules) have regions with partial charges
ionic bonds
1.
when an atom gains or gives up one or more electrons, it is called an ion

cations - ions that have lost one or more electrons; have a positive charge

anions - ions that have gained one or more electrons; have a negative charge

2.
the suffix –ide indicates an anion
polyatomic ions can also form

covalently bound atoms that lose or gain electrons or protons

only polyatomic ions can lose or gain protons

polyatomic cations = positive charge; polyatomic anions = negative charge
3.
an ionic bond is formed by the attraction between a cation and an anion
4.
an ionic compound is a substance held together by ionic bonds

ionic compounds dissociate into individual ions when dissolved in a polar substance, such as water

hydration – surrounding the ions with the ends water molecules with the opposite (partial) charge
G. hydrogen bonds
1.
weak interactions involving partially (+) charged hydrogen atoms
2.
the interaction is with another atom with a partial (-) charge
3.
can be within the same (large) molecule, or between molecules
4.
hydrogen bonds are common and important in living things

water forms hydrogen bonds

because they are weak, hydrogen bonds are relatively easy to manipulate

collectively, hydrogen bonds can be very strong – they hold together the two strands of DNA, for example
H. In aqueous systems (such as living organisms), the typical relative bond strengths are:
covalent bond > ionic bond > hydrogen bond
IX. Chemical Equations Describe Chemical Reactions
A. Reactants are written on the left
B. Products are written on the right
C. an arrow (
) is used to show the direction the reaction proceeds
C6H12O6 + 6 O2
6 CO2 + 6 H2O + Energy
D. double arrows of equal lengths (
) indicate equilibrium reactions (reactions proceeding simultaneously at equal
rates in both directions)
N2 + 3 H 2
2 NH3
E. Sometimes, different lengths of double arrows are used to indicate which direction is favored
CO2 + H2O
H2CO3
X. Oxidation-Reduction Reactions (redox reactions) Are Common in Biological Systems
A. oxidation is a chemical process in which an atom, molecule, or ion loses an electron(s)
B. reduction is the opposite – an electron is gained (charge is reduced)
C. oxidation and reduction are always paired (hence redox reactions)
D. example: rusting
1.
when iron rusts, iron oxide is formed by the oxidation of iron; this can be described by a chemical reaction as shown
below:

2.
4 Fe + 3 O2
2 Fe2O3
during the process iron atoms (Fe) become iron ions (Fe 3+):

4 Fe
4 Fe3+ + 12 e-
3.
therefore, we can say that iron atoms were oxidized to produce iron ions above
4.
on the flip side, the oxygen atoms gain electrons; we can say that the oxygen is reduced in the reaction:

3 O2 + 12 e-
6 O2-
E. oxygen is the most common oxidizing agent (hence the general term oxidation)
F.
in biological systems, typically molecules are oxidized and reduced
1.
very important in many processes such as photosynthesis, respiration
2.
electrons are less easily lost from molecules than from atoms

molecules typically will lose the equivalent of a complete hydrogen atom when oxidized

this means that both a proton and an electron are removed from the oxidized molecule and may be added to the
reduced molecule

thus, counting charge changes is not sufficient for analyzing redox reactions – look for movement of electrons in
redox reactions involving biological molecules
Chapter 3: Water and the fitness of the environment : What’s so great about water?
Overview: Life as we know it requires water. All organisms that we know of are made mostly of liquid water, and most of their
metabolism requires an aqueous medium. In addition, many organisms live in liquid water or in an environment dominated by water
in its various states (solid, liquid, or gas). Some numbers:
 cells are typically 70% or more water by mass
 about 75% of the Earth’s surface is covered by liquid water
But then, just being common on the Earth doesn’t make something essential for life. A large percentage of the Earth’s crust is sand,
but we don’t consider sand a requirement for life. What is it about water that makes it so special?
I.
The chemistry of water is dominated by the polar nature of water molecules.
A. oxygen atoms are electron seeking (electronegative), especially compared to hydrogen; thus for an oxygen-hydrogen bond:
1. the oxygen atom has a partial (-) charge
2. the hydrogen atoms have a partial (+) charge
B. the polar character of water allows water molecules to form many (up to 4) hydrogen bonds.
II. What properties of water are important for life?
A. four properties of water are critical for life as we know it, and all of them come in some way from water’s polar nature and
the resulting tendency of water to form hydrogen bonds and similar interactions
1. water is the principal solvent in living things
2. water exhibits both cohesive and adhesive forces
3. water helps maintain a stable temperature
4. ice (solid water) floats in liquid water
B. water is the principal solvent in living things
1. the highly polar character of water makes it an excellent solvent for other polar substances, and for ionic compounds
2. hydrophilic substances – interact readily with water
3. water does not readily dissolve nonpolar (hydrophobic) substances – thus, hydrophobic substances are good
components for membranes
C. water exhibits both cohesive and adhesive forces (due to hydrogen bonding)
1. cohesive forces are caused by the attraction of water molecules to other water molecules, and give water a high surface
tension (the ability of a water surface to withstand some stress)
2. adhesive forces cause water molecules to be attracted to other kinds of molecules; it is how things are made wet
3. capillary action, the tendency of water to move up narrow tubes even against gravity, results from cohesion and
adhesion; living organisms take advantage of this
D. water helps maintain a stable temperature
1. the unusual specific heat of water leads to temperature stability
 specific heat - the amount of energy required to raise the temperature of a specific amount of a substance one degree
Celsius (for water, 1 calorie = heat needed for 1 g of water to raise by one degree Celsius)
 the specific heat of water is much higher than most other substances, due to hydrogen bonding (as a comparison, the
specific heat of sand is about 0.2 calories for 1 g)
 thus, it requires the gain or loss of more energy (heat) to change the temperature of water than it does other
substances
 since much of the ecosphere is water, and most biological organisms are more than 70% water, this property of
water leads to temperature stability (which is critical for most living organisms)
2. the high heat of vaporization of water helps cool the ecosphere and biological organisms
 heat of vaporization is the amount of heat energy required to convert one gram of liquid into the gaseous state
 because of hydrogen bonds in liquid water, water has an extremely high heat of vaporization
 a commonly used unit for measuring energy is the calorie, the amount of heat (energy) required to cause the
temperature of one gram of pure water to rise one degree Celsius
 540 calories are required to convert one gram of liquid water into water vapor
 biological organisms take advantage of this property of water to cool themselves, examples sweating and cooling a
leaf
E. ice floats (ice is less dense than liquid water)
1. liquid water, like most substances, becomes denser as it cools – but only up to a point
2. at 4ºC (under standard atmospheric pressure), water begins to expand as it cools further – that is, it gets less dense from
then on – due to hydrogen bonds becoming locked in place
3. at 0ºC ice freezes into a crystal based on the placement of hydrogen bonds
4. floating ice keeps lakes, etc., from freezing solid and is important for temperature cycling on the planet
III. Acids and Bases
A. acids are proton donors
1. an acid is a substance that dissociates in solution to yield hydrogen ions (H +)
 HA (an acid)
H+ + A- (an anion)
2. note that hydrogen has an atomic number of 1, which means that the nucleus has only one proton
 when the atom loses its electron to become a hydrogen ion, all that remains is the proton
 thus, hydrogen ions are sometimes referred to as protons
 therefore, any substance that yields a proton is an acid, or an acid is a proton donor
B. bases are proton acceptors
1. a base is a substance that can accept a proton
2. bases either dissociate in water to produce hydroxide ions and a cation, or split water to form a cation and hydroxide ion:
NaOH
Na+ + OHor
B (a base) + HOH
BH+ + OHC. water tends to slightly dissociate into hydrogen and hydroxide ions (H+ and OH-)
HOH
H+ + OH-
in pure water, the concentrations of these ions are equal: [H +] = [OH-] = 10-7 M
(note that the designation M stands for molar, the moles of a substance per liter of solution)
2. the product of these remains constant: [H+] x [OH-] = 10-14
 acidic solutions have an elevated [H+], and thus reduced [OH-]
 basic solutions have an elevated [OH-], and thus reduced [H+]
D. the pH scale is a convenient short hand notation to express the proton concentration of a solution
1. the pH of a solution is defined as the reciprocal of the logarithm of the proton concentration in the solution, or -log[H+]
2. pure water (having a proton concentration of 10 -7 M) has pH = 7
3. a pH below 7 is acidic, and a pH above 7 is basic
4. the pH of most living cells is usually around 7.2 to 7.4
E. buffers minimize pH changes
1. weak acids and weak bases serve as buffers
2. living things use buffers to prevent dramatic changes in pH, which can kill them
3. carbonate/bicarbonate is an example of a biologically important buffer system
 CO2 + H2O
H2CO3
H+ + HCO3 because these reactions are equilibrium reactions, as H + is added to this system bicarbonate (HCO3-) and protons are
consumed to keep the proton concentration constant (pH constant) producing H 2CO3
 if OH- ions are added to the system, H + ions are consumed forming water. More H+ ions are produced by the
dissociation of H2CO3 to form protons and bicarbonate. This demonstrates how the pH is stabilized as acid or
base is added
IV. Some useful definitions
A. solvent – a liquid into which a substance dissolves
B. solute – the dissolved substance
C. solution = solvent + solute
D. salts – form from acids and bases
1. water is formed
2. the cation of the base and the anion of the acid form the salt
 HCl + NaOH
NaCl + HOH
E. electrolytes are salts, acids, or bases that form ions in water and thus can conduct an electrical current when dissolved in
water (pure water is a poor conductor of electricity, but put in a salt and it becomes an excellent conductor)
F. nonelectrolytes are substances like sugar that dissolve in water but do not become ionic
G. mixtures - a mixture of 2 or more elements and/or compounds; they can be broken down into elements and compounds by
simple physical means. There are two types:
1. heterogeneous mixtures - mixtures that are not of uniform composition throughout - a living organism is a good
example
2. homogeneous mixtures - mixtures that are completely uniform throughout - a salt water solution is a good example
1.
Chapter 3: What’s so great about water?
19. Draw a water molecule (structural formula) and then draw in four more
around it that are connected to it by hydrogen bonds.
20. List and describe at least four properties of water that result from its
polar nature/hydrogen bonds.
21. Describe how water acts as a temperature buffer (creates temperature
stability).
22. Define acids and bases.
23. What does pH stand for, and how does the pH scale work?
24. How do pH buffers work?
Overview: Life as we know it requires water. All organisms that we know of are made mostly of liquid water,
and most of their metabolism requires an aqueous medium. In addition, many organisms live in liquid water or
in an environment dominated by water in its various states (solid, liquid, or gas). Some numbers:
 cells are typically 70% or more water by mass
 about 75% of the Earth’s surface is covered by liquid water
But then, just being common on the Earth doesn’t make something essential for life. A large percentage of the
Earth’s crust is sand, but we don’t consider sand a requirement for life. What is it about water that makes it so
special?
I.
The chemistry of water is dominated by the polar nature of water molecules.
A. oxygen atoms are electron seeking (electronegative), especially compared to hydrogen; thus for an oxygen-hydrogen bond:
1.
the oxygen atom has a partial (-) charge
2.
the hydrogen atoms have a partial (+) charge
B. the polar character of water allows water molecules to form many (up to 4) hydrogen bonds.
II. What properties of water are important for life?
A. four properties of water are critical for life as we know it, and all of them come in some way from water’s polar nature and
the resulting tendency of water to form hydrogen bonds and similar interactions
1.
water is the principal solvent in living things
2.
water exhibits both cohesive and adhesive forces
3.
water helps maintain a stable temperature
4.
ice (solid water) floats in liquid water
B. water is the principal solvent in living things
1.
the highly polar character of water makes it an excellent solvent for other polar substances, and for ionic compounds
2.
hydrophilic substances – interact readily with water
3.
water does not readily dissolve nonpolar (hydrophobic) substances – thus, hydrophobic substances are good
components for membranes
C. water exhibits both cohesive and adhesive forces (due to hydrogen bonding)
1.
cohesive forces are caused by the attraction of water molecules to other water molecules, and give water a high surface
tension (the ability of a water surface to withstand some stress)
2.
adhesive forces cause water molecules to be attracted to other kinds of molecules; it is how things are made wet
3.
capillary action, the tendency of water to move up narrow tubes even against gravity, results from cohesion and
adhesion; living organisms take advantage of this
D. water helps maintain a stable temperature
1.
the unusual specific heat of water leads to temperature stability

specific heat - the amount of energy required to raise the temperature of a specific amount of a substance one degree
Celsius (for water, 1 calorie = heat needed for 1 g of water to raise by one degree Celsius)

the specific heat of water is much higher than most other substances, due to hydrogen bonding (as a comparison, the
specific heat of sand is about 0.2 calories for 1 g)

thus, it requires the gain or loss of more energy (heat) to change the temperature of water than it does other
substances

since much of the ecosphere is water, and most biological organisms are more than 70% water, this property of
water leads to temperature stability (which is critical for most living organisms)
2.
the high heat of vaporization of water helps cool the ecosphere and biological organisms

heat of vaporization is the amount of heat energy required to convert one gram of liquid into the gaseous state

because of hydrogen bonds in liquid water, water has an extremely high heat of vaporization

a commonly used unit for measuring energy is the calorie, the amount of heat (energy) required to cause the
temperature of one gram of pure water to rise one degree Celsius


540 calories are required to convert one gram of liquid water into water vapor
biological organisms take advantage of this property of water to cool themselves, examples sweating and cooling a
leaf
E. ice floats (ice is less dense than liquid water)
1.
liquid water, like most substances, becomes denser as it cools – but only up to a point
2.
at 4ºC (under standard atmospheric pressure), water begins to expand as it cools further – that is, it gets less dense from
then on – due to hydrogen bonds becoming locked in place
3.
at 0ºC ice freezes into a crystal based on the placement of hydrogen bonds
4.
floating ice keeps lakes, etc., from freezing solid and is important for temperature cycling on the planet
III. Acids and Bases
A. acids are proton donors
1.
an acid is a substance that dissociates in solution to yield hydrogen ions (H +)

2.
HA (an acid)
H+ + A- (an anion)
note that hydrogen has an atomic number of 1, which means that the nucleus has only one proton

when the atom loses its electron to become a hydrogen ion, all that remains is the proton

thus, hydrogen ions are sometimes referred to as protons

therefore, any substance that yields a proton is an acid, or an acid is a proton donor
B. bases are proton acceptors
1.
a base is a substance that can accept a proton
2.
bases either dissociate in water to produce hydroxide ions and a cation, or split water to form a cation and hydroxide ion:
Na+ + OH-
NaOH
B (a base) + HOH
or
BH+ + OH-
C. water tends to slightly dissociate into hydrogen and hydroxide ions (H+ and OH-)
HOH
1.
H+ + OH-
in pure water, the concentrations of these ions are equal: [H +] = [OH-] = 10-7 M
(note that the designation M stands for molar, the moles of a substance per liter of solution)
2.
the product of these remains constant: [H+] x [OH-] = 10-14

acidic solutions have an elevated [H+], and thus reduced [OH-]

basic solutions have an elevated [OH-], and thus reduced [H+]
D. the pH scale is a convenient short hand notation to express the proton concentration of a solution
1.
the pH of a solution is defined as the reciprocal of the logarithm of the proton concentration in the solution, or -log[H+]
2.
pure water (having a proton concentration of 10-7 M) has pH = 7
3.
a pH below 7 is acidic, and a pH above 7 is basic
4.
the pH of most living cells is usually around 7.2 to 7.4
E. buffers minimize pH changes
1.
weak acids and weak bases serve as buffers
2.
living things use buffers to prevent dramatic changes in pH, which can kill them
3.
carbonate/bicarbonate is an example of a biologically important buffer system

CO2 + H2O

because these reactions are equilibrium reactions, as H + is added to this system bicarbonate (HCO3-) and protons are
H2CO3
H+ + HCO3-
consumed to keep the proton concentration constant (pH constant) producing H 2CO3

if OH- ions are added to the system, H + ions are consumed forming water. More H+ ions are produced by the
dissociation of H2CO3 to form protons and bicarbonate. This demonstrates how the pH is stabilized as acid or
base is added
IV. Some useful definitions
A. solvent – a liquid into which a substance dissolves
B. solute – the dissolved substance
C. solution = solvent + solute
D. salts – form from acids and bases
1.
water is formed
2.
the cation of the base and the anion of the acid form the salt

HCl + NaOH
NaCl + HOH
E. electrolytes are salts, acids, or bases that form ions in water and thus can conduct an electrical current when dissolved in
water (pure water is a poor conductor of electricity, but put in a salt and it becomes an excellent conductor)
F.
nonelectrolytes are substances like sugar that dissolve in water but do not become ionic
G. mixtures - a mixture of 2 or more elements and/or compounds; they can be broken down into elements and compounds by
simple physical means. There are two types:
1.
heterogeneous mixtures - mixtures that are not of uniform composition throughout - a living organism is a good
example
2.
homogeneous mixtures - mixtures that are completely uniform throughout - a salt water solution is a good example
Chapter 4: Carbon and the molecular diversity of life : Life is based on molecules with carbon (organic molecules.
I.
Much of the chemistry of life is based on organic compounds
A. organic compounds have at least one carbon atom covalently bound to another carbon atom or to hydrogen; the chemistry of
organic molecules is organized around the carbon atom
B. carbon atoms have six electrons - 2 in level 1, and 4 in their valence (outer) shell (level 2)
1. Carbon is not a strongly electron seeking element, and it does not readily give up its electrons. Thus carbon does not
readily from ionic bonds. It almost always shares electrons, forming covalent bonds.
2. carbon can form up to 4 covalent bonds (and typically does form all four)
C. wide diversity in organic compounds
1. over 5 million identified
2. variety partially because carbon tends to bond to carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus
 hydrocarbons – contain only hydrogen and carbon
 single carbon-carbon bonds allow rotation around them and lend flexibility in molecules
3. building of organic macromolecules also leads to diversity
 carbon works well as a molecular “backbone” for forming long chain molecules due to the number and strength of
its bonds, particularly carbon-carbon bonds
 stronger carbon-carbon bonds can be made with double and triple covalent bonds
 carbon chains can branch
D. the shape of a molecule is important in determining its chemical and biological properties
1. the 4 bonds formed by carbon are formed at 109.5 degree angles from each other and form a pyramid with a triangular
base called a tetrahedron
2. when double bonds are formed the bonds are formed at angles 120 degrees apart, and they all lie in the same plane
3. These bond angles for carbon play a critical role in determining the shape of molecules.
4. generally there is freedom to rotate around carbon to carbon single bonds, but rotation around double bonds is not
permitted
II. Isomers are molecules that have the same molecular formula but different structures; there are two kinds of isomers
A. structural isomers - substances with the same molecular formula that differ in the covalent arrangement of their atoms;
example: ethanol and dimethyl ether (C2H6O)
B. stereoisomers - substances with the same arrangement of covalent bonds, but the order in which the atoms are arranged in
space is different; two important types for our use
1. cis-trans isomers
 associated with compounds that have carbon-carbon double bonds
 since there is no rotation around the double bond the other atoms attached to the carbons are stuck in place in
relationship to each other
 larger items together = cis; larger item opposite = trans
 examples: trans-2-butene and cis-2-butene
2. enantiomers – substances that are mirror images of each other and that cannot be superimposed on each other
 sometimes called optical isomers



typically, only one form of an enatiomer is found and/or used by organisms
the enantiomers are given designations such as [(+)- vs. (−)-] or [D- vs. L-] or [(R)- vs. (S)-]
biologically important enantiomers include
 amino acids (found in proteins) – most are L-amino acids (e.g. L-leucine, L-alanine, etc)
 sugars – most are D-sugars (e.g. D-glucose, D-fructose, etc.)
III. Functional groups determine most of the reactive properties (functions) of organic molecules
A. functional groups are groups of atoms covalently bonded to a carbon backbone that give properties different from a C-H
bond
B. the properties of the major classes of organic compounds (carbohydrates, lipids, proteins, and nucleic acids) are determined
mostly by their functional groups
C. learn these seven functional groups (note: X here stands for the “rest” of the molecule)
1. hydroxyl group (X-OH): polar; found in alcohols
2. carbonyl group (X-C=O): polar; found in aldehydes and ketones
3. carboxyl group (X-COOH): weakly acidic; found in organic acids (such as amino acids)
4. amino groups (X-NH2): weakly basic; found in such things as amino acids
5. sulfhydryl groups (X-SH): essentially nonpolar; found in some amino acids
6. phosphate groups (X-PO4H2): weakly acidic; found in such things as phospholipids and nucleic acids
7. methyl groups (X-CH3): nonpolar (thus hydrophobic); found in such things as lipids, other membrane components
Chapter 4: Life is based on molecules with carbon (organic
molecules).
25. Discuss the chemistry of carbon. How does it typically bond? What does
it typically bond to? What sort of shapes, angles, freedoms, etc. are
associated with the bonds that it makes?
26. Draw a tetrahedron.
27. Discuss isomers. What are they? What is the difference between
structural isomers and stereoisomers? Between cis-trans isomers and
enantiomers?
28. Draw an example of each of these:
structural isomers
cis-trans isomers
enantiomers
29. What is a functional group, and why is it useful to know them? Quiz
each other on the names and chemistry of the functional groups in the notes.
Chapter 4: Life is based on molecules with carbon (organic molecules).
I.
Much of the chemistry of life is based on organic compounds
A. organic compounds have at least one carbon atom covalently bound to another carbon atom or to hydrogen; the chemistry of
organic molecules is organized around the carbon atom
B. carbon atoms have six electrons - 2 in level 1, and 4 in their valence (outer) shell (level 2)
1.
Carbon is not a strongly electron seeking element, and it does not readily give up its electrons. Thus carbon does not
readily from ionic bonds. It almost always shares electrons, forming covalent bonds.
2.
carbon can form up to 4 covalent bonds (and typically does form all four)
C. wide diversity in organic compounds
1.
over 5 million identified
2.
variety partially because carbon tends to bond to carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus
3.

hydrocarbons – contain only hydrogen and carbon

single carbon-carbon bonds allow rotation around them and lend flexibility to molecules
building of organic macromolecules also leads to diversity

carbon works well as a molecular “backbone” for forming long chain molecules due to the number and strength of
its bonds, particularly carbon-carbon bonds

stronger carbon-carbon bonds can be made with double and triple covalent bonds

carbon chains can branch
D. the shape of a molecule is important in determining its chemical and biological properties
1.
the 4 bonds formed by carbon are formed at 109.5 degree angles from each other and form a pyramid with a triangular
base called a tetrahedron
2.
when double bonds are formed the bonds are formed at angles 120 degrees apart, and they all lie in the same plane
3.
These bond angles for carbon play a critical role in determining the shape of molecules.
4.
generally there is freedom to rotate around carbon to carbon single bonds, but rotation around double bonds is not
permitted
II. Isomers are molecules that have the same molecular formula but different structures; there are two kinds of isomers
A. structural isomers - substances with the same molecular formula that differ in the covalent arrangement of their atoms;
example: ethanol and dimethyl ether (C2H6O)
B. stereoisomers - substances with the same arrangement of covalent bonds, but the order in which the atoms are arranged in
space is different; two important types for our use
1.
cis-trans isomers

associated with compounds that have carbon-carbon double bonds

since there is no rotation around the double bond the other atoms attached to the carbons are stuck in place in
relationship to each other

larger items together = cis; larger items opposite = trans

examples: trans-2-butene and cis-2-butene
2.
enantiomers – substances that are mirror images of each other and that cannot be superimposed on each other

sometimes called optical isomers

typically, only one form of an enatiomer pair is found in and/or used by organisms

the enantiomers are given designations such as [(+)- vs. (−)-] or [D- vs. L-] or [(R)- vs. (S)-]

biologically important enantiomers include

amino acids (found in proteins) – most are L-amino acids (e.g. L-leucine, L-alanine, etc)

sugars – most are D-sugars (e.g. D-glucose, D-fructose, etc.)
III. Functional groups determine most of the reactive properties (functions) of organic molecules
A. functional groups are groups of atoms covalently bonded to a carbon backbone that give properties different from a C-H
bond
B. the properties of the major classes of organic compounds (carbohydrates, lipids, proteins, and nucleic acids) are determined
mostly by their functional groups
C. learn these seven functional groups (note: X here stands for the “rest” of the molecule)
1.
hydroxyl group (X-OH): polar; found in alcohols
2.
carbonyl group (X-C=O): polar; found in aldehydes and ketones
3.
carboxyl group (X-COOH): weakly acidic; found in organic acids (such as amino acids)
4.
amino group (X-NH2): weakly basic; found in such things as amino acids
5.
sulfhydryl group (X-SH): essentially nonpolar; found in some amino acids
6.
phosphate group (X-PO4H2): weakly acidic; found in such things as phospholipids and nucleic acids
7.
methyl group (X-CH3): nonpolar (thus hydrophobic); found in such things as lipids, other membrane components
Chapter 5: The structure and function of macromolecules : What are the major types of organic molecules?
IV. many biological molecules are polymers
A. polymers are long chains or branching chains based on repeating subunits (monomers)
1. example: proteins (the polymer) are made from amino acids (the monomers)
2. example: nucleic acids (the polymer) are made from nucleotides (the monomers)
B. very large polymers (hundreds of subunits or more) are called macromolecules
C. polymers are degraded into monomers by hydrolysis (“break with water”)
1. typically requires an enzyme to occur at a decent rate
2. hydrogen from water is attached to one monomer, and a hydroxyl from water is attached to the other
D. monomers are covalently linked to form polymers by condensation
1. also typically requires an enzyme to occur at a decent rate
2. typically the equivalent of a water molecule is removed (dehydration synthesis)
V. The four major classes of biologically important organic molecules are: carbohydrates, lipids, proteins or polypeptides (and
related compounds), and nucleic acids (and related compounds)
VI. carbohydrates include sugars, starches, and cellulose
A. carbohydrates contain only the elements carbon, hydrogen, and oxygen
B. the ratio works out so that carbohydrates are typically (CH 2O)n
C. carbohydrates are the main molecules in biological systems created for energy storage and consumed for energy production;
some are also used as building materials
D. grouped into monosaccharides, disaccharides, and polysaccharides
1. monosaccharides are simple sugars (a single monomer)
 have 3, 4, 5, 6, or 7 carbons
 referred to as trioses, tetroses, pentoses, hexoses, and heptoses
 examples of pentoses include ribose and deoxyribose (part of nucleic acids)
 examples of hexoses include glucose, fructose, and galactose; glucose is most abundant
 Examine the structural formulas for glucose, fructose, and galactose. Note that they are all isomers of each other (i.e.
they have the chemical formula C6H12O6). Glucose and galactose are structural isomers of fructose, while
glucose and galactose are diastereomers (a type of stereoisomer).
 pentose and hexose sugars actually form ring structures in solution
 this often creates diastereomers
 example: -glucose and -glucose
 note how carbons are given numbers to indicate position
2. disaccharides consist of two monosaccharide units
 the two monomers are joined by a glycosidic linkage or glycosidic bond
 formed when the equivalent of a water molecule is removed from the two monosaccharides
 an oxygen atom is bound to a carbon from each momomer
 typically, the linkage is between carbon 1 of one and 4 of the other
 maltose, sucrose, and lactose are common disaccharides
 maltose (malt sugar): has two glucose subunits
 sucrose (table sugar): glucose + fructose
 lactose (milk sugar): glucose + galactose
3. polysaccharides are macromolecules made of repeating monosaccharides units linked together by glycosidic bonds
 number of subunits varies, typically thousands
 can be branched or unbranched
 some are easily broken down and are good for energy storage (examples: starch, glycogen)
 some are harder to break down and are good as structural components (example: cellulose)
 starch is the main storage carbohydrate of plants
 polymer made from α-glucose units linked primarily between carbons 1 and 4
 amylose = unbranched starch chain (only have α1-4 linkages)
 amylopectin = branched starch chain (branches by linkages between carbons 1 and 6)
 plants store starches in organelles called amyloplasts, a type of plastid
 glycogen is the main storage carbohydrate of animals
 similar to starch, but very highly branched and more water-soluble
 is NOT stored in an organelle; mostly found in liver and muscle cells
 cellulose is the major structural component of most plant cell walls
 polymer made from -glucose units linked primarily between carbons 1 and 4 (similar to starch, but note that
the 1-4 linkage makes a huge difference)
 unlike starch, most organisms cannot digest cellulose
 cellulose is a major constituent of cotton, wood, and paper
 cellulose contains ~50% of the carbon in found in plants
 fibrous cellulose is the “fiber” in your diet
 some fungi, bacteria, and protozoa make enzymes that can break down cellulose
 animals that live on materials rich in cellulose, e.g. cattle, sheep and termites, contain microorganisms in their
gut that are able to break down cellulose for use by the animal
4. carbohydrates can be modified from the basic (CH2O)n formula
 many modified carbohydrates have important biological roles
 example: chitin – structural component in fungal cell walls and arthropod exoskeletons
 example: galactosamine in cartilage
 example: glycoproteins and glycolipids in cellular membranes
VII. lipids are fats and fat-like substances
A. lipids are a heterogeneous group of compounds defined by solubility, not structure
B. oily or fatty compounds
C. lipids are principally hydrophobic, and are relatively insoluble in water (some do have polar and nonpolar regions)
1. lipids consist mainly of carbon and hydrogen
2. some oxygen and/or phosphorus, mainly in the polar regions of lipids that have such regions
D. roles of lipids include serving as membrane structural components, as signaling molecules, and as energy storage molecules
E. major classes of lipids that you need to know are triacylglycerols (fats), phospholipids, and terpenes
F. triacylglycerols contain glycerol joined to three fatty acids
1. glycerol is a three carbon alcohol with 3 -OH groups
2.
a fatty acid is a long, unbranched hydrocarbon chain carboxyl group at one end
 saturated fatty acids contain no carbon-carbon double bonds (usually solid at room temp)
 unsaturated fatty acids contain one or more double bonds (usually liquid at room temp)
 monounsaturated – one double bond
 polyunsaturated – more than one double bond
 about 30 different fatty acids are commonly found in triacylglycerols; most have an even number of carbons
3. condensation results in an ester linkage between a fatty acid and the glycerol
 one attached fatty acid = monoacylglycerol
 two = diacylglycerol
 three = triacylglycerol
4. triacylglycerols (also called triglycerides) are the most abundant lipids, and are important sources of energy
G. phospholipids consist of a diacylglycerol molecule, a phosphate group esterified to the third -OH group of glycerol, and an
organic molecule (usually charged or polar) esterified to the phosphate
1. phospholipids are amphipathic; they have a nonpolar end (the two fatty acids) and a polar end (the phosphate and
organic molecule)
2. this is often drawn with a polar “head” and two nonpolar “tails”
3. the nonpolar (or hydrophobic) portion of the molecule tends to stay away from water, and the polar (or hydrophilic)
portion of the molecule tends to interact with water
4. because of this character phospholipids are important constituents of biological membranes
H. terpenes are long-chained lipids built from 5-carbon isoprene units
1. many pigments, such as chlorophyll, carotenoids, and retinal, are terpenes or modified terpenes (often called terpenoids)
2. other terpenes/terpenoids include natural rubber and “essential oils” such as plant fragrances and many spices
3. steroids are terpene derivatives that contain four rings of carbon atoms
 side chains extend from the rings; length and structure of the side chains varies
 one type of steroid, cholesterol, is an important component of cell membranes
 other examples: many hormones such as testosterone, estrogens
VIII. proteins are macromolecules that are polymers formed from amino acids monomers
A. proteins have great structural diversity and perform many roles
B. roles include enzyme catalysis, defense, transport, structure/support, motion, regulation; protein structure determines protein
function
C. proteins are polymers made of amino acid monomers linked together by peptide bonds
1. amino acids consist of a central or alpha carbon; bound to that carbon is a hydrogen atom, an amino group(-NH2), a
carboxyl group (-COOH), and a variable side group (R group)
 the R group determines the identity and much of the chemical properties of the amino acid
 there are 20 amino acids that commonly occur in proteins; pay attention to what makes an R group polar, nonpolar,
or ionic (charged) and thus their hydrophobic or hydrophilic nature
 most amino acids have enantiomers; when this is so, the amino acids found in proteins are nearly always of the Lconfiguration
 plants and bacteria can usually make their own amino acids; many animals must obtain some amino acids from their
diet (essential amino acids)
2. the peptide bond joins the carboxyl group of one amino acid to the amino group of another; is formed by a condensation
reaction
3. two amino acids fastened together by a peptide bond is called a dipeptide, several amino acids fastened together by
peptide bonds are called a polypeptide
D. the sequence of amino acids determine the structure (and thus the properties) of a protein
E. proteins have 4 levels of organization or structure
1. primary structure (1) of a protein is the sequence of amino acids in the peptide chain
2. secondary structure (2) of a protein results from hydrogen bonds involving the backbone, where the peptide chain is
held in structures, either a coiled α-helix or folded β-pleated sheet; proteins often have both types of secondary
structure in different regions of the chain
3. tertiary structure (3) of a protein is the overall folded shape of a single polypeptide chain, determined by secondary
structure combined with interactions between R groups (NOTE: book defines this in a confusing way, use my way)
4. quaternary structure (4) of a protein results from interactions between two or more separate polypeptide chains
 the interactions are of the same type that produce 2 and 3 structure in a single polypeptide chain
 when present, 4 structure is the final three-dimensional structure of the protein (the protein conformation)
 example: hemoglobin has 4 polypeptide chains
 not all proteins have 4 structure
5. ultimately the secondary, tertiary, and quaternary structures of a protein derive from its primary structure, but molecular
chaperones may aid the folding process
6. protein conformation determines function
7.
denaturation is unfolding of a protein, disrupting 2, 3, and 4 structure
 changes in temperature, pH, or exposure to various chemicals can cause denaturation
 denatured proteins typically cannot perform their normal biological function
 denaturation is generally irreversible
F. enzymes are biological substances that regulate the rates of the chemical reactions in living organisms; most enzymes are
proteins (covered in some detail later in this course)
G. “related compounds” –amino acids; modified amino acids; polypeptides too short to be considered true proteins; and
modified short polypeptides
IX. nucleic acids transmit hereditary information by determining what proteins a cell makes
A. two classes of nucleic acids found in cells: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
1. DNA carries the genetic information cells use to make proteins
2. RNA functions in protein synthesis according to mechanisms we will discuss later in the semester
B. nucleic acids are polymers made of nucleotide monomers
1. a nucleotide consists of
 a five-carbon sugar (ribose or deoxyribose)
 one or more phosphate groups, and
 a nitrogenous base, an organic ring compound that contains nitrogen
2. purines are double-ringed nitrogenous bases
3. pyrimidines are single-ringed nitrogenous bases
C. DNA typically contains the purines adenine (A) and guanine (G), and the pyrimidines cytosine (C) and thymine (T)
D. RNA typically contains the purines adenine (A) and guanine (G), and the pyrimidines cytosine (C) and uracil (U)
E. nucleotides are fastened together by phosphodiester bonds
1. the phosphate group of one nucleotide is fastened to the sugar of the adjacent nucleotide
2. the joining is yet another condensation reaction
3. the way that the are joined creates a polynucleotide strand with 5’ and 3’ ends
F. the sequence of the 4 bases fastened to the sugar-phosphate backbone is genetic information
G. DNA is typically a double stranded molecule
1. the two strands twist into a double helix
2. hydrogen bonds between the nitrogenous bases of opposite strands hold the strands together
3. the two strands are antiparallel
H. RNA is typically a single stranded nucleic acid molecule, having only a single polynucleotide chain
I. “related compounds” – nucleotides, modified nucleotides, dinucleotides
J. some single and double nucleotides with important biological functions:
1. adenosine triphosphate (ATP) is an important energy carrying compound in metabolism
2. cyclic adenosine monophosphate (cAMP) is a hormone intermediary compound
3. nicotinamide adenine dinucleotide (NAD+) is an electron carrier which is oxidized or reduced in many metabolic
reactions
Chapter 5: What are the major types of organic molecules?
30. Discuss hydrolysis and condensation, and the connection between them.
31. Carbohydrates: what are they, and what are they used for? What terms
are associated with them (including the monomers and the polymer bond
name)? Give some examples of molecules in this group.
32. Lipids: what are they, and what are they used for? What terms are
associated with them (including major classes and bond names)? Give some
examples of molecules in this group.
33. Polypeptides: what are they, and what are they used for? What terms are
associated with them (including the monomers and the polymer bond
name)? Give some examples of molecules in this group.
34. Discuss how to tell which of these categories an amino acid falls into:
hydrophobic or hydrophilic (and within the hydrophilic, polar or charged).
35. Discuss the four levels of protein structure.
36. Nucleic acids: what are they, and what are they used for? What terms
are associated with them (including the monomers and the polymer bond
name)? Give some examples of molecules in this group.
37. What are 5’ and 3’ ends? What does “antiparallel” mean in DNA?
38. What are ATP, cAMP, and NAD+? What are their roles in cells?
Chapter 5: What are the major types of organic molecules?
X. many biological molecules are polymers
A. polymers are long chains or branching chains based on repeating subunits (monomers)
1.
example: proteins (the polymer) are made from amino acids (the monomers)
2.
example: nucleic acids (the polymer) are made from nucleotides (the monomers)
B. very large polymers (hundreds of subunits or more) are called macromolecules
C. polymers are degraded into monomers by hydrolysis (“break with water”)
1.
typically requires an enzyme to occur at a decent rate
2.
hydrogen from water is attached to one monomer, and a hydroxyl from water is attached to the other
D. monomers are covalently linked to form polymers by condensation
1.
also typically requires an enzyme to occur at a decent rate
2.
typically the equivalent of a water molecule is removed (dehydration synthesis)
XI. The four major classes of biologically important organic molecules are: carbohydrates, lipids, proteins or polypeptides (and
related compounds), and nucleic acids (and related compounds)
XII. carbohydrates include sugars, starches, and cellulose
A. carbohydrates contain only the elements carbon, hydrogen, and oxygen
B. the ratio works out so that carbohydrates are typically (CH 2O)n
C. carbohydrates are the main molecules in biological systems created for energy storage and consumed for energy production;
some are also used as building materials
D. grouped into monosaccharides, disaccharides, and polysaccharides
1.
monosaccharides are simple sugars (a single monomer)

have 3, 4, 5, 6, or 7 carbons

referred to as trioses, tetroses, pentoses, hexoses, and heptoses

examples of pentoses include ribose and deoxyribose (part of nucleic acids)

examples of hexoses include glucose, fructose, and galactose; glucose is most abundant

Examine the structural formulas for glucose, fructose, and galactose. Note that they are all isomers of each other (i.e.
they have the chemical formula C6H12O6). Glucose and galactose are structural isomers of fructose, while
glucose and galactose are diastereomers (a type of stereoisomer).

pentose and hexose sugars actually form ring structures in solution

this often creates diastereomers

example: -glucose and -glucose

2.
3.
note how carbons are given numbers to indicate position
disaccharides consist of two monosaccharide units

the two monomers are joined by a glycosidic linkage or glycosidic bond

formed when the equivalent of a water molecule is removed from the two monosaccharides

an oxygen atom is bound to a carbon from each momomer

typically, the linkage is between carbon 1 of one and 4 of the other

maltose, sucrose, and lactose are common disaccharides

maltose (malt sugar): has two glucose subunits

sucrose (table sugar): glucose + fructose

lactose (milk sugar): glucose + galactose
polysaccharides are macromolecules made of repeating monosaccharides units linked together by glycosidic bonds

number of subunits varies, typically thousands

can be branched or unbranched

some are easily broken down and are good for energy storage (examples: starch, glycogen)

some are harder to break down and are good as structural components (example: cellulose)

starch is the main storage carbohydrate of plants



polymer made from α-glucose units linked primarily between carbons 1 and 4

amylose = unbranched starch chain (only have α1-4 linkages)

amylopectin = branched starch chain (branches by linkages between carbons 1 and 6)

plants store starches in organelles called amyloplasts, a type of plastid
glycogen is the main storage carbohydrate of animals

similar to starch, but very highly branched and more water-soluble

is NOT stored in an organelle; mostly found in liver and muscle cells
cellulose is the major structural component of most plant cell walls

polymer made from -glucose units linked primarily between carbons 1 and 4 (similar to starch, but note that
the 1-4 linkage makes a huge difference)

unlike starch, most organisms cannot digest cellulose

cellulose is a major constituent of cotton, wood, and paper

cellulose contains ~50% of the carbon in found in plants

fibrous cellulose is the “fiber” in your diet

some fungi, bacteria, and protozoa make enzymes that can break down cellulose

animals that live on materials rich in cellulose, e.g. cattle, sheep and termites, contain microorganisms in their
gut that are able to break down cellulose for use by the animal
4.
XIII.
carbohydrates can be modified from the basic (CH2O)n formula

many modified carbohydrates have important biological roles

example: chitin – structural component in fungal cell walls and arthropod exoskeletons

example: galactosamine in cartilage

example: glycoproteins and glycolipids in cellular membranes
lipids are fats and fat-like substances
A. lipids are a heterogeneous group of compounds defined by solubility, not structure
B. oily or fatty compounds
C. lipids are principally hydrophobic, and are relatively insoluble in water (some do have polar and nonpolar regions)
1.
lipids consist mainly of carbon and hydrogen
2.
some oxygen and/or phosphorus, mainly in the polar regions of lipids that have such regions
D. roles of lipids include serving as membrane structural components, as signaling molecules, and as energy storage molecules
E. major classes of lipids that you need to know are triacylglycerols (fats), phospholipids, and terpenes
F.
triacylglycerols contain glycerol joined to three fatty acids
1.
glycerol is a three carbon alcohol with 3 -OH groups
2.
a fatty acid is a long, unbranched hydrocarbon chain carboxyl group at one end

saturated fatty acids contain no carbon-carbon double bonds (usually solid at room temp)

unsaturated fatty acids contain one or more double bonds (usually liquid at room temp)

3.
4.

monounsaturated – one double bond

polyunsaturated – more than one double bond
about 30 different fatty acids are commonly found in triacylglycerols; most have an even number of carbons
condensation results in an ester linkage between a fatty acid and the glycerol

one attached fatty acid = monoacylglycerol

two = diacylglycerol

three = triacylglycerol
triacylglycerols (also called triglycerides) are the most abundant lipids, and are important sources of energy
G. phospholipids consist of a diacylglycerol molecule, a phosphate group esterified to the third -OH group of glycerol, and an
organic molecule (usually charged or polar) esterified to the phosphate
1.
phospholipids are amphipathic; they have a nonpolar end (the two fatty acids) and a polar end (the phosphate and
organic molecule)
2.
this is often drawn with a polar “head” and two nonpolar “tails”
3.
the nonpolar (or hydrophobic) portion of the molecule tends to stay away from water, and the polar (or hydrophilic)
portion of the molecule tends to interact with water
4.
because of this character phospholipids are important constituents of biological membranes
H. terpenes are long-chained lipids built from 5-carbon isoprene units
XIV.
1.
many pigments, such as chlorophyll, carotenoids, and retinal, are terpenes or modified terpenes (often called terpenoids)
2.
other terpenes/terpenoids include natural rubber and “essential oils” such as plant fragrances and many spices
3.
steroids are terpene derivatives that contain four rings of carbon atoms

side chains extend from the rings; length and structure of the side chains varies

one type of steroid, cholesterol, is an important component of cell membranes

other examples: many hormones such as testosterone, estrogens
proteins are macromolecules that are polymers formed from amino acids monomers
A. proteins have great structural diversity and perform many roles
B. roles include enzyme catalysis, defense, transport, structure/support, motion, regulation; protein structure determines protein
function
C. proteins are polymers made of amino acid monomers linked together by peptide bonds
1.
amino acids consist of a central or alpha carbon; bound to that carbon is a hydrogen atom, an amino group (-NH2), a
carboxyl group (-COOH), and a variable side group (R group)

the R group determines the identity and much of the chemical properties of the amino acid

there are 20 amino acids that commonly occur in proteins; pay attention to what makes an R group polar, nonpolar,
or ionic (charged) and thus their hydrophobic or hydrophilic nature

most amino acids have enantiomers; when this is so, the amino acids found in proteins are nearly always of the Lconfiguration

plants and bacteria can usually make their own amino acids; many animals must obtain some amino acids from their
diet (essential amino acids)
2.
the peptide bond joins the carboxyl group of one amino acid to the amino group of another; is formed by a condensation
reaction
3.
two amino acids fastened together by a peptide bond is called a dipeptide, several amino acids fastened together by
peptide bonds are called a polypeptide
D. the sequence of amino acids determine the structure (and thus the properties) of a protein
E. proteins have 4 levels of organization or structure
1.
primary structure (1) of a protein is the sequence of amino acids in the peptide chain
2.
secondary structure (2) of a protein results from hydrogen bonds involving the backbone, where the peptide chain is
held in structures, either a coiled α-helix or folded β-pleated sheet; proteins often have both types of secondary
structure in different regions of the chain
3.
tertiary structure (3) of a protein is the overall folded shape of a single polypeptide chain, determined by secondary
structure combined with interactions between R groups (NOTE: book defines this in a confusing way, use my way)
4.
5.
quaternary structure (4) of a protein results from interactions between two or more separate polypeptide chains

the interactions are of the same type that produce 2 and 3 structure in a single polypeptide chain

when present, 4 structure is the final three-dimensional structure of the protein (the protein conformation)

example: hemoglobin has 4 polypeptide chains

not all proteins have 4 structure
ultimately the secondary, tertiary, and quaternary structures of a protein derive from its primary structure, but molecular
chaperones may aid the folding process
F.
6.
protein conformation determines function
7.
denaturation is unfolding of a protein, disrupting 2, 3, and 4 structure

changes in temperature, pH, or exposure to various chemicals can cause denaturation

denatured proteins typically cannot perform their normal biological function

denaturation is generally irreversible
enzymes are biological substances that regulate the rates of the chemical reactions in living organisms; most enzymes are
proteins (covered in some detail later in this course)
G. “related compounds” –amino acids; modified amino acids; polypeptides too short to be considered true proteins; and
modified short polypeptides
XV. nucleic acids transmit hereditary information by determining what proteins a cell makes
A. two classes of nucleic acids found in cells: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
1.
DNA carries the genetic information cells use to make proteins
2.
RNA functions in protein synthesis according to mechanisms we will discuss later in the semester
B. nucleic acids are polymers made of nucleotide monomers
1.
a nucleotide consists of

a five-carbon sugar (ribose or deoxyribose)

one or more phosphate groups, and

a nitrogenous base, an organic ring compound that contains nitrogen
2.
purines are double-ringed nitrogenous bases
3.
pyrimidines are single-ringed nitrogenous bases
C. DNA typically contains the purines adenine (A) and guanine (G), and the pyrimidines cytosine (C) and thymine (T)
D. RNA typically contains the purines adenine (A) and guanine (G), and the pyrimidines cytosine (C) and uracil (U)
E. nucleotides are fastened together by phosphodiester bonds
F.
1.
the phosphate group of one nucleotide is fastened to the sugar of the adjacent nucleotide
2.
the joining is yet another condensation reaction
3.
the way that the are joined creates a polynucleotide strand with 5’ and 3’ ends
the sequence of the 4 bases fastened to the sugar-phosphate backbone is genetic information
G. DNA is typically a double stranded molecule
1.
the two strands twist into a double helix
2.
hydrogen bonds between the nitrogenous bases of opposite strands hold the strands together
3.
the two strands are antiparallel
H. RNA is typically a single stranded nucleic acid molecule, having only a single polynucleotide chain
I.
“related compounds” – nucleotides, modified nucleotides, dinucleotides
J.
some single and double nucleotides with important biological functions:
1.
adenosine triphosphate (ATP) is an important energy carrying compound in metabolism
2.
cyclic adenosine monophosphate (cAMP) is a hormone intermediary compound
3.
nicotinamide adenine dinucleotide (NAD+) is an electron carrier which is oxidized or reduced in many metabolic
reactions
Chapter 6: A tour of the Cell
XVI. Cell theory
A. All living organisms are composed of cells
1. smallest “building blocks” of all multicellular organisms
2. all cells are enclosed by a surface membrane that separates them from other cells and from their environment
3. specialized structures with the cell are called organelles; many are membrane-bound
B. Today, all new cells arise from existing cells
C. All presently living cells have a common origin
1. all cells have basic structural and molecular similarities
2. all cells share similar energy conversion reactions
3. all cells maintain and transfer genetic information in DNA
4. the genetic code is essentially universal
XVII. Cell organization and homeostasis
A. Plasma membrane surrounds cells and separates their contents from the external environment
B. Cells are heterogeneous mixtures, with specialized regions and structures (such as organelles)
C. Cell size is limited
1. surface area to volume ratio puts a limit on cell size
 food and/or other materials must get into the cell
 waste products must be removed from the cell
 thus, cells need a high surface area to volume ratio, but volume increases faster than surface area as cells grow larger
2. cell shape varies depending both on function and surface area requirements
XVIII. Studying cells – microscopy and fractionation
A. Most cells are large enough to be resolved from each other with light microscopes (LM)
1. cells were discovered by Robert Hooke in 1665; he saw the remains of cell walls in cork with a LMs, at about 30x
magnification
2. modern LMs can reach up to 1000x
3. LM resolution (clarity) is limited to about 1 m due to the wavelength of visible light (thus only about 500 times better
than the human eye, even at maximum magnification)
4. small cells (such as most bacteria) are about 1 m across, just on the edge of resolution
5. some modifications of LMs and some treatments of cells allow observation of subcellular structure in some cases
B. Resolution of most subcellular structure requires electron microscopy (EM)
1. electrons have a much smaller wavelength than light (resolve down to under 1 nm)
2. magnification up to 250,000x or more and resolution over 500,000 times better than the human eye
3. includes transmission (TEM) and scanning (SEM) forms
 transmission - electron passes through sample; need very thin samples (100 nm or less thick); samples embedded in
plastic and sliced with a diamond knife
 scanning – samples are gold-plated; electrons interact with the surface; images have a 3-D appearance
C. Cells can be broken and fractionated to separate cellular components for study
1. cells are broken (lysed) by disrupting the cell membrane, often using some sort of detergent
2. grinding and other physical force may be required, especially if cell walls are present
3. centrifugation is used to separate cellular components
 using a centrifuge, samples are spun at high speeds, resulting in exposure to a centrifugal force of thousands to
hundreds of thousands times gravity (example, 500,000 x G)
 results in a pellet and supernatant; cell components will be in one or the other depending on their individual
properties; intact membrane-bound organelles often wind up in pellets, depending on their density and the
centrifugal force reached (more dense = more likely in pellet)
 special treatments can determine whether a component ends up in the pellet or supernatant
 density gradients can also be used to subdivide pellet components based on their density; this can be used to separate
organelles from each other, for example Golgi apparatus from ER
XIX. Eukaryotic vs. prokaryotic cells
A. eukaryotic cells have internal membranes and a distinct, membrane-enclosed nucleus; typically 10-100 m in diameter
B. prokaryotic cells do not have internal membranes (thus no nuclear membrane)
1. main DNA molecule (chromosome) is typically circular; its location is called the nuclear area
2. other small DNA molecules (plasmids) are often present, found throughout the cell
3. plasma membrane is typically enclosed in a cell wall
4. often the cell wall is enclosed in an outer envelope or outer membrane
5. do not completely lack organelles; the plasma membrane and ribosomes are both present and are considered organelles
6. AKA bacteria, prokaryotic cells are typically 1-10 m in diameter
XX. Compartments in eukaryotic cells (cell regions, organelles)
A. two general regions inside the cell: cytoplasm and nucleoplasm
1. cytoplasm – everything outside the nucleus and within the plasma membrane
 contains fluid cytosol and organelles
2. nucleoplasm – everything within the nuclear membrane
B. membranes separate cell regions
1. have nonpolar regions that help form a barrier between aqueous regions
2. allow for some selection in what can cross a membrane (more details later)
XXI. nucleus – the “control center” of the cell
A. typically large (~5 m) and singular
B. nuclear envelope
1. double membrane surrounding the nucleus
2. nuclear pores – protein complexes that cross both membranes and regulate passage
C. chromatin – DNA-protein complex
1. have granular appearance; easily stained for microscopy (“chrom-” = color)
2. “unpacked” DNA kept ready for message transcription and DNA replication
3. proteins protect DNA and help maintain structure and function
4. chromosomes – condensed or “packed” DNA ready for cell division (“-some” = body)
D. nucleoli – regions of ribosome subunit assembly
1. appears different due to high RNA and protein concentration (no membrane)
2. ribosomal RNA (rRNA) transcribed from DNA there
3. proteins (imported from cytoplasm) join with rRNA at a nucleolus to from ribosome subunits
4. ribosome subunits are exported to the cytoplasm through nuclear pores
XXII. ribosomes – the sites of protein synthesis
A. ribosomes are granular bodies with three RNA strands and about 75 associated proteins
1. two main subunits, large and small
2. perform the enzymatic activity for forming peptide bonds, and serve as the sites of translation of genetic information into
protein sequences
B. prokaryotic ribosome subunits are both smaller than the corresponding subunits in eukaryotes
C. in eukaryotes
1. the two main subunits are formed separately in the nucleolus and transported separately to the cytoplasm
2. some are free in the cytoplasm while others are associated with the endoplasmic reticulum (ER)
XXIII. endomembrane system – a set of membranous organelles that interact with each other via vesicles
A. includes ER, Golgi apparatus, vacuoles, lysosomes, microbodies, and in some definitions the nuclear membrane and the
plasma membrane
B. endoplasmic reticulum (ER) – membrane network that winds through the cytoplasm
1. winding nature of the ER provides a lot of surface area
2. many important cell reactions or sorting functions require ER membrane surface
3. ER lumen – internal aqueous compartment in ER
 separated from the rest of the cytosol
 typically continuous throughout ER and with the lumen between the nuclear membranes
 enzymes within lumen and imbedded in lumen side of ER differ from those on the other side, thus dividing the
functional regions
4. smooth ER – primary site of lipid synthesis, many detoxification reactions, and sometimes other activities
5. rough ER – ribosomes that attach there insert proteins into the ER lumen as they are synthesized
 ribosome attachment directed by a signal peptide at the amino end of the polypeptide (see Ch. 17.4, p.326)
 a protein/RNA signal recognition particle (SRP) binds to the signal peptide and pauses translation
 at the ER the assembly binds to an SRP receptor protein
 SRP leaves, protein synthesis resumes (now into the ER lumen), and the signal peptide is cut off
 proteins inserted into the ER lumen may be membrane bound or free
 proteins are often modified in the lumen (example, carbohydrates or lipids added)
 proteins are transported from the ER in transport vesicles
C. vesicles – small, membrane-bound sacs
1. buds off of an organelle (ER or other)
2. contents within the vesicles (often proteins) transported to another membrane surface
3. vesicles fuses with membranes, delivering contents to that organelle or outside of the cell
D. Golgi apparatus (AKA Golgi complex) – a stack of flattened membrane sacs (cisternae) where proteins further processed,
modified, and sorted [the “post office” of the cell]
1. not contiguous with ER, and lumen of each sac is usually separate from the rest
2. has three areas: cis, medial, and trans
 cis face: near ER and receives vesicles from it; current model (cisternal maturation model) holds that vesicles
actually coalesce to continually form new cis cisternae
 medial region: as a new cis cisterna is produced, the older cisternae mature and move away from the ER
 in this region proteins are further modified (making glycoproteins and/or lipoproteins where appropriate, and )
 maturing cisternae may make other products; for example, many polysaccharides are made in the Golgi
 some materials are needed back a the new cis face and are transported there in vesicles
 trans face: nearest to the plasma membrane; a fully matured cisterna breaks into many vesicles that are set up to go
to the proper destination (such as the plasma membrane or another organelle) taking their contents with them
E. lysosomes – small membrane-bound sacs of digestive enzymes
1. serves to confine the digestive enzymes and their actions
2. allows maintenance of a better pH for digestion (often about pH 5)
3. formed by budding from the Golgi apparatus; special sugar attachments to hydrolytic enzymes made in the ER target
them to the lysosome
4. used to degrade ingested material, or in some cases dead or damaged organelles
 ingested material is found in vesicles that bud in from the plasma membrane; the complex molecules in those
vesicles is then digested
 can also fuse with dead or damaged organelles and digest them
5. digested material can then be sent to other parts of the cell for use
6. found in animals, protozoa; debatable in other eukaryotes, but all must have something like a lysosome
vacuoles – large membrane-bound sacs that perform diverse roles; have no internal structure
1. distinguished from vesicles by size
2. in plants, algae, and fungi, performs many of the roles that lysosomes perform for animals
3. central vacuole – typically a single, large sac in plant cells that can be 90% of the cell volume
 usually formed from fusion of many small vacuoles in immature plant cells
 storage sites for water, food, salts, pigments, and metabolic wastes
 important in maintaining turgor pressure
 tonoplast – membrane of the plant vacuole
4. food vacuoles – present in most protozoa and some animal cells; usually bud from plasma membrane and fuse with
lysosomes for digestion
5. contractile vacuoles – used by many protozoa for removing excess water
G. microbodies – small membrane-bound organelles that carry out specific cellular functions; examples:
1. lysosomes could be consider a type of microbody
2. peroxisomes – sites of many metabolic reactions that produce hydrogen peroxide (H 2O2), which is toxic to the rest of the
cell
 peroxisomes have enzymes to break down H2O2, protecting the cell
 peroxisomes are abundant in liver cells in animals and leaf cells in plants
 normally found in all eukaryotes
 example: detoxification of ethanol in liver cells occurs in peroxisomes
3. glyoxysomes – in plant seeds, contains enzymes that convert stored fats into sugar
XXIV. energy converting organelles
A. energy obtained from the environment is typically chemical energy (in food) or light energy
B. mitochondria are the organelles where chemical energy is placed in a more useful molecule, and chloroplasts are plastids
where light energy is captured during photosynthesis
C. mitochondria –the site of aerobic respiration
1. recall aerobic respiration: sugar + oxygen  carbon dioxide + water + energy
2. the “energy” is actually stored in ATP
3. mitochondria have a double membrane
 space between membranes = intermembrane space
 inner membrane is highly folded, forming cristae; provides a large surface area
 inner membrane is also a highly selective barrier
 the enzymes that conduct aerobic respiration are found in the inner membrane
 inside of inner membrane is the matrix, analogous to the cytoplasm of a cell
4. mitochondria have their own DNA, and are inherited from the mother only in humans
5. mitochondria have their own division process, similar to cell division; each cell typically has many mitochondria, which
can only arise from mitochondrial division
6. some cells require more mitochondria than others
7. mitochondria can leak electrons into the cell, allowing toxic free radicals to form
8. mitochondria play a role in initiating apoptosis (programmed cell death)
D. plastids – organelles of plants and algae that produce and store food
1. include amyloplasts (for starch storage), chromoplasts (for color, often found in petals and fruits), and chloroplasts
(for photosynthesis)
2. like mitochondria, have their own DNA (typically a bit larger and more disk-shaped than mitochondria, however)
3. derive from undifferentiated proplastids, although role of mature plastids can sometimes change
4. numbers and types of plastids vary depending on the organism and the role of the cell
5. chloroplasts get their green color from chlorophyll, the main light harvesting pigments involved in photosynthesis
(carbon dioxide + water + light energy  food(glucose) + oxygen)
6. chloroplasts have a double membrane
 the region within the inner membrane is the stroma; it is analogous to the mitochondrial matrix
 inner membrane is contiguous with an interconnected series of flat sacks called thylakoids that are grouped in
stacks called grana
 the thylakoids enclose aqueous regions called the thylakoid lumen
 chlorophyll is found in the thylakoid membrane, and the reactions of photosynthesis take place there and in the
stroma
 carotenoids in the chloroplast serve as accessory pigments for photosynthesis
E. endosymbiont theory
1. states that mitochondria and plastids evolved from prokaryotic cells that took residence in larger cells and eventually lost
their independence
2. the cells containing the endosymbionts became dependent upon them for food processing, and in turn provide them with
a protected and rich environment (a mutualistic relationship)
3. supporting evidence
F.



the size scale is right - mitochondria and plastids are on the high end of the size of typical bacteria
endosymbionts also have their own DNA and their own “cell” division; in many ways they act like bacterial cells
the DNA sequence and arrangement (circular chromosomes)of endosymbionts is closer to that of bacteria than to
that found in the eukaryotic nucleus
 endosymbionts have their own ribosomes, which are much like bacterial ribosomes
 the genetic code used by endosymbionts is more like that of bacteria than of eukaryotes
 there are other known, more modern endosymbiotic relationships: algae in corals, bacteria within protozoans in
termite guts
4. some genes appear to have been shuttled out of the endosymbionts to the nucleus
5. many of the proteins used by endosymbionts are actually encoded by nuclear genes and translated in the cytoplasm (or
on rough ER) and transported to the endosymbionts
6. DNA sequencing of endosymbionts is being used to trace the evolutionary history of the endosymbionts
 appears that endosymbiosis began about 1.5 to 2 billion years ago (around when the first eukaryotic cells appeared)
 mitochondria appear to have a monophyletic origin (one initial endosymbiotic event, giving rise to all mitochondria
in eukaryotic cells today)
 plastids appear to have a polyphyletic origin (several initial endosymbiotic events giving rise to different plastid
lines present today in algae and plants)
7. some argue that endosymbionts were simply derived within the early eukaryotic cells, along with the nuclear membrane
and the proliferation of other membrane surfaces common in eukaryotes but not prokaryotes
XXV. Cytoskeleton
A. eukaryotic cells typically have a size and shape that is maintained
1. the cytoskeleton is a dense network of protein fibers that provides needed structural support
2. the network also has other functions
 a scaffolding for organelles
 cell movement and cell division (dynamic nature to the protein fibers is involved here)
 transport of materials within the cell
B. the cytoskeleton is composed of three types of protein filaments: microtubules, microfilaments, and intermediate
filaments
C. microtubules are the thickest filaments of the cytoskeleton
1. hollow, rod -shaped cylinders about 25 nm in diameter
2. made of -tubulin and -tubulin dimers
3. dimers can be added or removed from either end (dynamic nature)
4. one end (plus end) adds dimers more rapidly than the minus end
5. can be anchored, where an end is attached to something and can no longer add or lose dimers
6. microtubule-organizing centers (MTOCs) serve as anchors
 centrosome in animal cells
 centrosome has two centrioles in a perpendicular arrangement
 centrioles have a 9x3 structure: 9 sets of 3 attached microtubules forming a hollow cylinder
 centrioles are duplicated before cell division
 play an organizing role for microtubule spindles in cell division (other eukaryotes must use some alternative MTOC
during cell division; still incompletely described)
7. microtubules are involved in moving organelles
 motor proteins (such as kinesin and dynein) attach to organelle and to microtubule
 using ATP as an energy source, the motor proteins change shape and thus produce movement
 microtubule essentially acts as a track for the motor protein
 motor proteins are directional; kinesin moves toward the plus end, dynein away from it
8. cilia and flagella are made of microtubules
 thin, flexible projections from cells
 used in cell movement, or to move things along the cell surface
 share the same basic structure; called cilia if short (2-10 m typically) and flagella if long (typically 200 m)
 central stalk covered by cell membrane extension, and anchored to a basal body
 stalk has two inner microtubules surrounded by nine attached pairs of microtubules
 9+2 arrangement
 dynein attached to the outer pairs actually fastens the pair to its neighboring pair
 dynein motor function causes relative sliding of filaments; this produces bending movement of the cilium or
flagellum
 the basal body is very much like the centriole
 has a 9x3 structure
 replicates itself
D. microfilaments are solid filaments about 7 nm in diameter
1.
2.
3.
composed of two entwined chains of actin monomers
linker proteins cross-link the actin chains with each other and other actin associated proteins
actin monomers can be added to lengthen the microfilament or removed to shorten it; this can be used to generate
movement
4. important in muscle cells; in conjunction with myosin, they are responsible for muscle contraction
5. also associate with myosin in many cells to form contractile structures, such as used in cell division
E. intermediate filaments
1. typically just a bit wider than microfilaments, this is the catch-all group for cytoskeletal filaments composed of a variety
of other proteins
2. the types of proteins involved differ depending on cell types and on the organism; apparently limited to animal cells and
protozoans
3. not easily disassembled, thus more permanent
4. a web of intermediate filaments reinforces cell shape and positions of organelles (they give structural stability)
5. prominent in cells that withstand mechanical stress
6. form the most insoluble part of the cell
XXVI. Outside the cell
A. Most prokaryotes have a cell wall, an outer envelope, and a capsule (capsule is also called glycocalyx or cell coat)
B. Most eukaryotic cells produce materials that are deposited outside the plasma membrane but that remain associated with it
1. plants have thick, defined cell walls made primarily of cross-linked cellulose fibers
 growing plant cells secrete a primary cell wall, which is thin and flexible
 after a plant cell stops growing, the primary cell wall is usually thickened and solidified, or a secondary cell wall is
produced between the primary cell wall and the plasma membrane
 secondary cell walls still contain cellulose, but typically have other material as well that strengthens them further
(for example, lignin in wood)
2. fungi typically have thinner cell walls than plants, made primarily of cross-linked chitin fibers
3. animals do not have cell walls, but their cells secrete varying amounts of compounds that can produce a glycocalyx and
an extracellular matrix (ECM)
 glycocalyx: polysaccharides attached to proteins and lipids on the outer surface of the plasma membrane
 typically functions in cell recognition and communication, cell contacts, and structural reinforcement
 often works through direct interaction with the ECM
 ECM: a gel of carbohydrates and fibrous proteins; several different molecules can be involved
 main structural protein is tough, fibrous collagen
 fibronectins are glycoproteins in the ECM that often bind to both collagen and integrins
 integrins are proteins in the plasma membrane that typically receive signals from the ECM
XXVII. Specialized contacts (junctions) between cells
cell junctions typically connect cells and can allow special transport between connected cells
A. anchoring junctions hold cells tightly together; one common type in animals is the desmosome
 desmosomes form strong bonds between cytoskeletons,of adjacent cells and hold them together
 materials can still pass in the space between cells with anchoring junctions
 NOT involved in the transport of materials between cells
B. tight junctions between some animal cells are used to seal off body cavities
 cell plasma membranes are adjacent to each other and held together by a tight seal
 materials cannot pass between cells held together by tight junctions
 NOT involved in the transport of materials between cells
C. gap junctions between animal cells act as selective pores
 proteins connect the cells
 those proteins are grouped in cylinders of 6 subunits
 the cylinder can be opened to form a small pore (less than 2 nm), through which small molecules can pass
D. plasmodesmata act as selective pores between plant cells
 plant cell walls perform the functions of tight junctions and desmosomes
 plant cell walls form a barrier to cell-to-cell communication that must be breached by the functional
equivalent of a gap junction
 plasmodesmata are relatively wide channels (20-45 nm) across the cell wall between adjacent cells; they
actually connect the plasma membranes of the two cells, and allow exchange of some materials between the
cells
Chapter 6: A Tour of the Cell
39. What are the 3 main tenets of cell theory?
40. What are the major lines of evidence that all presently living cells have a
common origin?
41. What is surface area to volume ratio, and why is it an important
consideration for cells?
42. What (usually) happens to surface area to volume ratio as cells grow
larger?
43. Compare and contrast:
 LM and EM
 SEM and TEM
Include the terms resolution and magnification in your discussions.
44. Describe cell fractionation. Why is it done, and how is it done? Include
the terms lyse, centrifugation, pellet, and supernatant in your discussion.
45. How do prokaryotic cells and eukaryotic cells differ from each other in
typical size and general organization?
46. Describe cytoplasm, cytosol, nucleoplasm, and the general role of
membranes in cells.
47. List as many organelles as you can think of. Describe their structures
and key functions.
48. Draw and label a typical animal cell and a typical plant cell, including
organelles.
49. Describe the nuclear envelope, nuclear pores, chromatin, chromosomes,
and nucleoli in terms of structures and key functions.
50. Name something that you KNOW must get out of the nucleus for cells to
function.
51. Describe the structure and function of ribosomes.
52. What is the endomembrane system (include organelle components)?
53. Diagram and describe the pathway from synthesis to final destination for
a secreted protein. Then do the same for a plasma membrane protein.
54. Diagram the cisternal maturation model for the Golgi.
55.








Describe the structure and function of:
ER
vesicles
vacuoles
Golgi apparatus
microbodies in general
lysosomes
peroxisomes
glyoxysomes
56. Draw a mitochondrion in cross-section and describe its structure and
functions.
57. Draw a chloroplast in cross-section and describe its structure and
functions.
58. Describe the endosymbiont theory. Include evidence for it, including
predictions that have proven true.
59. What are the functions of the cytoskeleton?
60. What are the three main types of cytoskeleton? Describe the structure
and function(s) of each type.
61.



Describe the structure and function(s) of:
motor proteins
MTOCs
centrosomes
 centrioles
 cilia and flagella
62. Describe the outer part and outside interface of a:
A. typical prokaryotic cell
B. typical plant cell
C. typical fungal cell
D. typical animal cell
63. Diagram and describe the animal cell glycocalyx and ECM interaction
(include collagen, fibronectin, and integrin).
Chapter 6: A Tour of the Cell
XXVIII. Cell theory
A. All living organisms are composed of cells
1.
smallest “building blocks” of all multicellular organisms
2.
all cells are enclosed by a surface membrane that separates them from other cells and from their environment
3.
specialized structures with the cell are called organelles; many are membrane-bound
B. Today, all new cells arise from existing cells
C. All presently living cells have a common origin
1.
all cells have basic structural and molecular similarities
2.
all cells share similar energy conversion reactions
3.
all cells maintain and transfer genetic information in DNA
4.
the genetic code is essentially universal
XXIX. Cell organization and homeostasis
A. Plasma membrane surrounds cells and separates their contents from the external environment
B. Cells are heterogeneous mixtures, with specialized regions and structures (such as organelles)
C. Cell size is limited
1.
surface area to volume ratio puts a limit on cell size

food and/or other materials must get into the cell

waste products must be removed from the cell

thus, cells need a high surface area to volume ratio, but volume increases faster than surface area as cells grow larger
2.
cell shape varies depending both on function and surface area requirements
XXX. Studying cells – microscopy and fractionation
A. Most cells are large enough to be resolved from each other with light microscopes (LM)
1.
cells were discovered by Robert Hooke in 1665; he saw the remains of cell walls in cork with a LM, at about 30x mag
2.
modern LMs can reach up to 1000x
3.
LM resolution (clarity) is limited to about 1 m due to the wavelength of visible light (only about 500 times better than
the human eye, even at maximum magnification)
4.
small cells (such as most bacteria) are about 1 m across, just on the edge of resolution
5.
some modifications of LMs and some treatments of cells allow observation of subcellular structure in some cases
B. Resolution of most subcellular structure requires electron microscopy (EM)
1.
electrons have a much smaller wavelength than light (resolve down to under 1 nm)
2.
magnification up to 250,000x or more and resolution over 500,000 times better than the human eye
3.
includes transmission (TEM) and scanning (SEM) forms

transmission - electron passes through sample; need very thin samples (100 nm or less thick); samples embedded in
plastic and sliced with a diamond knife

scanning – samples are gold-plated; electrons interact with the surface; images have a 3-D appearance
C. Cells can be broken and fractionated to separate cellular components for study
1.
cells are broken (lysed) by disrupting the cell membrane, often using some sort of detergent
2.
grinding and other physical force may be required, especially if cell walls are present
3.
centrifugation is used to separate cellular components

using a centrifuge, samples are spun at high speeds, resulting in exposure to a centrifugal force of thousands to
hundreds of thousands times gravity (example, 500,000 x G)

results in a pellet and supernatant; cell components will be in one or the other depending on their individual
properties; intact membrane-bound organelles often wind up in pellets, depending on their density and the
centrifugal force reached (more dense = more likely in pellet)

special treatments can determine whether a component ends up in the pellet or supernatant

density gradients can also be used to subdivide pellet components based on their density; this can be used to separate
organelles from each other, for example Golgi apparatus from ER
XXXI. Eukaryotic vs. prokaryotic cells
A. eukaryotic cells have internal membranes and a distinct, membrane-enclosed nucleus; typically 10-100 m in diameter
B. prokaryotic cells do not have internal membranes (thus no nuclear membrane)
1.
main DNA molecule (chromosome) is typically circular; its location is called the nuclear area
2.
other small DNA molecules (plasmids) are often present, found throughout the cell
3.
plasma membrane is usually enclosed in a cell wall that is often covered with a capsule (layer of proteins and/or sugars)
4.
do not completely lack organelles; the plasma membrane and ribosomes are both present and are considered organelles
5.
AKA bacteria, prokaryotic cells are typically 1-10 m in diameter
XXXII. Compartments in eukaryotic cells (cell regions, organelles)
A. two general regions inside the cell: cytoplasm and nucleoplasm
1.
cytoplasm – everything outside the nucleus and within the plasma membrane; contains fluid cytosol and organelles
2.
nucleoplasm – everything within the nuclear membrane
B. membranes separate cell regions
1.
have nonpolar regions that help form a barrier between aqueous regions
2.
allow for some selection in what can cross a membrane (more details later)
XXXIII. nucleus – the “control center” of the cell
A. typically large (~5 m) and singular
B. nuclear envelope
1.
double membrane surrounding the nucleus
2.
nuclear pores – protein complexes that cross both membranes and regulate passage
C. chromatin – DNA-protein complex
1.
have granular appearance; easily stained for microscopy (“chrom-” = color)
2.
“unpacked” DNA kept ready for message transcription and DNA replication
3.
proteins protect DNA and help maintain structure and function
4.
chromosomes – condensed or “packed” DNA ready for cell division (“-some” = body)
D. nucleoli – regions of ribosome subunit assembly
1.
appears different due to high RNA and protein concentration (no membrane)
2.
ribosomal RNA (rRNA) transcribed from DNA there
3.
proteins (imported from cytoplasm) join with rRNA at a nucleolus to from ribosome subunits
4.
ribosome subunits are exported to the cytoplasm through nuclear pores
XXXIV. ribosomes – the sites of protein synthesis
A. ribosomes are granular bodies with three RNA strands and about 75 associated proteins
1.
two main subunits, large and small
2.
perform the enzymatic activity for forming peptide bonds, serve as the sites of translation
B. prokaryotic ribosome subunits are both smaller than the corresponding subunits in eukaryotes
C. in eukaryotes
1.
the two main subunits are formed separately in the nucleolus and transported separately to the cytoplasm
2.
some are free in the cytoplasm while others are associated with the endoplasmic reticulum (ER)
XXXV. endomembrane system – a set of membranous organelles that interact with each other via vesicles
A. includes ER, Golgi apparatus, vacuoles, lysosomes, microbodies, and in some definitions the nuclear membrane and the
plasma membrane
B. endoplasmic reticulum (ER) – membrane network that winds through the cytoplasm
1.
winding nature of the ER provides a lot of surface area
2.
many important cell reactions or sorting functions require ER membrane surface
3.
ER lumen – internal aqueous compartment in ER

separated from the rest of the cytosol

typically continuous throughout ER and with the lumen between the nuclear membranes

enzymes within lumen and imbedded in lumen side of ER differ from those on the other side, thus dividing the
functional regions
4.
smooth ER – primary site of lipid synthesis, many detoxification reactions, and sometimes other activities
5.
rough ER – ribosomes that attach there insert proteins into the ER lumen as they are synthesized

ribosome attachment directed by a signal peptide at the amino end of the polypeptide (see Ch. 17.4, p.326)

a protein/RNA signal recognition particle (SRP) binds to the signal peptide and pauses translation

at the ER the assembly binds to an SRP receptor protein

SRP leaves, protein synthesis resumes (now into the ER lumen), and the signal peptide is cut off

proteins inserted into the ER lumen may be membrane bound or free

proteins are often modified in the lumen (example, carbohydrates or lipids added)

proteins are transported from the ER in transport vesicles
C. vesicles – small, membrane-bound sacs
1.
buds off of an organelle (ER or other)
2.
contents within the vesicles (often proteins) transported to another membrane surface
3.
vesicles fuses with membranes, delivering contents to that organelle or outside of the cell
D. Golgi apparatus (AKA Golgi complex) – a stack of flattened membrane sacs (cisternae) where proteins further processed,
modified, and sorted [the “post office” of the cell]
1.
not contiguous with ER, and lumen of each sac is usually separate from the rest
2.
has three areas: cis, medial, and trans

cis face: near ER and receives vesicles from it; current model (cisternal maturation model) holds that vesicles
actually coalesce to continually form new cis cisternae


medial region: as a new cis cisterna is produced, the older cisternae mature and move away from the ER

in this region proteins are further modified (making glycoproteins and/or lipoproteins where appropriate, and )

maturing cisternae may make other products; for example, many polysaccharides are made in the Golgi

some materials are needed back a the new cis face and are transported there in vesicles
trans face: nearest to the plasma membrane; a fully matured cisterna breaks into many vesicles that are set up to go
to the proper destination (such as the plasma membrane or another organelle) taking their contents with them
E. lysosomes – small membrane-bound sacs of digestive enzymes
1.
serves to confine the digestive enzymes and their actions
2.
allows maintenance of a better pH for digestion (often about pH 5)
3.
formed by budding from the Golgi apparatus; special sugar attachments to hydrolytic enzymes made in the ER target
them to the lysosome
4.
used to degrade ingested material, or in some cases dead or damaged organelles

ingested material is found in vesicles that bud in from the plasma membrane; the complex molecules in those
vesicles is then digested

F.
can also fuse with dead or damaged organelles and digest them
5.
digested material can then be sent to other parts of the cell for use
6.
found in animals, protozoa; debatable in other eukaryotes, but all must have something like a lysosome
vacuoles – large membrane-bound sacs that perform diverse roles; have no internal structure
1.
distinguished from vesicles by size
2.
in plants, algae, and fungi, performs many of the roles that lysosomes perform for animals
3.
central vacuole – typically a single, large sac in plant cells that can be 90% of the cell volume
4.

usually formed from fusion of many small vacuoles in immature plant cells

storage sites for water, food, salts, pigments, and metabolic wastes

important in maintaining turgor pressure

tonoplast – membrane of the plant vacuole
food vacuoles – present in most protozoa and some animal cells; usually bud from plasma membrane and fuse with
lysosomes for digestion
5.
contractile vacuoles – used by many protozoa for removing excess water
G. microbodies – small membrane-bound organelles that carry out specific cellular functions; examples:
1.
lysosomes could be consider a type of microbody
2.
peroxisomes – sites of many metabolic reactions that produce hydrogen peroxide (H 2O2), which is toxic to the cell
3.

peroxisomes have enzymes to break down H2O2, protecting the cell

peroxisomes are abundant in liver cells in animals and leaf cells in plants

normally found in all eukaryotes

example: detoxification of ethanol in liver cells occurs in peroxisomes
glyoxysomes – in plant seeds, contains enzymes that convert stored fats into sugar
XXXVI. energy converting organelles
A. energy obtained from the environment is typically chemical energy (in food) or light energy
B. mitochondria are the organelles where chemical energy is placed in a more useful molecule, and chloroplasts are plastids
where light energy is captured during photosynthesis
C. mitochondria –the site of aerobic respiration
1.
recall aerobic respiration: sugar + oxygen  carbon dioxide + water + energy
2.
the “energy” is actually stored in ATP
3.
mitochondria have a double membrane

space between membranes = intermembrane space

inner membrane is highly folded, forming cristae; provides a large surface area

inner membrane is also a highly selective barrier

the enzymes that conduct aerobic respiration are found in the inner membrane

inside of inner membrane is the matrix, analogous to the cytoplasm of a cell
4.
mitochondria have their own DNA, and are inherited from the mother only in humans
5.
mitochondria have their own division process, similar to cell division; each cell typically has many mitochondria, which
can only arise from mitochondrial division
6.
some cells require more mitochondria than others
7.
mitochondria can leak electrons into the cell, allowing toxic free radicals to form
8.
mitochondria play a role in initiating apoptosis (programmed cell death)
D. plastids – organelles of plants and algae that produce and store food
1.
include amyloplasts (for starch storage), chromoplasts (for color, often found in petals and fruits), and chloroplasts
(for photosynthesis)
2.
like mitochondria, have their own DNA (typically a bit larger and more disk-shaped than mitochondria, however)
3.
derive from undifferentiated proplastids, although role of mature plastids can sometimes change
4.
numbers and types of plastids vary depending on the organism and the role of the cell
5.
chloroplasts get their green color from chlorophyll, the main light harvesting pigments involved in photosynthesis
(carbon dioxide + water + light energy  food(glucose) + oxygen)
6.
chloroplasts have a double membrane

the region within the inner membrane is the stroma; it is analogous to the mitochondrial matrix

inner membrane is contiguous with an interconnected series of flat sacks called thylakoids that are grouped in
stacks called grana

the thylakoids enclose aqueous regions called the thylakoid lumen

chlorophyll is found in the thylakoid membrane, and the reactions of photosynthesis take place there and in the
stroma

carotenoids in the chloroplast serve as accessory pigments for photosynthesis
E. endosymbiont theory
1.
states that mitochondria and plastids evolved from prokaryotic cells that took residence in larger cells and eventually lost
their independence
2.
the cells containing the endosymbionts became dependent upon them for food processing, and in turn provide them with
a protected and rich environment (a mutualistic relationship)
3.
supporting evidence

the size scale is right - mitochondria and plastids are on the high end of the size of typical bacteria

endosymbionts also have their own DNA and their own “cell” division; in many ways they act like bacterial cells

the DNA sequence and arrangement (circular chromosomes) of endosymbionts is closer to that of bacteria than to
that found in the eukaryotic nucleus

endosymbionts have their own ribosomes, which are much like bacterial ribosomes

there are other known, more modern endosymbiotic relationships: algae in corals, bacteria within protozoans in
termite guts
4.
some genes appear to have been shuttled out of the endosymbionts to the nucleus
5.
many of the proteins used by endosymbionts are actually encoded by nuclear genes and translated in the cytoplasm (or
on rough ER) and transported to the endosymbionts
6.
DNA sequencing of endosymbionts is being used to trace the evolutionary history of the endosymbionts

appears that endosymbiosis began about 1.5 to 2 billion years ago (around when the first eukaryotic cells appeared)

mitochondria appear to have a monophyletic origin (one initial endosymbiotic event, giving rise to all mitochondria
in eukaryotic cells today)

plastids appear to have a polyphyletic origin (several initial endosymbiotic events giving rise to different plastid
lines present today in algae and plants)
7.
some argue that endosymbionts were simply derived within the early eukaryotic cells, along with the nuclear membrane
and the proliferation of other membrane surfaces common in eukaryotes but not prokaryotes
XXXVII.
Cytoskeleton
A. eukaryotic cells typically have a size and shape that is maintained
1.
the cytoskeleton is a dense network of protein fibers that provides needed structural support
2.
the network also has other functions

a scaffolding for organelles

cell movement and cell division (dynamic nature to the protein fibers is involved here)

transport of materials within the cell
B. the cytoskeleton is composed of three types of protein filaments: microtubules, microfilaments, and intermediate
filaments
C. microtubules are the thickest filaments of the cytoskeleton
1.
hollow, rod -shaped cylinders about 25 nm in diameter
2.
made of -tubulin and -tubulin dimers
3.
dimers can be added or removed from either end (dynamic nature)
4.
one end (plus end) adds dimers more rapidly than the minus end
5.
can be anchored, where an end is attached to something and can no longer add or lose dimers
6.
microtubule-organizing centers (MTOCs) serve as anchors

centrosome in animal cells

centrosome has two centrioles in a perpendicular arrangement

centrioles have a 9x3 structure: 9 sets of 3 attached microtubules forming a hollow cylinder

centrioles are duplicated before cell division

play an organizing role for microtubule spindles in cell division (other eukaryotes must use some alternative MTOC
during cell division; still incompletely described)
7.
microtubules are involved in moving organelles

motor proteins (such as kinesin and dynein) attach to organelle and to microtubule

using ATP as an energy source, the motor proteins change shape and thus produce movement
8.

microtubule essentially acts as a track for the motor protein

motor proteins are directional; kinesin moves toward the plus end, dynein away from it
cilia and flagella are made of microtubules

thin, flexible projections from cells

used in cell movement, or to move things along the cell surface

share the same basic structure; called cilia if short (2-10 m typically) and flagella if long (typically 200 m)

central stalk covered by cell membrane extension, and anchored to a basal body

stalk has two inner microtubules surrounded by nine attached pairs of microtubules

9+2 arrangement

dynein attached to the outer pairs actually fastens the pair to its neighboring pair

dynein motor function causes relative sliding of filaments; this produces bending movement of the cilium or
flagellum

the basal body is very much like the centriole

has a 9x3 structure

replicates itself
D. microfilaments are solid filaments about 7 nm in diameter
1.
composed of two entwined chains of actin monomers
2.
linker proteins cross-link the actin chains with each other and other actin associated proteins
3.
actin monomers can be added to lengthen the microfilament or removed to shorten it; can be used to generate movement
4.
important in muscle cells; in conjunction with myosin, they are responsible for muscle contraction
5.
also associate with myosin in many cells to form contractile structures, such as used in cell division
E. intermediate filaments
1.
typically just a bit wider than microfilaments, this is the catch-all group for cytoskeletal filaments composed of a variety
of other proteins
2.
the types of proteins involved differ depending on cell types and on the organism; apparently limited to animal cells and
protozoans
3.
not easily disassembled, thus more permanent
4.
a web of intermediate filaments reinforces cell shape and positions of organelles (they give structural stability)
5.
prominent in cells that withstand mechanical stress
6.
form the most insoluble part of the cell
XXXVIII.
Outside the cell
A. Most prokaryotes have a cell wall, an outer envelope, and a capsule (capsule is also called glycocalyx or cell coat)
B. Most eukaryotic cells produce materials that are deposited outside the plasma membrane but that remain associated with it
1.
plants have thick, defined cell walls made primarily of cross-linked cellulose fibers

growing plant cells secrete a primary cell wall, which is thin and flexible

after a plant cell stops growing, the primary cell wall is usually thickened and solidified, or a secondary cell wall is
produced between the primary cell wall and the plasma membrane

secondary cell walls still contain cellulose, but typically have other material as well that strengthens them further
(for example, lignin in wood)
2.
fungi typically have thinner cell walls than plants, made primarily of cross-linked chitin fibers
3.
animals do not have cell walls, but their cells secrete varying amounts of compounds that can produce a glycocalyx and
an extracellular matrix (ECM)


glycocalyx: polysaccharides attached to proteins and lipids on the outer surface of the plasma membrane

typically functions in cell recognition and communication, cell contacts, and structural reinforcement

often works through direct interaction with the ECM
ECM: a gel of carbohydrates and fibrous proteins; several different molecules can be involved

main structural protein is tough, fibrous collagen

fibronectins are glycoproteins in the ECM that often bind to both collagen and integrins

integrins are proteins in the plasma membrane that typically receive signals from the ECM
Chapter 7: Membrane structure and function
I.
Roles of biological membranes
A. membranes separate aqueous environments, so that differences can be maintained
1. the plasma membrane surrounds the cell and separates the interior of the cell from the external environment
2. membrane-bound organelles have their interior region separated from the rest of the cell
B. passage of substances across membranes is generally regulated, helping to establish and maintain appropriate environments
in the cell even as the outside environment changes
C. membranes provide a surface on which many chemical events can occur
1. enzymes embedded in membranes catalyze many chemical reactions, and the locations of reactants and products on one
side or the other of the membrane is often used to help control reaction rates
2. proteins and glycoproteins embedded in membranes are used for chemical recognition and signaling
II.
Physical properties of cell membranes: the lipid bilayer and the fluid mosaic model
A. biological membranes are lipid bilayers with associated proteins and glycoproteins
1. most of the lipids involved are phospholipids, although others like cholesterol and various glycolipids are also present
B. phospholipids molecules spontaneously form bilayers in aqueous environments due to their amphipathic nature and overall
cylindrical structure
1. amphipathic molecules have distinct hydrophobic and hydrophilic regions
2. recall the hydrophilic “head” and hydrophobic “tails” of phospholipids
 tails come from two chains of fatty acids linked to glycerol
 head comes from a polar organic molecule linked via a phosphate group to the glycerol backbone
3. the two tails combine with the head to give a roughly cylindrical shape to the phospholipids molecule, a shape that favors
the formation of lipid bilayers over lipid spheres
4. there are other amphipathic molecules, such as detergents (soaps, etc.), that come to a point at their single hydrophobic
tail, thus tending to form spheres instead of bilayers
detergents can “solubilize” lipids to varying degrees; high enough concentrations of detergents will disrupt cell
membranes
C. the fluid mosaic model describes the structure and properties of cell membranes
1. while a structural model including a lipid bilayer was proposed in the 1930s, early models sandwiched the lipid bilayer
with membrane-associated proteins
2. EM data after the 1950s showed that membrane bilayers are uniformly about 8 nm thick, too thin for the sandwich
model; also, isolated membrane proteins were often found to have a globular nature that did not fit the sandwich
model
3. in 1972, the fluid mosaic model was proposed where some proteins are imbedded in lipid bilayers that act as twodimensional fluids; this model explained the existing data and made two key predications that have been verified:
 materials, including embedded proteins, can be moved along the membrane due to its fluid properties
 digestion of certain “transmembrane” proteins applied to one side of a membrane will produce protein fragments
that differ from those found if digestion is done only on the other side
4. biological membranes act as two-dimensional fluids, or liquid crystals
 free to move in two dimensions, but not in the third, the molecules of the membrane can rotate or move laterally
 molecules rarely “flip” from one side of the membrane to the other (that would be movement in the third dimension)
 the fluidity of a membrane is a function of both temperature and the molecules in the membrane
 cells need membranes to be within a reasonable range of fluidity – too fluid and they are too weak, too viscous
and they are more like solid gels
 at a given temperature, phospholipids with saturated fats are less fluid than those with unsaturated fats
 in an unsaturated fat, a carbon-carbon double bond produces a “bend” that causes the phospholipids to be
spaced further away from its neighbors, thus retaining more freedom of motion
 the upshot is: at colder temperatures, unsaturated fats are preferred in cell membranes; at higher temperatures,
saturated fats are preferred
 other lipids, such as cholesterol, can stabilize membrane fluidity
 organisms control membrane fluidity by several means
 by regulating their temperature
 by changing the fatty acid profile of their membranes
 by adding fluidity modifiers or stabilizers like cholesterol
5. biological membranes resist having open ends
 a lipid bilayer will spontaneously “self-seal”
 usually, this results in nearly spherical vesicles with an internal, aqueous lumen
 the spherical tendency can be modified with structural elements, such as structural proteins
 winding membrane surfaces must be kept far enough apart and structurally supported to prevent them from selfsealing
 vesicle formation takes advantage of self-sealing as regions of membrane are pinched off by protein contractile
rings
 fusion of membrane surfaces can occur when they are in close proximity
 fusion is common between vesicles and various organelles
 contents of two separate membrane-bound lumens are mixed when fusion occurs
 fusion of vesicles with the plasma membrane delivers the material in the vesicle lumen to the outside of the cell
D. membrane-associated proteins
1. membrane proteins are classified as either integral or peripheral
 integral proteins are amphipathic proteins that are firmly bound to the membrane, and can only be released from
the membrane by detergents
 some integral proteins are transmembrane proteins, extending completely across the membrane
 hydrophobic alpha-helices are common in the membrane spanning domains of transmembrane proteins
 some wind back-and-forth across the membrane, but most only span the membrane once
 peripheral proteins are not embedded in the membrane; they are usually bound ionically or by hydrogen bonds to a
hydrophilic portion of an integral protein
2. the protein profile of one membrane side typically differs from that of the other side
 many more proteins are on the cytoplasmic side of the plasma membrane, as revealed by freeze-fracturing plasma
membranes
 the types of processing that a protein receives differs depending on the target side, or if it is integral
3. membrane proteins perform several functions, including acting as enzymes, regulating transport across the membrane,
and in cell signaling
III.
Transport and transfer across cell membranes
A. cell membranes are selectively permeable
1. some substances readily pass through, others do not
2. most permeable to small molecules and lipid-soluble substances
 water(!) and other small molecules like CO2 and O2 can pass through easily
5.
B.
C.
D.
E.
F.
 some examples of molecules that do not pass through easily: amino acids, sugars, ions
3. some passage across the membrane is assisted with special channels to allow or speed up the passage
4. the specific selectivity can vary depending on the membrane
diffusion across membranes is based on random motion of particles
1. particles move by random motion (kinetic energy); over time, the concentration across a membrane will tend to equalize
2. diffusion is the net movement of particles from an area with a high (initial) concentration to an area with a low (initial)
concentration; a difference in concentrations establishes a concentration gradient, which provides the energy for
diffusion
3. given enough time, equilibrium will be reached (the concentrations on both sides of the membrane will be equal)
4. often equilibrium is never reached due to continual removal and/or continual production of a substance
5. rate of diffusion is a function temperature and of the size, shape, and charge nature of the substance
osmosis is diffusion of a solvent across a membrane
1. in biology, the solvent is typically water
2. solutes do not travel across membranes with water, but they affect movement by affecting the concentration of water;
thus:
3. osmotic pressure is determined by the amount of dissolved substances in a solution; it is the tendency of water to move
into the solution
 when two solutions have the same osmotic pressure, they are isotonic
 when a solution has a higher osmotic pressure than another, it is hypertonic to the other solution; water will tend to
flow into the hypertonic solution
 conversely, a hypotonic solution has a relatively lower osmotic pressure; water will tend to flow out of the
hypotonic solution into the hypertonic solution
4. turgor pressure is hydrostatic pressure in cells with a cell wall
 a cell wall enables cells to take in extra amounts of water without bursting
 the cells take in water and push against the cell wall, which pushes back
 many cells use turgor pressure as part of maintaining structure; thus, if they lose turgor pressure, plants wilt
special integral membrane proteins assist in transport across membranes (carrier-mediated transport)
1. facilitated diffusion – when net transport follows a concentration gradient, but proteins are needed to assist in transport
 the carrier protein often provides a regulated channel or pore through the membrane
 typically used to transport ions and large molecules like glucose, although water channels also exist
 added energy is not required (concentration gradient provides the energy), and in some cases is harvested during
transport
2. carrier-mediated active transport requires energy to work against a concentration gradient
 energy is often supplied by ATP powering a protein “pump” that moves a substance against a gradient
 example: sodium-potassium pump in nearly all animal cells (moves 3 Na+ out, 2 K+ in)
 linked cotransport can also provide the energy for active transport
 Na+, K+, or H+ is transported down its gradient, providing energy
 another substance is transported at the same time against its gradient, using the energy
 the Na+, K+, or H+ gradient is often produced by active transport via a pump that uses ATP
large particles are transported across membranes via exocytosis and endocytosis
1. exocytosis - fusion of vesicles or vacuoles with the plasma membrane that results in secretion outside the cell or
discarding waste outside the cell
2. endocytosis – vesicles or vacuoles bud into the cell from the plasma membrane, bringing materials into the cell
 phagocytosis – large solid particles are ingested (including whole cells in some cases)
 pinocytosis – smaller regions of dissolved materials are ingested
 receptor-mediated endocytosis – receptor proteins in the plasma membrane bind to specific molecules, causing
protein conformational (shape) changes that lead to the formation of a coated vesicle
 typically, lysosomes bind with the vesicles or vacuoles formed via phagocytosis or receptor-mediated endocytosis
signal transduction is the transfer of information across the cell membrane
1. signal reception - special protein receptors in the cell membrane bind to signaling molecules outside the cell
2. signal transduction – the receptor, now activated, changes shape in some way and transfers information to the interior of
the cells (often though a series of protein activations and eventual formation of cAMP on the cytosolic side of the cell
membrane)
Chapter 7: Membranes
1.
What are the major roles of biological membranes?
2.
What about phospholipids makes a bilayer when mixed with water? Use the term
amphipathic, and contrast with what detergents do.
3.
Describe the fluid mosaic model: what does it mean to have a 2-dimensional fluid
and not a 3-dimensional one, and what does the “mosaic” term mean here?
4.
Discuss membrane fluidity: why it is important and the ways it can be adjusted.
5.
Contrast integral and peripheral membrane proteins.
6.
Define and discuss these terms related to transport/transfer across cell membranes:









selectively permeable
diffusion
concentration gradient
osmosis
tonics
isotonic
hypertonic
hypotonic
turgor pressure
7.
What is carrier-mediated transport? Differentiate between facilitated diffusion and
active transport.
8.
Describe how the sodium-potassium pump works.
9.
Explain linked cotransport.
10. Define the processes of exocytosis and endocytosis (include different forms of
endocytosis).
11. Summarize processes for transport of materials across membranes; include
information about which ones are active (energy-requiring).
12. Discuss information transfer across a membrane (signal transduction); why is it
needed, what are some concepts that you should associate with it?
13.
Differentiate between the following in terms of structure and function:




anchoring junctions (such as desmosomes)
tight junctions
gap juntions
plasmodesmata
Chapter 7: Membranes
I.
Roles of biological membranes
A. membranes separate aqueous environments, so that differences can be maintained
1.
the plasma membrane surrounds the cell and separates the interior of the cell from the external environment
2.
membrane-bound organelles have their interior region separated from the rest of the cell
B. passage of substances across membranes is generally regulated, helping to establish and maintain appropriate environments
in the cell even as the outside environment changes
C. membranes provide a surface on which many chemical events can occur
1.
enzymes embedded in membranes catalyze many chemical reactions, and the locations of reactants and products on one
side or the other of the membrane is often used to help control reaction rates
2.
II.
proteins and glycoproteins embedded in membranes are used for chemical recognition and signaling
Physical properties of cell membranes: the lipid bilayer and the fluid mosaic model
A. biological membranes are lipid bilayers with associated proteins and glycoproteins
1.
most of the lipids involved are phospholipids, although others like cholesterol and various glycolipids are also present
B. phospholipids molecules spontaneously form bilayers in aqueous environments due to their amphipathic nature and overall
cylindrical structure
1.
amphipathic molecules have distinct hydrophobic and hydrophilic regions
2.
recall the hydrophilic “head” and hydrophobic “tails” of phospholipids
3.

tails come from two chains of fatty acids linked to glycerol

head comes from a polar organic molecule linked via a phosphate group to the glycerol backbone
the two tails combine with the head to give a roughly cylindrical shape to the phospholipids molecule, a shape that favors
the formation of lipid bilayers over lipid spheres
4.
there are other amphipathic molecules, such as detergents (soaps, etc.), that come to a point at their single hydrophobic
tail, thus tending to form spheres instead of bilayers
5.
detergents can “solubilize” lipids to varying degrees; high enough concentrations of detergents will disrupt cell
membranes
C. the fluid mosaic model describes the structure and properties of cell membranes
1.
while a structural model including a lipid bilayer was proposed in the 1930s, early models sandwiched the lipid bilayer
with membrane-associated proteins
2.
EM data after the 1950s showed that membrane bilayers are uniformly about 8 nm thick, too thin for the sandwich
model; also, isolated membrane proteins were often found to have a globular nature that did not fit the sandwich
model
3.
in 1972, the fluid mosaic model was proposed where some proteins are imbedded in lipid bilayers that act as twodimensional fluids; this model explained the existing data and made two key predications that have been verified:

materials, including embedded proteins, can be moved along the membrane due to its fluid properties

digestion of certain “transmembrane” proteins applied to one side of a membrane will produce protein fragments
that differ from those found if digestion is done only on the other side
4.
biological membranes act as two-dimensional fluids, or liquid crystals

free to move in two dimensions, but not in the third, the molecules of the membrane can rotate or move laterally

molecules rarely “flip” from one side of the membrane to the other (that would be movement in the third dimension)

the fluidity of a membrane is a function of both temperature and the molecules in the membrane

cells need membranes to be within a reasonable range of fluidity – too fluid and they are too weak, too viscous
and they are more like solid gels

at a given temperature, phospholipids with saturated fats are less fluid than those with unsaturated fats

in an unsaturated fat, a carbon-carbon double bond produces a “bend” that causes the phospholipids to be
spaced further away from its neighbors, thus retaining more freedom of motion

the upshot is: at colder temperatures, unsaturated fats are preferred in cell membranes; at higher temperatures,
saturated fats are preferred


5.
other lipids, such as cholesterol, can stabilize membrane fluidity
organisms control membrane fluidity by several means

by regulating their temperature

by changing the fatty acid profile of their membranes

by adding fluidity modifiers or stabilizers like cholesterol
biological membranes resist having open ends

a lipid bilayer will spontaneously “self-seal”

usually, this results in nearly spherical vesicles with an internal, aqueous lumen

the spherical tendency can be modified with structural elements, such as structural proteins

winding membrane surfaces must be kept far enough apart and structurally supported to prevent them from selfsealing

vesicle formation takes advantage of self-sealing as regions of membrane are pinched off by protein contractile
rings

fusion of membrane surfaces can occur when they are in close proximity

fusion is common between vesicles and various organelles

contents of two separate membrane-bound lumens are mixed when fusion occurs

fusion of vesicles with the plasma membrane delivers the material in the vesicle lumen to the outside of the cell
D. membrane-associated proteins
1.
membrane proteins are classified as either integral or peripheral

integral proteins are amphipathic proteins that are firmly bound to the membrane, and can only be released from
the membrane by detergents


some integral proteins are transmembrane proteins, extending completely across the membrane

hydrophobic alpha-helices are common in the membrane spanning domains of transmembrane proteins

some wind back-and-forth across the membrane, but most only span the membrane once
peripheral proteins are not embedded in the membrane; they are usually bound ionically or by hydrogen bonds to a
hydrophilic portion of an integral protein
2.
the protein profile of one membrane side typically differs from that of the other side

many more proteins are on the cytoplasmic side of the plasma membrane, as revealed by freeze-fracturing plasma
membranes

3.
the types of processing that a protein receives differs depending on the target side, or if it is integral
membrane proteins perform several functions, including acting as enzymes, regulating transport across the membrane,
and in cell signaling
III.
Transport and transfer across cell membranes
A. cell membranes are selectively permeable
1.
some substances readily pass through, others do not
2.
most permeable to small molecules and lipid-soluble substances

water(!) and other small molecules like CO2 and O2 can pass through easily

some examples of molecules that do not pass through easily: amino acids, sugars, ions
3.
some passage across the membrane is assisted with special channels to allow or speed up the passage
4.
the specific selectivity can vary depending on the membrane
B. diffusion across membranes is based on random motion of particles
1.
particles move by random motion (kinetic energy); over time, the concentration across a membrane will tend to equalize
2.
diffusion is the net movement of particles from an area with a high (initial) concentration to an area with a low (initial)
concentration; a difference in concentrations establishes a concentration gradient, which provides the energy for
diffusion
3.
given enough time, equilibrium will be reached (the concentrations on both sides of the membrane will be equal)
4.
often equilibrium is never reached due to continual removal and/or continual production of a substance
5.
rate of diffusion is a function temperature and of the size, shape, and charge nature of the substance
C. osmosis is diffusion of a solvent across a membrane
1.
in biology, the solvent is typically water
2.
solutes do not travel across membranes with water, but they affect movement by affecting the concentration of water;
thus:
3.
osmotic pressure is determined by the amount of dissolved substances in a solution; it is the tendency of water to move
into the solution

when two solutions have the same osmotic pressure, they are isotonic

when a solution has a higher osmotic pressure than another, it is hypertonic to the other solution; water will tend to
flow into the hypertonic solution

conversely, a hypotonic solution has a relatively lower osmotic pressure; water will tend to flow out of the
hypotonic solution into the hypertonic solution
4.
turgor pressure is hydrostatic pressure in cells with a cell wall

a cell wall enables cells to take in extra amounts of water without bursting

the cells take in water and push against the cell wall, which pushes back

many cells use turgor pressure as part of maintaining structure; thus, if they lose turgor pressure, plants wilt
D. special integral membrane proteins assist in transport across membranes (carrier-mediated transport)
1.
facilitated diffusion – when net transport follows a concentration gradient, but proteins are needed to assist in transport

the carrier protein often provides a regulated channel or pore through the membrane

typically used to transport ions and large molecules like glucose, although water channels also exist

added energy is not required (concentration gradient provides the energy), and in some cases is harvested during
transport
2.
carrier-mediated active transport requires energy to work against a concentration gradient

energy is often supplied by ATP powering a protein “pump” that moves a substance against a gradient


example: sodium-potassium pump in nearly all animal cells (moves 3 Na+ out, 2 K+ in)
linked cotransport can also provide the energy for active transport

Na+, K+, or H+ is transported down its gradient, providing energy

another substance is transported at the same time against its gradient, using the energy

the Na+, K+, or H+ gradient is often produced by active transport via a pump that uses ATP
E. large particles are transported across membranes via exocytosis and endocytosis
1.
exocytosis - fusion of vesicles or vacuoles with the plasma membrane that results in secretion outside the cell or
discarding waste outside the cell
2.
endocytosis – vesicles or vacuoles bud into the cell from the plasma membrane, bringing materials into the cell

phagocytosis – large solid particles are ingested (including whole cells in some cases)

pinocytosis – smaller regions of dissolved materials are ingested

receptor-mediated endocytosis – receptor proteins in the plasma membrane bind to specific molecules, causing
protein conformational (shape) changes that lead to the formation of a coated vesicle

F.
typically, lysosomes bind with the vesicles or vacuoles formed via phagocytosis or receptor-mediated endocytosis
signal transduction is the transfer of information across the cell membrane
1.
signal reception - special protein receptors in the cell membrane bind to signaling molecules outside the cell
2.
signal transduction – the receptor, now activated, changes shape in some way and transfers information to the interior of
the cells (often though a series of protein activations and eventual formation of cAMP on the cytosolic side of the cell
membrane)
IV.
Specialized contacts (junctions) between cells
A. cell junctions typically connect cells and can allow special transport between connected cells
B. anchoring junctions hold cells tightly together; one common type in animals is the desmosome
1.
desmosomes form strong bonds, including merging of cytoskeletons, making it hard to separate the cells from each other
2.
materials can still pass in the space between cells with anchoring junctions
3.
NOT involved in the transport of materials between cells
C. tight junctions between some animal cells are used to seal off body cavities
1.
cell plasma membranes are adjacent to each other and held together by a tight seal
2.
materials cannot pass between cells held together by tight junctions
3.
NOT involved in the transport of materials between cells
D. gap junctions between animal cells act as selective pores
1.
proteins connect the cells
2.
those proteins are grouped in cylinders of 6 subunits
3.
the cylinder can be opened to form a small pore (less than 2 nm), through which small molecules can pass
E. plasmodesmata act as selective pores between plant cells
1.
plant cell walls perform the functions of tight junctions and desmosomes
2.
plant cell walls form a barrier to cell-to-cell communication that must be breached by the functional equivalent of a gap
junction
3.
plasmodesmata are relatively wide channels (20-45 nm) across the cell wall between adjacent cells; they actually
connect the plasma membranes of the two cells, and allow exchange of some materials between the cells
Chapter 8: An introduction to metabolism
Why do organisms need energy? How do organisms manage their energy needs?
V.
Energy and thermodynamics
A. Living organisms require energy to do work, any change in state or motion of matter
1. energy can be expressed in units of work (kJ) or heat energy (kcal); 1 kcal = 4.184 kJ
2. energy can change forms (energy conversion)
3. organisms carry out transformation in energy forms between potential energy (capacity to do work) and kinetic energy
(energy of motion, actively performing work)
4. organisms commonly use chemical bonds for storage and transfer of (potential) energy
5. work is required for the processes of life
B. Two laws of thermodynamics describe the constraints on energy usage
1. First law: the total amount of energy (+ matter) in a closed system remains constant (principle of conservation of
energy)
 The universe is a closed system
 Living things are open systems
2. Second law: in every energy conversion, some energy is converted to heat energy that is lost to the surroundings, and
thus cannot be used for work
 Every energy conversion increased the entropy of the universe.
 Energy converted to heat in the surroundings increases entropy (spreading of energy)
 no energy conversion is 100% efficient
 organisms must get a constant influx of energy because of energy is lost in conversions
VI.
Metabolic reactions include anabolism and catabolism, and involve energy transfers
A. Recall that metabolism is the sum of chemical activities in a organism
B. Metabolism can be divided into anabolism (anabolic reactions) and catabolism (catabolic reactions)
1. anabolic reactions are processes that build complex molecules from simpler ones
2. catabolic reactions are processes the break down complex molecules into simpler ones
C. Chemical reactions involve changes in chemical bonds and substance concentrations, along with changes in free energy
1. free energy = energy available to do work in a chemical reaction (such as: create a chemical bond)
 free energy changes depend on bond energies and concentrations of reactants and products
 bond energy = energy required to break a bond; value depends on the bond
 left undisturbed, reactions will reach dynamic equilibrium when the relative concentrations of reactants and
products is correct
 forward and reverse reaction rates are equal; concentrations remain constant
 cells manipulate relative concentrations in many ways, so that equilibrium is rare for key reactions
2. exergonic reactions – the products have less free energy than reactants
 the difference in energy is released and is available to do work
 exergonic reactions are thermodynamically favored; thus, they are spontaneous, but not necessarily fast (more on
activation energy later)
 catabolic reactions are usually exergonic
 ATP + H2O  ADP + Pi is highly exergonic in cellular conditions
3. endergonic reactions – the products have more free energy than the reactants
 the difference in free energy must be supplied (stored in chemical bonds)
 endergonic reactions are not thermodynamically favored, so they are not spontaneous
 an endergonic reaction is coupled with an exergonic reaction to provide the needed energy to drive an endergonic
reaction
 together, the coupled reactions must have a net exergonic nature
 reaction coupling requires that the reactions share a common intermediate(s)
EXAMPLE:

A  B (exergonic)
C  D (endergonic)
Coupled: A + C  B + D (overall exergonic)
Actually: A + C  I  B + D
 typically, the exergonic reaction in the couple is ATP + H 2O  ADP + Pi
anabolic reactions are usually endergonic
One way that organisms manage their energy needs is to use ATP as a ready energy source for many reactions.
VII. ATP is the main energy currency in cells
A. Recall ATP (adenosine triphosphate) is a nucleotide with adenine base, ribose sugar, and a chain of 3 phosphate groups
B. The last two phosphate groups are joined to the phosphate group chain by unstable bonds; breaking these bonds is relatively
easy, and releases energy; thus:
1. hydrolysis of ATP to ADP and inorganic phosphate (P i) releases energy
ATP + H2O  ADP + Pi
2. the amount of energy released depends in part on concentrations of reactants and products, but is generally ~30 kJ/mol
C. Intermediates are involved when ATP hydrolysis is coupled to a reaction to provide energy; often these involve
phosphorylated compounds, with the inorganic phosphate removed from ATP transferred onto another compound rather
than being immediately released
EXAMPLE:
glucose + fructose  sucrose + H2O (endergonic; requires ~27 kJ/mol)
ATP + H2O  ADP + Pi (provides ~30 kJ/mol)
coupled:
glucose + fructose + ATP + H2O  sucrose + H2O + ADP + Pi
intermediates:
glucose + fructose + ATP + H2O  glucose-P + fructose + ADP  sucrose + H2O + ADP + P
simplified:
glucose + fructose + ATP  sucrose +ADP + Pi
D. Thus, energy transfer in cellular reactions is often accomplished through transfer of a phosphate group from ATP
E. Making ATP involves an endergonic condensation reaction
1. reverse of an exergonic reaction is always endergonic
ADP + Pi  ATP + H2O (endergonic, usually requires more than ~30 kJ/mol)
2. must be coupled with an exergonic reaction; typically from a catabolic pathway
F. ATP is typically created in catabolic reactions and used in anabolic reactions, linking those aspects of metabolism
G. Cells maintain high levels of ATP relative to ADP
1. maximizes energy available from hydrolysis of ATP
2. ratio typically greater than 10 ATP: 1 ADP
H. Overall concentration of ATP still very low
1. supply typically only enough for a few seconds at best
2. instability prevents stockpiling
3. must be constantly produced
4. in a typical cell, the rate of use and production of ATP is about 10 million molecules per second
5. resting human has less than 1 g of ATP at any given time but uses about 45 kg per day
Redox reactions are used to harvest energy from some chemicals; the acceptors of that energy typically cannot be used directly as
energy currency.
VIII. Redox reactions are also used for energy transfer
A. Electrons can also be used for energy transfer
1. Redox reactions: recall reduction, gain electrons; oxidation, lose electrons; both occur simultaneously in cells
(generally no free electrons in cells)
2. Typically, the oxidized substance gives up energy with the electron, the reduced substance gains energy with the electron
3. Commonly occur as a chain of redox reactions or electron transfers (more on electron transport chains later)
4. As the electron is transferred to an acceptor molecule, it releases free energy that can be used for other chemical
reactions
5. Typically, a proton is removed as well when an electron is removed from covalent molecules; thus, the equivalent of a
hydrogen atom is transferred
B. Catabolism typically involves removal of hydrogen atoms from nutrients (such as carbohydrates), and the transfer of the
protons and electrons to intermediate electron acceptors
1. One common intermediate acceptor is nicotinamide adenine dinucleotide (NAD+)
 Use XH2 to represent a nutrient molecule:
XH2 + NAD+  X + NADH + H+
 Often, the reduced form is just called NADH
 Reduced state stores energy, which is partially released as free energy when NADH is oxidized
 The free energy usually winds up being used to make ATP
2. Other commonly used acceptors are NADP+, FAD, and cytochromes
 NADP+/NADPH – important in photosynthesis


FAD/FADH2 – flavin adenine dinucleotide
Cytochromes – small iron-containing proteins; iron serves as electron acceptor
Enzymes are a large part of the answer to how organisms manage their energy needs. Manipulation of reactions is essential to and
largely defining of life, and enzymes manipulate the speed of reactions. Understanding life requires understanding how enzymes
work.
IX.
Enzymes regulate chemical reactions in living organisms
A. An enzyme is an organic molecule (typically a protein) that acts as a catalyst
1. catalyst – substance that increases the rate of a chemical reaction without being consumed in the reaction (the catalyst
recycles back to its original state)
2. enzymes (catalysts) only alter reaction rate; thermodynamics still governs whether the reaction can occur – thus,
enzymes only catalyze reactions that are occurring anyway
B. Enzymes (catalysts) work by lowering the activation energy of a reaction
1. all reactions have a required energy of activation (the energy required to break existing bonds) that must be supplied in
some way before the reaction can proceed; also, reactants must come together
2. catalysts greatly reduce the activation energy requirement, making it easier for a reaction to occur
3. often, this reduction in activation energy is due to in part to the enzyme holding reactants (substrates) close together,
which also reduces the reliance on random collisions
C. Enzymes lower activation energy by forming a complex with the substrate(s)
1. the ability to form an enzyme-substrate complex is highly dependent on the shape of the enzyme
2. the site where the substrate(s) binds to the enzyme is called the active site
3. when the enzyme-substrate complex forms, there are typically shape changes in the enzyme and substrate(s) – this is
called induced fit
4. the enzyme-substrate complex is typically very unstable and short-lived; it breaks down into released product(s) and a
free enzyme that is ready to be reused
5. overall:
enzyme +substrate(s)  ES complex  enzyme + product(s)
D. Enzyme names
1. many names give some indication of substrate
2. most enzyme names end in –ase (example: sucrase)
3. some end in –zyme (example: lysozyme)
4. some traditional names are less indicative of enzyme function (example: pepsin)
E. Enzymes are generally highly specific
1. overall shape as well as spatial arrangements in the active site limit what enzyme-substrate complexes can readily form
2. the amount of specificity depends on the particular enzyme
 example of high specificity: sucrase splits sucrose, not other disaccharides
 example of low specificity: lipase splits variety of fatty acids from glycerol
3. enzymes are classified by the kind of reaction they catalyze
F. Many enzymes require cofactors to function
1. apoenzyme + cofactor  active enzyme (bound together)
2. alone, an apoenzyme or a cofactor has little if any catalytic activity
3. cofactors may or may not be changed by the reaction
4. cofactors can be organic or inorganic
 organic examples (coenzymes):
 ATP, NADH, NADPH, FADH2
 typically changed by the catalyzed reaction
 inorganic examples

metal ions like Ca2+, Mg2+, Fe3+, etc.
 typically not changed by the catalyzed reaction
5. most vitamins are coenzymes or part of coenzymes, or are used for making coenzymes
G. Enzymes are most active under optimal conditions
1. each enzyme has an optimal temperature
 most effective as a catalyst at the optimal temperature
 rate of drop-off in effectiveness away from optimal temperature depends on the enzyme
 high temperatures tend to denature enzymes
 human enzymes have temperature optima near human body temperature (37°C)
2. each enzyme has an optimal pH
 again, most effective at the optimum; drop-off varies
 extremes of pH tend to denature enzymes
 a particular organism shows more variety in enzyme pH optima than in temperature optima, but most of its enzymes
will still be optimal at the pH normally found in the cytosol of its cells
H. Metabolic pathways use organized “teams” of enzymes
1. the products of one reaction often serve as substrates for the next reaction
2. removing products (by having them participate the “next reaction”) improves reaction rate
3. multiple metabolic pathways exit in cells, overlapping in some areas and diverging in others
I. Cells can regulate enzyme activity to control reactions
1. increase substrate amount  increase reaction rate (up to saturation of available enzyme molecules)
2. increase enzyme amount  increase reaction rate (as long as substrate amount > enzyme amount)
3. compartmentation of the enzyme, substrate, and products can help control reaction rate
4. inhibitors and activators of enzymes
 inhibitors reduce or eliminate catalytic activity
 activators allow or enhance catalytic activity
 sometime, this uses an allosteric site – a receptor site on an enzyme where an inhibitor or activator can bind
 a common example of allosteric control is feedback inhibition, where the last product in a metabolic pathway
binds to an allosteric site of an enzyme in an early step of the pathway (often the first) and inhibits activity
of the enzyme
 irreversible inhibition – enzyme is permanently inactivated or destroyed; includes many drugs and toxins
 reversible inhibition – if inhibitor is removed, the enzyme activity can be recovered
 competitive inhibition – inhibitor is similar in structure to a substrate; competes with substrate for binding to
the active site
 noncompetitive inhibition – binds at allosteric site, alters enzyme shape to make active site unavailable
Chapter 8: Energy and Metabolism
1.
Discuss energy conversions and the 1st and 2nd law of thermodynamics. Be sure to use the terms
work, potential energy, kinetic energy, and entropy.
2.
What are Joules (J) and calories (cal)?
3.
The laws of thermodynamics are sometimes stated as: In energy conversions, “You can’t win, and
you can’t break even.” Explain.
4.
Differentiate between:
anabolism and catabolism
exergonic and endergonic reactions
5.
Why is ATP so darned important?
What is a phosphorylated intermediate?
How much ATP is in a cell at any given time?
Why must cells keep a high ATP/ADP ratio?
6.
What are redox reactions used for in cells? How (generally) can you tell which of two similar
compounds is reduced and which is oxidized? Give some examples of compounds commonly used in
redox reactions in cells.
7.
What do enzymes do for cells, and how do they do it? Be sure to use the following terms: catalyst (or
catalyze); activation energy, enzyme-substrate complex, active site, induced fit
8.
What are the four main things that enzymes do to lower activation energy?
9.
How are enzymes named (what suffixes indicate an enzyme)?
10. Explain the terms cofactor, apoenzyme, and coenzyme.
11. Discuss the effects of temperature and pH on enzyme activity.
12. What is a metabolic pathway?
13. How do cells regulate enzyme activity? Include the terms inhibitors, activators, allosteric site, and
feedback inhibition; also, differentiate between irreversible and reversible inhibition and between
competitive and noncompetitive inhibition.
Chapter 8: Energy and Metabolism
Why do organisms need energy? How do organisms manage their energy needs?
X.
Energy and thermodynamics
A. Living organisms require energy to do work, any change in state or motion of matter
1.
energy can be expressed in units of work (kJ) or heat energy (kcal); 1 kcal = 4.184 kJ
2.
energy can change forms (energy conversion)
3.
organisms carry out transformation in energy forms between potential energy (capacity to do work) and kinetic energy
(energy of motion, actively performing work)
4.
organisms commonly use chemical bonds for storage and transfer of (potential) energy
5.
work is required for the processes of life
B. Two laws of thermodynamics describe the constraints on energy usage
1.
2.
First law: the total amount of energy (+ matter) in a closed system remains constant (principle of conservation of energy)

The universe is a closed system

Living things are open systems
Second law: in every energy conversion, some energy is converted to heat energy that is lost to the surroundings, and
thus cannot be used for work

Also can be stated as: Every energy conversion increased the entropy of the universe.

Energy converted to heat in the surroundings increases entropy (spreading of energy)

Upshot: no energy conversion is 100% efficient

Just to maintain their current state, organisms must get a constant influx of energy because of energy lost in
conversions
XI.
Metabolic reactions include anabolism and catabolism, and involve energy transfers
A. Recall that metabolism is the sum of chemical activities in a organism
B. Metabolism can be divided into anabolism (anabolic reactions) and catabolism (catabolic reactions)
1.
anabolic reactions are processes that build complex molecules from simpler ones
2.
catabolic reactions are processes the break down complex molecules into simpler ones
C. Chemical reactions involve changes in chemical bonds and substance concentrations, along with changes in free energy
1.
free energy = energy available to do work in a chemical reaction (such as: create a chemical bond)

free energy changes depend on bond energies and concentrations of reactants and products

bond energy = energy required to break a bond; value depends on the bond

left undisturbed, reactions will reach dynamic equilibrium when the relative concentrations of reactants and
products is correct
2.

forward and reverse reaction rates are equal; concentrations remain constant

cells manipulate relative concentrations in many ways, so that equilibrium is rare for key reactions
exergonic reactions – the products have less free energy than reactants

the difference in energy is released and is available to do work

exergonic reactions are thermodynamically favored; thus, they are spontaneous, but not necessarily fast (more on
activation energy later)
3.

catabolic reactions are usually exergonic

ATP + H2O  ADP + Pi is highly exergonic in cellular conditions
endergonic reactions – the products have more free energy than the reactants

the difference in free energy must be supplied (stored in chemical bonds)

endergonic reactions are not thermodynamically favored, so they are not spontaneous

an endergonic reaction is coupled with an exergonic reaction to provide the needed energy to drive an endergonic
reaction

together, the coupled reactions must have a net exergonic nature

reaction coupling requires that the reactions share a common intermediate(s)
EXAMPLE:
A  B (exergonic)
C  D (endergonic)
Coupled: A + C  B + D (overall exergonic)
Actually: A + C  I  B + D


typically, the exergonic reaction in the couple is ATP + H 2O  ADP + Pi
anabolic reactions are usually endergonic
One way that organisms manage their energy needs is to use ATP as a ready energy source for many reactions.
XII.
ATP is the main energy currency in cells
A. Recall ATP (adenosine triphosphate) is a nucleotide with adenine base, ribose sugar, and a chain of 3 phosphate groups
B. The last two phosphate groups are joined to the phosphate group chain by unstable bonds; breaking these bonds is relatively
easy, and releases energy; thus:
1.
hydrolysis of ATP to ADP and inorganic phosphate (P i) releases energy
ATP + H2O  ADP + Pi
2.
the amount of energy released depends in part on concentrations of reactants and products, but is generally ~30 kJ/mol
C. Intermediates are involved when ATP hydrolysis is coupled to a reaction to provide energy; often these involve
phosphorylated compounds, with the inorganic phosphate removed from ATP transferred onto another compound rather
than being immediately released
EXAMPLE:
glucose + fructose  sucrose + H2O (endergonic; requires ~27 kJ/mol)
ATP + H2O  ADP + Pi (provides ~30 kJ/mol)
coupled:
glucose + fructose + ATP + H2O  sucrose + H2O + ADP + Pi
simplified:
glucose + fructose + ATP  sucrose +ADP + Pi
with intermediates:
glucose + fructose + ATP + H2O  glucose-P + fructose + ADP  sucrose + H2O + ADP + Pi
D. Thus, energy transfer in cellular reactions is often accomplished through transfer of a phosphate group from ATP
E. Making ATP involves an endergonic condensation reaction
1.
reverse of an exergonic reaction is always endergonic
ADP + Pi  ATP + H2O (endergonic, usually requires more than ~30 kJ/mol)
2.
F.
must be coupled with an exergonic reaction; typically from a catabolic pathway (more on that later)
Overall, ATP is typically created in catabolic reactions and used in anabolic reactions, linking those aspects of metabolism
G. Cells maintain high levels of ATP relative to ADP
1.
maximizes energy available from hydrolysis of ATP
2.
ratio typically greater than 10 ATP: 1 ADP
H. Overall concentration of ATP still very low
1.
supply typically only enough for a few seconds at best
2.
instability prevents stockpiling
3.
must be constantly produced
4.
in a typical cell, the rate of use and production of ATP is about 10 million molecules per second
5.
resting human has less than 1 g of ATP at any given time but uses about 45 kg per day
Redox reactions are used to harvest energy from some chemicals; the acceptors of that energy typically cannot be used directly
as energy currency.
XIII. Redox reactions are also used for energy transfer
A. Electrons can also be used for energy transfer
1.
Redox reactions: recall reduction, gain electrons; oxidation, lose electrons; both occur simultaneously in cells
(generally no free electrons in cells)
2.
Typically, the oxidized substance gives up energy with the electron, the reduced substance gains energy with the electron
3.
Commonly occur as a chain of redox reactions or electron transfers (more on electron transport chains later)
4.
As the electron is transferred to an acceptor molecule, it releases free energy that can be used for other chemical
reactions
5.
Typically, a proton is removed as well when an electron is removed from covalent molecules; thus, the equivalent of a
hydrogen atom is transferred
B. Catabolism typically involves removal of hydrogen atoms from nutrients (such as carbohydrates), and the transfer of the
protons and electrons to intermediate electron acceptors
1.
One common intermediate acceptor is nicotinamide adenine dinucleotide (NAD+)

Use XH2 to represent a nutrient molecule:
XH2 + NAD+  X + NADH + H+
2.

Often, the reduced form is just called NADH

Reduced state stores energy, which is partially released as free energy when NADH is oxidized

The free energy usually winds up being used to make ATP
Other commonly used acceptors are NADP+, FAD, and cytochromes

NADP+/NADPH – important in photosynthesis

FAD/FADH2 – flavin adenine dinucleotide

Cytochromes – small iron-containing proteins; iron serves as electron acceptor
Enzymes are a large part of the answer to how organisms manage their energy needs. Manipulation of reactions is essential to
and largely defining of life, and enzymes manipulate the speed of reactions. Understanding life requires understanding how
enzymes work.
XIV. Enzymes regulate chemical reactions in living organisms
A. An enzyme is an organic molecule (typically a protein) that acts as a catalyst
1.
catalyst – substance that increases the rate of a chemical reaction without being consumed in the reaction (the catalyst
recycles back to its original state)
2.
enzymes (catalysts) only alter reaction rate; thermodynamics still governs whether the reaction can occur – thus,
enzymes only catalyze reactions that are occurring anyway
B. Enzymes (catalysts) work by lowering the activation energy of a reaction
1.
all reactions have a required energy of activation (the energy required to break existing bonds) that must be supplied in
some way before the reaction can proceed; also, reactants must come together
2.
catalysts greatly reduce the activation energy requirement, making it easier for a reaction to occur
3.
often, this reduction in activation energy is due to in part to the enzyme holding reactants (substrates) close together,
which also reduces the reliance on random collisions
C. Enzymes lower activation energy by forming a complex with the substrate(s)
1.
the ability to form an enzyme-substrate complex is highly dependent on the shape of the enzyme
2.
the site where the substrate(s) binds to the enzyme is called the active site
3.
when the enzyme-substrate complex forms, there are typically shape changes in the enzyme and substrate(s) – this is
called induced fit
4.
the enzyme-substrate complex is typically very unstable and short-lived; it breaks down into released product(s) and a
free enzyme that is ready to be reused
5.
overall:
enzyme +substrate(s)  ES complex  enzyme + product(s)
D. the reduction in activation energy is due primarily to four things:
1.
an enzyme holds reactants (substrates) close together in the right orientation for the reaction, which reduces the reliance
on random collisions
2.
an enzyme may put a “strain” on existing bonds, making them easier to break
3.
an enzyme provides a “microenvironment” that is more chemically suited to the reaction
4.
sometimes the active site of the enzyme itself is directly involved in the reaction during the transition states
E. Enzyme names
F.
1.
many names give some indication of substrate
2.
most enzyme names end in –ase (example: sucrase)
3.
some end in –zyme (example: lysozyme)
4.
some traditional names are less indicative of enzyme function (example: pepsin)
Enzymes are generally highly specific
1.
overall shape as well as spatial arrangements in the active site limit what enzyme-substrate complexes can readily form
2.
the amount of specificity depends on the particular enzyme
3.

example of high specificity: sucrase splits sucrose, not other disaccharides

example of low specificity: lipase splits variety of fatty acids from glycerol
enzymes are classified by the kind of reaction they catalyze
G. Many enzymes require cofactors to function
1.
apoenzyme + cofactor  active enzyme (bound together)
2.
alone, an apoenzyme or a cofactor has little if any catalytic activity
3.
cofactors may or may not be changed by the reaction
4.
cofactors can be organic or inorganic


5.
organic examples (coenzymes):

ATP, NADH, NADPH, FADH2

typically changed by the catalyzed reaction
inorganic examples

metal ions like Ca2+, Mg2+, Fe3+, etc.

typically not changed by the catalyzed reaction
most vitamins are coenzymes or part of coenzymes, or are used for making coenzymes
H. Enzymes are most active under optimal conditions
1.
2.
each enzyme has an optimal temperature

most effective as a catalyst at the optimal temperature

rate of drop-off in effectiveness away from optimal temperature depends on the enzyme

high temperatures tend to denature enzymes

human enzymes have temperature optima near human body temperature (37°C)
each enzyme has an optimal pH

again, most effective at the optimum; drop-off varies

extremes of pH tend to denature enzymes

a particular organism shows more variety in enzyme pH optima than in temperature optima, but most of its enzymes
will still be optimal at the pH normally found in the cytosol of its cells
I.
Metabolic pathways use organized “teams” of enzymes
1.
the products of one reaction often serve as substrates for the next reaction
2.
removing products (by having them participate the “next reaction”) improves reaction rate
3.
J.
multiple metabolic pathways exit in cells, overlapping in some areas and diverging in others
Cells can regulate enzyme activity to control reactions
1.
increase substrate amount  increase reaction rate (up to saturation of available enzyme molecules)
2.
increase enzyme amount  increase reaction rate (as long as substrate amount > enzyme amount)
3.
compartmentation of the enzyme, substrate, and products can help control reaction rate
4.
inhibitors and activators of enzymes

inhibitors reduce or eliminate catalytic activity

activators allow or enhance catalytic activity

sometime, this uses an allosteric site – a receptor site on an enzyme where an inhibitor or activator can bind

a common example of allosteric control is feedback inhibition, where the last product in a metabolic pathway
binds to an allosteric site of an enzyme in an early step of the pathway (often the first) and inhibits activity
of the enzyme

irreversible inhibition – enzyme is permanently inactivated or destroyed; includes many drugs and toxins

reversible inhibition – if inhibitor is removed, the enzyme activity can be recovered

competitive inhibition – inhibitor is similar in structure to a substrate; competes with substrate for binding to
the active site

noncompetitive inhibition – binds at allosteric site, alters enzyme shape to make active site unavailable
Chapter 9: Cellular Respiration-Harvesting Chemical Energy
I.
Three terms describe the ways in which cells generate ATP
A. aerobic respiration – a generally efficient process that requires O2; most, but not all, organisms can use a form of this
process at least some of the time; also called cellular respiration (How is this different from breathing, and how is it
related to breathing?)
B. anaerobic respiration – processes similar to aerobic respiration but that do not use O 2; used mainly by bacteria that live in
anaerobic (O2-deficient) environments
C. fermentation – generally inefficient processes used mainly when other pathways cannot be used or when ATP is needed
quickly; fermentation processes do not use O2
II.
Aerobic respiration: a redox process
A. aerobic respiration, the most efficient form of cellular respiration, is used by most organisms
B. nutrients (typically glucose) are catabolized to water and carbon dioxide, and energy is stored in ATP
C6H12O6 + 6 O2 +6 H2O  6 CO2 + 12 H2O + energy (stored in 36-38 ATP molecules)
1. this is a redox process – glucose is oxidized to carbon dioxide, and oxygen is reduced to water
2. above equation is overall; aerobic respiration is actually is series of reactions
3. water is shown on both sides above because it is consumed in some reactions and generated in others
4. the overall process is the same as what you would get from burning glucose (but the energy would all be lost as heat)
C. aerobic respiration is a complex series of enzyme-catalyzed reactions that can be grouped into four types of reactions:
1. substrate-level phosphorylation – coupled reactions that directly phosphorylate ADP or GDP
2. dehydrogenation reactions – redox reactions that transfer hydrogen to NAD + or FAD
3. decarboxylation reactions – carboxyl groups are removed; CO2 is released
4. preparation reactions – molecules are rearranged to prepare for other reactions
5. of the above, only substrate-level phosphorylation and dehydrogenation provide energy for cells
III.
Aerobic respiration is conventionally divided into four stages
A. glycolysis
1. occurs in the cytosol (both in prokaryotes and eukaryotes)
2. overall, glucose is converted to 2 pyruvate molecules (a 3-carbon molecule)
3. released energy is stored in a net yield of 2 ATP and 2 NADH molecules
4. occurs under both aerobic and anaerobic conditions (no O 2 required)
5. actually a series of ten reactions, each catalyzed by a different enzyme; broken into two phases (energy investment and
energy capture)
6. first phase requires energy investment
 phosphorylation, using two ATP, charges the sugar with two phosphates
 2 molecules of glyceraldehyde 3-phosphate (G3P) are formed
7. second phase, the energy payoff phase, yields private and energy captured in ATP and NADH
 each G3P is converted to pyruvate, C3H3O3- (net of 2 pyruvates)
 aside: -ate and –ic acid forms are essentially equivalent in cells; for example, pyruvate and pyruvic acid
 produces 4 ATP (net of 2 ATP)
 produces 2 NADH + H+
8. overall:
C6H12O6 + 2 ADP +2 Pi + 2 NAD+  2 [C3H3O3- ]+ 2 ATP + 2 NADH + 4 H+ + 2 H2O
B. formation of acetyl coenzyme A (acetyl-CoA) from pyruvate (AKA pyruvate oxidation)
1. pyruvate is sent to the mitochondria in eukaryotes (stays in cytosol of prokaryotes)
2. set of three enzymes catalyze the reactions, grouped together in the pyruvate dehydrogenase complex
3. oxidative decarboxylation: a carboxyl group is removed from pyruvate (CO2 is produced)
4. remaining 2-carbon fragment is oxidized (loses 2 electrons); NADH is produced
5. remaining 2-carbon fragment, an acetyl group, is joined to coenzyme A (from B-vitamin pantothenic acid) to form
acetyl-CoA
6. overall:
C3H3O3- + NAD+ + CoA  acetyl-CoA + CO2 + NADH
and so far:
C6H12O6 + 2 ADP +2 Pi + 4 NAD+ + 2CoA  2 acetyl-CoA + 2 CO2 + 2 ATP + 4 NADH + 4 H+ + 2 H2O
C. citric acid cycle
1. AKA tricarboxylic acid cycle, TCA cycle, Krebs cycle
2. still in mitochondria of eukaryotes
3. series of 8 enzyme-catalyzed steps, and one side reaction where GTP + ADP  GDP + ATP
4. entry: acetyl-CoA + oxaloacetate  citrate + CoA
5. rest of cycle: citrate + H2O  2 CO2 + oxaloacetate + energy
 note there is no net gain or loss of oxaloacetate in the cycle
 energy is stored in three NADH and one FADH2 for each cycle, plus one ATP
6. overall:
acetyl-CoA +3 NAD+ + FAD + ADP + Pi  CoA + 2 CO2 + 3 NADH + 3 H+ + FADH2 + ATP +H2O
and so far:
7.
C6H12O6 + 4 ADP +4 Pi + 10 NAD+ + 2 FAD  6 CO2 + 4 ATP + 10 NADH + 10 H+ + 2 FADH2 + 4 H2O
note that at this point glucose has been completely catabolized, yet only 4 ATP have been formed; the rest of the energy
is stored in NADH and FADH2
D. oxidative phosphorylation: the electron transport chain and chemiosmosis
1. occurs in mitochondria of eukaryotes, and on membrane surface in prokaryotes
2. electrons from NADH and FADH2 are transferred to a chain of membrane-bound electron acceptors, and eventually
passed to oxygen
 acceptors include flavin mononucleotide (FMN), ubiquinone, iron-sulfur proteins, cytochromes
 in the end, electrons wind up on molecular oxygen, and water is formed
(NADH or FADH2) + ½ O2  H2O + (NAD+ or FAD) + energy
 lack of oxygen or compounds like cyanide stop the transport chain, and energy cannot be obtained from NADH and
FADH2 – this usually starves cells, killing them
3. hydrogen ions (protons) are pumped across the inner mitochondrial membrane, creating a concentration gradient with
high proton concentration in the intermembrane space
 energy for the pumping comes from energy lost as electrons are transferred
 gradient allows opportunity for energy capture
4. chemiosmosis produces ATP
 protons are charged and do not readily cross a cell membrane
5.
6.
IV.
 special protein channel, ATP synthase (also called ATP synthetase) allows proton transport with the gradient
 energy is captured and used to make ATP
energy from oxidation of NADH yields ~3 ATP (only ~2 if the electrons from the NADH from glycolysis wind up on
FADH2 after being shuttled across the mitochondrial membrane)
energy from oxidation of FADH2 yields ~2 ATP
Aerobic respiration theoretically yields 36 or 38 ATP molecules from one glucose molecule
Glycolysis
Citric Acid Cycle
FADH2 oxidation (2 x 2)
NADH oxidation (8 x 3, 2 x 2 or 3)
TOTAL
2 ATP
2 ATP
4 ATP
28-30 ATP
36-38 ATP
The actual yield is typically about 30 ATP per glucose. Why only ~30? Chemiosmosis doesn’t actually give round figures, and
some of the energy from the proton gradient is used for other things too, like bringing pyruvate into the mitochondrion. The
overall efficiency of aerobic respiration is typically about 32%; the rest of the energy from combustion of glucose is released as
heat (compare this to a car’s internal combustion engine, typically about 20-25% efficiency).
V.
Non-glucose energy sources
A. other substances can be oxidized to produce ATP in living systems
B. along with carbohydrates, proteins and lipids (fats) are generally major energy sources in foods; nucleic acids are not present
in high amounts in foods and thus aren’t as important in providing cells with energy
C. proteins are broken into amino acids, which can be broken down further
1. amino group is removed (deamination)
2. amino group may eventually be converted to urea and excreted
3. remaining carbon chain enters aerobic respiration at various points, depending on chain length
4. provide roughly the same amount of energy per unit weight as does glucose
D. lipids (focus on triacylglycerols)
1. lipids are more reduced than glucose (note less oxygen in lipids), thus more energetic
2. glycerol is converted to glyceraldehyde-3-phosphate (G3P), entering glycolysis
3. fatty acids are oxidized and split into acetyl groups that are combined with CoA to make acetyl-CoA (this process is
called  oxidation)
4. typically provides over twice as much energy per unit weight as glucose
5. as an example, oxidation of a 6-carbon fatty acid yields up to 44 ATP
VI.
Regulation of aerobic respiration
A. ATP/ADP balance regulates much of oxidative phosphorylation
1. ATP synthesis continues until ADP stores are largely depleted
2. rapid use of ATP leads to excess ADP, and thus speeds up aerobic respiration
B. phosphofructokinase, the enzyme for one of the earliest steps in glycolysis, is highly regulated
1. ATP, though a substrate, also serves as an allosteric inhibitor
2. citrate is also an allosteric inhibitor
3. AMP serves as an allosteric activator
VII.
A.
B.
C.
D.
Anaerobic respiration
bacteria that live in environments where O2 is not abundant perform anaerobic respiration
still uses an electron transport chain
some other compound such as NO3-, SO42- or CO2 serves as the ultimate electron acceptor
not as efficient as aerobic respiration (exact efficiency varies depending on the process and the species)
VIII. Fermentation
A. involves no electron transport chain
B. inefficient; net is 2 ATP per glucose molecule (only glycolysis works)
C. if glycolysis only, then NAD+ must be regenerated, thus fermentation, where NADH reduces an organic molecule
1. alcohol fermentation produces ethanol, CO2, and NAD+
 pyruvate is converted to ethanol and CO2 to regenerate NAD+
 ethanol is a potentially toxic waste product, and is removed from cells
 yeast (and many bacteria) perform alcoholic fermentation in low oxygen environments
 used in making alcoholic beverages, baking
2. lactic acid fermentation produces lactate and NAD+



pyruvate is reduced to lactate to regenerate NAD+
performed by some bacteria and fungi, and by animals (when muscles need energy fast)
used in making cheese, yogurt, sauerkraut
To review the materials in this chapter make yourself a chart like the one below. Practice to
recreate it several times initially using your book and then from memory
PROCESS
Where? (carbon)
(carbon)
Net
Net
Net
Other
compounds compounds ATP NADH FADH2 notable
in
out
made made made
items
glycolysis
acetyl-CoA
formation
citric acid cycle
oxidative
phosphorylation
TOTAL
Chapter 9: How do cells harvest energy?
14.
Differentiate between aerobic respiration, anaerobic respiration, and fermentation.
15. Write the overall chemical equation for aerobic respiration and note what gets
oxidized and what gets reduced.
16.
List and describe the 4 general types of reactions in aerobic respiration.
17.
Fill out aerobic respiration chart (class activity).
18. Describe the use of proteins as an energy source. Include discussion of relative
energy provision, pathway entry point(s), and key terms (amino acid, deamination).
19. Describe the use of triacylglycerol lipids as an energy source. Include discussion of
relative energy provision, pathway entry point(s), and key terms (glycerol, fatty acid, G3P,
 oxidation).
20. Differentiate between anaerobic respiration, alcohol fermentation, and lactic acid
fermentation. Include comparisons to aerobic respiration in terms of process and energy
yield; where these processes are found in nature; key terms and products (NAD+
regeneration, ethanol, CO2, lactic acid); and human uses of these processes.
Chapter 9: How do cells harvest energy?
IX.
Three terms describe the ways in which cells generate ATP
A. aerobic respiration – a generally efficient process that requires O2; most, but not all, organisms can use a form of this
process at least some of the time; also called cellular respiration (How is this different from breathing, and how is it
related to breathing?)
B. anaerobic respiration – processes similar to aerobic respiration but that do not use O2; used mainly by bacteria that live in
anaerobic (O2-deficient) environments
C. fermentation – generally inefficient processes used mainly when other pathways cannot be used or when ATP is needed
quickly; fermentation processes do not use O2
X.
Aerobic respiration: a redox process
A. aerobic respiration, the most efficient form of cellular respiration, is used by most organisms
B. nutrients (typically glucose) are catabolized to water and carbon dioxide, and energy is stored in ATP
C6H12O6 + 6 O2 +6 H2O  6 CO2 + 12 H2O + energy (stored in 36-38 ATP molecules)
1.
this is a redox process – glucose is oxidized to carbon dioxide, and oxygen is reduced to water
2.
above equation is overall; aerobic respiration is actually is series of reactions
3.
water is shown on both sides above because it is consumed in some reactions and generated in others
4.
the overall process is the same as what you would get from burning glucose (but the energy would all be lost as heat)
C. aerobic respiration is a complex series of enzyme-catalyzed reactions that can be grouped into four types of reactions:
XI.
1.
substrate-level phosphorylation – coupled reactions that directly phosphorylate ADP or GDP
2.
dehydrogenation reactions – redox reactions that transfer hydrogen to NAD + or FAD
3.
decarboxylation reactions – carboxyl groups are removed; CO2 is released
4.
preparation reactions – molecules are rearranged to prepare for other reactions
5.
of the above, only substrate-level phosphorylation and dehydrogenation provide energy for cells
Aerobic respiration is conventionally divided into four stages
A. glycolysis
1.
occurs in the cytosol (both in prokaryotes and eukaryotes)
2.
overall, glucose is converted to 2 pyruvate molecules (a 3-carbon molecule)
3.
released energy is stored in a net yield of 2 ATP and 2 NADH molecules
4.
occurs under both aerobic and anaerobic conditions (no O 2 required)
5.
actually a series of ten reactions, each catalyzed by a different enzyme; broken into two phases (energy investment and
energy payoff)
6.
7.
8.
first phase requires energy investment

phosphorylation, using two ATP, charges the sugar with two phosphates

2 molecules of glyceraldehyde 3-phosphate (G3P) are formed
second phase, the energy payoff phase, yields private and energy captured in ATP and NADH

each G3P is converted to pyruvate, C3H3O3- (net of 2 pyruvates)

aside: -ate and –ic acid forms are essentially equivalent in cells; for example, pyruvate and pyruvic acid

produces 4 ATP (net of 2 ATP)

produces 2 NADH + H+
overall:
C6H12O6 + 2 ADP +2 Pi + 2 NAD+  2 C3H3O3- + 2 ATP + 2 NADH + 4 H+ + 2 H2O
B. formation of acetyl coenzyme A (acetyl-CoA) from pyruvate (AKA pyruvate oxidation)
1.
pyruvate is sent to the mitochondria in eukaryotes (stays in cytosol of prokaryotes)
2.
set of three enzymes catalyze the reactions, grouped together in the pyruvate dehydrogenase complex
3.
oxidative decarboxylation: a carboxyl group is removed from pyruvate (CO2 is produced)
4.
remaining 2-carbon fragment is oxidized (loses 2 electrons); NADH is produced
5.
remaining 2-carbon fragment, an acetyl group, is joined to coenzyme A (from B-vitamin pantothenic acid) to form
acetyl-CoA
6.
overall:
C3H3O3- + NAD+ + CoA  acetyl-CoA + CO2 + NADH
and so far:
C6H12O6 + 2 ADP +2 Pi + 4 NAD+ + 2CoA  2 acetyl-CoA + 2 CO2 + 2 ATP + 4 NADH + 4 H+ + 2 H2O
C. citric acid cycle
1.
AKA tricarboxylic acid cycle, TCA cycle, Krebs cycle
2.
still in mitochondria of eukaryotes
3.
series of 8 enzyme-catalyzed steps, and one side reaction where GTP + ADP  GDP + ATP
4.
entry: acetyl-CoA + oxaloacetate  citrate + CoA
5.
rest of cycle: citrate + H2O  2 CO2 + oxaloacetate + energy
6.

note there is no net gain or loss of oxaloacetate in the cycle

energy is stored in three NADH and one FADH2 for each cycle, plus one ATP
overall:
acetyl-CoA +3 NAD+ + FAD + ADP + Pi  CoA + 2 CO2 + 3 NADH + 3 H+ + FADH2 + ATP +H2O
and so far:
C6H12O6 + 4 ADP +4 Pi + 10 NAD+ + 2 FAD  6 CO2 + 4 ATP + 10 NADH + 10 H+ + 2 FADH2 + 4 H2O
7.
note that at this point glucose has been completely catabolized, yet only 4 ATP have been formed; the rest of the energy
is stored in NADH and FADH2
D. oxidative phosphorylation: the electron transport chain and chemiosmosis
1.
occurs in mitochondria of eukaryotes, and on membrane surface in prokaryotes
2.
electrons from NADH and FADH2 are transferred to a chain of membrane-bound electron acceptors, and eventually
passed to oxygen

acceptors include flavin mononucleotide (FMN), ubiquinone, iron-sulfur proteins, cytochromes

in the end, electrons wind up on molecular oxygen, and water is formed
(NADH or FADH2) + ½ O2  H2O + (NAD+ or FAD) + energy

lack of oxygen or compounds like cyanide stop the transport chain, and energy cannot be obtained from NADH and
FADH2 – this usually starves cells, killing them
3.
hydrogen ions (protons) are pumped across the inner mitochondrial membrane, creating a concentration gradient with
high proton concentration in the intermembrane space
4.
5.

energy for the pumping comes from energy lost as electrons are transferred

gradient allows opportunity for energy capture
chemiosmosis produces ATP

protons are charged and do not readily cross a cell membrane

special protein channel, ATP synthase (also called ATP synthetase) allows proton transport with the gradient

energy is captured and used to make ATP
energy from oxidation of NADH yields ~3 ATP (only ~2 if the electrons from the NADH from glycolysis wind up on
FADH2 after being shuttled across the mitochondrial membrane)
6.
energy from oxidation of FADH2 yields ~2 ATP
XII.
Aerobic respiration theoretically yields 36 or 38 ATP molecules from one glucose molecule
Glycolysis
Citric Acid Cycle
FADH2 oxidation (2 x 2)
NADH oxidation (8 x 3, 2 x 2 or 3)
TOTAL
2 ATP
2 ATP
4 ATP
28-30 ATP
36-38 ATP
The actual yield is typically about 30 ATP per glucose. Why only ~30? Chemiosmosis doesn’t actually give round figures, and
some of the energy from the proton gradient is used for other things too, like bringing pyruvate into the mitochondrion. The
overall efficiency of aerobic respiration is typically about 32%; the rest of the energy from combustion of glucose is released as
heat (compare this to a car’s internal combustion engine, typically about 20-25% efficiency).
XIII. Non-glucose energy sources
A. other substances can be oxidized to produce ATP in living systems
B. along with carbohydrates, proteins and lipids (fats) are generally major energy sources in foods; nucleic acids are not present
in high amounts in foods and thus aren’t as important in providing cells with energy
C. proteins are broken into amino acids, which can be broken down further
1.
amino group is removed (deamination)
2.
amino group may eventually be converted to urea and excreted
3.
remaining carbon chain enters aerobic respiration at various points, depending on chain length
4.
provide roughly the same amount of energy per unit weight as does glucose
D. lipids (focus on triacylglycerols)
1.
lipids are more reduced than glucose (note less oxygen in lipids), thus more energetic
2.
glycerol is converted to glyceraldehyde-3-phosphate (G3P), entering glycolysis
3.
fatty acids are oxidized and split into acetyl groups that are combined with CoA to make acetyl-CoA (this process is
called  oxidation)
4.
typically provides over twice as much energy per unit weight as glucose
5.
as an example, oxidation of a 6-carbon fatty acid yields up to 44 ATP
XIV. Regulation of aerobic respiration
A. ATP/ADP balance regulates much of oxidative phosphorylation
1.
ATP synthesis continues until ADP stores are largely depleted
2.
rapid use of ATP leads to excess ADP, and thus speeds up aerobic respiration
B. phosphofructokinase, the enzyme for one of the earliest steps in glycolysis, is highly regulated
1.
ATP, though a substrate, also serves as an allosteric inhibitor
2.
citrate is also an allosteric inhibitor
3.
AMP serves as an allosteric activator
XV.
Anaerobic respiration
A. bacteria that live in environments where O2 is not abundant perform anaerobic respiration
B. still uses an electron transport chain
C. some other compound such as NO3-, SO42- or CO2 serves as the ultimate electron acceptor
D. not as efficient as aerobic respiration (exact efficiency varies depending on the process and the species)
XVI. Fermentation
A. involves no electron transport chain
B. inefficient; net is 2 ATP per glucose molecule (only glycolysis works)
C. if glycolysis only, then NAD+ must be regenerated, thus fermentation, where NADH reduces an organic molecule
1.
2.
alcohol fermentation produces ethanol, CO2, and NAD+

pyruvate is converted to ethanol and CO2 to regenerate NAD+

ethanol is a potentially toxic waste product, and is removed from cells

yeast (and many bacteria) perform alcoholic fermentation in low oxygen environments

used in making alcoholic beverages, baking
lactic acid fermentation produces lactate and NAD+

pyruvate is reduced to lactate to regenerate NAD+

performed by some bacteria and fungi, and by animals (when muscles need energy fast)

used in making cheese, yogurt, sauerkraut
PROCESS
Where?
(carbon)
compounds
in
(carbon)
compounds
out
Net
ATP
made
Net
NADH
made
Net
Other notable items
FADH2
made
glycolysis
acetyl-CoA
formation
citric acid cycle
oxidative
phosphorylation
TOTAL
Chapter 10: Photosynthesis
XVII. Organisms can be classified based on how they obtain energy and how they obtain carbon
A. energy source
1. chemotrophs can only get energy directly from chemical compounds
2. phototrophs can get energy directly from light (these organisms can use chemical compounds as energy sources as well)
B. carbon source
1. autotrophs can fix carbon dioxide, thus they can use CO 2 as a carbon source
2. heterotrophs cannot fix CO2; they use organic molecules from other organisms as a carbon source
C. combined, these lead to 4 possible groups:
1. photoautotrophs – carry out photosynthesis (use light energy to fix CO2, storing energy in chemical bonds of organic
molecules); includes green plants, algae, and some bacteria
2. photoheterotrophs – use light energy but cannot fix CO2; only nonsulfur purple bacteria
3. chemoautotrophs – obtain energy from reduced inorganic molecules and use some of it to fix CO2; some bacteria
4. chemoheterotrophs – use organic molecules as both carbon and energy sources; dependent completely on other
organisms for energy capture and carbon fixation; includes all animals, all fungi, most protests, and most bacteria
XVIII. The electromagnetic spectrum and visible light
A. visible light is a form of electromagnetic radiation
B. electromagnetic radiation consists of particles or packets of energy (photons) that travel as waves
1. amount of energy carried is inversely proportional to wavelength (distance from one wave peak to another)
2. spectrum ranges from short wavelength/high energy gamma rays to long wavelength/low energy radio waves
C. the portion of the spectrum visible to humans (thus what we call visible light) ranges from higher-energy violet at 380 nm to
lower-energy red at 760 nm; between lie all the colors of the rainbow
D. molecules can absorb photons, thus becoming energized; typically, an electron absorbs the energy
1.
2.
high energy: electron can be freed from the atom it was bound to (ionization)
moderate energy (of correct amount): electron moves to a higher-energy orbital
 electron can then be removed from the atom, going to an acceptor molecule
 electron can return to a lower energy level, emitting a photon (fluorescence) or a series of photons (mostly infrared,
experienced as heat)
 ground state – when all electrons in a atom fill only the lowest possible energy levels
XIX. Chloroplasts
A. in photosynthetic eukaryotes (plants and algae), photosynthesis occurs in chloroplasts
B. chloroplasts have both an inner and outer membrane
1. stroma – fluid-filled region inside the inner membrane
2. thylakoids – disklike membranous sacs found in stroma (interconnected with each other and inner membrane)
3. thylakoid lumen – fluid-filled region inside a thylakoid
4. granum – stack of thylakoids (plural: grana)
C. chlorophyll, the main light-harvesting molecule, is found in the thylakoid membrane
1. chlorophyll has a porphyrin ring and hydrocarbon side chain
2. light energy is absorbed by the ring
3. chlorophyll-binding proteins associate with chlorophyll in the membrane
4. chlorophyll has several forms; in plants, typically chlorophyll a (chl a) initiates photosynthesis
D. accessory pigments are also found in the thylakoid membrane
1. pigments are compounds that absorb light; we see them as the main color of light that they do not absorb well (thus they
scatter those colors or reflect them back)
2. all pigments have an absorption spectrum
3. chl a, a green pigment, absorbs violet-blue and red light
4. several accessory pigments, with absorption spectra that differ from chl a, aid in photosynthesis
 chl b is the main accessory pigment; a slight difference in the ring shifts its absorption spectrum
 carotenoids are important yellow and orange accessory pigments
 accessory pigments can transfer captured energy to chl a
 they also help protect chl a and other compounds from excess light energy (high light intensity can cause damage)
E. the relative rate of photosynthesis for a given radiation wavelength is an action spectrum
1. the action spectrum looks similar to the absorption spectrum of chl a, but is augmented by the absorption spectrum of the
accessory pigments
2. blue and red light are most effective for photosynthesis
3. action spectra can vary depending on species
F. photosynthetic prokaryotes have plasma membrane folds that act like thylakoid membranes
XX. Photosynthesis overview
A. photosynthesis converts energy from light into stored energy in chemical bonds
B. in the process, CO2 is fixed and used in synthesizing carbohydrates
C. overall reaction: 6 CO2 +12 H2O  C6H12O6 + 6 O2 + 6 H2O
1. water is on both sides because it is consumed in some steps and produced in others; overall, there is a net use of water
2. hydrogen atoms are transferred from water to carbon dioxide; yet another redox reaction
D. usually divided into light reactions and the C3 cycle; more details on these later, but in summary:
1. light reactions occur in the thylakoids; they capture light energy and consume water, producing O 2; energy is placed in
ATP and NADPH in the stroma
2. the C3 cycle occurs in the stroma; it consumes CO2 and energy (proved by ATP and NADPH), producing carbohydrates
E. in many ways this is the reverse of aerobic respiration
XXI. The light reactions of photosynthesis
A. overall:
12 H2O + 12 NADP+ + 18 ADP + 18 Pi + light energy  6 O2 + 12 NADPH + 12 H+ + 18 ATP + 18 H2O
B. the overall equation takes into account the amount of NADPH and ATP needed to create one molecule of glucose
C. light is captured in photosystems that contain antenna complexes and a reaction center
1. there are two types, Photosystem I and Photosystem II
2. antenna complexes are highly organized arrangements of pigments, proteins, and other molecules that capture light
energy
3. energy is transferred to a reaction center where electrons are actually moved into electron transport chains
 Photosystem I reaction center has a chl a absorption peak at 700 nm (P700)
 Photosystem II reaction center has a chl a absorption peak at 680 nm (P680)
4. chlorophyll molecule + light energy  an excited electron in the chlorophyll
5. the excited electron is captured by a carrier in the photosynthetic electron transport chain, thus reducing the carrier and
oxidizing the chlorophyll molecule (a redox reaction)
6. the electron can then be transferred down the electron transport chain, with energy harvest possible
D. noncyclic electron transport produces ATP and NADPH
1. P700 absorbs energy and sends an electron to an electron transport chain
2. eventually, the electron winds up on ferredoxin
3. when 2 electrons have reached ferredoxin, they can be used to make NADPH from NADP+ + H+; the NADPH is
released in the stroma
4. the electrons are passed down one at a time, and are replaced in P700 by electrons donated from P680
5. P680 absorbs energy and sends an electron to an electron transport chain
 this chain differs from the one that P700 uses
 eventually, the electron winds up on plastocyanin
 the ultimate electron acceptor for this chain is P700
6. P680+ can accept electrons from water in the thylakoid lumen; thus:
 2 P680+ + H2O  2 P680 + ½ O2 + 2 H+
 this is a big deal, nothing else in living systems can readily take electrons from water
 this consumes water and releases O2
7. a proton gradient is established, with high [H+] in the thylakoid lumen
 H+ produced in the lumen when water is split
 H+ consumed in stroma when NADPH is made
 H+ pumped into lumen using energy released as electrons move along the electron transport chain between P680 and
P700
 the overall gradient winds up being about a 1000-fold difference in [H+]
 gradient provides an energy source for making ATP using ATP synthase (chemiosmosis)
 compare this process (photophosphorylation) to oxidative phosphorylation
E. cyclic electron transport is possible for P700; all it can accomplish is to enhance the proton gradient that can be used to
make ATP
F. overall ATP generation is variable, depending on how much cyclic electron transport occurs
1. for every 2 electrons moved through the whole P680 – P700 noncyclic electron transport system, one NADPH is
produced and the proton gradient is enhanced enough for ~1 or more ATP
 the net amount of ATP needed for the rest of photosynthesis comes out to 1.5 ATP per molecule of NADPH; thus
the numbers in the equation at the start of this section
 cyclic electron transport can be used to make up the difference in ATP needed for the rest of photosynthesis, as well
as to produce extra ATP
 all of the ATP that is made is released in the stroma
XXII. carbon fixation by the C3 cycle (AKA the Calvin-Benson cycle or Calvin cycle)
A. overall:
12 NADPH + 12 H+ + 18 ATP + 18 H2O + 6 CO2  C6H12O6 + 12 NADP+ + 18 ADP + 18 Pi + 6 H2O
B. note that this consumes all of the products of the light reactions except O 2, and regenerates much of the reactants for the light
reactions, thus generating the overall result for photosynthesis:
12 H2O +6 CO2 + light energy  6 O2 + C6H12O6 + 6 H2O
C. the details of the 13 reactions involved in this process were described by Calvin and Benson in the 1950s
D. all 13 enzymes are in the stroma; 10 of them are also enzymes that work in aerobic respiration
1. enzymes can usually catalyze reactions in both directions – the intermediate ES complex looks the same in both cases
2. the direction of the reaction depends on thermodynamics, which is influenced by concentrations of all substances
involved in the reaction
E. the C3 cycle is broken into three phases: carbon fixation, carbon reduction, and RuBP regeneration
F. carbon fixation (AKA CO2 uptake):
1. CO2 combines with the 5-carbon compound ribulose 1,5-bisphosphate (RuBP)
 catalyzed by the enzyme ribulose bisphosphate carboxylase/oxygenase (abbreviated rubisco)
 rubisco is one of the most abundant proteins on earth
 the carboxylase function is used here
2. the resulting 6-carbon compound is unstable and immediately splits into 2 molecules of 3-phosphoglycerate (3-PGA)
3. the overall reaction is:
RuBP + CO2  2 (3-PGA)
4. to assimilate 6 CO2:
6 RuBP + 6 CO2  12 (3-PGA)
G. carbon reduction
1. 3-PGA is reduced to glyceraldehyde 3-phosphate (G3P) in two steps; in the process, ATP and NADPH are used
2. from 6 CO2 you get 12 G3P
3. 2 G3P are removed and used to make glucose or fructose (thus 6 carbons leave to make C 6H12O6)
4. the remaining 10 G3P are used to regenerate RuBP
H. RuBP regeneration
1. a series of ten reactions rearrange the 10 G3P to make 6 ribulose phosphate molecules, to which a phosphate is added to
make 6 RuBP
2. ATP is consumed for each RuBP formed (it is the source of the phosphate)
XXIII. photorespiration
A. sometimes, rubisco adds O2 to RuBP rather than a CO2 (the oxygenase function of RUBISCO)
B. this is most likely under conditions of conditions of low [CO 2] and high [O2]
C. the product cannot be used in the C3 cycle, and photorespiration is a drain on the overall efficiency of photosynthesis
D. some byproducts are broken down in part into CO2 and H2O; organic material is lost from the system, and no energy is
captured (no ATP are produced; in fact, some are consumed)
E. called photorespiration because it occurs in the light and consumes O2, while producing CO2 and H2O
F. for C3 plants (plants with only the C3 pathway), photorespiration rate increases as the rate of photosynthesis increases,
especially if stomata are closed – thus, bright, hot, dry days are inefficient days for C3 plants
G. the effect of photorespiration is minimal in C4 and CAM plants because they keep [CO2] high for RUBISCO
XXIV. supplemental carbon fixation pathways: C4 and CAM pathways
A. while the C3 pathway is used by all plants, some plants have supplemental pathways that increase the efficiency of
photosynthesis in either intense light or arid conditions
B. intense light – [CO2] becomes limiting; C4 pathway gets around this by increasing [CO2] for the C3 pathway
C. arid conditions – [H2O] is most limiting during the day; CAM pathway gets around this by allowing initial carbon fixation to
occur at night
D. C4 pathway (AKA Hatch-Slack pathway)
1. in mesophyll cells:
 pyruvate + ATP + H2O  phosphoenolpyruvate (PEP) + AMP + Pi
 PEP carboxylase binds CO2 even at very low [CO2] (binds it much better than RUBISCO binds CO2); PEP
carboxylase catalyzes:
PEP + CO2  oxaloacetate
 oxaloacetate + NADPH + H+  NADP+ + malate (usually)
2. malate is then sent to bundle sheath cells
3. in bundle sheath cells:
 malate + NADP+  CO2 + pyruvate + NADPH + H+
 greatly increases [CO2] in bundle sheath cells (10-60x), allowing the C3 pathway to proceed in those cells
 pyruvate is sent back to the mesophyll cells
4. overall, invests 12 more ATP per glucose or fructose than C3 alone; only worthwhile under intense light, but then it is
very worthwhile
5. examples of plants with a C4 pathway include corn, sugar cane, crabgrass
E. CAM pathway (crassulacean acid metabolism)
1. at night, when stomata are open and gas exchange can occur, cells perform reactions like the “mesophyll cell C 4
reactions”; malate (or a similar organic acid) is stored in vacuoles
2. during the day, the malate is released and cells perform reactions like the “bundle sheath cell C 4 reactions”; this allows
the C3 pathway to proceed during the day (when stomata are closed to prevent excessive water loss, and thus gas
exchange is not possible)
3. CAM plants include many desert plants such as cactuses
F. C4 works by altering the location of initial CO2 fixation, while CAM works by altering the time of initial CO2 fixation; all of
the plants still use the C3 cycle
Chapter 10: Photosynthesis
21.
22.
List and differentiate the 4 possible groups of organisms based on how they obtain energy and useful carbon.






Define the following:
electromagnetic radiation
photons
wavelength
ionization
fluorescence
ground state
23.
Rank major types of EM radiation from the highest energy content per photon to lowest; do the same for the major
colors of visible light (also note the wavelengths for the extremes of visible light).
24.


Draw a chloroplast cross-section and:
label: stroma, thylakoid membrane, thylakoid lumen, granum
label location of: chlorophyll, accessory pigments
25.


26.
Differentiate between absorption spectrum and action spectrum, and:
draw the typical absorption spectra for chl a, chl b, and carotenoids
draw the typical action spectrum for photosynthesis
Write the overall chemical equation for photosynthesis and note what gets oxidized and what gets reduced.
27.




28.
Go back to your chloroplast diagram and label where:
light energy is captured
photolysis occurs
ATP and NADPH are produced
carbohydrates are produced
Describe a photosystem (include terms antenna complex, reaction center)
29.








Diagram noncyclic electron transport, noting:
photosytems I (P700) and II (P680)
where photons are absorbed
electron transport chains
ferredoxin
NADPH production
plastocyanin
ATP production
photolysis
30.
Diagram cyclic electron transport, noting relevant items from the list given for the noncyclic diagram.
31.
Diagram the C3 cycle (whole class activity).
32.
Define photorespiration.
33.
Explain the extra cost of C4 and CAM pathways and what benefit they can provide.
34.
Diagram the C4/CAM pathway, noting where and how the two differ.
Chapter 10: Photosynthesis
XXV. Organisms can be classified based on how they obtain energy and how they obtain carbon
A. energy source
1.
chemotrophs can only get energy directly from chemical compounds
2.
phototrophs can get energy directly from light (these organisms can use chemical compounds as energy sources as well)
B. carbon source
1.
autotrophs can fix carbon dioxide, thus they can use CO 2 as a carbon source
2.
heterotrophs cannot fix CO2; they use organic molecules from other organisms as a carbon source
C. combined, these lead to 4 possible groups:
1.
photoautotrophs – carry out photosynthesis (use light energy to fix CO2, storing energy in chemical bonds of organic
molecules); includes green plants, algae, and some bacteria
2.
photoheterotrophs – use light energy but cannot fix CO2; only nonsulfur purple bacteria
3.
chemoautotrophs – obtain energy from reduced inorganic molecules and use some of it to fix CO 2; some bacteria
4.
chemoheterotrophs – use organic molecules as both carbon and energy sources; dependent completely on other
organisms for energy capture and carbon fixation; includes all animals, all fungi, most protests, and most bacteria
XXVI. The electromagnetic spectrum and visible light
A. visible light is a form of electromagnetic radiation
B. electromagnetic radiation consists of particles or packets of energy (photons) that travel as waves
1.
amount of energy carried is inversely proportional to wavelength (distance from one wave peak to another)
2.
spectrum ranges from short wavelength/high energy gamma rays to long wavelength/low energy radio waves
C. the portion of the spectrum visible to humans (thus what we call visible light) ranges from higher-energy violet at 380 nm to
lower-energy red at 760 nm; between lie all the colors of the rainbow
D. molecules can absorb photons, thus becoming energized; typically, an electron absorbs the energy
1.
high energy: electron can be freed from the atom it was bound to (ionization)
2.
moderate energy (of correct amount): electron moves to a higher-energy orbital

electron can then be removed from the atom, going to an acceptor molecule

electron can return to a lower energy level, emitting a photon (fluorescence) or a series of photons (mostly infrared,
experienced as heat)

ground state – when all electrons in a atom fill only the lowest possible energy levels
XXVII. Chloroplasts
A. in photosynthetic eukaryotes (plants and algae), photosynthesis occurs in chloroplasts
B. chloroplasts have both an inner and outer membrane
1.
stroma – fluid-filled region inside the inner membrane
2.
thylakoids – disklike membranous sacs found in stroma (interconnected with each other and inner membrane)
3.
thylakoid lumen – fluid-filled region inside a thylakoid
4.
granum – stack of thylakoids (plural: grana)
C. chlorophyll, the main light-harvesting molecule, is found in the thylakoid membrane
1.
chlorophyll has a porphyrin ring and hydrocarbon side chain
2.
light energy is absorbed by the ring
3.
chlorophyll-binding proteins associate with chlorophyll in the membrane
4.
chlorophyll has several forms; in plants, typically chlorophyll a (chl a) initiates photosynthesis
D. accessory pigments are also found in the thylakoid membrane
1.
pigments are compounds that absorb light; we see them as the main color of light that they do not absorb well (thus they
scatter those colors or reflect them back)
2.
all pigments have an absorption spectrum
3.
chl a, a green pigment, absorbs violet-blue and red light
4.
several accessory pigments, with absorption spectra that differ from chl a, aid in photosynthesis

chl b is the main accessory pigment; a slight difference in the ring shifts its absorption spectrum

carotenoids are important yellow and orange accessory pigments

accessory pigments can transfer captured energy to chl a

they also help protect chl a and other compounds from excess light energy (high light intensity can cause damage)
E. the relative rate of photosynthesis for a given radiation wavelength is an action spectrum
1.
the action spectrum looks similar to the absorption spectrum of chl a, but is augmented by the absorption spectrum of the
accessory pigments
F.
2.
blue and red light are most effective for photosynthesis
3.
action spectra can vary depending on species
photosynthetic prokaryotes have plasma membrane folds that act like thylakoid membranes
XXVIII. Photosynthesis overview
A. photosynthesis converts energy from light into stored energy in chemical bonds
B. in the process, CO2 is fixed and used in synthesizing carbohydrates
C. overall reaction: 6 CO2 +12 H2O  C6H12O6 + 6 O2 + 6 H2O
1.
water is on both sides because it is consumed in some steps and produced in others; overall, there is a net use of water
2.
hydrogen atoms are transferred from water to carbon dioxide; yet another redox reaction
D. usually divided into light reactions and the C3 cycle; more details on these later, but in summary:
1.
light reactions occur in the thylakoids; they capture light energy and consume water, producing O 2; energy is placed in
ATP and NADPH in the stroma
2.
the C3 cycle occurs in the stroma; it consumes CO2 and energy (proved by ATP and NADPH), producing carbohydrates
E. in many ways this is the reverse of aerobic respiration
XXIX. The light reactions of photosynthesis
A. overall:
12 H2O + 12 NADP+ + 18 ADP + 18 Pi + light energy  6 O2 + 12 NADPH + 12 H+ + 18 ATP + 18 H2O
B. the overall equation takes into account the amount of NADPH and ATP needed to create one molecule of glucose
C. light is captured in photosystems that contain antenna complexes and a reaction center
1.
there are two types, Photosystem I and Photosystem II
2.
antenna complexes are highly organized arrangements of pigments, proteins, and other molecules that capture light
energy
3.
energy is transferred to a reaction center where electrons are actually moved into electron transport chains

Photosystem I reaction center has a chl a absorption peak at 700 nm (P700)

Photosystem II reaction center has a chl a absorption peak at 680 nm (P680)
4.
chlorophyll molecule + light energy  an excited electron in the chlorophyll
5.
the excited electron is captured by a carrier in the photosynthetic electron transport chain, thus reducing the carrier and
oxidizing the chlorophyll molecule (a redox reaction)
6.
the electron can then be transferred down the electron transport chain, with energy harvest possible
D. noncyclic electron transport produces ATP and NADPH
1.
P700 absorbs energy and sends an electron to an electron transport chain
2.
eventually, the electron winds up on ferredoxin
3.
when 2 electrons have reached ferredoxin, they can be used to make NADPH from NADP+ + H+; the NADPH is
released in the stroma
4.
the electrons are passed down one at a time, and are replaced in P700 by electrons donated from P680
5.
P680 absorbs energy and sends an electron to an electron transport chain

this chain differs from the one that P700 uses
6.
7.

eventually, the electron winds up on plastocyanin

the ultimate electron acceptor for this chain is P700
P680+ can accept electrons from water in the thylakoid lumen; thus:

2 P680+ + H2O  2 P680 + ½ O2 + 2 H+

this is a big deal, nothing else in living systems can readily take electrons from water

this consumes water and releases O2
a proton gradient is established, with high [H+] in the thylakoid lumen

H+ produced in the lumen when water is split

H+ consumed in stroma when NADPH is made

H+ pumped into lumen using energy released as electrons move along the electron transport chain between P680 and
P700

the overall gradient winds up being about a 1000-fold difference in [H+]

gradient provides an energy source for making ATP using ATP synthase (chemiosmosis)

compare this process (photophosphorylation) to oxidative phosphorylation
E. cyclic electron transport is possible for P700; all it can accomplish is to enhance the proton gradient that can be used to
make ATP
F.
overall ATP generation is variable, depending on how much cyclic electron transport occurs
1.
for every 2 electrons moved through the whole P680 – P700 noncyclic electron transport system, one NADPH is
produced and the proton gradient is enhanced enough for ~1 or more ATP

the net amount of ATP needed for the rest of photosynthesis comes out to 1.5 ATP per molecule of NADPH; thus
the numbers in the equation at the start of this section

cyclic electron transport can be used to make up the difference in ATP needed for the rest of photosynthesis, as well
as to produce extra ATP

all of the ATP that is made is released in the stroma
XXX. carbon fixation by the C3 cycle (AKA the Calvin-Benson cycle or Calvin cycle)
A. overall:
12 NADPH + 12 H+ + 18 ATP + 18 H2O + 6 CO2  C6H12O6 + 12 NADP+ + 18 ADP + 18 Pi + 6 H2O
B. note that this consumes all of the products of the light reactions except O 2, and regenerates much of the reactants for the light
reactions, thus generating the overall result for photosynthesis:
12 H2O +6 CO2 + light energy  6 O2 + C6H12O6 + 6 H2O
C. the details of the 13 reactions involved in this process were described by Calvin and Benson in the 1950s
D. all 13 enzymes are in the stroma; 10 of them are also enzymes that work in aerobic respiration
1.
enzymes can usually catalyze reactions in both directions – the intermediate ES complex looks the same in both cases
2.
the direction of the reaction depends on thermodynamics, which is influenced by concentrations of all substances
involved in the reaction
E. the C3 cycle is broken into three phases: carbon fixation, carbon reduction, and RuBP regeneration
F.
carbon fixation (AKA CO2 uptake):
1.
CO2 combines with the 5-carbon compound ribulose 1,5-bisphosphate (RuBP)

catalyzed by the enzyme ribulose bisphosphate carboxylase/oxygenase (abbreviated rubisco)

rubisco is one of the most abundant proteins on earth

the carboxylase function is used here
2.
the resulting 6-carbon compound is unstable and immediately splits into 2 molecules of 3-phosphoglycerate (3-PGA)
3.
the overall reaction is:
RuBP + CO2  2 (3-PGA)
4.
to assimilate 6 CO2:
6 RuBP + 6 CO2  12 (3-PGA)
G. carbon reduction
1.
3-PGA is reduced to glyceraldehyde 3-phosphate (G3P) in two steps; in the process, ATP and NADPH are used
2.
from 6 CO2 you get 12 G3P
3.
2 G3P are removed and used to make glucose or fructose (thus 6 carbons leave to make C6H12O6)
4.
the remaining 10 G3P are used to regenerate RuBP
H. RuBP regeneration
1.
a series of ten reactions rearrange the 10 G3P to make 6 ribulose phosphate molecules, to which a phosphate is added to
make 6 RuBP
2.
ATP is consumed for each RuBP formed (it is the source of the phosphate)
XXXI. photorespiration
A. sometimes, rubisco adds O2 to RuBP rather than a CO2 (the oxygenase function of RUBISCO)
B. this is most likely under conditions of conditions of low [CO 2] and high [O2]
C. the product cannot be used in the C3 cycle, and photorespiration is a drain on the overall efficiency of photosynthesis
D. some byproducts are broken down in part into CO2 and H2O; organic material is lost from the system, and no energy is
captured (no ATP are produced; in fact, some are consumed)
E. called photorespiration because it occurs in the light and consumes O 2, while producing CO2 and H2O
F.
for C3 plants (plants with only the C3 pathway), photorespiration rate increases as the rate of photosynthesis increases,
especially if stomata are closed – thus, bright, hot, dry days are inefficient days for C3 plants
G. the effect of photorespiration is minimal in C4 and CAM plants because they keep [CO2] high for RUBISCO
XXXII. supplemental carbon fixation pathways: C4 and CAM pathways
A. while the C3 pathway is used by all plants, some plants have supplemental pathways that increase the efficiency of
photosynthesis in either intense light or arid conditions
B. intense light – [CO2] becomes limiting; C4 pathway gets around this by increasing [CO2] for the C3 pathway
C. arid conditions – [H2O] is most limiting during the day; CAM pathway gets around this by allowing initial carbon fixation to
occur at night
D. C4 pathway (AKA Hatch-Slack pathway)
1.
in mesophyll cells:

pyruvate + ATP + H2O  phosphoenolpyruvate (PEP) + AMP + Pi

PEP carboxylase binds CO2 even at very low [CO2] (binds it much better than RUBISCO binds CO2); PEP
carboxylase catalyzes:

PEP + CO2  oxaloacetate
oxaloacetate + NADPH + H+  NADP+ + malate (usually)
2.
malate is then sent to bundle sheath cells
3.
in bundle sheath cells:
4.

malate + NADP+  CO2 + pyruvate + NADPH + H+

greatly increases [CO2] in bundle sheath cells (10-60x), allowing the C3 pathway to proceed in those cells

pyruvate is sent back to the mesophyll cells
overall, invests 12 more ATP per glucose or fructose than C 3 alone; only worthwhile under intense light, but then it is
very worthwhile
5.
examples of plants with a C4 pathway include corn, sugar cane, crabgrass
E. CAM pathway (crassulacean acid metabolism)
1.
at night, when stomata are open and gas exchange can occur, cells perform reactions like the “mesophyll cell C 4
reactions”; malate (or a similar organic acid) is stored in vacuoles
2.
during the day, the malate is released and cells perform reactions like the “bundle sheath cell C4 reactions”; this allows
the C3 pathway to proceed during the day (when stomata are closed to prevent excessive water loss, and thus gas
exchange is not possible)
3.
F.
CAM plants include many desert plants such as cactuses
C4 works by altering the location of initial CO2 fixation, while CAM works by altering the time of initial CO2 fixation; all of
the plants still use the C3 cycle
Chapter 12: The Cell Cycle
XXXIII. Cell division in prokaryotes
A. typically, a prokaryotic cell divides by binary fission, splitting into two nearly equal halves
B. the main circular DNA molecule of the cell is replicated
1. replication begins at a replication origin and proceeds in both directions
2. two complete, identical circles are present by the end; each is attached to the plasma membrane
C. new plasma membrane and cell wall materials are laid down between the two DNA circles, eventually separating the
daughter cells
D. prokaryotic cells can have a generation time (general term for the period from the start of one cell division to the start of the
next cell division) as short as 20 minutes
XXXIV. Eukaryotic DNA molecules are organized in chromosomes
A. each chromosome is made of chromatin, a long DNA molecule with associated proteins
1. chromatin is packaged into dense chromosomes during cell division
 protects the DNA
 helps assure proper distribution of DNA during cell division
 the dense bodies can be stained and show up well under light microscopy
2. the chromosomes are unpacked (“decondensed”) when cells are not dividing
B. each chromosome contains hundreds to thousands of genes
1. genes are the functional units of heredity
2. typically, a gene contains the instructions to make a protein or RNA molecule
3. the complete DNA sequence for an organism is the genome; it contains the complete set of instructions for that organism
4. humans apparently have ~40,000 genes in the now-sequenced human genome
C. each species has a characteristic number of chromosomes
1. the number varies between species
2. chromosome number does not reflect the complexity of the organism
3. the assortment of chromosomes for an individual is the karyotype
4. humans have 46 chromosomes
D. chromosomes carry the genetic information of a cell from one cell generation to the next, and from one organism to its
offspring
XXXV. The eukaryotic cell cycle
A. the cell cycle describes the status of cells in relationship to growth and division
1. when cells reach a certain size, growth either stops or the cell must divide
2. most, but not all, eukaryotic cells are capable of dividing
3. cell division is generally a highly regulated process
4. the generation time for eukaryotic cells varies widely, but is usually 8-20 hours
B. cell cycle has two main phases – interphase and cell division (mitosis + cytokinesis)
C. interphase is divided into three parts, defined with respect to DNA replication
1. the DNA is completely replicated (genetic information duplicated) during the synthesis phase or S phase
2. the period before the S phase is a “gap” phase, G1 phase
 most cellular growth occurs in this phase
 this phase is usually the most variable with respect to time, and is typically longest
 cells that do not divide become arrested in this phase, then called G0
3. the period between the S phase and cell division is the G2 phase
 the G2 phase is usually short; cells in this phase are committed to and preparing for cell division
D. cell division has two main parts – mitosis and cytokinesis
1. mitosis is the process that distributes a complete copy of the duplicated genetic information to each daughter cell
2. cytokinesis is the process of dividing the cytoplasm into two separate cells
3. some cells can have mitosis without cytokinesis (most common in fungi and slime molds)
E. the current model of cell cycle regulation involves a highly conserved, genetically-controlled program that can be influenced
by external signals
1. there are three major checkpoints, found in G1, G2 and mitosis
2. key regulatory components for checkpoints are cyclins and cyclin-dependent protein kinases
3. hormones such as cytokinins in plants and various protein growth factors in animals can stimulate progression through
checkpoints in the right cells under the right conditions
4. other factors can serve as suppressors of cell division
5. cancer cells generally grow without needing stimulation by external growth factors and fail to respond to normal
suppressors of cell division
XXXVI. mitosis is generally be divided into 4 stages: prophase, metaphase, anaphase, and telophase (PMAT)
A. be aware that mitosis is a continuous process, the stages are defined only for our convenience
B. prophase – chromatin condenses to form chromosomes
1. each chromosome (duplicated during S phase) forms a pair of sister chromatids
 sister chromatids are joined at a centromere by protein tethers
 centromeres contain a kinetochore where microtubules will bind
 each sister chromatid has its own kinetochore
a system of microtubules, called the mitotic spindle, organizes between the two poles (opposite ends) of the cell
 each pole has a microtubule organizing center (MTOC)
 in animals and some other eukaryotes, centrioles are found in the MTOC; their exact role, if any, is unclear
3. by the end of prophase:
 the nuclear membrane has disappeared (actually divided into many small vesicles)
 nucleoli have disintegrated
 the sister chromatids are attached by their kinetochores to microtubules from opposite poles
4. some call the later part of prophase prometaphase, usually defined to include vesicularization of the nuclear membrane
and attachment of kinetochores to microtubules
5. in some eukaryotes the nuclear membrane never vesicularizes
C. metaphase – chromosomes line up along the midplane of the cell (the metaphase plate)
1. chromosomes are most condensed, most visible, and most distinguishable during metaphase
2. the mitotic spindle, now complete, has two types of microtubules
 kinetochore microtubules extend from a pole to a kinetochore
 polar microtubules extend from a pole to the midplane area, often overlapping with polar microtubules from the
other pole
3. the mitosis checkpoint appears to be here; progress past metaphase is typically prevented until the kinetochores are all
attached to microtubules
D. anaphase – sister chromatids separate and are moved toward opposite poles
1. the protein tethers at the centromere between the chromatids are broken
2. each former sister chromatid can now be called a chromosome
3. model for the mechanism that moves chromosomes to the poles
 motor proteins move the chromosomes towards the poles along the kinetochores microtubules
 kinetochore microtubules shorten as behind the moving chromosomes
 polar microtubules lengthen the entire spindle
 motor proteins on the polar microtubules slide them past each other, pushing them apart (the microtubules may
grow a bit, too)
 this pushes the MTOCs away from each other, and thus has the effect of pushing kinetochore microtubules from
opposite poles away from each other
4. overall, this process assures that each daughter cell will receive one of the duplicate sets of genetic material carried by
the chromosomes
E. telophase – the processes of prophase are reversed
1. the mitotic spindle is disintegrated
2. the chromosomes decondense
3. nuclear membranes reform around the genetic material to form two nuclei, each with an identical copy of the genetic
information
4. nucleoli reappear, and interphase cellular functions resume
XXXVII.
cytokinesis divides the cell into two daughter cells
A. cytokinesis usually begins in telophase and ends shortly thereafter
1. in animals, a cleavage furrow develops – usually close to where the metaphase plate was
 a microfilament (actin) ring contracts due to interactions with myosin molecules, forming a deepening furrow
 eventually, the ring closes enough for spontaneous separation of the plasma membrane, resulting in two separate
cells
2. in plants, a cell plate develops – usually close to where the metaphase plate was
 vesicles that originate from the Golgi line up in the equatorial region
 the vesicles fuse and add more vesicles, growing outward until reaching the plasma membrane and thus separating
the cells
 the vesicles contain materials for making the primary cell wall and a middle lamella
B. cytoplasm (and with it most organelles) is usually distributed randomly but roughly equally between daughter cells
C. sometimes cell division is a highly regulated polar division that purposefully distributes some materials unequally
2.
Chapter 12: The Cell Cycle (How do cells divide?)
35. Describe the typical cell cycle of prokaryotes. Include and define the terms binary
fission and generation time.
36.
Define:
 chromosome




chromatin
gene
genome
karyotype
37. Describe the human genome and karyotype in terms of: number of basepairs,
number of genes, and number of chromosomes.
38.
Draw a circle diagram of the eukaryotic cell cycle. Label all phases.
39. Discuss what goes on in each of the phases on the diagram. Note where checkpoints
exist. Also, discuss G0, and discuss cell cycle regulation in general terms.
40.
Describe what “PMAT” means.
41. With a partner, do the “chromosome dance” for mitosis. Make sure that you
distinguish between chromosomes and chromatids, and note at each stage the number of
sister chromatids per chromosome.
42.
Discuss what happens in each stage of mitosis.
43.
Describe cytokinesis in both plant cells and animal cells, noting the differences.
44. Describe what is meant by the term “polar division” and why this process was (and
still is) important in your development.
Chapter 12: The Cell Cycle (How do cells divide?)
XXXVIII.
Cell division in prokaryotes
A. typically, a prokaryotic cell divides by binary fission, splitting into two nearly equal halves
B. the main circular DNA molecule of the cell is replicated
1.
replication begins at a replication origin and proceeds in both directions
2.
two complete, identical circles are present by the end; each is attached to the plasma membrane
C. new plasma membrane and cell wall materials are laid down between the two DNA circles, eventually separating the cells
D. prokaryotic cells can have a generation time (general term for the period from the start of one cell division to the start of the
next cell division) as short as 20 minutes
XXXIX. Eukaryotic DNA molecules are organized in chromosomes
A. each chromosome is made of chromatin, a long DNA molecule with associated proteins
1.
2.
chromatin is packaged into dense chromosomes during cell division

protects the DNA; helps assure proper distribution of DNA during cell division

the dense bodies can be stained and show up well under light microscopy
the chromosomes are unpacked (“decondensed”) when cells are not dividing
B. each chromosome contains hundreds to thousands of genes
1.
genes are the functional units of heredity
2.
typically, a gene contains the instructions to make a protein or RNA molecule
3.
the complete DNA sequence for an organism is the genome; it contains the complete set of instructions for that organism
4.
humans apparently have ~20,000 genes in the now-sequenced human genome
C. each species has a characteristic number of chromosomes
1.
the number varies between species
2.
chromosome number does not reflect the complexity of the organism
3.
the assortment of chromosomes for an individual is the karyotype
4.
humans have 46 chromosomes
D. chromosomes carry the genetic information of a cell to the next generation, and to offspring
XL.
The eukaryotic cell cycle
A. the cell cycle describes the status of cells in relationship to growth and division
1.
when cells reach a certain size, growth either stops or the cell must divide
2.
most, but not all, eukaryotic cells are capable of dividing
3.
cell division is generally a highly regulated process
4.
the generation time for eukaryotic cells varies widely, but is usually 8-20 hours
B. cell cycle has two main phases – interphase and cell division (mitosis + cytokinesis)
C. interphase is divided into three parts, defined with respect to DNA replication
1.
the DNA is completely replicated (genetic information duplicated) during the synthesis phase or S phase
2.
the period before the S phase is a “gap” phase, G1 phase
3.

most cellular growth occurs in this phase

this phase is usually the most variable with respect to time, and is typically longest

cells that do not divide become arrested in this phase, then called G0
the period between the S phase and cell division is the G2 phase

the G2 phase is usually short; cells in this phase are committed to and preparing for cell division
D. cell division has two main parts – mitosis and cytokinesis
1.
mitosis is the process that distributes a complete copy of the duplicated genetic information to each daughter cell
2.
cytokinesis is the process of dividing the cytoplasm into two separate cells
3.
some cells can have mitosis without cytokinesis (most common in fungi and slime molds)
E. the current model of cell cycle regulation involves a highly conserved, genetically-controlled program that can be influenced
by external signals
1.
there are three major checkpoints, found in G1, G2 and mitosis
2.
key regulatory components for checkpoints are cyclins and cyclin-dependent protein kinases
3.
hormones such as cytokinins in plants and various protein growth factors in animals can stimulate progression through
checkpoints in the right cells under the right conditions
4.
other factors can serve as suppressors of cell division
5.
cancer cells generally grow without needing stimulation by external growth factors and fail to respond to normal
suppressors of cell division
XLI. mitosis is generally be divided into 4 stages: prophase, metaphase, anaphase, and telophase (PMAT)
A. be aware that mitosis is a continuous process, the stages are defined only for our convenience
B. prophase – chromatin condenses to form chromosomes
1.
2.
each chromosome (duplicated during S phase) forms a pair of sister chromatids

sister chromatids are joined at a centromere by protein tethers

centromeres contain a kinetochore where microtubules will bind

each sister chromatid has its own kinetochore
a system of microtubules, called the mitotic spindle, organizes between the two poles (opposite ends) of the cell
3.
4.

each pole has a microtubule organizing center (MTOC)

in animals and some other eukaryotes, centrioles are found in the MTOC
by the end of prophase:

the nuclear membrane has disappeared (actually divided into many small vesicles)

nucleoli have disintegrated

the sister chromatids are attached by their kinetochores to microtubules from opposite poles
some call the later part of prophase prometaphase, usually defined to include vesicularization of the nuclear membrane
and attachment of kinetochores to microtubules
5.
in some eukaryotes the nuclear membrane never vesicularizes
C. metaphase – chromosomes line up along the midplane of the cell (the metaphase plate)
1.
chromosomes are most condensed, most visible, and most distinguishable during metaphase
2.
the mitotic spindle, now complete, has two types of microtubules

kinetochore microtubules extend from a pole to a kinetochore

polar microtubules extend from a pole to the midplane area, often overlapping with polar microtubules from the
other pole
3.
the mitosis checkpoint appears to be here; progress past metaphase is typically prevented until the kinetochores are all
attached to microtubules
D. anaphase – sister chromatids separate and are moved toward opposite poles
1.
the protein tethers at the centromere between the chromatids are broken
2.
each former sister chromatid can now be called a chromosome
3.
model for the mechanism that moves chromosomes to the poles

motor proteins move the chromosomes towards the poles along the kinetochores microtubules

kinetochore microtubules shorten behind the moving chromosomes

polar microtubules lengthen the entire spindle

motor proteins on the polar microtubules slide them past each other, pushing them apart (the microtubules may
grow a bit, too)

this pushes the MTOCs away from each other, and thus has the effect of pushing kinetochore microtubules from
opposite poles away from each other
4.
overall, this process assures that each daughter cell will receive one of the duplicate sets of genetic material carried by
the chromosomes
E. telophase – the processes of prophase are reversed
1.
the mitotic spindle is disintegrated
2.
the chromosomes decondense
3.
nuclear membranes reform around the genetic material to form two nuclei, each with an identical copy of the genetic
information
4.
nucleoli reappear, and interphase cellular functions resume
XLII. cytokinesis divides the cell into two daughter cells
A. cytokinesis usually begins in telophase and ends shortly thereafter
1.
in animals, a cleavage furrow develops – usually close to where the metaphase plate was

a microfilament (actin) ring contracts due to interactions with myosin molecules, forming a deepening furrow

eventually, the ring closes enough for spontaneous separation of the plasma membrane, resulting in two separate
cells
2.
in plants, a cell plate develops – usually close to where the metaphase plate was

vesicles that originate from the Golgi line up in the equatorial region

the vesicles fuse and add more vesicles, growing outward until reaching the plasma membrane and thus separating
the cells

the vesicles contain materials for making the primary cell wall and a middle lamella
B. cytoplasm (and with it most organelles) is usually distributed randomly but roughly equally between daughter cells
C. sometimes cell division is a highly regulated polar division that purposefully distributes some materials unequally
Chapter 13: Meiosis and Sexual Life Cycles
I.
Different modes of reproduction require different types of cell division
A. asexual reproduction creates offspring that are genetically identical to each other and to the parent cell (clones)
1. only mitotic cell division, or something very similar, is required
2. the parent may split, bud, or fragment; sometimes, this involves mitotic cell division with unequal partitioning during
cytokinesis (cellular budding)
3. asexual reproduction is typically rapid and efficient compared to sexual reproduction
B. sexual reproduction occurs when specialized sex cells called gametes fuse to form a single cell called a zygote
1. usually the gametes that fuse are produced by different individuals, but they may be produced by the same individual
2. in plants and animals the gametes are called the egg and the sperm
3. the offspring are not genetically identical to their parents
4. this genetic recombination may render the offspring better adapted to the environment than either parent, or it may be
more poorly adapted than either parent
5. sexual reproduction must contain a mechanism to half the number of chromosomes at some point
 without such a mechanism, the number of chromosomes would double with each generation
 halving the chromosome number is accomplished through meiosis
II.
Diploid cells give rise to haploid cells during meiosis
A. the somatic (body) cells of animals and higher plants are diploid cells
1. each chromosome in a diploid cell has a partner chromosome
2. the partners are called homologous chromosomes
3. one member of each pair came from the father (paternal homolog), and one from the mother (maternal homolog)
4. thus, for humans, the 46 chromosomes are in 23 pairs
5. most pairs of homologous chromosomes contain very similar, but not identical, genetic information in each member of
the pair (more on this in the next unit, genetics)
sex chromosomes aren’t strictly homologous (an X chromosome has different genes than a Y chromosome), but they act
as if they are homologous during meiosis
7. a set of chromosomes (n) has one member for each homologous pair; a diploid cell has two complete sets (2n), while a
haploid cell has one set (n)
8. sometimes, cells have extra sets (3n or more; polyploid cells – common in plants, rare and usually fatal in animals)
B. meiosis reduces chromosome number, producing up to 4 haploid cells from one diploid cell
1. meiosis has two successive cell divisions after only one DNA replication
2. the two cell divisions are called meiosis I and meiosis II
 homologous chromosomes separate during meiosis I
 sister chromatids separate during meiosis II
 meiosis is best understood by following the chromosomes (and their kinetochores) – don’t confuse homologous
chromosomes with sister chromatids
III.
Meiosis I and meiosis II are each divided into prophase, metaphase, anaphase, and telophase (PMAT) with accompanying
cytokinesis
A. prophase I – chromatin condenses to form chromosomes, and homologous chromosomes pair
1. the process of homologous chromosomes pairing lengthwise is called synapsis
 the resulting structure, with 4 total chromatids (two sisters from each homologous chromosome), is called a bivalent
or a tetrad
 the tetrad is held together by a synaptonemal complex during early prophase I
 typically, enzymes cause breaks in the chromatids and genetic material may be exchanged between chromatids
(crossing-over or genetic recombination)
 genetic recombination greatly increases the potential for genetic variation in offspring
2. as in mitosis, sister chromatids are held together at centromeres and have kinetochores, but their kinetochores are
side-by-side and attach to spindle fibers from the same pole (thus both sister chromatids are later pulled to the same
pole)
3. by the end of prophase I:
 the spindle has formed
 the nuclear membrane has vesicularized
 nucleoli have disintegrated
 homologous chromosomes are attached by their kinetochores to spindle fibers from opposite poles
 homologous chromosomes are held together only at chiasmata, the sites where crossing-over occurred
B. metaphase I – tetrads line up along the midplane of the cell – the presence of tetrads (bundles with 4 total chromatids) is the
key distinguishing feature of metaphase I of meiosis
C. anaphase I – homologous chromosomes separate and are moved toward opposite poles
1. each pole gets one set of homologous chromosomes
2. the initial “maternal” or “paternal” chromosome sets are mixed and distributed randomly (crossing-over largely blurs
such identity anyway)
D. telophase I – after anaphase is completed, generally:
1. the spindle fibers disintegrate
2. the chromosomes partially decondense
3. nuclear membranes may form around the genetic material
4. cytokinesis occurs
E. interkinesis, the period between meiosis I and meiosis II, varies in length and distinctiveness
1. interkinesis differs from interphase because there is no S phase (no DNA replication)
2. typically, interkinesis is brief (some cells skip it altogether)
F. prophase II of meiosis is similar to prophase of mitosis, but is usually very short because the chromatin did not completely
decondense after meiosis I
G. metaphase II – similar to metaphase of mitosis
1. chromosomes line up along the midplane of the cell
2. sister chromatids are connected by their kinetochores (now on opposite sides) to spindle fibers from opposite poles
H. anaphase II – like mitotic anaphase, sister chromatids segregate toward opposite poles
I. telophase II – much like mitotic telophase:
1. the spindle is disintegrated
2. the chromosomes decondense
3. nuclear membranes reform around the genetic material to form nuclei
4. nucleoli reappear, and interphase cellular functions resume
5. cytokinesis usually begins during telophase II and ends shortly thereafter
IV.
Summary: key differences between mitosis and meiosis
A. mitosis has one DNA replication and one division, resulting in two genetically identical daughter cells; homologous
chromosomes do not pair, do not cross-over, and are not segregated
6.
B. meiosis has one DNA replication but two divisions (reductive division), resulting in up to four genetically distinct daughter
cells; in the process, homologous chromosomes pair (synapsis), cross-over (homologous recombination), and segregate
during meiosis
V.
The products of meiosis can vary between sexes and between species
A. in many eukaryotes, the zygote undergoes meiosis, and most of the life cycle is spent as haploid cells; gametes are then
produced by mitosis and fuse to make the zygote
B. in animals, the somatic (body) cells are typically diploid, and special germ line cells undergo meiosis to form haploid
gametes (gametogenesis)
1. male gametogenesis (spermatogenesis) typically produces 4 viable haploid sperm for each germ cell that undergoes
meiosis
2. female gametogenesis (oogenesis) typically produces 1 haploid egg cell (ovum) for each germ cell that undergoes
meiosis; the rest of the genetic material goes to polar bodies, cells that get little of the original cytoplasm and
eventually die
3. a sperm and an egg fuse to make a diploid zygote, which gives rise to the multicellular animal
C. plants and some algae have distinct alternation of generations
1. spores produced after meiosis divide (mitotically) into a multicellular haploid gametophyte, from which gametes are
eventually derived
2. the zygote gives rise (through mitotic divisions) to a multicellular diploid sporophyte, which produces specialized cells
that undergo meiosis to produce spores
Chapter 13: Meiosis and Sexual Life Cycles
45. Why is mitosis alone insufficient for the life cycle of sexually reproducing
eukaryotes?
46.






Define:
gamete
zygote
meiosis
homologous chromosomes
diploid
haploid
47. With a partner, do the “chromosome dance” for meiosis. Make sure that you
distinguish between tetrads, chromosomes, and chromatids, and note at each stage the
number of sister chromatids per chromosome.
48.
Summarize the key events of prophase I.
49. In which phase do sister chromatids segregate? In which phase do homologous
chromosomes segregate?
50.
Compare and contrast meiosis and mitosis.
51. Draw zygotic meiosis, gametic meiosis, and sporic meiosis (alternation of
generations). For each, note the organisms that use it.
52.
Describe Miller’s Ratchet, DNA repair, and the Red Queen hypotheses for sex.
Chapter 13: Meiosis and Sexual Life Cycles
I.
Different modes of reproduction require different types of cell division
A. asexual reproduction creates offspring that are genetically identical to each other and to the parent cell (clones)
1.
only mitotic cell division, or something very similar, is required
2.
the parent may split, bud, or fragment; sometimes, this involves mitotic cell division with unequal partitioning during
cytokinesis (cellular budding)
3.
asexual reproduction is typically rapid and efficient compared to sexual reproduction
B. sexual reproduction occurs when specialized sex cells called gametes fuse to form a single cell called a zygote
1.
usually the gametes that fuse are produced by different individuals, but they may be produced by the same individual
2.
in plants and animals the gametes are called the egg and the sperm
3.
the offspring are not genetically identical to their parents
4.
this genetic recombination may render the offspring better adapted to the environment than either parent, or it may be
more poorly adapted than either parent
5.
II.
sexual reproduction must contain a mechanism to half the number of chromosomes at some point

without such a mechanism, the number of chromosomes would double with each generation

halving the chromosome number is accomplished through meiosis
Diploid cells give rise to haploid cells during meiosis
A. the somatic (body) cells of animals and higher plants are diploid cells
1.
each chromosome in a diploid cell has a partner chromosome
2.
the partners are called homologous chromosomes
3.
one member of each pair came from the father (paternal homolog), and one from the mother (maternal homolog)
4.
thus, for humans, the 46 chromosomes are in 23 pairs
5.
most pairs of homologous chromosomes contain very similar, but not identical, genetic information in each member of
the pair (more on this in the next unit, genetics)
6.
sex chromosomes aren’t strictly homologous (an X chromosome has different genes than a Y chromosome), but they act
as if they are homologous during meiosis
7.
a set of chromosomes (n) has one member for each homologous pair; a diploid cell has two complete sets (2n), while a
haploid cell has one set (n)
8.
sometimes, cells have extra sets (3n or more; polyploid cells – common in plants, rare and usually fatal in animals)
B. meiosis reduces chromosome number, producing up to 4 haploid cells from one diploid cell
1.
meiosis has two successive cell divisions after only one DNA replication
2.
the two cell divisions are called meiosis I and meiosis II

homologous chromosomes separate during meiosis I

sister chromatids separate during meiosis II

meiosis is best understood by following the chromosomes (and their kinetochores) – don’t confuse homologous
chromosomes with sister chromatids
III.
Meiosis I and meiosis II are each divided into prophase, metaphase, anaphase, and telophase (PMAT) with accompanying
cytokinesis
A. prophase I – chromatin condenses to form chromosomes, and homologous chromosomes pair
1.
the process of homologous chromosomes pairing lengthwise is called synapsis

the resulting structure, with 4 total chromatids (two sisters from each homologous chromosome), is called a bivalent
or a tetrad

the tetrad is held together by a synaptonemal complex during early prophase I

typically, enzymes cause breaks in the chromatids and genetic material may be exchanged between chromatids
(crossing-over or genetic recombination)

2.
genetic recombination greatly increases the potential for genetic variation in offspring
as in mitosis, sister chromatids are held together at centromeres and have kinetochores, but their kinetochores are
side-by-side and attach to spindle fibers from the same pole (thus both sister chromatids are later pulled to the same
pole)
3.
by the end of prophase I:

the spindle has formed

the nuclear membrane has vesicularized

nucleoli have disintegrated

homologous chromosomes are attached by their kinetochores to spindle fibers from opposite poles

homologous chromosomes are held together only at chiasmata, the sites where crossing-over occurred
B. metaphase I – tetrads line up along the midplane of the cell – the presence of tetrads (bundles with 4 total chromatids) is the
key distinguishing feature of metaphase I of meiosis
C. anaphase I – homologous chromosomes separate and are moved toward opposite poles
1.
each pole gets one set of homologous chromosomes
2.
the initial “maternal” or “paternal” chromosome sets are mixed and distributed randomly (crossing-over largely blurs
such identity anyway)
D. telophase I – after anaphase is completed, generally:
1.
the spindle fibers disintegrate
2.
the chromosomes partially decondense
3.
nuclear membranes may form around the genetic material
4.
cytokinesis occurs
E. interkinesis, the period between meiosis I and meiosis II, varies in length and distinctiveness
F.
1.
interkinesis differs from interphase because there is no S phase (no DNA replication)
2.
typically, interkinesis is brief (some cells skip it altogether)
prophase II of meiosis is similar to prophase of mitosis, but is usually very short because the chromatin did not completely
decondense after meiosis I
G. metaphase II – similar to metaphase of mitosis
1.
chromosomes line up along the midplane of the cell
2.
sister chromatids are connected by their kinetochores (now on opposite sides) to spindle fibers from opposite poles
H. anaphase II – like mitotic anaphase, sister chromatids segregate toward opposite poles
I.
IV.
telophase II – much like mitotic telophase:
1.
the spindle is disintegrated
2.
the chromosomes decondense
3.
nuclear membranes reform around the genetic material to form nuclei
4.
nucleoli reappear, and interphase cellular functions resume
5.
cytokinesis usually begins during telophase II and ends shortly thereafter
Summary: key differences between mitosis and meiosis
A. mitosis has one DNA replication and one division, resulting in two genetically identical daughter cells; homologous
chromosomes do not pair, do not cross-over, and are not segregated
B. meiosis has one DNA replication but two divisions (reductive division), resulting in up to four genetically distinct daughter
cells; in the process, homologous chromosomes pair (synapsis), cross-over (homologous recombination), and segregate
during meiosis
V.
The products of meiosis can vary between sexes and between species
A. in many eukaryotes, the zygote undergoes meiosis, and most of the life cycle is spent as haploid cells; gametes are then
produced by mitosis and fuse to make the zygote
B. in animals, the somatic (body) cells are typically diploid, and special germ line cells undergo meiosis to form haploid
gametes (gametogenesis)
1.
male gametogenesis (spermatogenesis) typically produces 4 haploid sperm for each germ cell that undergoes meiosis
2.
female gametogenesis (oogenesis) typically produces 1 haploid egg cell (ovum) for each germ cell that undergoes
meiosis; the rest of the genetic material goes to polar bodies, cells that get little of the original cytoplasm and
eventually die
3.
a sperm and an egg fuse to make a diploid zygote, which gives rise to the multicellular animal
C. plants and some algae have distinct alternation of generations
1.
spores produced after meiosis divide (mitotically) into a multicellular haploid gametophyte, from which gametes are
eventually derived
2.
the zygote gives rise (through mitotic divisions) to a multicellular diploid sporophyte, which produces specialized cells
that undergo meiosis to produce spores
VI.
The origin and maintenance of sex is an evolutionary puzzle
A. Sexual reproduction dilutes the genes from the “best adapted” individuals, and thus must offer a significant advantage or
asexual reproduction will win out
B. Even when sex clearly benefits a population or species, it must directly benefit individuals or it will lose out via evolution
C. There may be no single hypothesis that explains “Why sex?” for all sexually reproducing organisms
D. Leading hypotheses for why sex occurs include Miller’s Ratchet, DNA repair, and the Red Queen
1.
Miller’s Ratchet – asexual populations tend to accumulate harmful mutations by chance over time, with no good way to
get rid of them – like turning a ratchet, you can’t go back; recombination can overcome this
2.
DNA Repair – many species reproduce sexually only during times of stress; some types of DNA repair (such as fixing
double-strand breaks) can only take place with a diploid cell, and that type of repair is most likely needed in times of
stress (also, this allows these species to overcome Miller’s Ratchet by simple recombination)
3.
Red Queen – sex allows for populations to “store” genetic diversity so that it is available for each generation; this only
provides an advantage if the environment provides ever-changing physical and/or biological constraints; an
‘evolutionary arms race’ between parasites and their hosts may be a key factor in producing such ‘treadmill
evolution’
Chapter 14: Mendel and the gene idea
VII.
the basic rules of inheritance were first demonstrated by Mendel
A. at the time of Mendel’s work, most thought that parental traits were fluids that “blend” in offspring
B. Mendel recognized that this model did not explain what he observed
C. Mendel chose a model system and carefully established testing conditions
1. he used pea plants that he could outcross or allow to self-fertilize
2. he chose traits that had two clear possible outcomes (yellow or green seeds, etc.)
3. he established true-breeding or “pure” lines to use for genetic crosses
D. terminology for genetic crosses
1. P generation (or P1) = parental generation
2. F1 generation = first generation offspring (from filial)
3. F2 generation = second generation offspring
4. phenotype – appearance or characteristic of an organism
5. genotype – genetic makeup of an organism, determines phenotype
6. gene – unit of heredity; controls a trait that determines a phenotype
7. locus – the location of a particular gene on a chromosome
8. alleles – alternative versions of a gene
9. dominant – allele that dominates over others in determining phenotype
10. recessive – allele whose phenotypic expression is “hidden” when a dominant allele is present
11. hybrid – offspring from a cross between two “pure” lines of different, competing phenotypes
VIII. rules and terminology for examination of genetic inheritance
A. Mendel’s law of segregation
1. when Mendel crossed pure lines of different, competing phenotypes, he found that the F1 generation was uniform and
matched one of the parents’ phenotypes
 example: P1 yellow seed X green seed  all F1 yellow seed
2. when F1 plants were crossed or selfed, the F2 plants had both P1 phenotypes in a ratio of roughly 3:1
 using offspring from above F1 X F1  F2 3 yellow seed: 1 green seed
3. thus, contrary to the popular belief of the time, recessive traits are not lost in a mixing of parental phenotypes – they are
merely hidden in some “carrier” individuals
4. Mendel explained these ratios with what we now call his law of segregation; stated in modern terms: individuals
normally carry two alleles for each gene, these alleles must segregate in production of sex cells
5. later investigations of cell division revealed the mechanism for segregation: the pairing and subsequent separation of
homologous chromosomes during meiosis
B. genotype vs. phenotype
1. phenotype is the actual appearance or characteristic, and is determined by genotype; knowing the phenotype will not
always directly reveal the genotype (recessive traits can be masked)
2. genotype is the listing of the actual alleles present; if you know the genotype, you should be able to predict the
phenotype
 genotypes are either homozygous or heterozygous
 homozygous – the homologous chromosomes have the same allele at the locus in question
 heterozygous – the homologous chromosomes have different alleles at the locus; if there is a dominant allele
the trait of the dominant allele will be expressed
 the same letter is used to indicate all alleles (superscripts or subscripts are sometimes needed, if there are more than
2 alleles known)
 DOMINANT ALLELES ARE CAPITALIZED; recessive alleles are lowercase
C. rules of probability govern genetic inheritance
1. the likelihood of a sex cell carrying a particular allele is determined by probability, its expected frequency of occurrence
(expressed in fractions, decimal fractions, percentages, or ratios)
2. the combination of sex cells to form a zygote is generally ruled by probability as well
3. thus, the rules of probability govern genetics
4. product rule – when independent but not mutually exclusive events are combined, you multiply their individual
probabilities to get the overall probability of the result (genetic crosses, X, are multiplications of probabilities)
5. sum rule– if there is more than one way to obtain a result (mutually exclusive events), you add their individual
probabilities to get the overall probability of the result
 the sum of all possibilities is one (no more, no less)
D. Punnett square – way of diagramming genetic crosses that uses the laws of probability
E. more terminology
1. test cross – mating an individual that has the dominant phenotype for a trait with an individual with the recessive
phenotype; this often will reveal the genotype of the dominant parent, or at least give some idea of the probably
genotype
2. monohybrid cross – cross between individuals that are both heterozygous for the gene that you are following; note that
these give a 3:1 phenotype ratio and a 1:2:1 genotype ratio
F. practice applying the law of segregation: following one gene in a cross
1. A pea plant with yellow seeds is crossed with a pea plant with green seeds (P 1 generation). All 131 offspring (F1
generation) have yellow seeds. What are the likely genotypes of the P 1 plants?
2. Two of the F1 plants from above are crossed. What are the expected ratios of phenotypes and genotypes in the F 2
generation?
3. be sure to work some examples on your own; the textbook and website have plenty of genetics problems – note how they
are typically presented as word problems and expect that format on your test
IX.
expanding the rules and terminology to follow two (or more) genes in a cross
A. law of independent assortment
1. dihybrid cross – cross between individuals that are both heterozygous for two different genes that you are following
2. when Mendel performed dihybrid crosses he found phenotype ratios of 9:3:3:1, which is explained by the product rule
3. this led to Mendel’s law of independent assortment: segregation of any one pair of alleles is independent of the
segregation of other pairs of alleles
 we now know that this is also a consequence of events in meiosis
 this doesn’t hold perfectly true for all genes (see genetic linkage below)
B. using the law of independent assortment in genetic problems
1. with independent assortment a dihybrid cross is simply two separate monohybrid crosses multiplied
2. avoid making tedious and difficult Punnett squares like in Fig. 14.8; pay attention in class for an easier method
 make sure to try some on your own
X.
Beyond simple genetics: Mendel picked easy fights
A. We have already seen that modifications must be made to Mendel’s laws for linked genes; there are other situations that do
not fit the “simple” cases that Mendel used
B. incomplete dominance – the heterozygote has a phenotype that is intermediate between the two homozygous states
1. really, the term dominance has no true meaning here
2. example: red, pink, and white snapdragon flowers
C. codominance – the heterozygote expresses characteristics of both alleles; very much like incomplete dominance
1. not an intermediate form, instead you see each allele distinctly expressed
2. roan cattle, expressing both red and white hairs, are a good example (the difference between incomplete dominance and
codominance is essentially a case of splitting hairs)
3. one of the best examples is the ABO human blood type, which will be covered below
4. how to spot codominance or incomplete dominance: monohybrid crosses with a 1:2:1 phenotype ratio
D. multiple alleles – it is very common for there to be more than two allele types for a give locus; any time there are three or
more alleles types involved, we say that there are multiple alleles
1. dominance relationships can vary between multiple alleles
2. example: rabbit coat color is influenced by a gene that has four known alleles
3. example: human ABO blood types
 the main blood type is determined by a single locus with three known alleles (I A, IB, iO)
 IA and IB alleles are codominant with respect to each other
 the IA allele leads to the expression of type A antigen on the surface of red blood cells
 the IB allele leads to the expression of type B antigen on the surface of red blood cells
 iO is a recessive allele; the iO allele does not lead to expression of a cell surface antigen
 resulting blood types:
 IAIA or IAiO genotype produce only the A antigen; blood type A
 IBIB or IBiO genotype produce only the B antigen; blood type B
 IAIB genotype produces both the A antigen and B antigen; blood type AB
 iOiO genotype produces no A or B antigens; blood type O
 blood transfusions (or any transplants) must be of the appropriate type, because the blood of individuals contains
antibodies against the antigens not contained on its red blood cells
 thus, type O can only accept type O blood or organs
 type AB can accept any type blood or organs (A, B, AB or O); etc.
 there are other blood type factors, such as Rh factor, that must be taken into account
 blood type is used in paternity or maternity cases only as a means to rule out possible parents
4. (tangent warning!) the other key component tested for human blood typing is the Rh factor
o while there are actually several Rh factors, one (antigen D) is most commonly tested and referred to as the Rh factor;
most Americans are Rh+
o expression of antigen D on red blood cell surfaces is controlled by a single gene; the dominant phenotype leads to
expression of the antigen (recessive = no expression)
o inheritance of the Rh factor is thus described by classical Mendelian inheritance; if you express the dominant
phenotype, you are Rh+; if you are Rh-, then you are homozygous recessive for the gene controlling the factor
o someone who is Rh- should not be given Rh+ blood or organs, because they will develop antibodies to antigen D
and reject the blood or organs
o the Rh factor can cause complications during pregnancy (something not seen with the ABO bloodgroup)
o there are other blood typings and tissue matchings that are done, but the ABO/Rh blood typing is the one most
commonly used (for example, ABO/Rh is usually all that matters for blood donation or reception
E. pleiotrophy: one gene, many phenotypes
1. one gene affects more than one characteristic
2. usually only one gene product is directly involved, and its status affects many things
3. many disease genes are pleiotrophic (examples, cystic fibrosis, sickle cell anemia)
F. one phenotype, many genes: gene interactions, epistasis, and polygenic inheritance
1. gene interactions – two or more genes interact to produce a novel phenotype
 examples: rooster combs; coat color in Labrador retrievers
 hallmark of gene interactions: exactly 4 phenotypes are found, and certain crosses will produce a 9:3:3:1 phenotype
ratio in offspring (thus indicating that they are dihybrid crosses)
epistasis – one gene influences the phenotype that a second gene usually controls, masking any effects of alleles at the
second gene; the name literally means “stopping” or “standing upon”
 example: albinism is generally epistatic
 spot epistasis by modification of dihybrid cross results, getting ratios like 9:7 or 9:3:4 instead of 9:3:3:1
3. polygenic inheritance – multiple, independent genes have similar, additive effects on a characteristic
 examples include height and skin color in humans
 most economically important traits are polygenic (cow milk production, cattle weight, corn crop yield, etc.)
 polygenic traits don’t fall easily into distinct categories; instead, they usually are measured traits (quantitative
traits)
 when plotted out for a population, polygenic traits produce a normal distribution curve if mating is random with
respect to the trait
G. also note that genotype is not the only basis for phenotype – environment can have a major impact on what phenotype is seen
for some traits
H. Do all of these exceptions invalidate Mendel’s laws?
1. No. Mendel’s laws explain the basic situation, and all of these exceptions are best understood in light of the mechanisms
that Mendel described. Scientists generally try to understand simple cases before moving on to the more baffling
ones, and often (as here) understanding the simpler cases helps form the basis for understanding the more
complicated ones.
 However…it is important to know about these “exceptions” and apparent exceptions, because most genetic
inheritance has some aspect of at least one of these “exceptions” in it.
XI.
Autosomal recessive genetic disorders
A. most genetic disorders are inherited as autosomal recessive traits
B. the recessive allele is usually a nonfunctional (or poorly functional) copy of a gene whose product is needed in metabolism
C. much genetic research with model organisms (mouse, fruit fly, etc.) uses such traits to determine gene identities and
functions
D. gene therapy is considered to be a promising possibility for treatment of many of these disorders
1. the idea usually is to put a functional copy of the gene into critical body cells
2. the problem is how to get the gene delivered to the cells where it is needed – sometimes a virus is used to infect cells,
with the virus actually carrying and expressing the desired gene
3. in some cases, particularly if blood is involved, it appears that blood stem cells may be able to be removed from the
patient, transformed (have new genetic material inserted), and then returned to the patient’s body
4. the most promising transformation mechanism uses embryonic stem cells and cloning
 take cells from a discarded embryo (relatively common from in vitro fertilization) and remove the nucleus
 replace the nucleus with one from a putative gene therapy patient, and grow lots of cells in culture
 perform a technique to the gene you want into the cells, then select for the cells that do what you want
 grow those cells in culture, treat them with hormones that cause them to differentiate into the cell type that you
want, and put those cells into the patient
Examples in humans
5. phenylketonuria (PKU)
 most common in those of western European descent; occurs in about 1 in 12,000 human births in the U.S.
 phenylalanine (an amino acid) is not metabolized properly, leading to a buildup of a toxic compounds that can lead
to severe mental retardation
 treated with a diet that dramatically reduces phenylalanine consumption; potential gene therapy target
6. sickle cell anemia
 most common in those of African descent; about 1 in 500 of African-Americans have it
 caused by a mutation in hemoglobin that makes it tend to crystallize when oxygen is not bound to it
 makes red blood cells take on a sickle shape, which can slow or even block blood flow through veins and
capillaries
 can damage tissues due to lack of oxygen and nutrients, and is very painful
 shortens lifespan of red blood cells, leading to anemia (low red blood cell count)
 treatments have increased life expectancy, including stimulating fetal hemoglobin production and bone marrow
transplants; work continues on gene therapy
 the heterozygous condition actually leads to increased resistance to malaria, and thus is favored when malaria is
present – about 1 in 12 African-Americans are heterozygous and thus “carriers” for sickle cell anemia
7. cystic fibrosis
 most common in those of European descent (in this group, about 1 in 2500 births, with about 1 in 20 phenotypically
normal, heterozygous carriers for the trait)
 abnormal mucus secretions, particularly in the lungs, due to a defect in Cl - ion transport
 life expectancy short (about 30 years); treatments are limited – has been a target for gene therapy trials
 heterozygous carriers may be less likely to die from diarrhea-inducing diseases (based on mouse model studies
involving cholera)
2.
XII.
Autosomal dominant genetic disorders in humans
A. severe dominant genetic disorders are not common, because they are usually are not passed on to the next generation
(affected individuals usually die before they have children)
B. those that do exist typically have late onset of disorder symptoms (late enough for those with the disorder to have had
children)
C. the best known autosomal dominant disorder is Huntington disease (AKA Huntington’s chorea, or HD)
1. occurs in about 1 in 10,000 human births in the U.S. (no heterozygous carriers – it is a dominant disorder)
2. affects central nervous system, leading to severe mental and physical deterioration
3. onset of symptoms usually in 30s or 40s
4. one of at least 9 known “trinucleotide repeat disorders” in humans
 HD is caused by a gene with a [CAG] repeat of 36-100x or more (normal allele has 6-35 of these repeats); more
repeats usually means earlier onset
 fragile X syndrome and myotonic dystrophy are two other examples of trinucleotide repeat disorders
D. hypercholesterolemia is the most common dominant genetic disorder known (estimates are that as many as 1 in 500 have
it); generally causes high cholesterol levels in the blood, leading to heart disease
XIII. Methods of studying human inheritance
A. ethics must be considered in studies of human genetics
1. most genetic research involves producing inbred lines and controlled genetic crosses
2. since we can’t (or shouldn’t) really do that with humans, we must use other means
3. isolated populations with typically large families are often used because they provide much inbreeding and many data
points
B. family pedigree analysis
1. pedigree – a chart summarizing phenotypes and/or genotypes within a family over several generations
2. standard symbols for pedigrees:
 generations are designated with capital roman numerals, starting with the oldest generation at the top
 each generation gets one row, and genetic parents are connected by a horizontal line
 males are square, females round
 each individual gets a number, going from left to right for each generation
 a vertical line connects parents to their offspring
 coloring is used to indicate phenotype (and, sometimes, known genotypes)
3. pedigree analyses only work well when a single locus is involved in determining a phenotype (so-called Mendelian
traits); still, many disorder genes have been identified and characterized with the help of pedigree analysis (some
human genetic disorders will be discussed later in this unit)
4. you need to be able to analyze pedigrees and determine which is the most likely mode of inheritance for a single-gene
trait among these choices: autosomal dominant, autosomal recessive, X-linked dominant, X-linked recessive
C. karyotyping
1. many genetic problems occur on the large-scale, chromosomal level
2. studies of karyotypes are often done to test for such problems
3. a karyotype display reveals the composition of chromosomes for an individual
 a cell sample is taken (white blood cells, amniocentesis, chorionic villus sampling, etc.)
 cells are grown in culture, and eventually treated to make chromosomes easy to photograph
 the chromosome images are then analyzed and used to create the karyotype display
4. chromosomes are identified by size, position of the centromeres, and staining patterns
D. human genome project
1. sequencing the human genome provides a means to greatly accelerate studies of human genetics
 the underlying genetic causes for gene-based traits can be studied more easily (including traits that involve multiple
genes)
 sequence variations can be readily analyzed
 more sophisticated genetic testing can be performed, leading to the potential for genetically tailored medical
treatment. (a “complete” draft of the human genome sequence (~3 billion basepairs) was made public in April
2003 [coinciding with the 50th anniversary of the Watson and Crick paper announcing the structure of DNA] –
there are ~35,000 genes in the genome, based on current interpretations of the sequence)
XIV. Genetic testing and screening in humans
A. conclusive tests for many genetic disorders are now available
B. especially with the completing of the sequencing of the human genome, more sophisticated “predictive probability” tests are
available, such as for alleles that are associated with higher rates of breast cancer
C. although testing gives more knowledge, it has limitations (there are often at best limited treatments for the disorder, and in
some cases the test only tells you if you are more or less likely to have a problem); testing leads to many ethical issues
and concerns that are still being addressed
Chapter 14: Genetics
53.





Compare and describe the relationship between:
P generation (or P1) / F1 generation / F2 generation
phenotype / genotype
gene / locus / alleles
dominant allele or trait / recessive allele or trait
homozygous / heterozygous / hybrid
54. Draw a Punnett square and list the predicted fractions for each genotype and
phenotype for this cross:
heterozygous (yellow seeds) X heterozygous (yellow seeds)
…where yellow seeds is dominant over green seeds
55. Problems from slides:
A pea plant with yellow seeds is crossed with a pea plant with green seeds (P1 generation).
All 131 offspring (F1 generation) have yellow seeds. What are the likely genotypes of the
P1 plants?
Two of the F1 plants from before are crossed. What are the expected ratios of phenotypes
and genotypes in the F2 generation?
56.
[make up about 3 two-gene crosses in class]
57.
Determine predicted results for the test cross used in the genetic linkage example.
58.
Discuss how you could map the third gene in the example on the slide.
59.
Give the phenotype ratio results for a cross between pink and snapdragons.
60.
[make up 2-3 blood group genetics problems in class]
61.
Describe three different ways in which sex is determined.
62.
Describe the homogametic and heterogametic sexes for humans and then for birds.
63.
[make up 2-3 sex linkage genetics problems in class]
64. Explain dosage compensation in fruit flies and then in mammals; for mammals, use
the terms Barr body and mosaicism
Chapter 14: Genetics
XV.
the basic rules of inheritance were first demonstrated by Mendel
A. at the time of Mendel’s work, most thought that parental traits were fluids that “blend” in offspring
B. Mendel recognized that this model did not explain what he observed
C. Mendel chose a model system and carefully established testing conditions
1.
he used pea plants that he could outcross or allow to self-fertilize
2.
he chose traits that had two clear possible outcomes (yellow or green seeds, etc.)
3.
he established true-breeding or “pure” lines to use for genetic crosses
D. terminology for genetic crosses
1.
P generation (or P1) = parental generation
2.
F1 generation = first generation offspring (from filial)
3.
F2 generation = second generation offspring
4.
phenotype – appearance or characteristic of an organism
5.
genotype – genetic makeup of an organism, determines phenotype
6.
gene – unit of heredity; controls a trait that determines a phenotype
7.
locus – the location of a particular gene on a chromosome
8.
alleles – alternative versions of a gene
9.
dominant – allele that dominates over others in determining phenotype
10. recessive – allele whose phenotypic expression is “hidden” when a dominant allele is present
11. hybrid – offspring from a cross between two “pure” lines of different, competing phenotypes
XVI. rules and terminology for examination of genetic inheritance
A. Mendel’s law of segregation
1.
when Mendel crossed pure lines of different, competing phenotypes, he found that the F 1 generation was uniform and
matched one of the parents’ phenotypes

2.
when F1 plants were crossed or selfed, the F2 plants had both P1 phenotypes in a ratio of roughly 3:1

3.
example: P1 yellow seed X green seed  all F1 yellow seed
using offspring from above F1 X F1  F2 3 yellow seed: 1 green seed
thus, contrary to the popular belief of the time, recessive traits are not lost in a mixing of parental phenotypes – they are
merely hidden in some “carrier” individuals
4.
Mendel explained these ratios with what we now call his law of segregation; stated in modern terms: individuals
normally carry two alleles for each gene, these alleles must segregate in production of sex cells
5.
later investigations of cell division revealed the mechanism for segregation: the pairing and subsequent separation of
homologous chromosomes during meiosis
B. genotype vs. phenotype
1.
phenotype is the actual appearance or characteristic, and is determined by genotype; knowing the phenotype will not
always directly reveal the genotype (recessive traits can be masked)
2.
genotype is the listing of the actual alleles present; if you know the genotype, you should be able to predict the
phenotype

genotypes are either homozygous or heterozygous

homozygous – the homologous chromosomes have the same allele at the locus in question

heterozygous – the homologous chromosomes have different alleles at the locus; if there is a dominant allele
the trait of the dominant allele will be expressed

the same letter is used to indicate all alleles (superscripts or subscripts are sometimes needed, if there are more than
2 alleles known)

DOMINANT ALLELES ARE CAPITALIZED; recessive alleles are lowercase
C. rules of probability govern genetic inheritance
1.
the likelihood of a sex cell carrying a particular allele is determined by probability, its expected frequency of occurrence
(expressed in fractions, decimal fractions, percentages, or ratios)
2.
the combination of sex cells to form a zygote is generally ruled by probability as well
3.
thus, the rules of probability govern genetics
4.
product rule – when independent but not mutually exclusive events are combined, you multiply their individual
probabilities to get the overall probability of the result (genetic crosses, X, are multiplications of probabilities)
5.
sum rule– if there is more than one way to obtain a result (mutually exclusive events), you add their individual
probabilities to get the overall probability of the result

the sum of all possibilities is one (no more, no less)
D. Punnett square – way of diagramming genetic crosses that uses the laws of probability
E. more terminology
1.
test cross – mating an individual that has the dominant phenotype for a trait with an individual with the recessive
phenotype; this often will reveal the genotype of the dominant parent, or at least give some idea of the probably
genotype
2.
monohybrid cross – cross between individuals that are both heterozygous for the gene that you are following; note that
these give a 3:1 phenotype ratio and a 1:2:1 genotype ratio
F.
practice applying the law of segregation: following one gene in a cross
1.
A pea plant with yellow seeds is crossed with a pea plant with green seeds (P1 generation). All 131 offspring (F1
generation) have yellow seeds. What are the likely genotypes of the P 1 plants?
2.
Two of the F1 plants from above are crossed. What are the expected ratios of phenotypes and genotypes in the F2
generation?
3.
be sure to work some examples on your own; the textbook and website have plenty of genetics problems – note how they
are typically presented as word problems and expect that format on your test
XVII. expanding the rules and terminology to follow two (or more) genes in a cross
A. law of independent assortment
1.
dihybrid cross – cross between individuals that are both heterozygous for two different genes that you are following
2.
when Mendel performed dihybrid crosses he found phenotype ratios of 9:3:3:1, which is explained by the product rule
3.
this led to Mendel’s law of independent assortment: segregation of any one pair of alleles is independent of the
segregation of other pairs of alleles

we now know that this is also a consequence of events in meiosis

this doesn’t hold perfectly true for all genes (see genetic linkage below)
B. using the law of independent assortment in genetic problems
1.
with independent assortment a dihybrid cross is simply two separate monohybrid crosses multiplied
2.
avoid making tedious and difficult Punnett squares like in Fig. 14.8; pay attention in class for an easier method
3.
we will work examples in class; be sure to try some on your own
C. genetic linkage – independent assortment does not always occur (see Ch. 15.1, 15.3)
1.
independent segregation of chromosomes during meiosis I leads to independent assortment
2.
independent assortment can lead to recombination

recombination – any process that leads to combinations of genotypes not seen in the parents

recombinant gametes – gametes that display a recombinant genotype

recombinant offspring – offspring whose phenotype reveals that they inherited genes from a recombinant gamete
3.
genes that are on the same chromosome may not sort independently; such genes are said to be linked
4.
an example will be used in class to show the effect of linkage on the results of a genetic cross
5.
crossing over breaks linkages between genes

recall crossing over during prophase I between homologous chromosomes; it is the only way to get genetic
recombination between genes that are on the same chromosome

the further apart two genes are, the more likely they are to have crossing over occur between them (thus leading to
genetic recombination)
6.
genetic maps of chromosomes

percentage of crossing over or recombination is calculated from 100 times the number of recombinant offspring
divided by the total number of offspring

map unit – by convention, one map unit = 1% recombination (the term cM or centiMorgan is sometimes used for
map units, in honor of a pioneer in gene mapping)

map distances between genes on the same chromosome are measured in map units

linkage group = all genes on a particular chromosome; tend to be inherited together

placement of a gene into a position in a linkage group is genetic mapping

map distances get less meaningful as they get large


as genes get further apart, the odds of multiple crossing over events between them increase

when distances approach 50 map units, the genes appear essentially unlinked

many chromosomes have an overall map length of well over 50 map units
genetic maps are useful in locating the actual physical location of genes
XVIII. Beyond simple genetics: Mendel picked easy fights
A. We have already seen that modifications must be made to Mendel’s laws for linked genes; there are other situations that do
not fit the “simple” cases that Mendel used
B. incomplete dominance – the heterozygote has a phenotype that is intermediate between the two homozygous states
1.
really, the term dominance has no true meaning here
2.
example: red, pink, and white snapdragon flowers
C. codominance – the heterozygote expresses characteristics of both alleles; very much like incomplete dominance
1.
not an intermediate form, instead you see each allele distinctly expressed
2.
roan cattle, expressing both red and white hairs, are a good example (the difference between incomplete dominance and
codominance is essentially a case of splitting hairs)
3.
one of the best examples is the ABO human blood type, which will be covered below
4.
how to spot codominance or incomplete dominance: monohybrid crosses with a 1:2:1 phenotype ratio
D. multiple alleles – it is very common for there to be more than two allele types for a give locus; any time there are three or
more alleles types involved, we say that there are multiple alleles
1.
dominance relationships can vary between multiple alleles
2.
example: rabbit coat color is influenced by a gene that has four known alleles
3.
example: human ABO blood types

the main blood type is determined by a single locus with three known alleles (I A, IB, iO)

IA and IB alleles are codominant with respect to each other

the IA allele leads to the expression of type A antigen on the surface of red blood cells

the IB allele leads to the expression of type B antigen on the surface of red blood cells

iO is a recessive allele; the iO allele does not lead to expression of a cell surface antigen

resulting blood types:


IAIA or IAiO genotype produce only the A antigen; blood type A

IBIB or IBiO genotype produce only the B antigen; blood type B

IAIB genotype produces both the A antigen and B antigen; blood type AB

iOiO genotype produces no A or B antigens; blood type O
blood transfusions (or any transplants) must be of the appropriate type, because the blood of individuals contains
antibodies against the antigens not contained on its red blood cells

4.

thus, type O can only accept type O blood or organs

type AB can accept any type blood or organs (A, B, AB or O); etc.

there are other blood type factors, such as Rh factor, that must be taken into account
blood type is used in paternity or maternity cases only as a means to rule out possible parents
(tangent warning!) the other key component tested for human blood typing is the Rh factor
o
while there are actually several Rh factors, one (antigen D) is most commonly tested and referred to as the Rh factor;
most Americans are Rh+
o
expression of antigen D on red blood cell surfaces is controlled by a single gene; the dominant phenotype leads to
expression of the antigen (recessive = no expression)
o
inheritance of the Rh factor is thus described by classical Mendelian inheritance; if you express the dominant
phenotype, you are Rh+; if you are Rh-, then you are homozygous recessive for the gene controlling the factor
o
someone who is Rh- should not be given Rh+ blood or organs, because they will develop antibodies to antigen D
and reject the blood or organs
o
the Rh factor can cause complications during pregnancy (something not seen with the ABO bloodgroup)
o
there are other blood typings and tissue matchings that are done, but the ABO/Rh blood typing is the one most
commonly used (for example, ABO/Rh is usually all that matters for blood donation or reception
E. pleiotrophy: one gene, many phenotypes
F.
1.
one gene affects more than one characteristic
2.
usually only one gene product is directly involved, and its status affects many things
3.
many disease genes are pleiotrophic (examples, cystic fibrosis, sickle cell anemia)
one phenotype, many genes: gene interactions, epistasis, and polygenic inheritance
1.
gene interactions – two or more genes interact to produce a novel phenotype

examples: rooster combs; coat color in Labrador retrievers

hallmark of gene interactions: exactly 4 phenotypes are found, and certain crosses will produce a 9:3:3:1 phenotype
ratio in offspring (thus indicating that they are dihybrid crosses)
2.
epistasis – one gene influences the phenotype that a second gene usually controls, masking any effects of alleles at the
second gene; the name literally means “stopping” or “standing upon”
3.

example: albinism is generally epistatic

spot epistasis by modification of dihybrid cross results, getting ratios like 9:7 or 9:3:4 instead of 9:3:3:1
polygenic inheritance – multiple, independent genes have similar, additive effects on a characteristic

examples include height and skin color in humans

most economically important traits are polygenic (cow milk production, cattle weight, corn crop yield, etc.)

polygenic traits don’t fall easily into distinct categories; instead, they usually are measured traits (quantitative
traits)

when plotted out for a population, polygenic traits produce a normal distribution curve if mating is random with
respect to the trait
G. also note that genotype is not the only basis for phenotype – environment can have a major impact on what phenotype is seen
for some traits
H. Do all of these exceptions invalidate Mendel’s laws?
1.
No. Mendel’s laws explain the basic situation, and all of these exceptions are best understood in light of the mechanisms
that Mendel described. Scientists generally try to understand simple cases before moving on to the more baffling
ones, and often (as here) understanding the simpler cases helps form the basis for understanding the more
complicated ones.
2.
However…it is important to know about these “exceptions” and apparent exceptions, because most genetic inheritance
has some aspect of at least one of these “exceptions” in it.
XIX. Sex determination and sex chromosomes (see Ch. 15.2)
A. sex determination varies between species
1.
hermaphroditic organisms – have both sexes in the same individual
2.
many animals have sex determined in response to environmental signals
3.
most animals have sex determined by genetic inheritance; sex chromosomes are involved
B. sex chromosomes
1.
homogametic sex – has a pair of similar sex chromosomes; all gametes that individual produces get that kind of sex
chromosome
2.
heterogametic sex – has two different sex chromosomes, and makes gametes with two different types of sex
chromosome
3.
all the other, non-sex chromosomes are called autosomes
4.
usually, the sex chromosome found in the homogametic sex is considerably larger, and the shorter sex chromosome
found only in the heterogametic sex has few genes
5.
in humans, females are XX and males are XY (not all do it this way – birds are essentially reversed in this)
6.
X and Y chromosomes have regions of homology (sequence similarity) that allow for pairing during meiosis I
7.
usually, but not always, the sex determining gene is on the Y chromosome

XXY humans are male (Klinefelter syndrome)

X_ humans are female (Turner syndrome)
C. sex-linked traits
1.
genes on sex chromosomes show inheritance patterns that do not fit traditional Mendelian ratios that describe what
happens to genes on autosomes
2.
in humans (and other species with XY sex determination), a gene found only on the X chromosome is said to be Xlinked (which is a type of sex-linked)

males only get one X chromosome, from the mother, and are hemizygous at every locus found only on the X
chromosome

thus, recessive X-linked alleles are expressed more often in males than in females

X-linked alleles are written with superscripts

we will work examples for X-linked inheritance in class; be sure to try some on your own
D. dosage compensation
1.
it is not always good to have twice as much of a chromosome, or half as much
2.
dosage compensation – a mechanism for equalizing the overall expression of an sex-linked genes in both males and
females

some organisms (like fruit flies) ramp up X-linked gene expression in the heterogametic sex

some (like humans and other mammals) use inactivation of most of one of the X chromosomes
3.
Barr body – condensed, mostly inactivated X chromosome visible during interphase in most mammalian cells
4.
variegation or mosaicism – mixes in phenotypic appearance in an organism due to expression of X-linked genes and
variable, random inactivation patterns for X chromosomes (example: calico cat)
XX.
Using genetics in breeding
A. inbreeding – the mating of closely related individuals (includes self-fertilization)
1.
typically done to enhance a desirable trait (quantitative or qualitative) that an individual has
2.
also done to produce homozygous lines (“true-breeding”)
3.
often produces genetically inferior individuals due to unmasking of deleterious recessive traits
B. outbreeding – mating of essentially unrelated individuals (unclear cut-off, beyond second cousins is generally considered
enough)
1.
hybrid vigor – progeny produced by outbreeding often show a clear genetic superiority as a group over their parents
when the parents are from mostly inbred lines
2.
the exact cause of hybrid vigor is not clear, and likely has multiple aspects

less expression of deleterious recessive traits certainly plays a role

heterozygote advantage – some positive attribute that is not found in any homozygous case

for example, sometimes expression of one of the allelic forms is good to have under one condition and the other
is good under a different condition; expressing both allelic forms allows the organism to do well in both
conditions, which may both come up during its life
XXI. Methods of studying human inheritance
A. ethics must be considered in studies of human genetics
1.
most genetic research involves producing inbred lines and controlled genetic crosses
2.
since we can’t (or shouldn’t) really do that with humans, we must use other means
3.
isolated populations with typically large families are often used because they provide much inbreeding and many data
points
B. family pedigree analysis
1.
pedigree – a chart summarizing phenotypes and/or genotypes within a family over several generations
2.
standard symbols for pedigrees:

generations are designated with capital roman numerals, starting with the oldest generation at the top

each generation gets one row, and genetic parents are connected by a horizontal line

males are square, females round
3.

each individual gets a number, going from left to right for each generation

a vertical line connects parents to their offspring

coloring is used to indicate phenotype (and, sometimes, known genotypes)
pedigree analyses only work well when a single locus is involved in determining a phenotype (so-called Mendelian
traits); still, many disorder genes have been identified and characterized with the help of pedigree analysis (some
human genetic disorders will be discussed later in this unit)
4.
you need to be able to analyze pedigrees and determine which is the most likely mode of inheritance for a single-gene
trait among these choices: autosomal dominant, autosomal recessive, X-linked dominant, X-linked recessive
C. karyotyping
1.
many genetic problems occur on the large-scale, chromosomal level
2.
studies of karyotypes are often done to test for such problems
3.
a karyotype display reveals the composition of chromosomes for an individual
4.

a cell sample is taken (white blood cells, amniocentesis, chorionic villus sampling, etc.)

cells are grown in culture, and eventually treated to make chromosomes easy to photograph

the chromosome images are then analyzed and used to create the karyotype display
chromosomes are identified by size, position of the centromeres, and staining patterns
D. human genome project
1.
sequencing the human genome provides a means to greatly accelerate studies of human genetics

the underlying genetic causes for gene-based traits can be studied more easily (including traits that involve multiple
genes)

sequence variations can be readily analyzed

more sophisticated genetic testing can be performed, leading to the potential for genetically tailored medical
treatment
2.
a “complete” draft of the human genome sequence (~3 billion basepairs) was made public in April 2003 [coinciding with
the 50th anniversary of the Watson and Crick paper announcing the structure of DNA] – there are ~25,000 genes in
the genome, based on current interpretations of the sequence
3.
links of interest:
http://www.ornl.gov/sci/techresources/Human_Genome/project/50yr/press4_2003.shtml
http://www.ornl.gov/TechResources/Human_Genome/publicat/primer/
http://www.ncbi.nlm.nih.gov/genome/guide/human/
http://www.genome.gov
http://www.genomenewsnetwork.org/
XXII. Autosomal recessive genetic disorders
A. most genetic disorders are inherited as autosomal recessive traits
B. the recessive allele is usually a nonfunctional (or poorly functional) copy of a gene whose product is needed in metabolism
C. much genetic research with model organisms (mouse, fruit fly, etc.) uses such traits to determine gene identities and
functions
D. gene therapy is considered to be a promising possibility for treatment of many of these disorders
1.
the idea usually is to put a functional copy of the gene into critical body cells
2.
the problem is how to get the gene delivered to the cells where it is needed – sometimes a virus is used to infect cells,
with the virus actually carrying and expressing the desired gene
3.
in some cases, particularly if blood is involved, it appears that blood stem cells may be able to be removed from the
patient, transformed (have new genetic material inserted), and then returned to the patient’s body
4.
the most promising transformation mechanism uses embryonic stem cells and cloning

take cells from a discarded embryo (relatively common from in vitro fertilization) and remove the nucleus

replace the nucleus with one from a putative gene therapy patient, and grow lots of cells in culture

perform a technique to the gene you want into the cells, then select for the cells that do what you want

grow those cells in culture, treat them with hormones that cause them to differentiate into the cell type that you
want, and put those cells into the patient
E. examples in humans
1.
phenylketonuria (PKU)

most common in those of western European descent; occurs in about 1 in 12,000 human births in the U.S.

phenylalanine (an amino acid) is not metabolized properly, leading to a buildup of a toxic compounds that can lead
to severe mental retardation

2.
treated with a diet that dramatically reduces phenylalanine consumption; potential gene therapy target
sickle cell anemia

most common in those of African descent; about 1 in 500 of African-Americans have it

caused by a mutation in hemoglobin that makes it tend to crystallize when oxygen is not bound to it

makes red blood cells take on a sickle shape, which can slow or even block blood flow through veins and
capillaries


can damage tissues due to lack of oxygen and nutrients, and is very painful

shortens lifespan of red blood cells, leading to anemia (low red blood cell count)
treatments have increased life expectancy, including stimulating fetal hemoglobin production and bone marrow
transplants; work continues on gene therapy

the heterozygous condition actually leads to increased resistance to malaria, and thus is favored when malaria is
present – about 1 in 12 African-Americans are heterozygous and thus “carriers” for sickle cell anemia
3.
cystic fibrosis

most common in those of European descent (in this group, about 1 in 2500 births, with about 1 in 20 phenotypically
normal, heterozygous carriers for the trait)

abnormal mucus secretions, particularly in the lungs, due to a defect in Cl - ion transport

life expectancy short (about 38 years); treatments are limited – has been a target for gene therapy trials

heterozygous carriers may be less likely to die from diarrhea-inducing diseases (based on mouse model studies
involving cholera)
XXIII. Autosomal dominant genetic disorders in humans
A. severe dominant genetic disorders are not common, because they are usually are not passed on to the next generation
(affected individuals usually die before they have children)
B. those that do exist typically have late onset of disorder symptoms (late enough for those with the disorder to have had
children)
C. the best known autosomal dominant disorder is Huntington disease (AKA Huntington’s chorea, or HD)
1.
occurs in about 1 in 10,000 human births in the U.S. (no heterozygous carriers – it is a dominant disorder)
2.
affects central nervous system, leading to severe mental and physical deterioration
3.
onset of symptoms usually in 30s or 40s
4.
one of at least 9 known “trinucleotide repeat disorders” in humans

HD is caused by a gene with a [CAG] repeat of 36-100x or more (normal allele has 6-35 of these repeats); more
repeats usually means earlier onset

fragile X syndrome and myotonic dystrophy are two other examples of trinucleotide repeat disorders

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=genomes.table.8377
D. hypercholesterolemia is the most common dominant genetic disorder known (estimates are that as many as 1 in 500 have
it); generally causes high cholesterol levels in the blood, leading to heart disease
XXIV. Genetic testing and screening in humans
A. conclusive tests for many genetic disorders are now available
B. especially with the completing of the sequencing of the human genome, more sophisticated “predictive probability” tests are
available, such as for alleles that are associated with higher rates of breast cancer
C. although testing gives more knowledge, it has limitations (there are often at best limited treatments for the disorder, and in
some cases the test only tells you if you are more or less likely to have a problem); testing leads to many ethical issues
and concerns that are still being addressed
1.
for a view of a dystopian future based on genetic testing, see the movie “GATTACA”
2.
to see how scientists are trying to address ethical concerns, visit
http://www.ornl.gov/sci/techresources/Human_Genome/elsi/elsi.shtml
Chapter 15: The chromosomal basis of inheritance
I.
Chromosome theory of inheritance Mendelian factors (genes) have specific locus on the chromosomes
 chromosomes undergo segregation and independent assortment
 Morgan used Drosophila as a model system and demonstrated gene chromosome relationships
 Morgan demonstrated that linked genes tend to be inherited together because they are near each other on the same
chromosomes
D. genetic linkage – independent assortment does not always occur
1. independent segregation of chromosomes during meiosis I leads to independent assortment
2. independent assortment leads to recombination
 recombination – any process that leads to combinations of genotypes not seen in the parents
 recombinant gametes – gametes that display a recombinant genotype
 recombinant offspring – offspring whose phenotype reveals that they inherited genes from a recombinant gamete
3. genes that are on the same chromosome may not sort independently; such genes are said to be linked
4. an example will be used in class to show the effect of linkage on the results of a genetic cross
5. crossing over breaks linkages between genes
 recall crossing over during prophase I between homologous chromosomes; it is the only way to get genetic
recombination between genes that are on the same chromosome
 the further apart two genes are, the more likely they are to have crossing over occur between them (thus leading to
genetic recombination)
6. genetic maps of chromosomes
 percentage of crossing over or recombination is calculated from 100 times the number of recombinant offspring
divided by the total number of offspring
 map unit – by convention, one map unit = 1% recombination (the term cM or centiMorgan is sometimes used for
map units, in honor of a pioneer in gene mapping)
 map distances between genes on the same chromosome are measured in map units
 linkage group = all genes on a particular chromosome; tend to be inherited together
 placement of a gene into a position in a linkage group is genetic mapping
 map distances get less meaningful as they get large
 as genes get further apart, the odds of multiple crossing over events between them increase
 when distances approach 50 map units, the genes appear essentially unlinked

many chromosomes have an overall map length of well over 50 map units
genetic maps are useful in locating the actual physical location of genes
XXV. Sex determination and sex chromosomes
A. sex determination varies between species
1. hermaphroditic organisms – have both sexes in the same individual
2. many animals have sex determined in response to environmental signals
3. most animals have sex determined by genetic inheritance; sex chromosomes are involved
B. sex chromosomes
1. homogametic sex – has a pair of similar sex chromosomes; all gametes that individual produces get that kind of sex
chromosome
2. heterogametic sex – has two different sex chromosomes, and makes gametes with two different types of sex
chromosome
3. all the other, non-sex chromosomes are called autosomes
4. usually, the sex chromosome found in the homogametic sex is considerably larger, and the shorter sex chromosome
found only in the heterogametic sex has few genes
5. in humans, females are XX and males are XY (not all do it this way – birds are essentially reversed in this)
6. X and Y chromosomes have regions of homology (sequence similarity) that allow for pairing during meiosis I
7. usually, but not always, the sex determining gene is on the Y chromosome
 XXY humans are male (Klinefelter syndrome)
 X_ humans are female (Turner syndrome)

XXX humans are female (likely to give birth to a XXY child)

XYY humans are male (Jacob’s syndrome)
C. sex-linked traits
1. genes on sex chromosomes show inheritance patterns that do not fit traditional Mendelian ratios that describe what
happens to genes on autosomes
2. a number of inherited diseases in humans are located in sex chromosomes. Examples: Hemophilia, color blindness
3. in humans (and other species with XY sex determination), a gene found only on the X chromosome is said to be Xlinked (which is a type of sex-linked)
 males only get one X chromosome, from the mother, and are hemizygous at every locus found only on the X
chromosome
 thus, recessive X-linked alleles are expressed more often in males than in females
 X-linked alleles are written with superscripts
 make sure to try some of the sex linked gene problems on your own
D. dosage compensation
1. it is not always good to have twice as much of a chromosome, or half as much
2. dosage compensation – a mechanism for equalizing the overall expression of an sex-linked genes in both males and
females
 some organisms (like fruit flies) ramp up X-linked gene expression in the heterogametic sex
 some (like humans and other mammals) use inactivation of most of one of the X chromosomes
3. Barr body – condensed, mostly inactivated X chromosome visible during interphase in most mammalian cells
4. variegation or mosaicism – mixes in phenotypic appearance in an organism due to expression of X-linked genes and
variable, random inactivation patterns for X chromosomes (example: calico cat)
XXVI. Alterations in chromosomes number or structure cause some genetic disorders in humans
1. Abnormal chromosome numbers
 aneuploidy- nondisjucntion of homologous chromosomes during meiosis may lead to formation of an embryo with
one extra chromosomes called trisomic (2n+ 1) or less chromosomes called monosomics (2n-1)
 some organisms may have more than two complete copies of chromosomes sets – Poloploidy. Polyploidy is
uncommon and lethal in most animals, but more prevalent in plants
 Example: Trisomy for 21: Down’s syndrome
2. Alterations in chromosomes structures:
 deletion or loss of a part of chromosomes- usually lethal
Loss of a piece of chr 5 leads to a child with cri-du chat (Cries of a cat) syndrome
 translocation of a part chromosomes to another sites
a piece of chromosome 9 to chromosome 22 is associated with CML leukemia
 Fragile sites - thin chromosomes at a particular point
fragile X has a CGG repeats more than 1000 times leading to break in X xhromosomes
Chapter 15: Chromosomal Abnormalities
65.





Define:
nondisjunction
polyploidy
aneupoidy
trisomy
monosomy
66. Describe each of the aneuploidies that can be found in an appreciable number of
human adults (chromosomal abnormality, common name of the syndrome if it has one,
phenotypes)
67.
Draw an inversion, a deletion, a duplication, and a reciprocal translocation.
68.
Describe trinucleotide repeat disorders.
XXVII. Abnormalities in chromosomal number
A. How does it happen? nondisjunction
1. nondisjunction - mistake in cell division where chromosomes do not separate properly in anaphase
 usually in meiosis, although in mitosis occasionally; in meiosis, can occur in anaphase I or II
2. polyploidy – complete extra sets (3n, etc.) – fatal in humans, most animals
3. aneuploidy – missing one copy or have an extra copy of a single chromosome
 three copies of a chromosome in your somatic cells: trisomy
 one copy of a chromosome in your somatic cells: monosomy
 most trisomies and monosomies are lethal well before birth in humans; exceptions covered below
 generally, autosomal aneuploids tend to be spontaneously aborted
 over 1/5 of human pregnancies are lost spontaneously after implantation (probably closer to 1/3)
 chromosomal abnormalities are the leading known cause of pregnancy loss
 data indicate that minimum 10-15% of conceptions have a chromosomal abnormality
 at least 95% of these conceptions spontaneously abort (often without being noticed)
B. aneuploidy in human sex chromosomes
1. X_ female (Turner syndrome)
 short stature; sterile (immature sex organs); often reduced mental abilities; about 1 in 2500 human female births
2. XXY male (Klinefelter syndrome)
 often not detected until puberty, when female body characteristics develop; sterile; sometimes reduced mental
abilities; testosterone shots can be used as a partial treatment; about 1 in 500 human male births
3. XYY male (XYY syndrome)
 usually tall, with heavy acne; some correlation with mild mental retardation and with aggressiveness; usually still
fertile; about 1 in 1000 human male births
4. XXX female (triple X syndrome)
 usually just like XX females, except for having 2 Barr bodies in somatic cells; HOWEVER, more likely to be sterile,
and if fertile, more likely to have XXY and XXX children; about 1 in 1000 human female births
C. aneuploidy in human autosomes
1. autosomic monosomy appears to be invariably fatal, usually very early in pregnancy
2. most autosomic trisomy is fatal, but sometimes individuals trisomic for autosomes 13, 15, 18, 21, or 22 survive to birth
and even beyond
 chromosome number reflects size; bigger number = smaller size, and usually fewer genes
 extra 13, 15, or 18 leads to multiple defects and usually death well before 1 year of age
 extra 22 is much like extra 21 (Down syndrome, covered below), but usually more severe, with shorter life
expectancy
3. trisomy 21 (Down syndrome): the only autosomal trisomy condition in humans that allows an appreciable number of
individuals to survive to adulthood
 found in about 1 in 750 live births; a phenotypically identical condition occurs that is not due to a true trisomy (it
involves a chromosomal translocation, covered later)

traits include abnormal facial appearance, high likelihood of mental retardation (degree varies considerably), and
increased likelihood of developing leukemia and Alzheimer’s disease
 likelihood of a child being born with Down syndrome increases with the age of the mother
 rate is as high as 1 in 16 live births for mothers age 45 and over at conception; not completely clear why the
odds go up so dramatically, likely a combination of factors; nondisjunction is more common in eggs than
sperm; appears that spontaneous rejection of aneuploid pregnancies is more common in younger women
XXVIII. Abnormalities in chromosomal structure: chromosomal rearrangements and fragile sites
A. in addition to nondisjunction errors, there can be errors in homologous chromosome pairing and in crossing over; these
produce chromosomal rearrangements
1. reciprocal translocation – nonhomologous chromosomes pair and exchange parts (if only one gets new material, this is
just called a translocation)
 can lead to deletions (loss of genetic material) and duplications (extra copies of genetic material)
 somewhat common in humans is a translocation of chromosome 21 to chromosome 14
 results in only 45 chromosomes in body cells of carrier (has one chr 14, one chr 21, one 14/21 = normal
phenotype), but that individual has a high chance of producing offspring that are essentially trisomy 21
(with one chr 14, two chr 21, and one 14/21)
 this is called translocation Down syndrome, accounting for about 3% of all phenotypic Down syndrome
individuals
2. inversion – part of a chromosome is “flipped” relative to the normal gene sequence; can lead to deletions and
duplications
3. deletion
 causes include losses from translocations, crossovers within an inversion, and unequal crossing over
 can also be caused by breaking without rejoining, usually leading to large deletions
 small deletions are less likely to be fatal; large deletions are usually fatal – but always, there is variation based on
what genes are lost
 some medium-sized deletions lead to recognizable human disorders
 several syndromes have been described that correspond to deletions of certain chromosomal regions; most
commonly found in live births in humans is deletion of the short arm of chr 5
 called cri du chat (cat’s cry) syndrome
 found in about 1 in 50,000 live births
 surviving infants have a distinctive cry, severe mental retardation, and shortened lifespan
4. duplication
 causes include extras from translocations, crossovers within an inversion, and unequal crossing over
 again, amount makes a difference, with larger duplications more likely to be fatal, but there is variation based on
what genes are duplicated
 duplications also provide raw material for genetic evolution; for example, there are many pseudogenes in humans
that are “inactivated” duplicates
B. fragile sites
1. some chromosomes have regions that are poorly connected to the rest of the chromosome;
 the “poor connection” is often a string rich in CGG or CGC repeats, and is inherited like a gene
 breaks from these fragile sites lead to loss of genetic material
2. human X can have such a site (fragile X syndrome)
 effects center on decreased mental capacity
 more prominent effects in males than females
 one of the trinucleotide repeat disorders:
 normally 5-55 CGG repeats
 diseased individuals have 200-1300 repeats
 like many trinucleotide repeat disorders, the repeat number may increase from one generation to the next
3. other fragile sites may play a role in cancer
Chapter 16: DNA: The Molecular basis of inheritance
I.
Evidence that DNA is the genetic material
A. What must genetic material do?
1. the genetic material must be able to replicate itself
2. must be able to control living processes
B. a model of genetic inheritance was in place in the early 1900s:
1. Mendel’s “laws” of genetics – inherit one copy of each gene from each parent
2. chromosomes as locations/carriers of genes
3. distribution of chromosomes in making sex cells explains Mendel’s laws
C. chromosomes are predominantly made of two things: protein and DNA
D. from the late 1800s until the mid-1900s, most biologists believed that the genetic material was made of proteins, and that
nucleic acids were inconsequential
1. proteins are very complex
2. proteins have much variety
E. DNA is required for genetic transformation of bacteria
1. studies by Griffith in the 1920s of pneumococcus in mice
 smooth (S) strain killed mice, rough (R) strain did not
 heat-killed S strain did not kill mice, but heat-killed S + R strain killed mice
 some “transforming principle” from the heat-killed S strain changed the R strain to make it deadly
2. studies by Avery and colleagues in the 1940s identified DNA as the “transforming principle” – but many were very
skeptical of this result
F. viruses inject DNA into bacteria and take them over: the Hershey-Chase experiments
1. viruses that infect bacteria are called bacteriophages (shortened as phages)
2. viruses execute a “genetic takeover” of cells
3. using radioactive isotopes, phage were labeled with either 35S to label proteins or 32P to label DNA
4. phage were incubated with bacteria to allow infection, and then shaken off the bacteria
5. centrifugation then separated the bacteria into the pellet, with phage in the supernatant
6. found that 35S stayed with the phage, while 32P was with the bacteria
7. Hershey and Chase concluded that phage injected DNA into bacteria to infect them
8. this convinced many more biologists that DNA is the genetic material, and the race to find the structure of DNA began
9. evidence gathered since the mid-1900s that DNA is the generic material has been overwhelming (much of the rest of this
unit will cover that evidence)
II.
Structure of DNA
A. recall the DNA polymer structure from deoxynucleotide monomers
1. deoxynucleotide has 5-carbon deoxyribose sugar, phosphate, and nitrogenous base
2. bases are the purines adenine (A) and guanine (G), and the pyrimidines thymine (T) and cytosine (C)
3. nucleotides are linked by a 3’, 5’ phosphodiester linkage
4. resulting chain has a 5’ end and a 3’ end
5. the phosphates and sugars are collectively called the “backbone” of the strand
6. this structure had been fully worked out by the early 1950s
B. Chargaff and colleagues had found that amounts of A = T and C = G
C. x-ray diffraction studies by Rosalind Franklin and Maurice Wilkins indicated a helical molecule
1. molecule has three repeating patterns that any model of its structure must account for
2. the data indicated a double helix
3. Franklin and Wilkins inferred that the bases are stacked like rungs of a ladder
4. DNA was envisioned as a twisted ladder, with the sugar-phosphate backbone forming the sides and basepairs forming
the rungs
D. the accepted model for the structure of the DNA double helix was published by James Watson and Francis Crick in 1953
1. model explained all three repeating patterns seen in x-ray diffraction, as well Chargaff’s data on base ratios
2. double helix with antiparallel strands
 each strand a nucleotide chain held together by phosphodiester linkages
 strands held together by hydrogen bonds between the bases (basepairs)
 A paired with T, with 2 hydrogen bonds predicted
 C paired with G, with 3 hydrogen bonds predicted
3. the strands were described as complementary: the sequence of one had to have an appropriate, complementary sequence
on the other for the molecule to hold together
4. the double-helix model strongly suggested a way to store information in the sequence of bases, which indeed appears to
be true
E. the determination of the DNA structure by Watson and Crick is considered the major landmark of modern biology
III.
DNA replication is semiconservative
A. DNA structure suggests an obvious replication mechanism
1. Watson and Crick noted that “specific [base]pairing…immediately suggests a possible copying mechanism for the
genetic material”
2. the model suggested that each strand could serve as a template for making a complementary strand, so-called
semiconservative replication
 one strand old, one new
3. competing, less-elegant models were conservative replication (both strands either old or new) and dispersive replication
(each strand a mix of old and new)
B. experiments with E. coli supported the semiconservative replication model
1. Meselson and Stahl used nitrogen isotopes to mark old vs. newly synthesized DNA strands
2.
3.
4.
IV.
bacteria grown in medium with 15N were transferred to medium with 14N; thus, old DNA strands had 15N and new ones
14
N
isolated DNA after one generation: DNA molecules all had roughly equal amounts of 15N and 14N – disproved
conservative replication
later generations: some 14N only, some still with roughly equal amounts of 15N and 14N – disproved dispersive replication
DNA replication: the process
A. overview
1. DNA replication requires the coordinated activity of many enzymes and other proteins
2. also requires the presence of nucleotide triphosphates
B. origins of replication
1. DNA replication begins at specific sites
 synthesis generally proceeds in both directions from an origin, creating a “replication bubble”
 there is usually only one origin of replication in the circular bacterial DNA
 eukaryotic chromosomes usually have several origins of replication each
2. both strands are replicated at the same time on both sides of the replication bubble, producing Y-shaped replication
forks on each side; the forks move as synthesis proceeds
C. unwinding and opening DNA
1. the twisted double helix must be unwound and the basepair bonds broken (“opening” the DNA molecule)
2. DNA helicase does the unwinding and opening
3. single-strand DNA binding proteins keep it open (also called helix-destabilizing proteins)
4. topoisomerases break and rejoin strands, resolving knots and strains that occur
D. direction of synthesis
1. DNA polymerases direct synthesis of new strands
2. synthesis proceeds by adding nucleotides onto the 3’ end of a strand
3. thus, synthesis can only proceed in the 5’  3’ direction
4. the nucleotide added is from a deoxynucleotide triphosphate; two phosphates are released in the process
E. priming new strands
1. DNA polymerase can only add onto an existing strand, so it can’t start the strand
2. primase starts the strand by making an RNA primer that is a few (usually about 10) ribonucleotides long
3. DNA polymerase can then add nucleotides starting at the end of the RNA primer
4. the RNA primer is later degraded and (usually) replaced with DNA
F. leading and laggings strands
1. the 5’  3’ directionality of synthesis complicates the replication activity
2. one strand being synthesized, the leading strand, has its 3’ end at the fork; thus, its synthesis can proceed continuously,
in the direction that the fork moves
3. the other, lagging strand has its 5’ end at the fork; it must be synthesized in the “opposite direction” from the leading
strand
 the lagging strand is thus made in short (100-1000 nucleotides) Okazaki fragments
 fragments are later joined by DNA ligase
G. DNA proofreading and DNA repair
1. DNA polymerase proofreads: initial error rate about 1 in 100,000; final rate about 1 in 100,000,000
2. cells have DNA repair mechanisms to fix most mistakes that get through as well as to fix most damaged DNA
H. the dead end: problem at the telomeres
1. the ends of chromosomes are called telomeres
2. they present special problems for DNA replication: the 5’ end RNA primer cannot be replaced with DNA, creating 5’
end gaps
3. this leads to shorting of chromosomes at the ends with each cell generation
4. in some cells, special telomerase enzymes can generate longer telomeres – telomerase is required in germ-line cells, and
active in cancer cells as well
V.
DNA packaging in chromosomes (see Ch. 19.1)
A. the DNA molecule is too long if not folded
1. bacteria have much less DNA in their cells than eukaryotes do, but even so the length of their DNA molecule if stretched
out would be 1000x the length of the cell itself
2. thus, even in the bacteria DNA must be “packaged”, folded and coiled to make it fit in the cell
3. eukaryotes have even more DNA, and use somewhat elaborate means to package the DNA even when it is in
“decondensed” chromatin
B. nucleosomes
1. nucleosomes are the main packaging mechanism for eukaryotic DNA
2. the nucleosome is made up of 8 protein subunits, acting like a “spool” for the DNA “thread”
3. the proteins are called histones
4. histones are positively charged, and thus able to associate with the negatively charged phosphates of the DNA backbone
5.
6.
the 8 proteins in a nucleosomes are 2 each of 4 different histones
nucleosomes are linked together with “linker DNA” regions, parts of the continuous DNA molecule that are not wound
on histones
7. overall this gives an appearance of nucleosomes as “beads” on a DNA “string”
8. nucleosome packaging of DNA is found throughout the cell cycle, except when DNA is being replicated
C. further packaging: histone H1 and scaffolding proteins
1. even during interphase, most of the DNA is packed tighter than just being wound on nucleosomes
2. this next packing step uses another histone, H1, that associates with the linker DNA regions
3. H1 binding leads to packing of nucleosomes into a chromatin fiber that is 30nm wide
4. those fibers form loops that are often held together by non-histone scaffolding proteins
5. more complex packing steps occur when chromosomes are fully condensed for cell division
Chapter 16: DNA: The Genetic Material
14. What must genetic material do?
15. Why did biologists used to think that proteins are the genetic material?
16. Describe Griffith’s experiments with genetic transformation and how they
(and follow-up experiments) helped determine the genetic material.
17. Describe the Hershey-Chase bacteriophage experiment, its results, and the
conclusion.
18. Discuss how Watson and Crick determined the structure of DNA (including
incorporation of Chargaff’s rules and X-ray diffraction results from
Franklin/Wilkins).
19. Draw the structure of DNA; indicate basepairs, 5’ and 3’ ends, antiparallel
nature.
20. Compare and contrast conservative, semiconservative, and dispersive
models of DNA replication.
21. Group activity on overhead: Meselson-Stahl experiment
22. Outline the process of DNA replication: what is required?
23. On a blank piece of paper, draw and label a replication fork (as completely
as you can from memory).
Chapter 16: DNA: The Genetic Material
VI.
Evidence that DNA is the genetic material
A. What must genetic material do?
1.
the genetic material must be able to replicate itself
2.
must be able to direct and control living processes
B. a model of genetic inheritance was in place in the early 1900s:
1.
Mendel’s “laws” of genetics – inherit one copy of each gene from each parent
2.
chromosomes as locations/carriers of genes
3.
distribution of chromosomes in making sex cells explains Mendel’s laws
C. chromosomes are made of two things: protein and DNA
D. from the late 1800s until the mid-1900s, most biologists believed that the genetic material was made of proteins, and that
nucleic acids were inconsequential
1.
proteins are very complex
2.
proteins have much variety
E. DNA is required for genetic transformation of bacteria
1.
2.
studies by Griffith in the 1920s of pneumococcus in mice

smooth (S) strain killed mice, rough (R) strain did not

heat-killed S strain did not kill mice, but heat-killed S + R strain killed mice

some “transforming principle” from the heat-killed S strain changed the R strain to make it deadly
studies by Avery and colleagues in the 1940s identified DNA as the “transforming principle” – but many were very
skeptical of this result
F.
viruses inject DNA into bacteria and take them over: the Hershey-Chase experiments
1.
viruses that infect bacteria are called bacteriophages (shortened as phages)
2.
viruses execute a “genetic takeover” of cells
3.
using radioactive isotopes, phage were labeled with either 35S to label proteins or 32P to label DNA
4.
phage were incubated with bacteria to allow infection, and then shaken off the bacteria
5.
centrifugation then separated the bacteria into the pellet, with phage in the supernatant
6.
found that 35S stayed with the phage, while 32P was with the bacteria
7.
Hershey and Chase concluded that phage injected DNA into bacteria to infect them
8.
this convinced many more biologists that DNA is the genetic material, and the race to find the structure of DNA began
9.
evidence gathered since the mid-1900s that DNA is the generic material has been overwhelming (much of the rest of this
unit will cover that evidence)
VII.
Structure of DNA
A. recall the DNA polymer structure from deoxyribonucleotide monomers
1.
deoxyribonucleotide has 5-carbon deoxyribose sugar, phosphate, and nitrogenous base
2.
bases are the purines adenine (A) and guanine (G), and the pyrimidines thymine (T) and cytosine (C)
3.
nucleotides are linked by a 3’, 5’ phosphodiester linkage
4.
resulting chain has a 5’ end and a 3’ end
5.
the phosphates and sugars are collectively called the “backbone” of the strand
6.
this structure had been fully worked out by the early 1950s
B. Chargaff and colleagues had found any one organism they tested had amounts of A ≈ T and C ≈ G
C. x-ray diffraction studies by Rosalind Franklin and Maurice Wilkins indicated a helical molecule
1.
molecule has three repeating patterns that any model of its structure must account for
2.
the data indicated a helix
D. the accepted model for the structure of the DNA double helix was published by James Watson and Francis Crick in 1953
1.
DNA was envisioned as a twisted ladder, with the sugar-phosphate backbone forming the sides and basepairs forming
the rungs
2.
model explained all three repeating patterns seen in x-ray diffraction, as well Chargaff’s data on base ratios
3.
double helix with antiparallel strands
4.

each strand a nucleotide chain held together by phosphodiester linkages

strands held together by hydrogen bonds between the bases (basepairs)

A paired with T, with 2 hydrogen bonds predicted

C paired with G, with 3 hydrogen bonds predicted
the strands were described as complementary: the sequence of one had to have an appropriate, complementary sequence
on the other for the molecule to hold together
5.
the double-helix model strongly suggested a way to store information in the sequence of bases, which indeed appears to
be true
E. the determination of the DNA structure by Watson and Crick is considered the major landmark of modern biology
VIII. DNA replication is semiconservative
A. DNA structure suggests an obvious replication mechanism
1.
Watson and Crick noted that “specific [base]pairing…immediately suggests a possible copying mechanism for the
genetic material”
2.
the model suggested that each strand could serve as a template for making a complementary strand, so-called
semiconservative replication

3.
one strand old, one new
competing, less-elegant models were conservative replication (both strands either old or new) and dispersive replication
(each strand a mix of old and new)
B. experiments with E. coli supported the semiconservative replication model
1.
Meselson and Stahl used nitrogen isotopes to mark old vs. newly synthesized DNA strands
2.
bacteria grown in medium with 15N were transferred to medium with 14N; thus, old DNA strands had 15N and new ones
14
3.
N
isolated DNA after one generation: DNA molecules all had roughly equal amounts of 15N and 14N – disproved
conservative replication
4.
IX.
later generations: some 14N only, some still with roughly equal amounts of 15N and 14N – disproved dispersive replication
DNA replication: the process
A. overview
1.
DNA replication requires the coordinated activity of many enzymes and other proteins
2.
also requires the presence of nucleotide triphosphates
B. origins of replication
1.
2.
DNA replication begins at specific sites

synthesis generally proceeds in both directions from an origin, creating a “replication bubble”

there is usually only one origin of replication in the circular bacterial DNA

eukaryotic chromosomes usually have several origins of replication each
both strands are replicated at the same time on both sides of the replication bubble, producing Y-shaped replication
forks on each side; the forks move as synthesis proceeds
C. unwinding and opening DNA
1.
the twisted double helix must be unwound and the basepair bonds broken (“opening” the DNA molecule)
2.
DNA helicase does the unwinding and opening
3.
single-strand DNA binding proteins keep it open (also called helix-destabilizing proteins)
4.
topoisomerases break and rejoin strands, resolving knots and strains that occur
D. direction of synthesis
1.
DNA polymerases direct synthesis of new strands
2.
synthesis proceeds by adding nucleotides onto the 3’ end of a strand
3.
thus, synthesis can only proceed in the 5’  3’ direction
4.
the nucleotide added is from a deoxynucleotide triphosphate; two phosphates are released in the process
E. priming new strands
F.
1.
DNA polymerase can only add onto an existing strand, so it can’t start the strand
2.
primase starts the strand by making an RNA primer that is a few (usually about 10) ribonucleotides long
3.
DNA polymerase can then add nucleotides starting at the end of the RNA primer
4.
the RNA primer is later degraded and (usually) replaced with DNA
leading and laggings strands
1.
the 5’  3’ directionality of synthesis complicates the replication activity
2.
one strand being synthesized, the leading strand, has its 3’ end at the fork; thus, its synthesis can proceed continuously,
in the direction that the fork moves
3.
the other, lagging strand has its 5’ end at the fork; it must be synthesized in the “opposite direction” from the leading
strand

the lagging strand is thus made in short (100-1000 nucleotides) Okazaki fragments

fragments are later connected by DNA ligase (which also joins together DNA strands when replication forks meet)
G. DNA proofreading and DNA repair
1.
DNA polymerase proofreads: initial error rate about 1 in 100,000; final rate about 1 in 100,000,000
2.
cells have DNA repair mechanisms to fix most mistakes that get through as well as to fix most damaged DNA
H. the dead end: problem at the telomeres
1.
the ends of chromosomes are called telomeres
2.
they present special problems for DNA replication: the 5’ end RNA primer cannot be replaced with DNA, creating 5’
end gaps
3.
this leads to shorting of chromosomes at the ends with each cell generation
4.
in some cells, special telomerase enzymes can generate longer telomeres – telomerase is required in germ-line cells, and
active in cancer cells as well
X.
DNA packaging in chromosomes
A. the DNA molecule is too long if not folded
1.
bacteria have much less DNA in their cells than eukaryotes do, but even so the length of their DNA molecule if stretched
out would be 1000x the length of the cell itself
2.
thus, even in the bacteria DNA must be “packaged”, folded and coiled to make it fit in the cell
3.
eukaryotes have even more DNA, and use somewhat elaborate means to package the DNA even when it is in
“decondensed” chromatin
B. nucleosomes
1.
nucleosomes are the main packaging mechanism for eukaryotic DNA
2.
the nucleosome is made up of 8 protein subunits, acting like a “spool” for the DNA “thread”
3.
the proteins are called histones
4.
histones are positively charged, and thus able to associate with the negatively charged phosphates of the DNA backbone
5.
the 8 proteins in a nucleosomes are 2 each of 4 different histones
6.
nucleosomes are linked together with “linker DNA” regions, parts of the continuous DNA molecule that are not wound
on histones
7.
overall this gives an appearance of nucleosomes as “beads” on a DNA “string”
8.
nucleosome packaging of DNA is found throughout the cell cycle, except when DNA is being replicated
C. further packaging: histone H1 and scaffolding proteins
1.
even during interphase, most of the DNA is packed tighter than just being wound on nucleosomes
2.
this next packing step uses another histone, H1, that associates with the linker DNA regions
3.
H1 binding leads to packing of nucleosomes into a 30 nm chromatin fiber
4.
30 nm fibers form looped domains that are ~300 nm wide and attached to non-histone scaffolding proteins

this level of packing is found only for some regions of DNA, except when chromosomes are condensed for cell
division
5.
the next step connects looped domains into an ~700 nm fiber that is considered fully condensed chromatin
Chapter 17: From gene to protein
I.
Genes generally are information for making specific proteins
A. in connection with the rediscovery of Mendel’s work around the dawn of the 20 th century, the idea that genes are responsible
for making enzymes was advanced
B. this view was summarized in the classic work Inborn Errors of Metabolism (Garrod 1908)
C. work by Beadle and Tatum in the 1940s refined this concept
1. found mutant genes in the fungus Neurospora that each affected a single step in a metabolic pathway
2. developed the “one gene, one enzyme” hypothesis
 later work by Pauling and others showed that other proteins are also generated genetically
 also, some proteins have multiple subunits encoded by different genes
 this ultimately led to the “one gene, one polypeptide” hypothesis
II. RNA (ribonucleic acid)
A. RNA serves mainly as an intermediary between the information in DNA and the realization of that information in proteins
B. RNA has some structural distinctions from DNA
1. typically single-stranded (although often with folds and complex 3° structure)
2. sugar is ribose; thus, RNA polymers are built from ribonucleotides
3. uracil (U) functions in place of T
C. three main forms of RNA are used: mRNA, tRNA, and rRNA
1.
2.
3.
4.
mRNA or messenger RNA: copies the actual instructions from the gene
tRNA or transfer RNA: links with amino acids and bring them to the appropriate sites for incorporation in proteins
rRNA or ribosomal RNA: main structural and catalytic components of ribosomes, where proteins are actually produced
all are synthesized from DNA templates (thus, some genes code for tRNA and rRNA, not protein)
III. Overview of gene expression
A. Central Dogma of Gene Expression: DNA  RNA  protein
1. the gene is the DNA sequence with instructions for making a product
2. the protein (or protein subunit) is the product
B. DNA  RNA is transcription
1. making RNA using directions from a DNA template
2. transcribe = copy in the same language (language used here is base sequence)
C. RNA  protein is translation
1. making a polypeptide chain using directions in mRNA
2. translate = copy into a different language; here the translation is from base sequence to amino acid sequence
D. there are exceptions to the central dogma
1. some genes are for an RNA final product, such as tRNA and rRNA (note: mRNA is NOT considered a final product)
2. for some viruses use RNA as their genetic material
 some never use DNA
 some use the enzyme reverse transcriptase to perform RNA  DNA before then following the central dogma
IV. Transcription: making RNA from a DNA template
A. RNA is synthesized as a complementary strand using DNA-dependent RNA polymerases
1. process is somewhat similar to DNA synthesis, but no primer is needed
2. bacterial cells each only have one type of RNA polymerase
3. eukaryotic cells have three major types of RNA polymerase
 RNA polymerase I is used in making rRNA
 RNA polymerase II is used in making mRNA and some small RNA molecules
 RNA polymerase III is used in making tRNA and some small RNA molecules
B. only one strand is transcribed, with RNA polymerase using ribonucleotide triphosphates (rNTPs, or just NTPs) to build a
strand in the 5’  3’ direction
1. thus, the DNA is transcribed (copied or read) in the 3’  5’ direction
2. the DNA strand that is read is called the template strand or sense strand
3. upstream means toward the 5’ end of the RNA strand, or toward the 3’ end of the template strand (away from the
direction of synthesis)
4. downstream means toward the 3’ end of the RNA strand, or toward the 5’ end of the template strand
C. transcription has three stages: initiation, elongation, and termination
D. initiation requires a promoter – site where RNA polymerase initially binds to DNA
1. promoters are important because they are needed to allow RNA synthesis to begin
2. promoter sequence is upstream of where RNA strand production actually begins
3. promoters vary between genes; this is the main means for controlling which genes are transcribed at a given time
4. bacterial promoters
 about 40 nucleotides long
 positioned just before the point where transcription begins
 recognized directly by RNA polymerase
5. eukaryotic promoters (for genes that use RNA polymerase II)
 initially, transcription factors bind to the promoter; these proteins facilitate binding of RNA polymerase to the site
 transcription initiation complex
 completed assembly of transcription factors and RNA polymerase at the promoter region
 allows initiation of transcription (the actual production of an RNA strand complementary to the DNA template)
 genes that use RNA polymerase II commonly have a “TATA box” about 25 nucleotides upstream of the point where
transcription begins
 actual sequence is something similar to TATAAA on the non-template strand
 sequences are usually written in the 5’3’ direction of the strand with that sequence unless noted otherwise
6. regardless of promoter specifics, initiation begins when RNA polymerase is associated with the DNA
 RNA polymerase opens and unwinds the DNA
 RNA polymerase begins building an RNA strand in the 5’3’ direction, complementary to the template strand
 only one RNA strand is produced
E. elongation
1. RNA polymerase continues building the RNA strand in a linear fashion, unwinding and opening up the DNA along the
way
the newly synthesized RNA strand easily separates from the DNA and the DNA molecule “zips up” behind RNA
polymerase, reforming the double helix
termination: the end of RNA transcription
1. in prokaryotes, transcription continues until a terminator sequence is transcribed that causes RNA polymerase to release
the RNA strand and release from the DNA
2. termination in eukaryotes is more complicated and differs for different RNA polymerases
 still always requires some specific sequence to be transcribed
 for RNA pol II the specific sequence is usually hundreds of bases before the actual ending site
2.
F.
V. The genetic code
A. the actual information for making proteins is called the genetic code
B. the genetic code is based on codons: sequences of three bases that instruct for the addition of a particular amino acid (or a
stop) to a polypeptide chain
1. codons are thus read in sequences of 3 bases on mRNA, sometimes called the triplet code
2. codons are always written in 5’3’ fashion
3. four bases allow 43 = 64 combinations, plenty to code for the 20 amino acids typically used to build proteins
4. thus, a 3-base or triplet code is used
5. see the genetic code figure
 don’t try to memorize the complete genetic code
 do know that the code is degenerate or redundant: some amino acids are coded for by more than one codon (some
have only one, some as many as 6)
 know that AUG is the “start” codon: all proteins will begin with methionine, coded by AUG
 know about the stop codons that do not code for an amino acid but instead will end the protein chain
 be able to use the table to “read” an mRNA sequence
6. the genetic code was worked out using artificial mRNAs of known sequence
7. the reading of the code 3 bases at a time establishes a reading frame; thus, AUG is very important as the first codon
establishes the reading frame
8. the genetic code is nearly universal – all organisms use essentially the same genetic code (strong evidence for a common
ancestry among all living organisms)
C. mRNA coding region
1. each mRNA strand thus has a coding region within it that codes for protein synthesis
2. the coding region starts with the AUG start, and continues with the established reading frame
3. the coding region ends when a stop codon is reached
4. the mRNA strand prior to the start codon is called the 5’ untranslated region or leader sequence
5. the mRNA strand after the stop codon is called the 3’ untranslated region or trailing sequence
6. collectively, the leader sequence and trailing sequence are referred to as noncoding regions of the mRNA
VI. Translation: using information in mRNA to direct protein synthesis
A. in eukaryotes, mRNA is moved from the nucleus to the cytoplasm (in prokaryotes, there is no nucleus so translation can
begin even while transcription is underway – see polyribosomes later)
B. the site of translation is the ribosome
1. ribosomes are complexes of RNA and protein, with two subunits
2. ribosomes catalyze translation (more on this role later)
C. ultimately, peptide bonds must be created between amino acids to form a polypeptide chain
1. recall that peptide bonds are between the amino group of one amino acid and the carboxyl group of another
2. primary polypeptide structure is determined by the sequence of codons in mRNA
3. the ribosome acts at the ribozyme that catalyzes peptide bond formation
D. tRNAs bring amino acids to the site of translation
1. tRNAs are synthesized at special tRNA genes
2. tRNA molecules are strands about 70-80 bases long that form complicated, folded 3-dimensional structures
3. tRNAs have attachment sites for amino acids
4. each tRNA has an anticodon sequence region that will form a proper complementary basepairing with a codon on an
mRNA molecule
5. tRNA is linked to the appropriate amino acid by enzymes called aminoacyl-tRNA synthetases
 the carboxyl group of each specific amino acid is attached to either the 3' OH or 2' OH group of a specific tRNA
 there is at least one specific aminoacyl-tRNA synthetase for each of the 20 amino acids used in proteins
 ATP is used as an energy source for the reaction
 the resulting complex is an aminoacyl-tRNA; this is also called a charged tRNA or activated tRNA
 the amino acid added must be the proper one for the anticodon on the tRNA
6. there are not actually 64 different tRNAs
 three stops have no tRNA

some tRNAs are able to be used for more than one codon
 for these, the third base allows some “wobble” where basepairing rules aren’t strictly followed
 this accounts for some of the degeneracy in the genetic code
 for note how often the 3rd letter in the codon does not matter in the genetic code
 there are usually only about 45 tRNA types made by most organisms
E. the mRNA and aminoacyl-tRNAs bond at the ribosome for protein synthesis
1. the large ribosome subunit has a groove where the small subunit fits
2. mRNA is threaded through the groove
3. the large ribosomal subunit has two depressions where tRNAs attach (A and P binding sites), and a third site called the
exit site (E site)
 the E site is where uncharged tRNA molecules are moved and then released
 the P site is where the completed part of the polypeptide chain will be attached to tRNA
 the A site is where the new amino acid will enter on an aminoacyl-tRNA as a polypeptide is made
4. the tRNAs that bond at these sites basepair with mRNA
 pairing is anticodon to codon
 must match to make proper basepairs, A-U or C-G, except for the allowed wobbles at the 3 rd base
F. translation has three stages: initiation, elongation, and termination
1. all three stages have protein “factors” that aid the process
2. many events within the first two stages require energy, which is often supplied by GTP (working effectively like ATP)
G. initiation – start of polypeptide production
 an initiation complex is formed
 begins with the loading of a special initiator tRNA onto a small ribosomal subunit
 the initiator tRNA recognizes the codon AUG, which is the initiation start codon
 AUG codon codes for the amino acid methionine
 the initiator tRNA thus is charged with methionine; written as tRNA Met
 next the small ribosomal subunit binds to an mRNA
 for prokaryotes, at the ribosome recognition sequence in the mRNA's leader sequence
 for eukaryotes, at the 5’ end of the mRNA (actually at the 5’ cap, more on that later)
 the initiator tRNA anticodon will then basepair with the start codon
 the large ribosomal subunit then binds to the completed initiation complex
 in the completed initiation complex the initiator tRNA is at the P site
 proteins called initiation factors are help the small subunit bind to the initiator tRNA and mRNA
 assembly of the initiation complex also required energy from GTP (and ATP in eukaryotes)
2. elongation – the addition of amino acids to the growing polypeptide chain
 the aminoacyl-tRNA coding for the next codon in the mRNA then binds to the A site of the ribosome
 has to have proper anticodon-codon basepairs form with the mRNA (again wobble occurs for some)
 the binding step requires energy, supplied by GTP
 proteins called elongation factors assist in getting the charged tRNA to bind
 the amino group of the amino acid on the tRNA in the A site is then in alignment with the carboxyl group of the
amino acid in the P site
 peptide bond formation can spontaneously occur
 the peptide bond formation is catalyzed by the ribosome itself, with energy that had been stored in the
aminoacyl-tRNA molecule
 in the process, the amino acid at the P site is released from its tRNA
 this leaves an unacylated tRNA in the P site, and a tRNA in the A site which now contains the growing peptide
chain of the protein
 notice that protein synthesis proceeds from the amino end of the polypeptide to the carboxyl end (NC)
 translocation then takes place
 the ribosome assemble essentially moves three nucleotides along the mRNA
 the ribosome moves relative to the mRNA so that a new, exposed codon now sits in the A site
 the unacylated tRNA is moved from the P site to the E site, where it is released
 the tRNA-peptide is moved from the A site to the P site
 the translocation process also requires energy from GTP
 elongation factor proteins assist with translocation
 now everything is set up for another elongation step
 note again that polypeptides are synthesized on ribosomes starting at the amino terminal end and proceeding to the
carboxy terminal end (NC)
 note also that mRNA's are made from their 5' end to their 3' end, and they are also translated from their 5' end to
their 3' end (5’3’)
3. termination
 a stop codon signals the end for translation (UAA, UGA, and UAG are universal stop codons)


no tRNA matches the stop codon; instead, it a termination factor (AKA release factor) binds there
the termination factor causes everything to dissociate, freeing the polypeptide, mRNA, last tRNA, and ribosomal
subunits all from each other (think of the termination factor as a little molecular bomb)
H. for an average-sized polypeptide chain (~300-400 amino acids long) translation takes less than a minute
I. polyribosomes
1. an mRNA is typically being translated by many ribosomes at the same time
2. once one ribosome has initiated, and elongation has occurred, a second ribosome initiates, and subsequently a third, and
so on
 typically as many as 20 ribosomes may be synthesizing protein from the same message
 these complexes are called polyribosomes
 in prokaryotes, ribosomes initiate and begin elongation even before RNA polymerase ends transcription
 thus, transcription and translation are nearly simultaneous
 that leads to polyribosomes of prokaryotes being closely associated with DNA
J. mRNAs do not stick around forever – they are quickly degraded (as fast as in about 2-5 minutes in most prokaryotes)
VII. Differences between prokaryotes and eukaryotes in transcription and translation: in eukaryotes, the mRNA is modified before
leaving the nucleus
A. the initial transcript is called precursor mRNA (or pre-mRNA, or heterogeneous nuclear RNA, or hnRNA)
B. the first modification is 5’ mRNA capping
1. happens early, when eukaryotic mRNAs are just being formed and are 20 - 30 nucleotides long
2. a set of enzymes found in the nucleus adds a 5’ cap to the message
3. the cap consists of a modified guanine residue, called 7-methylguanylate
4. this cap is required for binding to eukaryotic ribosomes (so an uncapped mRNA cannot be translated in eukaryotes)
5. also appears that the cap makes eukaryotic mRNAs less susceptible to degradation and to promote the transport of the
mRNA out of the nucleus
C. the 3’ tail: polyadenylation
1. a polyadenylation signal in the mRNA trailing sequence signals for the addition of a “tail” on the 3’ end of the mRNA
2. the tail is a series of adenines, and is called a poly-A tail
3. polyadenylation is the process of putting the tail on
 enzymes recognize the polyadenylation signal and cut the RNA strand at that site
 the enzymes then add 100 - 250 adenine ribonucleotides to the mRNA chain
4. the roles of polyadenylation
 starting the process leads to termination of transcription
 may make mRNAs less susceptible to degradation
 may help get mRNA out of the nucleus
 may help in initiation of translation
D. interrupted coding sequences: introns and exons
1. the transcript made from the DNA in eukaryotes is often much larger than the final mRNA
2. some stretches of bases called introns “interrupt” the sequence and must be removed
 the number of introns varies, from none for some genes up to dozens or more for others
 different alleles of the same gene may even vary in intron number
 the regions that will not be removed are called exons
3. the process of removing introns is called RNA splicing
 the signals for splicing are short sequences at the ends of introns
 particles called snRNPs associate with the mRNA in a complex called the spliceosome
 snRNPs are made of small RNA molecules and proteins
 the spliceosome catalyzes cutting out and removing an intron and joining together the exons
 RNAs in some of the snRNPs act as ribozymes in the splicing process
 note that the spliceosome is not always required, but it usually is needed
4. Why do exons exist?
 in some cases, alternative RNA splicing allows one DNA sequence to direct synthesis of two or more different
polypeptides (this may be very common in humans)
 exons tend to code for specific domains within proteins
 a domain is a region within the protein that has a specific function
 exons with “junk DNA” intron regions between them may be easy to move around and rearrange to make new
proteins
 this leads to the notion that many proteins consist of such functional domains which can be readily shuffled
around during evolution to produce new proteins with novel catalytic functions, a process is referred to as
exon shuffling; this does indeed appear to have played a prominent role in evolution in eukaryotes
VIII. Modern definition of genes
A. complications in some scenarios make it necessary to modify the definition of a gene
B. a more inclusive definition: a gene is a nucleotide sequence with information for making a final product polypeptide or RNA
product
C. the usual flow of information is still DNA  RNA  polypeptide
IX. Mutations are changes in the DNA sequence
A. mutations may occur as accidents during DNA replication, or may be induced by DNA-damaging radiation or chemicals
1. DNA-damage inducers are called mutagens
2. many mutagens increase the likelihood of cancer, and are thus carcinogens
3. some DNA regions are more prone to mutations; they are called mutational hot spots (trinucleotide repeats are one
example)
4. organisms have mechanisms to repair damage to DNA and to proofread DNA during replication, but mutations still
occur (usually at a very low rate)
B. the mutations that are most likely to lead to genetic changes (for good or bad) are those in the coding regions of genes
1. mutations that result in the substitution of one base for another are referred to as point mutations or base substitution
mutations
 if the point mutation does not actually cause a change in what amino acid is coded for, it is called a silent mutation
 if the point mutation causes a change in what amino acid is coded for, it is called a missense mutation
 if the point mutation result in the formation of a stop codon where an amino previously was coded for, it is called a
nonsense mutation
 nonsense mutations result in the premature termination of the protein sequence, and thus an active protein is
usually not formed
 missense mutation example: sickle cell anemia (see, in part, page 298)
 missense at 6th codon in hemoglobin  chain (counted after protein processing)
 in DNA a T is replaced with an A; this leads to valine instead of glutamic acid in the protein
 resulting hemoglobin is “sticky” with other hemoglobin chains, crystallizing easily
Normal hemoglobin  chain
DNA:
CAC GTG GAC TGA GGA CTC CTC
RNA:
GUG CAC CUG ACU CCU GAG GAGProtein: val-his-leu-thr-pro-glu-gluSickle cell anemia hemoglobin  chain
DNA:
CAC GTG GAC TGA GGA CAC CTC
RNA:
GUG CAC CUG ACU CCU GUG GAGProtein: val-his-leu-thr-pro-val-glu2. mutations that shift the reading frame (when nucleotides are either added or deleted) are called frameshift mutations
C. some mutations are caused by pieces of DNA that can jump around the genome
1. such jumping DNA is called a transposon or transposable element
2. transposons exist in both prokaryotes and eukaryotes; for most their normal function (if any) is unknown, but some
larger ones can provide benefits by moving copies of useful genes with them
X. Gene Regulation – there are a few points from Ch. 19.2 that you need to know
A. gene expression is regulated
B. regulation allows for different expression under different conditions
1. a given cell type will only express genes appropriate for that cell type
2. gene expression can be changed in response to the environment
3. constitutive genes (housekeeping genes) are constantly transcribed, with little or no regulation
C. proteins that regulate transcription are called transcription factors
1. transcription factors often bind directly to DNA
2. transcription factors usually are activated or inactivated based on signals
3. signals are some sort of change in the internal environment of the cells
4. signals can be information from the environment (such as hormones), or as simple as running out of a food molecule or
having a new food source
5. most transcription factors associate with promoters
 promoter sequence determines what transcription factions can bind to the promoter to help initiate transcription
 different promoter sequences allow for differences in expression
6. repressors – transcription factors that suppress or stop gene expression
7. activators – transcription factors that either activate ( “turn on”) gene expression, or to enhance gene expression
D. sometimes DNA sequences away from the promoter can also affect transcription
1. such sequences can be upstream or downstream of the coding region, or even within the coding region or introns
2.
3.
they are usually within a few kilobases of the coding region, and often within a few hundred bases
enhancers – DNA regions, often far from the promoter, where activators will bind either directly or indirectly
Chapter 17: Genes and How They Work
24. What do genes do? How do we define a gene? Discuss the derivation of the
“one gene, one polypeptide” model, tracing the history through Garrod,
Beadle and Tatum, and Pauling.
25. How does RNA differ from DNA structurally?
26. What are the structural and functional differences between mRNA, tRNA
and rRNA?
27. Explain the “central dogma of gene expression”.
28. What is the difference between transcription and translation? How will
you keep these similar-sounding terms clear in your head?
29. What three steps must most (perhaps all) biological processes have?
30. Describe the events of initiation, elongation, and termination of
transcription. Be sure to use key terms like upstream, downstream,
promoter, etc.
31. How does transcription differ between prokaryotes and eukaryotes?
32. What is a codon?
33. What is the genetic code?
34. Why are the “words” in the genetic code three bases long?
35. Diagram a mature mRNA.
36. Describe the events of initiation, elongation, and termination of translation.
Be sure to use key terms like ribosome, ribozyme, anticodon, activated
tRNA, EPA sites, translocation, termination factor, etc. Also, be sure to
note
a. how the reading frame is established
b. the direction of reading mRNA (5’ and 3’ ends)
c. the direction of protein synthesis (N- and C- ends)
37. Can mRNAs be used more than once? What are the consequences of this?
38. What special things are different about eukaryotic mRNA production
compare to prokaryotic mRNA production? Be sure to address key terms
such as pre-mRNA, 5’ cap, poly-A tail, RNA splicing, intron, and exons.
39. How does alternative splicing work?
40. How does exon shuffling work? Be sure to include the term “domain” in
your explanation.
41. What is the modern definition of a gene?
42. What are mutations, and how can they be good, bad, or neutral?
43. What is the difference between these three types of point mutation:
a. silent mutation
b. missense mutation
c. nonsense mutation
44. What is a frameshift mutation, and why does it usually have a huge impact?
45. What are transposons?
46. Why is regulation of gene expression important?
47. How can, for example, a cell in the retina of your eye make different
proteins from a cell in your liver when both cells have exactly the same
DNA?
48. What are constitutive genes, transcription factors, repressors, activators,
and enhancers?
Chapter 17: Genes and How They Work
XI. Genes generally are information for making specific proteins
A. in connection with the rediscovery of Mendel’s work around the dawn of the 20 th century, the idea that genes are responsible
for making enzymes was advanced
B. this view was summarized in the classic work Inborn Errors of Metabolism (Garrod 1908)
C. work by Beadle and Tatum in the 1940s refined this concept
1.
found mutant genes in the fungus Neurospora that each affected a single step in a metabolic pathway
2.
developed the “one gene, one enzyme” hypothesis
3.
follow-up work by Srb and Horowitz illustrated this even more clearly

later work by Pauling and others showed that other proteins are also generated genetically

also, some proteins have multiple subunits encoded by different genes

this ultimately led to the “one gene, one polypeptide” hypothesis
XII. RNA (ribonucleic acid)
A. RNA serves mainly as an intermediary between the information in DNA and the realization of that information in proteins
B. RNA has some structural distinctions from DNA
1.
typically single-stranded (although often with folds and complex 3D structure)
2.
sugar is ribose; thus, RNA polymers are built from ribonucleotides
3.
uracil (U) functions in place of T
C. three main forms of RNA are used: mRNA, tRNA, and rRNA
XIII.
1.
mRNA or messenger RNA: copies the actual instructions from the gene
2.
tRNA or transfer RNA: links with amino acids and bring them to the appropriate sites for incorporation in proteins
3.
rRNA or ribosomal RNA: main structural and catalytic components of ribosomes, where proteins are actually produced
4.
all are synthesized from DNA templates (thus, some genes code for tRNA and rRNA, not protein)
Overview of gene expression
A. Central Dogma of Gene Expression: DNA  RNA  protein
1.
the gene is the DNA sequence with instructions for making a product
2.
the protein (or protein subunit) is the product
B. DNA  RNA is transcription
1.
making RNA using directions from a DNA template
2.
transcribe = copy in the same language (language used here is base sequence)
C. RNA  protein is translation
1.
making a polypeptide chain using directions in mRNA
2.
translate = copy into a different language; here the translation is from base sequence to amino acid sequence
D. there are exceptions to the central dogma
1.
some genes are for an RNA final product, such as tRNA and rRNA (note: mRNA is NOT considered a final product)

some viruses use RNA as their genetic material (some never use DNA; some use the enzyme reverse transcriptase to
perform RNA  DNA before then following the central dogma)
XIV.
Transcription: making RNA from a DNA template
A. RNA is synthesized as a complementary strand using DNA-dependent RNA polymerases
1.
process is somewhat similar to DNA synthesis, but no primer is needed
2.
bacterial cells each only have one type of RNA polymerase
3.
eukaryotic cells have three major types of RNA polymerase

RNA polymerase I is used in making rRNA

RNA polymerase II is used in making mRNA and some small RNA molecules

RNA polymerase III is used in making tRNA and some small RNA molecules
B. only one strand is transcribed, with RNA polymerase using ribonucleotide triphosphates (rNTPs, or just NTPs) to build a
strand in the 5’  3’ direction
1.
thus, the DNA is transcribed (copied or read) in the 3’  5’ direction
2.
the DNA strand that is read is called the template strand
3.
upstream means toward the 5’ end of the RNA strand, or toward the 3’ end of the template strand (away from the
direction of synthesis)
4.
downstream means toward the 3’ end of the RNA strand, or toward the 5’ end of the template strand
C. transcription has three stages: initiation, elongation, and termination
D. initiation requires a promoter – site where RNA polymerase initially binds to DNA
1.
promoters are important because they are needed to allow RNA synthesis to begin
2.
promoter sequence is upstream of where RNA strand production actually begins
3.
promoters vary between genes; this is the main means for controlling which genes are transcribed at a given time
4.
bacterial promoters

about 40 nucleotides long, positioned just before the point where transcription begins, recognized directly by RNA
polymerase
5.
eukaryotic promoters (for genes that use RNA polymerase II)

initially, transcription factors bind to the promoter; these proteins facilitate binding of RNA polymerase to the site

transcription initiation complex

completed assembly of transcription factors and RNA polymerase at the promoter region

allows initiation of transcription (the actual production of an RNA strand complementary to the DNA template)

genes that use RNA polymerase II commonly have a “TATA box” about 25 nucleotides upstream of the point where
transcription begins
6.

actual sequence is something similar to TATAAA on the non-template strand

sequences are usually written in the 5’3’ direction of the strand with that sequence unless noted otherwise
regardless of promoter specifics, initiation begins when RNA polymerase is associated with the DNA

RNA polymerase opens and unwinds the DNA

RNA polymerase begins building an RNA strand in the 5’3’ direction, complementary to the template strand

only one RNA strand is produced
E. elongation
1.
RNA polymerase continues building the RNA strand, unwinding and opening up the DNA along the way
2.
the newly synthesized RNA strand easily separates from the DNA and the DNA molecule “zips up” behind RNA
polymerase, reforming the double helix
F.
termination: the end of RNA transcription
1.
in prokaryotes, transcription continues until a terminator sequence is transcribed that causes RNA polymerase to release
the RNA strand and release from the DNA
2.
termination in eukaryotes is more complicated and differs for different RNA polymerases

still always requires some specific sequence to be transcribed

for RNA pol II the specific sequence is usually hundreds of bases before the actual ending site
XV. The genetic code
A. the actual information for making proteins is called the genetic code
B. the genetic code is based on codons: sequences of three bases that instruct for the addition of a particular amino acid (or a
stop) to a polypeptide chain
1.
codons are thus read in sequences of 3 bases on mRNA, sometimes called the triplet code
2.
codons are always written in 5’3’ fashion
3.
four bases allow 43 = 64 combinations, plenty to code for the 20 amino acids typically used to build proteins
4.
thus, a 3-base or triplet code is used
5.
see the genetic code figure

don’t try to memorize the complete genetic code

do know that the code is degenerate or redundant: some amino acids are coded for by more than one codon (some
have only one, some as many as 6)

know that AUG is the “start” codon: all proteins will begin with methionine, coded by AUG

know about the stop codons that do not code for an amino acid but instead will end the protein chain

be able to use the table to “read” an mRNA sequence
6.
the genetic code was worked out using artificial mRNAs of known sequence
7.
the reading of the code 3 bases at a time establishes a reading frame; thus, AUG is very important as the first codon
establishes the reading frame
8.
the genetic code is nearly universal – all organisms use essentially the same genetic code (strong evidence for a common
ancestry among all living organisms)
C. mRNA coding region
XVI.
1.
each mRNA strand thus has a coding region within it that codes for protein synthesis
2.
the coding region starts with the AUG start, and continues with the established reading frame
3.
the coding region ends when a stop codon is reached
4.
the mRNA strand prior to the start codon is called the 5’ untranslated region or leader sequence
5.
the mRNA strand after the stop codon is called the 3’ untranslated region or trailing sequence
6.
collectively, the leader sequence and trailing sequence are referred to as noncoding regions of the mRNA
Translation: using information in mRNA to direct protein synthesis
A. in eukaryotes, mRNA is moved from the nucleus to the cytoplasm (in prokaryotes, there is no nucleus so translation can
begin even while transcription is underway – see polyribosomes later)
B. the site of translation is the ribosome
1.
ribosomes are complexes of RNA and protein, with two subunits
2.
ribosomes catalyze translation (more on this role later)
C. ultimately, peptide bonds must be created between amino acids to form a polypeptide chain
1.
recall that peptide bonds are between the amino group of one amino acid and the carboxyl group of another
2.
primary polypeptide structure is determined by the sequence of codons in mRNA
3.
the ribosome acts at the ribozyme that catalyzes peptide bond formation
D. tRNAs bring amino acids to the site of translation
1.
tRNAs are synthesized at special tRNA genes
2.
tRNA molecules are strands about 70-80 bases long that form complicated, folded 3-dimensional structures
3.
tRNAs have attachment sites for amino acids
4.
each tRNA has an anticodon sequence region that will form a proper complementary basepairing with a codon on an
mRNA molecule
5.
tRNA is linked to the appropriate amino acid by enzymes called aminoacyl-tRNA synthetases

the carboxyl group of each specific amino acid is attached to either the 3' OH or 2' OH group of a specific tRNA

there is at least one specific aminoacyl-tRNA synthetase for each of the 20 amino acids used in proteins

ATP is used as an energy source for the reaction; the resulting complex is an aminoacyl-tRNA; this is also called a
charged tRNA or activated tRNA; the amino acid added must be the proper one for the anticodon on the tRNA
6.
there are not actually 64 different tRNAs

three stops have no tRNA

some tRNAs are able to be used for more than one codon

for these, the third base allows some “wobble” where basepairing rules aren’t strictly followed; this accounts
for some of the degeneracy in the genetic code (note how often the 3 rd letter in the codon does not matter in
the genetic code)

there are usually only about 45 tRNA types made by most organisms
E. the mRNA and aminoacyl-tRNAs bond at the ribosome for protein synthesis
1.
the large ribosome subunit has a groove where the small subunit fits
2.
mRNA is threaded through the groove
3.
the large ribosomal subunit has two depressions where tRNAs attach (A and P binding sites), and a third site (E site)
4.
F.

the E site (exit site) is where uncharged tRNA molecules are moved and then released

the P site is where the completed part of the polypeptide chain will be attached to tRNA

the A site is where the new amino acid will enter on an aminoacyl-tRNA as a polypeptide is made
the tRNAs that bond at these sites basepair with mRNA

pairing is anticodon to codon

must match to make proper basepairs, A-U or C-G, except for the allowed wobbles at the 3 rd base
translation has three stages: initiation, elongation, and termination
1.
all three stages have protein “factors” that aid the process
2.
many events within the first two stages require energy, which is often supplied by GTP (working effectively like ATP)
G. initiation – start of polypeptide production

an initiation complex is formed

begins with the loading of a special initiator tRNA onto a small ribosomal subunit

the initiator tRNA recognizes the codon AUG, which is the initiation start codon

2.

AUG codon codes for the amino acid methionine

the initiator tRNA thus is charged with methionine; written as tRNAMet
next the small ribosomal subunit binds to an mRNA

for prokaryotes, at the ribosome recognition sequence in the mRNA's leader sequence

for eukaryotes, at the 5’ end of the mRNA (actually at the 5’ cap, more on that later)

the initiator tRNA anticodon will then basepair with the start codon

the large ribosomal subunit then binds to the completed initiation complex

in the completed initiation complex the initiator tRNA is at the P site

proteins called initiation factors help the small subunit bind to the initiator tRNA and mRNA

assembly of the initiation complex also requires energy from GTP (eubacteria) or ATP (eukaryotes)
elongation – the addition of amino acids to the growing polypeptide chain


the aminoacyl-tRNA coding for the next codon in the mRNA then binds to the A site of the ribosome

has to have proper anticodon-codon basepairs form with the mRNA (again wobble occurs for some)

the binding step requires energy, supplied by GTP

proteins called elongation factors assist in getting the charged tRNA to bind
the amino group of the amino acid on the tRNA in the A site is then in alignment with the carboxyl group of the
amino acid in the P site

peptide bond formation can spontaneously occur

the peptide bond formation is catalyzed by the ribosome itself, with energy that had been stored in the
aminoacyl-tRNA molecule

in the process, the amino acid at the P site is released from its tRNA

this leaves an unacylated tRNA in the P site, and a tRNA in the A site which now contains the growing peptide
chain of the protein


notice that protein synthesis proceeds from the amino end of the polypeptide to the carboxyl end (NC)
translocation then takes place

the ribosome assemble essentially moves three nucleotides along the mRNA

the ribosome moves relative to the mRNA so that a new, exposed codon now sits in the A site

the unacylated tRNA is moved from the P site to the E site, where it is released

the tRNA-peptide is moved from the A site to the P site

the translocation process also requires energy from GTP

elongation factor proteins assist with translocation


now everything is set up for another elongation step
note again that polypeptides are synthesized on ribosomes starting at the amino terminal end and proceeding to the
carboxy terminal end (NC)

note also that mRNA's are made from their 5' end to their 3' end, and they are also translated from their 5' end to
their 3' end (5’3’)
3.
termination

a stop codon signals the end for translation (UAA, UGA, and UAG are universal stop codons)

no tRNA matches the stop codon; instead, it a termination factor (AKA release factor) binds there

the termination factor causes everything to dissociate, freeing the polypeptide, mRNA, last tRNA, and ribosomal
subunits all from each other (think of the termination factor as a little molecular bomb)
H. for an average-sized polypeptide chain (~300-400 amino acids long) translation takes less than a minute
I.
polyribosomes
1.
an mRNA is typically being translated by many ribosomes at the same time
2.
once one ribosome has initiated, and elongation has occurred, a second ribosome initiates, and subsequently a third, and
so on
J.

typically as many as 20 ribosomes may be synthesizing protein from the same message

these complexes are called polyribosomes

in prokaryotes, ribosomes initiate and begin elongation even before RNA polymerase ends transcription

thus, transcription and translation are nearly simultaneous

that leads to polyribosomes of prokaryotes being closely associated with DNA
mRNAs do not stick around forever – they are quickly degraded (as fast as in about 2-5 minutes in most prokaryotes)
XVII. Differences between prokaryotes and eukaryotes in transcription and translation: in eukaryotes, the mRNA is modified before
leaving the nucleus
A. the initial transcript is called precursor mRNA (or pre-mRNA, or heterogeneous nuclear RNA, or hnRNA)
B. the first modification is 5’ mRNA capping
1.
happens early, when eukaryotic mRNAs are just being formed and are 20 - 30 nucleotides long
2.
a set of enzymes found in the nucleus adds a 5’ cap to the message
3.
the cap consists of a modified guanine residue, called 7-methylguanylate
4.
this cap is required for binding to eukaryotic ribosomes (so an uncapped mRNA cannot be translated in eukaryotes)
5.
also appears that the cap makes eukaryotic mRNAs less susceptible to degradation and to promote the transport of the
mRNA out of the nucleus
C. the 3’ tail: polyadenylation
1.
a polyadenylation signal in the mRNA trailing sequence signals for the addition of a “tail” on the 3’ end of the mRNA
2.
the tail is a series of adenines, and is called a poly-A tail
3.
polyadenylation is the process of putting the tail on
4.

enzymes recognize the polyadenylation signal and cut the RNA strand at that site

the enzymes then add 100 - 250 adenine ribonucleotides to the mRNA chain
the roles of polyadenylation

starting the process leads to termination of transcription

may make mRNAs less susceptible to degradation

may help get mRNA out of the nucleus

may help in initiation of translation
D. interrupted coding sequences: introns and exons
1.
the transcript made from the DNA in eukaryotes is often much larger than the final mRNA
2.
some stretches of bases called introns “interrupt” the sequence and must be removed
3.
4.

the number of introns varies, from none for some genes up to dozens or more for others

different alleles of the same gene may even vary in intron number

the regions that will not be removed are called exons
the process of removing introns is called RNA splicing

the signals for splicing are short sequences at the ends of introns

particles called snRNPs associate with the mRNA in a complex called the spliceosome

snRNPs are made of small RNA molecules and proteins

the spliceosome catalyzes cutting out and removing an intron and joining together the exons

RNAs in some of the snRNPs act as ribozymes in the splicing process

note that the spliceosome is not always required, but it usually is needed
Why do exons exist?

in some cases, alternative RNA splicing allows one DNA sequence to direct synthesis of two or more different
polypeptides (this may be very common in humans)

exons tend to code for specific domains within proteins

exons tend to code for specific domains within proteins

a domain is a region within the protein that has a specific function

exons with “junk DNA” intron regions between them may be easy to move around and rearrange to make new
proteins

this leads to the notion that many proteins consist of such functional domains which can be readily shuffled
around during evolution to produce new proteins with novel functions

such exon shuffling does indeed appear to have played a prominent role in evolution in eukaryotes
XVIII. Modern definition of genes
A. complications in some scenarios make it necessary to modify the definition of a gene
B. a more inclusive definition: a gene is a nucleotide sequence with information for making a final polypeptide or RNA product
C. the usual flow of information is still DNA  RNA  polypeptide
XIX.
Mutations are changes in the DNA sequence
A. mutations may occur as accidents during DNA replication, or may be induced by DNA-damaging radiation or chemicals
1.
DNA-damage inducers are called mutagens
2.
many mutagens increase the likelihood of cancer, and are thus carcinogens
3.
some DNA regions are more prone to mutations; they are called mutational hot spots (trinucleotide repeats are one
example)
4.
organisms have mechanisms to repair damage to DNA and to proofread DNA during replication, but mutations still
occur (usually at a very low rate)
B. the mutations that are most likely to lead to genetic changes (for good or bad) are those in the coding regions of genes
1.
mutations that result in the substitution of one base for another are referred to as point mutations or base substitution
mutations

if the point mutation does not actually cause a change in what amino acid is coded for, it is called a silent mutation

if the point mutation causes a change in what amino acid is coded for, it is called a missense mutation

if the point mutation result in the formation of a stop codon where an amino previously was coded for, it is called a
nonsense mutation

nonsense mutations result in the premature termination of the protein sequence, and thus an active protein is
usually not formed

missense mutation example: sickle cell anemia (see, in part, page 84)

missense at 6th codon in hemoglobin  chain (counted after protein processing)

in DNA a T is replaced with an A; this leads to valine instead of glutamic acid in the protein

resulting hemoglobin is “sticky” with other hemoglobin chains, crystallizing easily
Normal hemoglobin  chain
DNA:
CAC GTG GAC TGA GGA CTC CTC
RNA:
GUG CAC CUG ACU CCU GAG GAG-
Protein:
val-his-leu-thr-pro-glu-glu-
Sickle cell anemia hemoglobin  chain
2.
DNA:
CAC GTG GAC TGA GGA CAC CTC
RNA:
GUG CAC CUG ACU CCU GUG GAG-
Protein:
val-his-leu-thr-pro-val-glu-
mutations that shift the reading frame (when nucleotides are either added or deleted) are called frameshift mutations
C. some mutations are caused by pieces of DNA that can jump around the genome
1.
such jumping DNA is called a transposon or transposable element
2.
transposons exist in both prokaryotes and eukaryotes; for most their normal function (if any) is unknown, but some
larger ones can provide benefits by moving copies of useful genes with them
XX. Gene Regulation – there are a few points from Ch. 18 that you need to know
A. gene expression is regulated
B. regulation allows for different expression under different conditions
1.
a given cell type will only express genes appropriate for that cell type
2.
gene expression can be changed in response to the environment
3.
constitutive genes (housekeeping genes) are constantly transcribed, with little or no regulation
C. proteins that regulate transcription are called transcription factors
1.
transcription factors often bind directly to DNA
2.
transcription factors usually are activated or inactivated based on signals
3.
signals are some sort of change in the internal environment of the cells
4.
signals can be information from the environment (such as hormones), or as simple as running out of a food molecule or
having a new food source
5.
most transcription factors associate with promoters

promoter sequence determines what transcription factions can bind to the promoter to help initiate transcription

different promoter sequences allow for differences in expression
6.
repressors – transcription factors that suppress or stop gene expression
7.
activators – transcription factors that either activate (“turn on”) gene expression, or that enhance gene expression
D. sometimes DNA sequences away from the promoter can also affect transcription
1.
such sequences can be upstream or downstream of the coding region, or even within the coding region or introns
2.
they are usually within a few kilobases of the coding region, and often within a few hundred bases
3.
enhancers – DNA regions, often far from the promoter, where activators will bind either directly or indirectly
Chapter 20: DNA Technology and Genomics
XXI.
A.
B.
C.
D.
General outline of genetic engineering
DNA cleavage
Production of recombinant DNA
Cloning of the recombinant DNA
Screening clones
XXII. Manipulating DNA: DNA cleavage and Production of Recombinant DNA
A. restriction enzymes: molecular scissors with a twist
1. restriction enzymes, also called restriction endonucleases, are enzymes that cut DNA molecules in specific places
2. restriction enzymes vary considerably
 hundreds of different kinds of restriction enzymes are known (recognizing different DNA sequences)
 recognized sequence length varies (most common are “4-base cutters” and “6-base cutters”)
 placement of cut varies; some leave “sticky ends”, others “blunt ends”
 most recognized sequences are palindromic
 the sequence on one strand matches that of the complementary strand read in the opposite direction
 thus 5'-AGCGCT-3' would have a complementary strand 3'-TCGCGA-5' or reading from 5' to 3', 5'-AGCGCT3'
3. restriction enzymes are mostly from bacteria, and their natural role is to destroy DNA from invading viruses
B. making recombinant DNA
1. restriction enzymes are used to cut up DNA of interest and a “vector” into which you want to place the DNA, making
restriction fragments
2. particularly when sticky ends are involved, the target DNA restriction fragment can form basepairs with the vector
3. DNA ligase is then used to join the DNA strand backbones
XXIII. Cloning of recombinant DNA: using vectors
A. cloning is the process of making many genetically identical cells from cell containing recombinant DNA
1. the gene piece introduced in the recombinant DNA is said to be the DNA that is cloned
2. recombinant DNA is introduced to cells by a vector; the vector is usually maintained in the altered cell line
B. a vector is a means of delivering recombinant DNA to an organism
1. vectors must have a way of getting into the host organism (transformation)
2. vectors must have some way of being propagated
 some types of vectors remain free but are copied and distributed in cell division
 some type of vectors have the inserted DNA integrate all or in part with the host DNA
3. vector DNA sequence must be known enough so that restriction sites can be accurately predicted and used
C. most commonly, vectors are either plasmids, viruses, or yeast artificial chromosomes (YACs)
1. plasmids as vectors
 the most commonly used vectors today are plasmids
 plasmids are small, circular DNA molecules with at least one replication origin
 most bacterial cells contain several plasmids
 some eukaryotic cells commonly have plasmids (such as the yeast Saccharomyces cerevisiae)
 plasmids vary in what organisms can maintain them (largely based on the type of replication origin they carry)
 most plasmids carry genes that are expressed, again with variations depending on the host cell
2. viruses as vectors
 viruses infect cells with their DNA; recombinant DNA in a virus can thus be transferred into cells
 some of this “transduction” occurs naturally, but genetic engineers control and exploit the process
3. yeast artificial chromosomes (YACs) as vectors
 eukaryotes can support and maintain larger pieces of DNA as chromosomes
 YACs have the required elements of chromosomes (centromere, telomeres) and can be used as vectors for large
segments of recombinant DNA in some eukaryotes
D. vectors typically include a selectable marker and a cloning site
1. selectable markers usually are a gene for a product that the host cell cannot make, such as an antibiotic resistance factor
2.
the cloning site on a vector is engineered with many possible sites for restriction enzyme cutting, where foreign DNA
can be inserted
E. the piece of foreign DNA inserted at a cloning site is said to be cloned, and the combined foreign DNA + vector is called
recombinant DNA
XXIV. Screening
A. Often many clones are made with various DNA pieces inserted
B. Screening is used to find the DNA of interest; typically:
1. a selectable marker is used to ensure that the vector is present
2. a second type of selectable marker is tested to ensure that the vector contains inserted DNA (that is, make sure it is
recombinant DNA)
3. cells from cell colonies that pass the screens to this point are used as sources for making large numbers of cells; DNA
from these cells is then subjected to other treatments to help identify cell lines containing the DNA of interest (for
example, the probing covered later in these notes)
XXV. DNA libraries
A. the first step in working with the DNA of a species is to break the whole genome into manageable bits for study; this is done
by creating DNA libraries
B. vectors serve as the “books” in a DNA library – each “book” has a different piece of inserted DNA
C. two main types of libraries are genomic libraries and cDNA libraries
D. genomic libraries
1. raw genomic DNA is broken into fragments
 sometimes the breaking is done mechanically
 sometimes the breaking is done with restriction enzymes
 often a combination is used
2. the broken DNA pieces are put into vectors and then the vectors into host cells
3. cells lines are maintained for each library piece (often, the whole genome is represented multiple times in the library for
completeness)
4. the cell lines are given unique identifiers, and DNA probing techniques (described later) can be used to determine what
lines carry particular cloned DNA sequences
E. cDNA (complementary DNA) libraries
1. a more refined approach than genomic libraries, this type of library is based mainly on the coding regions of DNA
2. mRNAs are isolated from a cell and converted into complementary DNA using the enzyme reverse transcriptase
3. the cDNA is then inserted into vectors and the library is made and maintained just like a genomic library
4. different types of cDNA libraries can be made, reflecting the conditions under which cells made the original mRNAs
5. again, DNA probing techniques are used to find which lines have a cDNA of interest
XXVI. Techniques used to manipulate and study DNA before and after cloning include: PCR, DNA gel electrophoresis,
probing, DNA sequencing, and RFLPs
A. DNA sequence amplification: PCR (polymerase chain reaction) is used to get enough DNA to work with
1. DNA polymerase can build a DNA strand provided there is a template strand, a primer, and dNTPs
(deoxyribonucleotides of each type: dATP, dCTP, dGTP, and dTTP)
 denaturation: heating a DNA molecule will eventually denature (“melt”) the double strands into separate single
strands, breaking the hydrogen bonds between A-T and C-G basepairs; this can provide potential template
strands
 annealing of primers: when the DNA cools, basepairs will reform; if small, specific DNA primers are added in
excess compared to the amount of target (template) DNA molecules, the DNA primers will tend to bind to the
target DNA strands and keep the original double helices from reforming
 primer extension: then, DNA polymerases can add dNTPs to make a complementary DNA strands, starting at the
3’ ends of the primers
 if you repeat this through a series of cycles, you will exponentially make new DNA strands that cover a specific
region of DNA, defined by the specific primers used – a polymerase chain reaction, where each cycle essentially
doubles the amount of your target DNA fragment
2. PCR works well only when the DNA polymerase used can withstand temperatures that melt DNA strands
 such enzymes are found in organisms that grow under very hot conditions (such as thermophilic bacteria from hot
springs)
 these are called heat-stable DNA polymerases (the best known one is Taq polymerase)
3. typically, the PCR works like this:
 DNA melting is done 94°C (just a bit under the boiling temperature of water) for a minute or less

B.
C.
D.
E.
DNA annealing is done at a temperature around 50°C for a minute or less, but this varies depending on the DNA
primers used and their optimal annealing temperature – you want to avoid getting too cool, where some
nonspecific annealing can occur
 DNA synthesis (primer extension) is performed at the optimal temperature for the heat-stable DNA polymerase,
usually 72°C; the time given to extension is roughly 1 min per kilobase of DNA in the final target size
 the process then moves to back to DNA melting, and the “cycle” is repeated for up to ~35 cycles
 often, an extra melting period is put before any cycles (since larger DNA strands are harder to melt), and an extra
extension period is put after all cycles end (to finish up as many strands as possible)
4. PCR greatly amplifies the target DNA sequence
 starting with a single double-stranded DNA molecule (the minimal extreme):
 after 4 cycles one has 24 = 16 DNA molecules
 after 20 cycles one has 220 = 1,048,576 DNA molecules
 with wise primer choices, a segment of DNA can be amplified to make enough molecules for useful study
 thus, given enough sequence knowledge and a small DNA sample, any piece of DNA from any individual can
usually be amplified through PCR to useful quantities
 PCR products can be used for such things as the raw material for cloning, for probing DNA libraries, and for DNA
sequencing
DNA gel electrophoresis
1. the overall DNA molecule is negatively charged, and will migrate though a viscous material such as a gel if a voltage
difference is supplied (moving toward the positive pole)
2. the speed of migration through a gel will be determined in part by the size of the DNA molecule; the longer the
molecule, the slower it moves
3. thus, relative migration rate through a gel can be used to determine the approximate size of a DNA fragment
4. this mostly holds true for RNA as well, but different conditions must be used to prevent degradation of RNA (which is
much more common, and much more of a problem, than DNA degradation)
probing
1. DNA and RNA fragments can be transferred to a filter, denatured, and incubated with probe molecules that will
hybridize (bond by forming correct basepairs) with specific sequences
2. the probe molecules (usually DNA fragments) can be made with some nucleotides that are either radioactive or
fluorescent, thus “labeling” the probe – and, when the probe is used, labeling the sites on the filter where the probe is
able to hybridize
3. if DNA is on the filter and being probed, this is called a Southern blot or DNA gel blot (after the inventor)
4. if RNA is being probed, this is called a Northern blot or RNA gel blot
5. an analogous process with proteins is called a Western blot (there antibodies are used as probes)
DNA sequencing
1. a DNA sequence can be determined using special nucleotides and migration differences of DNA strands through a gel
based on size
2. special ddNTPs (dideoxyribonucleotide triphosphates) are used for sequencing
3. when a ddNTP is incorporated into a growing DNA strand, it prevents further elongation of the DNA strand
 there is no 3’-OH on which to add the next nucleotide, so the strand stops
 strand length is thus set by where the stop occurs
4. sequencing typically involves 4 polymerization mixtures
 usually, each mixture has labeled primers that allow DNA visualization
 each mixture also has a DNA polymerase and multiple copies of single-stranded template DNA
 each mixture also has all 4 normal dNTPs
 the mixtures differ in the ddNTP included (one will be ddATP, one ddCTP, one ddGTP, one ddTTP); the ddNTP is
included in a small amount relative to the dNTPs
 at the end, each mixture will have a number of newly-synthesized DNA strands with a variety of sizes, but within a
given mixture you will know what ddNTP is at the 3’ end of each of the stands
5. the labeled mixes are run on a gel and separated by size; the gel is then read from shortest (thus fastest, and closest to the
bottom) up to the longest (thus slowest, and closest to the top) fragment – a letter is assigned based on the ddNTP
that was used for the mixture that was run in that gel lane
restriction fragment length polymorphisms (RFLPs)
1. DNA cut by restriction enzymes and run on a gel can produce distinguishable DNA bands
2. sequence differences between organisms (between species, or even within the same species) can result in different bands
3. thus, given the right restriction enzymes or set of enzymes, RFLPs can serve as a “DNA fingerprint” for an individual
4. DNA sequencing is the most reliable means of identification, and as it becomes cheaper and more available it is
replacing some uses of RFLP analysis; however, RFLP analysis likely will always be quicker and cheaper than
sequencing, and is still used heavily (RFLP analysis is much more reliable than older techniques like actual
fingerprint matching)
XXVII. Applications of genetic engineering (some examples)
A. transgenic organism - any organism with a foreign gene(s) incorporated in it
B. uses of transgenic organisms
1.
2.
3.
4.
5.
as drug makers
 many gene products have potential medical uses; a useful protein or enzyme can often be made in bulk via genetic
engineering
 a case in point: the human insulin gene has been made in E. coli for over two decades (much safer than insulin from
other animals, which is not identical to human insulin)
 another example: human growth hormone – much safer than the old process of purifying from cadavers
as medical models
 transgenic mice for modeling disease
 transgenic organisms for basic research on disease-related topics such as cell division
as gene therapy tools – viruses to deliver DNA to human cells
tools used to make better tools
 cloned restriction enzymes, Taq polymerase, etc.
 sometimes cloned enzymes are modified to improve them for specific uses
improved food sources – examples:
 golden rice, engineered to make enough beta carotene to reduce vitamin A deficiencies in many societies
 insect-resistant cotton, corn, etc. – express a bacterial gene that codes for a toxin that kills insects that try to feed on
the plant
 herbicide resistance
C. safety guidelines
1.
2.
potential misuses (both intentional and accidental) are a concern
stringent guidelines are in place to prevent such things as producing and releasing a “super virus,” “super bacteria,” or
“super weed” that would become a serious medical and/or ecological disaster
3. genetically engineered organisms that are released into the environment in some way are closely monitored on a case-bycase basis – example of Bt corn
4. much concern over genetic engineering exists in the general public (especially in Europe), so things such as labeling of
genetically modified foods is a controversial issue
Chapter 22: Descent with Modification: A Darwinian Viwe of Life
I.
Darwin’s voyage
A. Charles Darwin (1809-1882) received a degree in theology, but also was trained in the type of field biology common in the
early 19th century (most prominent biologists of the time were field biologists who studied and classified organisms in
their natural environments)
B. Darwin signed on as the captain’s companion on board the H.M.S. Beagle, on which he took a five-year voyage from 18311836 exploring South America and surrounding islands, as well as islands in the South Pacific
C. His private work on the voyage was as a naturalist, collecting and cataloging thousands of species
D. He was most impressed by the similarities between species in the Galapagos islands (in the Pacific west of Ecuador) and their
similarities to species from South America; this did not fit well with the divine design model that he had been trained
under and that was still prominent at the time
E. There was much discussion by immediate predecessors and contemporaries of Darwin about how the divine design model did
not mesh well with observation of the extremes of variation among species, the idea of extinct species represented in the
fossil record, and the functional similarities between the anatomy of extremely divergent species; the idea that evolution
occurs thus was “in the air” at the time, but attempts to find a convincing mechanism fell short (such as Lamarck’s
acquired characteristics model)
F. Recall Darwin’s theological training – Darwin was well aware of the impact that a workable, testable theory of evolution
would have, and the intense controversy and scrutiny it would draw; thus, while he worked out most of his theory of
evolution shortly after his trip on the Beagle, he spent 20 years accumulating evidence and doing experiments before
finally publishing the idea
G. Darwin was spurred on to publish when Alfred Russel Wallace shared his independent work where he had reached similar
conclusions to Darwin; they first presented the theory of evolution by natural selection together in 1858
H. Darwin published his first version of the book On the Origin of Species by Means of Natural Selection in 1859; in it, he laid
out the entire argument with all of the evidence that he had been gathering ever since his voyage on the Beagle
I. Darwin’s book had immediate and dramatic impact; the force of his argument and evidence convinced many scientists
quickly, but of course it stirred tremendous controversy as well; Darwin made several revisions of his work in response to
some of the most reasonable criticisms, as well as focusing on human evolution in The Descent of Man (1871)
II. Evidence supporting the theory of evolution
A. the fossil record
1.
2.
fossils provide direct evidence for change over time
 fossils range from mineralized casts or imprints (most commonly of bone, teeth, and shells, but sometimes of softer
tissues) to actual body parts preserved in bogs, tar, amber, or ice
 fossils provide evidence of intermediates between extant and extinct forms
 many relatively complete examples of transitions in body forms are known, such as the evolutionary lineage of
horses and the transition of terrestrial species to modern whales
 the fossil record provides tests of evolution as an explanation for the history of life on Earth – fossils can be dated,
and the age of fossils invariably matches the predicted place of those body forms in the history of life on Earth
fossils most commonly form in sedimentary rocks in aquatic environments
 the fossil record is biased toward organisms with hard parts that lived in aquatic or arid environments, where decay
is slow and incorporation in rocks can occur with reasonable speed
 organisms that lived in places of rapid decay are thus biased against in the fossil record
B. dating fossils
1.
2.
3.
4.
relative position in rock layers
 sedimentary layers most commonly have the youngest layers nearer the surface, and are progressively older as you
go deeper
 large-scale geological events can be used to correlate rock strata from different sites; other dating methods are also
used to correlate rock strata
association with index fossils that have been dated by other means from other locations
radioisotope dating
 each radioisotope has characteristic, constant rates of decay
 some allow for measurement of when a rock was formed or when an organism died
 example: potassium-40 decaying to argon-40
 when magma cools to solid rock, no argon is in the rock (escapes as the rock forms)

once the rock hardens, the radioactive clock begins – potassium-40 in the rock decays to argon-40
 measurement of the amounts of potassium-40 and argon-40 in the rock today are used to determine an age range
for when the rock could have been formed
 half-life of 1.3 billion years: used for fossils tens of millions to billions of years old
 another example: carbon-14 decaying to nitrogen-14 (half-life of 5730 years) – used for organic remains hundreds to
tens of thousands of years old
there are hundreds of well-studied sites with fossils that can be dated in some way; no truly incongruous fossils have
been found
C. comparative anatomy of related species
1.
2.
3.
organs or structures that have similar form due to a common evolutionary origin are called homologous features
 example: the similarity between the human arm, the dolphin's flipper, the bat's wing, and the bird's wing
 example: plant leaves, cactus needles, flower sepals and petals
not all organs or structures with functional similarity have a common origin
 such cases are called homoplastic features, or analogous features
 resemblance between homoplastic features is superficial – consider an insect's wing and a bird's wing
 independent evolution of similar features in distantly related organisms is called convergent evolution
vestigial structures – a feature that once had a role in the evolutionary history of a species but that no longer functions
 natural selection will logically lead to degeneration of unused features
 however, it is not easy to completely remove by natural selection – thus, vestiges are left behind
 examples: human appendix, wisdom teeth; whale pelvis and hind legs
D. distribution of plants and animals
biogeography – the study of the past and present geographical distribution of organisms
organisms on islands are most closely related (in form and genetically) to those from the nearest mainland, not those
from similar islands in different parts of the world
3. the modern theory of plate tectonics and reconstruction of the history of land masses on Earth explains much of the
observed fossil distributions matching with timings of geographic isolations that would be expected for some modern
distributions of species (example: the dominance of marsupials in Australia)
E. related species have similar patterns of development
1. very young embryos of reptiles, birds, mammals, and humans are indistinguishable
2. studies of developmental biology are revealing the common genetic basis for such similarities – “devo/evo” study is one
of the hottest fields in biology today
F. molecular comparisons among organisms
1. the “big test” for the theory of evolution by natural selection was this:
 evolution by natural selection on inherited traits predicts that genetic sequence information will provide a record of
evolutionary change and evolutionary relationships
1.
2.

2.
3.
4.
these genetic records should correlate with evolutionary relationships that have been established by other means,
such as biogeography and comparative anatomy
 evolution has passed this test with flying colors
the virtual universality of the genetic code is compelling evidence of a common ancestor
changes in proteins and nucleic acids provide a record of evolutionary change
 DNA sequencing provides a means to measure genetic similarities and differences between species
 sequences of amino acids in proteins can also be used – these provide an indirect comparison of DNA sequences
 DNA and protein sequencing can be used to create a phylogenetic tree, diagrams showing the relatedness between
species and lines of descent
 DNA sequencing can also be used in some cases as a molecular clock to make some inference about when any two
species diverged from each other (last shared a common ancestor)
 example – humans and chimpanzees: ~98% sequence identity, diverged about 6 million years ago
detailed molecular studies have clearly documented microevolution in the case of the emergence of antibiotic-resistant
bacteria
III. The central role of evolution in modern biology
A. the modern synthetic theory of evolution is accepted today by most biologists as a robust and well-supported model that can
be trusted enough to form the central framework for the study of life
B. nearly all biologists today agree with the famous statement by the evolutionary geneticist T. Dobzhansky: “Nothing in
biology makes sense except in the light of evolution.”
C. studies of evolution itself today focus largely on the causal processes of evolution, such as the speed of evolutionary change
and the role of chance in evolution, and on molecular comparisons between and within species by DNA sequencing
Chapter 22: Evolution
69. Describe the major ideas on evolution and related topics that had a significant
influence on Charles Darwin as he developed the concept of evolution by natural selection.
Describe the logical reasoning behind Darwin’s concept of natural selection.
70.
71. Explain the terms microevolution and macroevolution (in their true scientific
meanings), and describe how microevolution can lead to macroevolution.
72.





Discuss these major lines of evidence for evolution:
fossil record
anatomical evidence (comparisons, vestigial structures, “design” flaws)
distribution of organisms
developmental comparisons
molecular comparisons
73.
Explain how fossils are dated.
74.
Discuss how DNA sequence comparisons and “molecular clocks” work.
75.
What is the “modern synthesis”?
I.
Historical perspective – ideas on evolution and related topics up to Darwin
A. divine design and perfection model
1.
espoused by Aristotle, the ancient Greek philosopher (284-322 B.C.) whose ideas on biology dominated most thinking
on the subject until the renaissance
2.
species were viewed on a scale from simple to complex
3.
all organisms were seen as moving toward perfection (which was associated with complexity)
4.
based on divine intervention and design (thus supernatural, outside the true realm of science)
5.
now discredited in biology, but still part of the social consciousness
B. fossils
1.
fossils were known for centuries before Darwin
2.
fossils reveal organisms unlike any living today, and the idea that some fossils represent species that had become extinct
was recognized even by Leonardo da Vinci (1452-1519)
C. acquired traits
1.
mostly associated with Lamarck (1744-1829)
2.
still focused on a model of organisms driven toward complexity, but involved an explanation with natural causes
3.
postulated that changes or “acquired characteristics” during an organism’s life could be passed on to offspring
4.
famous example was Lamarck’s model for how giraffes developed long necks – he claimed that stretching of the neck in
one generation would lead to offspring with longer necks
5.
understanding of genetic inheritance has led to rejection of acquired traits models
D. birth of modern geology – Lyell, uniformitarianism, and the ancient Earth
1.
prior to the early 1800s, the world view of most was that the Earth is very young (around 6000 years old)
2.
in the early 1800s, geologists began to apply scientific reasoning to studies of geological processes, and quickly
recognized that these processes require that the Earth be very old (billions of years) to occur naturally
3.
this “uniformitarian” model of geological processes was made famous by Lyell’s Principles of Geology, which
influenced Charles Darwin
4.
the uniformitarian model is essentially the basis of geology today; confirming tests of this model include dating rocks
using radioisotope ratios (more on that later)
E. artificial selection
1.
it was well known that domesticated animals and plants had been breed over centuries by humans to produce different
varieties, indicating that the characteristics of a species can be modified by selection
2.
some examples are different breeds of dogs and the “wild cabbage” lineage of cabbage, broccoli, cauliflower, Brussels
sprouts, collards, kale, etc.
F.
population limits that would allow selection to act naturally were recognized
1.
Malthus (1766-1834) wrote the most influential works on this subject
2.
mathematically, populations will grow geometrically if unchecked
3.
food supplies rarely can be expected to grow faster than arithmetically, thus putting a limit on population growth
II. Darwin’s voyage
A. Charles Darwin (1809-1882) received a degree in theology, but also was trained in the type of field biology common in the
early 19th century (most prominent biologists of the time were field biologists who studied and classified organisms in
their natural environments)
B. Darwin signed on as the captain’s companion on board the H.M.S. Beagle, on which he took a five-year voyage from 18311836 exploring South America and surrounding islands, as well as islands in the South Pacific
C. His private work on the voyage was as a naturalist, collecting and cataloging thousands of species
D. He was most impressed by the similarities between species in the Galapagos islands (in the Pacific west of Ecuador) and their
similarities to species from South America; this did not fit well with the divine design model that he had been trained
under and that was still prominent at the time
E. There was much discussion by immediate predecessors and contemporaries of Darwin about how the divine design model did
not mesh well with observation of the extremes of variation among species, the idea of extinct species represented in the
fossil record, and the functional similarities between the anatomy of extremely divergent species; the idea that evolution
occurs thus was “in the air” at the time, but attempts to find a convincing mechanism fell short (such as Lamarck’s
acquired characteristics model)
F.
Recall Darwin’s theological training – Darwin was well aware of the impact that a workable, testable theory of evolution
would have, and the intense controversy and scrutiny it would draw; thus, while he worked out most of his theory of
evolution shortly after his trip on the Beagle, he spent 20 years accumulating evidence and doing experiments before
finally publishing the idea
G. Darwin was spurred on to publish when Alfred Russel Wallace shared his independent work where he had reached similar
conclusions to Darwin; they first presented the theory of evolution by natural selection together in 1858
H. Darwin published his first version of the book On the Origin of Species by Means of Natural Selection in 1859; in it, he laid
out the entire argument with all of the evidence that he had been gathering ever since his voyage on the Beagle
I.
Darwin’s book had immediate and dramatic impact; the force of his argument and evidence convinced many scientists
quickly, but of course it stirred tremendous controversy as well; Darwin made several revisions of his work in response to
some of the most reasonable criticisms, as well as focusing on human evolution in The Descent of Man (1871)
III. Darwin’s theory: evolution occurs by natural selection
A. Darwin proposed that species evolve by natural selection; his theory of evolution was based on four general observations:
1.
overproduction – each species produces more offspring than will survive to maturity
2.
variation – individuals in a population vary, and some of the variation is heritable (this was expanded by others later, as
genetics came to be understood)
3.
competition – there is competition among the individuals of a population for limited resources (struggle for existence)
4.
differential reproductive success – individuals that possess more favorable characteristics (in the pool of variation) are
more likely to survive and reproduce; those with less favorable characteristics are less likely to survive and reproduce
B. thus, natural selection will produce a population of individuals more suited to their environment through time
C. when populations are separated (such as the geographic separation of islands from each other and a nearby continent), natural
selection on two separate populations can produce two distinct populations with different characteristics – resulting in two
separate species
D. note that for this theory to explain the current variety of species on Earth, there is a need for a long amount of time for natural
selection to produce the variety observed; thus, the idea of an ancient Earth hundreds of millions to billions of years old is
crucial
E. note also that this theory really has two major branches: microevolution, or changes of a population over time, and
macroevolution, or the formation of species
IV. Evidence supporting the theory of evolution
A. the fossil record
1.
fossils provide direct evidence for change over time

fossils range from mineralized casts or imprints (most commonly of bone, teeth, and shells, but sometimes of softer
tissues) to actual body parts preserved in bogs, tar, amber, or ice

fossils provide evidence of intermediates between extant and extinct forms

many relatively complete examples of transitions in body forms are known, such as the evolutionary lineage of
horses and the transition of terrestrial species to modern whales

the fossil record provides tests of evolution as an explanation for the history of life on Earth – fossils can be dated,
and the age of fossils invariably matches the predicted place of those body forms in the history of life on Earth
2.
fossils most commonly form in sedimentary rocks in aquatic environments

the fossil record is biased toward organisms with hard parts that lived in aquatic or arid environments, where decay
is slow and incorporation in rocks can occur with reasonable speed

organisms that lived in places of rapid decay are thus biased against in the fossil record
B. dating fossils
1.
relative position in rock layers

sedimentary layers most commonly have the youngest layers nearer the surface, and are progressively older as you
go deeper

large-scale geological events can be used to correlate rock strata from different sites; other dating methods are also
used to correlate rock strata
2.
association with index fossils that have been dated by other means from other locations
3.
radiometric dating

each radioisotope has characteristic, constant rates of decay

some allow for measurement of when a rock was formed or when an organism died

example: potassium-40 decaying to argon-40

when magma cools to solid rock, no argon is in the rock (escapes as the rock forms)

once the rock hardens, the radioactive clock begins – potassium-40 in the rock decays to argon-40

measurement of the amounts of potassium-40 and argon-40 in the rock today are used to determine an age range
for when the rock could have been formed


half-life of 1.3 billion years: used for fossils tens of millions to billions of years old
another example: carbon-14 decaying to nitrogen-14 (half-life of 5730 years) – used for organic remains hundreds to
tens of thousands of years old
4.
there are hundreds of well-studied sites with fossils that have been dated in some way; no truly incongruous fossils have
been found
C. comparative anatomy of related species
1.
2.
3.
organs or structures that have similar form due to a common evolutionary origin are called homologous features

example: the similarity between the human arm, the dolphin's flipper, the bat's wing, and the bird's wing

example: plant leaves, cactus needles, flower sepals and petals
vestigial structures – a feature that once had a role in the evolutionary history of a species but that no longer functions

natural selection will logically lead to degeneration of unused features

however, it is not easy to completely remove by natural selection – thus, vestiges are left behind

examples: human appendix, wisdom teeth; whale pelvis and hind legs
not all organs or structures with functional similarity have a common origin

such cases are called homoplastic features, or analogous features

resemblance between homoplastic features is superficial – consider an insect's wing and a bird's wing

independent evolution of similar features in distantly related organisms is called convergent evolution
D. distribution of plants and animals
1.
biogeography – the study of the past and present geographical distribution of organisms
2.
organisms on islands are most closely related (in form and genetically) to those from the nearest mainland, not those
from similar islands in different parts of the world
3.
the modern theory of plate tectonics and reconstruction of the history of land masses on Earth explains much of the
observed fossil distributions matching with timings of geographic isolations that would be expected for some modern
distributions of species (example: the dominance of marsupials in Australia)
E. related species have similar patterns of development
1.
very young embryos of reptiles, birds, mammals, and humans are indistinguishable
2.
studies of developmental biology are revealing the common genetic basis for such similarities – “devo/evo” study is one
of the hottest fields in biology today
F.
molecular comparisons between organisms
1.
the “big test” for the theory of evolution by natural selection was this:

evolution by natural selection on inherited traits predicts that genetic sequence information will provide a record of
evolutionary change and evolutionary relationships

these genetic records should correlate with evolutionary relationships that have been established by other means,
such as biogeography and comparative anatomy

evolution has passed this test with flying colors
2.
the virtual universality of the genetic code is compelling evidence of a common ancestor
3.
changes in proteins and nucleic acids provide a record of evolutionary change

DNA sequencing provides a means to measure genetic similarities and differences between species

sequences of amino acids in proteins can also be used – these provide an indirect comparison of DNA sequences

DNA and protein sequencing can be used to create a phylogenetic tree, diagrams showing the relatedness between
species and lines of descent

DNA sequencing can also be used in some cases as a molecular clock to make some inference about when any two
species diverged from each other (last shared a common ancestor)

4.
example – humans and chimpanzees: ~98% sequence identity, diverged about 6 million years ago
detailed molecular studies have clearly documented microevolution in the case of the emergence of antibiotic-resistant
bacteria
V. The modern synthesis of evolutionary theory combines Darwin’s concept of natural selection with genetics
A. although Mendel was a contemporary of Darwin, remember that his work was largely unrecognized until around 1900
B. how traits are inherited was central to Darwin’s theory of evolution, and thus Darwin (and others) were keenly interested in
finding working models of inheritance
C. when genetic mechanisms came to be widely understood, they were quickly combined with Darwin’s model in the modern
synthesis, also called Neo-Darwinism or the synthetic theory of evolution
1.
this model emphasizes the genetics of populations
2.
evolution is seen as working by natural selection on individuals to change the genetic makeup of populations over
successive generations
D. mutations play a key role in providing a source of genetic variation
1.
without genetic variation, evolution cannot occur
2.
mutations are necessary to produce genetic variation
3.
while many mutations have no impact and many others are harmful, it is critical to recognize that some mutations are
advantageous
VI. The central role of evolution in modern biology
A. the modern synthetic theory of evolution is accepted today by most biologists as a robust and well-supported model that can
be trusted enough to form the central framework for the study of life
B. nearly all biologists today agree with the famous statement by the evolutionary geneticist T. Dobzhansky: “Nothing in
biology makes sense except in the light of evolution.”
C. studies of evolution itself today focus largely on the causal processes of evolution, such as the speed of evolutionary change
and the role of chance in evolution, and on molecular comparisons between and within species by DNA sequencing
Chapter 23: The Evolution of Population (Microevolution)
VII. Historical perspective – ideas on evolution and related topics up to Darwin
A. divine design and perfection model
1. espoused by Aristotle, the ancient Greek philosopher (284-322 B.C.) whose ideas on biology dominated most thinking
on the subject until the renaissance
2. species were viewed on a scale from simple to complex
3. all organisms were seen as moving toward perfection (which was associated with complexity)
4. based on divine intervention and design (thus supernatural, outside the true realm of science)
5. now discredited in biology, but still part of the social consciousness
B. fossils
1. fossils were known for centuries before Darwin
2. fossils reveal organisms unlike any living today, and the idea that some fossils represent species that had become extinct
was recognized even by Leonardo da Vinci (1452-1519)
C. acquired traits
1. mostly associated with Lamarck (1744-1829)
2. still focused on a model of organisms driven toward complexity, but involved an explanation with natural causes
3. postulated that changes or “acquired characteristics” during an organism’s life could be passed on to offspring
4. famous example was Lamarck’s model for how giraffes developed long necks – he claimed that stretching of the neck in
one generation would lead to offspring with longer necks
5. understanding of genetic inheritance has led to rejection of acquired traits models
D. birth of modern geology – Lyell, uniformitarianism, and the ancient Earth
1. prior to the early 1800s, the world view of most was that the Earth is very young (around 6000 years old)
2. in the early 1800s, geologists began to apply scientific reasoning to studies of geological processes, and quickly
recognized that these processes require that the Earth be very old (billions of years) to occur naturally
3. this “uniformitarian” model of geological processes was made famous by Lyell’s Principles of Geology, which
influenced Charles Darwin
4. the uniformitarian model is essentially the basis of geology today; confirming tests of this model include dating rocks
using radioisotope ratios (more on that later)
E. artificial selection
1. it was well known that domesticated animals and plants had been breed over centuries by humans to produce different
varieties, indicating that the characteristics of a species can be modified by selection
2. some examples are different breeds of dogs and the “wild cabbage” lineage of cabbage, broccoli, cauliflower, Brussels
sprouts, collards, kale, etc.
F. population limits that would allow selection to act naturally were recognized
1. Malthus (1766-1834) wrote the most influential works on this subject
2. mathematically, populations will grow geometrically if unchecked
3. food supplies rarely can be expected to grow faster than arithmetically, thus putting a limit on population growth
VIII. Darwin’s theory: evolution occurs by natural selection
A. Darwin proposed that species evolve by natural selection; his theory of evolution was based on four general observations:
1. overproduction – each species produces more offspring than will survive to maturity
2. variation – individuals in a population vary, and some of the variation is heritable (this was expanded by others later, as
genetics came to be understood)
3. competition – there is competition among the individuals of a population for limited resources (struggle for existence)
4. differential reproductive success – individuals that possess more favorable characteristics (in the pool of variation) are
more likely to survive and reproduce; those with less favorable characteristics are less likely to survive and reproduce
B. thus, natural selection will produce a population of individuals more suited to their environment through time
C. when populations are separated (such as the geographic separation of islands from each other and a nearby continent), natural
selection on two separate populations can produce two distinct populations with different characteristics – resulting in two
separate species
D. note that for this theory to explain the current variety of species on Earth, there is a need for a long amount of time for natural
selection to produce the variety observed; thus, the idea of an ancient Earth hundreds of millions to billions of years old is
crucial
E. note also that this theory really has two major branches: microevolution, or changes of a population over time, and
macroevolution, or the formation of species
IX. The modern synthesis of evolutionary theory combines Darwin’s concept of natural
selection with genetics
A. although Mendel was a contemporary of Darwin, remember that his work was largely unrecognized until around 1900
B. how traits are inherited was central to Darwin’s theory of evolution, and thus Darwin (and others) were keenly interested in
finding working models of inheritance
C. when genetic mechanisms came to be widely understood, they were quickly combined with Darwin’s model in the modern
synthesis, also called Neo-Darwinism or the synthetic theory of evolution
1. this model emphasizes the genetics of populations
2. evolution is seen as working by natural selection on individuals to change the genetic makeup of populations over
successive generations
D. mutations play a key role in providing a source of genetic variation
1. without genetic variation, evolution cannot occur
2. mutations are necessary to produce genetic variation
3. while many mutations have no impact and many others are harmful, it is critical to recognize that some mutations are
advantageous
X. Microevolution is a change in allele frequencies or genotype frequencies in a population over time
A. population – a group of individuals capable or interbreeding and producing fertile offspring, and that are more or less
isolated from other such groups
B. gene pool – all alleles present in a population at a given time
C. phenotype frequency – proportion of a population with a given phenotype
D. genotype frequency – proportion of a population with a given genotype
E. allele frequency – proportion of a specific allele in a population
1. diploid individuals have two alleles for each gene
2. if you know genotype frequencies, it is easy to calculate allele frequencies
3. example:
 population (1000) = genotypes AA (490) + Aa (420) + aa (90)
 allele number (2000) = A (490x2 + 420) + a (420 + 90x2) = A (1400) + a (600)
 freq[A] = 1400/2000 = 0.70
 freq[a] = 600/2000 = 0.30
 note that the sum of all allele frequencies is 1.0
XI. Genetic equilibrium in populations: the Hardy-Weinberg theorem
A. the Hardy-Weinberg theorem describes the frequencies of genotypes in a population based on the frequency of occurrence
of alleles in the population that is in a state of genetic equilibrium (that is, not evolving)
1. the usual case for calculations: if allele “A” is dominant to “a”, and they are the only two alleles possible at the A-locus,
then
 p = freq[A] = the frequency of occurrence of the A-allele in the population
 q = freq[a] = the frequency of occurrence of the a-allele in the population
2. Then p + q = 1 (following the sum rule for probability)
3. Allele associations follow the product rule for probability, so you multiply to predict the genotype frequencies:
 ( p + q ) x ( p + q ) = p2 + 2 pq + q2
 p2 = frequency of homozygous dominant genotypes
 2 pq = frequency of heterozygous genotypes
 q2 = frequency of homozygous recessive genotypes
 note that ( p + q ) x ( p + q ) = 1 x 1 = 1, so p2 + 2 pq + q2 = 1
B. Hardy-Weinberg equilibrium
1. if the Hardy-Weinberg theorem can be used to accurately predict genotype frequencies from allele frequencies for a
population then the population is in Hardy-Weinberg equilibrium or genetic equilibrium
2. in such cases you can use data from one generation to predict the allele, genotype, and phenotype frequencies for the
next generation
3. such populations are not evolving, but are static instead
C. the assumptions of this model are:
1. large population size (due to statistical constraints, to minimize genetic drift)
2. no migration – no exchange of alleles with other populations (no gene flow)
3. no mutations of the alleles under study occur
4. random mating of all genotypes
5. no natural selection
XII. Microevolution thus can be described as deviation from Hardy-Weinberg equilibrium, where the allele or genotype
frequencies in a population change over time
A. consequences of small population size: genetic drift
1. Consider taking a small sample of individuals from a larger population. If only two individuals were picked they cannot
reflect the allele frequency in the larger population. Neither can 3, 4, or 5 individuals, but as the selected sample gets
larger it becomes more likely that the sample reflects the allele frequency in the larger population.
2. genetic drift is a change in gene frequencies of populations because of small population size
3. genetic drift tends to decrease genetic variation within a population
4. genetic drift tends to increase genetic variation between populations
5. two general mechanisms lead to small population sizes
 genetic bottlenecks are created by dramatic reduction in population size – endangered species face a genetic
bottleneck on a species-wide scale, and suffer lasting effects even if population size later recovers
 founder effect – when a new population is established, typically only a few individuals (founders) are involved in
colonizing the new area; this is common for islands
B. migration – when individuals leave or join a population
1. migrating individuals carry their alleles with them (gene flow), usually resulting in changes in allele frequencies
2. gene flow tends to decrease genetic variation between populations
C. mutations increase variation in the gene pool of a species
1. remember that mutations may be neutral, harmful, or beneficial
2.
even at the risk of harmful effects, mutations are necessary to increase variation in the population so that natural
selection can produce organisms more suited to their environment
D. nonrandom mating
1. if individuals do not mate at random, then Hardy-Weinberg equilibrium is not achieved
2. the most common cases of nonrandom mating involve mating between individuals of similar genotypes, either by choice
or location
 such inbreeding does not change allele frequencies, but increases the frequency of homozygous genotypes
 inbreeding depression is seen in some cases, where inbred individuals have lower fitness that non-inbred individuals
 fitness – relative ability of a genotype to contribute to future generations
 fertility declines and high juvenile mortality associated with “unmasking” harmful recessive alleles can reduce
fitness for inbred individuals
 hybrid vigor also leads to higher relative fitness for hybrids
 self-fertilization is the most extreme case of inbreeding
3. assortive mating – mates are selected by phenotypes
 positive assortive mating – selection for the same phenotype; works like inbreeding for the genes governing that
phenotype, and for loci closely linked to those genes
 negative assortive mating – selection for the opposite phenotype
 less common than positive assortive mating
 leads to a decrease in homozygous genotypes for the genes governing the selected phenotype, and for loci
closely linked to those genes
E. natural selection changes allele frequencies in a way that leads to adaptation to the environment
1. fitness is the ability of an organism to compete successfully and pass its alleles on to the next generation
2. populations undergoing natural selection are evolving, with alleles that contribute to better fitness increasing in
frequency over successive generations
3. natural selection only operates based on the current environment – as environmental conditions change, different alleles
will be selected for
4. sexual selection (mate choices based on inherited characteristics) is an aspect of natural selection
5. there are 3 types of natural selection
 stabilizing selection – occurs in populations well adapted to their environments, selecting against phenotypic
extremes
 this is probably the type of selection most commonly faced by populations
 example - human birth weight
 directional selection – permits species to adapt to environmental change by favoring selection of one extreme over
the other; example – peppered moth
 disruptive selection – when more than one extreme phenotype is favored over intermediate phenotypes
 really a special case of direction selection, where there are trends in more than one direction
 can produce a genetic “split” in a population and thus serve as a mechanism for speciation
 example – pocket mice in New Mexico
XIII. Genetic variation must exist for natural selection to occur
A. the ultimate source of genetic variation is mutations
B. once variation exists, it can be affected by independent assortment and genetic recombination during gamete formation
1. consider the cross AaBb x AaBb – 9 different genotypes arise
2. this involves only 2 alleles at 2 loci; if there were 6 alleles possible at just 5 loci, over 4 million genotypes are possible
3. thus, given that there are thousands of genes in an organism, and that many alleles are possible at most of these loci, it
becomes clear that in nature there is great genetic variability
C. the demonstrated presence of two or more alleles at a given locus is genetic polymorphism
1. biologists have produced tools for studying the genetic polymorphism of populations at the molecular level (RFLP, DNA
sequencing, etc.)
2. these tools can be used to demonstrate and study polymorphism in populations without necessarily knowing the specific
genes involved
D. genetic polymorphisms can be maintained by heterozygote advantage or hybrid vigor
1. when either the homozygous dominant or recessive is more suited to an environment than the heterozygote, the
homozygous genotype will be more likely to be fixed in the population
2. but when heterozygous genotypes have advantage over either of the homozygous genotypes, variation tends to increase
in the population
3. example - sickle cell anemia and malaria resistance
E. genetic polymorphisms can be maintained due to frequency-dependent selection
1. there are cases where the frequency of a given genotype affects the degree to which it is or isn't selected in the
population
2.
F.
example - predator/prey relationships, where individuals with a rare phenotype may be ignored by a predator, but as they
become more abundant the selective advantage decreases because the predator is more likely to notice them
much of the genetic variation in a population will produce no selective advantage, i.e. it is neutral
1. the role of neutral variation in evolution is debated today
2. remember that what is neutral in one context may not be neutral in another context, so as environments change some
previously neutral variation may be acted on by natural selection
Chapter 23: Population Genetics (Microevolution)
76.
Explain what terms in the Hardy-Weinberg equation give:
 allele frequencies (dominant allele, recessive allele, etc.)
 each genotype frequency (homozygous dominant, heterozygous, etc.)
 each phenotype frequency
77.
[do some pop gen problems from slides, and make some more up if there is time]
78.
Describe the assumptions of the Hardy-Weinberg equilibrium model.
79. Describe conditions that can keep populations from establishing or maintaining
genetic equilibrium.
80.
Explain three main types of natural selection.
81. Discuss the importance of genetic variation for evolution, and the concept of neutral
variation.
82. Give a hypothetical example of how genetic variation that was once neutral may no
longer be neutral.
XIV.
Microevolution is a change in allele frequencies or genotype frequencies in a population over time
A. population – a localized group of individuals capable of interbreeding and producing fertile offspring, and that are more or
less isolated from other such groups
B. gene pool – all alleles present in a population at a given time
C. phenotype frequency – proportion of a population with a given phenotype
D. genotype frequency – proportion of a population with a given genotype
E. allele frequency – proportion of a specific allele in a population
1. diploid individuals have two alleles for each gene
2. if you know genotype frequencies, it is easy to calculate allele frequencies
3. example:
 population (1000) = genotypes AA (490) + Aa (420) + aa (90)
 allele number (2000) = A (490x2 + 420) + a (420 + 90x2) = A (1400) + a (600)
 freq[A] = 1400/2000 = 0.70
 freq[a] = 600/2000 = 0.30
 note that the sum of all allele frequencies is 1.0
XV. Genetic equilibrium in populations: the Hardy-Weinberg theorem
A. the Hardy-Weinberg theorem describes the frequencies of genotypes in a population based on the frequency of occurrence
of alleles in the population that is in a state of genetic equilibrium (that is, not evolving)
1.
the usual case for calculations: if allele “A” is dominant to “a”, and they are the only two alleles possible at the A-locus,
then
 p = freq[A] = the frequency of occurrence of the A-allele in the population
 q = freq[a] = the frequency of occurrence of the a-allele in the population
2.
3.
Then p + q = 1 (following the sum rule for probability)
Allele associations follow the product rule for probability, so you multiply to predict the genotype frequencies:
 ( p + q ) x ( p + q ) = p2 + 2 pq + q2
 p2 = frequency of homozygous dominant genotypes
 2 pq = frequency of heterozygous genotypes
 q2 = frequency of homozygous recessive genotypes
 note that ( p + q ) x ( p + q ) = 1 x 1 = 1, so p2 + 2 pq + q2 = 1
B. Hardy-Weinberg equilibrium
1. if the Hardy-Weinberg theorem can be used to accurately predict genotype frequencies from allele frequencies for a
population then the population is in Hardy-Weinberg equilibrium or genetic equilibrium
2.
3.
in such cases you can use data from one generation to predict the allele, genotype, and phenotype frequencies for the
next generation
such populations are not evolving, but are static instead
C. the assumptions of this model are:
1. large population size (due to statistical constraints, to minimize genetic drift)
XVI.
2.
no migration – no exchange of alleles with other populations (no gene flow)
3.
no mutations of the alleles under study occur
4.
random mating of all genotypes
5.
no natural selection
Microevolution thus can be described as deviation from Hardy-Weinberg equilibrium, where the allele or genotype
frequencies in a population change over time
A. consequences of small population size: genetic drift
1.
Consider taking a small sample of individuals from a larger population. If only two individuals were picked they cannot
reflect the allele frequency in the larger population. Neither can 3, 4, or 5 individuals, but as the selected sample gets
larger it becomes more likely that the sample reflects the allele frequency in the larger population.
2.
genetic drift is a change in gene frequencies of populations because of small population size
3.
genetic drift tends to decrease genetic variation within a population
4.
genetic drift tends to increase genetic variation between populations
5.
two general mechanisms lead to small population sizes

genetic bottlenecks are created by dramatic reduction in population size – endangered species face a genetic
bottleneck on a species-wide scale, and suffer lasting effects even if population size later recovers

founder effect – when a new population is established, typically only a few individuals (founders) are involved in
colonizing the new area; this is common for islands
B. migration – when individuals leave or join a population
1.
migrating individuals carry their alleles with them (gene flow), usually resulting in changes in allele frequencies
2.
gene flow tends to decrease genetic variation between populations
C. mutations increase variation in the gene pool of a species
1.
remember that mutations may be neutral, harmful, or beneficial
2.
even at the risk of harmful effects, mutations are necessary to increase variation in the population so that natural
selection can produce organisms more suited to their environment
D. nonrandom mating
1.
if individuals do not mate at random, then Hardy-Weinberg equilibrium is not achieved
2.
the most common cases of nonrandom mating involve mating between individuals of similar genotypes, either by choice
or location

such inbreeding does not change allele frequencies, but increases the frequency of homozygous genotypes

inbreeding depression is seen in some cases, where inbred individuals have lower fitness that non-inbred individuals

3.

fitness – relative ability of a genotype to contribute to future generations

fertility declines and high juvenile mortality associated with “unmasking” harmful recessive alleles can reduce
fitness for inbred individuals

hybrid vigor also leads to higher relative fitness for hybrids
self-fertilization is the most extreme case of inbreeding
assortive mating – mates are selected by phenotypes

positive assortive mating – selection for the same phenotype; works like inbreeding for the genes governing that
phenotype, and for loci closely linked to those genes

negative assortive mating – selection for the opposite phenotype
 less common than positive assortive mating
 leads to a decrease in homozygous genotypes for the genes governing the selected phenotype, and for loci
closely linked to those genes
E. natural selection changes allele frequencies in a way that leads to adaptation to the environment
1.
fitness is the ability of an organism to compete successfully and pass its alleles on to the next generation
2.
populations undergoing natural selection are evolving, with alleles that contribute to better fitness increasing in
frequency over successive generations
3.
natural selection only operates based on the current environment – as environmental conditions change, different alleles
will be selected for
4.
sexual selection (mate choices based on inherited characteristics) is an aspect of natural selection
5.
there are 3 types of natural selection

stabilizing selection – occurs in populations well adapted to their environments, selecting against phenotypic
extremes
 this is probably the type of selection most commonly faced by populations
 example - human birth weight

directional selection – permits species to adapt to environmental change by favoring selection of one extreme over
the other; example – peppered moth

disruptive selection – when more than one extreme phenotype is favored over intermediate phenotypes
 really a special case of direction selection, where there are trends in more than one direction
 can produce a genetic “split” in a population and thus serve as a mechanism for speciation
 example – pocket mice in New Mexico
XVII. Genetic variation must exist for natural selection to occur
A. the ultimate source of genetic variation is mutations
B. once variation exists, it can be affected by independent assortment and genetic recombination during gamete formation
1. consider the cross AaBb x AaBb – 9 different genotypes arise
2. this involves only 2 alleles at 2 loci; if there were 6 alleles possible at just 5 loci, over 4 million genotypes are possible
3. thus, given that there are thousands of genes in an organism, and that many alleles are possible at most of these loci, it
becomes clear that in nature there is great genetic variability
C. the demonstrated presence of two or more alleles at a given locus is genetic polymorphism
1. biologists have produced tools for studying the genetic polymorphism of populations at the molecular level (RFLP, DNA
sequencing, etc.)
2. these tools can be used to demonstrate and study polymorphism in populations without necessarily knowing the specific
genes involved
D. genetic polymorphisms can be maintained by heterozygote advantage or hybrid vigor
1. when either the homozygous dominant or recessive is more suited to an environment than the heterozygote, the
homozygous genotype will be more likely to be fixed in the population
2. but when heterozygous genotypes have advantage over either of the homozygous genotypes, variation tends to increase
in the population
3. example - sickle cell anemia and malaria resistance
E. genetic polymorphisms can be maintained due to frequency-dependent selection
1. there are cases where the frequency of a given genotype affects the degree to which it is or isn't selected in the
population
2. example - predator/prey relationships, where individuals with a rare phenotype may be ignored by a predator, but as they
become more abundant the selective advantage decreases because the predator is more likely to notice them
F.
much of the genetic variation in a population will produce no selective advantage, i.e. it is neutral
1. the role of neutral variation in evolution is debated today
2. remember that what is neutral in one context may not be neutral in another context, so as environments change some
previously neutral variation may be acted on by natural selection
Chapter 24: The Origin of Species (Macroevolution)
I.
Macroevolution is essentially the formation of new species (speciation) and accompanying events
A. species: “Kind of living thing”; the word “species” is both plural and singular
B. relatively easy to define for sexual organisms, hard for asexual organisms and extinct species
1. biological species concept (for sexual organisms)
 a species is one or more populations whose members are capable of interbreeding and producing fertile offspring,
and whose members are reproductively isolated from other such groups
 not always clear-cut, because some can interbreed under “artificial” conditions but don’t appear to do so in nature
 sometimes, “race” and “subspecies” designations are used, but often different specific epithets are used when there
are clear morphological differences involved
2. asexual species – definition based on biochemical (think DNA sequence) and morphological differences; no solid rules
 also includes use of “race,” “subspecies,” and “strain” designations
 in asexual species, microevolution over time directly leads to macroevolution (speciation)
phylogenetic species concept or evolutionary species concept
 a species is a single line of descent (lineage with a unique genetic history) that maintains its distinctive identity from
other lineages
 this is a more comprehensive concepts (it works for both sexual and asexual species)
 but, it can be hard to clearly define and agree upon “distinctive identity”
C. the basis of macroevolution in sexual species is microevolution coupled with reproductive isolation
II. Reproductive isolation can occur in a variety of ways
A. reproductive isolation is any means of preventing gene flow between two species; for a new species to evolve from an
existing (sexually reproducing) species, there must be a reproductive isolating mechanism in place
B. reproductive isolating mechanisms can be classified as either prezygotic or postzygotic
1. prezygotic barriers – prevent fertilization (zygote formation) between gametes from two species
 habitat isolation (or ecological isolation) – isolation by differences in habitat occupied at the time of mating;
examples: some garter snakes; some flycatchers
 temporal isolation – isolation by differences in timing of mating; examples: mating seasons in some skunks;
flowering time in some plants; mating time in some fruit flies
 behavioral isolation – differences in behavior that cause reproductive isolation; examples: mating calls, courtship
patterns, and other mating rituals; can be an aspect of sexual selection (selective pressure that comes from
mating choices)
 mechanical isolation – differences in physical aspects make successful mating impossible; examples: many flower
species; dragonflies may attempt interspecies mating, but the physical structure of their genitalia prevents
successful mating
 gametic isolation – mating occurs, but the sperm and egg can not fuse; examples: sperm cannot penetrate the egg of
the different species, such as between sea urchins species, as well as in many other animal species; in plants,
often pollen grains do not get the proper signal to germinate when on a stigma of a different species
2. postzygotic barriers – reproductive isolation after fertilization has occurred
 hybrid inviability – (the most common type of postzygotic barrier) normal development of the zygote formed from
the mating of two species does not occur and the embryo is aborted, or if development is completed the offspring
is very frail; examples: crosses between different iris species, cross between bullfrog and leopard frog; crosses
between some salamander subspecies
 hybrid sterility – a zygote of a hybrid proceeds through normal development, but is reproductively sterile
 sometimes due to other barriers such as behavioral isolation (don’t make the right mating call, etc.)
 most often due to problems in meiosis (example: male donkey [n=31] x female horse [n=32] generates sterile
mule [2n=63, not an even number, pairing problems during meiosis])
 hybrid breakdown – a zygote of a hybrid proceeds through normal development, and the interspecific hybrid
reproduces, but the F2 generation and beyond have problems with reproduction; examples: crosses between
sunflower species result in 80% hybrid breakdown in the F 2 generation; crosses between some rice strains
C. the genetic basis for some reproductive barriers have been identified (the basis will vary depending on the species involved)
III. Reproductive isolation is the key to cladogenic speciation
A. speciation (the evolution of new species) has two general forms, anagenic and cladogenic
B. anagenic speciation is the gradual change of one species into a new form, with the “new” species form replacing the “old”
form; this is essentially microevolution on the whole species level – the number of species does not change
C. cladogenic speciation, or branching evolution, occurs when two or more species are present where only one existed before;
these species share a common ancestor
1. a cluster of species that share a common ancestor is a clade
2. cladogenic speciation increases the number of species
3. two separate species are said to diverge from the point where they shared a common ancestor – the gene pools of these
species are separated from the point of divergence on
D. cladogenic speciation occurs when a population is different enough from its ancestral species so that no genetic exchange can
occur between them
1. the appearance of a reproductive isolating mechanism produces two or more species where once there was one
2. The question of macroevolution becomes, what creates reproductive isolation?
3. there is no easy way to define when cladogenic speciation is complete – often some level of hybridization can persist
when there is essentially no gene flow between the “species” or “subspecies” involved
IV. Cladogenic speciation has two modes: allopatric speciation and sympatric speciation
A. allopatric speciation – one population becomes geographically separated from the rest of the species
1. the separated population encounters different selective pressures from the rest of the species, and also is usually
subjected to a genetic bottleneck (thus its gene pool changes due to genetic drift)
2. after a long period of time, the population has diverged enough from the parent species that it is reproductively isolated
from the parent species if they come in contact
3. likely the most common means of cladogenic speciation
3.
4.
examples of mechanisms for geographic isolation: founders on an island, rivers shifting course, glaciation, land bridge
appearance and removal, mountain formation
B. sympatric speciation – a species achieves reproductive isolation and evolves in the same geographic location as its ancestral
species
1. polyploidy (extra sets of chromosomes) is a major factor in sympatric speciation in plants
 autopolypoidy – multiple sets from one parent species; example – plants around Agent Orange sites
 hybridization + allopolyploidy – closely related species produce a hybrid that must double its chromosome number
to reproduce successfully; a new, viable hybrid species is thus formed
2. disruptive selection – when disruptive selection occurs, hybrids are selected against
 there is thus strong selective pressure for the development of reproductive isolation mechanisms
 example – food preference specializations in Lake Victoria cichlids (over 500 species, likely rapid speciation from a
common ancestor less than 13,000 years ago)
C. adaptive radiation (rapid production of many species from a common ancestor) is most easily produced by a combination of
allopatric speciation and sympatric speciation
1. pioneers on an island, or pioneering fish in Lake Victoria, are separated from their ancestral species allopatrically
2. the presence of a variety of open ecological niches in such regions also gives ample opportunity for sympatric speciation
by disruptive selection
3. groups of species that derived by adaptive radiation, like the Lake Victoria cichlids, Galapagos finches, Hawaiian
Drosophila , and Hawaiian silverswords, thus experience sympatric and allopatric speciation simultaneously
V. Macroevolution involves both rapid and gradual divergence
A. Darwin's original theory suggested that evolution occurs gradually (gradualism model)
1. there is some fossil evidence for this, but in many cases there is a lack of transitional forms
2. the fossil record by its very nature is incomplete, which would explain some of the lack of transitional forms, but there is
an alternative: punctuated equilibrium
B. punctuated equilibrium theory states that evolutionary change can be rapid, and that this rapidity explains much of the lack
of transitional forms in the fossil record
1. rapid change means that the transitional forms are around for only a short time (on the order of thousands of years), and
thus are far less likely to be preserved as fossils
2. between periods of rapid change are long periods of relative stasis, with little evolutionary change and thus little change
in form; these long periods (on the order of millions of years) greatly increase the likelihood of such forms being
preserved as fossils
3. first advanced by Stephen Jay Gould and Niles Eldredge in 1972
4. note that "rapid" evolution still takes thousands of years, which in geological time is a relatively short period, but is long
in human terms
C. both gradualism and punctuated equilibrium have the same underlying mechanisms (reproductive isolation and genetic
divergence); they differ in the rate of genetic divergence predicted
D. there is abundant fossil evidence for both gradualism and punctuated equilibrium; apparently both modes can occur,
depending on the situation
E. biologists disagree about the relative importance of gradualism and punctuated equilibrium in evolution, and the clarity of
distinction between the two
Chapter 24: The Origin of Species (Macroevolution)
83.
Discuss the biological species concept, including its limitations.
84.
Discuss the phylogenetic or evolutionary species concept, including its limitations.
85. Explain what a reproductive isolating mechanism (RIM) is and the difference
between prezygotic and postzygotic barriers.
86.
Define and give an example of each of the 8 RIMs covered in the notes.
87.
Explain the difference between anagenic and cladogenic speciation.
88.
Explain the difference between allopatric and sympatric speciation.
89. What is adaptive radiation, and how can it be an example of both allopatric and
sympatric speciation?
90.
What is the difference between punctuated equilibrium and gradualism?
VI. Macroevolution is essentially the formation of new species (speciation) and accompanying events
A. species: “Kind of living thing”; the word “species” is both plural and singular
B. relatively easy to define for sexual organisms, hard for asexual organisms and extinct species
1.
biological species concept (for sexual organisms)

a species is one or more populations whose members are capable of interbreeding and producing fertile offspring,
and whose members are reproductively isolated from other such groups

not always clear-cut, because some can interbreed under “artificial” conditions but don’t appear to do so in nature

sometimes, “race” and “subspecies” designations are used, but often different specific epithets are used when there
are clear morphological differences involved
2.
3.
asexual species – definition based on biochemical (think DNA sequence) and morphological differences; no solid rules

also includes use of “race,” “subspecies,” and “strain” designations

in asexual species, microevolution over time directly leads to macroevolution (speciation)
phylogenetic species concept or evolutionary species concept

a species is a single line of descent (lineage with a unique genetic history) that maintains its distinctive identity from
other lineages

this is a more comprehensive concepts (it works for both sexual and asexual species)

but, it can be hard to clearly define and agree upon “distinctive identity”
C. the basis of macroevolution in sexual species is microevolution coupled with reproductive isolation
VII. Reproductive isolation can occur in a variety of ways
A. reproductive isolation is any means of preventing gene flow between two species; for a new species to evolve from an
existing (sexually reproducing) species, there must be a reproductive isolating mechanism in place
B. reproductive isolating mechanisms can be classified as either prezygotic or postzygotic
1.
prezygotic barriers – prevent fertilization (zygote formation) between gametes from two species

habitat isolation (or ecological isolation) – isolation by differences in habitat occupied at the time of mating;
examples: some garter snakes; some flycatchers

temporal isolation – isolation by differences in timing of mating; examples: mating seasons in some skunks;
flowering time in some plants; mating time in some fruit flies

behavioral isolation – differences in behavior that cause reproductive isolation; examples: mating calls, courtship
patterns, and other mating rituals; can be an aspect of sexual selection (selective pressure that comes from
mating choices)

mechanical isolation – differences in physical aspects make successful mating impossible; examples: many flower
species; dragonflies may attempt interspecies mating, but the physical structure of their genitalia prevents
successful mating

gametic isolation – mating occurs, but the sperm and egg can not fuse; examples: sperm cannot penetrate the egg of
the different species, such as between sea urchins species, as well as in many other animal species; in plants,
often pollen grains do not get the proper signal to germinate when on a stigma of a different species
2.
postzygotic barriers – reproductive isolation after fertilization has occurred

hybrid inviability – (the most common type of postzygotic barrier) normal development of the zygote formed from
the mating of two species does not occur and the embryo is aborted, or if development is completed the offspring
is very frail; examples: crosses between different iris species, cross between bullfrog and leopard frog; crosses
between some salamander subspecies

hybrid sterility – a zygote of a hybrid proceeds through normal development, but is reproductively sterile

sometimes due to other barriers such as behavioral isolation (don’t make the right mating call, etc.)

most often due to problems in meiosis (example: male donkey [n=31] x female horse [n=32] generates sterile
mule [2n=63, not an even number, pairing problems during meiosis])

hybrid breakdown – a zygote of a hybrid proceeds through normal development, and the interspecific hybrid
reproduces, but the F2 generation and beyond have problems with reproduction; examples: crosses between
sunflower species result in 80% hybrid breakdown in the F 2 generation; crosses between some rice strains
C. the genetic basis for some reproductive barriers have been identified (the basis will vary depending on the species involved)
VIII.
Reproductive isolation is the key to cladogenic speciation
A. speciation (the evolution of new species) has two general forms, anagenic and cladogenic
B. anagenic speciation is the gradual change of one species into a new form, with the “new” species form replacing the “old”
form; this is essentially microevolution on the whole species level – the number of species does not change
C. cladogenic speciation, or branching evolution, occurs when two or more species are present where only one existed before;
these species share a common ancestor
1.
a cluster of species that share a common ancestor is a clade
2.
cladogenic speciation increases the number of species
3.
two separate species are said to diverge from the point where they shared a common ancestor – the gene pools of these
species are separated from the point of divergence on
D. cladogenic speciation occurs when a population is different enough from its ancestral species so that no genetic exchange can
occur between them
1.
the appearance of a reproductive isolating mechanism produces two or more species where once there was one
2.
The question of macroevolution becomes, what creates reproductive isolation?
3.
there is no easy way to define when cladogenic speciation is complete – often some level of hybridization can persist
when there is essentially no gene flow between the “species” or “subspecies” involved
IX. Cladogenic speciation has two modes: allopatric speciation and sympatric speciation
A. allopatric speciation – one population becomes geographically separated from the rest of the species
1.
the separated population encounters different selective pressures from the rest of the species, and also is usually
subjected to a genetic bottleneck (thus its gene pool changes due to genetic drift)
2.
after a long period of time, the population has diverged enough from the parent species that it is reproductively isolated
from the parent species if they come in contact
3.
likely the most common means of cladogenic speciation
4.
examples of mechanisms for geographic isolation: founders on an island, rivers shifting course, glaciation, land bridge
appearance and removal, mountain formation
B. sympatric speciation – a species achieves reproductive isolation and evolves in the same geographic location as its ancestral
species
1.
polyploidy (extra sets of chromosomes) is a major factor in sympatric speciation in plants

autopolypoidy – multiple sets from one parent species; example – plants around Agent Orange sites

hybridization + allopolyploidy – closely related species produce a hybrid that must double its chromosome number
to reproduce successfully; a new, viable hybrid species is thus formed
2.
disruptive selection – when disruptive selection occurs, hybrids are selected against

there is thus strong selective pressure for the development of reproductive isolation mechanisms

example – food preference specializations in Lake Victoria cichlids (over 500 species, likely rapid speciation from a
common ancestor less than 13,000 years ago)
C. adaptive radiation (rapid production of many species from a common ancestor) is most easily produced by a combination of
allopatric speciation and sympatric speciation
1.
pioneers on an island, or pioneering fish in Lake Victoria, are separated from their ancestral species allopatrically
2.
the presence of a variety of open ecological niches in such regions also gives ample opportunity for sympatric speciation
by disruptive selection
3.
groups of species that derived by adaptive radiation, like the Lake Victoria cichlids, Galapagos finches, Hawaiian
Drosophila , and Hawaiian silverswords, thus experience sympatric and allopatric speciation simultaneously
X. Macroevolution involves both rapid and gradual divergence
A. Darwin's original theory suggested that evolution occurs gradually (gradualism model)
1.
there is some fossil evidence for this, but in many cases there is a lack of transitional forms
2.
the fossil record by its very nature is incomplete, which would explain some of the lack of transitional forms, but there is
an alternative: punctuated equilibrium
B. punctuated equilibrium theory states that evolutionary change can be rapid, and that this rapidity explains much of the lack
of transitional forms in the fossil record
1.
rapid change means that the transitional forms are around for only a short time (on the order of thousands of years), and
thus are far less likely to be preserved as fossils
2.
between periods of rapid change are long periods of relative stasis, with little evolutionary change and thus little change
in form; these long periods (on the order of millions of years) greatly increase the likelihood of such forms being
preserved as fossils
3.
first advanced by Stephen Jay Gould and Niles Eldredge in 1972
4.
note that "rapid" evolution still takes thousands of years, which in geological time is a relatively short period, but is long
in human terms
C. both gradualism and punctuated equilibrium have the same underlying mechanisms (reproductive isolation and genetic
divergence); they differ in the rate of genetic divergence predicted
D. there is abundant fossil evidence for both gradualism and punctuated equilibrium; apparently both modes can occur,
depending on the situation
E. biologists disagree about the relative importance of gradualism and punctuated equilibrium in evolution, and the clarity of
distinction between the two
Chapter 25: The Origin and Evolutionary History of Life on Earth
91. What is the best current estimate of the age of the Earth, and what is the evidence
for that estimate?
92.
What are considered to be the four requirements for life to begin on Earth?
93. Describe the contributions of Oparin and Haldane and of Miller and Urey to models
of the origin of life on Earth.
94.
Briefly discuss at least three different models for how life began on Earth.
95. What are protobionts and microspheres, and what does their existence imply about
how cellular life began?
96.
Explain the RNA world hypothesis and how in vitro evolution tests it.
97.
What are microfossils, and to what age to the oldest ones found on Earth date?
98.
What are stromatolites?
99.
What are banded iron formations, and why are they important?
100. When did oxygenation of Earth’s atmosphere occur, and what were the key
consequences of it?
101. When do eukaryotic cells appear in the fossil record?
102. When was Precambrian time and what were the major events during that time
period?
103. For each of the “big five” mass extinctions, give when they occurred, their likely
causes if known, and key consequences of them.
104. Outline the relative history, dominant organisms, and key events of each of the
periods of the Paleozoic, Mesozoic, and Cenozoic eras.
105. What is the sixth extinction?
Chapter 25: The Origin and Evolutionary History of Life on Earth
I.
Chemical conditions of the early Earth that could have fostered the origin of life
A. the Earth is about 4.6 billion years old (time of the first likely solid surface)
1.
supported by radioisotope dating of
 oldest known Earth minerals (date to 4.4 billion years ago, or 4.4 bya)
 oldest known rocks on Earth (4.1 bya)
 oldest known meteorites (4.6 bya; for the age of the solar system)
2.
some models go out to 6 billion years, it is hard make a rule for a definitive starting point of planet formation
B. Earth’s early atmosphere (when life first appears in the fossil record) most likely consisted of CO 2, H2O, CO, H2, N2, and
small amounts of NH3, H2S, and CH4 – note the lack of O2, which is a major constituent of today’s atmosphere
C. Four requirements for the current chemical evolution model were likely met in the early Earth
1.
little or no free oxygen
2.
abundant energy sources (volcanism, thunderstorms, and bombardment with particles and radiation from space were all
likely present as energy sources; especially important is more UV radiation than today)
 the sun was hotter, producing more UV light
 the Earth had no ozone layer to filter out most of the UV light coming in
3.
chemical building blocks of water, dissolved mineral ions, and atmospheric gases
4.
time (there was plenty of time before the first traces of life from 3.8 bya])
D. attempts to mimic the early Earth’s atmosphere and chemical profile have led to production of organic molecules from
simpler materials after energy is added
1.
1920s – Oparin and Haldane independently proposed that organic molecules could form spontaneously from simpler raw
materials when sufficient energy is supplied in a reducing (energy-rich, electron-adding) environment
2.
1950s – Miller and Urey made a “reducing atmosphere” of H2O, H2, NH3, CH4 in a spark chamber; after sparking, they
found that amino acids and other organic compounds had formed
3.

designed to mimic what was thought at the time to have been Earth’s early atmosphere

later experiments with different “reducing atmospheres” that were thought to be better matches to the likely
atmosphere of the early Earth produced all 20 amino acids used in proteins, various sugars and lipids, and
components of DNA and RNA nucleotides

current models of the Earth’s early atmosphere are that in general the atmosphere was not reducing, but that there
were likely many local environments that were reducing – especially near volcanic activity
organic polymers can form spontaneously from monomer building blocks on some sand, clay, or rock surfaces
E. there are several models for exactly where and how life as we know it on Earth began
1.
prebiotic broth hypothesis – life began from an “organic soup” in the oceans
2.
bubble hypothesis – a variation on the prebiotic broth, with “oily bubbles” from an organic soup interacting with land
surfaces at shallow seas or seashores
3.
4.
iron-sulfur world hypothesis – life began from an “organic soup” interacting with mineral surfaces at hydrothermal
vents in the ocean floor, with abundant iron and sulfur there impacting the early metabolism that developed
deep-hot biosphere hypothesis – life began in an “organic soup” deep within the Earth
5.
exogenesis – Earth was seeded with life from an extraterrestrial source
II. A model for how the first cells could have originated and functioned
A. protobionts have been produced that resemble living cells
1.
microspheres, a type of protobiont, form spontaneously when liquid water is added to abiotically produced polypeptides
2.
microspheres can grow, divide, and maintain internal chemistry different from their surroundings
3.
microspheres show that some spontaneous production and maintenance of organization is possible, but are incomplete as
a model for formation of the first cells
B. genetic reproduction was crucial in the origin of true cells
1.
2.
RNA likely was first (RNA world hypothesis)

RNA can catalyze a variety of reactions, including some self-catalytic reactions

RNA can also store genetic information

in vitro evolution of RNA has shown that the RNA world hypothesis is feasible – selection can act on selfreplicating RNA molecules in vitro
DNA likely came later and had the selective advantage of greater stability
III. First life, however it came to be (or, Enough theory, Dr. Bowling, give me some dates to learn for the test!)
A. the first evidence of life in the fossil record are isotopic carbon “fingerprints” in rocks from ~3.8 bya
B. the first evidence of cells are microfossils of prokaryotic cells in fossils of stromatolites dated to ~3.5 bya
1. stromatolites are rocklike structures made up of layers of bacteria and sediment
2. in some areas stromatolites are still being formed today
C. the first cells were most likely anaerobic heterotrophs
1. there was likely an abundance of organic molecules available for food early on
2. later, as organic molecules became scarcer, photosynthetic organisms were favored
D. the first photosynthetic organisms were likely the purple and green sulfur bacteria, which use H 2S as a hydrogen donor
IV. Life changes the planet: oxygenating Earth’s oceans and atmosphere
A. cyanobacteria were likely the first photosynthetic organisms to use H 2O as a hydrogen donor, releasing O2 into the
environment
1. stromatolites from as old as 3.5 bya containing what appear to be fossil cyanobacteria
2. many stromatolites with what appear to by fossil cyanobacteria date to about 2.5 bya
B. banded iron formations from about 2.5 bya indicate the release of O2 into the oceans
C. by 2 bya, O2 levels began to build up in the atmosphere
D. the presence of O2 had a profound impact on life on Earth
1. O2 is toxic to organisms that don’t have protective mechanisms; many died as O 2 levels built up
 creates an oxidizing atmosphere, which can destroy precious reduced organic molecules
 some anaerobic organisms survive (even today) only in environments with little to no oxygen
 some evolved adaptations to the presence of oxygen
 some organisms developed means to use O2 in respiration to extract more energy from foods (aerobic respiration)
2.
the formation of the ozone layer (O3) soon after oxygenation of the atmosphere provided protection from UV radiation
and allowed life to expand to regions at and near the Earth’s surface
V. Eukaryotic cells descended from prokaryotic cells
A. eukaryotes first appear in the fossil record about 2 bya, long after prokaryotic cells
B. DNA sequencing provides evidence of common ancestry of life on Earth, with eukaryotes splitting from Archaea about 2 bya
C. recall the endosymbiotic theory – model for how at least some of the eukaryotic cell organelles came to exist
VI. History of life on Earth (organized by divisions of geological time)
A. basis for the divisions
1. divisions of geological time are based major changes in types of organisms found in the fossil record (each division has
its own characteristic set of commonly found fossils and unique fossil forms)
2. many of the transitions between the divisions are marked by major extinction events, where many organisms apparently
died out over a short period of time because they disappear form the fossil record from that point on
3. although there are many major extinction events in the fossil record, by most measures five stand out above the rest; you
need to know these “big five” mass extinction events
B. Precambrian time, from 4.6 bya up to 542 million years ago (mya); the fossil record is very spotty prior to 542 mya
1. we have already covered some of the major events of that time period (origin of life, oxygenation of the oceans and
atmosphere)
2. Snowball Earth??? 800 mya – 635 mya
3. ended with the Ediacaran Period (635-542 mya), which is widely recognized as having the oldest animal fossils
C. Paleozoic era (542-251 mya)
1. Cambrian period (542-488 mya)
 Cambrian explosion - fossils of multicellular organisms are abundant in this period
 all contemporary animal phyla are represented in Cambrian fossils, as well as many extinct groups
 this is the biggest expansion in diversity found in the fossil record
 Burgess shale – most famous example of Cambrian fossils
2.
Ordovician period (488-444 mya)
 abundant numbers and diversification of trilobites, brachiopods, and molluscs
 first coral reefs
 first terrestrial plants
 Ordovician period ended in a mass extinction event (1st of the big five)
 likely due to an ice age, perhaps in conjunction with a gamma ray burst
 decimated the trilobites and brachiopods, along with many other groups of marine organisms
3.
Silurian period (444-416 mya) – first vascular plants; first true terrestrial animals
4.
Devonian period (416-359 mya) – jawed fishes, amphibians, insects, and vascular plants first appear; jawed fishes
diversify and dominate the seas (Age of Fishes), and vascular plants diversify and dominant the land
 Devonian period ended in a mass extinction event (2nd of the big five)
5.
Carboniferous period (359-299 mya) – reptiles first appear; amphibians diversify and are the dominant terrestrial
carnivores (Age of Amphibians); most of today’s major coal deposits are the remains of organisms that lived in this
period
6.
Permian period (299-251 mya) – by the end of this period, the continents have merged as the Pangaea supercontinent
7.
the era ended (251 mya) with a mass extinction event (3rd of the big five)
 the largest mass extinction on record
 more than 90% of the marine species and 70% of land vertebrates that are in the fossil record at the end of the
Permian never appear in the fossil record again
 the mass extinction event apparently took place in a time span of only a few hundred thousand years, which is fast in
the geological time scale
D. Mesozoic era (251-65 mya)
1. diversification and dominance by reptiles – the whole era is often called the Age of Reptiles (sometime called the Age of
Dinosaurs, many non-dinosaur reptiles were prominent)
2.
Triassic period (251-200 mya)
 dinosaurs and mammals first appear
 gynmnosperms are the dominant land plants

ended with a mass extinction event (4th of the big five) that paved the way for the dinosaurs to rise to prominence
3.
Jurassic period (200-146 mya)
 dinosaurs dominate the land (and other large reptiles dominate the seas and the skies)
 birds evolve from a dinosaur lineage
4.
Cretaceous period (146-65 mya)
 flowering plants evolved around the early Cretaceous and diversified quickly
 many animals (especially insects) appear to have coevolved with flowering plants (different species affecting each
other’s evolution)
5.
the era ended (65 mya) with a mass extinction event (5th of the big five)
 dinosaurs essentially all died out (unless you count birds as dinosaurs, which some scientists do)
 most gymnosperms also died out, as did many marine organisms
 evidence points to the impact of a large extraterrestrial body as a likely cause of the extinction event
 a major impact almost certainly occurred at this time; iridium layers worldwide and deposits from tsunamis
around the Gulf of Mexico coast of the time provide clear evidence of this
 a large crater site (Chicxulub crater) in the Yucatán Peninsula of Mexico is likely the result of this impact
 the extent to which such an impact could affect the biosphere is still debated, but is accepted by more and more
scientists as at least a contributing factor to this massive extinction event
E. Cenozoic era (65 mya – present)
1. usually called the Age of Mammals, but birds, insects, and flowering plants have also undergone massive diversification
and have all achieved some measure of “dominance” in the biosphere during this era
2.
two periods, Paleogene (65-23 mya) and the Neogene (23 mya – present), although an older division into Tertiary (65~2 mya) and Quaternary (~2 mya – present) is still often referred to
3.
the Neogene has been marked by many ice ages, the rise of humans, and mass extinctions; most of these mass extinctions
may have been caused by the ice age climate, humans, or both; the current mass extinction event (we are in one
now, the sixth extinction) is mostly caused by humans
Chapter 26: The Tree of Life
VII. Chemical conditions of the early Earth that could have fostered the origin of life
A. the Earth is about 4.6 billion years old (time of the first likely solid surface)
1. supported by radioisotope dating of
 oldest known Earth minerals (date to 4.4 billion years ago, or 4.4 bya)
 oldest known rocks on Earth (4.1 bya)
 oldest known meteorites (4.6 bya; for the age of the solar system)
2. some models go out to 6 billion years, it is hard make a rule for a definitive starting point of planet formation
B. Earth’s early atmosphere (when life first appears in the fossil record) most likely consisted of CO 2, H2O, CO, H2, N2, and
small amounts of NH3, H2S, and CH4 – note the lack of O2, which is a major constituent of today’s atmosphere
C. Four requirements for the current chemical evolution model were likely met in the early Earth
1. little or no free oxygen
2. abundant energy sources (volcanism, thunderstorms, and bombardment with particles and radiation from space were all
likely present as energy sources; especially important is more UV radiation than today)
 the sun was hotter, producing more UV light
 the Earth had no ozone layer to filter out most of the UV light coming in
3. chemical building blocks of water, dissolved mineral ions, and atmospheric gases
4. time (there was plenty of time before the first traces of life from 3.8 bya])
D. attempts to mimic the early Earth’s atmosphere and chemical profile have led to production of organic molecules from
simpler materials after energy is added
1. 1920s – Oparin and Haldane independently proposed that organic molecules could form spontaneously from simpler raw
materials when sufficient energy is supplied in a reducing (energy-rich, electron-adding) environment
2. 1950s – Miller and Urey made a “reducing atmosphere” of H2O, H2, NH3, CH4 in a spark chamber; after sparking, they
found that amino acids and other organic compounds had formed
 designed to mimic what was thought at the time to have been Earth’s early atmosphere
 later experiments with different “reducing atmospheres” that were thought to be better matches to the likely
atmosphere of the early Earth produced all 20 amino acids used in proteins, various sugars and lipids, and
components of DNA and RNA nucleotides

current models of the Earth’s early atmosphere are that in general the atmosphere was not reducing, but that there
were likely many local environments that were reducing – especially near volcanic activity
3. organic polymers can form spontaneously from monomer building blocks on some sand, clay, or rock surfaces
E. there are several models for exactly where and how life as we know it on Earth began
1. prebiotic broth hypothesis – life began from an “organic soup” in the oceans
2. bubble hypothesis – a variation on the prebiotic broth, with “oily bubbles” from an organic soup interacting with land
surfaces at shallow seas or seashores
3. iron-sulfur world hypothesis – life began from an “organic soup” interacting with mineral surfaces at hydrothermal
vents in the ocean floor, with abundant iron and sulfur there impacting the early metabolism that developed
4. deep-hot biosphere hypothesis – life began in an “organic soup” deep within the Earth
5. exogenesis – Earth was seeded with life from an extraterrestrial source
VIII. A model for how the first cells could have originated and functioned
A. protobionts have been produced that resemble living cells
1. microspheres, a type of protobiont, form spontaneously when liquid water is added to abiotically produced polypeptides
2. microspheres can grow, divide, and maintain internal chemistry different from their surroundings
3. microspheres show that some spontaneous production and maintenance of organization is possible, but are incomplete as
a model for formation of the first cells
B. genetic reproduction was crucial in the origin of true cells
1. RNA likely was first (RNA world hypothesis)
 RNA can catalyze a variety of reactions, including some self-catalytic reactions
 RNA can also store genetic information
 in vitro evolution of RNA has shown that the RNA world hypothesis is feasible – selection can act on selfreplicating RNA molecules in vitro
2. DNA likely came later and had the selective advantage of greater stability
IX. First life, however it came to be (or, Enough theory, Dr. Bowling, give me some dates to learn for the test!)
A. the first evidence of life in the fossil record are isotopic carbon “fingerprints” in rocks from ~3.8 bya
B. the first evidence of cells are microfossils of prokaryotic cells in fossils of stromatolites dated to ~3.5 bya
1. stromatolites are rocklike structures made up of layers of bacteria and sediment
2. in some areas stromatolites are still being formed today
C. the first cells were most likely anaerobic heterotrophs
1. there was likely an abundance of organic molecules available for food early on
2. later, as organic molecules became scarcer, photosynthetic organisms were favored
D. the first photosynthetic organisms were likely the purple and green sulfur bacteria, which use H2S as a hydrogen donor
X. Life changes the planet: oxygenating Earth’s oceans and atmosphere
A. cyanobacteria were likely the first photosynthetic organisms to use H 2O as a hydrogen donor, releasing O2 into the
environment
1. stromatolites from as old as 3.5 bya containing what appear to be fossil cyanobacteria
2. many stromatolites with what appear to by fossil cyanobacteria date to about 2.5 bya
B. banded iron formations from about 2.5 bya indicate the release of O2 into the oceans
C. by 2 bya, O2 levels began to build up in the atmosphere
D. the presence of O2 had a profound impact on life on Earth
1. O2 is toxic to organisms that don’t have protective mechanisms; many died as O 2 levels built up
 creates an oxidizing atmosphere, which can destroy precious reduced organic molecules
 some anaerobic organisms survive (even today) only in environments with little to no oxygen
 some evolved adaptations to the presence of oxygen
 some organisms developed means to use O2 in respiration to extract more energy from foods (aerobic respiration)
2. the formation of the ozone layer (O3) soon after oxygenation of the atmosphere provided protection from UV radiation
and allowed life to expand to regions at and near the Earth’s surface
XI. Eukaryotic cells descended from prokaryotic cells
A. eukaryotes first appear in the fossil record about 2 bya, long after prokaryotic cells
B. DNA sequencing provides evidence of common ancestry of life on Earth, with eukaryotes splitting from Archaea about 2 bya
C. recall the endosymbiotic theory – model for how at least some of the eukaryotic cell organelles came to exist
XII. History of life on Earth (organized by divisions of geological time)
A. basis for the divisions
1. divisions of geological time are based major changes in types of organisms found in the fossil record (each division has
its own characteristic set of commonly found fossils and unique fossil forms)
2.
B.
C.
D.
E.
many of the transitions between the divisions are marked by major extinction events, where many organisms apparently
died out over a short period of time because they disappear form the fossil record from that point on
3. although there are many major extinction events in the fossil record, by most measures five stand out above the rest; you
need to know these “big five” mass extinction events
Precambrian time, from 4.6 bya up to 542 million years ago (mya); the fossil record is very spotty prior to 542 mya
1. we have already covered some of the major events of that time period (origin of life, oxygenation of the oceans and
atmosphere)
Paleozoic era (542-251 mya)
1. Cambrian period (542-488 mya)
 Cambrian explosion - fossils of multicellular organisms are abundant in this period
 all contemporary animal phyla are represented in Cambrian fossils, as well as many extinct groups
 this is the biggest expansion in diversity found in the fossil record
2. Ordovician period (488-444 mya)
 abundant numbers and diversification of trilobites, brachiopods, and molluscs
 first coral reefs
 first terrestrial plants
 Ordovician period ended in a mass extinction event (1st of the big five)
 likely due to an ice age, perhaps in conjunction with a gamma ray burst
 decimated the trilobites and brachiopods, along with many other groups of marine organisms
3. Silurian period (444-416 mya) – first vascular plants; first true terrestrial animals
4. Devonian period (416-359 mya) – jawed fishes, amphibians, insects, and vascular plants first appear; jawed fishes
diversify and dominate the seas (Age of Fishes), and vascular plants diversify and dominant the land
 Devonian period ended in a mass extinction event (2nd of the big five)
5. Carboniferous period (359-299 mya) – reptiles first appear; amphibians diversify and are the dominant terrestrial
carnivores (Age of Amphibians); most of today’s major coal deposits are the remains of organisms that lived in this
period
6. Permian period (299-251 mya) – by the end of this period, the continents have merged as the Pangaea supercontinent
7. the era ended (251 mya) with a mass extinction event (3rd of the big five)
 the largest mass extinction on record
 more than 90% of the marine species and 70% of land vertebrates that are in the fossil record at the end of the
Permian never appear in the fossil record again
 the mass extinction event apparently took place in a time span of only a few hundred thousand years, which is fast in
the geological time scale
Mesozoic era (251-65 mya)
1. diversification and dominance by reptiles – the whole era is often called the Age of Reptiles (sometime called the Age of
Dinosaurs, many non-dinosaur reptiles were prominent)
2. Triassic period (251-200 mya)
 dinosaurs and mammals first appear
 gynmnosperms are the dominant land plants
 ended with a mass extinction event (4th of the big five) that paved the way for the dinosaurs to rise to prominence
3. Jurassic period (200-146 mya)
 dinosaurs dominate the land (and other large reptiles dominate the seas and the skies)
 birds evolve from a dinosaur lineage
4. Cretaceous period (146-65 mya)
 flowering plants evolved around the early Cretaceous and diversified quickly
 many animals (especially insects) appear to have coevolved with flowering plants (different species affecting each
other’s evolution)
5. the era ended (65 mya) with a mass extinction event (5th of the big five)
 dinosaurs essentially all died out (unless you count birds as dinosaurs, which some scientists do)
 most gymnosperms also died out, as did many marine organisms
 evidence points to the impact of a large extraterrestrial body as a likely cause of the extinction event
 a major impact almost certainly occurred at this time; iridium layers worldwide and deposits from tsunamis
around the Gulf of Mexico coast of the time provide clear evidence of this
 a large crater site (Chicxulub crater) in the Yucatán Peninsula of Mexico is likely the result of this impact
 the extent to which such an impact could affect the biosphere is still debated, but is accepted by more and more
scientists as at least a contributing factor to this massive extinction event
Cenozoic era (65 mya – present)
1. usually called the Age of Mammals, but birds, insects, and flowering plants have also undergone massive diversification
and have all achieved some measure of “dominance” in the biosphere during this era
2. two periods, Paleogene (65-23 mya) and the Neogene (23 mya – present), although an older division into Tertiary (65~2 mya) and Quaternary (~2 mya – present) is still often referred to
3.
the Neogene has been marked by many ice ages, the rise of humans, and mass extinctions; most of these mass extinctions
may have been caused by the ice age climate, humans, or both; the current mass extinction event is mostly caused
by humans
Ecology
XIII.
What is ecology?
A. Ecology is the scientific study of interactions between ___________
1. term ecology comes from the Greek oikos, _______, and logos, to study
B. biotic and abiotic factors
1. What are biotic factors? Give examples.
2. What are abiotic factors? Give examples.
C. climate
1. What is climate?
2. What abiotic factors are the major components of climate?
3. What effects do bodies of water have on climate?
4. What effects do mountains have on climate?

Include descriptions of how elevation affects temperature, and of rain shadows.
5. What effects do seasons have on climate?

Describe what causes seasons; include the terms solstice and equinox in your description.
D. biomes
1. What are biomes?
2. aquatic biomes

List the major aquatic biomes and their defining physical features (there are 8, giving you space here).

define the following: photic zone, aphotic zone, benthic zone

Describe the process of turnover in a lake, and why it is important.

What is eutrophication, and what are some likely consequences of it?
3. terrestrial biomes
XIV.

List the major terrestrial biomes and their characteristic vegetation types and climate (there are 8).

define the following: climograph, ecotone

Be sure that you can interpret a climograph (like figure 52.20).
population ecology
A. Population ecology is the study of populations in relation to __________
B. A population is:
C. define the following: density, dispersion, range
D. How does the mark-recapture method to estimate population size work? Include the formula and definition of the terms in
the formula.
E. What is demography?
F.
define and be able to use/interpret:
1. life tables
2. survivorship curves
3. reproductive tables
G. define and be able to use/interpret the exponential population growth model
H. define and be able to use/interpret the logistic population growth model
1. define and understand the terms K and r
2. describe K-selection and r-selection

What sort of life tables and survivorship curves would you expect for each type?

give examples of organisms of each type

If given a typical life history for an organism be able to categorize it as K-selected and r-selected.
I.
List and describe six density-dependent factors known to affect population growth rates.
J.
Describe how population cycles may be linked between predators and their prey.
K. Human population history and future
1. Be sure that you understand figures 53.22-26.
2. What was industrial revolution and how did it affect human population growth?
3. What is the demographic transition and how does it affect human population growth?
4. What is the global carrying capacity for humans?
XV. community ecology
A. Community ecology is the study of __________
B. A biological community is:
C. describe the following interspecific interactions in general terms of the +/-/0 system
1. competition

define the terms (ecological) niche, resource partitioning, and character displacement
2. predation

Describe how these defenses can help animals avoid predation:

camouflage

warning coloration

Batesian mimicry

Müllerian mimicry
3. herbivory
4. parasitism
5. mutualism

What is the difference between obligate and facultative mutualism?
6. commensalism
D. What is symbiosis? Which interspecific interactions are types of symbiosis?
E. What is keystone species and a pivotal niche?
F.
What is a food web? How do energetic limits affect food webs/chains?
G. Describe ecological succession, primary succession, and secondary succession.
XVI.
ecosystems
A. Diagram the biogeochemical cycles of
1. water
2. carbon
3. nitrogen
4. phosphorus
B. Describe how biomagnification (biological magnification) of a toxin works in an ecosystem.
C. How we almost killed ourselves: the ozone hole story (see fig 55.25)
1. Describe the importance of the ozone layer.
2. Describe how human activities led to depletion of the ozone layer.
3. Describe what humans have done about the depletion of the ozone layer.
D. How we still might kill ourselves: global warming (see fig 55.21)
1. Describe the greenhouse effect and why CO2 is called a greenhouse gas.
2. Describe how human activities increase CO2 in the atmosphere, the logic behind how that leads to global warming, and
the evidence that global warming is occurring.
3. Describe what effects global warming may have. What is the feed-forward effect of thawing tundra?
4. Describe what humans have done about the global warming.
E. Define ecosystem biodiversity, species biodiversity, genetic biodiversity
F.
Describe the value of biodiversity in
1. maintaining the global ecosystem and biogeochemical cycles
2. providing unique resources such as food, remediation, drugs
3. intrinsic value of biodiversity
G. The sixth extinction, or how we are killing lots of things and perhaps ultimately ourselves as well.
1. What is habitat loss and how is it affecting life on Earth today?
2. What are introduced species and how are they affecting life on Earth today?
3. What is overexploitation and how is it affecting life on Earth today?
4. What is the sixth extinction? What can humans do about it?