INTRODUCTION TO BIOLOGY
UNIT ONE
Introduction to the Study of Life
Chemistry for Non-Majors
The Basic Units of Life
Taxonomy
Nuclear Divisions
DNA and Protein Synthesis
CERRITOS COLLEGE
SUMMER 2004
LECTURER – L. L. HARRIS
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A Note to My Students*: (You are responsible for the meanings of underlined terms!)
The word "biology" comes from two Greek words: BIOS, meaning life, and LOGOS, meaning discourse.
The science of biology is thus "the study of life". A grand undertaking! Life, of course, cannot manifest
itself without the presence of living things, and so we can subdivide biology into microbiology, the study of
microorganisms, zoology, the study of animals, and botany, the study of plants. Indeed, even as living
things may be composed of many differing types, biology can be further divided into many subunits. For
example, microbiology may be divided into bacteriology, the study of bacteria; virology, the study of
viruses (Are they living?); and more. Zoology may be divided into entomology, the study of insects;
ichthyology, the study of fish; herpetology, the study of both the amphibians (frogs, toads, salamanders,
and more) and the reptiles (snake, lizards, turtles, and more); ornithology, the study of birds; mammalogy;
the study of mammals; and many, many more. The botany student may choose to specialize as well;
botany may also be divided into such topics as mycology, the study of fungi; phycology, the study of algae;
bryology, the study of mosses; and still more.
Other subsciences of biology which are also fundamental to the study of life are anatomy, the study of
structure (both gross and microscopic); ecology, the study of interrelations of living organisms and their
living and non-living surroundings; genetics, the study of how characteristics are passed on from one
generation to succeeding generations; physiology, the study of functioning of an organism and its parts;
and still scores of others. Each and every one of these subsciences may be broken down still further. As
an example, an entomologist (one who studies entomology) may specialize in beetles, fleas, or butterflies.
At the same time two or more subsciences may be combined to produce still a third subscience such as
mammalian genetics, bacterial physiology, or even physiological ecology.
Thus, it is obviously impossible in one semester (or even a lifetime) to more than skim the surface of the
science of biology. Consequently, the name of our course, Introduction to the Biological Sciences, is an
apt one, for we will not attempt to cover all phases of biology, but we will instead pick and choose from
those areas that I feel demonstrate the basic oneness of life.
Alfred Lord Tennyson, sums up our philosophy of biology much better than we would be able to in his
poem, "Flower in the Crannied Wall":
Flower in the crannied wall,
I pluck you out of the crannies,
I hold you here, root and all, in my hand
Little flower – but if I could understand
What you are, root and all, and all in all,
I should know what God and man is.
During this semester, we shall "pluck" a variety of life's "flowers" and attempt to understand some of the
marvels of life held in them.
Welcome to class!
L. L. Harris
(*Adapted from a letter written by the late Prof. Mark Hoffman to his biology students at Santa Monica College)
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Biology 120
Cerritos College
Introduction to Biology
I. Just for Starters
What is Biology?
“The Study of Life” (From Old Greek: BIOS - life and LOGOS - discourse [study])
What is Science?
"Dependable knowledge"
Why is Science Dependable?
“Scientific Method”
II. More on the Scientific Method
A. Defined – Commitment to systematic observation & testing. Further defined as followed “steps”:
B. Observe some aspect of the natural world
C. Develop the Hypothesis – hypothesis is a tentative explanation of the observation
D. Design Experiment to Test Hypothesis
To be scientific – hypothesis must be "testable" (see text on "untestable" observations)
E. Collect Data and Analyze Data
F. Accept or Reject Hypothesis
G. More on the Experimental Design
1. Faulty Design = Faulty Data
Good Data → Objective, not subjective Quantitative, not qualitative
Repeatability → Rigorous testing
2. Components of Design:
Experimental group – subjects used to test hypothesis
Independent variable – condition(s)/event(s) under study
Dependent variables – condition(s)/event(s) that could possibly change because of the
independent variable(s)
Controlled variables – conditions that could affect outcome of an experiment, but do not
because they are held constant
Experimental control – subject(s) treated in every respect as experimental group with one
important exception; the one variable that you are testing!
Value of the Control – Comparisons! Correction of design "flaws"
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H. More on the Analysis/Interpretation of Data
Based on objective data – either ACCEPT or REJECT the hypothesis
Suspend judgment – test again and again
“Rigorous Testing”
“Repeatability”
I. Theory: A related set of hypotheses to explain some aspect of the natural world.
And even the theory is still subject to challenge!
III. Characteristics of Living Organisms
A. DNA is present in all living things
B INTERDEPENDENCY ON OTHER ORGANISMS; either directly or indirectly. “Energy Flow”
Home Assigned Vocabulary: (define, give examples)
1. Producers – _______________________________________________________________
2. Consumers – ______________________________________________________________
3. Decomposers – _____________________________________________________________
C METABOLIC ACTIVITY
METABOLISM: Sum total of processes used by an organism to extract and transform energy.
Energy used assures maintenance, growth, and reproduction
ANABOLIC PROCESSES: Biosynthesis; make large molecules
from smaller molecules. Stores “energy”
A + B → AB
CATABOLIC PROCESSES: Digestion; break down a large molecule into smaller
molecules. Releases “energy”
AB → A + B
D HOMEOSTASIS: Maintaining the internal environment within some narrow tolerable range.
Examples – Blood Sugar, Blood pH, Body Temperature, ...
E REPRODUCE: capacity by which instructions for heritable traits are passed from parent to offspring
F. CAPACITY TO EVOLVE: based ultimately on variations in traits that arise through mutations in DNA.
In Addition: Living things are subject to the same physical laws as non-living things:
FIRST LAW OF THERMODYNAMICS: Total amount of energy (matter) available in the universe
remains constant. It cannot be created or destroyed; it can only undergo conversion from one form
into another.
SECOND LAW OF THERMODYNAMICS: If left to itself, a system will spontaneously undergo
conversion to a less organized form. Entropy is the measure of the degree of disorder.
As a rule – Entropy increases. However, Living systems can resist entropy if continual energy supply
is put into the system.
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IV. Levels of Organization:
(Also see Figure in your text)
BIOSPHERE – zones of Earth where life is found; includes above and below ground level!
ECOSYSTEM – interactions of biotic and abiotic factors of an area (narrow and broad definitions)
COMMUNITY – all biotic factors that interact with each other (either directly of indirectly)
POPULATION – interacting members of same species
ORGANISM – individual; a species
ORGAN SYSTEM – collection of organs that perform a general task for the organism
ORGAN – collection of different tissue types that perform a specific function for the organism
TISSUE – collection of similar cells
CELL – basic living unit of structure and function
ORGANELLE – “machinery” performing certain tasks for the cell; these are what makes the cell alive
MOLECULE – combinations of atoms (can be atoms of the same kind or of different kinds)
ATOM – smallest unit of an element (pure substance) that still displays the properties of the element
SUBATOMIC PARTICLES – protons, neutrons, electrons, and others; defines an atom
V. Taxonomy
A. Defined – The process of describing species and placing that species into a classification (category)
Attempts to answer the questions: What are they? How do they fit in with all the rest?
B. Beginnings – Why Classify?
First Reason → Man's need to do so! My Friend – My Enemy Good to Eat – Bad to Eat
Second Reason → Common names are confusing! Many common names for same organism!
C. Father of Taxonomy – Carl Linnaeus (formerly Carl Linne)
"Systemae Naturae" (1758) – proposed a hierarchical system of classification
Scientific Names were used to name a species
D. More on the Hierarchical System of Taxonomy
Classification based on relationships
Taxon (pl. Taxa) – category of classification
Hierarchical System – system of GRADED ORDER
Trend from top to bottom: Most General → Less General → → → More Specific → Specific
Taxon:
Kingdom
Phylum
Class
Order
Family
Genus
species
Analogy:
Country
State
City
Street
House #
Surname
1st name
Examples:
Animalia
Chordata
Amphibia
Anura
Bufonidae
Bufo
punctuates
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Mammalia
Primates
Homonidae
Homo
sapiens
Memory Devices: ________________________________________________________________
_________________________________________________________________
E. More On Scientific Names
Binomial nomenclature – organism gets 2 names! General name & Specific name together
Genus species → Capitalize first letter of genus name; leave species name in lower case
Underline – tells a printer to set in italics font
Use Latin – “dead language”; no favoritism to any one country
Examples of Scientific Names:
Bufo punctatus
Homo erectus
Homo sapiens
F. Species Defined – A group of very similar organisms that have the ability to breed with one another
and produce fertile offspring. (Hybrids, are not true species; infertile or low fertility)
VI. The Domains/Kingdoms
(How are they defined? This is a HOME ASSIGNMENT)
Domain of Eubacteria (Bacteria) – _____________________________________________________________
Formerly Kingdom Monera
Domain of Archaebacteria (Archaea) – _________________________________________________________
Formerly Kingdom Monera:
Domain of Eukarya – _______________________________________________________________________
_____________________________________________________________________________________
Kingdom Protista –______________________________________________________________________
___________________________________________________________________________________
Kingdom Fungi – _______________________________________________________________________
_____________________________________________________________________________________
Kingdom Plantae –______________________________________________________________________
_____________________________________________________________________________________
Kingdom Animalia – ____________________________________________________________________
_____________________________________________________________________________________
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Scientific Methodology
Tribal Magic
Philosophy
"It is precisely because it is fashionable for
Americans to know no science, even though
they may be well educated otherwise, that
they so easily fall prey to nonsense."
-- Isaac Asimov
"The Armies of the Night"
Art
Science
Pure
(Because it's there)
Applied
(To help humanity)
OBSERVATION -------------------->
Not what one wants to perceive, or ought to perceive, or try to
perceive, but what one does perceive.
PROBLEM --------------------------->
Question asking – show curiosity; take nothing for granted; be
skeptical!
HYPOTHESIS ----------------------->
A possible answer to your question, but a relevant, testable one;
knowledge of the field should obviously help in this process, but
hunches, intuition, and pure luck also play a role.
EXPERIMENTS ---------------------> "Where is the evidence?" This is the process that separates
OR
science from most other fields of endeavor; one must supply
REPEATED OBSERVATIONS
some data to support his/her hypothesis. Data is repeatable!
DISPROVE or SUPPORT ------------> Note avoidance of the word "proof" – If it is used, it is understood
HYPOTHESIS
HYPOTHESIS
that it means relative proof, that is, acceptable for the level of our
knowledge at the moment (and is open to further research); absolute
proof is outside the realm of science.
THEORY ---------------------------->
The knowledge derived from testing of many related hypotheses;
theories have predictive value, and are utilized to devise more
hypotheses for further testing. Theories are the strongest
statements made ... but that does not imply that they are absolute.
THEORIES EVOLVE AND CHANGE AS NEW INFORMATION
BECOMES AVAILABLE!!
OUTSIDE THE REALM OF SCIENCE
1. If the methods of science cannot be utilized, i.e., if something is not measurable or testable: One must be able
to disprove the phenomenon if it is to be considered within the area of science. Note that this eliminates all
supernatural phenomena from consideration.
2. Value judgments and moral decisions: Scientists can and should have values and should possess morality
(as should everyone!), but they cannot explain their results on the basis of these traits. They can make
decisions about what kind of scientific research is appropriate for them.
3. Purposes and goals: These are more properly the realm of philosophical systems. For example, to state that
the purpose of evolution was to give rise to humans is unscientific because it is untestable. Science deals with
functions, not purposes.
4. Explanations of a philosophical/religious nature: These are not subject to the methods of science. No data!
"There is no expedient to which a man will not resort to avoid the real labor of thinking." – Sir Joshua Reynolds
(1723 - 1792)
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Biology 120
Cerritos College
Origins of Life on Planet Earth
I. SPONTANEOUS GENERATION DEBATES
The big question -- What gives rise to LIFE?
Once upon a time, many people believed some life forms would arise “spontaneously” from inanimate
sources. That is, “life from non-life”.
Examples:
Worms arise from mud. Rats from dirty old rags. Maggots from rotting flesh.
Most men of science did not believe this. They supported a concept of “life from life”.
Louis Pasteur in 1862 – Broth in a Goose-Necked Flask versus a Straight-Necked Flask
He divided a nutritious broth into two flasks; one straight-necked fand the other a goose-necked. He
boiled the broths and then let them cool. Days later the broth in the straight-necked flask was
cloudy – broth in the swan-necked flask was clear. Several more days – straight-necked flask had
molds growing on the broth surface – broth in the swan-necked flask was still clear. Fast-forward
to 2003 – broth in the goose-necked flask is STILL CLEAR.
Conclusion: Under present day conditions – Life arises from Life
“BIOGENESIS”
II. SPONTANEOUS GENERATION OF LIFE MOLECULES
A. Bottom Line: Theorists today support the idea that LIFE MOLECULES did spontaneously arise from
nonliving matter under the physical conditions that prevailed on early Earth.
THE BIG BANG – Stellar explosions give rise to Solar System – 4.6 billion years ago!
B. Speed up to 20th Century: Alexander Oparin, a Russian Scientist, offered a hypothesis!
Published in 1922 and again in 1936 a discussion on what may have happened to
spontaneously generate the stuff life is made of – “life molecules”.
1. Earth's Early Atmosphere
Hydrogen gas (H2)
Methane (CH4)
Hydrogen Cyanide (HCN)
Carbon Dioxide (CO2)
Nitrogen (N2
Ammonia (NH3)
Carbon Monoxide (CO)
Water Vapor (H2O)
Hydrogen Sulfide (H2S)
Important Note: NO OXYGEN GAS (O2)!
Earth cooled – Storms came – Flooding creates seas – Erosion adds minerals to Seas
The gases dissolved into Earth’s seas/oceans. A "Primordial Soup", but Energy to cook it?
2. Summary of Physical Conditions Favoring Formation of Life Molecules On Early Earth
a.
b.
c.
d.
e.
Elements of C H O N (& S) in the gases of the atmosphere
Near-Anaerobic Conditions that favor certain chemical reactions
Liquid Water favored by distance from Sun
Gravity that holds water on Earth's surface
Energy for driving chemical reactions? Solar Heat, Radiation (UV light, others), Lightning, other
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3. Assumptions for the Spontaneous Assembly of Organic Compounds
a. Assume proposed physical & chemical conditions of early Earth to be correct.
b. Assume physical, chemical, and evolutionary principles known to be true today can be applied
to the early Earth conditions.
c. Ask if there could be a series of events that could lead to spontaneous assembly of organic
compounds that, in turn, could lead to the first living systems.
d. Design experiments that could test a proposed series of events that would have led to the first
living systems.
III. TESTING OPARIN’S HYPOTHESIS
A. Stanley Miller (A young doctoral student in Harold Urey's lab) – 1953
In a reaction chamber Miller added a SOUP
containing a mixture of H2, CH4, NH3, H2O.
For a week's time he kept the mixture in motion
and all the while he shot it through with electrical
currents that were to simulate lightning flashes.
At the end of the experiment he assayed his SOUP;
discovered several amino acids and even some
nucleotides had formed.
Experiment is easy to repeat. Miller continued to
get the same results.
Change soup ingredients and different "life molecules”
were be made by this abiotic system. Example, add
inorganic phosphate to he original soup – ATP forms!
B. Beyond Miller – A Discussion (Text has more on experiments proposing events that led to CELLS)
But these "building blocks" of Miller’s are not living! They are just the stuff that living things are made
from! What events would have led to these "building blocks" to build even one living cell?
Fossils dating 3.5 BYA show early cells. (Prior to this, it is estimated that for 300-500 million years
the soup was gathering "life" molecules.)
What would it take for these molecules to become "self-replicating" systems?
The "self-replicating" system today's scientists speak of is: DNA  RNA  polypeptide
But is this the correct order? Did DNA need to come first? Maybe RNA was the more important
player in life's early history. Current thought is that RNA did come first!
The exact sequence of events is not known. We leave this subject by stating simply that there are
good reasons to believe that given the conditions of the early Earth some reactions were much
more probable than others. (paraphrased from text)
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Biology 120
Cerritos College
Inorganic Chemistry for Non-Majors
I. Atoms and Molecules
A. Organization of Matter
1. Elements – Substances that contain only one kind of atom
Example: Carbon is an element. A one carat diamond is pure carbon
109 elements are currently listed in the Periodic Table – more are being added!
Memory device for the most common elements in living organisms: C HOPKINS CaFe, Mg NaCl
carbon
iodine
magnesium
hydrogen
nitrogen
sodium
oxygen
sulfur
chloride
phosphorous
calcium
potassium
iron
THE BIG 4 : C H O N
2. Atoms – The smallest portion of an element that still displays the properties of the element
3. Subatomic Particles – Protons, Neutrons, and Electrons (and others!)
Protons – electrically positive (+ charge), found in nucleus (weight = 1)
The # of protons = the atomic number
Change proton number – no longer the same element
Neutrons – electrically neutral (0 charge), found in nucleus (weight=1)
Neutrons + Protons = mass number
Change # of neutrons → Isotope of the atom
Causes variation in mass number 12C 14C 32P
Radioactive isotopes – decay; have a 1/2 life; used as tracers in bio experiments;
dating techniques, clinical applications
Electrons – electrically negative (-), found orbiting nucleus (weight = 0)
Held in orbit by attraction to proton's + charge
Electrons are the atom's ENERGY!
ORBITAL: An orbit is region of space around the nucleus where an electron is found at
any instant. There are 2 (usually) e-’s per orbit
SHELLS: Regions around nucleus where orbitals are found. The ENERGY LEVELS of the
electrons. Shells like to be filled! “Octet Rule”
Very Important: Most atoms do not have filled outermost shells!
What was meant by ENERGY OF THE ATOM?
Distance an electron is from the nucleus represents the amount of energy it has.
Electrons at a greater distance from nucleus have greater potential energy than
electrons nearer the nucleus.
Energy comes from the sun. Electrons will absorb this energy and are said to be
"excited". Jump to a higher energy level. Potential Energy = “stored energy”
When an electron returns to its previous shell the extra energy is released.
Released energy = kinetic energy (Capable of work if properly “harnessed”))
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If an atom is “neutral” it has an equal number of protons and electrons.
# Negative Charges + # Positive Charges = ZERO
This is not how we find most atoms in nature.
Atoms combine with other atoms or exist as IONS.
This is how an atom can satisfy its outermost shell!
Ions = Electrically charged atoms
Gain an electron would yield a negative ion
Lose an electron would yield a positive ion
Examples:
Na+ has a positive charge -- lost an e- to have an outermost shell that is filled.
Cl- has a negative charge -- gained an e- to achieve a filled outermost shell.
II. Bonds Between Atoms
A. Chemical Bonds – A union between the electron structure of two or more atoms or ions
Bonds are an ENERGY RELATIONSHIP between the electrons of atoms
Bonds represent potential energy – breaking a bond releases ENERGY!
B. Types of Bonds
1. Ionic Bonds – bonds between ions, opposite charges attract
2. Covalent Bonds – sharing of electrons to fill outer shell.
Single covalent bonds: 2 atoms, 1 pair e-'s shared
Double covalent bonds: 2 atoms, 2 pair e-'s shared
Triple covalent bonds: 2 atoms, 3 pair e-'s shared
HH
O=O
NN
POLARITY – Is the sharing of electrons equal or unequal?
1. Non-polar Covalent Bonds: EQUAL SHARING – Protons of atoms exert the
same amount of pull for the electrons.
2. Polar Covalent Bonds: UNEQUAL SHARING – One atom’s protons pull more
for the shared electrons than do the protons of the other atom.
Hydrogen Bonds – weak bond between an electronegative atom interacting with a hydrogen atom
that is involved in a covalent bond with another molecule (atom). Important in the nature of
WATER, DNA, and RNA.
************************************************************************************************************************
Hydrophobic - Hydrophilic Interactions
Water is polar molecule – what does that mean to other molecules surrounded by water?
Polar molecules are attracted to the polar H2O; are hydrophilic (love water)
Nonpolar molecules are not attracted to polar H2O; hydrophobic (fear water)
ANALOGY: Vinegarette Dressing – Shaking bottle breaks up some of the bonds between water and oil
molecules. Mixture doesn't last long. Oil and water are repulsive to each other! More attracted to
their own kind – H2O molecules begin to regroup pushing the oil out of their way.
************************************************************************************************************************
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III. Acids, Bases, Buffers, and Salts
A. Acid – Substance that releases a hydrogen ion in solution. AKA Proton donor
B. Base – Substance that combines with a H ion in solution. AKA Alkaline
AKA Proton acceptor or hydroxyl (OH-) donor.
C. The pH Scale – 0->14 is a measure of acidity and basicity. pH means "Power of Hydrogen"
[H+] = [OH-]; pH value is 7.0 (neutral pH)
pH < 7.0 is acid pH > 7.0 is basic
A change of only 1.0 on the pH scale means a
ten-fold change in hydrogen ion concentration.
pH 4.0 → pH 5.0
pH 4.0 is 10X more acidic than pH 5.0
0
7
14
pH 4.0 → pH 7.0
pH 4.0 is 1000X more acidic than pH 7.0
D. Buffers – substances that resist changes in pH by taking up excess H + or OH-.
Arterial blood has pH of 7.4; changes to 7.2 or 7.6 are usually fatal
(Homeostatic Range: pH 7.35 – pH 7.45)
E. Salts – Salt is an ionic compound formed in the reaction of an acid and a base:
HCl + NaOH → H2O + NaCl
Salts dissociate into their ions when placed in water. “Ionization”
Ions in solution are called "Electrolytes"
Water molecules also ionize – water behaves as an acid and base
IV. Water Molecules and Cell Organization (HOME ASSIGNMENT – here are my notes – read the book!)
Three properties of water that cells depend on: 1. Cohesion property
2. Temperature stabilization
3. Solvent property
A. Cohesion Property
H2O molecules are highly attracted to other H2O molecules. Attractiveness for each other is due
to H bonding. Negative regions (Oxygen Atom) of a water molecule are attracted to the positive
regions (Hydrogen atoms) of adjacent water molecules. In a drop of water the H bonds exert a
constant inward pull on the molecules at the surface of drop. “SURFACE TENSION” is the reason
a drop of water holds that shape. This cohesiveness (along with other factors) allows water to be
carried in small tubes from the roots of a plant up to the highest branches and leaves of the plant.
B. Temperature Stabilization
Water is an ideal liquid for maintenance of living cells:
1. High Specific Heat – H2O absorbs lots of heat before its temperature rises significantly.
2. High Heat of Vaporization – H2O molecules resist separating from each other.
However, when enough E is absorbed bonds are broken and the water molecules at the
surface can escape. EVAPORATION lowers surface temperature of water
3. High Heat of Fusion – Liquid H2O resists changing to a solid at 0oC (32oF).
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C. Solvent Properties of Water
Water is polar and will dissolve polar molecules.
SOLVENT: A fluid material in which other substances can be dissolved.
SOLUTE: The material dissolved by the solvent.
SOLVENT + SOLUTE = SOLUTION
Salts (such as NaCl) will dissolve when placed in water.
Water and the Organization Underlying the Living State
To quote text book: None of the activities associated with the term "living" proceeds without water.
The organization of cells is dependent on water and water interactions with other molecules.
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Basics of Chemistry Worksheet
(includes several Home Assignments)
1. ________________________________________ is defined as anything that has mass and occupies space.
2. The subject of #1 is composed of fundamental substances called __________________________________.
3. What was the mnemonic device (given you in lecture) that can help you to remember the major and minor
elements of your body?
_____________________________________________________________________________
4. Of these, what are the (full) names of the MAJOR elements? _____________________________________
____________________________________________________________________________________
5. What are the names of the MINOR elements? __________________________________________________
_____________________________________________________________________________________
6. What is a “trace element”? Define and give examples: ____________________________________________
_____________________________________________________________________________________
7. Atoms are composed of "subunits". What are the names of the three major "subunits"?
______________________________________________________________________
8. Of these "subunits", ________________________ have a positive charge and ________________________
carry a negative charge. The third subunit is not electrically charged.
9. Of these "subunits", which ones are found in the nucleus? ________________________________________
10. The total number of _____________________________ in the nucleus equals the atomic number of the unit.
11. Atomic Mass (Weight) is equal to the total number of ____________________________________________.
12. Uncharged atoms will have an equal number of ______________________ and ______________________.
13. An atom that loses or gains an uncharged subunit is called an ____________________________ of that atom.
14. An atom that loses or gains a positive charged subunit is called a ___________________________________.
15. A charged atom has either lost or gained one or more ____________________________________________.
16. A charged atom is called an ___________________. They are also known as _________________________
when they are present in a solution.
17. A combination of two or more atoms of the same kind is called a ____________________________________.
18. A combination of two or more atoms of different kinds is called a ____________________________________.
19. Combinations (#17, #18) are united by ________________________________ of which there are three types.
20. Unions called ______________________ are formed by the attraction of positive and negative charged atoms.
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21. Unions called ___________________________ occur when the negative charged subunits are not completely
transferred in attempting stability. Instead they are "shared" by units involved.
22. These unions (#21) are said to be ____________________ if sharing is "equal" and ___________________
if sharing is not "equal".
23. ________________________________ are the 3rd type of union in which covalently bonded hydrogen atoms
are joined with an electronegative unit. (Hint: important for water and nucleic acids like DNA)
24. An _____________________________ reaction is one in which two or more atoms or molecules join to form
more complex substance. These are also called Synthesis Reactions.
25. A _______________________________ reaction is one in which a large complex substance is broken down
down into smaller substances. These are also called Digestive Reactions.
26. The term _____________________________ refers to the sum total of #24 and #25 reactions carried out by
living cells/organisms in order to extract and transform energy.
27. A _______________________________ is defined as anything that increases the rate of chemical reactions.
28. Biological substances that increase chemical reaction rates are called ______________________________.
29. Organic compounds differ from inorganic compounds by the presence of both ________________________
and ________________________ atoms in their molecular formulae.
30. According to #29, salts are examples of ORGANIC / INORGANIC substances.
31. All salts are united by ______________________ bonds that form in the reactions of strong acids and bases.
32. An acid is a substance that releases _________________________________ ions when dissolved in water.
33. A base is a substance that releases ______________________________________ when dissolved in water.
34. Bases are also known as ________________________ and are acceptors of ________________________.
35. The pH of a solution is primarily determined by its concentration of _________________________________.
36. The lower the pH the more _____________ a solution. The higher the pH the more ____________ a solution.
37. So-called "pure" water has a pH of ________________ and represents an equal concentration of #32 and #33.
38. ___________________________ are substances that behave as acids when pH rises and behave as bases
when the pH of a solution falls.
39. Strong bases become STRONGER / WEAKER ______________ when combined with a ____________ acid.
40. In a summary equation of a chemical reaction – _______________________ are shown to the left of the arrow
and ____________________ are shown to the right of the arrow.
41. Solutions are mixtures composed of substances generally known as _______________ and ______________
42. Mixtures differ from Molecules in that a mixture can be ____________________________________________
________________________________________________________________________________________
15
Biology 120
Cerritos College
Organic Chemistry for Non-Majors
I. The Chemical Constituents of Cells
A. Inorganic Compounds
Common examples: Salts, H2O, O2, CO2, NH3
B. Organic Compounds
How organics differ from inorganic compounds → organic compounds will have both C and H atoms.
II. Organic Compounds of Cells: Carbohydrates, Lipids, Proteins, and Nucleic Acids
A. Carbohydrates
Molecular formula = (CH2O)n
(Where n does not equal less than 3)
Common names: Sugars and Starches
Function: Structural and as Energy Source
Structural Levels: Monosaccharides – taste sweet
Disaccharides – taste sweet
Polysaccharides (aka Starches) – do not taste sweet
Note "-ose" suffix tells you it is a carbohydrate (there are exceptions to using –ose for all)
1. Monosaccharides
Building blocks (monomers) of large Carbohydrates
Simple Sugars - GLUCOSE, principle energy source for most organisms, is made by green
plants in the process called Photosynthesis.
GLUCOSE = (CH2O)6 = C6H12O6
Other examples include: Fructose and Galactose
2. Disaccharides (an "Oligosaccharide")
Composed of 2 monosaccharide subunits joined in a Condensation (aka Dehydration) Reaction:
GLUCOSE + GLUCOSE → MALTOSE + WATER
C6H12O6 + C6H12O6 → C6H22O11 + H2O
Others:
GLUCOSE + FRUCTOSE → SUCROSE + WATER
Sucrose = table sugar; plant's transport form of glucose
GLUCOSE + GALACTOSE → LACTOSE + WATER
Lactose = milk sugar
Digestion of a disaccharide into its monosaccharides via a Hydrolysis Reaction:
MALTOSE + H2O → GLUCOSE + GLUCOSE
C6H22O11 + H2O → C6H12O6 + C6H12O6
16
3. Starches (AKA Polysaccharides)
Carbohydrate composed of many monosaccharide subunits.
Examples:
Amylose – long chains of glucose units; storage form of glucose in plants (Plant Starch)
Glycogen – long chains of glucose units; storage form of glucose in animals (Animal Starch)
Cellulose – Structural polysaccharide of plant cell walls – the “fiber” in your diet
Chitin – Structural polysaccharide of bug's exoskeleton
B. Proteins
1. Function
Structural and Metabolic Processes
Structural examples:
Metabolic examples:
Hair, Skin
Enzymes, Hormones
2. Structure of Proteins
Amino Acids are the monomers of Proteins
Amino Acids are composed of C, H, O, N and some contain S
3. Composition of Amino Acids
20 biologically active amino acids
Amino Acid:
R
|
H2N – C – C – OH
| ||
H O
Carboxyl Group = COOH (ionized as COO-)
Amino Group = NH2 (ionized as +NH3)
R Group = side chain varies for different AAs.
4. Covalent Bondings between AAs = Peptide Bonds
a. Peptide bonds form by Condensation Rxns (removal of a H 2O found between the
carboxyl end of one AA and the amino end of the second AA.
b. Bonding continues → peptides, polypeptides, and proteins
5. Structural Levels of a Protein
a. Primary Structure
AA sequence
(may also include Cys-Cys bonds); determined by DNA (gene)
b. Secondary Structure
Coils (Helices) or Pleated Sheets of the 1o structure; determined by H-bondings
↑
All Proteins
Some Proteins
↓
c. Tertiary Structure
Foldings of 2o structure → "globular" protein; determined by R-group interactions
Essential to the activity of the metabolic protein
Creates the ACTIVE SITE (aka "binding site")
Sensitive to high heat and pH extremes = Denaturation
d. Quartenary Structure
Combining of several "globular protein" subunits
Example – Hemoglobin and Ion Channels in cell membranes
Hemoglobin = C3032H4816O872N780S8Fe4
17
C. Lipids
Non-polar hydrocarbons.
What does this say about interactions with H 2O? Answer: Lipids are hydrophobic!
Functions: Structural Materials and as Energy Stores.
Important Lipids:
Fats
Oils
Phospholipids
Waxes
Steroids
Fats and Oils are composed of Glycerides
Glyceride = 1-3 fatty acid tails attached to a Glycerol via a condensation reaction
Fatty Acid = long chains of C with H atoms with a carboxyl end (COOH)
FATS:
Solid at room temperature
Saturated – single covalent bonds between Carbon atoms
OILS:
Liquid at room temperature
Unsaturated – contains one or more double covalent bonds between C atoms.
PHOSPHOLIPIDS:
Important constituent of Cell Membrane
Have a hydrophilic end: Phosphate Head
Have a hydrophobic end: 2 Fatty Acid Tails
WAXES:
Fatty Acid Tails bonded to either an Alcohol or C-ring.
Bee's Wax – made by bees to make honeycomb
Cerumen (aka Ear Wax) – trap dust, small critters
Cutin Wax – plant product, "waterproof" leaves & fruits; also discourages insects
STEROIDS:
No Fatty Acid Component
Some have chain structure, others have ring structure
Cholesterol – animal steroids
Sex hormones, bile acids, Synthesis of Vitamin D
Phytosterol – plant steroids
D. Nucleic Acids
1. Composed of units called Nucleotides
2. Composition of a Nucleotide
a. Phosphate Group
(phosphoric acid)
b. 5-carbon Sugar
(either deoxyribose or ribose)
c. One of Five Nitrogenous Bases (Adenine, Guanine, Thymine, Cytosine, and Uracil)
Common Examples: Deoxyribonucleic Acid (DNA) Ribonucleic Acid (RNA)
Important Derivatives: NADPH FADH NADH
Very Important Derivative: Adenosine Triphosphate (ATP) "Biological $$"
SUGAR – ADENOSINE
|
P
.
|
The bonds between the Ps are of high potential energy.
P
Breaking of the 3rd bond releases the greatest kinetic energy.
|
P
18
Organic Compounds Worksheet
1. The four (4) major categories of organic compounds are ___________________________________________
____________________________________________________________________________________
2. Monosaccharides are the building blocks of all _________________________________; molecules commonly
known as sugars and starches.
3. Twenty different amino acids are the building blocks of all ____________________________________; these
are molecules that have important structural and metabolic functions for the cell/organism.
4. Five different nucleotides are the building blocks of the _____________________________; these molecules
are important in heredity and cellular information – and their derivatives are very important too!
5. A nucleotide is composed of three types of molecules – these are ___________________________________
___________________________________________________________________________________
6. The fourth type of organic compound, the _______________ include neutral fats, phospholipids, and steroids.
7. Disaccharides and Polysaccharides are formed in a chemical reaction called _________________________ in
which a water molecule is "removed".
8. Disaccharides and Polysaccharides are digested in reactions called ____________________ in which a water
molecule is "added" to break the bonds between the sugar units.
9. The building blocks of neutral fats are _________________________________________________________.
10. Neutral fats are commonly known as ______________ and ________________; important as energy stores.
11. Unsaturated fats are distinguished from saturated fats by the presence of one or more __________________
bonds; saturated fats do not contain these, instead its C-backbone is saturated with hydrogen atoms.
12. Water and Oil don't mix; water is a _________________ molecule and oil is a ________________ molecule.
13. The hydrophilic end of a phospholipid is its ______________ and the hydrophobic end is its _____________.
14. Hydrophilic molecules are POLAR / NONPOLAR and hydrophobic molecules are POLAR / NONPOLAR.
15. The single most important molecule in steroid chemistry is ______________________; essential to life due to
its role in species reproduction, synthesis of Vitamin D, inflammations, and general metabolic processes.
16. A mRNA molecule is a copy of a _________________; instructions for a polypeptide located along the DNA.
17. Molecules of mRNA are made during ___________________; this occurs in the cell's __________________.
18. Polypeptides are made during ____________________; this occurs in the cell's ______________________.
19. Peptide bonds are formed when the ______________ end of one amino acid reacts with the _____________
end of a second amino acid. Again, the bond is formed when a water molecule is "removed".
20. The amino acid sequence is the Primary / Secondary / Tertiary / Quaternary structure of the polypeptide.
21. The polypeptide's active site is characteristic to the Primary / Secondary / Tertiary / Quaternary structure.
22. The _______________________ structure is determined by the interactions of the various ________ groups
of the amino acids and their position in the polypeptide chain.
19
Biology 120
Cerritos College
Cell Structure & Function
I. The Cell Theory
Proposed by German botanist Schleiden & German zoologist Schwann: (1839)
a. All organisms are composed of one or more cells.
b. The cell is the basic living unit of organization.
In 1850, Russian physiologist Rudolph Virchow added:
c. All cells arise from preexisting cells.
II. Types of Cells
Prokaryotic Cells
The earliest of cells
Prokaryotic means “first nucleus” (or early nucleus) refers only to a region in the cell where
the nuclear material (DNA) is found. This region is called the NUCLEOID (nucleus-like)
Extended Definition refers to fact that there are no membrane-bound organelles (including DNA)
All Prokaryotic Cells are members of the Kingdom Monera
Eukaryotic Cells
Means “good nucleus” (or true nucleus). Refers to the fact that nuclear material is membrane-bound;
All organelles are also membrane-bound, discreet features in the cell
Autotrophic Cells
Some prokaryotic and eukaryotic cells are Autotrophic
"Self-feeders"; produce their own food through photosynthesis or by chemiosynthesis
Includes: Cyanobacteria (fossil record, 3.5 bya)
All members of the Kingdom Plantae (except those that are parasitic)
Some members of the Kingdom Protista
Heterotrophic Cells
Literally "other-feeder"; must obtain their food from "outside sources"
Most members of the Kingdoms Monera & Protista
All members of the Kingdoms Animalia and Fungi
Unicellular Organisms
Single-celled "organism"; all life processes are conducted by the single cell
Heterotrophic Cells
Literally "other-feeder"; must obtain their food from "outside sources"
Most members of the Kingdoms Monera & Protista
All members of the Kingdoms Animalia and Fungi
Only a few members of the Kingdom Plantae (parasitic plants)
Unicellular Organisms
Single-celled "organism"; all life processes conducted by the single cell.
Multicellular Organisms
Composed of many cells; specialized cells accomplish a "division of labor" for organism’s survival
III. Generalized Animal Cell Anatomy
A. PLASMA MEMBRANE – outermost boundary of the single cell. Defines the cell and separates the
internal events in the cell from the external events occurring outside the cell. AKA Cell Membrane.
"FLUID MOSAIC MODEL": Phospholipid Bilayer (fluid) & embedded Protein Chunks (mosaic)
Review: hydrophobic & hydrophilic ends of a phospholipid
Proteins present as channels for letting things inside or outside the cell; many more roles
THE PLASMA MEMBRANE IS SELECTIVELY PERMEABLE!!
20
B. NUCLEUS – membrane bound compartment of the cell that holds the blueprints for all materials
made by the cell. A major part of the subject here is called Protein Synthesis (later!).
Nucleus has the hereditary information known as DNA
Contains the nucleolus and chromatin
1. NUCLEOLUS – dense region within nucleoplasm, holds RNA
2. CHROMATIN → CHROMOSOMES (composed largely of DNA)
C. CYTOPLASM – all material between the nucleus and the cell membrane. Composed of cell's little
organs (called organelles) and the liquid (the cytosol) in which they are suspended
D. ORGANELLES – little organs. They makes the cell alive.
1. CENTROSOME w/ CENTRIOLES – function in nuclear divisions (mitosis and meiosis)
2. RIBOSOMES – carpenter's workbench for proteins
3. ENDOPLASMIC RECTICULUM – refinements and packaging; “circulatory system” of the cell.
ROUGH ER – studded with ribosomes, indicates that proteins are being made
SMOOTH ER – no ribosomes, no protein synthesis. Lipid synthesis, "detox" centers in liver
4. GOLGI APPARATUS – refinement center, packaging center; makes transport vesicles
5. MITOCHONDRIA – powerhouse of the cell (ATP); Beginnings as a Symbiotic Relationship
between a prokaryote and eukaryote?
6. LYSOSOMES –powerful digestive enzymes. Cell Aging Tay-Sachs Disease Autophagy
7. VACUOLES/VESICLES – storage sites for water, fats, ...
******************************************************************************************************************
ENDOCYTOSIS – Vesicle formation for obtaining extracellular material for purposes of bringing
materials into the cell.
PHAGOCYTOSIS – Cellular eating
PINOCYTOSIS – Cellular drinking
EXOCYTOSIS – Vesicle formation for moving digested matter out of the cell. Also used for the
secretion of cell products to outside the cell.
Important Note: The membranes of Vesicles and Vacuoles are “phospholipid bilayers” just like the Cell
Membrane. Note how activities of endocytosis and exocytosis affect the cell membrane!
******************************************************************************************************************
IV. Generalized Plant Cell Anatomy
Has many of the same features as the Animal Cell. Unique to the plant cell are the following features:
CELL WALL – Made of the carbohydrate CELLULOSE (the roughage, fiber in our diets). Is made by the
cell and transported outside the cell. Mechanical support structure for the cell/plant
PLASTIDS – Storage organelles, some store pigments, others store starch
Example: CHLOROPLAST -- chlorophyll pigment & P/S machinery
LARGE WATER VACUOLE – mechanical support; H2O store
What it lacks: CENTROSOMES (CENTRIOLES), LYSOSOMES
V. Cell Functioning (Lab Supported!)
A. Active vs. Passive Transport Processes
BROWNIAN MOVEMENT – random movement of molecules due to their inherent kinetic energy
ACTIVE TRANSPORT – ATP is spent to move materials across an unfavorable gradient
(low concentration → higher) Examples: Endocytosis and Exocytosis
PASSIVE TRANSPORT – ATP not required as a favorable gradient exists (higher → lower)
21
Molecules in area of high concentration will be more likely to bombard one another and
“move” into areas of lower concentration.
B. Types of Passive Transport
DIFFUSION – passive movement of "particles" from regions of higher particle concentration into
regions of lower particle concentration. Eventually, an equilibrium is achieved in the medium
Special Diffusions:
OSMOSIS – diffusion of solute molecules across a selectively permeable membrane
DIALYSIS – diffusion of solvent molecules across a selectively permeable membrane
Transports via Pressure Gradients:
BULK FLOW – movement of solutes/solvents in the same direction due to a favorable
pressure gradient. Typical of movements in “tubes”
FILTRATION – movement of solutes/solvents across a selectively permeable membrane
due to a hydrostatic pressure gradient (or gravity)
C. Solutions = Solutes + Solvents
Solvents are substances that can dissolve solids
Solutes are dissolved solids
Types of Solutions:
HYPERTONIC – as compared to a second solution, it has a higher solute concentration
HYPOTONIC – as compared to a second solution, it has a lower solute concentration
ISOTONIC – as compared to a second solution, it has the same solute concentration
VI. Limits on Cell Size
Ever wonder why most cells are so darn small? Measured in micrometers!
Small size is more efficient – materials that cross membrane will also travel through cytosol.
Most movement is by simple diffusion and diffusion works well over short distances
If a cell were allowed to get larger and larger – we would find that the surface area of the sphere (cell)
increases at a different rate from that of the volume. As size increases: Surface Area = μm2
Volume = μm3
A Closer Look at the Problem: Begin with a hypothetical cell that has a diameter of 1.0 μm
(We will cheat on the geometry by ignoring pi!)
Double the size?
Triple the size?
Quadruple it?
S.A.  2 x 2 = 4
Vol.  2 x 2 x 2 = 8
sa/v = .5
S.A.  3 x 3 = 9
Vol.  3 x 3 x 3 = 27
sa/v = .33
S.A.  4 x 4 = 16
Vol.  4 x 4 x 4 = 64
sa/v = .25
Large cells have a poor surface area to volume ratio – may not insure transport of materials (good & bad) in a
physiologically significant time period. “Physiological timeframe” means fast enough to mean cell’s survival!
22
Small cells have a large SA relative to their Volume – diffusions will be able to occur in a physiologically
significant timeframe. Distance for diffusion is shorter – good for cell’s survival!
Biology 120
Cerritos College
Nuclear Divisions
I. Prokaryotic Nuclear Divisions
Prokaryotic Fission – Ancestor of eukaryotic nuclear divisions; see figure in text.
II. Eukaryotic Nuclear Divisions
A. Mitosis
1. Defined – nuclear division of somatic cells
2. Function – growth; replacement of “lost” cells; also asexual reproductions & regenerations
3. Significance – maintains chromosome number in resulting nucleii
diploid → diploid
haploid → haploid
B. Meiosis
1. Defined – nuclear reduction division
2. Function – reduce the chromosome number to one-half (diploid → haploid)
3. Significance – fertilization event restores the diploid number (haploid + haploid → diploid)
4. Dominant Types of Meiotic Divisions
1. Sporic Meiosis (Plants)
2. Gametic Meiosis (Animals)
III. Cytokinesis
Defined – cytoplasmic division between two daughter cells; a cytoplasmic sharing.
Purpose – creates separate cells; increase cell numbers
Significance – increase cell numbers, keep cells small
Events
a. Animal Cell – cleavage furrow formation
b. Plant Cell – cell plate formation
E. Special Note: Cytokinesis does not occur for all cells!
A.
B.
C.
D.
IV. Cell Cycle and A Closer Look at Mitosis
A. Interphase
1. Two Growth Periods Interrupted by a Synthesis Period
2. Synthesis of DNA (copy made; joined as "sisters")
Semiconservate Replication – copies DNA
Copies = Sister Chromatids joined at Centromeres
B. Mitosis – 4 Stages Generalized description to apply to both Animals & Plants
1. Prophase – sister pairs (chromatids) of DNA condense; nuclear membrane "lost"
2. Metaphase – sister chromatids align at equator; microtubule system activated
3. Anaphase – centromere linkage “breaks” between sisters; segregation of sisters to opposite
poles of cell
4. Telophase – nuclear membrane reforms around both sets of segregated chromosomes
Summary Diagram:
23
V. Meiosis – A Closer Look at Reduction Division
A. Homologues – pair of chromosomes in 2n organism
Similar in Appearance* and Information* (genes)
One from Mom, the other from Dad
* Exception to this rule: The Sex Chromosomes; the 23rd pair of chromosomes in Humans. Don't look
the same and both don't necessarily carry same information, but behave as homologues during meiosis.
B. Meiotic Stages – Two Rounds of Division
1. Meiosis I (“Round 1”)
Follows an Interphase that is very similar to the Interphase that precedes mitosis
a. Prophase I – homologous non-sister chromatids usually exchange pieces of DNA
“Cross-Over” makes for new combinations of same, but different information
on the chromosome. This offers “variation” in the possible offspring.
b. Metaphase I – homologues (as sister chromatids) line up at equatorial plane (Tetrad)
c. Anaphase I – homologues segregate to opposite poles; still as joined sister chromatids
d. Telophase I – no nuclear membrane reforms; reduction is achieved. (Two Haploid Cells)
2. Interkinesis – similar to Interphase, but no DNA copies made; important note – still have sisters!
3. Meiosis II (“Round 2”)
a. Prophase II – same as in mitosis; no Cross-Over occurs (Why not?)
b. Metaphase II – same as in mitosis
c. Anaphase II – same as in mitosis; sisters separate and segregate
d. Telophase II – same as in mitosis; nuclear membrane forms around segregated
chromosomes
Summary Diagram:
C. Cytokinesis
1. Gametic Meiosis (Animals)
a. Male (4 spermatozoa) – equal cytokinesis
b. Female (1 ovum, 3 polar bodies) – unequal cytokinesis
24
2. Sporic Meiosis (Plants) – we will save this for later!
a. Male (microspores)
b. Female (megaspores)
A COMPARISON OF THE NUCLEAR DIVISIONS
MITOSIS AND MEIOSIS IN THE ANIMAL AND PLANT KINGDOMS
Mitosis:
Meiosis:
(1) An equational division which
separates sister chromatids in
anaphase.
(1) The first stage is a “reduction division”
that separates homologous chromosomes
at anaphase I; sister chromatids separate in
an equational division at anaphase II.
(2) One division per cycle, i.e., one cytoplasmic division (cytokinesis) per
equational chromosomal division.
(2) Two divisions per cycle; that is, two
cytoplasmic divisions, one after reductional
chromosomal division and one following
equational chromosomal division.
(3) Chromosomes fail to synapse; no
tetrad forms; genetic exchange
between chromosomes does not occur.
(3) Chromosomes synapse and form a tetrad;
genetic exchange occurs between the
non-sister homologues. (“Cross-Over”)
(4) Two cellular products (daughter cells)
are produced per cycle.
(4) Four cellular products are produced per
complete cycle.
(5) Genetic content of mitotic products
are identical.
(5) Genetic content of meiotic products are
different; new chromosomes composed
of genes from maternal and paternal
homologues. (See #3)
(6) Chromosome number of daughter cells
is the same as that of the parental cell.
(6) Chromosome number of meiotic
products is half that of parental cell.
(7) Mitotic products are usually capable of
undergoing additional mitotic divisions.
(7) Meiotic products cannot undergo another
meiotic division although they may
undergo mitotic divisions.
(8) Normally occurs in most all somatic cells.
(8) Occurs only in specialized cells of the
germinative (germ) line.
(9) Begins at zygote stage and continues
through the life of most organisms.
(9) Occurs in higher organism of reproductive
age. Gametes of animals and the spores
25
Used to make gametes of land plants.
of land plants.
Biology 120
Cerritos College
DNA & PROTEIN SYNTHESIS
I. Introduction
Johann Meischner in 1868:
ASSAY cells were from PUS and FISH SPERM – also lots of blood from injured soldiers in wartime.
Organelle of interest was the NUCLEUS
Material found was ACIDIC and high in PHOSPHOROUS
He called the substance NUCLEIN – Today it is known as DEOXYRIBONUCLEIC ACID
In Meischner's day – his discovery was not what we would call “Earth shattering”
Today – genes are instructions encoded along a chromosome.
Today – chromosomes are made of DNA, a nucleic acid
II. Structure of Nucleic Acids
Composed of NUCLEOTIDES:
A. NUCLEOTIDES
1. 5-carbon sugar – DEOXYRIBOSE OR RIBOSE
2. PHOSPHATE GROUP – PHOSPHORIC ACID
3. NUCLEOTIDE BASE – PURINES & PYRIMIDINES
a. Purines
(Double Ring Structure)
1. Adenine
2. Guanine
b. Pyrimidines
(Single Ring Structure)
1. Thymine
2. Cytosine
3. Uracil
SUGAR and PHOSPHORIC ACID bond together
BASE is attached to the 5-C sugar
B. TYPES OF NUCLEIC ACID
1. Deoxyribonucleic Acid (DNA)
a. 5 carbon sugar is Deoxyribose
b. Nucleotide bases "All Turtles Chew Grass"
1. Adenine
2. Thymine
3. Cytosine
4. Guanine
c. Double Stranded
Strands held together by hydrogen bonds between bases
A with T (2 H bonds)
C with G (3 H bonds)
d. Strands twist to form a spiral : DOUBLE HELIX.
Watson & Crick - pieced together work performed by several other researchers;
deduced the structure of DNA. Received the Nobel Prize for Medicine in 1953
2. Ribonucleic Acid (RNA)
a. 5 carbon sugar is Ribose
b. Nucleotide bases "All Ungulates Chew Grass"
1. Adenine
2. Uracil
3. Cytosine
4. Guanine
c. Single Stranded
III. DNA Replication
A. Hydrogen bonds break - double strand "unzips".
26
B. "Old" strand acts as TEMPLATE for making "new" strand; Old strand determines sequence of new strand
C. New strand "complements" old strand; with opposite bases
D. This process is called SEMICONSERVATIVE REPLICATION: New double strand is 1/2 old and 1/2 new!
IV. Protein Synthesis
A. Central Dogma in Biology
codes for
DNA
codes for
mRNA
(Transcription)
POLYPEPTIDE
(Translation)
B. 20 biologically significant amino acids yet thousands of different polypeptides (proteins).
C. Triplicate Code
A sequence of 3 bases codes for one amino acid
Each AA is coded for by a 3 LETTER NAME spelled by a 4 LETTER ALPHABET!
The 3 letter name is termed a "CODON"
D. Degenerate Code
A code in which some words have the same meaning is said to be a degenerative code
Example: ACU ACC ACA ACG All code for Threonine
Why a Triplicate Code?
1. If only 1 nucleotide long – (41) – would only account for 4 AA. What would code for the other 16 AA's?
2. If only 2 nucleotides long – (42) – only 16 combinations. What would code for the remaining 4 AA's?
3. But if 3 nucleotides long – (43) – 64 codons would be possible. But, now, what about all the excess?
Are some AAs yet to be discovered? Not Likely
Are some of these codons just a whole lot of nonsense? No
Are some of these codons signals? Yes!
All but 3 of the 64 codons specify an AA – These 3 signal "TERMINATION"; an end to Protein Synthesis
E. Transcription
1. Process of copying DNA instructions (GENE) by the RNA
In copying DNA by RNA:
A -> U
G -> C
(“Transcription”)
T -> A
C -> G
2. RNA is single-stranded.
3. Three types of RNA
a. mRNA – Messenger RNA "The CARPENTER"
1. Carries codons for synthesis of a polypeptide
2. It is the transcribed DNA
3. Is carried out of the nucleus and taken to a ribosome
b. rRNA – Ribosomal RNA “Carpenter's "WORKBENCH"“
1. Ribosomes composed of 2 subunits – 50 S & 30 S
2. Ribosome assembles when mRNA binds to 30S subunit
Then the 50S subunit fits on top the mRNA/30S
The mRNA is sandwiched between the 2 subunits
c. tRNA – Transfer RNA "Carpenter’s Apprentice”
1. Carries the amino acid to the ribosome
2. There is a different tRNA for each AA
Has an attachment site for its AA
27
3. Has an "ANTICODON" that binds to an RNA CODON
If Codon is AAG Anticodon is UUC
F. Translation – process that builds a polypeptide by reading the instructions along the mRNA copy of the gene
a. mRNA enters cytoplasm. Attaches its 5' end to 30S subunit
b. tRNA anticodon aligns with starting codon on mRNA
c.
Larger ribosome subunit connects = INITIATION COMPLEX.
d. Ribosome moves along mRNA strand  Exposes next codon
e. A complementary tRNA ANTICODON for CODON attaches
f.
Positioning of 2 tRNAs holds 2 AAs so that a peptide bond forms between the AAs
g
First tRNA detaches – goes to find AA coded by its anticodon
REPEAT STEPS d – g FOR THE mRNA STRAND UNTIL A “STOP CODON” IS REVEALED
h. Ribosome eventually exposes a “stop” codon on the mRNA.
i. Polypeptide is released by ribosome – ribosome disassembles. End of Protein Synthesis.
V. Mutations
A. The genetic code is a triplicate code that shows degeneracy:
3 bases code for an Amino Acid “CODON”
Most Amino Acids have more than one Codon (This is very fortunate!)
B. The genetic code is universal – It is the same for every living organism
C. A random change in DNA sequence of bases which results in altered polypeptide is called a MUTATION
D. Substances causing mutations = "MUTAGENIC AGENTS" = UV light; X-rays; and many chemicals
E. Mutations of the DNA can be: HARMFUL even life-threatening; HELPFUL; or OF NO CONSEQUENCE
Many single base mutations probably do occur! But because of the degenerative code – good chance
that the resulting codon will still represent the same amino acid. Therefore no change in the resulting
polypeptide chain. (Only Methionine & Tryptophan codons have no degeneracy.)
SUBTITUTION MUTATIONS:
Example: SICKLED-CELL ANEMIA – caused by a single amino acid substitution in the hemoglobin
molecule of Red Blood Cells. Valine is bonded instead of Glutamic Acid
Hb A (normal):
--AA--AA--AA--PRO–GLU–GLU–LYS--AA--AA--AAHb S (sickled-cell): --AA--AA--AA--PRO–VAL–GLU–LYS--AA--AA--AAFRAMESHIFT MUTATIONS
1. DELETIONS – Loss of one or more bases from the DNA
2. INSERTIONS – Add an extra base (or more)along the DNA
Where in the gene these mutations occur will determine the severity of the altered polypeptide.
28
VI. Cellular Application and Disclaimer Statements
A. Participating Proteins
Transcription and Translation Enzymes act as signals and enzymes in nucleus and cytoplasm.
B. Cell differentiation
Nucleated cells in body (except eggs & sperm) have identical copies of every gene
However, different cells have different functions
Many of the genes on a chromosome are not "expressed".
Nucleated cell has a complete "library" but some of the books (genes) can not be "checked out"
But what if you could go to the cell and read all the books? This is the idea of CLONING!
C. Gene Regulation
Process that determines which genes are expressed and which genes are not expressed
Transcriptional and Translational Controls
Editing of mRNA in nucleus and in cytoplasm
Cleaving of polypeptide made at ribosome
D. DNA Fingerprinting
(LAB SUPPORTED)
1. DNA molecules are extracted from nucleated cells
2. DNA subjected to enzymes that break molecule into fragments called Restriction Fragment Length
Polymorphisms (RFLPs)
3. Load RFLPS onto one end of a thin gel plate and pass an electric current through gel.
Large RFLPs migrate through the gel at slower rate than short RFLPs. A banding pattern results.
Electrophoretic Analysis of RFLPs is used to:
Show % relatedness of two individuals
Attempt to show guilt (or innocence) of suspect(s) in criminal cases
Identify location of genes – Human Genome Project
Prenatal diagnosis of possible genetic disorders
29
The Genetic Code (for mRNA Codons)
First Base of
the Codon
U
U
Phenylalanine
Phenylalanine
Leucine
Leucine
Second Base of the Codon
C
A
Serine
Tyrosine
Serine
Tyrosine
Serine
STOP
Serine
STOP
G
Cysteine
Cysteine
STOP
Tryptophan
Third Base of
the Codon
U
C
A
G
C
Leucine
Leucine
Leucine
Leucine
Proline
Proline
Proline
Proline
Histidine
Histidine
Glutamine
Glutamine
Arginine
Arginine
Arginine
Arginine
U
C
A
G
A
Isoleucine
Isoleucine
Isoleucine
Methionine
Threonine
Threonine
Threonine
Threonine
Asparagine
Asparagine
Lysine
Lysine
Serine
Serine
Arginine
Arginine
U
C
A
G
G
Valine
Valine
Valine
Valine
Alanine
Alanine
Alanine
Alanine
Aspartic Acid
Aspartic Acid
Glutamic Acid
Glutamic Acid
Glycine
Glycine
Glycine
Glycine
U
C
A
G
How to Read the Codon Chart: (Easier than reading a road map!)
1. The 1st base of the mRNA Codon will indicate which ROW of Amino Acids (or STOP) is signified by the full Codon. You have limited the
possible 20 Amino Acids to a 4-line ROW containing between five to seven different Amino Acids.
2. The 2nd base of the mRNA Codon will indicate which COLUMN of Amino Acids (or STOP) is signified by the full Codon. You have now
limited the possible five to seven Amino Acids to a 4-line BLOCK of one or two Amino Acids (or a STOP).
3. 3rd base of the mRNA Codon will indicate a specific Amino Acid signified by the full Codon. Having determined the BLOCK by following
steps 1 and 2, now go to the grouping of UCAG on the far right-hand side of chart for that BLOCK/ROW and select the line in the BLOCK
that is for the third nucleotide base of the mRNA Codon.
EXAMPLE: mRNA Codon GAC. (1) Find G in far left-hand column of chart. Possible Amino Acids are Valine, Alanine, Aspartic Acid, Glutamic
Acid, or Glycine. (2) Find A in the midcolumns of chart. Possible amino acids now are either Aspartic or Glutamic Acid. (3) Find C in the UCAG
grouping in the right-hand column that corresponds to the BLOCK. C is the 2nd line of block, therefore mRNA Codon GAC is for Aspartic Acid.
Messenger RNA is synthesized, one chain of DNA (in region of a gene) serving as a template. This mRNA then goes into the cytoplasm and
becomes associated with ribosome subunits. Various tRNAs in the cytoplasm pick up amino acids for which they are specific and bring them to
the ribosome as it moves along the mRNA. Each tRNA Anticodon momentarily bonds to its exposed complementary mRNA Codon. This ordering
of tRNA molecules along the mRNA thereby puts in order the amino acids that are then linked together by peptide bonds. Synthesis of a
polypeptide chain proceeds one amino acid at a time in an orderly sequence as the ribosome move along. As each tRNA donates its amino acid
to the growing polypeptide it uncouples from mRNA and moves into the cytoplasm, where it will again pick up another amino acid specified by its
anticodon. Thus, tRNA is readied once again. These events will continue until a STOP codon along the mRNA is revealed.
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DNA-RNA WORKSHEET
PART ONE - TRANSCRIPTION & TRANSLATION
1. STUDY THE STRING OF NUCLEOTIDES SHOWN FOR EACH PROBLEM; DECIDE IF THE SEQUENCE
IS mRNA or DNA (SINGLE-STRANDED).
2 IF IT IS DNA - Transcribe it as to form the mRNA transcript. IF IT IS mRNA – Reverse the transcript
as to form the DNA "template"
3. TRANSLATE THE TRANSCRIPT – DETERMINE THE AMINO ACID SEQUENCE. Use the mRNA codon
chart found in your text, your lab manual, or your Lecture Outline.
*ANSWER KEY IS POSTED IN A DISPLAY CASE IN THE NATURAL SCIENCE BUILDING*
A.
1. DNA / mRNA
-T---C---G---C---C---A---C---G---T---C---A---G---C---A---T-2. -___-___-___-___-___-___-___-___-___-___-___-___-___-___-___3. -___________-___________-___________-___________-___________B.
1. ssDNA / mRNA
--G---A---C---G---U---C---C---A---C---A---U---C---G---A---C-2. -___-___-___-___-___-___-___-___-___-___-___-___-___-___-___3. -___________-___________-___________-___________-___________C.
1. ssDNA / mRNA
--T---C---A---C---A---G---G---C---C---A---C---A---A---G---A-2. -___-___-___-___-___-___-___-___-___-___-___-___-___-___-___3. -___________-___________-___________-___________-___________D.
1. ssDNA / mRNA
--A---C---C---A---C---G---A---U---U---U---G---A---C---C---A-2. -___-___-___-___-___-___-___-___-___-___-___-___-___-___-___3. -___________-___________-___________-___________-___________-
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