NOTES FOR BIOLOGY 101: Dr. Charles Masarsky,
Instructor (Chapter, Table & Figure numbers refer to the Campbell, et al text.)
LAB #1: Scientific Method: PP 3-7 in the lab manual, with modifications TBA.
LECTURE #1: Chapters 1&2
What Is Science?
Scientists seek to enlarge their knowledge of nature in a self-correcting way.
Someone cannot simply announce that his or her latest hunch is “new knowledge” and be
considered a scientist. A scientist is required to describe the process by which they
gathered observations that led them to this “new knowledge”. Other scientists can then
duplicate the same process or develop additional processes for gathering observations –
also known as data – relevant to the alleged “new knowledge”. If repeated future
observations fit the “new knowledge”, it gains scientific support. If some observations do
not fit, the “new knowledge” must be revised to explain all existing observations. Any
“new knowledge” in science must be tested with repeated, independent observations. It is
this self-correcting aspect of science that makes it different from most other methods of
gaining knowledge.
One method of gathering data is descriptive research. For example, the Spanish
scientist Santiago Ramon y Cajal looked at nerve cells in brain tissue and spinal cord
tissue under his microscope in the late nineteenth century. Everything he had read about
this tissue told him that the nerve cells are all directly connected to each other. However,
when he looked in his microscope, he saw gaps between the nerve cells in this tissue. He
carefully described his technique for preparing and examining his tissue samples. After a
number of years, many other scientists reported that they independently observed the
gaps first described by Cajal. Eventually, these gaps (later named “synapses”) were
considered critical to our understanding of the nervous system, and Cajal received the
Nobel Prize.
Another method of gathering data is experimental research. First, a scientist develops
an educated guess that will form the groundwork for an investigation into some aspect of
nature. Such an educated guess is called a hypothesis, from a Greek root meaning
“groundwork” (the word “hypothetical” comes from the same root). Often, a scientist’s
hypothesis will grow out of the observations typical of descriptive research. This is
followed by a type of reasoning that goes from the specific to the general. Such reasoning
is called inductive reasoning or induction. For example, in 1964, Aklilu Lemma, an
Ethiopian scientist, described a large number of dead snails close to where a group of
women were washing their clothing in a stream. He found out that the women were using
a local berry for soap. He hypothesized that the reason these specific snails were dying
was because the berry was poisonous to this variety of snail in general. Lemma’s
hypothesis was significant, because this particular type of snail carries a disease that
afflicts some 200 million people worldwide (schistosomiasis).
1
The next stage of experimental research is to develop a means of testing the
hypothesis. This usually requires a deduction – a form of reasoning that goes from the
general to the specific. For example, if the local berry is poisonous to the disease-carrying
snails in general, then an extract of the berry should kill live snails in the laboratory. This
type of formal test of a hypothesis that comes from deductive reasoning is an experiment.
Lemma did, in fact, perform this experiment. Dr. Makhubu continued this line of research
on the berry at the University of Swaziland, and the berry is now being used in the fight
against schistosomiasis.
Biology as a Science
Biology is the science of life. Living things and living processes can be studied with both
descriptive and experimental methods at many levels of organization. Some fields of
study within biology concern themselves with the largest level of biological organization
– the biosphere – the life-bearing layer of the planet Earth. Other fields of study within
biology study smaller-scale levels of organization. The smallest level of biological
organization is the molecule – the domain of biochemistry and molecular biology. Before
biologically significant molecules can be understood, even smaller levels of organization
have to be discussed. These levels form the domain of basic chemistry.
Basic Chemistry
Matter takes up space and has mass. An element is a form of matter that cannot be
broken down into another substance by chemical reactions. The smallest bit of an element
you can have without turning it into some other form of matter is an atom.
Atoms are composed of subatomic particles. The subatomic particles we will discuss
are protons, neutrons, and electrons. Most of the mass of an atom is in the protons and
neutrons, with the mass of the electrons being almost negligible. The unit used to
represent the mass of subatomic particles is the Dalton or the atomic mass unit (AMU). A
proton’s mass is approximately one AMU; same for a neutron’s mass.
An atom’s protons and neutrons are located in the center of the atom – the nucleus.
The electrons orbit about the atom.
The number of protons in the nucleus of an atom of a particular element is its atomic
number. Every atom of an element has the same atomic number. The atomic number is
written as a subscript to the left of the symbol for that element.
For example, the four most common elements in living organisms are carbon,
hydrogen, nitrogen and oxygen. Their chemical symbols, with their atomic numbers are
6C, 1H, 8O, and 7N. Other biologically significant elements include (but are not limited
to) phosphorus (15P), sulfur (16S), calcium (20Ca), potassium (19K), and sodium (11Na).
Although the atomic number of every atom of an element is the same, the atomic mass
can be different. Atoms of the same element but of differing atomic mass are called
2
isotope of that element. The atomic mass is usually noted as a superscript just above the
atomic number. Write the notation for the most common isotope of carbon – carbon
twelve:_____________. Some isotopes are unstable, and the nucleus will shed particles
and energy from time to time. These are radioactive isotopes. An example that is
important in certain lines of research is carbon fourteen.
LAB 2: Scientific Method, pages 7-9 in lab manual with modifications TBA
LECTURE 2: Chemical Bonding, Chapter 2, continued
The electrons orbiting the nucleus of an atom occupy various energy levels or
electron shells. The electrons in an electron shell have a natural tendency to pair up. Each
electron shell can only accommodate so many pairs of electrons. The number of electrons
orbiting an atom is normally the same as the number of protons in the nucleus. A diagram
of how the electrons are arrayed in their electron shells around a particular atom is called
an electron configuration.
The first electron shell can accommodate no more than one pair of electrons. So,
the electron configuration of 1H would be:
The electron configuration of helium (2He) would be:
Notice that the one electron shell of a helium atom is completely filled. An atom in which
the outer electron shell is completely filled is very stable – it does not have any tendency
to enter chemical reactions with other atoms. The chemical behavior of an atom depends
on the number of electrons in the outermost electron shell. This shell is called the valence
shell, and the electrons in that shell are called the valence electrons. Atoms with
completed valence shells, such as helium, do not readily enter chemical reactions with
other atoms.
The next two electron shells can accommodate a maximum of 4 electron pairs
each. An electron shell fills with unpaired electrons first; then the electrons begin to pair
up. So, the electron configuration of 6C would be:
The electron configuration of 7N would be:
The electron configuration of 8O would be:
The presence of unpaired electrons in the valence shell gives an atom a tendency
to chemically bond with other atoms. Chemical bonds tend to complete the valence shell
in one or both of the atoms involved with the bond. The periodic chart arranges atoms
with similar chemical properties in the same row. For example, He, Ne and Ar are all in
3
the same row, and they all have a completed outer valence shell – no unpaired electrons.
Therefore, these elements do not readily form chemical bonds.
H, on the other hand, has one unpaired electron in its valence shell. Therefore,
each H atom can form a single bond with another atom. For example, one H bond can
bond with another. By sharing their electrons, the H atoms complete each other’s valence
shells. This molecule of hydrogen would be represented in this way:
H-H
O has two unpaired electrons in its valence shell. Therefore, it can form two single
bonds, such as in water (H2O):
O
/ \
H H
O can also form double bonds, as in molecular oxygen:
O=O
C has four. N has three. These are also the number of bonds an atom of each of those
elements can form. The number of unpaired electrons in an atom’s valence shell also
represents the number of chemical bonds it can form, and is called the atom’s valence.
The sorts of chemical bonds in which the electrons are shared between atoms are
called covalent bonds. Sometimes the electrons in a covalent bond are shared more or
less equally between atoms. Such a covalent bond is called a nonpolar covalent bond.
The covalent bonds in molecular hydrogen and molecular oxygen are examples.
The amount of attraction an atom has for the electrons in a chemical bond is called
electronegativity. If one atom in a chemical bond is more electronegative than another, it
tends to hold the electron more closely. Such a bond is called a polar
covalent bond. For example, oxygen is more electronegative than hydrogen. Therefore,
the water molecule has a slightly negative pole at the oxygen side and a slightly positive
pole at the side with the two hydrogen atoms. Water is a polar molecule.
Extremely electronegative atoms can completely strip away an electron from another
atom. For example chlorine (17Cl) has one unpaired electron in its valence shell. So does
11Na. However, if chlorine completes its pair, it also completely fills its valence shell.
This makes chlorine very electronegative. When it bonds with sodium, it completely
strips away sodium’s one valence electron. In effect, sodium is left with a complete
valence shell (the second electron shell), because the one unaccompanied electron has
been stripped away from the third electron shell. Chorine also has a complete valence
shell (the third electron shell). This type of bond is called an ionic bond.
The formation of chemical bonds between atoms of different elements creates a
substance different than the original elements. For example, hydrogen and oxygen are
4
both colorless, odorless gasses at room temperature. Yet, when one oxygen atom and two
hydrogen atoms are combined with covalent bonds, they form water – a liquid at room
temperature.
To take another example, sodium is a metal, and chlorine is a toxic gas. Neither
substance is edible. Yet, when you combine an atom of each with an ionic bond, you
have table salt, which is often used to flavor food. (In general, ionic bonds form salts).
These substances such as water and table salt formed by fixed ratios of elements are
called compounds. They have properties completely different from the properties of the
individual elements composing them. These different properties that appear as you
combine simple components (such as atoms of elements) into entities with more
complexity (such as molecules of compounds) are called emergent properties.
Another example of emergent properties is the combination of one atom of carbon
– usually a black solid at room temperature – with four atoms of the colorless, odorless
gas hydrogen. The result is a combustible gas called methane. The molecular formula (a
“recipe” indicating the ratio of the elements composing a compound) for this gas is CH4.
The structural formula (a diagram indicating the single and double bonds) is:
H
|
H-C-H
|
H
Another example: hydrogen and nitrogen are both odorless gasses at room
temperature. However, combine them into ammonia, and you have a gas with a powerful
odor. Nitrogen, with a valence of three can combine with three hydrogen atoms. The
molecular formula for ammonia is NH3. The structural formula is:
The making and breaking of chemical bonds are called chemical reactions. The
starting materials are reactants, and the end results are products. If a reaction converts all
of the reactants into products, it is an irreversible reaction. However, most reactions are
reversible. For example, when hydrogen and nitrogen form ammonia, some of the
ammonia reverts to the original reactants. The chemical equation for this reaction looks
like this:
3H2 + N2 __________ 2NH3
LAB 3: Selected Properties of Water
In your experience, does water tend to flow uphill or downhill? _____________
A stalk of celery contains a great deal of water. Develop a hypothesis about what would
happen to the water in a stalk of celery placed in an upright position; would the water
move up or down in the stalk?__________________________________________
5
Experiment #1: Place 100 ml of water in a graduated cylinder, and add enough food
coloring to give it a definite color. Place a stalk of celery in the cylinder so that the
bottom of the stalk reaches all the way down to the bottom of the beaker. Put this
experimental preparation aside while you go on to the rest of the lab. When you remove
the celery stalk from the graduated cylinder at the end of the lab, do the results support or
refute your
hypothesis?______________________________________________________________
_______________________________________________________________________
Do these results suggest that water molecules are neutral, or that water molecules have
the ability to cling to the sides of a small tube, allowing a column of water to rise up a
plant?___________________________________________________________________
________________________________________________________________________
*
*
*
A water molecule is composed of two hydrogen atoms and one oxygen atom. Using
the periodic table in the back of your lab manual, calculate the mass of the typical water
molecule in A.M.U. (round off to the nearest A.M.U.). __________________________
Staples are made of steel. Steel is composed mostly of the element iron, also known as
ferrium, the chemical symbol for which is Fe. Using the periodic table, what is the atomic
mass of an iron atom? _________ Based on this information, plus your own personal
experience, which would you expect to be heavier – water or steel? ________ Based on
this understanding, develop a hypothesis about whether or not a steel staple will float or
sink in water.___________________________________________________________
Experiment #2: Hold a steel staple a few inches above the surface of a beaker of water.
Drop the staple. Do the results support or refute your hypothesis?__________________
Experiment #3: Place a steel staple on a piece of tissue paper. Using the tissue paper like
a stretcher or a hammock, gently lay the paper on the surface of the water. Observe what
happens to the staple. Do the results support or refute your
hypothesis?______________________________________________
Does the behavior of the steel staple suggest that water molecules are neutral, or
does this behavior suggest that water molecules are polar entities that can cling to each
other strongly enough to create a sort of “skin” on the surface of a quiet body of
water?____________________________________________________________ At a
naturally-occurring quiet body of water such as a pond, can you observe something that
behaves in a manner similar to the staple in Experiment 3? If so,
what?___________________________________________________________
*
*
*
In your experience, can two objects occupy the same space at the same time?
__________ Based on your answer, if you took an object whose volume was 10 ml and
6
another object whose volume was also 10 ml, how much space would you hypothesize
both objects together would occupy:________________________________________.
Experiment #4: Place 10 ml of water in a graduate cylinder. In another graduated
cylinder measure out 10 ml of table salt. You now have two 10 ml objects. Now, combine
them in one cylinder. How much space is occupied by these two objects
together?____________________ Do these results support or refute your
hypothesis?___________________________________ Table salt is primarily NaCl.
Molecules of NaCl are held together with ionic bonds, with the Na side being positively
charged and the Cl side being negatively charged. What property would a substance need
to be an excellent solvent of
NaCl?__________________________________________________________________
_______________________________________________________________________
*
*
*
Based on your experience, is sweating a common reaction of the human body to hot
weather? _____________ If the evaporation of water only took a small amount of heat,
would the human body’s reaction to hot weather be a good cooling
strategy?____________ How about if the evaporation of water took a large amount of
heat?______________________________________________
LECTURE 3: Chemistry of Water, Chapter 3
Because oxygen is more electronegative than hydrogen, and because the water
molecule is asymmetrical the molecule ends up having a positive pole and a negative
pole, like a battery or a magnet. The existence of poles makes water a polar molecule.
Just as the positive pole of a magnet will attract the negative pole of another magnet, the
positively charged hydrogen side of one water molecule will attract the negatively
charged oxygen side of another. This attraction between water molecules is the basis for
hydrogen bonding.
See Figure 3.2.
One of water’s emergent properties due to hydrogen bonding is the fact that water
molecules will attract each other. This property is called cohesion. A closely related
emergent property is the attraction of water for other substances. This property is called
adhesion. These two properties together explain the transport of water in plants such as a
tree (See Figure 3.3) or a stalk of celery (as in your lab experiment). Adhesion allows
water to stick to the walls of the water-conducting cells within the plant. Cohesion
preserves the integrity of this rising column of water, preventing the column from
breaking up.
A property directly resulting from cohesion is the formation of an ordered
arrangement of molecules that creates a sort of “skin” at the interface between a quiet
7
body of water and air. This property is called surface tension. Surface tension explains
the behavior of the paper clip in your lab experiment, and the water strider in Figure 3.4.
The energy of motion of any body is called kinetic energy. The total amount of
kinetic energy of the molecules composing any particular object is its heat. The average
kinetic energy of the molecules at a particular location in a particular object is that
location’s temperature. For example, a swimmer’s body may have a higher temperature
than the ocean they are swimming in, but the total heat of the ocean will be immensely
greater than the total heat in the swimmer’s body.
The amount of heat required to raise the temperature of one gram of a substance
one degree Centigrade is that substance’s specific heat. The specific heat of water is 1
cal/g/oC. This is greater than the specific heat of most substances, because the kinetic
energy of the heat must overcome the hydrogen bonds between water molecules before
the molecules will move faster. This makes water a good heat buffer, keeping most places
on earth within a range sustainable for life. (See Figure 3.5.)
Compared to most liquids, more heat is required to evaporate water. This is also
due to hydrogen bonding. One result of the heat absorbed and then carried away by water
during evaporation is evaporative cooling. This mechanism is the reason that sweating
and panting enable animals to cool themselves during hot weather.
Hydrogen bonding also causes water molecules to organize themselves into a
crystalline lattice when liquid water is frozen (Figure 3.6). This lattice structure locks the
water molecules into a less dense configuration than the than they assume in the liquid
form. Therefore, ice floats. Therefore, liquid water remains under a frozen pond, a frozen
lake, or the Arctic ice, enabling marine and aquatic life to survive.
The polar nature of the water molecule enables the oxygen end to pull at anything
with a positive charge, and the hydrogen to pull at anything with a negative charge. For
example, in table salt (NaCl), the oxygen ends of several water molecules will surround
the Na+ ion, while the hydrogen ends of several water molecules will surround the Cl- ion
(Figure 3.7). In other words, the polarity of the water molecule makes it a very versatile
solvent. A substance dissolved in water, such as table salt, is called a solute. Any solution
with water as the solvent is an aqueous solution. The vast majority of chemical reactions
in living organisms take place in aqueous solution.
If you take the molecular mass of a substance, but express it in grams, you have a
mole of that substance. A mole of a substance always contains the same number of
molecules (approximately 6.02 x 1023, which is called Avogadro’s number). If you
dissolve a mole of solute into one liter of water, you have a one molar (1 M) solution. For
example, table salt is NaCl. The atomic mass of Na is 23 AMU (rounded off to the
nearest AMU or Dalton), and the atomic mass of Cl is 35 AMU. Therefore, the molecular
mass of one molecule of table salt is 58 AMU. To make a 1 M solution, you would
dissolve 58 grams of NaCl into 1 liter of water. Biological functions require specific
molarities of certain substance to proceed normally.
In pure water, a very small percentage of molecules will break up into ions: H+
and OH-. If there are more H+ than OH-, you no longer have pure water, but a solution
known as an acid. If your have more OH- ions, you have a base. There is a scale to
represent how acid or how basic a solution is; it is called the pH scale (Figure 3.9). Pure
water has a pH of 7. The “ultimate” acid would have a pH of 0. The “ultimate” base
8
would have a pH of 14. Biological functions in any organism require a certain range of
pH levels.
Substances that resist changes in pH are called buffers. These substances can be
critically important in maintaining pH within tolerable limits for a particular organism.
9
LAB 4: Microscope – pp 12- 21
LECTURE 4: Building Blocks of Carbon-Based Molecules, Chapter 4
Hydrogen has 1 unpaired electron in its outer shell, giving it a valence of 1.
Oxygen has a valence of 2. Nitrogen has a valence of 3.
Carbon is very chemically versatile, because it has a valence of 4, giving it the ability
to bond with 4 other atoms. This makes it the backbone of a diversity of molecules.
Figure 4.4
10
Molecules formed of carbon and hydrogen only are hydrocarbons. They are found in
petroleum, and are major constituents of fats. Both petroleum and fats are formed with
mostly non-polar bonds, making them difficult to mix with water = hydrophobic.
Hydrocarbons can vary in length, they may include both single and double bonds, they
can involve branching, and can sometimes form ring structures.
Organic molecules with the same number of atoms of the same elements but different
structures are called isomers.
Figure 4.5
Figure 4.7
11
Although hydrocarbons are hydrophobic, they can be attached to certain other
chemical groups with more polar bonds. The resulting organic molecule becomes more
hydrophilic, and therefore soluble in water, and available for chemical reactions in
aqueous solution. These important portions of organic molecules are called functional
groups.
Functional groups include:
Hydroxyl group: When this group is the major functional group, the molecule is an
alcohol, which usually ends in the suffix “ol”.
-OH.
Carbonyl group: When this is the major functional group, and it is located at the
end of the carbon skeleton, it is an aldehyde. If it is within the carbon skeleton, it is called
a ketone.
\
C=O
/
Carboxyl group: When this is the major functional group, the molecule is an
organic acid. The H of this group tends to dissociate, giving up an H+ ion.
O
//
-C
\\
OH
Amino group: When this is the major function group the molecule is an amine. If it
also has a carboxyl group, it is called an amino acid.
H
/
-N
\
H
Sulfhydryl group: When this is the major functional group, the molecule is called a thiol.
-SH
Phosphate group: When this is the major functional group, the molecule is an organic
phosphate.
O
||
-O-P-O|
O
Methyl group: When this is the major functional group, molecule is a methylated
Figure 4.10
compound. (-CH3)
12
LAB 5: Microscope, p. 21-end
LECTURE 5: Macromolecules, Part I, Chapter 5
There are four main classes of large biological molecules: carbohydrates, lipids,
proteins, and nucleic acids. Some of these molecules are huge molecules called
macromolecules. Macromolecules are polymers (poly = many; meris = part), which are
made up of smaller units called monomers.
The typical monomer has at least one hydrogen atom and at least one hydroxyl
group at some site on the molecule. Building up polymers is generally done by bonding a
hydrogen atom from one monomer with a hydroxyl group from another, leaving the
original monomers bonded together and releasing a molecule of water. This process is
dehydration synthesis.
The reverse process – breaking a polymer down to smaller fragments, and
eventually to its individual monomers – is done by adding water. This process is
hydrolysis.
You can almost think of this as a more complex form of the changes you see
when water interacts with table salt. Adding water breaks the salt molecules down into
smaller units (sodium and chlorine ions) – a process analogous to hydrolysis. Taking the
water away (by evaporation, for instance) allows the sodium and chlorine to get back
together again, to form the larger unit – molecules of table salt.
See Figure 5.2
13
Carbohydrates
Think, “hydrated carbon”. The molecular formula for any carbohydrate is some
multiple of carbon plus a molecule of water – CH2O. The monomers of carbohydrates are
simple sugars, called monosaccharides. Sugars, including monosaccharides, usually end
in the suffix “–ose”.
Simple sugars are classified in two basic ways. One form of classification is by
the number of carbons in the molecule. For example, any 3-carbon sugar is a triose; any
5-carbon sugar is a pentose; any 6-carbon sugar is a hexose. Glucose is one of the more
important 6-carbon sugars in biology. Any hexose, including glucose has the molecular
formula C6H12O6.
The other form of monosaccharide classification is by the location of the carbonyl
group, which all simple sugars have. If the carbonyl group appears at one end of the
carbon skeleton, it is an aldehyde, which makes the sugar an aldose. Glucose is an
example of an aldose. On the other hand, if the carbonyl group appears within the carbon
skeleton, it is a ketone, which makes the sugar a ketose. For example, fructose, like
glucose, is a hexose, but it differs from glucose in being a ketose.
See Figure 5.3
The carbon atoms in a monosaccharide are numbered, with the carbon at the end
closest to the carbonyl group being carbon #1.
In aqueous solution, monosaccharides exist in both linear and ring forms.
See Figure 5.4
When monosaccharides are joined by dehydration synthesis, the resulting bond
between monosaccharides is called a glycosidic linkage.
See Figure 5.5
Very large carbohydrates include energy storage molecules, such as starch in
plants and glycogen in animals. Some large carbohydrates are not for energy storage, but
are used for structural purposes, such as cellulose and chitin.
See Figures 5.6, 5.8, and 5.10
14
Lipids
Lipids are mostly non-polar, and therefore hydrophobic. The most
characteristic lipids are fats. One building block of fat is the three-carbon alcohol known
as glycerol:
H
|
H-C-OH
|
H-C-OH
|
H-C-OH
|
H
The other building block of fat is a long hydrocarbon chain with a carboxyl group
at one end – a fatty acid:
O H HH
\\ | | |
C-C-C-C…………….etc.
/ | | |
OH H H H
In a dehydration synthesis reaction, the carboxyl group of the fatty acid gives up
its OH group, while an OH group of glycerol gives up a hydrogen atom. The result is the
creation of a water molecule and a bond between the carbon of the fatty acid’s carboxyl
and the oxygen of glycerol’s OH – an ester linkage. One fatty acid forms an ester linkage
to each OH site on the glycerol molecule. This combination of glycerol and 3 fatty acids
is a fat, aka a triglyceride.
If all of the bonds in the carbon skeletons of the fatty acids composing a fat are
single bonds, then the molecule is completely saturated with hydrogen – a saturated fat.
Saturated fats are solid at room temperature, and are often found in animal fats (the fats
in meat or in butter, for example). If some of the bonds in the carbon skeletons of the
fatty acids composing a fat are double bonds, then the molecule is not completely
saturated with hydrogen – an unsaturated fat. Unsaturated fats are liquid at room
temperature, and are often found in vegetable and fish oils. Certain isomers of
unsaturated fats – the trans isomers – are reputed to be even more of a risk factor for
cardiovascular disease than saturated fats. For this reason, there has been a lot of negative
press about trans fats.
See figures 5.11 and 5.12
15
In a phospholipid, there are two fatty acids attached to glycerol instead of
three. The third position on the glycerol is occupied by a phosphate group, which carries
a slight negative charge. This creates a long fatty acid “tail” which is non-polar, and
therefore hydrophobic, with a polar phosphate “head” which is hydrophilic. This feature
comes into play in the formation of the plasma membrane of a cell. The major building
block of such a membrane is a double layer of phospholipids, with the hydrophobic tails
inside and the hydrophilic heads in contact with the water outside.
Additional small molecules can be attached to the phosphate, creating a variety of
phospholipids.
See Figures 5.13 and 5.14
16
Cholesterol is a lipid with composed of four hydrocarbon rings, with a
hydroxyl group at one end. Cholesterol and all molecules built on cholesterol are called
steroids. Steroids are components of certain cell membranes and certain hormones.
See Figure 5.15
17
Nucleic Acids
In the 1980s, a series of satellite probes rendezvoused with Halley’s
comet, and analyzed the gasses in its tail. The basic elements necessary for life – carbon,
hydrogen, oxygen and nitrogen – are all present in the comet’s tail. Also, the % of each
element is approximately the same as that in a typical living organism. Yet, the tail of a
comet is not a living organism. You need more than just the right elements to make
something alive. A living organism is not just matter; it’s matter organized by biological
information. At the molecular level, this information is stored and handled by a class of
compounds called nucleic acids.
The monomer of a nucleic acid is called a nucleotide, which consists of a pentose,
a nitrogenous base, and a phosphate group. The pentose is either ribose or deoxyribose.
There is a numbering system for each of the five carbons in the pentose; the carbon that
sticks up from the ring is the #5 carbon, usually written as “5’carbon” (“five prime
carbon”). A phosphate group is attached to the 5’ carbon. A nitrogenous base is attached
to the 1’ carbon (the carbon at the end closest to the carbonyl group, in the sugar’s linear
form).
A nucleic acid built up from ribose monomers is ribose nucleic acid, or RNA. A
nucleic acid built up from deoxyribose monomers is deoxyribose nucleic acid or DNA.
DNA uses four nitrogenous bases: adenine, thymine, guanine and cytosine. In RNA,
adenine, guanine and cytosine are also used, but uracil replaces thymine.
Joining nucleotides together to form a polymer is accomplished by two pentose
sugars being linked by a phosphate group. This creates a backbone of repeating sugarphosphate units, with nitrogenous bases extending from the backbone. One free end of
the polymer is attached to the 5’ carbon, and is called the “5’ end”, while the opposite
end is attached to the 3’ carbon, the “3’ end”. The sequence of bases is the code for the
biological information that will organize matter into a living organism.
See Figure 5.27
18
DNA consists of two polynucleotide chains spiraled around each other, with each
base on one chain linked by hydrogen bonds to a base on the other chain. The result is a
molecule that looks like a spiral staircase, or a twisted ladder. This structure was first
described by James Watson and Francis Crick in 1953, and is called a double helix.
(Watson and Crick didn’t figure out the double helix all by themselves. Their work was
made possible by many years of research by other scientists, including Gordon Avery,
Maurice Wilkins, and Rosalind Franklin, among many others.)
The bases do not connect randomly. An adenine on one strand can only link to a
thymine on the opposite strand. A guanine on one strand can only connect to a cytosine
on the other. Also, moving from one end of the DNA molecule to the other, you are
moving from the 5’ end to the 3’ end of one strand, and the 3’ end to the 5’ strand of the
other, sort of like a divided highway.
A modified nucleic acid – adenosine triphosphate – usually abbreviate ATP, is
essential in any reactions involving the expenditure of energy.
See Figure 5.28
19
LAB 6: Chemical Aspects of Life, p. 26-31
LECTURE 6: Macromolecules, Part II, Chapter 5, continued
Proteins
Remove water from a typical living organism, and approximately 50% of
the dry weight will consist of proteins. The monomers from which proteins are built are
amino acids. Each amino acid consists of a carbon attached to a carboxyl group, a
hydrogen atom, an amino group, and a side-chain or “R group”:
H R O
\ | //
N-C-C
/
| \
H
H OH
Each amino acid is basically the same, except for the R group. The R group can
be as simple as a hydrogen atom; this would be the amino acid glycine. It can be as
complex as a nine-carbon side-chain with a double ring structure; this would be the
amino acid tryptophan. The R group determines the special chemical properties of the
amino acid. The R group can make the amino acid polar, non-polar, acidic or basic.
See Figure 5.17
Chains of amino acids, called polypeptides, are formed by dehydration synthesis.
A hydrogen atom from the amino group of one amino acid is combined with the hydroxyl
from the carboxyl group of another amino acid. A water molecule is released, and the two
amino acids are linked by a carbon-nitrogen bond, called a peptide bond. A chain formed
in this manner – a polypeptide – will have a free amino group at one end and a free
carboxyl group at the other.
See Figure 5.18
20
Long polypeptides with a complex three-dimensional structure are called
proteins. There are four levels of protein structure. One level is simply the sequence of
amino acids from the amino end to the carboxyl end of the polypeptide chain. This is
called the primary structure.
The polypeptide chain usually forms some sort of coil or pleated sheet. This shape
is held together by hydrogen bonds, and is called the secondary structure.
This coil or pleated sheet is folded into a more complex structure when in aqueous
solution. This is formed when water drives hydrophobic areas to the inside of the protein
molecule, with hydrophilic areas on the outside, in contact with the water. Ionic
interactions and bonds between sulfur atoms, called disulfide bridges, further maintain
this complex shape. This complex shape is the tertiary structure.
The final level of protein structure is created by more than one polypeptide chain
linked together. For example, a blood protein called hemoglobin has four chains wrapped
around each other. The structural protein collagen has three chains.
There are approximately 1.2 proteins of known primary structure. We only know
the full structure of approximately 8,500 of them.
The three-dimensional structure of protein determines its function. There are all
sorts of proteins with a variety of functions.
A protein’s three-dimensional structure is often a delicate thing. It often depends
on the existence of a specific range of temperatures, a specific range of pH, a polar or
non-polar environment, and a number of other factors. When these factors are altered, the
three-dimensional structure of the protein can be disrupted or destroyed. This disruption
of the protein’s structure is called denaturation. A familiar example of irreversible
denaturation takes place in the proteins of an egg when you boil it.
See Figures 5.21, 5.23 and Table 5.1
21
LAB 7: Enzymes, Part I, pp 34-38
LECTURE 7: Examination I (Note: I will announce any changes in the planned
exam schedule. This will only happen if the overall course schedule is disrupted due to
inclement weather or other unforeseen circumstances.)
LAB 8: Enzymes, Part II, pp 38-40
LECTURE 8: Introduction to the Cell, Chapter 6
It is quite difficult to see objects smaller than 0.3 millimeter in diameter, and most
cells are smaller than 100 micrometers (0.1 millimeter) in diameter. Therefore the
exploration of the cell requires the use of microscopes. Thanks to the development of the
microscope shortly before 1600, many observations of the microscopic world were made
during the 17th century. Hooke first described the cell in 1665, and van Leeuwenhoek
first described microorganisms shortly thereafter.
The light microscopes of today can achieve magnification of approximately
1,000x the object’s actual size, allowing clear visualization of 0.2-micrometer objects.
This allows visualization of all animal and plant cells, much of the internal structure of
these cells, and many bacteria. A micrometer is 1/1,000,000 (one millionth) of a meter. A
nanometer is 1/1,000,000,000 (one billionth) of a meter.
Visualization of the smallest bacteria, viruses, very small structures of animal and
plant cells and individual molecules requires the use of the electron microscope.
All cells are surrounded by a plasma membrane. The basic structure of any
plasma membrane is a double layer (or bilayer) of phospholipids, with the hydrophilic
phosphate heads on the outside and the hydrophobic fatty acid tails on the inside.
Embedded in this basic structure are various proteins and carbohydrates that provide
channels for certain substances to move into or out of the cell and receptor sites for the
recognition of certain chemical signal, among other functions. The plasma membrane
contains a fluid called cytosol. All cells also contain chromosomes, which carry most or
all of the cell’s DNA, and ribosomes – small pieces of cellular machinery where proteins
are synthesized. Small pieces of cellular machinery – including ribosomes – are called
organelles.
See Figure 6.7
Relatively small (typically1-10 micrometers) and primitive organisms such as bacteria
and archaea (more about these in a later lecture on classification) are prokaryotes.
Prokaryotic cells do not have any membrane-bound organelles. There is no true nucleus;
the DNA is located in a “nucleoid region” of the cell. Outside the plasma membrane is a
rigid cell wall. Outside the cell wall there is often a jelly-like capsule.
See Figure 6.6
22
Animals, plants, fungi, and microorganisms called protists are eukaryotes.
Eukaryotic cells are usually larger than prokaryotic cells, and have a much more complex
internal structure. The most striking feature of the eukaryotic cell is the presence of
membrane-bound organelles. The membranes of the organelles have the same
phospholipid bilayer framework as the plasma membrane. Many of these organelles are
connected, either by physical contact between their membranes, or by indirect contact
through tiny sacs of membrane (vesicles). This connected series of membrane-bound
organelles within the cell is referred to as the endomembrane system.
One structure on the endomembrane system is the nucleus, which contains most
of a eukaryotic cell’s DNA intertwined with specialized proteins. This complex of DNA
and protein is called chromatin. The DNA-bearing chromatin within the nucleus is
organized into a number of individual units called chromosomes. The nucleus also
contains ribosomal RNA, which will be combined with certain proteins to form the
building blocks of ribosomes. In addition, there is messenger RNA in the nucleus, which
carries the genetic instructions coded in the DNA to the ribosomes located outside of the
nucleus.
See Figures 6.10 & 6.11
23
Connected to the nuclear membrane is an extensive network of membranes called
the endoplasmic reticulum – the next structure of the endomembrane system. Some
regions of endoplasmic reticulum have ribosomes attached – rough endoplasmic
reticulum. These regions of the endoplasmic reticulum are devoted to the synthesis and
transport of certain proteins. Portions of the endoplasmic reticulum devoid of ribosomes
– smooth endoplasmic reticulum – are involved in a number of functions, including the
synthesis and transport of lipids, the detoxification of certain poisons, and the storage of
certain ions.
The next portion of the endomembrane system – the Golgi apparatus, processes
many of the substances produced and transported by the endoplasmic reticulum. The
Golgi apparatus is a cellular version of a package delivery system such as UPS or FedEx.
The packages delivered by the Golgi apparatus are vesicles. Larger vesicles are called
vacuoles.
See Figures 6.12, 6.13, & 6.14
24
One type of vesicle formed by the endoplasmic reticulum and then refined and
released by the Golgi apparatus is the lysosome – a sac of digestive enzymes. These are
found in animal cells only. Another characteristic of animal cells is a small organelle
called a centrosome, which contains centrioles; these organelles become important in cell
division.
Plant cells also have unique characteristics. A large vacuole in a plant cell, called
a central vacuole, serves as a storage compartment for nutrients and pigments, a place
where waste products are broken down to harmless chemicals, and a place where
macromolecules are hydrolyzed to their monomers. Just outside the plasma membrane, a
plant cell has a cell wall; a structure composed mostly of the polysaccharide cellulose,
which protects the cell and maintains its shape. There are small pores through the cell
walls that allow one plant cell to connect to another one; these pores are called
plasmodesmata. One of the most striking features of a plant cell is an organelle
containing a green pigment called chlorophyll. Chlorophyll – located in organelles called
chloroplasts - captures the energy of sunlight, and utilizes that energy to convert carbon
dioxide and water into simple sugars.
See Figures 6.9, 6.15, 6.14, & 6.18
25
Although most of a eukaryotic cell’s DNA is located in its nucleus, the
chloroplast contains its own DNA. Another organelle containing its own DNA is the
mitochondrion. The mitochondria are the energy-producing organelles of the cell. It is
here that sugars and other nutrients react with oxygen in a process that results in carbon
dioxide, water and ATP; this process is called cellular respiration. A cell may contain
hundreds or even thousands of mitochondria.
A membrane-enclosed compartment similar to a vesicle, but not formed by the
Golgi apparatus, is the peroxisome. This organelle synthesizes hydrogen peroxide (H2O2),
which is a caustic chemical. It is helpful in breaking down certain toxins, breaking down
macromolecules into smaller components, and several other functions. When there is an
excess of hydrogen peroxide, enzymes within the peroxisome break it down into water.
See Figure 6.17 and 6.19
26
A network of protein tubules and filaments maintains the structure of a cell. This
network is called the cytoskeleton. In addition to structural support, some types of
filaments can become shorter or longer. The cell can use this property to move, to change
its shape, or to move components around within the cytoplasm. Sometimes motile protein
tubules (microtubules) project to the outside of the cell, to form flagella or cilia.
See Table 6.1 and Figures 6.23, 6.25, & 6.27
27
LAB 9: Physical Aspects of Life: Diffusion, Osmosis, Plasmolysis
LECTURE 9: Membranes, Chapter 7
In the current concept of what membranes are like, the phospholipids,
which compose the framework of any biological membrane, are in constant lateral
movement. Smaller molecules such as H2O, O2, and CO2 are able to move through the
shuffling phospholipid molecules. Embedded in this moving (fluid) bilayer of
phospholipids is a mosaic of various proteins. This concept is called the fluid mosaic
model.
Plant cells have unsaturated fatty acids in their phospholipids. These unsaturated
fatty acids make plant cells resistant to freezing. Animal cells have saturated fatty acids
in their phospholipids, making them somewhat vulnerable to freezing. However, animal
membranes often include cholesterol molecules, which add a little bit of resistance to
freezing.
The embedded proteins serve a number of functions. Some of them transport
various substances across the membrane. Others are enzymes. Some are involved in
sending or receiving signals. A specialized group of proteins serve as identification tags.
There are other functions as well.
See Figures 7.5 and 7.9
28
Methods of transport across a membrane include diffusion. This is movement
from high concentration to low concentration, and does not require the expenditure of
cellular energy (does not require ATP). Therefore, it is a type of passive transport.
When water moves across a membrane from high to low concentration, this is a
form of passive transport called osmosis. Animal cells are vulnerable to changes in shape
due to osmotic pressures. For example, if you placed an animal cell in a solution with a
greater concentration of solute than the cytoplasm (a hypertonic solution), water would
leave the cell, causing it to collapse. If you placed an animal cell in a solution with a
lesser concentration of solute than the cytoplasm (a hypotonic solution), water would rush
into the cell and cause it to burst (lyse). The shape of a plant cell is supported by its cell
wall, so a hypertonic solution will not collapse the cell. However, the plasma membrane
more-or-less caves in within the cell wall (plasmolysis). The plasma membrane of a plant
cell will press against the cell wall in a hypotonic solution – such a cell is called turgid.
Some substances can diffuse across a membrane, but only if they are assisted by
specialized transport proteins. This form of passive transport is called facilitated
diffusion.
See Figures 7.11, 7.13 & 7.15
29
Forms of transport across a membrane that require ATP expenditure are forms of
active transport. Some of the most important active transport mechanisms are those that
help maintain a slight negative electrical charge on the inside of a cell and a slight
positive charge on the outside. It is as if a membrane’s outside is a positive pole – like the
positive pole of a battery or a magnet. The inside of the membrane forms a negative pole.
This existence of positive and negative poles creates a voltage across the membrane,
called a membrane potential. The existence of this membrane potential means that
cations (positively charged ions) are drawn into the cell and anions (negatively charged
ions) are driven out.
In animals, the main active transport mechanism that creates the membrane
potential is the sodium-potassium pump. This mechanism pumps Na+ ions out of the cell,
and K+ ions into the cell, with more Na+ going out than K+ coming in. The end result is a
slight positive charge on the inside of the membrane, positive charge outside.
In plants, fungi and bacteria, the membrane potential is created mainly by a
mechanism called the proton pump, which actively transports H+ ions out of the cell,
leaving the inside relatively negative, and the outside relatively positive.
In addition to the active transport mechanisms related to membrane potential,
there are mechanisms for transporting “bulk” – large molecules or particles – into and out
of the cell. These mechanisms involve the creation of membrane packages. Bulk transport
into the cell is called endocytosis. Endocytosis of a solid is called phagocytosis, and the
resulting package is called a food vacuole. Endocytosis of a liquid is called pinocytosis,
and results in a vesicle called a pinocyte. Receptor-mediated endocytosis involves the
engulfing of a receptor protein and the molecule it has recognized. The process opposite
endocytosis – exocytosis – removes substances from the cell by joining a vesicle to the
plasma membrane. This process is useful in secretion and excretion.
See Figures 7.16, 7.18 & 7.20
30
LAB 10: Cell Structure: pp 47-53
LECTURE 10: Cell Division, Chapter 12
The phases of cell division in eukaryotic cells are collectively called the cell
cycle. The cell cycle includes interphase, mitosis and cytokinesis. Interphase occupies the
majority of the cell cycle. During this time, the cell is mostly growing and occupying
itself with everything else it does besides dividing. The only event during interphase
directly related to cell division is the duplication of the cell’s nuclear DNA – the creation
of a copy of the cell’s genome. As a result of this DNA duplication, each chromosome is
also duplicated. During most of interphase, each chromosome consists of two arms of
DNA-protein complex (chromatids) joined together by a centromere. After duplication,
each of these arms is linked to a sister chromatid, which carries a copy of the original
chromatid’s genetic information. At this point, the chromosomes are not condensed into
compact bodies visible under the light microscope; they are in a sort of wispy, uncoiled
form.
The first phase of mitosis is prophase. (Note: In your text, the phase called
“prophase” in most texts is divided into “prophase and prometaphase”. For the purpose
of this class, the events described in your text’s description of prophase and
prometaphase will all be part of prophase. This will bring the description of mitosis in
line with the description in your lab manual.) During this phase, the nuclear membrane
dissolves, the chromosomes condense into their visible forms. The nuclear envelope (the
nuclear membrane) fragments and disappears. The centrosomes move to opposite poles
of the cell. A number of short microtubules extend from the centrosomes in animal cells,
creating a star-like formation called asters. Longer microtubules form a structure called
the mitotic spindle. Some of the microtubules reach the centromere of each chromosome,
attaching to a protein structure called the kinetochore – these are called the kinetochore
microtubules. Other microtubules interact with the microtubules from the opposite pole
of the cell, to complete the spindle. The sister chromatids of the chromosomes are joined
all along their length by specialized proteins.
In metaphase, which is typically the longest phase of mitosis, the microtubules of
the mitotic spindle manipulate the chromosomes towards the center of the cell. At this
point, if the centrosomes look like the North and South poles of the earth, the
chromosomes are arranged along the equator. This chromosome arrangement is called the
metaphase plate. Each kinetochore is attached to kinetochore tubules from opposite
poles.
In anaphase, an enzyme breaks down the specialized protein holding the sister
chromatids together. The sister chromatids separate, the centromere breaks apart, and two
identical chromosomes move to opposite poles of the cell.
In telophase, two nuclei form, and envelop the chromosomes. The chromosomes
become less condensed, reverting to their wispy interphase structure. This is the final
phase of mitosis.
See Figure 12.6
31
In cytokinesis, the last stage of the cell cycle, the cytoplasm divides to form two
new (daughter) cells. In animal cells, this division of the cytoplasm takes place at a
structure called the cleavage furrow. In plant cells, vesicles filled with the materials for
the construction of a cell wall are released by the Golgi apparatus and move to the middle
of the cell, forming a cell plate. This cell plate divides the cell into two daughter cells,
complete with new cell walls.
Prokaryotes – including bacteria – have much simpler cellular structures, and
therefore much simpler cell division. A bacterial cell simply replicates its single circular
chromosome, while the cell as a whole elongates to twice its original length. Afterwards,
the plasma membrane pinches inwards and creates two new bacterial cells. This process
does not involve a mitotic spindle, and is called binary fission.
See Figures 12.9, 12.10, and 12.11
32
In multicellular organisms, there are chemical signals that control the cell cycle.
For example, if you remove cells from the tissues of a multicellular organism and grow
the cells on a culture dish, the cells will usually divide until they form a single layer of
cells, and then cell division stops. This phenomenon is controlled by biochemical signals
given off by the cells when they reach a certain density, and is called density-dependent
inhibition.
In animal cells, division will usually not happen unless they are anchored to some
surface, such as the inside of the culture dish or the extracellular matrix of the tissue to
which they belong. When cell division depends in this way on anchorage to a surface, it
is called anchorage dependence.
Occasionally, a cell in a multicellular organism transforms to a state in which it
divides without the normal controls such as anchorage dependence and density-dependent
inhibition. A mass of such cells is called a tumor. If the tumor stays put, it is benign. For
example, a wart is an example of a benign tumor. If the tumor extends crab-like
appendages of itself to invade the surrounding tissue, such a tumor is no longer benign,
but is cancerous, and is called a malignant tumor. When pieces of the malignant
cancerous tumor break off and travel through the body, this process is called metastasis,
and the cancer is called a metastatic cancer.
See Figures 12.19 & 12.20
LAB 11: Cell Division: pp 53-60.
LECTURE 11: Cellular Respiration, Chapter 9
When a fuel is burned, the fuel reacts with oxygen; this is what most of us mean
when we say, “oxidation”. In chemistry, the term oxidation has a more general meaning –
it may or may not involve actual oxygen at all. In this more general sense, the term
oxidation means the loss of one or more electrons from a reactant. A specific example
would be the reaction of hydrogen with oxygen. The hydrogen, being less
electronegative, loses an electron to the oxygen. Therefore the hydrogen has been
oxidized. The opposite situation, the acquisition of one or more electrons, is reduction.
Therefore, in the aforementioned example, oxygen is reduced. Such reactions are often
called redox (reduction-oxidation) reactions.
Cellular respiration is a redox reaction in a food molecule such as glucose is
oxidized to carbon dioxide, while oxygen is reduced to water. This does not happen all at
once, as in a fire; it happens in a controlled, step-by-step manner, with each step
controlled by an enzyme. Cellular respiration takes place mostly in the mitochondria of
eukaryotic cells and the plasma membranes of many prokaryotic cells. The reaction
produces energy, primarily in the form of ATP:
33
C6H12O6 + 6O2 Æ 6CO2 + 6 H2O + Energy (ATP)
In the first phase of cellular respiration – glycolysis (“sugar splitting”) – the main
oxidation agent is not oxygen itself, but a positively-charged organic molecule derived
from the vitamin niacin – nicotinamide adenine dincucleotide (NAD+). In a series of
reactions involving NAD+ and ten different enzymes, glucose is oxidized to two
molecules of pyruvate (the ionized form of pyruvic acid). In the process, two molecules
of water are formed, along with energy in the form of two molecules of ATP. Glycolysis
takes place entirely in the cellular fluid – the cytosol. In the absence of oxygen, or in
organisms that normally live in an oxygen-poor environment, glycolysis is followed by a
reaction to renew the NAD+ for use in a new round of glycolysis. The end product of this
reaction – fermentation – is lactate (an ionized form of lactic acid) or ethanol. If oxygen
is present, cellular respiration proceeds to the next step, which takes place in the
mitochondrion of eukaryotes or the cytosol of certain prokaryotes – the citric acid cycle
(aka the Krebs cycle).
Figures 9.8 , 9.9 and 9.18
The citric acid cycle consists of eight steps in which a pyruvate molecule is
oxidized to carbon dioxide. In addition to NAD+, another oxidizing agent is also used in
this process – a molecule derived from the vitamin riboflavin called flavin adenine
dincucleotide (FAD). At the end of each round of the citric acid cycle, three molecules of
CO2 and one molecule of ATP are produced. This happens twice for each original glucose
molecule, because each glucose produces two molecules of pyruvate. Therefore, at the
end of glycolysis and the citric acid cycle, the oxidation of glucose has produced four
molecules of ATP.
Glycolysis has also produced two molecules of reduced NAD+ - NADH – for
every original glucose molecule. The two turns of the citric acid cycle produce an
additional eight NADH molecules, along with two molecules of the reduced form of FAD
– FADH2. NADH and FADH2 – are fed into the electron transport chain, the next phase
of cellular respiration.
See Figures 9.11 and 9.12
34
The electron transport chain utilizes a series of enzymes and electron carriers to
oxidize NADH and FADH2. One of the key electron carriers in the electron transport
chain is coenzyme Q (aka ubiquinone). The transfer of electrons is used to create a
gradient of H+ ions within different compartments of the mitochondrion – a process
called chemiosmosis. The pressure of this H+ gradient is used to activate an enzyme
called ATP synthase. This process is very productive of ATP molecules – 32 to 34 ATP
molecules are produced by the electron transport chain and chemiosmosis per glucose
molecule. All told, 36-38 ATP molecules are produced by complete cellular respiration of
one glucose molecule.
See Figures 9.13, 9.14, 9.16, and 9.17
35
LAB 12: Recipe Analysis
The following recipe for apple and banana fritters was modified from The Grand
Diplome Cooking Course, Volume 2, Anne Willan (Editor), The Danbury Press, 1972. p.
58.
I. Fritter Batter
Ingredients:
½ cup flour
Pinch of salt
2 egg yolks
1 tablespoon vegetable oil
½ cup milk
1 egg white
Method:
Sift flour with salt into a bowl, make a well in the center and add egg
yolks and oil. Add milk gradually, mixing to form a smooth batter, and beat thoroughly.
Store at cool room temperature (do not refrigerate) for 30 minutes. Just before use, whip
the egg white until stiff, and then fold into batter.
II. The Fritters Per Se
Ingredients:
2-3 tart apples
2 bananas
2 teaspoons lemon juice
fritter batter
approx ½ inch frying oil in frying pan
granulated sugar (for sprinkling)
Method:
Pare and core apples and cut into ½ inch slices. Peel bananas and cut
diagonally into 3-4 pieces. Sprinkle the fruit slices with lemon juice.
Heat the oil to 350-375 degrees F. Coat half of the fruit with batter. Remove from
batter with a slotted spoon and place into the oil. Fry until golden brown. Drain fried
fritters on paper towels, then arrange on a platter.
Repeat with the remaining fruit. Sprinkle the finished fritters with powdered sugar
before serving.
36
Questions for Recipe Lab
H
|
H-C-OH
|
H-C-OH
|
H-C-OH
|
H
1. What is the name of this monomer?___________ What large biological molecules
does this monomer contribute to?______________ What recipe ingredients are
especially rich in this type of biological molecule?________________________
If you substituted butter for vegetable oil in the batter, what would it be harder or
easier to beat, and why? _________________________________________
H
R O
\ | //
N-C-C
/
| \
H H OH
2. What is the name of this monomer? _________ What large biological molecules are
composed of this monomer?_____________ What recipe ingredients are especially rich
in this type of biological molecule?______________________________ As the fritters
are browned, what is the heat of frying doing to the structure of these biological
molecules?_____________________ Can this process be reversed?_____________
What sorts of bonds are being affected by the heat in this process?______________
3. Is the pH of these fritters high, low, or neutral, and
why?_______________________________________________________
4. In which ingredients would you find sugars?_____________________
Starches?____________________________________ Structural
carbohydrates?______________________________________
37
5. If you decided to serve these fritters with wine, what alcohol would be found in
that beveredge?_______________________ Draw the structural formula for that
alcohol:
What stage and process of cellular respiration is responsible for that alcohol?
________________ Is that a high-yield or low-yield process in terms of ATP
production?_____________________________
LECTURE 12: Meiosis, Chapter 13
The basic unit of hereditary information is the gene. The genes in eukaryotes are
coded in the DNA located in the chromosomes. A gene’s specific place on a chromosome
is called its locus.
Some organisms can reproduce without a partner, producing genetically identical
copies of themselves – clones. This is accomplished through mitosis or binary fission,
and is called asexual reproduction. This form of reproduction does not produce very
much variation from one generation to the other. What little variation does occur takes
place entirely due to accidental changes in genes – mutations.
There is another form of reproduction that requires two parents, and produces great
variation from one generation to the other – sexual reproduction. This form of
reproduction requires a type of cell division involving a process called meiosis, in which
each original cell produces four cells with half the usual number of chromosomes. These
cells are called gametes. Meiosis alternates with fertilization in the life cycle of a sexually
reproducing organism.
Cell not involved in gamete production are called somatic cells. In humans, each
somatic cell has 46 chromosomes. 23 of these are from one’s biological mother, and 23
from one’s biological father. If images of chromosomes are arranged starting with the
longest, the result is a karyotype. Most maternal chromosomes can be paired with a
paternal chromosome of equal length; these paired chromosomes are called homologous
chromosomes or homologs. The chromosomes determining a person’s gender are called
the X and Y chromosomes; collectively they are the sex chromosomes. All other
chromosomes are autosomes.
The number of chromosomes in each set – maternal and paternal – is referred to as n.
The number of chromosomes in the normal somatic cell (46 for humans) containing both
sets is referred to as 2n. A cell containing 2n chromosomes is diploid cell, while a cell
containing n chromosomes is a haploid cell. In meiosis, one diploid cell (a germ cell)
produces four haploid cells (gametes).
See Figures 13.2, 13.3, 13.4, 13.5, & 13.7
38
The phase of a germ cell’s life cycle prior to meiosis – interphase – is characterized by
the replication of the chromosomes – just as in mitosis.
The first phase of meiosis is prophase I. Just as in mitosis, the nucleus disintegrates,
and a spindle forms. What is different is that homologous chromosomes pair up and align
with each other – a process called synapsis. This pairing of a chromosome with its two
sister chromatids and a homologous chromosome with its sister chromatids is called a
tetrad. During this process, segments of homologous chromosomes may get stuck to each
other; these stuck-together segments are called chiasmata. At these places, DNA from
one chromosome may be exchanged with the DNA of its homolog – a process called
crossing over. The DNA of these chromosomes is now a new combination of genes; such
chromosomes are called recombinant chromosomes. The creation of recombinant
chromosomes by crossing over during the synapsis of prophase I is one source of
variability in sexual reproduction.
In metaphase I, the pairs of homologous chromosomes – the tetrads – are lined up in a
metaphase plate. Not all of the maternal chromosomes are on the same side of the plate;
neither are all of the paternal chromosomes.
In anaphase I, enzymes break down the proteins responsible for causing the homologs
to stick to each other, and the homologs move towards opposite poles of the cell. Because
of the arrangement noted in metaphase I, not all of the paternal chromosomes will end up
on the same side; neither will all of the maternal chromosomes. This phenomenon is
called independent assortment.
In telophase I, the movement of the homologous chromosomes away from each other
is complete. New nuclei may or may not form, depending on the species. Cytokinesis
follows, just as in mitosis.
Prophase II, metaphase II, anaphase II, and telophase II resemble the equivalent
phases of mitosis, except that sister chromatid separation will take place with only the
haploid number of chromosomes. Also, due to the crossing over that took place in
prophase I, not all of the sister chromatids are identical any more. After cytokinesis, the
original germ cell has yielded four gametes.
Due to crossing over, any gamete you produce can have any one of 223 combinations
of your maternal and paternal chromosomes. If one of your gametes meets someone
else’s in the fertilization process, approximately 70 trillion combinations are possible.
Added to this is the variation due to crossing over. When you consider all of these
factors, it is understandable that sexual reproduction is a powerful generator of genetic
variation.
See Figures 13.8, 13.9, 13.11 &13.12
39
LAB 13: Review for Lab Midterm
LECTURE 13: Exam 2
40
LAB 14: Midterm Test
LECTURE 14: Mendelian Genetics, Chapter 14
Beginning around 1857, an Austrian monk by the name of Gregor Mendel began a
series of experiments on heredity. He chose pea plants, because there are many varieties,
and they are normally self-pollinating, so pea plants tend to be true-breeding: tall plants
produce only tall plants, plants with green seeds only offspring with green seeds, and so
forth. A pea plant can only be pollinated by a pea plant other than itself if the gardener
carries out the pollination artificially; this enabled Mendel to perform carefully controlled
crosses.
Up until the time of Mendel’s work, it was assumed that hereditary material from both
parents would simply blend. So, if you pollinated a tall pea plant with a short pea plant,
you would get a pea plant intermediate in height. If you crossed a pea plant with green
seeds with one with yellow seeds, you would get a plant bearing yellow-green seeds. This
was called the blending hypothesis of inheritance.
Much to Mendel’s surprise, when he crossed a pea plant with purple flowers with a
plant with white flowers, all of the plants of the next generation produced exclusively
purple flowers, not a pale purple. These results refuted the blending hypothesis. In an
experiment like this, the original purple and white flowers are the parental generation,
usually symbolized by the letter P. The next generation is the first filial generation,
usually symbolized by the letter F with the subscript 1: F1. When Mendel crossed one F1
plant with another, the resulting F2 plants had either pure purple or pure white flowers.
The ratio of purple to white flowers in this generation was 3:1. Mendel got similar results
when performing crosses involving stem length, seed color, seed size, and a number of
other characteristics.
Mendel developed a new hypothesis to replace the blending hypothesis. First, he
proposed that heritable factors (which in modern parlance, we call genes) come in two or
more alternative forms, accounting for differences in inherited characteristics. Today, we
refer to these alternative forms as alleles. Second, he proposed that each organism
inherits two alleles, one from each parent. Third, if the alleles in an organism differ, one
will dominate, and completely determine the observable expression of the inherited
character in the organism. The allele that dominates is called the dominant allele, and the
other is the recessive allele. Fourth, when an organism creates gametes, the two alleles
for a heritable character separate, with any one gamete having a 50:50 chance of getting
one allele or the other. This is called the law of segregation.
The genetic makeup of a parental organism’s gametes and the resulting genetic
makeup of possible offspring – genotype – and the observable expression of the trait
inherited by the offspring – phenotype – can be diagrammed in a format called the
Punnett square for clear analysis. When you do this, taking dominance and segregation
into account, you have a very good explanation of Mendel’s experimental results.
See Figures 14.1, 14.2, 14.3, Table 14.1, Figure 14.5 & 14.6
41
An organism with a pair of identical alleles for a trait is homozygous, while one with
two different alleles is heterozygous. To find out whether a plant with the dominant
phenotype (purple flowers, for instance) is homozygous or heterozygous, you can cross it
with an organism of recessive phenotype. This is called a testcross. In the plant in
question is homozygous, the testcross will produce offspring with all dominant
phenotypes, just like the F1 generation in Mendel’s experiment with purple and white
flowers. If the plant in question is heterozygous, ¼ of the offspring will have the
recessive phenotype, just like the F2 generation in Mendel’s experiment.
In later experiments, Mendel went on to follow two heritable characters in his crosses
instead of one. He found that the two characters are not transmitted to the progeny as a
package, but rather each pair of alleles segregates independently of each other pair of
alleles during gamete formation. This is known as the law of independent assortment.
See Figures 14.7, 14.8, & 14.9
42
The pea plant characteristics that Mendel was fortunate enough to choose were fairly
simple to follow, because they exhibited complete dominance. There are some instances
in other organisms that demonstrate incomplete dominance. For example, if you breed
red snapdragons with white snapdragons, you get a pink flower.
There are also instances where there are more than two alleles – multiple alleles. An
example of great practical significance in health care is the ABO system of antigens
(substances that can cause an immune response) on red blood cells. Allele “IA” causes a
person’s red blood cells to produce the A antigen. Allele “IB” causes the red blood cells to
have the B antigen. Allele “i” does not cause the production of any antigen in the ABO
blood group. Any human receives one of these alleles from their biological mother and
one from their biological father. The combinations of alleles represent the four blood
groups.
In Mendel’s pea plants, each gene seemed to be responsible for a single trait. There
are some genes, however, which create more than one phenotypic effect. This
phenomenon is called pleiotrophy. For example, there are plants in which one gene
controls both flower color and seed color.
Sometimes a gene at one locus affects the expression of a gene at a second locus epistasis. For example, black fur is dominant to brown in certain species of mice. The
alleles are generally represented as B for black and b for brown. However, these alleles
alone will not determine the mouse’s fur color. There is an epistatic gene for pigment,
and only if the dominant allele is present – C – will there be color at all. If the mouse has
inherited the recessive pigment allele from both parents – cc – then the mouse will be
albino.
Since you cannot carry out experimental breeding experiments on human beings,
human genetics is studied examining matings that have already occurred. This process is
called pedigree analysis. A number of human traits follow Mendelian inheritance
patterns, and can easily be studied by pedigree analysis.
See figures 14.10, 14.11, 14.12, 14.15, 14.16 & 14.17.
43
LAB 15: Mendelian Genetics, pp 66-82 – selected topics
LECTURE 15: Chromosomal Basis of Inheritance, Chapter 15
In the late nineteenth century, cytologists discovered and observed chromosomes in
dividing cells. Mendel’s Law of Segregation and Law of Independent assortment seemed
to correspond with the behavior of these chromosomes. These observations led to the
theory that chromosomes carried the genes described by Mendel.
The chromosome theory of inheritance was strengthened by Morgan’s work with the
species Drosophila melanogaster. This species of fruit fly has four easily-observed
chromosomes – three autosomes and the sex chromosomes. Just as in humans, the male
genotype is XY, and female genotype is XX.
Morgan discovered a male fruit fly with a mutant phenotype – white eyes. The typical
– or wild – phenotype is red eyes. When he crossed the mutant male with a normal
female, all of the offspring had red eyes, suggesting that the wild-type allele is dominant.
However, in the F2 generation, only male flies had the mutant trait. This suggested that
the allele for this trait was located on the X chromosome, with no corresponding allele on
the Y. This was the first evidence of a specific gene being carried by a specific
chromosome.
A gene located on either sex-linked chromosome is a sex-linked gene. In humans, sexlinked genes are responsible for a number of traits, including normal color vision, and its
mutant allele, color blindness.
Only one X chromosome is active in a cell. If the individual is female (in a species
where the XX individual is female), one X becomes inacitivated. The inactivated X
chromosome is visible as a compact object in the nucleus called a Barr body. Which X
chromosome will become inactivated is random, so the individual becomes a mosaic of
cells in which either the paternal X or the maternal X is active.
See Figures 15.2, 15.3, 15.4, 15.5, 15.7 & 15.8.
44
Morgan found some traits that did not seem to obey the Law of Independent
Assortment, but rather seemed to be inherited together. He concluded that the genes for
these traits must be located on the same chromosome. Such genes are called linked genes.
Sometimes, linked genes undergo recombination as a result crossing over, and wind
up on different chromosomes. The further apart two genes are on a chromosome, the
more likely this is to happen. The percentage of recombination of two linked genes is
expressed as the number of map units apart they are on the chromosome.
See Figures 15.9, 15.10, & 15.11
45
Sometimes, there are errors in the process of meiosis, such that homologous
chromosomes are not separated during meiosis I, or sister chromatids fail to separate
during meiosis II. This is called nondisjunction. The result is one gamete with an extra
chromosome, and one gamete with a chromosome missing. In the resulting zygotes, one
will be monosomic for that chromosome, and the other will be trisomic.
For example, trisomy of chromosome 21 in humans results in Down syndrome, which
causes mental retardation, heart defects, and a number of other health problems. Human
males with an extra X chromosome (Klinefelter syndrome) and human females with a
missing X chromosome (Turner syndrome) are sterile.
There are traits not inherited through chromosomal DNA, but rather through the DNA
of the organelles. Chloroplasts in plants and mitochondria in all eukaryotes contain their
own DNA.
See Figure 15.13, 15.16, 15.19.
46
LAB 16: Mendelian Genetics, pp 66-82 – selected topics
LECTURE 16: Molecular Genetics, Chapter 16
The chromosome theory of inheritance implied that the genetic code was located on
one of the chemical components of the chromosome, but which one? The code either had
to be on DNA or on protein.
In 1928, a British medical doctor (Frederick Griffith) mixed a harmless strain of the
bacteria Streptococcus pneumonia with the cellular remains of heat-killed cells of a
disease-causing (pathogenic) form of the bacteria. Some of the harmless bacteria turned
into pathogenic bacteria. Griffith had no evidence that DNA from the pathogenic strain
was the culprit, but today we recognize that cells can incorporate external DNA, thereby
changing the cell’s genotype and phenotype. This process is called transformation.
Following up on Griffith’s experiment, American bacteriologist Oswald Avery used
treatments to inactivate the RNA, the DNA, or the protein of the heat-killed pathogenic
bacteria. Only when he allowed the DNA to remain intact did transformation take place.
By 1944, Avery and his colleagues were able to announce that DNA was the
transforming agent – a major piece of evidence indicating that DNA is the molecule that
contains the genetic code.
In 1950, the biochemist Chargaff demonstrated that different species had different
percentages of the four nitrogenous bases in their DNA – further evidence of the role of
DNA as the molecule of inheritance. Chargaff also noted that the adenine was always
present in the same ratio as thymine, while guanine was always present in the same ratio
as cytosine. Any future model of DNA’s structure would have to take this into account.
Further evidence implicating DNA as the carrier of the genetic code came from an
experiment by Alfred Hershey and Martha Chase in 1952 involving a virus. There is a
virus known as the T2 phage, which infects the bacterium Escherichia coli. When
infection takes place, the virus forces the bacterial cell to make copies of the virus. It was
known from previous research that the T2 phage consists almost entirely of protein and
DNA, just like a chromosome. Hershey and Chase prepared batches of T2 phage tagged
with a radioactive isotope of sulfur, and another batch with a radioactive isotope of
phosphorus. DNA is rich in phosphorus, while protein is rich in sulfur; therefore, the
isotopes would enable the scientists to track protein and DNA movements into the
infected cells. They found that only the radioactive phosphorus entered the bacteria,
indicating that the viruses injected DNA, not protein, into the cells to infect them.
See Figures 16.2, 16.3, 16.4, and 16.5
47
After absorbing the results published by Griffith, Avery, Chargaff, Hershey and
Chase, the scientific community was in substantial agreement that DNA was the
substance of heredity. Now, the race was on to figure out the three-dimensional structure
of this critically important molecule.
One of the scientists working on the problem was Rosalind Franklin of King’s
College, England. She was gathering data on DNA structure by passing x-rays through
fibers of DNA, and photographing the resulting patterns. This technique is called x-ray
diffraction. Another King’s College scientist, Maurice Wilkins, took one of Franklin’s xray diffraction photographs to James Watson at Cambridge. Based on Franklin’s data,
Watson and his research partner Francis Crick quickly solved the DNA puzzle with their
now-familiar double helix model in 1953. Their model positioned adenine in such a way
that it could form hydrogen bonds only with thymine, and guanine could only hydrogen
bond with cytosine. This explained Chargaff’s findings. This rule for base pairing also
implied that one strand of DNA could form a template for the other. Based on this,
Watson and Crick proposed a mechanism for DNA replication in 1954.
In the years since the critical publications by these scientists, molecular biology has
acquired much additional information about the DNA replication process.
See Figures 16.6, 16.1, 16.7, 16.8, and 16.9
FYI, See Figures 16.12, 16.13, 16.14, 16.15, and 16.17.
48
The DNA replication process is not free of error. An error in sequence takes place in
approximately one out of every 100,000 bases. There are systems of enzymes in all
organisms studies so far that proofread and repair the base sequence in replicating DNA,
to limit the number of errors that get passed down to the next generation of cells. One of
the more important systems is called nucleotide excision repair. On the other hand,
certain factors in the environment can increase the number of errors in DNA replication.
These factors can be chemical (asbestos, certain components of cigarette smoke, etc.) or
physical (x-rays, ultraviolet rays, etc.).
In eukaryotes, the ends of DNA molecules are sometimes lost in the replication
process. Fortunately, the segments of DNA at the ends of the molecule do not contain
genes. These non-coding segments of DNA are called telomeres. With each successive
mitotic division, a telomere tends to shorten. Once the telomere is gone, actual gene
degeneration may take place. There are some scientists who hypothesize that telomere
shortening may be one of the molecular components of the aging process.
See Figures 16.18, 16.19 and 16.20
49
LAB 17: The DNA Molecule
LECTURE 17: Protein Synthesis, Chapter 17
Bread mold can grow on a very minimally nutritious jelly or agar called minimal
medium. In the late 1930s, George Beadle and Edward Tatum bombarded bread mold
with x-rays, and discovered mutant bread mold that did not grow on minimal medium. By
preparing a series of media with various amino acid combinations, they discovered that
only one amino acid supplement was necessary for the mutant mold to grow. From this,
they determined that the mutation must involve a single gene that produces a single
enzyme involved in the synthesis of a single amino acid. This led them to the idea that
each gene was responsible for the production of one enzyme – the one gene – one enzyme
hypothesis. Today, we understand that genes may carry the code for all sorts of proteins
and smaller polypeptides, not just enzymes. Also, genes can carry the code for specific
RNA molecules that never get translated into proteins. The most frequent genes code for
polypeptides, so one gene – one protein covers most situations (the more complete rule
would be one gene – one polypeptide or RNA).
In the eukaryotic nucleus, when it is time for a gene to become active, the DNA
molecule will “unzip” to expose the base sequence of that gene. A strand of RNA will be
synthesized according to a base-pairing rule similar to the one for replicating a new DNA
molecule. The only difference is that adenine in DNA will form a hydrogen bond with
uracil from RNA rather than thymine. The resulting strand of RNA carries the genetic
code for the polypeptide out of the nucleus, and is called messenger RNA or mRNA.
Because mRNA carries a transcript of the gene, the process of producing the mRNA
strand is called transcription.
After transcription, the information coded on the mRNA must be translated into the
polypeptide – a process called translation. Translation takes place at the ribosome.
See Figures 17.2 and 17.3
50
The “letters” of the DNA “language” are the bases are the bases adenine, thymine,
guanine and cytosine. The “words” are each three bases long, each three-base sequence
standing for an amino or a “start” or “stop” signal directing RNA where to begin
translating the protein. These three-base sequences are called triplets.
The mRNA language is the same language, just a slightly different “dialect”, in which
uracil is substituted for thymine, as explained before. The three-base sequences in mRNA
are called codons. At the ribosome, the mRNA will be exposed one codon at a time.
Floating in the cytoplasm of the cell are short segments of RNA only three bases long.
These short pieces of RNA are each attached to an amino acid. This RNA is called
transfer RNA or tRNA. The three-base sequence on the tRNA is the complementary
sequence to the codon representing that amino acid, and is called an anticodon. The
anticodon will base-pair with the codon, placing the first amino acid in just the right
place.
For example, let’s say the first amino acid in a protein is phenylalanine. The DNA
triplet for the amino acid phenylalanine is adenine-adenine-adenine, or AAA. The mRNA
codon is UUU. At the ribosome, the tRNA anticodon AAA pairs with the mRNA codon
UUU. The tRNA is attached to the amino acid phenylalanine. The first amino acid is now
in place.
After this, the ribosome will expose the next mRNA codon, which will be joined by a
tRNA anticodon, placing the next amino acid in the right sequence. This is done again
and again, until all of the amino acids have been placed in the proper sequence. The
tRNA disengages from the amino acids, and the translation of the protein is complete.
Naturally, a complex series of enzymes control the processes of transcription and
translation.
See Figures 17.4, 17.5, and 17.13.
FYI, See Figures 17.7, 17.8,17.9, 17.10, 17.11, 17.12, and 17.14-17.21
51
LAB 18: Taxonomy, pp 86-89 (Note: Your lab manual uses a five-kingdom system of
taxonomy. This is a bit different from the system in Chapter 26 of your textbook, which
uses a system of three domains. I will explain this a bit during the lab with, hopefully, a
minimum of confusion.)
LECTURE 18: Exam 3
LAB 19: Taxonomy, pp 86-89
LECTURE 19: Darwinian Theory, Chapter 22
The ancient Greek philosopher, Aristotle, maintained that species were unchanging,
and had been present since the world’s earliest times. Each species had a particular level
of complexity, one species being higher or lower than another on the “scale of Nature”.
The eighteenth Century Swedish physician and botanist, Linnaeus, also saw species as
unchanging entities present since the beginning of Creation. He developed a system of
grouping similar species together in genera (plural for genus). Since the time of
Linnaeus, the scientific name for any organism is a two-part or binomial name. The genus
name is capitalized, and the species name is not; both parts of the binomial name are
underlined or italicized. For example, the scientific name for our species is Homo
sapiens.
During the late eighteenth and early nineteenth Centuries, the French scientist Georges
Cuvier compared fossils from layers or strata of sedimentary rock laid down at different
times. He noticed that the older the stratum, the more dissimilar its fossils were compared
to current life forms. He also noted that from one stratum to the next, some new species
appeared, while other species disappeared. These were important observations supporting
the idea that species were not unchanging categories
A new graduate of Cambridge University in divinity by the name of Charles Darwin
was a naturalist by inclination. In 1831, he joined the survey ship HMS Beagle in a fiveyear voyage around the world. During this time, he collected a huge number of plant and
animal specimens, both contemporary and fossilized. His observations of coral atolls led
him to believe that they took approximately one million years to form – suggesting that
the earth is much older than many of his contemporaries supposed. He found fossils of
marine organisms high in the Andes, suggesting that these mountains were once under an
ocean, yet another indication of the earth’s great age and changeability. Darwin also
noted that the animals of the Galapagos Islands, while somewhat similar to mainland
South American animals, were clearly unique species. Darwin hypothesized that South
American animals had colonized the Galapagos, and that these animals had somehow
adapted to their new habitat, thereby changing into new species.
Back home in England, Darwin pondered his experiences. In 1844, he crystallized his
ideas in an essay on what he called descent with modification. He further developed these
ideas in the 1858 book, On the Origin of Species. (The term “evolution” was not used
52
until the book’s sixth edition.) The key idea behind descent with modification is the
process of natural selection. In brief, Darwin maintained the following:
1. Members of a population of organisms often show a great deal of variation in
heritable traits.
2. All species are capable of producing more offspring than the environment can
support. Therefore, many of those offspring do not survive. (The book, Essay on
the Principle of Population by Thomas Malthus influenced this idea. Malthus
maintained that the human food supply could not keep up with human population
growth in the long run. Darwin applied this idea to the broader natural world.)
3. Some individuals will have heritable traits better suited to survival in a given
environment than other individuals. These individuals are more likely to pass on
their traits to future generations.
4. Over time, these traits will become increasingly common in a particular natural
habitat. The local population of a particular species becomes more and more of a
match to the little bit of nature in which it finds itself. In essence nature itself
selects certain heritable traits for survival – natural selection.
See Figures 22.5, 22.6, 22.7, 22.10, 22.11, 22.12
53
Evidence for Darwin’s natural selection concept comes in many forms. John Endler at
the University of California, Santa Barbara has studied a species of guppies with an
enormous amount of variation in adult male color pattern. Endler’s field observations
indicated that the more brightly colored the male, the more likely he is to attract a female
to mate with, and thereby pass on his coloration to the next generation. On the other
hand, the more predators of adult guppies there are, the more likely is the brightly colored
adult male guppy to be eaten, and thereby fail to pass on his coloration to the next
generation. When Endler followed up his field observations with a controlled experiment,
he found that the choice of predator makes a significant difference in guppy color
patterns in 22 months – 15 guppy generations.
There are strains of the human immunodeficiency virus (HIV) that are resistant to the
drug 3TC. In the absence of 3TC, this trait is not an advantage; this strain of HIV
replicates more slowly than non-resistant viruses. However, studies indicate that within
3-8 weeks of beginning 3TC therapy, 100% of a patient’s HIV will be resistant.
Modern-day paleontologists have confirmed Cuvier’s observations many times over;
fossilized organisms differ from modern-day organisms, with many older species having
become extinct. Also the older the rock strata, the more different the fossilized organisms
are from modern life forms. Where it is possible to track a type of organism through
successively more modern rock strata, evolutionary changes are seen over time. For
example, a series of fossils unearthed recently show a gradual transition from life on land
to ocean-dwelling life in ancestors of the modern whale.
There are many modern organisms with body parts that have retained similar
structures, even though they have evolved different functions – evidence of common
ancestry. These structurally similar body parts are called homologous structures, and the
phenomenon is called homology. For example, the forelimbs of the bat, the whale, the cat
and the human share the same basic skeletal structure, even though each species uses the
limb very differently. This is evidence of common ancestry among mammals.
Some homologous structures are not apparent in the adult organism, but are
readily seen in the embryo. All vertebrate embryos have a tail and a pair of gill slits. In
fish, these structures develop into a true tail and a set of gills; in humans, they do not.
Some homologous structures inherited from an ancestor species no longer serve a
significant function in the modern species. For example, the land-living ancestor of the
whale had a fully developed pelvis and hind limbs. Modern whales have small
remainders of these bones, but they no longer form functional hind limbs. Such
homologous body parts of marginal significance are called vestigial structures.
Some homologous structures are only recognizable at the molecular level. Some
genes found in bacteria are also found in humans, suggesting the existence of a distant
common ancestor. In a sense, genetic code itself is the ultimate homology – it is the same
in all species known to exist.
See Figures 22.13, 22.14, 22.15, 22.16, 22.17, & 22.18
54
LAB 20: Looking at Homologous Structures, I (Not in your lab manual)
LECTURE 20: Origin of Species, Chapter 24
It is easy to see how a population of a particular species can change over time through
natural selection, but when does this change become sufficient to consider the population
to be a new species? The development of new species is called speciation.
External similarities or differences are easily observed, but they are not reliable guides
to whether or not individuals belong to the same species. For example, there are birds that
look strikingly similar, but are members of different species. On the other hand, all dogs
are members of the same species, but a poodle does not look much like a boxer or a
greyhound. Humans also show a great variety in external characteristics.
In 1942, biologist Ernst Mayr proposed the biological species concept. This concept
holds that a species is a group of populations whose members have the potential to
interbreed in nature and produce viable, fertile offspring. While there are situations in
which this concept does not readily apply, it is very useful in most situation involving
multicellular, sexually reproducing organisms.
If the biological species concept is valid, then speciation depends on the
development of barriers to certain organisms interbreeding. The existence of such barriers
is called reproductive isolation. There are a number of factors which can reproductively
isolate a population, leading to the development of a new species.
For example, a population of organisms can be geographically isolated. Over
time, as differing forces of natural selection act the isolated populations, they may
become sufficiently different so that they can no longer interbreed. This process is called
allopatric speciation (Greek: allos = other; patra = homeland). This is the type of
speciation Darwin hypothesized when he found unique species on the Galapagos Islands.
Although unique, these species were more similar to those found in nearby South
America than they were to anything found in far-away Europe, Africa, Asia, or Australia.
Darwin reasoned that mainland South American organisms happened onto these islands,
and developed generations of reproductive isolation into new species. Similar geographic
isolation is provided by the Hawaiian Islands; these islands also are home to unique
species.
A further example of allopatric speciation can be seen in North America, where
two distinct but related species of squirrels live on opposite sides of the Grand Canyon.
Also, distinct but related species of frogs live on Madagascar and India; geological
evidence suggests that these landmasses were once connected, then drifted apart millions
of years ago.
See Figures 24.2, 24.5, 24.6, 24.7, & 24.9
55
Speciation can also take place without geographic separation. This is called
sympatric (Greek: syn = together; patra = homeland) speciation. For example, mutation
or other genetic change may give rise to populations better adapted to various food
sources within the same habitat. For example, there have historically been some 600
species of a type of fish known as cichlids in Lake Victoria, Africa. Different species of
cichlids have adapted to different food sources within the same lake. Over time, cichlids
with different diets have developed differing male breeding colors, creating a genuine
reproductive barrier between species.
Interestingly enough, this reproductive barrier may be breaking down. Pollution in
Lake Victoria over the past 30 years has made the water murky. This has obscured the
differences in male breeding color, leading to matings between species. Since the
speciation was relatively recent, the offspring are often viable. This merging has
contributed to the reduction in the number of species of Lake Victoria cichlids.
Sympatric speciation can be brought on by a mutation in a single gene. There are
two species of snail in Japan in which a difference in a single gene caused a difference in
the direction of the shell’s spiral. The difference in shell direction causes a difference in
genital positioning, creating a complete reproductive barrier. These snails are distinct
species. In other organisms, speciation is related to multiple genes with complex
interactions.
See Figures 24.12, 24.26, & 24.19
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LAB 21: Looking at Homologous Structures, II
LECTURE 21: Bacteria and Archaea, Chapter 27
Prokaryotes are unicellular organisms without membrane-bound organelles. They
typically have cell walls, which are biochemically different from the cell walls of
eukaryotes like plants and fungi. Prokaryotic cell walls are composed of a combined
carbohydrate-protein polymer called peptidoglycan.
Organisms of one of the prokaryotic domains – bacteria – can be characterized by
different abilities of their cell walls to take up stains. For example, Gram stain can be
used to categorize bacteria into species that take up the stain – Gram-positive bacteria,
and those that do not take up the stain – Gram-negative bacteria. For a number of
biochemical reasons, Gram-negative bacteria are more likely to cause human disease than
Gram-positive bacteria.
Outside the cell wall, many prokaryotes have a sticky layer of polysaccharide or
protein – a capsule. Capsules and extensions called fimbriae enable prokaryotes to adhere
to surfaces or to each other.
Some prokaryotes have the ability to move. Usually, a whip-like appendage called
a flagellum makes this movement possible. Some species can cover 50 times their body
length per second. That would be like a human being running at a speed of approximately
190 mph.
A prokaryote’s genome is usually located in a single circular chromosome. Many
prokaryotes also have smaller bits of DNA called plasmids.
See Figures 27.3, 27.4, 27.5, 27.6, & 27.8
57
Prokaryotes reproduce quite rapidly through a cell division process quite a bit
simpler than eukaryotic mitosis - binary fission. Some prokaryotic species can produce a
new generation every 20 minutes. This rapid reproductive rate gives prokaryotes the
ability to genetically change in a relatively short period of time. For example, a
spontaneous mutation in a single gene of a typical species of intestinal bacteria – E. coli –
will happen about one in every 10 million cell divisions. However, the rapid reproductive
rate of this bacterium, some 20 billion new bacteria are produced every day in the
average human being’s intestines, leading to some 2,000 mutations in that one gene
alone. When one considers all 4,300 genes in the E. coli genome, the average human
being has some 9 million mutant bacteria generated in their intestines every day.
In addition to mutation, prokaryotes can also ingest DNA from other members of
its species or closely related species. This is called transformation. Also, viruses that
infect bacteria – bacteriophages - can carry bacterial genes from one cell to another. This
is called transduction. In addition, genetic material can be transferred from one bacterial
cell to another cell of the same or different species through a tube called a sex pilus. This
is called conjugation. All of these processes – mutation, transformation, transduction and
conjugation – combined with rapid rates of reproduction – give prokaryotes the ability to
adapt very rapidly to environmental pressures. For example, if you attack disease-causing
bacteria with an antibiotic, the likelihood of at least some mutant bacteria in your body
carrying genetic resistance to the antibiotic is high. These survivors will then make copies
of themselves through binary fission, and/or pass on their resistance to other bacteria
through transformation, transduction or conjugation. You will soon have a very high
population of bacteria resistant to that antibiotic.
When faced with harsh environmental conditions, some bacteria form a tough
wall around its chromosome called and endospore. An endospore can survive dry
conditions, boiling water, and very high levels of salinity. When environmental
conditions are more favorable, the bacterium reconstitutes a full, active cell. Bacteria
have been brought back to active life after lying dormant as endospores in 118-year-old
cans of meat, 166-year-old bottles of beer, 3,000,000-year-old layers of Siberian
permafrost, and even 250,000,000-year-old salt deposits. (Sources for this information:
1.“A Case of Bacterial Immortality,” Nature, 10-19-2000, p. 844; 2. “Earth’s Hidden
Life,” Economist, 12-21-1996, p. 111, 3. “Sleeping Beauty,” New Scientist, 10-21-2000,
p. 12.).
See Figures 27.10, 27.11, 27.12, and 27.9
58
Prokaryotes, and all other organisms for that matter, can be categorized according
to their mode of nutrition. Organisms that obtain energy form light are phototrophs.
Those that gain energy from chemicals are chemotrophs. Organisms that need only
inorganic carbon sources such as carbon dioxide are autotrophs. Those that require at
least one organic nutrient are heterotrophs. These categories combine to describe the four
major modes of nutrition: photoautotrophs, chemoautotrophs, photoheterotrophs, and
chemoheterotrophs. Prokaryotes are represented in all four groups.
Mode of oxygen metabolism is another way of categorizing organisms. Among
prokaryotes there are obligate aerobes (organisms which need oxygen for survival),
obligate anaerobes (organisms for whom oxygen is poisonous), and facultative anaerobes
(organisms that can use oxygen when present, but can live without it).
One of the most important types of prokaryotes – in fact, one of the most
important types of organisms altogether – are the cyanobacteria (in some older texts,
these are referred to as blue-green algae). These are capable of photosynthesis. Much of
the atmosphere’s free oxygen supply is the result of these prokaryotes. Cyanobacteria are
abundant wherever there is fresh or salt water.
The ancestors of modern-day cyanobacteria are the most likely generators of the
first free oxygen in earth’s atmosphere; this event is recorded in reddish bands of iron
oxide in rock strata dated at 2.7 billion years old. Eukaryotic photosynthetic organisms,
including green plants, may very well owe their chloroplasts to these older cyanobacteria.
A chloroplast contains a single circular chromosome, is sensitive to certain antibiotics,
and has bacteria-like ribosomes and nucleotide sequences – all characteristics of
cyanobacteria. It has been hypothesized that early large cells ingested ancient
cyanobacteria, and the two organisms cooperated with each other. This hypothetical
model is called endosymbiosis.
Some cyanobacteria can also take atmospheric nitrogen and use it to synthesize
amino acids – a process called nitrogen fixation. Nitrogen-fixing cyanobacteria are often
found in close association with the roots of eukaryotic plants, which cannot fix their own
nitrogen.
In some species of cyanobacteria, one cell cannot carry out photosynthesis and
nitrogen fixation at the same time. Therefore, colonies form in which some cells are
photosynthetic and some cells are nitrogen fixing. This ability to form colonies is a
characteristic of many other types of prokaryotes besides cyanobacteria. When a surfacecoating colony of prokaryotes is formed, it is called a biofilm. Biofilms can cause a great
deal of damage when they form on the surface of medical or industrial equipment or as
plaque on human teeth.
See Table 27.1, Figures 25.8, 25.9, 27.14 & 27.15
59
A bit earlier, some feats of bacterial survival in the form of endospores were
described. Even more amazing, though, are some species in the domain archaea. Some of
these do not have to go dormant to survive extreme environments. On the contrary, they
thrive in extreme environments. Some archaea can live active lives in high-salinity
environments such as the Great Salt Lake and temperatures beyond the boiling point of
water. These organisms are called extremophiles.
See Figure 27.17
60
LAB 22: Looking at Homologous Structures, III
LECTURE 22: Protists, Plants, and Fungi; Chapters 28, 30, 31,35, 38
Most eukaryotes are unicellular. In older classification systems, these are
considered members of the kingdom protista. Today, they are still called protists
informally. There is biochemical evidence to suggest that protists aquired mitochondria
by ingesting and establishing symbiotic relationships with ancient prokaryotes.
Eukaryotic algae seem to have aquired chloroplasts by ingesting and establishing a
symbiotic relationship with cyanobacteria. As mentioned in an earlier lecture, this
process is called endosymbiosis. There are some motile eukaryotes which possess
chloroplasts. These seem to have evolved by the engulfing of algae by larger eukaryotes
– secondary endosymbiosis.
An interesting example of the photosynthetic protist is the diatom. These algae
consist of single cells surrounded by a crystal-like silica wall. A live diatom can
withstand pressures equal to those under each leg of a table supporting an elephant. The
silica walls of many species are almost jewel-like in shape. They form an important part
of plankton on oceans and lakes, which provide food for larger eukaryotes – including
whales. There are some 100,000 modern diatom species and many more in fossilized
form known as diatomaceous earth.
An interesting group of motile photosynthetic protists are the euglenids. When
sunlight is unavailable, some euglenids can become heterotrophic – even predatory.
Some species, such as those in the genus Euglena, have light detectors, enabling them to
move toward light of appropriate intensity, thereby enhancing photosynthesis.
Paramecia, amoeba, and many other organisms are part of the diversity of the
protists.
See Figures 28.2, 28.3, 28.7, 28.11, & 28.13
61
Plants are multicellular photosynthetic autotrophs. The cell wall of a plant is
composed of the polysaccharide cellulose. The body plan of the typical plant consists of
roots, stems and leaves. Roots anchor the plant in the soil, absorb minerals and water, and
sometimes serve a storage function. Root systems consisting of one main vertical root
that gives off smaller branches are called taproot systems. Taproots penetrate deeply into
the soil, helping the plant adapt to habitats where water is not close to the surface.
Nutrient storage is common in taproots; carrots, turnips, beets and other root crops have
taproot systems.
A fibrous root system has no main root, but consists of a mat of thin roots just
below the soil surface. Most grasses have fibrous root system.
Both taproots and fibrous roots often give off thousands of tiny root hairs, which
vastly increase the root’s surface area for enhanced absorption.
Stems in some species are modified for nutrient storage. This results in structures
such as bulbs (as in onions) and tubers (as in potatoes).
Leaves are the main photosynthetic organs, with a diversity of shapes.
The typical plant has two types of vascular tissue: xylem for the transport of water
and minerals, and phloem for the transport of organic nutrients such as sugars and amino
acids.
The first seed-bearing plants developed some 360 million years ago. In these
plants, the male gamete is enclosed in a tough wall – a pollen grain. These can be carried
long distances by wind or animals, greatly increasing the likelihood of fertilizing a female
gamete.
Some plants have specialized structures to support this process of sexual
reproduction – the flower. The typical flower consists of green sepals enclosing petals,
which are often brightly colored, especially when the plant is insect-pollinated. Pollen
grains are produced by the male part of the flower, the anther. The female part of the
flower consists of a sticky stigma that captures pollen. The style leads from the stigma to
the ovary.
The fertilized female gamete in the ovary develops into an embryo, and is
surrounded by a food supply and a protective coat – the seed. Seeds can remain dormant
for days, months, or even years until it lands in favorable conditions. Some plants
develop a further layer of nutrition and protection around the seed – the fruit.
See Figures 35.2, 35.3, 35.5, 35.6, 30.7, 38.4, 30.8, 30.9, & 30.11
62
Fungi are chemoheterotrophs that secrete digestive enzymes to break down organic
nutrients in their surroundings. Unicellular fungi are called yeasts. The bodies of
multicellular fungi are typically composed of tube-like filaments one-cell thick called
hyphae. The cell walls of fungi are composed of chitin – the same substance found in the
external skeletons of arthropods. An extension of many hyphae into the material the
fungus is feeding on is called the mycelium. Some fungi have specialized hyphae capable
of capturing and feeding on small prey, such as worms. The mycelium of some individual
forest mushrooms cover the area of 1,800 football fields, and may be more than 1,900
years old – they are the largest living organisms by size and weight on the planet earth.
Many fungi reproduce sexually. The cells of fungi are normally haploid. In sexual
reproduction, hyphae of different individuals unite – a process called plasmogamy. After
a period of time that varies between species, the haploid nuclei join to produce diploid
cells. This is called karyogamy. The diploid cells then undergo meiosis, producing
genetically unique haploid cells, which are released as spores. The wind or water can
carry spores a great distance before they find favorable conditions and germinate.
In asexual reproduction in multicellular fungi, spores are produced by mitosis of
haploid cells. This mode of reproduction is common among molds. Asexual reproduction
among yeasts also involves mitosis; the daughter cell is smaller in size than the parent
cell – this is called budding.
While some fungi cause disease in humans and other organisms, they serve many
beneficial purposes. Some species of sac fungi and mushrooms are edible. Certain yeasts
are crucial for brewing, baking and the ripening of certain cheeses. The decomposition of
dead animals and plants by fungi is essential for the normal function of earth’s
ecosystems. Some plants have symbiotic relationships with fungi that help the plant resist
insects, head, drought, and certain toxins. Some animals have symbiotic fungi in their
digestive systems to aid the digestive process. Some fungi form symbiotic relationships
with cyanobacteria or green algae – these are called lichens. The first antibiotic –
penicillin – was extracted from a mold, and many of today’s pharmaceuticals are fungal
products.
See Figures 31.1, 31.2, 31.4, 31.5, 31.6, 31.7, 31.9, 31.17, 31.18, 31.22, & 31.26
63
LAB 23: Looking at Homologous Structures, IV
LECTURE 23: Exam 4
LAB 24: Lab Review, I
LECTURE 24: Invertebrates, Chapters 32 & 33
There are some 1.3 million identified species of animals – multicellular heterotrophic
eukaryotes.
Different animals are characterized by different overall structures or body plans. One
aspect of the body plan is symmetry. There is a type of symmetry in which any plane
through the center of the animal will divide it into mirror images, but there is no left and
right side – like a flowerpot. This is called radial symmetry – the sea anemone has this
sort of symmetry. The other type of symmetry is the type in which there is a definite left
and right side – like a shovel, and only one plane will divide the animal into mirror
images. This is bilateral symmetry – the lobster has this sort of symmetry. Animals with
bilateral symmetry also have a dorsal (top) and ventral (bottom) side, and an anterior
(front) and posterior (back) end. Many animals with bilateral symmetry also have a
concentration of sensory equipment at the anterior end. When this is part of the body plan
it is called cephalization.
During embryonic development, most animals develop distinct cell layers that will
later form into various tissues and organs. Some animals have only two embryonic layers
– an outer ectoderm and an inner endoderm. All bilaterally symmetrical animals –
bilateralians – have a third embryonic layer sandwiched in between the ectoderm and the
endoderm – the mesoderm.
Most bilateralians have a cavity separating the digestive tract from the outer body – a
coelom (“SEE loam”). When the cavity is formed entirely from mesoderm, it is a true
coelom, and the animal is a coelomate. If the cavity is a mixture of tissues it is called a
pseudocoelom, and the animal is a pseudocoelomate. A few bilateralians have on cavity –
acoelomates.
Animals without a backbone – invertebrates – constitute 95% of the known animal
species. We will consider the major phyla (the next taxonomic classification down from
domains and kingdoms) of invertebrates.
Simple, asymmetrical animals with no true tissues, the sponges live out their lives in a
fixed location. They capture and digest food particles suspended in the water in which
they live. Sponges are hermaphrodites. Sperm are released into the water and are carried
by the current to fertilize eggs in nearby individuals. A swimming larva is formed, and
then it finds a place to settle down – for life. Taxonomists used to classify them in the
phylum porifera, though that is currently undergoing revision.
See Figures 32.4, 32.5, 32.7, 32.8, & 33.4
64
Animals in phylum Cnidaria (“nigh DARE ee uh”) have radial symmetry around a
central digestive sac. A mobile cnidarian is a medusa. Jellies (jellyfish) are familiar
examples. A sessile cnidarian is a polyp. Hydras, corals, and sea anemones are examples.
Cnidarians have tentacles arrayed around the opening that is both mouth and anus. Prey is
stung by specialized cells in these tentacles, and drawn into the digestive sac. The
stinging cells, called cnidocytes, are unique in the animal kingdom; any animal that
grows their own cnidocytes belongs to the phylum Cnidaria. Undigested remains are
expelled through the mouth/anus. Many species of corals secrete a hard external skeleton
of calcium carbonate. As successive generations leave behind their skeletal remains, coral
reefs are built up. Coral reefs are critically important as habitats for many other species
and for removing carbon dioxide from the atmosphere. Some coral reefs are so large, they
included coral islands large enough to build towns on. The Great Barrier Reef in
Australia can be seen from space.
The phylum Platyhelminthes consists of flatworms. They are acoelomate bilateralians
that have no respiratory or circulatory organs, depending on their flat shape to accomplish
gas and water exchange by simple diffusion. There are both free-living species such as
the planarian and parasites such as the tapeworm.
Species within the phylum Mollusca are bilateralian coelomates with a three-part body
plan. A muscular foot is used for movement, a visceral mass contains most of the internal
organs, and the mantle is a fold of tissue protecting the visceral mass. The mantle in some
species secretes a hard shell.
Gastropods are the most numerous types of molluscs. The most familiar of these are
snails and slugs, which are both cephalized, with eyes at the tips of tentacles. The foot of
a gastropod ripples or moves by means of cilia. The mantle is the gas exchange area in
land-based gastropods, while aquatic or marine species have gills. Most gastropods graze
on algae or plants; a few are predators.
Bivalves include such familiar animals as clams, oysters, mussels and scallops. The
body plan of a bivalve includes a two-part shell that can be shut tight for defense. Most
bivalves are suspension feeders, like the sponges. A few species have sensory organs
such as eyes and tentacles along the outer edge of the mantle.
Cephalopods are predators with tentacles and poisonous beak-like jaws and with welldeveloped sensory organs and complex brains. They include squids, cuttlefish, and
octopuses. Most cephalopods travel by squirting water, creating a kind of jet propulsion.
Many species of cephalopods can camouflage themselves by changing color. Only the
chambered nautilus has an external shell. The now-extinct ammonites were shelled
cephalopods, like the nautilus, and were sometimes the size of truck tires. There are giant
species of squid that reach 18 meters in length.
See Figures 33.5, 33.6, 33.7, 33.9, 33.10, 33.12, 33.15, 33.18, 33.20, 33.21
65
The phylum Annelida consists of worms with a bilateralian, coelomate, segmented
body plan. They range from 1 mm to more than 3 m in length. One of the most familiar
and important type of annelid is the earthworm. The earthworm has a specialized blood
vessels pump – a primitive type of heart. Bristles composed of chitin help the worm
anchor one part of its body as another part lengthens or shortens. It has a well-developed
nervous system, including a brain-like formation at the head end. They are crossfertilizing hermaphrodites; even though each worm has both sets of sex organs, they have
to align with another worm to mate. As worms eat and dig their way through the soil,
they till and aerate it, making it much more valuable to farmers.
In some marine annelids, the bristles are attached to leg-like extensions of its body.
These extensions are rich in blood vessels, enabling them to function in gas exchange – a
primitive type of gill. Some of these marine annelids live in tubes built from surrounding
materials or their own secretions.
Leeches are annelids that suck blood from other animals, including humans. Some
species of leech can consume ten times their own body weight in blood, after which they
do not have to eat again for months.
The phylum Nematoda consists of species of bilateralian, coelomate, non-segmented
round worms. Some species are free-living in the soil or water. A number of species live
as parasites within the tissues of plants and animals. A nematode parasitic in humans is
responsible for the disease trichinosis. This parasite is generally aquired from raw or
undercooked meat, especially pork.
More than one million species have been discovered in the phylum Arthropoda. These
are bilateralian coelomates. An arthropod has a segmented body protected by an
exoskeleton, with jointed appendages. Early arthropods, such as the trilobites, had little
variation from segment to segment. In modern arthropods, there has been a diversity of
specialization in these segments. The exoskeleton is composed of various combinations
of protein and chitin, and becomes paper-thin over the joints for flexibility. While many
aquatic and marine species exist, the exoskeleton provides the support and the protection
from drying out that make life on land possible. The down side of the exoskeleton is that
it limits the animal’s growth. Therefore, an arthropod must molt its exoskeleton and
secrete a new one whenever growth is required – a process that uses much of the animal’s
energy and renders it temporarily vulnerable. Arthropod antennae have sensory receptors
for both touch and smell.
Horseshoe crabs are arthropods which closely resemble their fossilized ancestors of
hundreds of millions of years ago.
Arachnids are predators and parasites, including spiders, scorpions, ticks and mites.
Spiders have the unique ability to spin webs of silk.
Millipedes and centipedes are notable for their large number of legs.
See Figures 33.22, 46.1, 33.23, 32.24, 33.25, 33.26, 33.27, 33.31, 33.33, & 33.34
66
One group of arthropods – the insects – includes more known species than all other
life forms combined. An insect’s wings are an extension of the exoskeleton. The ability to
fly is a great advantage, either in predation or in escaping predation. Many insects
develop into their adult form from a non-flying worm-shaped form called a larva. The
change from the larva to the adult is a process called metamorphosis. Insects have a
complex relationship with humans. On the one hand, we depend on bees, flies and other
insects to pollinate agriculturally important plants. On the other hand, some insects are
disease-carrying parasites. Also, plant-eating insects compete with humans for food
crops; in some areas of the world, insects consume 75% of the annual crop.
Crustaceans are mostly marine and aquatic arthropods. They are the only arthropods
with two pair of antennae. They include crabs, shrimp, lobsters, crayfish, barnacles, and
various types of krill.
The phylum Echinodermata includes sea stars (starfish), sea urchins, sand dollars and
sea cucumbers. Although many species have radial symmetry as adults, they are
considered bilateralians, since they all have bilateral symmetry at least in their larval
form. Although casual inspection would make you suppose they have an exoskeleton,
echinoderms actually have a hard endoskeleton under a thin skin. They have a network of
canals that pump water through their bodies – a water vascular system. They also have
tube feet for locomotion and gas exchange. The water vascular system and tube feet are
unique features of the echinoderm body plan.
As different as echinoderms are from humans, biochemical evidence – including
DNA evidence – suggests that the phylum Echinodermata is the closest relative to our
own phylum – Chordata.
See Figures 33.35, 33.36, 33.37, 33.38, 33.39, & 33.40
67
LAB 25: Lab Review II
LECTURE 25: Vertebrates, Chapter 34
There is a small animal that spends most of its adult life with its tail buried in the sea
floor, while its front end eats. It is shaped like a narrow blade-like fish – hence its name:
the lancelet. When it leaves its burrow it even swims like a fish, with side-to-side
undulations of its body – but it is not a fish. It has no vertebral column, yet it is a member
of the phylum that includes vertebrates – the phylum Chrodata. Running down the
lancelet’s back is a rod of fluid-filled cells encased in fibrous tissue – a notochord.
During the lancelet’s embryonic development, a plate of ectoderm rolls into a neural tube
that develops into a hollow nerve cord just dorsal to the notochord. The anterior portion
of the lancelet has a series of narrow openings – pharyngeal slits – through which water
passes, allowing it to filter food particles from the water. Unlike a worm, in which the
anus is the most posterior structure, the lancelet’s body extends past the anus, forming a
post-anal tail. These four characteristics – a notochord, a hollow nerve cord dorsal to the
notochord, pharyngeal slits, and a post-anal tail – are present in all members of the
phylum Chordata, although some chordates only have these characteristics during the
embryonic stage of development. Lancelets, sea squirts, and hagfish are the only
invertebrates in this phylum.
Most chordates have a vertebral column. In the majority of vertebrates, the vertebral
column encloses a major portion of the nerve cord, which in vertebrates is called the
spinal cord. In many vertebrate species, the vertebral column (in fact, the skeleton as a
whole) contains little or no bone, but is composed of cartilage. This is a primary
characteristic of a group of vertebrates whose name – chondrichthyans (“con DRIK thee
anz”) – means “cartilage fish”. These include rays, skates, and one of the most successful
groups of predators on the planet – sharks. Sharks are heavier than water; therefore, they
swim almost all the time to avoid sinking to the bottom. This constant swimming also
keep water moving into their mouth and out of their gills (a special adaptation of the
pharyngeal slits). During rare periods of rest, sharks work their jaws to keep water
moving over the gills. In addition to eyes, the shark has a good sense of smell as well as
specialized organs to detect electrical fields – including those fields generated by the
muscle contractions of prey animals. There are no eardrums. Instead, the shark’s entire
body conducts sound vibrations to its inner ear.
True fish usually have bony skeletons. They do not need to move constantly, because
the typical fish has an air sac called a swim bladder, which enables it to control its
buoyancy. Thanks to the swim bladder, a fish can hover motionless without sinking – a
tremendous advantage for a stalking predator animal or for a hiding prey animal. Fish are
very diverse and numerous, including more than 27,000 species. The vast majority of
vertebrates are fish.
See Figures 34.4, 34.3, 34.5, 34.15, 34.16, & 34.17
68
Water is the most important compound in the body of a living thing, so the
development of vertebrates that can leave the water was a momentous evolutionary event.
There are fish that have lungs and can live out of the water for long periods of time – a
handy ability when a pond or creek dries up. There are not many species of these
lungfish, however. Today, it is mostly the amphibians that have mastered this life style of
sometimes being in the water and sometimes being out of it. This group of animals
includes salamanders, apodans (legless amphibians) and frogs. While most amphibians
have lungs, their closeness to water enables them to rely on a thin, moist skin for most
gas exchange. The species with lungs move air into them with movements of their mouth
and throat.
Frogs have a fish-like larval stage, complete with gills, called a tadpole. It undergoes a
metamorphosis during which it develops legs, lungs, eardrums, and a digestive system
adapted to a carnivorous diet. Various species of frogs have evolved anti-predatory
features in their skin, such as distasteful or poisonous mucus, as well as protective
coloration. In frogs and most other amphibians, the male grasps the female and spills his
sperm over the eggs as the female sheds them.
Fully land-based animals evolved ways to take their water with them, both during
embryonic development and adult life. One adaptation of reptiles and mammals is the
development of the amniotic egg. The amnion is a membrane, which acts as a shock
absorber and also bathes the embryo. In a sense, the amniotic egg surrounds the embryo
in a miniature pond. Shells surround the amniotic eggs of many species, further
protecting the egg from dehydration.
Rather than using motions of the mouth and throat to move air into the lungs like
amphibians, reptiles and mammals use their rib cage to do so – a much more efficient
mode of breathing. This frees them from the necessity to breathe through the skin,
allowing a thicker, water-resistant skin to develop
See Figures 34.22 & 34.25.
69
Reptile skin has scales composed of the protein keratin – the same protein found in
human skin and nails. Many reptile species make use of external heat – seeking the sun
when they are too cold – to maintain optimal body temperature. An animal that relies
strongly on external heat to maintain body temperature is ectothermic. This is a very
good energy-conservation system; an ectothermic reptile can survive on 10% of the food
energy required by an endothermic (warm-blooded) animal such as a mammal.
Lizards range in adult size from 16 mm (small enough to stand on a dime) to 3 m (the
Komodo dragon). Snakes are, in a sense, legless lizards. In fact, some snakes have
vestigial pelvic and limb bones. Elastic skin and loose jawbones enable most snakes to
swallow prey much larger than their head. Some snakes have specialized heat sensors,
improving their ability to detect hidden prey at night.
Turtles are reptiles with shells fused to their vertebrae, clavicles and ribs. Fossilized
turtles have been dated at approximately 220 millions years old. Closely related to the
turtles, and appearing in the fossil record at around the same time are the alligators and
crocodiles. There is an exhibit in the Smithsonian Museum of Natural history in which
the skeleton of a fossilized crocodile is shown side-by-side with the skeleton of a modern
crocodile. If you are not a specialist in these species, you probably can’t tell the skeletons
apart.
Birds are now classified as endothermic reptiles. Most birds fly, and flight involves a
number of adaptation. Acute vision and fine muscle control are required for flight, and
these abilities require a larger brain (relative to overall body size) than the brains of
amphibians or non-flying reptiles. A form of keratin, the same protein in the snake’s
scales, is the main protein in feathers. Birds lack a urinary bladder, teeth, and their
gonads remain small except during mating season – all adaptation to save body weight to
make flight easier. Another weight-saving adaptation is the existence of air spaces in the
bones of many birds. Some birds soar, with little flapping of their wings. The
hummingbird, on the other hand, flaps its wings continually when flying. Some birds
engage in elaborate courtship dances. The oldest bird fossil has been dated at 150 million
years old.
See Figures 34.26, 34.27, 34.28, & 34.29
70
Mammals have mammary glands, skin covered with hair or fur with a fat layer
underneath, a four-chambered heart, and a diaphragm to improve the efficiency of
breathing. Also characteristic of mammals is a variety of teeth for chewing a variety of
foods. Like reptiles, mammals surround their embryos with an amnionic membrane, but
only a few species lay eggs (the platypus and the spiny anteaters). A few species
complete the embryo’s development in a pouch called a marsupium. These animals
include the possum, the kangaroo, and a number of other species. In most mammals,
embryonic development is completed within the uterus of the mother.
Primates include lemurs, tarsiers, monkeys and apes (humans are classified with the
apes). Primates are mammals with digits that have flat nails instead of claws or talons.
They have thumbs that are separate from and more moveable than the other fingers. The
fingers have skin ridges (fingerprints in humans).
See Figures 34.32, 34.33, 34.34, 34.35, 34.36, & 34.38
71
LAB 26: Final Lab Exam
LECTURE 26: Human Evolution
(Some information is this lecture is from The Origin of Humankind by Richard Leakey,
Basic Books, New York, 1994.)
In the late 1960’s, two biochemists from the University of California at Berkeley –
Allan Wilson and Vincent Sarich – compared the structures of certain blood proteins in
chimpanzees, gorillas and humans. These proteins have known rates of mutation.
Therefore, they can serve as a sort of “molecular clock”. The more different the blood
proteins are, the longer ago the species diverged. Based on this molecular evidence, they
concluded that the common ancestor of humans and apes lived some 5 million years ago.
More recent molecular clock evidence has revised this estimate to more like 7 million
years ago. No fossils of this common ancestor have been discovered so far.
Skeletal remains from the time of ape-human divergence are hard to find, and are
usually very incomplete. Most finds are a skull fragment here, a bit of pelvis there.
However, a very fortunate find was made in 1974 in Ethiopia. A 40% complete skeleton
of a 3-foot tall female that walked erect was found, and was dated at approximately 3.2
million years old. The fossil was named “Lucy”. Lucy is a member of the species
Australopithecus afarensis. Her brain was not particularly large – about one-third the size
of the brain of a human of equal size. There have been several species grouped in the
Australopithecus genus, with the oldest fossilized remains having been discovered in East
Africa, particularly Ethiopia, Tanzania, and Kenya. Australopiths are believed to have
been bipeds – that is, they were capable of walking upright on two legs. Bipedalism frees
the upper limbs to grip tools and weapons – it is an important evolutionary step.
There are several methods of determining whether or not a fossilized skeleton
belonged to a biped or not. For example, the large hole in the skull through which the
spinal cord exits – the foramen magnum – is located at the back of the skull of a
quadruped. In a biped, it is located in a more central location, so that the skull is balanced
over the spine in the upright position. Fossilized Australopithecus skulls were consistent
with bipedalism. Also, footprints have been found associated with the Australopiths.
Combined with evidence from the pelvic bones, the evidence of bipedalism in the
Australopiths is reasonably strong.
However, there are a number of characteristics of Australopithecus more ape-like than
human-like. Their lower limbs were short in comparison to their upper limbs. Their
shoulder joints were oriented more upward than forward. Their phalanges (finger and toe
bones) were long and curved rather than short and straight. All of these characteristics are
more useful for tree-dwelling quadrupeds than surface-dwelling bipeds. When CAT scans
were done of Australopithecus skulls, the structure of their balance organs in their inner
ears was more ape-like than human-like. Although Australopiths had developed human-
72
like bipedalism on the ground, they may have spent a significant amount of their time
living an ape-like life in the trees.
The earliest fossils belonging to our own genus Homo are those of Homo habilis.
These fossils have been dated at approximately 2.5 million years old. Homo habilis had a
much larger brain than any members of the Australopithecus species, almost half the size
of a modern human brain. CAT scans of the skulls inner of Homo habilis fossils reveal
human-like inner ears. Their legs were substantially longer than their arms, and their
phalanges and shoulders were similar to those of a modern human. Clearly, Homo habilis
was more completely adapted than the Australopiths to a bipedal life on the ground.
Besides bipedalism and increased brain size, another milestone on the way to the
modern human was the use of relatively complex stone tools. Simple stone tool use is
known among apes. For example, chimpanzees have been observed to place hard nuts on
flat rocks and open them with smaller rounded rocks. However, these are “found” tools.
The chimpanzee uses the rocks as he or she finds them – there is no sculpting of the
stones to a particular shape. The first deliberately formed tools appeared approximately
2.5 million years ago. While it is not clear whether or not Australopiths made stone tools,
Homo habilis definitely did (thus the name, which means “handy man”).
Approximately 1.9 to 1.7 years ago, a species of Homo with a larger brain capacity
appeared – Homo erectus. Some authors use the term Homo ergaster to describe this
species; others consider them to be separate. In this lecture, I will stick with the name
Homo erectus. This new species of Homo made more sophisticated stone tools than
Homo habilis. Richard Leaky and Kamoya Kimeu discovered a 1.5-million-year-old
fossil of a nearly complete Homo erectus skeleton near Lake Turkana, Kenya in 1984.
It is not known whether one of the Australopithecus species gave rise to the early
Homo species, or whether they were separate lines of evolution from a common ancestor.
No Australopithecus fossils have been found dated earlier than 1 million years ago. From
this, it is assumed that the Australopiths were extinct by 1 million years ago. Some late
version of Homo erectus is presumed to be the direct ancestor of Homo sapiens.
Neanderthals were considered a separate species – Homo neanderthalis – when first
discovered in 1856. Today, most scientists consider the Neanderthals to be an early
subspecies of Homo sapiens (Homo sapiens neanderthalis). The Neanderthals had a
better-developed tool kit than previous hominids, and also buried their dead. At least one
100,000 year-old Neanderthal burial site has been found. Different scientists place the
appearance of the first Neanderthals at different points in time, but it was approximately
200,000 years ago. No Neanderthal remains have been found dated more recently than
28,000 years ago.
Modern humans – Homo sapiens sapiens – appeared some 195,000 years ago and
migrated out of Africa some 115,000 years ago. Modern humans and Neanderthals
coexisted in many parts of the world up to 28,000 years ago, but DNA studies show little
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evidence of interbreeding. Art objects began to appear some 77,000 years ago, and the
cave paintings of France and Spain began to appear approximately 36,000 years ago.
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LECTURE 27: Course Review, I
LECTURE 28: Course Review, II
LECTURE 29: Final Lecture Exam
(Next: Protein synthesis=ch 17=2-28 lecture; Origin of Species = ch 24 = 4-1
lecture; (Test III?) Phylogeny=ch 26 (no lecture); Bacteria and Archaea = Ch 27 = part
of 4-17 lecture; Protists = ch 28 = 4-22 lecture; Plants = ch 29 (no lecture); Fungi = ch
31 =part of 4-24 lecture; (Test IV?) Invertebrates (2?) = ch 33 = 4-3 & 4-15 lecture +
handouts; vertebrates (2?) = 4-15 & 4-17 lecture + handouts (Final) Total 25 lectures)
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