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Energetics: Cellular Respiration and
Photosynthesis
A. ENERGY
1. First Law of Thermodynamics Energy can be changed from one form into another, but cannot
be created nor destroyed.
Energy can be stored in various forms then changed into other forms. For example, energy in
glucose is oxidized to change the energy stored in chemical bonds into mechanical energy. In all
energy conversions some of the useful energy is converted to heat and so dissipates.
Scientists have developed the notion of potential energy, which is "stored" energy. Molecules
contain potential energy in bonds. When the bonds are broken, other bonds form, and some
unusable heat is always produced.
2. Second Law of Thermodynamics In all energy exchanges and conversions, it is proven that if
no energy leaves or enters the system under study, the potential energy of the final state will
always be less than the potential energy of the initial state.
a) Exergonic Reaction
If the reaction releases energy, then the potential energy of the final state is less
than the potential energy of the initial state. This type of reaction is called an
exergonic reaction. These reactions occur without any energy being added.
b) Endergonic Reaction
These reactions need energy to complete the reaction. The energy added is
greater than the difference between the reactants and the products.
3. Entropy
Another factor besides the gain or loss of heat affects the change in potential energy - entropy.
Entropy means the disorder of a system. The final state has more entropy and less potential
energy than the initial state.
The second law states that in other terms all natural processes tend to proceed in such a
direction that disorder/randon-mess increases.
B. OXIDATION/REDUCTION REACTIONS
The reactions that occur when an atom gains or loses one or more electrons are called
oxidation/reduction reactions. The use of chemical energy in living organisms involves
oxidation/reduction reactions.
Oxidation is the loss of an electron. In this example the Fe2+ ion has been oxidized; it lost an
electrons and a negative charge.
Reduction is the gain of an electron. When the oxygen receives an electron, it gains a negative
charge.
Electron carriers: Some compounds can accept and donate electrons readily, and these are
called electron carriers in organisms. There are a number of molecules that serve as electron
carriers.
One molecule is NAD (Nicotinamide adenine dinucleotide) and is used in anaerobic respiration.
NADP (Nicotinamide adenine dinucleotide phosphate) is another used in photosynthesis. These
molecules readily give up 2 electrons (oxidized) and gain 2 electrons (reduced). Along with the
electrons the molecules accept 2 hydrogens to offset the negative charge of the electrons.
When the electron moves to a lower energy level, energy is released.
C. ATP
1. ATP as Energy
Cells need energy to drive reactions. The molecule that supplies the energy is ATP (This reaction
is called ATP hydrolysis). When the third phosphate is removed by hydrolytic cleavage, 7 kcal of
energy is released per mole of ATP.
ATP + H20 --> ADP +
Phosphate + Energy (7 Kcal)
When the second phosphate is removed, the same amount of energy is released.
ADP + H20 ------> AMP + Phosphate + Energy (7 Kcal)
The bonds between the two phosphates are not strong bonds. In fact, these bonds are easily
broken releasing 7 Kcal of energy per mole. 7 Kcal of energy is enough to drive endergonic
reactions in the cell.
All the energy does not come from the moving of electrons to a lower energy level. In fact, the
rearrangement of electrons in other orbitals (i.e.. ATP ----> ADP) results in a structure with less
energy.
Enzymes catalyzing the hydrolysis of ATP are ATPases.
Sometimes the terminal phosphate group is transferred to another molecule. The addition of a
phosphate group is called PHOSPHORYLATION. Enzymes that catalyze this reaction are called
KINASES. In these phosphorylation reactions, energy is transferred from the phosphate group in
ATP to the phosphorylated compound. This newly energized compound will participate in other
reactions.
2. Production of ATP
ATP originates when anaerobic respiration (fermentation) takes place in the
absence of oxygen. What happens is that sugar is broken down into smaller
molecules and energy is released. The energy is used to generate ATP from
ADP and P.
ADP + P ------> ATP
Sugar ---------> smaller molecules
The breakdown of the sugar takes place through a series of chemical reactions. Living organisms
have developed numerous and different fermentation pathways; however, most organisms use
the following Embden-Meyerhoff pathway, named for the two discoverers.
The anaerobic respiration pathway takes glucose (C 6 H 120 6 ) and breaks it down into two
molecules of pyruvate (three carbon compound). This occurs in the cytoplasm of the cell. The
pyruvate can take two pathways in anaerobic respiration:
a. Pyruvate will be converted to alcohol (ethanol) and carbon dioxide. This is
called alcohol fermentation and is the basis of our wine, beer and liquor industry.
b. The pyruvate will be converted to lactic acid. This is called lactic acid
fermentation. Lactic acid is what makes your muscles burn during prolonged
exercise, this process is also used to make yogurt.
The overall reaction for alcohol fermentation looks like this:
C6H1206 --->2CH 3CH 20H + 2 C02 + Energy
Chapter 9 "How Cells Make ATP: Glycolysis &
Respiration"
ATP adenosine triphosphate = "the cell's energy currency" $$
I. An Overview of Glucose Oxidation
review:
oxidation = loss of e-
reduction = gain of e-
Glucose + Oxygen ----> Carbon dioxide + water + Energy
G = -686 Kcal/mole ---->energy used to add a phosphate molecule: ADP + P = ATP
There is a need to convert glucose (sugar) which is stored chemical energy into ATP which is
usable cell energy
RememberATP - P = ADP
ADP - P = AMP
OR
AMP+P=ADP
ADP+P=ATP
exergonic, energy liberating
endergonic, energy intake
2 major stages in the oxidation of glucose (in living cells)
1) Glycolysis (in cytoplasm )
2) Respiration (mitochondria)
(a ) Kreb's Cycle
(b) electron transport
Aerobic Respiration, the production of energy in the presence of oxygen, occurs in the
mitochondria. Aerobic respiration produces 21-36 ATP molecules per molecules of glucose.
Compare this to the 2 ATP molecules which are produced in anaerobic respiration.
A.
INTRODUCTION TO AEROBIC RESPIRATION
1. Glucose
Although carbohydrates, fats, and proteins can all be processed and consumed as fuel, we
usually track glucose in the production of energy. The breakdown of glucose is exergonic, having
a free energy change of -686 kilocalories per mole of glucose (recall that a negative -G indicates
that the products of the chemical reaction store less energy than the reactants).
2. Energy
This energy is stored as ATP. ATP is the chemical equivalent of a loaded spring; the close
packaging of the three negatively charged phosphate groups is an unstable, energy-storing
arrangement (like charges repel). The chemical "spring" tends to "relax" from the loss of a
terminal phosphate. The cell taps this energy source by using enzymes (kinases) to transfer
phosphate groups from ATP to other compounds, which are then said to be phosphorylated.
Adding the phosphate primes a molecule to undergo some kind of change that performs work,
and the molecule loses its phosphate group in the process.
In order to understand the process of making energy, we must briefly review redox reactions.
a. Reduction
Gaining electrons, hydrogen or losing oxygen.
b. Oxidation
Losing electrons, hydrogen or the gaining of oxygen. An electron loses potential energy when it
shifts from a less electronegative atom towards a more electronegative one. A redox reaction that
relocates electrons closer to oxygen releases chemical energy which can be put to work.
the combustion of glucose, sugar is oxidized and oxygen is reduced. Meanwhile, electrons lose
potential energy along the way.
c. Change in Covalent Status
Usually, organic molecules that have an abundance of hydrogen are excellent fuels because their
bonds are a source of electrons with high potential energy. They also have the potential to drop
the energy when they move closer to oxygen. The important point in aerobic respiration is the
change in covalent status of electrons as hydrogen is transferred to oxygen. This is what liberates
the energy.
At key steps in aerobic respiration, hydrogen atoms are stripped from the glucose, but they are
not directly transferred to oxygen. They are passed to a coenzyme called NAD+ (nicotinamide
adenine dinucleotide) which functions as the oxidizing agent.
Enzymes called dehydrogenases remove a pair of hydrogen atoms from the substrate. These
enzymes deliver two electrons along with one proton to NAD+, forming NADH. The other proton
is released as a hydrogen ion into the surrounding solution.
Electrons lose very httle potential energy when they are transferred by dehydrogenases from
glucose (organic molecules) to NAD. Thus, each NADH molecule formed during respiration
represents stored energy that can be used to make ATP when the electrons complete their
journey from NADH to oxygen.
3. Mitochondria Review
The mitochondrion is surrounded by two membranes. The outer is smooth and the inner folds
inwards. The inner folds are called cristae. Within the inner compartment of the mitochondrion,
surrounding the cristae, there is a dense solution known as the matrix. The matrix contains
enzymes, co-enzymes, water, phosphates, and other molecules needed in respiration.
The outer membrane is permeable to most small molecules, but the inner one permits the
passage of only certain molecules, such as pyruvic acid and ATP.
Proteins are built into the membrane of the cristae. These proteins are involved with the Electron
Transport Chain. The inner membrane is about 80% protein and 20% lipids. 95% of the ATP
generated by the heterotrophic cell is produced by the mitochondrion.
II. GLYCOLYSIS The first step in aerobic respiration is called Glycolysis. Glycolysis closely
resembles anaerobic respiration.
translation= " glucose " - "splitting"
1. Overall Reaction
takes place in a series of 9 reactions, each mediated by a different enzyme (very well-controlled)
1 molecule glucose (6-carbon sugar) split into 2 molecules of pyruvic acid (3-carbons each)
ATP---> ADP energy used (steps 1, 3)
ADP---> ATP ( steps 6, 9) energy is yielded (stored)
9 Glycolysis Steps
[Step 1] Energy input required
Terminal P from an ATP (-->ADP) is bonded to the C6 of a glucose
Taken from the Univ. of V
Page.

G = - 3.3 (enzyme: hexokinase)
[Step 2] glucose - 6 - phosphate-----------------> fructose - 6 - phosphate
atoms rearranged

G = + 0.4 (enzyme: phosphoglucoisomerase)
[Step 3] fructose - 6 - phosphate-----------------> fructose 1,6 diphosphate
Phosphate added to C1
G = - 3.4 (enzyme: phosphofructokinase)
splits into two products
[Step 4] fructose -1, 6 - diphosphate----------------->
dihydroxyacetone phosphate
G = + 5.7 ( enzyme: aldolase)
AND
glyceraldehyde
phosphate*
Our 6-carbon sugar is split into TWO 3-carbon products
dihydroxyacetone phosphate --------------------------> glyceraldehyde phosphate
(enzyme: isomerase)
*Ultimately, all of the dihydroxyacetone phosphate will be converted into
glyceraldehyde phosphate so each step is actually x 2 from here
(because each of the two molecules will proceed through Steps 5- 9 )
[Step 5]
2 Glyceraldehyde phosphate molecules are oxidized 2 hydrogens(with e- are
removed and NAD+ is reduced to NADH and H+
Also, a free phosphate attaches to the glyceraldehyde phosphates
+Pi
2 Glyceraldehyde phosphate---------------> 1, 3 Diphosphoglycerate (x2)
NAD+ is reduced to NADH and H+
Pi = free phosphates, not taken from another molecule such as ATP
NAD = nicotinamide adenine dinucleotide (niacin derivative)
G = + 1.5 (enzyme: trios phosphate dehydrogenase)
[Step 6]
a P is released from each 1,3 diphosphoglycerate molecule and
is used to "recharge" 2 ADP 'S----> 2 ATP'S
thus, converting the 1,3 diphosphoglycerate to 3-phosphoglyceric acid
(highly exergonic= large G to pull preceding reactions forward)
(x2) 1,3 Diphosphoglycerate-----------------------------> 3-phosphoglyceric
acid
ADP---> ATP
G = - 4.5 (enzyme: phosphoglycerate kinase)
(x 2) [Step 7] The remaining P group is enzymatically transferred from
the 3C to
the 2C
G = + 1.0 (enzyme: phosphoglyceromutase)
3- phosphoglyceric acid-----------------------> 2 - phosphoglyceric acid
(x 2) [Step 8] A molecule of H2O removed
2 - phosphoglyceric acid----------------> phosphoenolpyruvic acid
H2O
G = + 0.4 (enzyme: enolase)
(x 2) [Step 9] Another phosphate P is transferred to ADP
( highly exergonic, pulls 2 preceding rxns!!!)
phosphoenolpyruvic acid--------------------> pyruvic acid
ADP-->
ATP
G = - 7.5 ( enzyme: pyruvate kinase)
III. Anaerobic Pathways:
Pyruvic acid can take one of 2 main pathways
Aerobic ( with O2)
Anaerobic( without O2)-several ways...produces minimal ATP
with other byproducts:
---> lactic acid (or one of several organic acids)
Produced by a variety of microorganisms + animal cells+ muscle fatigue (low pH).
When O2 goes up & ATP demand is reduced, lactic acid is converted back into pyruvic acid
---> ethanol
example: grapes ( with yeast " blooms") crushed; sugar in grape juice is metabolized by yeast
cells without O2 until all sugar is used up (12- 17% alcohol) ="fermentation"
FERMENTATION: The earliest form of energy production in prokaryotes
There are two phases in fermentation: The first 5 steps are the energy investment steps and the
last 4-6 steps are the energy production steps.
Glucose enters the cell through facilitated diffusion.
1. Initially glucose is phosphorylized by ATP. This step keeps the glucose in the
cell.
Glucose -----> Glucose-6-P
Enzyme: Hexokinase
ATP ------> ADP Net use of 1 ATP
2. Fructose is an isomer of glucose.
Glucose-6-P -------> Fructose-6-P
Enzyme: Phosphoglucoisomerase
3. Another phosphorylization. This is an example of reaction coupling. Fructose6-P will convert back to glucose 6-P. However, if phosphorylated immediately,
the anaerobic pathway will continue.
Fructose P ----------------------> Fructose1,6-P Enzyme: Phosphofructokinase
ATP------>ADP Net use of 2 ATP
4. The enzyme Aldolase splits the 6 carbon molecule into 2 three carbon
molecules.
Fructose-1,6-P-----------------> 2
Glyceraldehyde-3-P
Pi
enzyme: Aldolase
5. The electron carrier NAD accepts two electrons from glyceraldehyde (oxidizes
the compound). Glyceraldehyde accepts a phosphate (inorganic source); an
exergonic reaction G=-10.3 kcal/mole).
2 Glyceraldehyde-3-P ------> 2
Diphosphoglycerate-1,3-P
2 NAD ------> 2 NADH
Enzyme: Triosephosphate dehydrogenase
6. A phosphate from Diphosphoglycerate is taken from the molecule and added
to ADP to form ATP.
2 Diphosphoglycerate --------------> 2
phosphoglycerate-3-P
2 ADP ------> 2 ATP
Enzyme: Phosphoglycerate kinase
Net production: 0 ATP molecules (two used and
two produced per molecule of glucose).
7. Phosphate is transferred to an adjacent carbon.
2 Phosphoglycerate-3-P ------------> 2
Phosphoglycerate-2-P
Enzyme: Phosphoglyceromutase
8. Water is removed from phosphoglycerate-2-P to form PEP.
2 Phosphoglycerate-2-P ------------> 2
phosphoenolpyruvate
remove water
Enzyme: Enolase
9. The phosphate from phosphoenolpyruvate is removed and added to ADP to
form ATP.
2 Phosphoenolpyruvate -------------------> 2
Pyruvate (pyruvic acid)
Enzyme: Pyruvate kinase
2 ADP -------> 2 ATP Net ATP production: 2 ATP
10. A carbon and 2 oxygens are removed from pyruvate to form a two carbon
compound called acetaldehyde.
2 Pyruvate ---------------> 2 Acetaldehyde + 2
C02
11. Acetaldehyde accepts 2 electrons from the NADH molecule. This addition
causes acetaldehyde to be converted to ethanol.
2 Acetaldehyde ---------------> 2 Ethanol
2 NADH --------> 2 NAD+
12. NADH donates two electrons to pyruvate which is converted to lactic acid.
NADH-------->NAD+
2 Pyruvate-------> 2 Lactic Acid
In anaerobic respiration, the organism invests 2 ATPs into the process and
receives 4 ATPs back. The net gain is 2 ATPs.
In anaerobic respiration, there is a molecule called NAD that received 2 electrons
to become NADH. The cell has only a limited supply of NAD and ff it is all
converted to NADH, the breakdown of glucose would stop. This is overcome by
converting NADH back to NAD by giving the electrons to acetaldehyde to
produce ethanol.
Fermentation is an inefficient form of making energy. The end products, which
are excretions into the environment, can still be converted into simpler
compounds, releasing more energy.
Breaks down pyruvic acid to CO2 + H2O + ATP
(the oxidation of food molecules within the cell)
IV. Aerobic Pathway
2 stages:
1. The Krebs Cycle
Takes place in the presence of oxygen (aerobic)
2. The Electron Transport Chain (ETC)
aka the Electron Transport System (ETS)
In eukaryotic cells, takes place in the MITOCHONDRIA Fig. 9-7 p. 192
2 membranes *inner "cristae" - folded
"matrix"- dense solution of enzymes, coenzymes, water, etc. found within the cristae
A PRELIMINARY STEP: The Oxidation of Pyruvic Acid
The products NADH and Pyruvate (pyruvic acid) are formed in the cytoplasm of
the cell. The remainder of aerobic respiration takes place in the mitochondria.
Note: NADH cannot enter the inner chamber of the mitochondrion, but it can
pass its electrons to a shuttle carrier on the surface of the inner membrane and
build up a supply of interior electrons. The pyruvate can enter the mitochondrion.
Here the pyruvate is altered so that it can take part in the rest of the process.
A. PRODUCTION OF ACETYL CoA
Pyruvate can be further oxidized. The carbon and oxygen atoms of the carboxyl
group are removed and two acetyl groups are left. These react with NAD+, give
two electrons to NAD+ (this is converted to NADH), and CoA adds on to form
Acetyl CoA, a large complex molecule from pantothenic acid (vitamin B.)
2 pyruvate + 2 NAD + 2 Co-enz A -> 2
Acetyl CoA + 2 NADH + 2 C02
Pyruvic acid passes from the cytoplasm (where its produced thru glycolysis) and
crosses the outer & inner membranes of the mitochondria
Before entering the Krebs Cycle, the 3-C Pyruvic Acid molecule is oxidized: the
carbon and oxygen atoms of the carboxyl group are removed (into CO 2) and a 2C acetyl group is left (CH3CO)
In the course of this rxn, the carboxyl hydrogen reduces a molecule of NAD+ to
NADH
The acetyl is momentarily accepted by a "coenzyme A" molecule-->Acetyl CoA
This links glycolysis to the Krebs Cycle:
From here the Acetyl CoA can enter the Krebs (aka, Citric Acid) Cycle
(discovered in 1930 by Hans Krebs). Acetyl CoA moves into the mitochondria
and is completely dismantled by the enzymes in the mitochondria.
B. KREBS CYCLE (citric acid cycle)
Discovered 1937 by British biochemist Sir Hans Adolf Krebs
As the Krebs Cycle dismantles pyruvate, CO2 is Produced. The carbon and
oxygen come from the pyruvate, which is being tom apart. The electrons are
what's important.
The Krebs's cycle only gives us two molecules of ATP. Added with the two
molecules of ATP made in Glycolysis, the total is now a meager four molecules
of ATP. The remainder of the ATPs come from the Electron Transport System,
which takes the electrons produced in the Krebs's cycle and makes ATP.
In general:
1. 2-C acetyl combines with 4-C oxaloacetic acid to form a 6-C citric acid
2. Two carbons (per cycle) are oxidized to CO2 which regenerates a molecule of
oxaloacetic acid
Each turn of the cycle uses up one acetyl group and regenerates a oxaloacetic
acid, then begins the cycle again.
Energy is released by breaking C-H and C-C bonds and is stored by transforming
ADP to ATP (1 molecule per turn of the cycle) and to convert NAD+ to NADH and
H+ (3x per cycle)
Also, FAD (flavin adenine dinucleotide) is converted to FADH2 (one molecule per
cycle)
1. No oxygen is required in Krebs Cycle
2. All e- and p+ are accepted by NAD+ or FAD
There are nine steps in the Kreb's cycle and the aim is to totally dismantle the
Acetyl CoA using only its electrons.
Here are the steps:
1) 2 Acetyl CoA + 2 Oxaloacetate + 2 H,O -> 2 Citrate + 2 CoA
2) 2 Citrate -> 2 cis-Aconitate + 2 H20
3) 2 cis-Aconitate + 2 H2 0 -> 2 Isocitrate
4) 2 Isocitrate + 2 NAD+ -> 2 Oxalosuccinate + 2 NADH 2 Oxalosuccinate + 2
NADH-> 2 a-Ketoglutarate + 2 C02
5) 2 a-Ketoglutarate + 2 CoA + 2 NAD+ -> 2 Succinyl CoA + 2 C02 + 2 NADH
In the next reaction, the high energy bond is formed. GDP is changed to GTP (Guanine instead of
Adenine) as the CoA is released. We don't know why the cell uses GDP instead of ADP, but the
terminal phosphate in the GTP is transferred to ADP in order to form ATP.
6) 2 Succinyl CoA + 2 P + 2 GDP -> 2 Succinate + 2 CoA + 2 GTP 2 GTP + 2
ADP -> 2 GDP + 2 ATP
7) 2 Succinate + 2 FAD -> 2 Fumarate + 2 FADH 2
8) 2 Fumarate + 2 H,O -> 2 Malate
9) 2 Malate + 2 NAD+ -> 2 Oxaloacetate + 2 NADH
We have totally taken apart the glucose molecule. Only four ATPs have resulted, 2 from
glycolysis and 2 from the GTPS. But we still have a lot of hydrogens in the form of NADH and
FADH2 and a lot of electrons.
Total electron carriers:
Glycolysis (fermentation) 2 NADH
Pyruvate to Acetyl CoA 2 NADH
Citric Acid Cycle
Step4 2 NADH
Step 5 2 NADH
Step 7 2 FADH 2
Step 9 2 NADH
Total 24 electrons
The electrons will go through the electron transport chain to produce energy, and the hydrogen
ions will pass into the outer compartment of the mitochondria.
The Krebs Cycle
KREBS CYCLE SUMMARY:
START---> oxaloacetic acid + Acetyl CoA + ADP + Pi + 3 NAD+ + FAD
END---> oxaloacetic acid + 2CO2 + CoA + ATP + 3NADH + (3H+) + FADH2 + H2O
V. Electron Transport
Some energy from breaking the C-H and C-C glucose is stored in ATP (from ADP + P)
Most energy is passed to electron - carriers (NAD+) and FAD
(these e- are at a high energy level)
Electron Transport Chain transfers these electrons (stepwise) down to the lower energy level of
oxygen
As stated before, the mitochondria has two sets of membranes. The outer membrane is simple in
structure and highly permeable. The inner membrane is highly convoluted and forms extensive
folds/shelves called cristae that reach into the center of the organelle. The folding of the inner
membrane allows for thousands of protein chain copies in each mitochondrion.
Transport Chain carriers are called CYTOCHROMES (consist of protein and a heme group =
atom of iron enclosed in a porphyrin ring) Fig. 9-12 p. 196 (note the similarity to hemoglobin!)
electrons are "passed down" a "staircase" of cytochromes and the energy released in lowering
the energy level is stored in additional ATP molecules...called Oxidative Phosphorylation
remember, the energy from lowering electrons can do this: ADP + P = ATP
---> for every e- passed down the chain from NADH, 3 ATP's are formed
---> for every 2e- from FADH2, 2 ATP's are formed
VI. Phosphorylation by Chemiosmosis
When hydrogen protons (H+) build up on the inside of the mitochondria, a Chemiosmotic Gradient
is set up
(1) a proton gradient is established across the inner membrane of the mitochondrion, and (2)
potential energy is stored, and released as protons travel across the membrane. This energy is
used to phosphorylate ADP (into ATP)
enzyme involved: ATP synthetase
A. OXIDATIVE PHOSPHORYLATION: CHEMIOSMOTIC COUPLING
Production of ATP from ADP and P is powered by a proton gradient. This mechanism is known
as chen-dosmotic coupling. Chemiosmotic refers to the fact that the production of ATP molecules
is a chemical process and a transport process across a semipermeable membrane.
Two events take place in chemiosmotic coupling:
1) The
proton gradient is established across the inner mitochondrial membrane.
2) Potential energy stored in the gradient is released and captured to form ATP
from ADP and phosphate.
The proton gradient is established as electrons move down the ETC. At three different times in
the ETC, there is a signfficant drop in potential energy held by the electrons. These are the three
reactions: Fe-S-> Q, Cyt C, -> Cyt C, and Cyt a 3-> 0 2 . As a result, relatively large amount of
energy is released. This energy powers the pumping of H+ from the mitochondrial matrix through
the inner membrane to the space that separates the inner and outer membrane. Once in that
space, the protons are free to leave the mitochondrion.
The electron carriers in the chain are positioned so that the electrons travel in a zig zag manner from the inner to the outer surface of the inner membrane. Each time the electrons travel to the
inside surface, the electrons pick up two H+. When the electrons travel to the outer surface, they
release two H+. The actual number of protons moved is not known. It is known, however, that at
least six protons are moved.
T'he difference in the proton gradient on the outside of the inner membrane represents the
potential energy. The potential energy results from a difference in pH and electric charge. H+ are
allowed to flow back into the inner matrix through channels called ATP synthetase channels.
Once the H+ flow through the channels, ATP is formed from ADP and phosphate. It is not known
how many flowing H+ it takes to form an ATP molecule (3 ATPs from 1 NADH and 2 ATPs from
FADH 2)
Oxygen acts as the final electron acceptor. Once the oxygen accepts the electrons, it is converted
into water. That is why you need to breathe in oxygen. If oxygen were not there to accept the
electrons, the electron transport system would get backed up, no energy would be produced, and
without energy, there would be no life. Cyanide is a powerful poison because it blocks the transfer
of electrons from cyt a3 to oxygen.
T'he Electron Transport System produces 17 to 32 molecules of ATP. Add this to the previous
total of four ATP molecules produced in Glycolysis and the Krebs Cycle, and we now have a total
of 21 to 36 molecules of ATP from each molecule of glucose oxidized.
Oxygen is used as the final electron acceptor. Carbon dioxide is produced during the Krebs Cycle
and most of the energy is produced from the ETC and H+ concentration/ gradient.
B. OTHER CATABOLIC PATHWAYS
Starch is broken down into monosaccharides. The monosaccharides are phosphorylated to
glucose-6-P and enter glycolysis.
Fats are split into glycerol and fatty acids. The fatty acids are cut up into two carbon fragments
and slipped into the Krebs cycle as Acetyl CoA. Glycerol slips in as Glyceraldehyde-3-P.
Proteins are broken down into amino acids. Amino acids have the amino group removed. The
carbon skeleton is either converted into an acetyl group or a larger compound that can enter
glycolysis. If the amino group is not used, it is excreted as urea.
C. HOW ELSE CAN THIS AFFECT YOU?
In the muscle tissue, there are a lot of mitochondria. During heavy exertion a great deal of ATPs
can be used. Muscle systems usually workaerobicary;but, inlargeranitnals,itisiinpossibleforthe
circulatorysystem to bring enough oxygen to the tissues during heavy exertion. Therefore, we
have two back up systems.
1. Creatine Phosphate This transfers a phosphate to ADP in order to form ATP.
Creatine Phosphate + ADP -> Creatine + ATP. As the creatine phosphate is used
up, there is another quick source of energy.
2. Anaerobic Glycolysis
NADH combines with pyruvate to form lactic acid (lactate). Lactic acid
accumulates quickly during intensive use of muscle. This is the bum that is felt
when exercising. Animals can remove lactic acid in two ways.
a. Lactic acid combines with oxygen from the circulatory system. The oxygen
reverses the lactic acid to pyruvate which proceeds in the aerobic pathway.
b. Lactic acid can be washed away by the circulatory system and carried to the
liver. In the liver, the lactic acid can be metabolized back into glucose with
oxygen.
After periods of heavy exertion, the muscle tissue will be depleted of creatine phosphate and the
liver and muscles will be loaded with lactate. This causes pain. When the activity stops, it takes a
long time, and lots of oxygen and ATP, for the lactic acid to be metabolized and for the creatine to
regenerate into creatine phosphate.
During this time, a person will breathe hard and try to take in as much oxygen as possible. This is
called oxygen debt. How long it takes to recuperate depends on physical condition. The better
condition people are, the more oxygen they can take in and the heart can pump more blood with
the oxygen to their tissues.
Runners enlarge their lung capacity, increasing their capillary beds. The heart becomes stronger
and can pump more blood with each stroke, which increases the ability for runners to utilize
oxygen.
Remember that starch and glycogen are polymers of glucose. These polymers are broken down
into single glucose molecules during a process called phosphorolysis. During this process the
bond is split by an enzyme that places a phosphate on the #1 carbon of the glucose molecule.
This makes Glucose-l-P which is changed to Glucose-6-P.
Runners in the marathon who have hit "the wall" have used up all of the glucose in their bodies.
All that is left are fat and proteins which will be broken down for energy. This is very dangerous
since the heart is a muscle that is made up of protein. This is why runners try to load up with
carbohydrates before a big race.
Chapter 10. " Photosynthesis, Light, and
Life"
I. Introduction:
1st photosynthetic organisms 3 to 3.5 billion years old probably responsible for changing the
earth's atmosphere (use CO2 and H2O to synthesize glucose and O2)
II. The Nature of Light
Isaac Newton - discovered prism divides white light into the visible light spectrum
James Maxwell - discovered light (visible) is only a small part of a larger electromagetic spectrum
(Fig. 10-3 p. 207)
1 nm (nanometer) = 10-9 m
variation in this WAVELENGTH () makes different lights
all light travels at approx. 300,000 km/sec
Albert Einstein: (1905) proposed that light travels in both waves and particles " photons " (packets
of energy)
Photons for different light are inversely energetic to the wavelength ex: Violet light has short ,
but large amounts of energy in each photon
Essay: " No Vegetable Grows in Vain"


Van Helmont
Priestley



Ingenhousz
Lavoisier
de Saussure
III. The Fitness of Light
"Why does so narrow a region of the EM spectrum have such an important impact on life?"
(biorhythms, seasons, photosynthesis, visible colors, etc)
1. Life forms held together with weak H-bonds, etc. Easily disrupted by strong light (such as high
photon energy or low such as UV light) drives e- out of atoms. Conversely, low photon energy
or high  (such as IR light) is absorbed by H2O in cells to heat up
2. Most radiation that reaches thru earths atmosphere is in the spectrum ( higher energy is filtered
out by O2 & O3, lower energy  screened by CO2 and H2O in clouds)
IV. Chlorophyll and Other Pigments
Pigments absorb light of certain wavelengths (reflect some wave
lengths back, or transmit other wavelengths). Different pigments
absorb light energy at different wavelengths = absorption
spectrum
- In plants, chlorophyll a is directly involved in the transformation of light energy into chemical
energy
-Most photosynthetic cells also contain chlorophyll b and/or carotenoids ( red, orange, yellow) =>
most prevalent is beta-carotene
(Chlorophyll is a large molecule with a central Magnesium atom held in a porphyrin ring, like Fe in
hemoglobin) Fig. 10-6 p. 211
The presence of the " secondary" pigments allow photosynthetic cells to capitalize on the greatest
range of 's
When pigments absorb light, electrons within the pigment molecules are boosted to a higher
energy level
V. Photosynthetic Membranes: the Thylakoid
A. Thylakoid: the structural unit of photosynthesis is usually a form of a flattened sac, or vesicle.
These form the internal membranes of a CHLOROPLAST.
---can be up to 500,000 chloroplasts per square mm of leaf surface
B. The Structure of the CHLOROPLAST
similar in structure to the mitochondria: surrounded by 2 membranes that are separates by an
intermembrane space
3rd layer inside: grana (stacks of thylakoids), surrounded by a dense solution: the stroma
Figure 10-11 p. 214
CO2 + 2H2O ------------------------> (CH2O)n + H2O + 2O
VI. The Stages of Photosynthesis
1905 - F.F Blackman: Light/Temp. dependance
"Light" rxns - temp. dep.
"Dark" rxns - temp. indep.
A. "Light-Dependent Reactions" (aka Energy-Capturing Rxns) need light energy to occur
- trap light energy by exciting electrons in chlorophyll --> energy is used to form ATP from ADP,
and to reduce NADP+ to NADPH. Water molecules also broken down.
Occurs in the thylakoids.
B. "Light-Independent Reactions" (aka the Carbon-Fixing Rxns) are enzymatic; can take place
in/out of light, but need the products of light rxns to work
Energy in the form of ATP & NADPH (from previous set of rxns) used to reduce carbon (from
CO2) into sugar molecules (" carbon fixation")
Occurs in the stroma.
VII . Energy-Capturing
1. The Photosystems
In the thylakoids, chlorophyll and other molecules are packed into units called photosystems,
made up of 250-400 pigment molecules each
Photons of light hit chlorophyll and boost an electron to a higher energy level...imagine electrons
bouncing around like in a pinball machine when excited
2 different photosystems, based on "antennae molecules"
PS I = chlor. a molecule called P700 (actually a dimer of two
molecules)because peak absorbance is at 700nm PS II = P680
2. The Light-Trapping Rxns
The two photosystems work independently and continuously Fig. 10-14 p. 218
The boosted electrons are passed down an Electron Transport Chain (remember the last
chapter?) and the energy released is used to turn ADP--->ATP "phosphorylation"
Also, WATER is split into 2 H and an O
The oxygen is let off and the H get passed through photosystems
Water ------> PS II -------------------> PS I ---------------------> NADP
ADP--->ATP
+H =NADPH
This involves yet another Chemiosmotic Gradient Fig. 10-16 p. 220
Van Niel's Hypothesis (Stanford U., 1930's) previously, it had been believed that the O 2 given off
in light reactions came from the splitting of CO2
Van Niel studied autotrophic bacteria "purple sulfur bacteria" which did NOT use H2O in their
food-making proceses:
light
CO2 + 2H2S ------------------------> (CH2O)n + H2O + 2 S
So general equation is:
CO2 + 2H2A ------------------------> (CH2O)n + H2O + 2 A
Which proves it is the " H2A" that is in fact split to release the gas
Later, "heavy" oxygen18(radioactive isotope) was traced through a plant to prove it.
3. CYCLIC ELECTRON FLOW
"Photosynthetic Phosphorylation"
There is evidence that PS I can work independently to form ATP (no NADPH is formed)
Electrons are boosted from P700 to the primary electron acceptor in PSI
They do not travel down the PS I "staircase"
Instead, the e- are shunted to the electron transport chain that connects PS II to PS I and end up
back in the P700 molecule
* this can be used by a eukaryotic cell when an additional supply of energy (ATP) is needed, but
no oxygen is released, and no carbon dioxide is reduced
VIII. The Carbon-Fixing Reactions
CO2 taken in through STOMATA in leaf
Here, the ATP and NADPH from the Light-Dependent Reactions (stored energy) is used to
reduce carbon into sugars
1. The Calvin Cycle - the three-carbon pathway
-analogous to the Kreb's Cycle in many ways
-takes place in the stroma
The starting (and ending) compound is a 5-C sugar with 3 phosphates attached =RuBP
Ribulose biphosphate
CO2 binds to RuBP ------------> RuBPCO2
which then splits into 2 molecules of PGAL (phosphoglyceraldehyde) 3-C* each
(enzyme: RuBP carboxylase)
* = this is why it's called the "three carbon pathway")
6 turns of the cycle = one 6-C molecule of sugar (glucose)
overall equation:
6RuBP + 6 CO2 + 18 ATP + 12 NADPH + 12 H+ + 12 H2O
ends up as
6RuBP + glucose + 18 Pi + 18ADP + 12 NADP+ + H2O (liberated)
Problems with C3 photosynthesis:
1. oxygen competes with carbon dioxide for the active site on RuBP carboxylase
enzyme
2. RuBP carboxylase has relatively low affinity for carbon dioxide, esp. at low
concentrations
2. The Four-Carbon Pathway
an alternative to C3
see Fig. 10-22 pp. 224-225
While most plants bind CO2 to RuBP in 1st step of the light-independent rxns (3-C pathway),
some plants can go through a 4-C pathway
1. ...binds CO2 to PEP (phosphoenolpyruvate) to form a 4-carbon
compound called oxaloacetic acid (like Kreb's !)
2. ...the CO2 is then transferred to RuBP and enters the Calvin
Cycle, but not until it goes through an additional series of
reactions called the "Hatch-Slack Pathway" (catalyzed by
enzyme: PEP carboxylase)
= higher CO2 affinity; keeps CO2 gradient in leaf
C-4 is better in drought-ridden areas or with "crowded" leaves
(little gas exchange)
Maximizes the minimal CO2 PEP binds CO2 faster at lower conc.
Ex: C3 Kentucky bluegrass -vs- C4 crabgrass
*you must be able to COMPARE & CONTRAST the pathways
Molecular Genetics
"The Chemical Basis of Heredity"
*Definitely check out this link!!! Nucleic Acids
The Double Helix
1. The Chemistry of Heredity
Chromosomes are composed of atoms arranged into molecules "molecular genetics "
What was "The Language of Life" - early studies asked: protein (20 AA’s) or DNA (only 4
bases)? No one was sure back then
2. The DNA Trail
A. "Sugar-Coated Microbes" and the Transforming Factor
1928 Frederick Griffith - trying to develop pneumonia vaccine
2 types :
Virulent (encapsulated with in polysaccharide coat)
Nonvirulent (nonencapsulated)
Then, infected mice with both
(1) heat-killed virulent
which
(2) non-virulent
groups
(3) heat killed & nonvirulent
died !?
extracts from killed virulent bacteria could make the living , harmless bacteria into the virulent
type = " TRANSFORMATION "
B. The Nature of DNA
1869- DNA First isolated by German physician, Friedrich Miesscher
1914- Robert Feulgen found DNA staining with fuchsin ( red dye )
1920- P.A. Levene - biochemically broke down DNA into



5-C sugar (deoxyribose)
Phosphate
4 Nitrogen bases (adenine/guanine= purines; thymine/cytosine= pyrimidines )
Each unit - "Nucleotide"
C. The Bacteriophage Experiments
1940- Max Delbruck and Salvador Luria
Used Bacteriophages (a group of viruses that attack bacteria)
(7 phages attack E.coli bacteria ) T1 - T7
advantages: small, cheap, easy to maintain in lab, replicated in 25 minutes
? which part carried the info?
viruses made of: (1) protein coat; and (2) DNA
1952- Hershey & Chase
Labeled virus DNA with 32P and viral protein with 35S ; allowed to incubate with E. coli, then spun
down to separate the genetic material from the protein coats - Found only in the 32P inside
bacterial DNA
= DNA is the carrier if genetic info!
D. Further Evidence for DNA
Alfred Mirsky - All somatic cells (of a species) contain same amount of DNA (gametes contain
1/2)
(Erwin) CHARGAFF’S RESULTS :
compared amounts of each 4 N-bases --> found that they DO NOT always occur in equal l : l : l : l
, but proportions are same with in a species
ex : Human
30.4 % Adenine
30.1 % Thymine
19.9 % Cytosine
19.6 %
Guanine
The Watson-Crick Model
1950’s - Cambridge U.
A. The Known Data
1.
2.
3.
4.
5.
DNA molecule was very large and long and composed of nucleotides containing the 4 N-bases
Levene’s Data
Linus Pauling - protein chains often arranged in helix where AA’s are held together with H-bonds
X-ray Diffraction : Maurice Wilkins &Rosalind Franklin DNA showed helical pattern
Chargaff’s experiments (base ratios) A=T ; G=C
Nucleotides: monomers that come together to form a nucleic acid. They contain
either a ribose or
deoxyribose sugar ( ribose has one more oxygen in tis molecule), phosphate,
and a nitrogenous base
(purine = guanine or adenine, pyrimidine = cytosine, thymine ,or uracil).
Pyrimidines are constructed of a
single ring while purines are characterized by a double ring. The nucleotides are
joined together by
phosphodiester bonds.
Purines and Pyrimidines
Base Pair Combinations
Base pairing rule. A-T, A-U, C-G. DNA has a double helix shape, while RNA is
single stranded.
B. Building the Model
"Double Helix" twisted ladder
1. two sides : alternating sugar phosphate "rungs" :paired N- bases ( A-T / C-G ) discovered
2.
3.
4.
5.
complementary bases
each base covalently bonded to the sugar-phosphate unit
bases paired with H-bonds (relatively weak )
purine & pyrimidine always paired
Strands have a direction
5’ end = P attached to 5th C in the sugar
3’ end = 3rd C is "free"
Base sequence normally written in 5’ to 3’ direction "AntiParallel"
Ex :
(5’) - TTCAGTACATTGCCA - (3’)
(3’) - AAGTCATGTAACGGT- (5’)


proposed by Watson & Crick
Shared 1962 Nobel Prize (with Wilkins )
4. DNA Replication
"An essential property of genetic material is the ability to provide for exact copies if itself"
Replication :



DNA helix "unzips" down the center by separating at the H-bonds between base pairs
The two separated (single) strands then act as TEMPLATES (patterns for new strands to form
against )
free nucleotides "float" in to attach to the exposed complementary bases on each single strand of
DNA, thus forming a "new" strand against each "old" strand = semi conservative replication
A. Confirmation of Semiconservative Replication
Meselson and Stahl : used "heavy" nitrogen isotope (15N) to "mark" DNA molecules




grew E.coli on 15N medium until it’s DNA contained lots of "heavy" strands
then transferred the cells to normal medium ("light" 14N)
centrifuged the "new" replicated cells to separate the DNA types (CsCl )
found that the new cells contained 1/2 heavy and 1/2 light DNA
= CONFIRMED SEMICONSERVATIVE REPLICATION
B. Mechanics of DNA Replication
Replication of DNA takes place ONCE per cell cycle, during the S phase
Rapid process : humans = 50 nucleotides synthesized/second ( prokaryotes= 500
nucleotides/sec )
***** Requires several enzymes, many steps *****
"Origin of Replication"- specific nucleotides sequence that starts the process



It requires special initiator proteins and enzymes called helicases which break the H-bonds,
opening up the helix
Topoisomerases - enzymes that break and reconnect strandsto prevent supercoiling upon
disconnection
DNA polymerases - catalyze synthesis of new strands
Eukaryotes - "bidirectional" replication
Prokaryotes- single replication origin, "theta replication"
RNA Primers and the Direction of Synthesis
Primer: formed from nucleotides, which start the attachment to DNA strand (RNA primase)
"replication fork"
Reiji Okazaki - Discovered the leading/ lagging strands
Leading strand : synthesized continuosly against one side of "fork"
Lagging strand : synthesized as a series of fragments against the other side of "fork
"Okazaki fragments" (make up Lagging strands)
Prok: 1000- 2000 nucleotides long
Euk: 100 - 200 nucleotides long
DNA Ligases- connect the newly synthesized DNA segment, like "glue"
C. PROOFREADING : Mistakes happen; DNA Repair


DNA polymerase can only add more nucleotides to the 3’ end of a strand if the preceding
nucleotides are correctly paired on the template strand
DNA repair enzymes can "snip out" incorrect sequence , starting again with the 1st correct one
encountered
D. The Energetics of DNA Replication
Powered by extra phosphates (triphosphates)
ex: adenine is added to DNA strand as"deoxyadenosine
triphosphate " (dATP) and guanine added as "deoxyguanosine
triphosphate" (dGTP)
As the phosphate bonds are made, to attach the nucleotide to teh DNA molecule, the extra
phosphates are removed (thus releasing energy)
E. DNA As A Carrier Of Information
each base triplet codes for a specific AA , which in turn make up protein chains
Any combination is possible
number of base pairs in a virus = 5000
number of base pairs in 46 human chromosomes = 5 billion
some trivia:

A small DNA molecule may be ~5500 nucleotides long

A typical human germ cell (reproductive) has about 1 billion nucleotides in
it and is about 3.5 m in length when unwound!

Different species of organisms may be defined by the number of
chromosomes in their cells. For example: every human has 46
chromosomes per cell (except gametes); goldfish = 94; carrot = 18; fruit
fly= 8; onion= 16;
The Human Genome Project Begun in 1990, the U.S. Human Genome Project is
a 13-year effort coordinated
by the U.S. Department of Energy and the National Institutes of Health. The
project originally was planned to last 15 years, but rapid technological advances
have accelerated the expected completion date to 2003. Project goals are to:
identify all the estimated 80,000-100,000 genes in human DNA, determine the
sequences of the 3 billion chemical bases that make up
human DNA, store this information in databases, develop tools for data
analysis, and address the ethical, legal, and social issues that may arise from
the project.
THE GENETIC CODE AND ITS TRANSLATION
I. Genes and Proteins
A. Inborn Errors of Metabolism
1908 Sir Archibald Garrod
"Certain diseases that are caused by the body’s inability to perform particular chemical process are
hereditary in nature." Ex: alkaptonuria :enzyme deficiency caused by a gene deletion
B. One Gene - One Enzyme
Synthesis of all substances in living things dictated by enzymes
Specificity of different enzymes is a result of their 1 degree structure (sequence of linked AA’s)
Beadle and Tatum’s experiments with Neurospora crassa (red bread mold)
1.
2.
3.
brief life cycle
easy to grow in large quantities in lab
Most of it’s life cycle= HAPLOID (no homologous pairings) lets mutations be seen immediately.
4.
5.
6.
Meiosis takes place in saclike reproductive structures called asci
History of chromosome mapping studies on mold
Could live on minimal medium and still synthesize all aa’s (with enzymes [=genes])
X-ray = mutations = loss of enzyme = lack of an AA (ex. Arg.)= could only grow on Arg-supplemented
media
Beadle and Tatum proposed that a single gene (thru a single mutation = immediate result)
codes for a single specific enzyme = Nobel Prize
(Not necc. true = only some proteins are enzymes)
* also true of structural proteins, or hormones
C. The Structure of Hemoglobin
Linus Pauling- proposed that some diseases involving hemoglobin (sickle cell anemia) are caused by a
variation in the normal protein structure of the hemoglobin molecule (a protein)
Electrophoresis of hetero/homozygous sc patients
Vernon Ingram: Later learned that the sc hemoglobin is caused by one changed AA (out of 300)
D. The
Viral Coat
add’l studies showed how changes in viral DNA led to change in
(bacteriophages)
protein coat of virus
II. From DNA to Protein: The Role of RNA
A. The Central Dogma
DNA codes for specific RNA, which in turn codes for specific protein
B. RNA as a messenger
3 kinds of RNA play role (intermediates) leading from DNA to protein





mRNA (messenger) - Is a copy (transcript) of DNA sequences
single stranded
each new mRNA strand is transcribed from one (template) DNA strand by the
same base-pairing principle
mRNA has 5’ and 3’ end
mRNA bases pair complementary to DNA(unzipped, exposed bases)
DNA------->RNA complement ="Transcription"
A----U
T----A
C----G
G----C
mRNA nucleotides "float in" to add to 3’ end of strand (antiparallel to DNA strand)
RNA strand forms using enzyme: RNA POLYMERASE
* always builds from 3’ to 5’ along DNA strand
III. THE GENETIC CODE



proteins can be made of different numbers and combos of 20 AA’s
DNA and RNA only contain 4 possible bases => 3 bases code for each AA,
giving
4 x 4 x 4 = 64 possible base triplet combinations (RNA = "codons")
A. Breaking the Code
Marshall Nirenberg and Heinrich Matthaei (NIH)
added mRNA from various cells into E. coli and found that the "foreign" mRNA induced the E. coli to
produce proteins anyway...
Prepared 20 tubes of E. coli, ribosomes, ATP, enzymes, and AA’s. Each tube contained one radioactive
AA Synthetic "Poly-U"
mRNA (U-U-U-U...) was added and it was found that the U-U-U- bacteria synthesized only the radioactive
phenylalanine (Therefore U-U-U = phe)
(See figure 15-9 pp. 309)
IV. Protein Synthesis
A) 3 types of RNA
Messenger RNA



DNA double helix "unzips" forming 2 individual strands
mRNA is transcribed against one srand (5’-> RNA 3’)
Specific nuleotide sequences code for start of mRNA synthesis:
PROMOTORS; and stop of mRNA synthesis: TERMINATES

Finished mRNA strands are 500-10,000 nucleotides long
TRANSFER RNA



Small, ~80 nucleotides long , cloverleaf structure
More than 20 kinds, each carries a specific AA at the 3’ end
The "Wobble Phenomenon": There are only 40 different types of t-RNA and 64
codons. This means that some of the t-RNA can pair up with several different
codons. This can occur because the third base of a t-RNA molecule can form a
hydrogen bond with more than one kind of base. U in the third position can bond
with A or G in the corresponding position.
RIBOSOMAL RNA
3 types:



1,500 nucleotides in length
3,000 nucleotides in length
100 nucleotides in length
structural elements of the ribosomes
Ribosomal RNA- most abundant type of RNA in cells
Ribosomes: 2 subunits 2/3 RNA, 1/3 protein
mRNA
* of the 64 possible 3-base codes, 61 code for AA’s 3 code for "stop"; i.e. chain termination
AUG = methionine; sometimes "START"
B) Translation: the synthesis of proteins
involving the transfer of information from one language (nucleotides) to another (amino acids)
Takes place in 3 stages: initiation, elongation, termination
1. Initiation: begins when the smaller ribosomal subunit attaches to a strand of mRNA at its 5’ end
(initiator codon)
Next, the tRNA anticodon pairs with the initiator(mRNA) codon
Usually:
mRNA (5’)-AUG-(3’)
tRNA (3’)-UAC-(5’) -met (carries within its Amino acid)
2. Elongation: 2nd mRNA codon is "read" by anticodon tRNA (so the 2nd AA is brought into place);
then the 3rd triplet is translated, and so on....
as the ribosomal moves along the mRNA strand "reading" it...
3. Termination: translation ends AA strand when ribosome ‘reads" a STOP
V. Redefining Mutations
ex. Sickle cell anemia = abnormal hemoglobin (protein chain)
450 nucleotides - one mistake glutamic acid (...GAG...) subbed by valine(...GUC...)
"Point Mutations" a single nucleotide substitution
"Frame Shifts" caused by deletion or addition of a single nucleotide
TRANSCRIPTION
1. DNA unzips, mRNA nucleotides "float" in to form a complementary mRNA strand using the DNA as a
template
2. mRNA detaches from DNA template and attaches to a ribosome at 5’ end
3. tRNA anticodons "plug into" mRNA codons starting at its 3’ end
4. AA’s are based (peptide bonds) in sequence to finish the protein
"THE MOLECULAR GENETICS OF PROKARYOTES AND VIRUSES"
research: pneumococci, Escherichia coli, bacteriophages, TMV
Recombinant DNA: involves modifying/combining DNA from a variety of different sources and
inserting these altered molecu;es into other cells, in which the "new"genes are expressed
I. The E.coli Chromosome
*bacterial chromosome is a single, continuous (circular) thread of double- stranded DNA.
*Approx. 1 mm long when fully extended (only 2mm in diameter); *contains about 4.7 million base pairs.
*Prokaryotic Cells Replicate DNA in a bidirectional fashion (Replication)
*Replication begins at a specific base sequence.
"Origin of Replication"
diagram
II. Transcription and Its Regulation



Transcription begins when RNA polymerase (enzyme) begins formation of an
mRNA strand along DNA strand, beginning at promotor site.
A segment af DNA that codes for one specific protein is known as a structural
gene
There may be several "start" and "stop" codons along the mRNA strand,
marking the beginning and end of each structural gene.
"leader" sequence (of nucleotides) at 5’ end
"trailer" sequence (of nucleotides) at 3’ end
A) The
Need for Regulation
Bacteria cell goal: to grow and multiply rapidly
Can double number every 20 minutes!
Regulated by several means:


B) The
1) induced by presence of a material (ex. Lactose presence induced E. coli to synthesize betagalactosidase enzyme)
2) inhibition: presence of substance prevents formation of an enzyme "repressible" (ex: E.
coli; tryptophan inhibits tryptophan forming enzymes)
Operon Model (1865 Nobel Prize)
-arose from study of mutant cells
(by Francois Jacob and Jacques Monod and Andre Lwoff)
Operator: DNA sequence (nucleotides) that interacts with a repressor to regulate the transcription of
structural genes
Regulator: can be located anywhere on the bacterial chromosome
*This gene codes for a repressor protein
Repressor: protein that can bind to the operator gene, thus obstructing the promotor (blocks the
RNA polymerase from moving along ("reading") the molecule-> no mRNA transcription can occur
*when the repressor in removal, mRNA transcription begins
studies done on E. Coli cells making enzyme: beta-galactosidase "blocked" by repressor binding to
operator
lac operon:
CAP- Catabolite activator protein: a regulatory protein that exerts a positive effect on the operon
CAP combines with cyclic AMP molecule: this CAP-cAMP complex binds to the promotor and
maximizes transcription
III. Plasmids and Conjugation
Although bacterial chromosomes carry all the genes neccessary for growth and reproduction of the cell,
they also carry additional DNA molecules called Plasmids (carry between 2-> 30 genes; small)
2 important types:
"sex factor" plasmids = F (fertility)
"drug resistance" plasmids = R (resistance)
A.The F Plasmid
contain 25 genes
F+ (male) "donor" cells: make pili (protein "bridges" that form to connect 2 cells for
transfer of genetic material)
F- cells lack the F plasmid and can’t form pili (female) "recipient" cells
Conjugation: transfer of DNA from one cell to another by cell-by-cell contact
"rolling circle replication"
Sometimes the F factor gene can be incorporated within the main bacterial chromosome: called a "high
frequency replication" Hfr Cell
This can then transfer a portion of bacterial chromosome to a F- cell:
diagram
B. R Plasmids
1. Carry antibotic resistance genes
2. Can have up to 10 resistance genes per plasmid
3. Allow for species-to-species transfer
ex: E. coli -> Shigella (dysentary)
IV. Viruses
- a molecule of nucleic acid encased in a protein coat (capsid)
- contain no other "cell machinery", but can move from cell to cell and utilize the host cell’s "machinery" to
replicate the viral DNA
Viral nucleic acids vary: may be either DNA or RNA; double or single-stranded, circular or linear
CHARACTERISTICS:
1. Contain a small amount of DNA(or RNA) surrounded by protein
ex: T7 bacteriophage has DNA
and 100 genes
2. Small viruses that don’t have room for a lot of DNA uses overlapping genes
3. Retroviruses (ex: HIV) are RNA viruses that use an enzyme (called Reverse Transcriptase to make DNA
to replicate itself during infection stage)
A. Viruses as Vectors
Lysogenic- viruses incorporate their DNA into a cell’s chromosome.
The cell may then cause a sudden eruption of viral activity (can remain latent for many generations)
Temperate bacteriophages- viruses that can integrate their DNA into bacterial chromosome at specific
sites
Prophage- an integrated bacteriophage
Lytic cycle- occurs one in about every 10,000 cell divisions, when prophages break loose from the host
chromosome (causing release of more viruses) ----> can be induced in lab with UV light, X-rays, etc...
B. Transduction
the transfer of cellular DNA from one host cell to another by means of viruses
1. General Transduction
diagram
2. Restricted Transduction
diagram
C. Introducing Lambda
Lambda is the best studied of the temperate bacteriophages
Viral form: linear, double-stranded (2 free ends)
When inserted into a bacterial cell, it becomes circular
integrase- enzyme used to insert a DNA into bacterial chromosome
V. Transposons
segments of DNA that are integrated into chromosomal DNA
1. Also contain a gene for transposase which inserts it into a new site
2. At each end, they contain a sequence of repeats*
*direct repeats -ATTCAG-ATTCAG*used to I.D. insertion points
= recombinant DNA
*indirect repeats -ATTCAG-GACTTA-> Can carry genes for mutations, protein synthesis, drug resistance, etc...
RECOMBINANT DNA: THE TOOLS OF THE TRADE
I. Isolation of the Specific DNA segments
DNA molecules are difficult to analyse because of their size and complexity -must break down into
uniform samples of manageable size using Restriction Enzymes (synthesized by some bacterial
cells or Reverse Transcriptase(encoded by nucleic acid of some RNA viruses)
A. Restriction Enzymes:
- discovered early 1970’s
- used by cells to cleave foreign DNA
- cleave DNA at very specific sites: Recognition Sequences
Examples:
a.
5’- GTT AAC-3’
3’- CAA TTG-5’
Bacterial cells can "protect" their own DNA from their restriction enzymes by "methylation"(adding -CH3
group to the recognition sequence to "hide" it) *use an enzyme to methylate
Cleavage:
1. Straight cut
2. Sticky ends- can join with any other segment cut by the same enzyme (forms H-bonds between bases)
Genomic DNA (gDNA)
: DNA fragments produced by restriction enzymes (gDNA fragments may now be "stung together" from a
variety of different sources)
Reverse Transcriptase: cDNA
retrovirus: type of fanimal virus that carries only RNA when it infects a cell in order to replicate itself, it must turn the RNA into
DNA sequence using an enzyme called reverse transcriptase (RNA cannot be replicated!)
Complementary DNA (cDNA): produced from reverse transcriptase; can be spliced into other DNA segments by means of
"artificial" sticky ends (ex: .... TTTTT) a repeating nucleotide sequence --> can be added to any other DNA
strand to which .... AAAAA sticky end has been added.
Synthetic Oligonucleotides
Scientists have developed methods for synthesizing short segments of
DNA or RNA in a laboratory; ("Oligo-" means "few") uses condensation reactions to link series of 12 to
20 nucleotides together
II. Clones and Vectors
how to obtain gDNA, cDNA, and oligonucleotides in large quantities?
A. Plasmids as Vectors
"new" gene can be inserted(must also be cut out with EcoRI so that sticky ends are complementary)
Once "new" gene is inserted, the bacterial cell (plasmid) may be cultured and mass-produced in laboratory, thus also mass producing the
desired recombination of DNA
- good up to about 4,000 base pairs at length
B. Lambda
and Cosmids
Specifically modified bacteriophage "Lambda" are used to replicate larger segments (up to 20, 000 base pairs) of DNA(cut out a
large plasmid section and replace it with desived gDNA fragment)
Cosmids: constructed of a DNA segment flanked by "cohesive regions" (COS) of bacteriophage lambda.
III. Nucleic Acid Hybridization
by heating DNA, the Hydrogen bonds between paired bases are broken (disrupting the helix) - can be used to get new combinations of DNADNA or DNA-RNA (hybrid)
A. Radioactive
Probes
used to "mark" specific DNA or RNA sequences
1. Specific segment must be located and isolated
2. "Tagged" with a radioactive isotope (usually carried on gDNA or cDNA or oligonucleo tides)
IV. DNA Sequence
Electrophoresis using different cleavages (restriction enzymes)
Frederick Sanger: worked out nucleic acid sequence of insulin (1980 Nobel Prize)
The Molecular Genetics of Eukaryotes
pp. 355 - 381
Many marked differences between Eukaryotic & Prokaryotic DNA:
1.
2.
3.
4.
Far greater quantity of DNA in eukaryotic cells
Great deal of repetition in Eukaryotic DNA (much lacks any function)
Eukaryotic chromosome has more protein mixed with the DNA
More complexity in the protein-coding sequences in Eukaryotic
I. The Eukaryotic Chromosome


made up of a protein-DNA complex called CHROMATIN
60% protein by weight
Trivia: a DNA filament is so thin, tiny, that a strand reaching from earth to sun would weigh only 1/2 gram!
Humans have 46 chromosomes in the nucleus of each cell
Trivia: Each chromosome is 3-4 cm long; each cell, therefore, contains about 2m , which = 25 billion km
(length) of DNA in your entire body!
Characteristics:
Each DNA is Double-stranded & twisted into a HELIX
Helix is usually coiled tightly in Right-handed twist called B-form DNA
Also comes in 2 other forms:
A-DNA : right-handed twist, not very tightly coiled
Z-DNA : left-handed twist (see pg. 356 diagrams)
A. Structure of the Chromosome
"chromatin" = 60% protein, 40% DNA
protein type called HISTONES
Histones are positively charged (basic) & are thus attracted to (-) acidic DNA
Histones primarily responsible for the folding & packaging of DNA
5 Distinct types of Histones:
H1: about 30 million molecules per cell
also H2A, H3B, H3, H4:
a) About 60 million molecules EACH per cell
b) Very similar in all eukaryotic organisms
NUCLEOSOME: the fundamental packaging unit of chromatin
*see diagrams on page 357!!
DNA filament wrapped 2x (like thread
around a spool)
Upon condensation into "rods" (in mitosis & mitosis) forms "Looped Domain" configuration
B. Replication of the Chromosome
Semi-conservative Replication (Meselson & Stahl)
Remember! (review)
Nucleotides in Triphosphate form "float in"
Strand forms only in 5' to 3' direction(using DNA polymerase)
while 3' to 5' strand is assembled in a series of Okazaki fragments,
then joined together by DNA ligase
Prokaryotic cell: bidirectional replication starting from a single replication origin
Eukaryotic cell: many replication origins, bidirectional synthesis takes place until replication forks merge;
much slower replication (humans replicate at about 50 base pairs/second/replication fork)
II. Regulation of Gene Expression in Eukaryotes
Eukaryotes are multicellular & each cell type is differentiated by types of proteins produced. Some cells
produce different proteins at different stages, in sequence. How? Why? = carefully controlled gene
expression(regulation)
(How does each cell "Know" what protein to produce, and when?)
A. Condensation of the Chromosome & Gene Expression
2 types of Chromatin:


Euchromatin - more open
Heterochromatin - more condensed
Transcription of DNA to mRNA (for gene expression/protein synthesis) only takes place during
INTERPHASE, when euchromatin is dispersed
"Puffing" can be observed in insect chromosomes - puffs indicate that DNA must "unwind" to make itself
available for transcription
(Fig. 18-9 pp. 360)
B. Methylation & Gene Expression
Once DNA is formed, enzymes Methylate (-CH3)
Certain nucleotides of cytosine (=Methylcytosine)
perhaps to inhibit (block) gene expression
C. Regulation by Specific Binding Proteins
regulating proteins bind to turn genes on/off
III. The Eukaryotic Genome



The amount of DNA per cell is the same for all organisms within a species
The amount of DNA between different species varies greatly ex. Drosophila 1.4 x 100000000
base pairs haploid genome about 70x that of E. coli
Humans 3.5 x 1,000,000,000 base pairs = 25x that of Drosophila, somewhat more equal to a toad!
Eukaryotic Cells have a great excess of DNA (prokaryotes are more "thrifty" = max. of all DNA); only 110% of DNA in Eukaryotic codes for actual proteins!
About 1/2 of the nucleotide sequences are repeated (100's of times). Why so repetitious? (Same gene may
be coded for many times)
A. INTRONS
Protein-coding sequences of eukaryotic genes are NOT continuous (interrupted by NON coding sequences)
= INTRONS
EXONS = coding sequences
B. Classes of DNA: Repeats & NonRepeats
1. Simple-sequence DNA: Multiple copies of the same base sequences (reassociates very quickly when
broken up)



many short, repetive sequences
usually found around the centromere and at ends "caps" of the chromosome (ex: Drosophila has
the sequence -ACAACT- repeated 12 million times)
probably important for chromosome structure & integrity
2. Intermediate-Repeat DNA - Makes up about 20-40% of DNA in multi- cellular organisms (reassociates
more slowly)





longer sequences than simple-sequence DNA (150-300 nucleotides)
similar (but not identical) to one another "families"
scattered throughout the chromosome
sequences have some known functions
some of the best-studied intermediate-repeat sequences are the genes coding for histones &
ribosomal RNA
3. Single-Copy DNA



nucleotide sequences that are not repeated, or are repeat only a few times
make up 50-70% of DNA
only about 1% translates into actual proteins
Transcription Units - composed of introns & extrons - are separated by great distance of "Spacer" DNA
C. Gene Families

genes that are made up of similar nucleoticle sequences (ex. different types of hemoglobin in
same organism)
IV. Transcription & Processing of mRNA in Eukaryotes
begins with attachment of an RNA polymerase(enzyme) to a particular nucleotide sequence(promoter)
along one strand of DNA helix - this serves as a TEMPLATE for assembly of mRNA nucleotides
-In Eukaryotes, each structuralgene is transcribed separately (unlike prokaryotes, which can transcribe in
groups)
-In Eukaryotes, there are 3 different RNA polymerases which transcribe for 3 different types of RNA
A. mRNA Modification & Editing
In Eukaryotes, mRNA transcription must be completed and mRNA is then modified before it goes through
cytoplasm to the ribosome




a 7-methylguanine "cap" is added to the 5' end to aid in attachment to ribosome
a string of adenine -A-A-A-A- is added to 3' end "poly-A tail" (?? function)
introns are excised(before reaching ribosome) and exons spliced together
mRNA molecules are transported through cytoplasm by association with
mRNP's(ribonucleoprotein particles)
V. Genes on the Move
A. Antibody-coding genes
Anti bodies - complex globular proteins produced in large quantities by special WBC's (lymphocytes) in
response to presence of foreign molecules(Anitgens)
Problem: We are capable of producing specialized antibody proteins for over 10 million different antigens.
We don't have enough DNA to possibly carry all those genes?!
Answer: Antibodies all made of different combinations of Constant(C) and Variable(V) chains
would only require a reasonable # of different genes, moved around in different combinations
(rearrangement of genes)
B. VIRUSES
proviruses - piece of viral DNA incorporated into a eukaryotic chromosome


highly moveable, transferable
also, Retroviruses (RNA) can incorporate themselves into host DNA
C. Eukaryotic Transposons




can move nucleotide sequences from one chromosome place to another
can cause mutations when inserted into a structural gene or promoter sequence
in Eukaryotes, many transposons are copied into RNA, then back to DNA for insertion (unlike
prokaryotes)
can form "pseudogenes" (lack introns) = non-functional
VI. GENES, VIRUSES, & CANCER
ONCOGENES - thought to regulate CANCER; certain cell's growth/division



cells normal growth is disrupted, multiply & destroy other tissues
a few cancers cancers have been linked to viruses
hypothesis - when the normal regulatory genes are disrupted, causing the oncogenes to "turn on",
causing rapid cell growth/division (can be caused by viral disruption)
VII. TRANSFERS OF GENES BETWEEN EUKARYOTIC CELLS
A. To Cells in Test Tubes
SV40 virus can be used to transfer a rabbit gene into monkey cells
(exposing cells to Ca2Cl stimulates uptake of NEW DNA)
B. To Fertilized Mouse Eggs
see figure 18-23 pp. 378
C. To Drosophila Embryos
Mendelian Genetics
Ch. 11 From An Abbey Garden - The Beginning Of Genetics
I. Early Ideas About Heredity
Egyptians, Babylonians - Animal & Plant breeding, selective crosses for better
agriculture
Greeks believed in some interesting hybrids (ex: minotaur)
17th century - Abiogenesis (for small creatures)
II. The First Observations
Anton Van Leewenhoek - sperm (animalcules) " Spermists "
Regnier deGraaf - " Ovists "
III. Blending Inhertance
19th century: believed that gametes "blend" characteristics (hereditary mixture)
example: Black & White = Gray
Problem: this concept would lead all creatures toward uniformity (thus contradicting evolution)
When does Gray & Gray = Black /White? How do characteristics skip a generation?
IV. The Contributions of Mendel
Gregor Mendel - Austrian monk (born 1822 ) was experimenting with GENES around same time
Darwin was writing On The Origin of Species; he didn't know about "genes" , per se, he called
them "factors"
"Each parent contains PAIRS of 'factors'. One of this pair is donated by each parent to their
offspring."
We now know these factors to be genes, or more specifically, ALLELES
A. Mendel's Experimental Method
Garden peas - available, easy to grow, rapid generations several varieties "Bred true" for : Tall,
short, yellow seeds, green seeds, smooth seeds, wrinkled seeds, etc.
Contain both male and female flower parts (can self-pollinate)
Mendel manipulated flowers so he could restrict plants to artificial cross-pollination
Scientific Method :
Tested very specific hypotheses (well-planned experiments)
Studied offspring of first, second, third generations
Counted offspring (type) and statistically analyzed results
Well-organized data (easily observed, conclusions, repeatability)
B. The Principle of Segregation
Mendel chose 7 characteristics which "bred true" and did test-crosses to check F1 generation
(first filial) (see fig.11-1 pg. 239)
When he cross-pollinated purebred (homozygous) round-seeded plants with purebred
(homozygous) wrinkled-seeded plants, he found ALL of their offspring were round-seeded!
Why? Where did the trait for wrinkled-seeds go?
IMPORTANT OBSERVATION- "Principle of Dominance and Recessiveness": "One allele
(dominant) may mask another (recessive)"
Then...to check to see if the recessives were "carried", he re-crossed the F1 offspring to see what
traits came out in the F2 generation.
Found :
Dominant genes ex: round seed round
5,474
Recessive genes wrinkled seeds
1,850
total: 7,324 ...found a uniform 3:1 ratio dominant
to recessive traits expressed
The Principle of Segregation " Every individual carries a pair of factors for each trait, and
members of each pair separate (Segregate) during the formation of gametes " = Mendel’s First
Law
Alleles
Yellow seeds (dominant) Y Heterozygous Yy
Green seeds (recessive) y Homozygous yy or YY
" Alleles " = alternate forms of the same gene
Phenotype : the outward appearance of an organism (yellow / green)
Genotype : the actual genetic makeup (allelic pairing) of an organism
Punnett Squares : used to visualize a test cross
Probability
Monohybrid Crosses
Sample problem: complete a Punnett square to show the outcome of a pure tall
plant crossed with a short plant (F1):
y = green
Y = yellow <---- letter of dominant allele, capitalized
= 4 Yy (heterozygous) genotype
= 100% yellow seeds
Now, cross those to find the F2 outcome:
= 1 YY : 2 Yy : 1yy (1:2 :1) genotypic
= 3 yellow, 1 green (3 :1) phenotypic
example: tall and short pea plants
C. The Principle of Independent Assortment
Mendel also studied plants that carried 2 characteristics
ex :
round, yellow peas / wrinkled, green
remember! each parent carries 2 alleles for each trait
Dihybrid Cross (Punnett square = 16 boxes )
RRYY x rryy gives offspring of all varieties : round yellow, round green, wrinkled
yellow , wrinkled green
" When gametes are formed, the alleles of one gene for a trait segregate independently of the
alleles of a gene for another trait "
= Principle of Independent Assortment " (Mendel’s 2nd Law)
V. Mutations
1902 Dutch botanist - Hugo DeVries
studying Mendelian genetics on primroses, discovered that, white the offspring (results) are
generally predictable, sometime an abrupt change occurs => these changes in genes are then
passed on to successive generations.
Mutations - abrupt changes in a gene which are passed on to successive generations (Mutants)
ex : Wrinkled peas arose from a random mutation of smooth peas
A. Mutation and the Evolutionary Theory
Darwin’s theory failed to explain how variations can persist in populations
How can an offspring who has inherited traits from both parents be BETTER
adapted than either parent?
Mutations (random) give many more possibilities (for offspring) than simple
Mendelian genetics!
Meiosis and Sexual Reproduction
1. MEIOSIS AND SEX CELLS: SEXUAL REPRODUCTION
A. INTRODUCTION
In higher organisms, plants and animals, each individual is diploid. A diploid organism has a
complete set of chromosomes in every cell and is 2n (diploid means'double set'). The organism
gets one set from the mother and the other set from the father. The two partners produce
gametes which are joined to produce an offspring. However, two problems must be solved in
sexual reproduction.
1) If fertilization occurs and the gametes join,
why isn't the genetic material doubled?
2) How is it possible for each parent to give half
of the genetic material?
The answer is meiosis, a process in which a diploid or double set of chromosomes is reduced to
a haploid (n), or a single, set of chromosomes. It is a process that guarantees that the number of
chromosomes remains stable from generation to generation. In humans the diploid number = 46
(2n = 46), the haploid number = 23 (n = 23); in fruit
flies: 2n = 8, n = 4.
B. HOMOLOGOUS CHROMOSOMES
1. Chromosomes
In humans there are 46 chromosomes. Each chromosome consists of a double helix molecule of
DNA. The DNA is folded with proteins to make up a chromosome. One chromosome represents
hundreds or thousands of genes, and each gene is a specific region of the DNA molecule. A
gene's specific location on the chromosome is called the its locus. The 46 chromosomes are
actually 23 pairs of chromosomes. The members of each pair are called homologous
chromosomes (homologues). The two homologues are functionally equivalent and contain the
same kinds of genes arranged in the same order.
2. Autosomes
One set of chromosomes that does not occur as homologues occurs in males. The X
chromosome and the Y chromosome are not homologues, but pair up in meiosis. In
females, there are two X chromosomes that are homologues. These chromosomes are
the sex chromosomes and the other 22 pairs of chromosomes are called autosomes.
3. Homologues During meiosis, three things happen to the homologues.
a. The homologues pair up.
b. The homologues exchange genetic information. This is called crossing
over.
c.The newly scrambled chromosomes separate and go into different
daughter cells in such a way that each daughter cell contains only one of
each pair of homologues. These cells are called gametes or sex cells.
C. MEIOSIS AND LIFE CYCLES
Meiosis occurs at different times during the life cycle of different organisms. In protists
and fungi, meiosis occurs right after the fusion of the two mating cells. The mating cells
are usually haploid and the fusion produces a diploid cell. Immediate meiosis restores
the haploid lifestyle.
In all plants, a multicellular haploid phase alternates with a multicellular diploid phase.
The typical fem is diploid and is called a sporophyte. The diploid sporophyte produces
haploid spores through meiosis. A spore will grow into a small haploid plant called a
gametophyte. These produce male and female sex cells (gametes) via mitosis. The
gametes will join to form a diploid cell that will grow into the fem that you see. This
alternation between diploid and haploid is called alternation of generations.
Animals, including humans, are diploid organisms that produce haploid gametes. Two
haploid gametes will join to produce a diploid zygote. Most of the lifecycle in animals is
in the diploid state.
1. Mitosis vs. Meiosis
a. Mitosis
Occurs in haploid, diploid, and polyploid cells.
b. Meiosis
Occurs only in diploid and polyploid cells. The nucleus divides twice producing
four nuclei. The chromosomes replicate only once, so each nucleus contains half
of the number of chromosomes.
c. Haploid Chromosome Each haploid chromosome is a new combination of old chromosomes
because of crossing over.
D. MEIOSIS I
There are two stages of Meiosis: Meiosis I and Meiosis II. Meiosis I is the
replication of chromosomes, crossing over of the chromosomes, and reduction in
the chromosome number from diploid to haploid. Meiosis I is often called the
reduction division.
1. Premeiotic Interphase
GI, S (replication of the chromosomes), and G,.
Meiotic Prophase I: The first stage.
This is long and complex compared with mitotic prophase.
a. Nuclear membrane disappears.
b. Spindle fibers form.
c. The chromosomes condense.
d. The homologous chromosomes pair up by touching each other in the
appropriate places. First there is a lot of random movement of chromosomes until
the homologous chromosomes find each other. It is important, for example, that
chromosome #13 finds homologous chromosome #13. When the two
homologous touch each other in the same place, a specialized structure called
the synaptonemal complex holds the homologues together.
T'he meiotic cell of a human now has 23 genetic entities called tetrads, each packet containing
four chromatids and two centromeres. This is the point when crossing over occurs. A special
enzyme causes the chromatids to unwind, revealing the strands of DNA. A complex series of
events happen and the genetic material is exchanged between h6mologues.
Crossing over may occur at the introns.
Crossing over - exchange of segments of one chromosome with corresponding segment of its
homologue (can alter the genetic makeup of chromosomes)
Several thousand base pairs of one strand pairs with the chromatid on another homologues.
There are breakages and the chromatids untangle themselves. Meanwhile other enzymes are
repairing the breaks in the DNA. This process makes new chromatids and is a source of genetic
variation within a population.
After crossing over, the homologues begin to pull away from each other, except at the crossing
over points called the chiasmata (chiasma - singular).
2. Metaphase I
In the first metaphase, the tetrads are brought to the metaphase plate. The synaptonemal
complex is lined up on the metaphase plate.
3. Anaphase I
There is no separation of the centromeres, but the synaptonemal complex separates. This means
that the homologues separate andmovetooppositepoles.Thefirstmeiotic divisionreduces the
chromosomenumber by half.
4. Telophase I In this phase, the nucleus reorganizes and the nuclear membrane
reforms. The chromosomes decondense.
5. Cytokinesis I In this phase, the cytoplasmic division occurs.
E. MEIOSIS II
Division of the chromosomes, analogous to mitosis.
1. Meiotic Interphase
This involves GI and G, phases only. There is no S phase in this interphase. This phase may be
brief or last a long time.
2. Prophase II As in mitotic prophase, there are two sister chromatids attached
to a centromere. The chromosomes condense, the nucleus disappears, and the
spindle apparatus forms.
3. Metaphase II Centromeres move to the metaphase plate during metaphase II.
4. Anaphase II During anaphase II, centromeres divide, and sister chromatids
separate and move to the opposite poles.
5. Telophase II During telophase II, the nuclear membrane reforms and
chromosomes decondense.
6. Cytokinesis II The cytoplasm divides.
F. SUMMARY OF MEIOSIS From one pair of homologues, there are four, unique chromatids
from prophase I, if crossing over has occurred. Each unique chromatid ends up in one of the four
cells that are the products of meiosis.
T'he amount of genetic material was reduced by one half in meiosis I and divided in meiosis II.
Each resulting cell (gamete) is haploid.
1. Meiosis in Males
In the male each of these haploid cells is called a spermatid. These spermatid will undergo
cellular differentiation to become gametes (sperm).
2. Meiosis in Females
Meiosis is begun but is only partly completed in human females shortly before birth. All oocytes
remain in the last stage of meiotic prophase I. In humans, meiotic prophase I can last up to 50
years.
In spite of not continuing to metaphase I, the paired meiotic chromosomes are very active,
making large amounts of ribosomes and mRNA.
By the time the oocyte is ready to be released. It is a large cell filled with yolk, mRNA, ribosomes,
etc. The oocyte will not resume meiosis until released from the ovary. Even then meiosis will not
be completed unless the oocyte meets a sperm and is fertilized. When this happens, many
changes occur in the oocyte including the completion of meiosis.
In females, the cell constituents are not divided evenly and most of the cytoplasm ends up in one
cell. Only one cell will develop into the egg. About the time of ovulation, the oocyte's mitotic
spindle forms off to one side of the oocyte. The normal reduction division occurs, but one of the
two daughter cells has most of the cytoplasm. The other daughter cell is very small and becomes
the first polar body. The other bigger cell is known as the secondary oocyte.
At fertilization, the head of the sperm enters the egg. A second meiotic division occurs after
fertilization. As the cell divides there is the formation of another polar body and the fertilized cell
retains all of the cytoplasmic material.
3. Importance of Meiosis
a. Sexual reproduction is are shuffling of the genes of all the successful
individuals of the population. There are virtually an infinite possibility
combinations of genes.
b. The reduction and division of the chromosomes in the egg and sperm makes
fertilization possible and enables the maintenance of a constant chromosome
number within a species.
"Genes and Gene Interactions"
1900 - Mendels’ work resurfaced and was followed up by Hugo deVries
1909 - Thomas Hunt Morgan: worked with Drosophila melanogaster
easy to breed & maintain in laboratory
3 mm long
produce a new generation very 2 weeks
lay 100’s of eggs
I. The Reality of The Gene
TH Morgan : "Genes are located on chromosomes"
A. Sex Determination
autosome - "body chromosomes" - determine traits (carry genes)
sex chromosomes - determine sex (male and female)
XX -> homogametic
XY / XO --> heterogametic
Fruit flies - 8 pairs of chromosomes (7 pairs of autosomes,1 pair sex chromosomes)
Humans - 23 pairs (1 pair sex / 22 pairs autosomes)
B. Sex linkage
Morgan - observed white eyed recessive trait carried on X w (mutant)
X (normal) = "Wild type" red - eyed
XY XX XwY XwX XwXw -
II. Broadening the concept of the Gene
A. Allele Interactions
Incomplete dominance / codominance
B. Gene Interactions
account for most phenotypes
ex: Chickens (combs)
RR = rose comb
(R=rose, r=single comb)
Rr =
PP or Pp = pea comb (P=pea, p= single comb)
pp = single comb
RP = " Walnut comb " - novel phenotype (due to gene interaction) "incomplete doninace"
"codominance"
C. Epistasis "Standing Upon"
Gene A may mask the effects of gene B
example:
c or C = white, p or P = purple
cc PP = white
cc Pp = white
Cc pp = white
CC pp = white
Cc Pp = purple
CC Pp = purple
CC PP = purple
CC Pp = purple
D. Genes and The Environment :
ex : temperature (environmental factors) affects plant growth
Primrose Flowers
white, when raised at about 30 C (86 F)
red @ room temp.
also- sex of some reptiles determined by their incubation temp.
E. Expressivity and Penetrance :
When the expression of a gene is altered by environmental factors or other genes
1. The degree to which a genotype is expressed in phenotype varies (expressivity)
ex : polydactyly ( # of digits varies , size varies )
2. The proportion of individuals that show the phenotype (of a particular genotype) varies
ex : polydactyly; may have polydactyl genotype, but normal phenotype
F. Polygenic inheritance:
A trait affected by a number of genes (polygenes);
ex : height, shape, weight, color, metabolic
rate, behavior
= Wide variability in expression (continuous variation)
ex : white coat color in cats
also may affect eye color and hearing (high % are white = coated, blue-eyed, and deaf)
III . Genes and Chromosomes
G . Pleiotropy : A single gene affects more than one characteristic;
A. Linkage :
Contradicts the Law of Independent Assortment
certain genes tend to be distributed to gametes together ; "Linkage group" increased by exposure to mutagens ( X-rays, UV light, etc. )
B. Recombination :
Portions of homologous chromosomes may exchange parts at beginning of meiosis (Fig. 13.16
pp. 275) "crossing over"
C. Chromosome Mapping :
"Loci"- positions of gene along the chromosome
* gene crossover frequency is directly related to the physical distance between them (text
diagram)
Further apart = more likely to crossover
A.H. Sturtevant (1913) - 1st mapping
IV. Abnormalities in Chromosome Structure :
Recombination does not affect the order of genes on a chromosome but in some cases, it is
possible for pieces of chromosomes to break a part and rejoin in different order or on a different
chromosome
Deletion : whole segment is lost (usually lethal)
Duplication : gene segment attaches to its homologue (segment appear twice on
same chromosome)
Translocation : a gene segment is transferred to another, nonhomologous
chromosome
Inversion : segment breaks off and reattaches upside- down
Human Genetics : past, present, and future
Humans are Difficult to study :
Most people don’t have accurate records of ancestors beyond 3 generations ( except royalty )
Many, complicated chromosomes ( hard to map )
Long generation intervals
I. The Human Karyotype
46 chromosomes = 44 autosomes; 2 sex
Isolate cells during metaphase, take picture of chromosomes blow up, cut out, pair up
homologues, order by size (see Fig.19-2 pg. 383) - can use size, centromere location ( stained )
banding patterns (Fig.19-3)
II. Chromosomes Abnormalities
"Mistakes" during mitosis or meiosis
Nondisjunction - sister chromatids fail to separate; results in gametes with 24 or 21 chromosomes
(usually not viable)
A. Autosomal nondisjunction
Down Syndrome - trisomy (triplet) at chromosome 21
Physical: short, stock body, thick neck, large tongue, speech defect, susceptibility
to infections wide variety of mental retardation
may also be caused by translocation on to pair 14
Probability increases in older mothers
also:
Edwards Syndrome (Trisomy 18)
Patau Syndrome (Trisomy 13)
certain types of cancer have been associated with nondisjunctions
B. Sex Chromosome Abnormalities
XXY, XXXY, XXX, XO
Usually sexually underdeveloped, sterile, may be some physical sign and/or retardation
associated
XO= Turners Syndrome
XXY= Klinefelters Syndrome
XYY= "supermale" Syndrome
C. Chromosomal Deletions
"Arm" of one or more chromosomes deleted (Wilm’s tumor)
D. Prenatal Detection
Amniocentesis, CVS
III. PKU, Sickle cell Anemia, and other Recessives
A. Phenylketonuria
Lack enzyme required to convert phenylalanine (amino acid) to tyrosine. Phenylalanine
accumulates in blood/urine and harms nerve cells, causing progressive mental retardation
Avoidance: test at birth, give diet low in phenylalanine thru development so
phenotype remains normal)
B. Albinism
-Caused by recessive alleles (homozygous) 1/15,000 infants
-Born with normal phenotype, but as the phenylalanine accumulates, show symptoms
-Lack of pigmentation, inability to make brown pigment (melanin)
-Melanin produced from (aa) tyrosine missing one or more enzymes in the conversim process
(Fig. 19-9 pg. 388)
C. Tay - Sachs Disease
Homozygotes appear normal at birth, after 8 months listlessness, blindness, brain damage occur
(1/3,600 births); esp. European Jews; 1of 28 heterozygous
= absence of enzyme in lipid metabolism; lipid deposits accumulate in brain cells
D. Sickle cell Anemia
-Originated in Africa - associated with malaria - resistance (heterozygous advantage)
-Caused by single AA substitution in the beta chain of hemoglobin (valine subbed for glutamic
acid)
-Caused abnormally - shaped red blood cells = blockages in blood vessels, joints, organs
(painful, life-threatening)
-Heterozygous individuals generally "normal"
IV. Dwarfs & other Dominants
Achondroplastic dwarfism
Huntington’s Disease - progressive destruction of brain cells usually after age 30
detection : RFLP’s "restriction fragment-length polymorphisms"
V. Sex- linked Traits
Colorblindness 3 retinal pigment genes
Hemophilia Factor VIII plasma pigment
Muscular Dystrophy muscle-wasting diseases (cardiac or skeletal )
"Dystrophin" gene; 1/3,500 boys; usually appears age 2-6, die by 20’s; can be accompanied by
mental retardation