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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 ReactionIf 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 ReactionThese reactions need energy to complete the reaction. The energy added is greater than the difference between the reactants and the products.

3. EntropyAnother 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 ATPATP 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 Oxidationreview: oxidation = loss of e- reduction = gain of e-Glucose + Oxygen ----> Carbon dioxide + water + EnergyG = -686 Kcal/mole ---->energy used to add a phosphate molecule: ADP + P = ATPThere is a need to convert glucose (sugar) which is stored chemical energy into ATP which is usable cell energyRemember-ATP - P = ADP OR AMP+P=ADPADP - P = AMP ADP+P=ATPexergonic, energy liberating endergonic, energy intake2 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 Reactiontakes 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

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

Taken from the Univ. of Virginia web Page.

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 acidADP---> 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

- H

2O

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 acidADP---> ATP

G = - 7.5 ( enzyme: pyruvate kinase)

III. Anaerobic Pathways:Pyruvic acid can take one of 2 main pathwaysAerobic ( 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 prokaryotesThere 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. Fructose-6-P will convert back to glucose 6-P. However, if phosphorylated immediately, the anaerobic pathway will continue.

Fructose P ----------------------> Fructose-1,6-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 Pathway2 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. 1922 membranes *inner "cristae" - folded

"matrix"- dense solution of enzymes, coenzymes, water, etc. found within the cristaeA PRELIMINARY STEP: The Oxidation of Pyruvic AcidThe 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 CoAPyruvate 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 mitochondriaBefore entering the Krebs Cycle, the 3-C Pyruvic Acid molecule is oxidized: the carbon and oxygen atoms of the carboxyl group are removed (into CO2) and a 2-C 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 CoAThis 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 acid2. Two carbons (per cycle) are oxidized to CO2 which regenerates a molecule of oxaloacetic acidEach 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

http://encarta.msn.com/find/Concise.asp?ti=00EED000

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 NADHPyruvate to Acetyl CoA 2 NADH

Citric Acid CycleStep4 2 NADHStep 5 2 NADH

Step 7 2 FADH 2Step 9 2 NADH

Total 24 electronsThe 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+ + FADEND---> oxaloacetic acid + 2CO2 + CoA + ATP + 3NADH + (3H+) + FADH2 + H2OV. 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 oxygenAs 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 Phosphorylationremember, 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 ChemiosmosisWhen 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 LightIsaac 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 lightsall light travels at approx. 300,000 km/secAlbert 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 photonEssay: " 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 up2. 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. 211The 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 levelV. Photosynthetic Membranes: the ThylakoidA. 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 surfaceB. 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. 214CO2 + 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 workEnergy 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-Capturing1. The PhotosystemsIn the thylakoids, chlorophyll and other molecules are packed into units called photosystems, made up of 250-400 pigment molecules eachPhotons of light hit chlorophyll and boost an electron to a higher energy level...imagine electrons bouncing around like in a pinball machine when excited2 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. 218The 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 photosystemsWater ------> PS II -------------------> PS I ---------------------> NADP ADP--->ATP +H =NADPHThis involves yet another Chemiosmotic Gradient Fig. 10-16 p. 220Van Niel's Hypothesis (Stanford U., 1930's) previously, it had been believed that the O2 given off in light reactions came from the splitting of CO2Van Niel studied autotrophic bacteria "purple sulfur bacteria" which did NOT use H2O in their food-making proceses:

lightCO2 + 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 gasLater, "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 PSIThey 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 reducedVIII. The Carbon-Fixing ReactionsCO2 taken in through STOMATA in leaf Here, the ATP and NADPH from the Light-Dependent Reactions (stored energy) is used to reduce carbon into sugars1. The Calvin Cycle - the three-carbon pathway -analogous to the Kreb's Cycle in many ways-takes place in the stromaThe starting (and ending) compound is a 5-C sugar with 3 phosphates attached =RuBPRibulose biphosphateCO2 binds to RuBP ------------> RuBPCO2which 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 H2Oends up as6RuBP + 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 C3see Fig. 10-22 pp. 224-225While 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 vaccine2 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 LuriaUsed Bacteriophages (a group of viruses that attack bacteria)(7 phages attack E.coli bacteria ) T1 - T7advantages: 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 & ChaseLabeled 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 DNAAlfred 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 speciesex : Human 30.4 % Adenine 30.1 % Thymine 19.9 % Cytosine 19.6 % Guanine

The Watson-Crick Model1950’s - Cambridge U.A. The Known Data

1. DNA molecule was very large and long and composed of nucleotides containing the 4 N-bases 2. Levene’s Data 3. Linus Pauling - protein chains often arranged in helix where AA’s are held together with H-bonds 4. X-ray Diffraction : Maurice Wilkins &Rosalind Franklin DNA showed helical pattern 5. Chargaff’s experiments (base ratios) A=T ; G=C

Nucleotides: monomers that come together to form a nucleic acid. They contain either a ribose ordeoxyribose 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 asingle ring while purines are characterized by a double ring. The nucleotides are joined together byphosphodiester 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 complementary bases

2. each base covalently bonded to the sugar-phosphate unit 3. bases paired with H-bonds (relatively weak ) 4. purine & pyrimidine always paired

5. Strands have a direction

5’ end = P attached to 5th C in the sugar3’ 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 ReplicationMeselson 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 phaseRapid 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" replicationProkaryotes- single replication origin, "theta replication"RNA Primers and the Direction of SynthesisPrimer: formed from nucleotides, which start the attachment to DNA strand (RNA primase)

"replication fork"Reiji Okazaki - Discovered the leading/ lagging strandsLeading 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 longEuk: 100 - 200 nucleotides longDNA 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 ReplicationPowered 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 Informationeach base triplet codes for a specific AA , which in turn make up protein chainsAny combination is possiblenumber of base pairs in a virus = 5000number 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 coordinatedby 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

http://www.er.doe.gov/production/ober/hug_top.html

http://vector.cshl.org/dnaftb/15/concept/index.html

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 ProteinsA. 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 deletionB. One Gene - One EnzymeSynthesis of all substances in living things dictated by enzymesSpecificity 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. brief life cycle 2. easy to grow in large quantities in lab 3. Most of it’s life cycle= HAPLOID (no homologous pairings) lets mutations be

seen immediately. 4. Meiosis takes place in saclike reproductive structures called asci 5. History of chromosome mapping studies on mold 6. 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 mediaBeadle 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 HemoglobinLinus 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 patientsVernon Ingram: Later learned that the sc hemoglobin is caused by one changed AA (out of 300)D. The Viral Coatadd’l studies showed how changes in viral DNA led to change in protein coat of virus (bacteriophages)II. From DNA to Protein: The Role of RNAA. The Central Dogma

DNA codes for specific RNA, which in turn codes for specific proteinB. RNA as a messenger3 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----UT----A C----GG----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 strandIII. 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 CodeMarshall 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 RNAMessenger 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 RNA3 types:

1,500 nucleotides in length 3,000 nucleotides in length 100 nucleotides in length

structural elements of the ribosomesRibosomal RNA- most abundant type of RNA in cellsRibosomes: 2 subunits 2/3 RNA, 1/3 proteinmRNA* of the 64 possible 3-base codes, 61 code for AA’s 3 code for "stop"; i.e. chain terminationAUG = methionine; sometimes "START"B) Translation: the synthesis of proteinsinvolving the transfer of information from one language (nucleotides) to another (amino acids)Takes place in 3 stages: initiation, elongation, termination1. 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) codonUsually: 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 STOPV. Redefining Mutationsex. 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 nucleotideTRANSCRIPTION1. DNA unzips, mRNA nucleotides "float" in to form a complementary mRNA strand using the DNA as a template2. mRNA detaches from DNA template and attaches to a ribosome at 5’ end3. tRNA anticodons "plug into" mRNA codons starting at its 3’ end4. 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 expressedI. 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"diagramII. 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’ endA) The Need for RegulationBacteria cell goal: to grow and multiply rapidlyCan double number every 20 minutes!Regulated by several means:

1) induced by presence of a material (ex. Lactose presence induced E. coli to synthesize beta-galactosidase enzyme)

2) inhibition: presence of substance prevents formation of an enzyme "repressible" (ex: E. coli; tryptophan inhibits tryptophan forming enzymes)

B) The 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 genesRegulator: can be located anywhere on the bacterial chromosome *This gene codes for a repressor proteinRepressor: 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 beginsstudies done on E. Coli cells making enzyme: beta-galactosidase "blocked" by repressor binding to operatorlac operon:CAP- Catabolite activator protein: a regulatory protein that exerts a positive effect on the operonCAP combines with cyclic AMP molecule: this CAP-cAMP complex binds to the promotor and maximizes transcriptionIII. 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 CellThis can then transfer a portion of bacterial chromosome to a F- cell:diagramB. R Plasmids1. Carry antibotic resistance genes2. Can have up to 10 resistance genes per plasmid3. Allow for species-to-species transferex: 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 linearCHARACTERISTICS:1. Contain a small amount of DNA(or RNA) surrounded by protein ex: T7 bacteriophage has DNA and 100 genes2. Small viruses that don’t have room for a lot of DNA uses overlapping genes3. 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 VectorsLysogenic- 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 sitesProphage- an integrated bacteriophageLytic 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. Transductionthe transfer of cellular DNA from one host cell to another by means of viruses = recombinant DNA1. General Transductiondiagram2. Restricted TransductiondiagramC. Introducing LambdaLambda is the best studied of the temperate bacteriophages Viral form: linear, double-stranded (2 free ends) When inserted into a bacterial cell, it becomes circularintegrase- enzyme used to insert a DNA into bacterial chromosomeV. Transposonssegments of DNA that are integrated into chromosomal DNA1. Also contain a gene for transposase which inserts it into a new site2. At each end, they contain a sequence of repeats**direct repeats -ATTCAG-ATTCAG- *used to I.D. insertion points*indirect repeats -ATTCAG-GACTTA- -> Can carry genes for mutations, protein synthesis, drug resistance, etc...

RECOMBINANT DNA: THE TOOLS OF THE TRADEI. Isolation of the Specific DNA segmentsDNA 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 SequencesExamples: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 methylateCleavage:1. Straight cut2. 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: cDNAretrovirus: 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 togetherII. 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 lengthB. Lambda and CosmidsSpecifically 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 Hybridizationby heating DNA, the Hydrogen bonds between paired bases are broken (disrupting the helix) - can be used to get new combinations of DNA-DNA or DNA-RNA (hybrid)A. Radioactive Probesused to "mark" specific DNA or RNA sequences 1. Specific segment must be located and isolated2. "Tagged" with a radioactive isotope (usually carried on gDNA or cDNA or oligonucleotides)IV. DNA SequenceElectrophoresis using different cleavages (restriction enzymes)Frederick Sanger: worked out nucleic acid sequence of insulin (1980 Nobel Prize)

The Molecular Genetics of Eukaryotespp. 355 - 381Many marked differences between Eukaryotic & Prokaryotic DNA:

1. Far greater quantity of DNA in eukaryotic cells 2. Great deal of repetition in Eukaryotic DNA (much lacks any function) 3. Eukaryotic chromosome has more protein mixed with the DNA 4. 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 cellTrivia: 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 HELIXHelix is usually coiled tightly in Right-handed twist called B-form DNAAlso comes in 2 other forms:A-DNA : right-handed twist, not very tightly coiledZ-DNA : left-handed twist (see pg. 356 diagrams)A. Structure of the Chromosome"chromatin" = 60% protein, 40% DNAprotein type called HISTONESHistones are positively charged (basic) & are thus attracted to (-) acidic DNAHistones primarily responsible for the folding & packaging of DNA5 Distinct types of Histones: H1: about 30 million molecules per cell

also H2A, H3B, H3, H4: a) About 60 million molecules EACH per cellb) Very similar in all eukaryotic organismsNUCLEOSOME: the fundamental packaging unit of chromatin

*see diagrams on page 357!!DNA filament wrapped 2x (like threadaround a spool)

Upon condensation into "rods" (in mitosis & mitosis) forms "Looped Domain" configuration

B. Replication of the ChromosomeSemi-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 ligaseProkaryotic cell: bidirectional replication starting from a single replication originEukaryotic 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 EukaryotesEukaryotes 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 Expression2 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 ExpressionOnce DNA is formed, enzymes Methylate (-CH3)Certain nucleotides of cytosine (=Methylcytosine)perhaps to inhibit (block) gene expressionC. Regulation by Specific Binding Proteinsregulating proteins bind to turn genes on/offIII. 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 1-10% 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. INTRONSProtein-coding sequences of eukaryotic genes are NOT continuous (interrupted by NON coding sequences) = INTRONSEXONS = coding sequences B. Classes of DNA: Repeats & NonRepeats1. 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 multicellular 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" DNAC. 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 Eukaryotesbegins 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 RNAA. mRNA Modification & EditingIn 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 MoveA. Antibody-coding genesAnti 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) chainswould only require a reasonable # of different genes, moved around in different combinations (rearrangement of genes)B. VIRUSESproviruses - 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, & CANCERONCOGENES - 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 CELLSA. To Cells in Test TubesSV40 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. 378C. 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 agricultureGreeks 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 = GrayProblem: 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 MendelGregor 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, ALLELESA. Mendel's Experimental MethodGarden 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 generationsCounted offspring (type) and statistically analyzed resultsWell-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 5,474Recessive genes wrinkled seeds 1,850 total: 7,324 ...found a uniform 3:1 ratio dominant to recessive traits expressedThe 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 YyGreen 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 CrossesSample 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. Mutations1902 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 populationsHow 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 Reproduction1. 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 CYCLESMeiosis 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 deVries1909 - Thomas Hunt Morgan: worked with Drosophila melanogaster

easy to breed & maintain in laboratory3 mm longproduce 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 -> homogameticXY / XO --> heterogameticFruit 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 Xw (mutant) X (normal) = "Wild type" red - eyed XY - XX - XwY - XwX -XwXw -II. Broadening the concept of the Gene A. Allele InteractionsIncomplete dominance / codominance

B. Gene Interactions account for most phenotypesex: Chickens (combs) RR = rose comb (R=rose, r=single comb)Rr = PP or Pp = pea comb (P=pea, p= single comb)pp = single combRP = " 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 = purplecc PP = white cc Pp = whiteCc 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 phenotypeF. 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)G . Pleiotropy : A single gene affects more than one characteristic; 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 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 mappingIV. 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 meiosisNondisjunction - 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 AbnormalitiesXXY, XXXY, XXX, XOUsually sexually underdeveloped, sterile, may be some physical sign and/or retardation associatedXO= Turners SyndromeXXY= Klinefelters SyndromeXYY= "supermale" SyndromeC. Chromosomal Deletions "Arm" of one or more chromosomes deleted (Wilm’s tumor)D. Prenatal Detection Amniocentesis, CVSIII. PKU, Sickle cell Anemia, and other RecessivesA. PhenylketonuriaLack 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 dwarfismHuntington’s Disease - progressive destruction of brain cells usually after age 30 detection : RFLP’s "restriction fragment-length polymorphisms"V. Sex- linked TraitsColorblindness 3 retinal pigment genesHemophilia Factor VIII plasma pigmentMuscular 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

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