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Practice Exam Solutions

Question 1

a) Which of the following would be incorporated into an RNA molecule? Circle all that apply.

O O
O P O O P O
O G O A
CH 2 O CH 2 O
H H H H H H
H H
OH H OH OH

A B C D E

b) Which of the above could be found in the produced proteins? List all that apply.
Molecule E

One of the proteins that you produce is ATP synthase. ATP synthase is a protein complex found in the
mitochondrial membrane. It converts the energy stored in the H+ electrochemical gradient into ATP.

c) Would you expect the ATP synthase found in human cells to produce ATP during anaerobic or
aerobic conditions? Explain your choice.
Aerobic. The H+ electrochemical gradient is produced by the movement of electrons through the electron
transport chain. The first protein in the electron transport chain accepts electrons from NADH and FADH2,
these electrons from NADH and FADH2 are ultimately transferred to O2. Without O2 as the terminal electron
acceptor, the H+ electrochemical gradient cannot be formed and ATP synthase could not produce ATP.

d) If an inhibitor of ATP synthase is added to cells where ATP synthase is active, glycolysis almost
immediately stops. Explain why inhibiting ATP synthase in these cells influences glycolysis.
When ATP synthase is inhibited, movement of electrons along the electron transport is also inhibited. This in
turn means that NADH (and FADH2) cannot unload electrons to the electron transport chain, thus NAD+ is not
regenerated. NAD+ is required for glycolysis to continue.

e) ATP synthase is a multimer composed of several different polypeptide chains. What is the highest
level (order) of protein structure seen in ATP synthase?
Quaternary

1

For each experiment. Heating a protein to 90 ºC disrupts the intermolecular. At 4 minutes. so at 2 minutes. so function is not restored. You study the effects that different treatments have on the activity of this enzyme. the energy of this gradient is used to make ATP. the protease has had time to destroy all of the ATP synthase molecules. non-covalent bonds and forces such as ionic bonds. The protease acts at a certain rate. the activity was measured at the end of the treatment. The protein loses its normal 3-dimensional shape and thus loses its function. H+ ions are moved across a membrane. glucose is broken down into pyruvate. lots of NADH and some FADH2 and CO2 . ii. As electrons are passed from one protein to another in this chain. Once the primary structure of the enzyme is altered the shape and function is also destroyed. g) Briefly describe events that precede the synthesis of ATP by ATP synthase. Once returned to normal temperature. Explain why there is a difference between a 2-minute and a 4-minute treatment with protease and why full enzyme activity is not restored in either experiment 3 or 4. generating ATP and NADH. Explain why 90 ºC eliminates the enzyme activity and why enzyme activity is restored after experiment 1 and 2. Through glycolysis. but other ATP synthase will remain intact. 2 .Question 1. Four different experiments are listed below. so no activity remains. The accumulated electron carriers NADH and FADH2 donate electrons to the first protein of the electron transport chain. some of the ATP synthase molecules have been destroyed. An H+ electrochemical gradient is established. Begin with one molecule of glucose and end with the formation of water. The sample was then returned to the pre-treatment conditions and the enzyme activity was measured again. and van der Waals forces. continued f) You obtain a large amount of ATP synthase that has high activity at room temperature. The pyruvate enters the citric acid cycle which produces a small amount of additional ATP. and a reduced amount of activity is measured. the protein may refold into its native conformation and thus its activity is restored. hydrogen bonds. A return to pre-treatment conditions cannot mend the broken peptide bonds. and as the H+ ions move through the ATP synthase molecule. Experiment Activity of enzyme at end Activity of enzyme after return Treatment of treatment (before return to pre-treatment conditions to pre-treatment conditions) Heat to 90 ºC for none high 1 2 minutes Heat to 90 ºC for none high 2 4 minutes Add a protease for 2 medium medium 3 minutes Add a protease for 4 none none 4 minutes i. The activity before each treatment was high.

i i) How many unique primary protein structures compose the LMGT protein complex? Two ii) What protein secondary structure is part of the LMGT protein complex? α-helix iii) What is the strongest type of bond that maintains the quaternary structure of LMGT? Covalent. and Lysine b) LMGT is composed of four polypeptides (two γ polypeptides and two δ polypeptides). Figure B shows a cross section of two of the polypeptides. Draw the chemical structure of PUNY. N-termini N-termini S S Phospholipid bilayer δ S S γ δ γ membrane S S Figure A Figure B a) In Figure B. disulfide bond c) Describe how the polypeptides of the LMGT protein can be surrounded by non-polar hydrocarbons but allow charged proteins and ions to transit the membrane. Name three amino acids that would likely be found at the N- termini of these polypeptides. d) One of the small molecules permitted to pass through the LMGT channel is PUNY. The positively charged amino acids: Arginine. PUNY is composed of asparagine-proline-alanine with asparagine at the amino terminus. The LMGT protein must have non-polar amino acids on the surfaces associated with the lipid part of the membrane and charged or polar amino acids lining the pore of the channel.Question 2 The protein complex. LMGT is composed of four polypeptides as shown in Figure A. LETMEGOTHRUIN (LMGT for short). a tripeptide. Histidine. H O H O H O Circle the peptide bonds. acts as a channel or pore through which charged proteins and ions can cross the phospholipid bilayer of the membrane. + H3 N C C N C C N C C O- CH 2 CH 2 CH 2 H CH3 C CH 2 O NH 2 3 . the amino termini (N-termini) are closely associated with the phosphate groups at the surface of the phospholipid bilayer.

4 . Glutamic acid is also (-) charged and would repel. ii) What is the strongest interaction possible between the amino acid in region 2 and the substrate? Choose from Covalent. or Hydrogen bonds or van der Waals forces. Ionic bonds iii) What is the strongest interaction possible between the amino acids in region 3 and the substrate? Choose from Covalent. or Hydrogen bonds or van der Waals forces. it is polar and can form hydrogen bonds with region 1. Ionic.Question 3 A drug company has isolated the protein shown in schematic below. or Hydrogen bonds or van der Waals forces. Hydrogen bonds. it is (+) charged and can form ionic bonds with region 2. van der Waals forces c) The drug company has asked you to design a protein that binds tightly in this pocket. Given the diagram above… i) What is the strongest interaction possible between the amino acid in region 1 and the substrate? Choose from Covalent. Alanine would only interact with van der Waals forces ii) Would Lysine or Glutamic Acid interact more strongly with region 2? Why? Lysine. H 3C CH region 3 C H3 C H3 C H2 O region 1 CH H 3C C N H2 C H2 region 2 _ O O C CH2 a) What amino acid is present in region 2? Aspartic acid b) The substrate for this protein has not been identified. i) Would Alanine or Serine interact more strongly with region 1? Why? Serine. Ionic. Ionic.

depending upon whether the cell is in anaerobic and aerobic conditions. Fermentation uses the end product of glycolysis. Question 4 ADP ATP a) Complete the diagram below for glycolysis. Glycolysis. the Citric Acid Cycle. Here a chemiosmotic mechanism produces ATP. pyruvate. so why can’t the phenylalanine version of the protein bind? Phenylalanine has a large side chain that prevents the substrate from fitting into the pocket. Its side-chain may create steric hinderence. What are the two different pathways? Fermentation and Respiration d) How does the energy outcome of these two different pathways varies. autosomal dominant inheritance No X-linked dominant inheritance No 5 . explain what the difference would be. In respiration. continued d) You design many proteins that bind tightly in this pocket. The Citric Acid Cycle produces additional ATP and energy rich electron carriers NADH and FADH2. what is the probability of child ? being affected? autosomal recessive inheritance Yes 2/3 X ½ X ½ X-linked recessive inheritance Yes ½ X ½ or 0 if girl and ½ if boy. ? Mode of inheritance Yes/No If yes. The NADH from glycolysis and the Citric Acid Cycle and FADH2 from the Citric Acid Cycle is shuttled to the mitochondria where the electrons are donated to the respiratory chain. glucose pyruvate NAD+ NADH b) Would the diagram for glycolysis be the same for both anaerobic and aerobic conditions? Yes the diagram would be the same. The NADH produced in glycolysis must be regenerated so that glycolysis can continue. You substitute phenylalanine for isoleucine and find this prevents binding of this protein. This effectively regenerates NAD+. the pyruvate is oxidized to form Acetyl CoA. and the respiratory chain combined yield approximately 36 ATP/glucose. so glycolysis and fermentation together generate about 2 ATP/glucose. Phenylalanine and isoleucine form the same kinds of interactions with the binding pocket. as an electron acceptor.Question 3. One of them has isoleucine associated with region 3. If not. Question 5 Which of the following modes of inheritance is consistent with the pedigree shown below? Assume complete penetrance. which enters the Citric Acid Cycle (also called the Kreb’s Cycle). but does not supply any additional energy. c) There are two different pathways for the end product of glycolysis.

2) bitter or smooth (use B or b). decaffeinated 3 nutty. smooth. decaffeinated strain to a true breeding plain. smooth. *In each case. caffeinated Ignore the traits that do not exhibit Mendelian inheritance. You cross a true breeding nutty. now how many of each phenotype and genotype do you expect? 100 aaBB } Plain. smooth (9/16) 25 AAbb 50 Aabb } 75 Nutty bitter (3/16) 25 aaBB 50 aaBb } 75 Plain smooth (3/16) 25 aabb } 25 Plain bitter ii) Assume that there is 0% recombination between the A/a and B/b genes. smooth. smooth (¼) 100 AaBb 100 AaBb } Nutty. and highly decaffeinated or caffeinated (use D or d).Question 6 As a plant geneticist. The first (F1) generation is 10 plants: 7 nutty. bitter. smooth. you have identified three traits that contribute tothe taste of certain coffee beans. smooth. caffeinated a) Which traits are not exhibiting classic Mendelian inheritance? Caffeinated. The strains produce beans that can be either 1) plain or nutty (use A or a). If there are 400 plants in the F2 generation. how many of each phenotype and genotype do you expect? 25 AABB 50 AaBB 50 AABb 100 AaBa } 225 Nutty. bitter (¼) 6 . decaffeinated X nutty. i) Assume that none of the traits are linked. If there are 400 plants in the F2 generation. You have isolated strains of coffee plants that breed true for each trait. and caffeinated strain. decaffienated b) Which traits are dominant Mendelian traits? Nutty and Smooth c) You crosses two F1 plants: nutty. smooth (½) 100 AAbb } Nutty. use the uppercase letter for the allele associated with the dominant phenotype and the lower case letter for the allele associated with the recessive phenotype.

dGTP. Explain why replication of the genome would fail in a cell that lacks DNA ligase? The lagging strand is copied by making a series of small Okazaki fragments. and a template strand. Describe what the 3’ to 5’ exonuclease activity is used for. Would replication of the top strand in region 2 be continuous or discontinuous? discontinuous ii. the newly made DNA will have gaps in the backbone. dCTP). The 3’ to 5’ exonuclease activity is used to excise a mismatch base. b) Some polymerases also have a 3’ to 5’ exonuclease activity. a primer. 5’ 3’ 3’ 5’ Region 1 Region 2 i. 7 . Each of these fragments must be linked together by DNA ligase. dTTP. Without DNA ligase to join the Okazaki fragments. c) Below is a schematic of an origin of replication.Question 7 All DNA polymerases can make a new DNA strand in the 5’ to 3’ direction. DNA polymerases require what three non-protein components? Deoxyribonucleiotides (dATP. a) To accomplish this. which forms the phosphodiester bond between the 3’ OH and the 5” phosphate.