Chemistry 153A Practice Final Exam KEY First letter of your last name _____ Question # 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 TOTAL TOTAL

COURSE SCORE FINAL COURSE GRADE Value 25 5 10 10 7 14 18 15 18 20 20 16 25 17 15 ______________________________ Signature

INSTRUCTIONS READ EACH QUESTION CAREFULLY! SHOW YOUR CALCULATIONS! WRITE YOUR LAST NAME IN THE SPACE PROVIDED ON EVERY PAGE OF THE EXAM. NO CREDIT WILL BE GIVEN FOR ANYTHING WRITTEN ON THE BACK OF A PAGE OR IN A SPACE OTHER THAN THAT PROVIDED FOR YOUR ANSWER. ANSWERS MUST BE BRIEF AND TO THE POINT. WHERE WORD LIMITS ARE GIVEN, NO CREDIT WILL BE GIVEN FOR THE PART OF YOUR ANSWER THAT SIGNIFICANTLY EXCEEDS THAT LIMIT. Numbers in parentheses represent the point values. Gas constant: R= 8.31 x 10-3 kJ/ oK/mole Faradays constant: 96.5 kJ V-1 mol-1

Score

___________KEY______________ Print your full name

(Last Name First)

______________________________ Print your TA's name ______________________________ Time and day of your discussion section I have read the instructions below.

Page 2 1. (25) a. b. The complexity of living cells is indicated by the _Number _ and average _Size (Molecular weight)_ of different molecules of which they are composed. or

The statement that water is amphoteric means that a water molecule can be a _Proton__ donor or acceptor and can thus form a _hydroxide_ ion or a _hydronium_ ion.

c. The extraordinary cohesiveness of water is attributed to extensive _hydrogen_ _bonding_ between molecules. d. pH is a property of a _solution__ while pKa is a property of a _weak acid__.

e. If a weak acid is dissolved in a solution at a pH that is greater than its pKa by one pH unit or less, the addition of H+ to the solution will result in increased _protonation_ of the weak acid. This will tend to minimize the change in the _pH___ of the solution. f. The inductive effect of the -carboxyl group of an -amino acid will tend to lower_ the pKa of the -amino group, and the electrostatic effect of that same -carboxyl group will tend to _raise _ the pKa of the -amino group. The peptide plate concept arises from the restriction of rotation around bonds due to steric hindrance. TRUE FALSE Would you expect polar amino acids at the outer surfaces of proteins to be more likely to hydrogen bond to water molecules or to each other. _water________ Why? They will be in close contact with many more water molecules than with other polar amino acid side chains. Would you expect an -helix of polyalanine to be disrupted by placing the polypeptide in an organic solvent? _No____ Explain your answer. [ 40 words] The hydrogen bond stabilizing the -helix will be strong in the apolar organic solvent, and contact of alanine side chains with an organic solvent at the surface of the helix would not be unfavorable.

g. h.

i.

2. (5) Which of the following forms of alanine would you be unlikely to detect in aqueous solution at any pH? [correct answer is indicate by a check mark]

CH3
+

CH3 COOH H2N C H Alanine COOH

+

CH3 H3N C H Alanine COO H2N

CH3 C H Alanine COO

H3N

C H Alanine

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3. (10) Below is a depiction of the relative radial positions of amino acid residues of an alpha helix, looking down the axis of the helix.
8 15 4 11 18 1 12 5 16 9 2

7
14 3 10 17 6

13

Circle the polypeptide below that would be most likely to form an amphipathic -helix? [check
marked below]

10 11 12

13 14 15 16 17 18 19

ser-val-ala-asn-ala-leu-met-lys-val-ala-thr-asp-phe-asp-gln-glu-leu-his-ala ser-trp-tyr-phe-ala-thr-met-leu-his-ala- phe-arg-trp -ile-gly-glu-leu-his-ala arg-leu-ser-ala-lys-val-glu-ile-asp-phe-his-asp-cys-gln-met-tyr-ala-asn-ala

4.(10) a.(2) How do you calculate the number of possible stereoisomers of a monosaccharide? # of stereoisomers = 2 , where n = # of chiral centers (carbons) b. (2) Which has more stereoisomers, an aldopentose or a ketohexose? they have the same #_ c. (6) While doing ecological research in the Masi Mara plains of Africa, a friend of yours discovers a new sub-species of Thompson Gazelle that seems to have a selective survival advantage, enabling its population to grow rapidly relative to the general population of Thompson Gazelles. On closer observation your friend observes that the new sub-species is capable of faster bursts of speed, making it more successful at fleeing from lions, leopards, and cheetahs. As a renowned biochemist and geneticist, you join her to investigate the nature of the mutations leading to this enhanced ability. You find that there appear to be some mutations affecting the carbohydrate storage enzymes of this sub-species leading to a change in the structure of a particular polysaccharide. What is the identity of this polysaccharide and the nature of the structural change? [ 30 words] A mutation in a gene coding for a glycogen storage enzyme has resulted in synthesis of glycogen molecules that are more highly branched. The resulting increase in non-reducing ends allows faster mobilization of glucose providing a potential for more rapid release of energy for running.
n

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5.

(7)

a. Which of the following lipids is not a component of biological membranes? ______C__________ A. glycerophospholipids B. sphingophospholipids C. triacylglycerols D. cholesterol b. Triacylglycerols provide highly reduced energy storage. TRUE FALSE

c. Integral membrane proteins always have a higher percentage of hydrophobic residues than soluble aqueous proteins do. TRUE FALSE d. A membrane rich in stearic acid would be less fluid than one rich in oleic acid. TRUE FALSE e. Glycerol is the parent compound for the major lipids of the myelin sheath. TRUE f. Biological membranes are rich in phosphate. TRUE FALSE FALSE

g. The bonds between fatty acids and glycerol in glycerolipids are ____ester______ linkages. 6. (14) Evidence indicates that some of the following events occur as hemoglobin carries out its natural function. Indicate the proposed normal sequence of these events reflecting their cause and effect relationships by assigning each event a number indicating the order of occurrence. If two events seem to occur simultaneously give the lower number to the event that causes the other. Use an X to indicate any event that does not normally occur. __1__ Red blood cells containing Hb enter the lungs where pO2 is high. __4__ Weak interactions at polypeptide contact points become strained. __6___ All subunits change to the R state in a concerted event. __8___ Additional O2 molecules bind with increased affinity. __5___ Interchain H-bonds and salt bridges of the T-state break. __X___ The heme iron, Fe2+, becomes oxidized to Fe3+. __9___ Red blood cells containing Hb carry oxygen to the tissues where pO2 is low. __2___ The first O2 binds with low affinity to the heme iron of an -chain of deoxy-Hb. __3___ The F-helix shifts toward the heme ring tending to induce a conformational change in the entire polypeptide (subunit). _10___ Certain Hb residues become protonated as bound O2 dissociates from Hb. __X___The R-state is stabilized by protonation of certain Hb residues and binding of 2,3 bisphosphoglycerate __X___ The first O2 binds with low affinity to the heme iron of an -chain of deoxy-Hb. __X___ Additional subunits (polypeptides) change to the R-state in sequence as additional O2 binds until all binding sites are occupied.

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__7___ New interchain H-bonds and salt-bridges form, stabilizing the R-state

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7. (18)

A diagram of one stage of the reaction mechanism of the enzyme, subtilisin, is shown below. This enzyme is mechanistically related to trypsin and chymotrypsin, but not evolutionarily related.
His-64 Ser-221

N C H O H R2 N H C
CH

O H N H N H O
Ser-125

H2 C N N

H2 C

Asn 155

H2 C

O
Asp32

C C H2

R1

H2 C

a. (2)

Draw a single circle encompassing all the atoms of the reaction intermediate that originated as part of the substrate.

b. (10) Suggest a role played in the catalysis by each of the following residues. Mention general catalytic mechanisms where appropriate, but also state specifically how the effects of each residue help to increase the rate of the reaction. [ 25 words each] Asp-32: His-64: Electrostatic catalysis: Electrostatic stabilization of his+

Acid/Base Catalysis: Proton acceptor and donor

Ser-221: Covalent catalysis: Nucleophile - forms covalent bond to carbonyl carbon of substrate/intermediate Asn-155: Preferential binding of transition state (intermediate): forms hydrogen bond to oxyanion of tetrahedral intermediate Ser-125: c. (6) Stabilizes binding of substrate to enzyme via hydrogen bonding

Draw curved arrows on the diagram indicating the movement of electrons in the expected next step of the catalytic mechanism. Explain the immediate result of this step either in words or by drawing a diagram of the result. [ 30 words] In the next step, the amide bond breaks as the newly forming primary amino group accepts a proton from his-64. A new covalently enzyme bound intermediate ester forms.

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(15)

Nearly all organisms carry out glycolysis. However, a few anaerobic bacteria, such as Pseudomonas, utilize an alternative pathway, known as the Entner-Doudoroff pathway, for the catabolism of glucose. It is shown below. O O C CH2OH CH2OPO3= ATP ADP H C OH O H2O + NAD NADH + H+ O H H H HO C H H H H H C OH HO OH H OH HO OH H OH glucokinase H C OH glucose-6-phosphate dehydrogenase OH H CH2OPO3= H OH 6-Phosphogluconate glucose glucose 6-Phosphate
6-phosphogluconate dehydratase COOPO 3= CHOH H+ + NADH Pi + NAD CHO CHOH KDPG-aldolase O C C O H C H H C OH H C OH CH2OPO3= 2-keto-3-deoxy-6phosphogluconate (KDPG) H 2O COOADP ATP COOC O COOC O O

H 2O

CH2OPO3= 1,3-bisphosphoglycerate ADP

glyceraldehyde-3-P dehydrogenase

CH2OPO3= 3-phosphoglycerate

1,3-bisphosphoglycerate kinase ATP COOCOOphosphoglycerate CHOPO3= CHOH C OPO3= mutase enolase pyruvate kinase CH2OH CH2OPO3= CH2 3-phosphoglycerate 2-phosphoglycerate phosphoenolpyruvate

CH3 pyruvate

CH3 pyruvate 2H+

pyruvate decarboxylase

2
a. (7) b. (4) c. (4)

CH2OH CH3

2NAD

2NADH + 2H +

2CO2

alcohol dehydrogenase

CHO CH3

Would the final two reactions of this pathway be necessary to an aerobic organism utilizing the Entner-Doudoroff pathway? Why? [ 40 Words]

glucose + ADP + Pi + 2H+ 2 ethanol + 2 CO2 + ATP + H2O

Write a balanced equation summarizing the net result of this pathway.

No, because NAD+ can be regenerated by the electron transport chain reactions.

Why do you suppose early evolution (natural selection) produced so many more anaerobic organisms that utilized glycolysis than the Entner-Doudoroff pathway? [ 35 Words]

It is more efficient at energy extraction and conservation in the form of 2 ATP per glucose as compared to 1 ATP per glucose generated by the Entner-Doudoroff pathway.

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9. (18)

Pyruvate is a central metabolite of the aerobic cell. Name and draw the structures of three metabolic intermediates which can be made in a mammalian muscle cell directly from pyruvate in a net reaction catalyzed by a single enzyme or enzyme complex. Place an asterisk next to the carbon at which you would expect to find 14C originating from carbon # 2 of pyruvate as the result of this reaction. Name the enzyme or complex and specify the intracellular conditions (metabolic status) that would favor that particular reaction over the others. Compound Enzyme & Conditions Favoring Reaction
[name & structure]

COOO CH2 COO-

Pyruvate carboxylase high [AcCoA] need for carbon compounds low energy needs

Oxaloacetate

COOH OH CH2

Lactate dehydrogenase high muscle activity need for rapid ATP synthesis anaerobic metabolism

L-Lactate

O H3 C SCoA

Pyruvate dehydrogenase low [AcCoA], low NADH need for energy

Acetyl-coenzyme A

10. (20)

Briefly state the metabolic role of the reaction catalyzed by each of the following enzymes and give the class to which the enzyme belongs. [ 30 words each] a. Isocitrate lyase: lyase: part of the glyoxylate bypass to achieve net synthesis (replenish) oxaloacetate b. 3-phosphoglycerol dehydrogenase: oxidoreductase: shuttles electrons from cytoplasmic NADH into electron transport chain c. phosphoglycerate kinase: transferase: substrate level phosphorylation of ADP to make ATP - part of glycolysis

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d. hexokinase: transferase: 1st step of glycolysis - phosphorylates glucose by transfer of phosphate from ATP. Traps glucose in the cell.

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11.

(20)

a. b. c.

The following cofactors participate in the reactions catalyzed by the pyruvate dehydrogenase complex. Write the full name of each specific structure drawn below on the line directly beneath it. Show on the next line, the enzyme (E1,E2 or E3), if any, to which each cofactor is tightly bound. Circle the reactive atom(s) of each.
CH3 NH2 CH2 N

+
S

CH2

CH2

O O O P O P OOOCH2
- OOC

(CH2 ) 4

CH S S

CH2

CH3

A.

thiaminepyrophospate____

B. __lipoic acid _______ ___ E-2____

O CH3 N NH N CH2 (CHOH) 3 CH2 O O P O AMP ON O

__E-1______
CH3OH O O CH2 ADP (3'P) CH3 O C CH C NH CH2 CH2 C NH

CH2

CH2 SH CH3

C.

__Coenzyme A ______________ __None___

D.__flavin adenine dinucleotide __E-3_____

12.(16) a. (6) Since the oxidation of NADH in electron transport results in the synthesis of more ATP, why doesnt the aerobic

cell use NAD+ exclusively as the electron acceptor in metabolic oxidation-reductions instead of sometimes using FAD? [ 50 words]

NADH does not have a high enough reduction potential to oxidize some metabolic intermediates (e.g., alkane to alkene) FADs reduction potential is high enough to accept electrons from some of these compounds.
b.(10) Describe the role played by CoQ in energy metabolism. Include its properties, possible oxidation states, location,
relationship to other components of the electron transport and the postulated role of Q cycling (details of Q cycling not required). [ 75 words]

CoQ is a mobile electron carrier of the electron transport chain. It is very hydrophobic and thus soluble in the interior of the lipid bilayer of the mitochondrial inner membrane. It diffuses laterally in the membrane to contact and bind the active sites of complex I, complex II or flavoprotein dehydrogenase (FH). It accepts electrons from the redox center of any of these sites and carries them to complex III where the electrons are passed along. It has three oxidation states known as ubiquinone (fully oxidized), ubi-semiquinone and unbiquinol (fully reduced). Ubiquinone acquires two electrons at I, II or FH to become fully reduced to ubiquinol. At complex III it apparently cycles through all three oxidation states in a complex process that enables single electrons to be passed one at a time through the subsequent redox centers (one-electron carriers) with concomitant translocation of 4 protons from matrix to cytosol per CoQ reoxidized. This latter process is known as Q cycling.

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13.(25) a. (6) Write a balanced net equation summarizing the TCA cycle beginning with acetylCoA.(no
structures)

AcCoA+ 2H2O+ 3NAD++ FAD+ GDP+ Pi 2CO2+ 3 NADH + 3H+ + FADH2 + GTP + CoA
b. (3) Write a balanced net equation summarizing the synthesis of -ketoglutarate from acetylCoA and Oxaloacetate in an aerobic cell. (no structures) AcCoA + oxaloacetate + H2O + NAD+ -ketoglutarate + NADH + H+ + CO2 c. (3) Assume that the -ketoglutarate generated in part (b) above is used in an amino acid synthesis pathway. What impact could the this process ultimately have on the ability of the cell to continue to carry out the TCA cycle and why? [ 40 Words]

It would ultimately lead to the depletion of oxaloacetate. This would result in the cells inability to carry out the TCA cycle unless oxaloacetate is replenished.
d. (3) Write a net balanced equation illustrating a means by which aerobic plant cells compensate for the effects discussed in your answer to (c) above. (no structures)

2 AcCoA+ 2 NAD+ + FAD + 2H2O oxaloacetate 2 NADH + 2 H+ + FADH2 + 2CoA

e. (10) Calculate (and itemize) the energetic cost of the process in (d) above per acetylCoA molecule utilized as compared to the use of acetylCoA into the complete TCA cycle. Specify each source of energetic cost and give your final answer in terms of ATP equivalents using the old values for P/O ratios. Item of energy cost

2 NADH from isocitrate dehydrogenase reaction 2 NADH from -ketoglutarate dehydrogenase rx 2 GTP from succinylCoA synthetase 1 FADH2 from succinate dehydrogenase 16 ATP equivalents lost per 2 acetylCo utilized
TOTAL ATP EQUIVALENTS per acetylCoA utilized

ATP equivalents 6 6 2 2 16 8

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14.

(17)

Refer to the table below in answering the following questions.

Go of phosphate hydrolysis Compound Go (kJ/mol) -61.9 PEP -49.4 1,3-bisphosphoglcerate -43.1 Acetylphosphate -43.1 Phosphocreatine -32.2 Phosphoarginine -33.5 PPi -32.2 ATP AMP +PPi -3O.5 ATP ADP +Pi -20.9 Glucose-1-phosphate -13.8 Fructose-6-phosphate -13.8 Glucose-6-phosphate -9.2 Glycerol-3-phosphate

a. (6)

The phosphorylated compounds, phosphocreatine and phosphoarginine, are sometimes used as energy reservoirs in muscle tissue. Calculate the standard free energy change for the generation of phosphoarginine via phosphoryl transfer from ATP. Go kJ/mol ATP + H2O ADP + Pi -30.5 arginine + Pi phosphoarginine + H2O +32.2 ATP + arginine phosphoarginine + ADP +1.7 Assuming that the necessary enzyme catalysis is always available, under what conditions would you expect the reaction in (a) above to occur in the direction of formation of phosphoarginine in the cell? [ 35 words] Go = -RT ln Keq thus Go = - ln Keq RT ln Keq = -0.68

b. (3)

1.7 kJ/mol = -ln Keq 2.5 kJ/mol

Keq = 0.51 thus the reaction will proceed to the right when the ratio ([phosphoarginine] [ADP]) / ([ATP] [arginine]) < 0.51
c. (8) Explain the large difference between Go for hydrolysis of phosphate from carbon #1 of glucose-1-phosphate and Go for hydrolysis of phosphate from carbon # 1 of 1,3bisphosphoglycerate? Suggest a thermodynamic explanation for this observed difference (i.e. plausible reasons for relative stability of products of hydrolysis). [ 70 words]

Glucose phosphorylated at C-1 is an acetal, while the dephosphorlyated form is a hemiacetal in equilibrium with an aldehyde. The dephosphorylation at C-1 of 1,3bisphosphoglycerate converts an ester to a carboxylic acid. Both products are much more stable (have lower free energy) than their respective reactants, making both dephosphorylations highly spontaneous. However, the carboxylic acid has a greater resonance stabilization relative to the ester than the aldehyde has relative to the acetal. Thus it has a greater relative stability contributing to a greater favorable free energy change.

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15.(15) a. (6) If the actual E for the net electron transport complex I reaction, NADH + H+ + CoQ NAD+ + CoQH2, is +0.36 V, and it takes 5.5 kcal/mole to pump protons across the inner mitochondrial membrane. Approximately how many moles of protons could possibly be translocated by complex I per mole of NADH oxidized? [No credit unless you show all of your
calculations.]

1kcal = 4.184 kJ, thus it takes 23kJ/mol of protons pumped under these conditions. G = - nFE G = - nF(0.36) = (2)(96.5kJ/mol)(0.36) = -69kJ/mol -69kJ/mol = 3 protons could be translocated per transfer of electrons from NADH to CoQ -23kJ/mol

b. (6) Assuming the same conditions as for part a, (i.e. G = -23 kJ/mol for protons flowing into mitochondrial matrix from cytoplasm and assuming intramitochondrial concentrations of 0.005M ATP, 0.01M Pi, and 0.0001M ADP, what minimum number of protons flowing through the ATP synthase is required to drive the synthesis of 1 ATP?

For ATP synthesis: G = Go+ RTln [ATP]/ [ADP] [Pi] = 30.5kJ/mol + (2.5kJ/mol)(ln5000)
= 30.5kJ/mol + (2.5kJ/mol)(8.5)

= 30.5kJ/mol + 21.3kJ/mol = 51.8 kJ/mol 51.8 kJ/mol needed per ATP per proton = 2.25 , but pumping of fractional 23kJ/mol provided protons is obviously not possible

Thus it will take flux of at least 3 protons per ATP

c. (3) If the order of participation in the electron transport chain is that electrons are passed to cytochrome b566 before they are passed to cytochrome a, which would you expect to have the higher reduction potential? ___ cytochrome a _____