NAME ______
Biochem 462
Final Exam
5/12/2003
Constants you may need:
N = 6.022 x 1023Avagodro’s number
F = 96500J/(V mole)Faraday constant
R = 8.31 J/(K mole)Gas constant
c = 3.00 x 108 m/sspeed of light
h = 6.63 x 10-34 J sPlank’s constant
Half reaction standard reduction potentials you may need:
½ O + 2 H+ + 2e- H2O E0’ = 0.816
Cytochrome c1(Fe3+) + e- Cytochrome c1(Fe2+)E0’ = 0.220
UQ + 2 H+ + 2e- UQH2E0’ = 0.060
UQ + H+ + e- UQH•E0’ = 0.030
FAD + 2 H+ + 2e- FADH2E0’ = 0.003
NAD+ + 2H+ 2e- NADH2E0’ = -0.320
Succinate + CO2 + 2H+ + 2e- -ketoglutarate + H2OE0’ = -0.670
Multiple choice - there is only one right answer to each problem in this section unless otherwise noted (50%)
1)The matching of the correct amino acid to the correct tRNA is performed by
a)Aminoacyl tRNA synthetase
b)tRNA
c)mRNA
d)The ribosome
2)During protein synthesis, the actual peptide bond formation is not catalyzed by a protein. Instead the enzyme is an RNA molecule. What kind of RNA molecule is it?
a)mRNA
b)tRNA
c)rRNA
d)dsRNA
3)Given the same total number of carbons, oxidation of which of these biochemicals would generate the most energy in the form of ATP? Assume that oxidation is complete forming CO2 and water in the body.
a)Glucose
b)Glycogen
c)Cellulose
d)Triglycerides
4)The carbon-carbon bonds in the fatty acids that are part of vegetable oils are
a)All single (saturated) bonds
b)All double (unsaturated) bonds
c)Alternating single and double bonds
d)Mostly single bonds with up to several double bonds
5)The degree to which the fatty acids in phospholipids are saturated is important because
a)The more unsaturated the fatty acid, the more stable the bilayer formed by the phospholipid.
b)Membrane bilayer fluidity is in part determined by how saturated the fatty acids in the phospholipids are.
c)The surface charge on the membrane is determined by the saturation level of the fatty acids in the phospholipid and the surface charge controls the electrochemical gradient.
d)Saturated fatty acids in the phospholipid are not broken down as rapidly as unsaturated fatty acids and therefore must be replace less often.
6)Which of the following statements best characterizes the biological membrane of a living cell.
a)Fluid-like, with integral protein complexes and lipid molecules able to move relative to each other within the plane of the membrane.
b)Rigid, with integral membrane proteins cross-linked in such a way as to form a hard outer shell for the cell’s protection.
c)A porous barrier though which ions flow freely as is necessary to maintain an appropriate osmotic balance.
d)An impermeable barrier through which molecules cannot pass.
7)Approximately how thick is a typical cell membrane?
a)1 nm
b)5 nm
c)25 nm
d)100 nm
8)What is the standard free energy change for moving glucose from the inside of a biological membrane to the outside. Careful! Think about the definition of a standard free energy change.
a)positive
b)negative
c)zero
d)depends on the concentrations of glucose inside and outside the cell.
9)How many electrons are involved in the reduction of NAD+?
a)One electrons.
b)Two electrons.
c)NAD+ can either accept one or two electrons.
d)The number varies and can in fact be fractional.
10)The bacterium Rhodobacter sphaeroides is a facultative anaerobe which lives as a photoheterotroph under anaerobic conditions when light is available. Please translate that into normal English:
a)This bacterium can live only live in the absence of oxygen and in the presence of light. It needs no additional carbon source.
b)This bacterium can live only live in the absence of oxygen and uses light as an energy source but needs an additional carbon source.
c)This bacterium can live either in the presence or absence of oxygen, but when oxygen is lacking it can perform photosynthesis and fix carbon (does not need another carbon source).
d)This bacterium can live either in the presence or absence of oxygen, and when oxygen is lacking it performs photosynthesis but still needs additional carbon sources (it cannot fix carbon).
11)Glycolysis is regulated predominantly at three reactions in the pathway. What do these three reactions have in common?
a)They all consume ATP.
b)They all involve large free energy changes.
c)The three enzymes involved are all membrane bound.
d)They all involve the net oxidation of the substrate.
12)The reaction forming pyruvate from PEP drives the production of ATP from ADP. Mechanistically speaking, this substrate-level phosphorylation is driven by what kind of reaction?
a)Hydrolysis of a phosphate bond.
b)Oxidation of an alcohol to ketone.
c)An enol – keto tautomerization.
d)A decarboxylation step.
13)Mechanistically, the formation of isocitrate from citrate in the TCA cycle by aconitase involves what kind of reaction?
a)A reduction of one carbon followed by the oxidation of another.
b)A dehydration forming a double bond followed by hydration in the opposite orientation.
c)A phosphorylation of one carbon coupled to the transfer of the hydroxyl to the neighboring carbon and dephosphylation.
d)The formation of a radical intermediate, followed by intramolecular radical movement between carbons and subsequent quenching by OH•.
14)The conversion of succinate to fumarate in the Krebs cycle is best described as a:
a)One electron oxidation
b)One electron reduction
c)Two electron oxidation
d)Two electron reduction.
15)What is the chemical property of quinones that makes them ideal for coupling electron transfer to proton pumping?
a)They take up protons upon reduction and give them off upon oxidation.
b)They take up protons upon oxidation and give them off upon reduction.
c)They can only go from one side of the membrane to the other when they are reduced.
d)They can only go from one side of the membrane to the other when they are oxidized.
16)The coupling of ATP synthesis to proton translocation across the membrane involves what kind of mechanism?
a)A pH dependent phophorylation reaction that only occurs when the pH on the inside of the mitochrondrion is made high enough by pumping protons out.
b)ATP synthase uses the proton to protonate ATP, and in so doing depletes the unprotonated ATP population, forcing the equilibrium between ADP and ATP to thermodynamically favor ATP.
c)Proton translocation through the ATP synthase enzyme results in a series of conformational changes in the enzyme, and it is these conformational changes that provide the power needed to make ATP from ADP.
d)Protonation of one of the amino acids in the ATP binding site changes the binding constant for ATP, releasing the product and driving the reaction forward.
17)What is the ultimate electron acceptor in the linear photosynthetic electron transfer chain of plants?
a)Light
b)Oxygen
c)Water
d)NADP+
18)How is the energy of light coupled to electron transfer during photosynthesis?
a)Light energy absorbed by a chlorophyll molecule (or complex) effectively makes this molecule a better reductant and it acts as the initial donor in electron transfer.
b)Light energy absorbed by a chlorophyll molecule (or complex) effectively makes this molecule a stronger acid, allowing it to transfer both protons and electrons.
c)Light energy absorbed by a chlorophyll molecule (or complex) causes the molecule to ionize and the solvated electron produced is injected into the electron transfer chain.
d)Light energy absorbed by a chlorophyll molecule causes it to heat up, making it more reactive towards the neighboring molecule.
19)Glycolysis and Gluconeogenesis differ in three of the reactions. What do these reactions all have in common?
a)They all consume ATP in one direction and generate it in the other.
b)They all involve large free energy changes.
c)The three enzymes involved are all membrane bound.
d)The all involve the net oxidation of the substrate in one direction and reduction in the other.
20)Breakdown of fatty acids involves:
a)A cyclic reaction in which carbon dioxide is released at each step.
b)A cyclic reaction in which acetyl-CoA is released at each step.
c)A cyclic reaction in which malonyl-CoA is released at each step.
d)A cyclic reaction in which succinyl-CoA is released at each step.
21)Synthesis of fatty acids involves:
a)A cyclic reaction in which carbon dioxide is reacted at each step, increasing the chain length by one.
b)A cyclic reaction in which acetyl-CoA is reacted with the growing chain at each step increasing the chain length by two.
c)A cyclic reaction in which malonyl-CoA is reacted with the growing chain at each step increasing the chain length by three.
d)A cyclic reaction in which malonyl-CoA is reacted with the growing chain at each step, increasing the chain length by two.
22)What types of organisms can assimilate nitrate?
a)Plants only
b)Bacteria only
c)Animals only
d)Plants and bacteria but not animals
23)What are the three major entry points for ammonia into biomolecules (you must pick all three of the right answers below in order to receive credit):
a)Addition of ammonia to ketoglutarate to form glutamate
b)Addition of ammonia to glutamate to form glutamine.
c)Addition of ammonia to pyruvate to form alanine.
d)The formation of carbamoyl phosphate from ammonia, carbon dioxide and ATP.
24)An example of a well-known second messenger used for hormone function is:
a)Insulin
b)ATP
c)cAMP
d)messenger RNA
Short Answer (40%)
25)Of the 64 possible codons in the genetic code, 61 normally code for the standard 20 amino acids. What do the other three code for?
26)The following is a Fischer projection of D-fructose. Next to it draw the Fischer projection of L-fructose.
CH2OH
|
C=O
|
HO-C-H
|
H-C-OH
|
H-C-OH
|
CH2OH
27) Name two differences between prokaryotic and eukaryotic translation.
28)Why do we use fat (saturated triglyceride) as the primary means of long term energy storage instead of glycogen? Phrase your answer in terms of the difference in oxidation/reduction level of carbon in the two molecules.
29)What is the free energy change for transporting one mole of glucose from the inside of the membrane to the outside if the glucose concentration on the inside is 10 mM and the glucose concentration on the outside is 100 mM? Constants are given on the front of the exam.
30)Write down a balanced chemical equation for the oxidation of succinate to fumarate in the TCA cycle.
31)Write down the overall reaction for Complex IV in the photosynthetic electron transport chain of mitochondria and calculate the standard reduction potential for this reaction using the half reaction values given on the front page of the exam.
32) Biology tends to use the same answers to common problems many times in different contexts. To go from pyruvate to PEP during gluconeogenesis (the reverse of the catabolic reactions of glycolysis), a biotin dependent carboxylation reaction is used followed by a decarboxylation. Where else is this same basic approach used in a synthetic pathway in order to reverse a step in the corresponding degradation pathway that has a large free energy change? Name the two specific reactions I am referring to by giving either the enzyme names or by describing the chemical reactions.
33) Another set of parallel reaction mechanisms is found in two of the decarboxylation reactions of sugar catabolism. Pyruvate dehydrogenase catalyzes the TPP dependent decarboxylation of pyruvate forming acetyl-CoA. Later in the TCA cycle there is a very similar TPP dependent decarboxylation reaction that uses an essentially identical mechanism. Name the specific reaction by giving either the enzyme name or by writing down the chemical reaction.
34)Hormones play a major role in controlling carbon metabolism in your body. Often they control the balance between the synthesis of molecules used for long term energy storage and their breakdown. Name two different points in metabolism that we have discussed where hormones exert this kind of control:
Hormones regulate the synthesis vs. breakdown of ______
And
Hormones regulate the synthesis vs. breakdown of ______
35)The formation of ammonia from N2(gas) is actually a thermodynamically favorable process. Yet nitrogen fixing bacteria end up spending 16 ATP molecules in this process. Why is this necessary?
36)Cholera is a major disease that kills many people in the world, particularly young children in third world countries. The toxin directly interferes with hormone mediated control. Describe briefly how it does this. Make sure you specify the molecular point of action.
Broader Understanding (10%)
37)Consider how glucose and ammonia could be used as the starting materials in a cell to produce glutamine using the pathways you have learned. Each of the parts to this question can be answered independently of the others, so if you do not know how to do one part, just go on to the next.
a)(4%) Describe how you would get from glucose to glutamine. You do not need to write out all the reactions, you can describe it in words. I will start the answer for you so you can see what kind of detail I am looking for in your answer:
Glucose enters glycolysis and is converted to pyruvate. Then…
b)(2%) Now lets say a fair amount of glutamine had built up. How would the body shut off further production of glutamine (at what point in the synthesis of glutamine would feed back inhibition act most strongly)?
c)(4%) If you answered part (a) correctly, you ended up using part of the TCA cycle in your pathway, effectively breaking the cycle so that oxaloacetate is never reformed to start the cycle over again. Given that glucose is present as the carbohydrate starting material, how do you replenish the oxaloacetate needed to keep the TCA cycle going if you are using intermediates in the TCA cycle up as raw materials for making amino acids?