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Bis Winter 2011 First Midterm Exam

1. Which of the following treatments would leave a proteins information content
A. Removing all the R groups from amino acids.
B. Rearranging the same amino acids in the sequence
C. Exchanging one amino acid for a different one.
D. Denaturing the amino acid by heating.
E. Hydrolyzing all of the peptide bonds.
2. Two pyruvate molecules are produced from one molecule of glucose by glycolysis.
What determines whether these pyruvates are reduced to lactate (or ethanol) or are
oxidized by the TCA (Krebs) cycle?
A. One pyruvate will always be reduced, and the other will always enter into the
TCA cycle
B. Availability of CO2 allows use of TCA cycle.
C. Availability of O2 or another outside respiratory electron acceptor allows use of
TCA cycle.
D. High levels of NADH force pyruvate reduction; at low NADH levels, oxidation of
pyruvate through the TCA cycle is allowed.
E. TCA cycle is used if cells require a lot of energy.

3. *Which one of the following reactions is NOT an oxidation-reduction (redox) reaction?
A. NADH + 1/2O2 + H+ <-> NAD+ + H2O
B. R-CH=CH-CH3 + H2O <-> RCH2-CH(OH)-CH3
C. FAD + H2O <-> FADH2 + 1/2O2
D. NADH + acetaldehyde <-> NAD+ + ethanol
E. AH2 + B <-> A + BH2

4. What distinguishes photosynthesis (as done in plants) and aerobic respiration? (FILL
A. One consumes CO2, the other produces CO2
B. One uses light to excite electrons, the other uses PMF
C. One uses the ATPase to make ATP, the other uses only substrate-linked
D. One uses light to excite electrons, the other uses the electron transport chain
E. One produces O2, the other consumes O2

5. What makes an amino acid hydrophobic?
A. polar R group
B. non-polar R group
C. positively charged R group
D. negatively charged R group
E. R group that disrupts protein secondary structure


6. What does a respiring heterotroph use as the proximal electron acceptor (first in the
process of fuel oxidation)?
D. CO2
E. O2
7. *The organisms that produced the oxygen gas in Earths atmosphere in ancient times
were -A. Heterotrophic eukaryotes
B. Autotrophic eukaryotes
C. Autotrophic prokaryotes
D. Heterotrophic prokaryotes
E. Completely unlike any modern organisms
8. A properly-folded protein tends to be globular with a hydrophobic (greasy) center
and an outer surface with exposed polar and charged R-groups. How is this structure
generated? (Choose two contributing factors).
A. Weak hydrogen bonds between O and H atoms of different peptide bonds
generate secondary structure (string of wieners).
B. Amino-acid R groups are rearranged in the sequence so that they all move
toward the center.
C. Substrates and other proteins bind to the polar and charged R groups and
holding them on the surface as the protein folds.
D. Weak interactions between different R groups are formed and disrupted until
the most stable structure is achieved.
E. Hydrophobic (greasy) R-groups, react to form covalent bonds that generate the
solid protein core.
9. Biological communities around hydrothermal vents persist in the dark. This would
seem to violate thermodynamics, which requires some continuous outside energy
source. How might these isolated communities live by standard redox chemistry?
A. They can violate thermodynamics, because of the high temperatures involved.
B. They use as electron donors H2, H2S and other reduced compounds that
emerge from the vents.
C. The communities use as fuel the biological deposits formed by earlier
life forms (oil deposits).
D. They get oxygen that diffuses down to them from the surface atmosphere to
use as an electron acceptor.
E. They are autotrophs that use heat instead of light as a source of energy.


10. Suppose you believe that the first life form was an autotroph. Which of the
following lifestyles seems most likely?
A. non-cyclic photosynthesizer (photo-autotroph)
B. fermenter
C. respirer
D. a light-independent autotroph, e.g using H2 to reduce CO2.
E. cyclic photosynthesizer
We discussed a series of major biological metabolic inventions (the toys of
life), some of which are listed below.
1. Substrate-linked phosphorylation (e. g. G3PO4 dehydrogenase).
2. Electron transport using redox reactions to pump protons)
3. ATPsyntase (interconverting PMF and ATP)
4. Photo-center (using light to excite an electron
5. TCA cycle (oxidizing pyruvate to CO2 and H2O)
6. Rhodopsin (direct pumping of protons by light)
7. Splitting water to release oxygen and reducing power.
8. Fixing CO2 using Rubisco

Use the toy numbers above to answer the questions below

11. Which of the above toys is the source of ATP for a fermenting organism.
A. Combination of 1 and 3
B. Toy number 5
C. Combination 2 and 3.
D. Exclusively toy 1
E. Use toy 2 in combination with an outside electron acceptor
12. What form of metabolism uses toys 2,3,4 and 7?
A. Aerobic respiration
B. Photo-autotrophy
C. Cyclic photosynthsis
D. Anerobic respiration
E. Light independent heterotroph (e.g. methanogen)

13. During aerobic respiration, electrons are taken from NADH (H+),
transported by a multi-step pathway and then used to reduce O2 to H2O.
Why not save all these steps and use NADH to reduce O2 directly?
A. This has occurred in humans, which have a streamlined metabolism.
B. This would release energy in a way that it could not be used to do work.
C. The single step is energetically unfavorable

D. A single step would not be reversible
E. Both (A) and (D) are correct


14. What organism obtains small carbon-containing molecules for biosynthesis by
OXIDIZING an outside carbon-containing compound ?
A. a respiring heterotroph
B. a fermenting heterotroph
C. a photosynthesizing autotroph
D. A and B
E. A and C
15. What organism gets small carbon-containing molecules for biosynthesis by
REDUCING an outside carbon compound?
A. a respiring heterotroph
B. a fermenting heterotroph
C. a photosynthesizing autotroph
D. A and B
E. A and C
16. ATP has two high-energy phospho-diester bonds (labeled I and II in the figure
below) and can use them to carry energy to a variety of reactions.
Energy is usually delivered by hydrolyzing the outside bond (I), producing ADP +
PO4. In some reactions, however, the inside bond (II) is hydrolyzed,
producing AMP + PO3-O-PO3. In what sorts of reactions do you think the inside
bond (II) might by hydrolyzed? (FILL TWO BUBBLES)
A. When the cell has too much free phosphate.
B. For reactions that are highly unfavorable and need more energy.
C. When its essential to assure that the reaction does not go in reverse.
D. When small doses of energy are needed.
E. At low temperature when all reactions are moving slowly and the cell needs
the added energy to attain a sufficient reaction rate.

17. *The immediate source of energy for ATP synthesis in chloroplasts and
photosynthetic bacteria is
A. Electron transport
B. The electrochemical proton gradient (PMF)
C. Light
D. Energized chlorophylls

The figure above presents the effects of substrate concentration heat and on the rate of
a particular reaction. Answer the questions below by filling in the bubble corresponding
to one of the letters (A B C D E) in the figure.
18. Which line gives evidence that the catalyst can be saturated? (A,B,C,D,E ?)

19. Which line is most likely to describe an enzyme-catalyzed reaction? (A,B,C,D,E?)

20. What aspect of the data can be used to estimate of the catalytic efficiency
( reaction rate of catalyst-bound molecules)?
A. The maximum initial slope of line A.
B. The rate approached by line A at high substrate concentrations (Vmax).
C. Half the reaction rate Vmax in line A
D. The ratio of the reaction rate in line B to the initial rate of line A.
E. The reaction rate seen in line C just before it drops.
21. What aspect of the data can be used to estimate of the binding affinity of
substrate for the catalyst?
A. The concentration at which Vmax is achieved
B. The reaction rate seen at the lowest substrate concentration.
C. The concentration at which the reaction rate reaches of Vmax.
D. The concentration that just begins to inhibit the reaction rate (line A).
E. The substrate concentration just at the point that temperature causes a
rate drop in line C.

In the figure above, the letters A, B, C, D, E represent values that can be used
to answer the questions below.
22. Which TWO values are NOT affected by heat? (FILL IN TWO BUBBLES)
23 Which TWO values are affected by BOTH heat AND catalysis?

24 Which value would be changed by a catalyst but not by heat?

25 Which SINGLE value dictates the forward rate constant (kF) with and without a catalyst?

26 Which SINGLE value determines the ratio of reactant concentrations (PxQ)/(MxN) at equilibrium?

27. What SINGLE value has no effect on the reaction rate, even far from equilibrium?

28 What is the effect of a catalyst on the reaction described in the figure?
A. It increases the forward rate constant, but not the back rate constant
B. Changes the steady state concentration of reactants such that the
reaction becomes more favorable (more P,Q, less M,N at equilibrium).
C. Reduces barriers to both forward and backward reaction by lowering the
transition state energy.
D. Specifically increases the forward reaction rate by reducing the FORWARD
activation energy .
E. The catalyst has very little effect in this reaction because the transition state
is so high.

29. *What are the products of non-cyclic photosynthesis (systems I + II) in plants and
cyanobacteria? (ONE BUBBLE)
B. NADP+ and ATP
D. NADPH, O2 and ATP
E. NADP+, O2 and ATP

30. *Which of the following statements is INCONSISTENT with the first and
second laws of thermodynamics?
A. Living organisms can create energy
B. Chemical energy can be converted to light energy
C. The total energy of a system is available to do work.
D. Potential energy may be used to do work.
E. both A and C.
31. Most biological metabolic reactions proceed at an extremely slow rate in the
absence of a catalyst. Choose two ways to explain why this happens
(mechanistically or functionally). (FILL TWO BUBBLES)
A. The transition state energy of these reactions is much higher than the energy of
the substrates, so the rate constants are extremely tiny without a catalyst.
B. In the confined space within a cell, products get concentrated and the
reactions come rapidly to steady state.
C. Metabolism is only possible if the rates of useful reactions exceed the rates of
the large array of other reactions. Life can dictate its metabolism only by
developing catalysis.
D. The catalysts do increase reaction rates, but the measured uncatalyzed rates
are much faster than they would need to be for a cell to function.
E. The catalysts are required because they allow more energy to be obtained
from poor fuel molecules.
32. The figure shows an alpha helix located in the middle
of a folded protein. How is the depicted portion oriented?
A. Amino terminus at the bottom
B. Amino terminus at the top
C. A protein has an amino terminus at both ends.
D. The orientation of a protein cannot be determined from the
amount of molecular structure shown.
E. The orientation can only be determined if you see the
structure of one end of the protein.
33. What does non-cyclic photosynthesis achieve
that can not be provided by a cyclic photosynthsizer? (FILL TWO BUBBLES)
A. Formation of PMF
B. Formation ATP
C. A source of reducing power for biosynthesis.
D. The ability to return excited electrons to its own photo-center
E. Ability to fix CO2.

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