Name:
BIOCHEMISTRY I (CHEM 360)
EXAM 3
November 25, 2015
There are six pages, TEN questions, and a total of 115 points in this exam,
which gives 15 extra points on top of that required for a “perfect” paper.
Please read each question carefully and possibly more than once. Good luck…
(8)
1.
A labeled oxaloacetate (see below) is allowed to enter the citric acid cycle in a cellular study.
1.1.
Identify 13C in aconitate (or in isocitrate if you cannot remember the structure of aconitate!)
1.2.
Provide the structure of the first citric acid cycle metabolite in the study, where the labeled carbon
cannot be detected.
(12)
2.
Pyruvate dehydrogenase complex deficiency (PDCD) is a neurodegenerative disorder commonly observed
in children.
2.1.
The shortage of which common metabolite is caused due to PDCD?
2.2.
Which common metabolic pathway is severely slowed down due to PDCD?
2.3.
Elevated levels of which amino acid is a diagnostic lead for PDCD?
(19)
3.
A reaction related to glycolysis, but one which does not link glycolysis to the citric acid cycle can be
analyzed in terms of the half-reactions given below.
3.1.
Write the spontaneous overall reaction which occurs when you mix pyruvate, lactate,
NAD+ and NADH, all at 1.0 M concentrations, together in the presence of appropriate
enzyme(s).
Note that you will need to calculate E in order to predict the direction of the overall
reaction. Give also the value of E below.
3.2.
Calculate G0’ for the overall reaction (in the direction you predicted)
Show your work.
(The Faraday constant, F, is 96.5 kJ/V.mol)
3.3.
Which one of the following statements is correct for the overall reaction you have written
above?
(a) The reaction generates “reducing power”
(b) The reaction uses up “reducing power”
(c) The reaction is the basis for “lactic acidosis”, which causes pain in the joints and
muscles after strenuous exercise.
(d) The reaction generates ATP
3.4.
Explain your choice of the answer in 3.3, and justify the “metabolic objective” of the
reaction.
(7)
4.
Glucose enters some cells by simple diffusion through channels and pores, but glucose enters red blood
cells by passive transport. On the plot below, indicate which line represents diffusion through a channel or
pore, and which line represents passive transport.
Explain why the rates of the two processes (and the shapes of the two plots) are different.
Page 2
(14)
Question submitted by Kailee
5.
In the conversion of glyceraldehyde-3-phosphate into 1,3-bisphosphoglycerate the active site of the enzyme
glyceraldehyde-3-phosphate dehydrogenase illustrated below somewhat resembles that of a serine protease.
5.1.
Use curly arrows in Fig. 1 to show the formation of the tetrahedral intermediate with
glyceraldehyde-3-phosphate. Draw the tetrahedral intermediate in Fig. 2 using relevant side
chains shown in Fig. 1.
5.2.
Using curly arrows in Fig. 2 to show how the tetrahedral intermediate undergoes oxidation (with
the relevant oxidizing agent) to give an acyl enzyme.
5.3.
In Fig. 3 give the structure of the acyl enzyme formed as well as the structures of a new metabolite
formed as a result of the redox process.
Fig. 2
Fig. 1
Fig. 3
5.4.
In Fig. 3 outline the final phosphorylation step of the
acyl enzyme into 1,3-bisphosphoglycerate
Page 3
(24)
6.
Circle the best correct answer (only ONE) for the multiple-choice questions below.
6.1.
Which of the following two pathways is not likely to occur together?
(1) glycolysis and Krebb’s cycle (2) glyoxylate pathway and gluconeogenesis
(3) gluconeogenesis and glycogen synthesis
(4) glycogenolysis and glycolysis
6.2.
Once inside the cell, glucose is rapidly phosphorylated to glucose-6-phosphate. What is the main
purpose of this phosphorylation?
(1) To keep glucose inside the cell
(3) To form a high-energy compound
(2) To prevent mutarotation
(4) To activate PFK-1
6.2.
Out of the following fatty acids which one has the lowest melting point?
6.4.
For the reaction below what is the most likely value for G?
ATP
(1) 0 kJ/mole
6.5.
+
(2) 30 kJ/mole
(3) -30 kJ/mole (4) It cannot be predicted
Which class of membrane proteins can be removed from the membrane by changing the ionic
strength of the solution?
(1) integral
(4) all of the above
6.6.
2 ADP
AMP
(2) peripheral
(3) fatty acid-anchored
How many ATP molecules are produced in the triose stage of glycolysis for each molecule of
glucose?
(1) 1
(2) 2
(3) 3
(4) 4
(5) ATP is consumed, not produced.
Page 4
6.7.
Which of the following is true of glycogen synthesis and breakdown?
(1) Synthesis is catalyzed by the same enzyme which catalyzes breakdown.
(2) The immediate product of glycogen breakdown is free glucose
(3) Phosphorylation activates the enzyme responsible for glycogen degradation, and deactivates
the enzyme responsible for glycogen synthesis.
(4) Under normal circumstances glycogen synthesis and glycogen breakdown occur
simultaneously at high rates.
(5) The glycogen molecule “grows” at its reducing end.
6.8.
All but one of the compounds below is likely to undergo a C-C bond cleavage reaction in the
presence of an “aldolase like” enzyme. Which compound will not undergo such reaction?
(11)
7.
Some proteins exhibit “phosphoryl-group-transfer potential” through the side chains of their amino acids,
and are considered as phosphorylating agents.
Certain amino acid side chains are given below. Circle the side chain with the lowest phosphoryl-group
transfer potential (weakest phosphorylating agent).
7.1.
The phosphorylating potential of these amino acids can be quantified by hydrolyzing each of their
side chains. What parameter would you be measuring by doing so?
7.2.
Assign “0” for the “parameter” (your answer for 7.1) of the structure you circled. Give its units.
Now estimate a numerical value (with units) for a structure you have not circled (indicate its
letter). Tabulate both of the values below.
Page 5
(8)
8.
A strain of Mycobacterium marinum, which has recently taken up residence at the Ala Wai Boat Harbor,
bypasses some of the reactions of the citric acid cycle to produce glyoxylate. However, instead of isocitrate,
the organism uses the precursor below:
8.1.
Identify the structure of the missing product which is formed along with glyoxylate
8.2.
How do you think with the unusual “by-pass” reactant will affect the “Ala Wai resident” above?
What will be the impact on gluconeogenesis? Explain.
(8)
9.
When 13C labeled glucose at a certain position is fed to various living organisms, 3-phosphoglycerate
labeled at C-1 (carboxylate) can be isolated. Predict the position of 13C in glucose.
Show your work (no points for blind-guessing).
Note that there may be more than one position labeled in glucose which might yield the 3-phosphoglycerate
above.
(7)
10.
Phosphatidylinositol-4,5-bisphosphate,
messengers”.
10.1.
PIP2,
undergoes
hydrolysis
Draw the structures of the two “second messengers”.
(The hydrolysis site of PIP2 is indicated by an arrow in boldface)
10.2.
Give the name of the enzyme which catalyzes the hydrolysis
Page 6
to
produce
two
“secondary