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BIOCHEMISTRY (CHEM 360)
EXAM 3
November 26, 2014
There are six pages, TEN questions, and a total of 116 points in this exam.
Please read each question carefully and possibly more than once. Good luck…
(12)
1.
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
The only reaction where a C-C bond is formed in the citric acid cycle is given below:
In a mutant organism the cycle is fueled by an acyl CoA different than acetyl CoA at the end of
which a “citrate alternative”, Y, is produced.
Y undergoes a reaction catalyzed by an enzyme similar to aconitase to give the metabolite below:
1.1.
Identify the acyl CoA and the metabolite Y
1.2.
The metabolite in the reaction below bypasses several reactions in the citric acid cycle
and undergoes a reaction catalyzed by a lyase. Identify the structure of the missing
metabolite.
(15)
2.
Circle the best correct answer for the multiple choice questions given below:
7.1.
Elevated levels of certain amino acids in the body can be detected during starvation.
Which of the following amino acids is most likely to be detected?
(1) Alanine
2.2.
(3) tryptophan
(4) cysteine
(5) valine
If aconitase produced 2S,3R isocitrate rather than 2R,3S isocitrate, and if isocitrate
dehydrogenase could utilize the 2S,3R stereoisomer, what would be the consequence for
the citric-acid cycle?
(1)
(2)
The loss of one NADH during each turn of the cycle.
The citric-acid cycle could not operate, since isocitrate could not be
decarboxylated.
There would be no consequence.
The citric acid cycle could not operate, since -ketoglutarate could not be
decarboxylated.
(3)
(4)
2.3.
(2) histidine
If you were to compare the fatty-acid content of triacylglycerols in vegetable oil with
those in butter, what general trends would you expect to find?
(1) Butter would contain a higher percentage of more highly polyunsaturated fatty
acids than vegetable oil.
(2) Butter would contain a higher percentage of short, polyunsaturated fatty
acids than vegetable oil
(3) Butter would contain a lower percentage of polyunsaturated fatty acids than
vegetable oil
(4) Butter would contain a higher percentage of arachidonic acid than vegetable oil.
(5) Butter would contain fatty acids at approximately the same length and degree of
unsaturation as fatty vegetable oil.
2.4.
The immediate degradation product of glycogen by phosphorylase is
(1)
(2)
(3)
(4)
(5)
2.5.
fructose-1,6-bisphosphate
glucose-6-phosphate
fructose-6-phosphate
glucose
glucose-1-phosphate
If glucose was phosphorylated by an enzyme bound phosphate rather than
ATP during the first step of anaerobic glycolysis (all other steps remaining the
what would be the net ATP yield of glycolysis?
(1) 1
(2) 2
(3) 3
(4) 4
(5) 5
Page 2
same),
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3.
In 1,3-Bisphosphoglycerate (1,3-BPG) shown below one of the phosphates contains a labeled
phosphorus atom (32P). 1,3-BPG is one of the metabolites which generates ATP in the glycolysis
pathway. The following questions are aimed to trace the origins phosphate groups in the molecule.
3.1.
Phosphate with 32P
(i) Name (or write the structure of) the first glycolysis metabolite to which the
phosphate can be traced
Glucose-6-phosphate
(ii) Name the enzyme which catalyzed the phosphorylation of the glycolysis metabolite
in (i)
hexokinase
(iii) Name the coenzyme or reagent containing 32P which functioned as the
phosphorylating agent
ATP
3.2.
Phosphate with the unlabeled P
(i) Name the first glycolysis metabolite to which the phosphate can be traced
1,3-BPG
(ii) Name the enzyme which catalyzed the phosphorylation (along with another reaction)
GAP-dehydrogenase
(iii) Identify the source of the phosphate with the unlabeled P
enzyme bound phosphate
3.3.
Circle the phosphate in 1,3-BPG which is transferred to ADP
Page 3
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4.
Complete the following reactions by showing the full structures of the missing products
Please do not use abbreviations.
4.1.
4.2.
4.3.
(9)
5.
The reaction below is one of the earlier steps of a well-known metabolic pathway. Complete the
reaction and identify the pathway.
gluconeogenesis
(please note that this is the corrected version of the question)
Page 4
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6.
A number of electron transfer reactions take place within the pyruvate dehydrogenase (PDH)
complex during the conversion of pyruvate into acetyl CoA.
The standard reduction potentials (Eo’ ) for two of these half reactions are given.
6.1.
Write the spontaneous overall reaction which would take place, if you mixed lipoic acid,
dihydrolipoic acid, FAD and FADH2 together, all at 1.0 M concentration and in the
presence of the PDH complex.
6.2.
Calculate E and G0’ for the overall reaction (in the direction you predicted –note that
you may have to carry out these calculations, before you predict the direction of overall
reaction).. Show your work.
(The Faraday constant, F, is 96.5 kJ/V.mol)
6.3.
In the answer for 6.1 you will have written either lipoic acid or dihydrolipoic acid at the
end of the series of reactions within PDH complex. Write the structure of whichever
(lipoic acid or dihydrolipoic acid) is formed at the end of the spontaneous reaction in 6.1.
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7.
Amino acids resulting from the degradation of proteins can be further metabolized by conversion
to intermediates of the citric acid cycle. If the degradation of a labeled protein leads to the labeled
amino acid below,
7.1.
Write the structure of the first intermediate of the citric acid cycle into which the amino
acid is converted and also identify the labeled carbon.
7.2.
Identify the labeled carbon at the end of one turn of the citric acid cycle.
both carbons will be labeled
Page 5
(7)
8.
In the absence of oxygen, citric acid cycle is not used in the oxidation of acetyl CoA. Under these
conditions pyruvate dehydrogenase (PDH) is deactivated by phosphorylation.
The phosphorylation of PDH is catalyzed by PDH-phosphorylase kinase.
8.1.
Patients in shock experience decreased delivery of O2 to tissues, decreased activity of the
PDH complex and increased anaerobic mechanism. To alleviate these effects patients are
sometimes given dichloroacetate (DCA), which is likely to have an inhibitory effect.
What would be inhibited by DCA?
PDH-phosphorylase kinase
8.2.
Many cancer cells grow anaerobically, and PDH is not active in these cells.
Speculate the effect of DCA on cancer cells. Outline your train of thought.
Inhibiting PDH-phosphorylase kinase would activate PDH, which allow the citric acid
cycle to function at its full rate, thus maintain aerobic conditions. Limiting anaerobic
conditions would impede the proliferation of cancer cells
submitted by Kiana
(7)
9.
The reaction below is a “post-glycolysis” step and can be interpreted as a means to metabolize
excess pyruvate in anaerobic conditions (linked to question 8).
9.1.
Write the structure of the missing product
9.2.
Suggest an additional “metabolic function” for the reaction above (having to do with
glycolysis), since the product does not serve much of a purpose and gets converted back
into pyruvate in the liver.
The reaction generates NAD+, which helps to maintain the rate of the only oxidation step
in glycolysis
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10.
Although “Aldolase” type enzymes are commonly known to catalyze C-C bond cleavage in the
glycolysis pathway, they also catalyze amino acid transformations (also undergoing C-C bond
cleavage). Complete the reaction below and outline the mechanism of the reaction with curly
arrows in the presence of a representative (generic) enzyme illustrating acid or base catalysis.
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