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UNIVERSITY OF EAST ANGLIA
School of Biological Sciences
Main Series UG Examination 2012-2013
BIOCHEMISTRY
BIO-2B01
Time allowed: 2 hours
Answer ALL questions in Section A, ALL PARTS of the question in Section B, and
ONE question from Section C.
Write answers to EACH SECTION in a SEPARATE booklet.
The maximum number of marks available for your answers in SECTION A is 40 marks
The maximum number of marks available for your answer in SECTION B is 30 marks
The maximum number of marks available for your answer in SECTION C is 30 marks
The TOTAL number of marks available for the paper is 100
Numbers in square brackets [ ] indicate the relevant mark applied to each part of the
question.
Notes are not permitted in this examination.
Do not turn over until you are told to do so by the Invigilator.
BIO-2B01
Module Contact: Dr Richard Bowater, BIO
Copyright of the University of East Anglia
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SECTION A: MULTIPLE CHOICE AND SHORT ANSWER QUESTIONS
Answer ALL questions. Unless stated otherwise all multiple choice questions have
ONE answer.
1.
Erythrose 4-phosphate is a precursor of:
a)
b)
c)
d)
e)
[1 mark]
Aspartic acid
Cysteine
Phenylalanine
Serine
Threonine
2.
An important intermediate in the biosynthetic pathway to aromatic amino
acids is:
[1 mark]
a) Benzoic acid
b) Lactate
c) Orotate
d) Shikimate
e) α-ketoglutarate
3.
5-Phosphoribosyl-1-pyrophosphate (PRPP) is a synthetic precursor for all of
the following except:
[1 mark]
a)
b)
c)
d)
e)
4.
AMP
Arginine
Histidine
Tryptophan
UMP
Precursors for the biosynthesis of the pyrimidine ring system include:
[1 mark]
a)
b)
c)
d)
e)
Carbamoyl phosphate and aspartate
Glutamate, NH3, and CO2
Glycine and succinyl-CoA
Glycine, glutamine, CO2, and aspartate
Inosine and aspartate
Section A continues/ . . .
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. . . /Section A continued
5.
Which one of the following types of mechanisms does not play a role in the
reversible alteration of enzyme activity?
[1 mark]
a)
b)
c)
d)
e)
Activation by cleavage of an inactive zymogen
Allosteric response to a regulatory molecule
Alteration of the synthesis or degradation rate of an enzyme
Covalent modification of the enzyme
Interactions between catalytic and regulatory subunits
6.
Which one of the following conditions is not caused by a dietary deficiency of
a vitamin?
[1 mark]
a)
b)
c)
d)
e)
Werner-Korsakoff Syndrome
Pellagra
Phenylketonuria
Beri-Beri
Rickets
7.
Which of the following best describes the function of nicotinamide adenine
dinucleotide?
[1 mark]
a)
b)
c)
d)
e)
A 1 electron 1 proton carrier
A 1 electron 2 proton carrier
A 2 electron 1 proton carrier
A 4 electron 2 proton carrier
A 2 electron 2 proton carrier
8.
Which one of the following glucose transporters is constitutively expressed in
the membranes of pancreatic beta cells?
[1 mark]
a)
b)
c)
d)
e)
GLUT1
GLUT2
GLUT3
GLUT4
GLUT5
Section A continues/ . . .
TURN OVER
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. . . /Section A continued
9.
Which of the following statements is true?
[1 mark]
a) Fatty acid biosynthesis takes place in the cytosol, uses NADH as a
cofactor and requires the participation of the 3-carbon intermediate
propionyl-CoA
b) Fatty acid biosynthesis takes place in the mitochondria, uses
NADPH as a cofactor and requires the participation of the 3-carbon
intermediate propionyl-CoA
c) Fatty acid biosynthesis takes place in the cytosol, uses NADH as a
cofactor and requires the participation of the 3-carbon intermediate
malonyl-CoA
d) Fatty acid biosynthesis takes place in the mitochondria, uses
NADPH as a cofactor and requires the participation of the 3-carbon
intermediate malonyl-CoA
e) Fatty acid biosynthesis takes place in the cytosol, uses NADPH as
a cofactor and requires the participation of the 3-carbon
intermediate malonyl-CoA
10.
In Fatty Acid Synthase Type I, Malonyl CoA is esterified to the SH group of
which one of the following?
[1 mark]
a)
b)
c)
d)
e)
Cysteine
4’-Phosphopantetheine
Coenzyme A
Lipoic Acid
Glutathione
11.
The type of membrane transport that uses ion gradients as the energy
source is:
[1 mark]
a)
b)
c)
d)
e)
Facilitated diffusion
Passive transport
Primary active transport
Secondary active transport
Simple diffusion
Section A continues/ . . .
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. . . /Section A continued
12.
Oligomycin and 2,4-dinitrophenol (DNP) are inhibitors of mitochondrial
aerobic phosphorylation. Which of the following statements correctly describes the
mode of action of these two inhibitors?
[1 mark]
a) 2,4-dinitrophenol inhibits the respiratory chain, and oligomycin
inhibits the synthesis of ATP
b) Oligomycin and 2,4-dinitrophenol inhibit the synthesis of ATP
c) Oligomycin, and 2,4-dinitrophenol compete with O2 for cytochrome
oxidase (Complex IV)
d) Oligomycin inhibits synthesis of ATP and 2,4-dinitrophenol inhibits
the respiratory chain
e) Oligomycin inhibits the respiratory chain, whereas 2,4-dinitrophenol
prevents the synthesis of ATP
13.
Which of the following statements about the chemiosmotic theory is correct?
[1 mark]
a) Electron transfer in mitochondria is accompanied by an asymmetric
release of protons on one side of the inner mitochondrial
membrane
b) It predicts that oxidative phosphorylation can occur even in the
absence of an intact inner mitochondrial membrane
c) The effect of uncoupling reagents is a consequence of their ability
to carry electrons through membranes
d) The membrane ATP synthase has no significant role in the
chemiosmotic theory
e) For each proton transported out of the mitochondria, one electron
must be transferred along the electron transfer chain
14.
During oxidative phosphorylation, the proton motive force that is generated
by electron transport is used to:
[1 mark]
a)
b)
c)
d)
e)
Create a pore in the inner mitochondrial membrane
Generate the substrates (ADP and Pi) for the ATP synthase
Induce a conformational change in the ATP synthase
+
Oxidize NADH to NAD
Reduce O2 to H2O
Section A continues/ . . .
TURN OVER
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. . . /Section A continued
15.
Which of the following is not involved in the specificity of signal transduction?
[1 mark]
a)
b)
c)
d)
e)
16.
Scatchard analysis can provide information on:
a)
b)
c)
d)
e)
17.
[1 mark]
Enzyme cascades
Enzyme mechanisms
Gated ion channels
Protein phosphorylation
Receptor-ligand interactions
Which of the following does not involve cyclic AMP?
a)
b)
c)
d)
e)
18.
Interactions between receptor and signal molecules
Location of receptor molecules
Structure of receptor molecules
Structure of signal molecules
Transmembrane transport of signal molecules by receptor
molecules
[1 mark]
Regulation of glycogen synthesis and breakdown
Regulation of glycolysis
Signalling by acetylcholine
Signalling by epinephrine
Signalling by glucagon
How is trypsinogen converted to trypsin?
[1 mark]
a) A protein kinase-catalyzed phosphorylation event converts
trypsinogen to trypsin
b) Binding of Ca2+ to trypsinogen converts it to trypsin
c) Proteolysis of trypsinogen forms trypsin
d) Trypsinogen dimers bind an allosteric modulator, cAMP, causing
dissociation into active trypsin monomers
e) Two inactive trypsinogen dimers pair to form an active trypsin
tetramer
Section A continues/ . . .
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. . . /Section A continued
19.
A patient has been poisoned by a rodenticide of the coumarin-type. Which of
the following is likely to be an effective treatment?
[1 mark]
a)
b)
c)
d)
e)
Warfarin
Vitamin K
Calcium chloride
-carboxy glutamic acid
Oxygen
20.
Which of the following describes the overall conformation of a protein, taking
account of the organisation of multiple polypeptide chains, including any ligands
such as cofactors and metal ions?
[1 mark]
a)
b)
c)
d)
e)
The primary structure of a protein
The secondary structure of a protein
The tertiary structure of a protein
The quaternary structure of a protein
The gene sequence associated with a protein
21.
From the following seven options, select the option(s) that best fit the
biochemical descriptions of cytochromes P450 that are outlined below. Each option
may be used once, more than once, or not at all.
[5 marks]
List of seven options:
a)
b)
c)
d)
e)
f)
g)
CYP1A1
CYP2A1
CYP1A3
CYP2C9
CYP2D6
Class I
Class II
Biochemical descriptions of cytochromes P450:
i) Which cytochromes P450 receive electrons from ferredoxins?
ii) Which cytochromes P450 share > 55% sequence identity?
iii) Which cytochrome P450 is found in the liver and processes several
commonly used drugs including warfarin?
iv) Which cytochrome P450 is present in high levels in many persons
of Ethiopian and Saudi Arabian origin?
Section A continues/ . . .
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. . . /Section A continued
22.
Describe how to prepare 250 ml of 0.2 M phosphate buffer pH 6.8,
containing 0.2 M KCl. Note that to obtain phosphate buffer at pH 6.8, the molar ratio
of KH2PO4 to Na2HPO4 should be 1.15:1.00. The relevant molecular masses are
given in Table 1 below.
[5 marks]
Chemical
KCl
Na2HPO4
KH2PO4
Table 1
Molar mass (g.mol-1)
74.55
142.0
136.1
23.
Fill in the missing words ((a)-(e)) in the following statements. Note that the
answer to part (c) is a number. (Write your answers in your answer booklet, do not
write your answers on the exam paper.)
[5 marks]
‘(a)___________ enzymes catalyse the (b)________ cleavage of peptide
bonds. Catalysis by serine proteases is essentially a (c)_______-step process
and proceeds via a (d)_________ intermediate known as the (e)_________
complex.’
24.
Trypsin is an example of a hydrolase enzyme. The x-ray structure of purified
trypsin has been solved and the position of atoms present within the active site is as
follows:
A
B
C
Section A Q24 continues/…
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…/Section A Q24 continued
The “catalytic triad” that is present in all serine proteases consists of 3 specific, but
different, types of amino acids. The catalytic triad for trypsin is highlighted above,
with the 3 amino acids designated as “A”, “B” and “C”. Use the information above
and the image to answer the following questions:
a)
What general types of reactions are catalysed by “Hydrolases”?
[1 mark]
b)
For the 3 amino acids highlighted in the image above, which of them is the
catalytic serine? (Answer “A”, “B” or “C”.)
[1 mark]
c)
Trypsin has a “primary specificity” that relates to the type of peptide bonds
that it cleaves. What is the primary specificity of trypsin?
[1 mark]
d)
Name a related serine protease that has different primary specificity. Include
details of its primary specificity.
[2 marks]
END OF SECTION A
Section B begins on next page/ . . .
TURN OVER
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SECTION B:
Answer ALL PARTS of the question
25.
A sample of lactate dehydrogenase (LDH) has been purified. Throughout the
purification protocol the specific activity of LDH in the sample was determined using
an assay involving NADH, which has an extinction coefficient at 340 nm of 6.22 x 103
M-1.cm-1. (Note that NAD+ has an extinction coefficient of zero at 340nm.) The
following data refer to experiments that used cuvettes of 1 cm path length.
a)
What reaction is catalysed by LDH? In your answer, include details about
any cofactors that are required during the reaction.
[4 marks]
b)
As the sample became more pure in terms of its LDH content, what would
you expect to happen to its specific activity for LDH? Briefly, explain your answer.
[4 marks]
c)
The assays of LDH activity were set up as a 4.0 ml solution with an initial
absorbance at 340 nm of 0.95. How much NADH (in moles) was present in this
sample?
[6 marks]
d)
For the most pure sample of LDH, 0.01 ml of the sample was found to
contain 12 micrograms of protein. Calculate the concentration of protein in the
sample in mg.ml-1.
[3 marks]
e)
Assuming the sample referred to in part (d) is composed entirely of LDH and
that the relative molar mass (Mr) of LDH is 35,000, what is the concentration of the
sample analysed in part (d)? Give your answer in M to 2 decimal places. [3 marks]
f)
For the sample referred to in part (d), the LDH activity assay produced an
absorbance change at 340 nm of 0.52 per minute when 0.05ml of sample was
added to the reaction volume of 4.0 ml. For this sample, what was the specific
activity of LDH (in μmol NADH min-1 .mg protein-1)?
[8 marks]
g)
If the LDH assays were repeated in the presence of oxamate, what would
you expect to happen to the rate of LDH activity? Briefly, justify your answer.
[2 marks]
END OF SECTION B
Section C begins on next page/ . . .
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SECTION C: ESSAY QUESTION
Answer ONE question
[30 marks]
26.
The selective translocation of small metal ions across biological membranes
is achieved through the use of membrane proteins. Using appropriate examples,
compare and contrast how the transport of metal ions across membranes is
achieved by membrane proteins that use passive diffusion or active transport
mechanisms.
27.
Ribonucleotide reductase from Escherichia coli converts ribonucleotides to
their deoxy form. Describe the various biochemical reactions that are performed by
this enzyme, making sure that you provide a specific description of the ways in which
its various polypeptides are arranged. What allosteric regulatory reactions influence
the activity of this enzyme?
28.
Compare and contrast the mechanisms by which animal cells respond to
growth factors and adrenaline. In your answer include details about the mechanism
of interaction between these ligands and the cell surface receptors.
END OF PAPER
BIO-2B01
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BIO-2B01 EXAMINATION MARKERS 2012-13
[Do not print this when printing to take to Examinations Office! This is for our
information only.]
Question No.
Section A
Section B
Section C Q26
Section C Q27
Section C Q28
BIO-2B01
1st Marker
Prof J Butt
Dr R Bowater
Dr T Clarke
Dr R Bowater
Dr Charles Brearley
2nd Marker
Prof V Ellis
Dr Charles Brearley
Dr N Watmough
Dr N Watmough
Dr T Clarke
Version 1