Download BIO-5002A - BIOCHEMISTRY

UNIVERSITY OF EAST ANGLIA
School of Biological Sciences
Main Series UG Examination 2015-2016
BIOCHEMISTRY
BIO-5002A
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 the Answer Grid or 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.
Graph paper is provided.
Notes are not permitted in this examination.
Do not turn over until you are told to do so by the Invigilator.
BIO-5002A
Copyright of the University of East Anglia
Module Contact: Dr Richard Bowater, BIO
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SECTION A: MULTIPLE CHOICE AND SHORT ANSWER QUESTIONS
Answer ALL questions. Answer multiple choice questions in the answer grid provided
and attach this to your booklet for Section A.
1.
The synthesis of purine and pyrimidine nucleotides differ in that:
[1 mark]
a) ATP is required in the synthesis of purines but not in the synthesis of
pyrimidines
b) purine biosynthesis starts with the formation of PRPP
(phosphoribosyl pyrophosphate), whereas pyrimidines incorporate
PRPP near the end of the pathway
c) pyrimidine formation requires a tetrahydrofolate (THF) derivative,
whereas purine formation does not
d) pyrimidine biosynthesis is tightly regulated in the cell, whereas
purine biosynthesis is not
e) pyrimidines go through many steps, adding a single carbon or
nitrogen each time, whereas the basic skeleton for purines is formed
from two main precursors
2.
An important intermediate in the biosynthetic pathway to aromatic amino acids is:
[1 mark]
a)
b)
c)
d)
e)
3.
One amino acid directly involved in the purine biosynthetic pathway is:
a)
b)
c)
d)
e)
4.
benzoic acid
lactate
orotate
shikimate
α-ketoglutarate (2-oxo-glutarate)
[1 mark]
alanine
aspartate
glutamate
leucine
tryptophan
Which of the following molecules is not an inhibitor of glutamine synthetase?
[1 mark]
a)
b)
c)
d)
e)
AMP
valine
histidine
glycine
glucosamine-6-phosphate
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Section A continued. . .
5.
In which of the following enzymes would you not expect to find a domain known as a
"Rossmann fold"?
[1 mark]
a)
b)
c)
d)
e)
6.
Which of the following enzymes is not part of the fatty acid synthase found in the
cytosol of mammalian cells?
[1 mark]
a)
b)
c)
d)
e)
7.
Alcohol Dehydrogenase
Acetyl-CoA Carboxylase
Acetaldehyde Dehydrogenase
Carbonyl Oxidoreductase
Lactate Dehydrogenase
Ketoacyl synthase
Enoyl CoA isomerase
Malonylacetyl transferase
Thioesterase
Dehydratase
Which of these statements about facilitated diffusion across a membrane is true?
[1 mark]
a) Facilitated diffusion involves a specific membrane protein that lowers
the activation energy for movement of the solute through the
membrane
b) Facilitated diffusion can increase the magnitude of a transmembrane
concentration gradient of the diffusing solute
c) Facilitated diffusion is dependent upon the solubility of the
transported solute in the nonpolar interior of the lipid bilayer
d) Facilitated diffusion is responsible for the transport of gases, such as
O2, N2, and CH4, across biological membranes
e) The rate of solute transport never reaches saturation
8.
Upon the addition of 2,4-dinitrophenol (DNP) to a suspension of mitochondria
carrying out oxidative phosphorylation linked to the oxidation of malate, all of the
following occur except:
[1 mark]
a)
b)
c)
d)
e)
the rate of ATP production increases
oxygen consumption increases
the P/O ratio drops from a value of approximately 2.5 to zero
the proton gradient dissipates
the rate of transport of electrons from NADH to O2 becomes maximal
Section A continues on next page/ . . .
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Section A continued. . .
9.
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) The chemiosmotic theory 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
10.
Which of the following statements is not true about cytochrome P450 enzymes?
[1 mark]
a)
b)
c)
d)
The active site contains magnesium
They belong to a general class of enzymes called monooxygenases
There are over 30 different cytochrome P450 enzymes
Variation in the cytochrome P450 enzyme profile between individuals
can explain individual variation in drug susceptibility
e) Human cytochrome P450 enzymes are bound to membranes
11.
Which of the following is not involved in the specificity of signal transduction?
[1 mark]
a)
b)
c)
d)
e)
12.
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
Scatchard analysis can provide information on:
a)
b)
c)
d)
e)
[1 mark]
enzyme cascades
enzyme mechanisms
gated ion channels
protein phosphorylation
receptor-ligand interactions
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Section A continued. . .
13.
Which of the following does not involve cyclic AMP?
a)
b)
c)
d)
e)
14.
Regulation of glycogen synthesis and breakdown
Regulation of glycolysis
Signalling by acetylcholine
Signalling by epinephrine (adrenaline)
Signalling by glucagon
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)
15.
[1 mark]
Warfarin
Vitamin K
Calcium chloride
γ-carboxy glutamic acid
Oxygen
Ubiquitin is a:
a)
b)
c)
d)
e)
[1 mark]
component of the electron transport system
protease
protein kinase
protein phosphorylase
protein that tags another protein for proteolysis
For all remaining questions in Section A, please use an answer booklet. Remember
to attach your multiple choice answer grid to the booklet.
Section A continues on next page/ . . .
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Section A continued. . .
For all remaining questions in Section A, please use an answer booklet. Remember
to attach your multiple choice answer grid to the booklet.
16.
Answer ALL parts (a), (b), (c) and (d).
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
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) Serine proteases have a “primary specificity” that relate to the “P1” residue of the
substrate. What is the primary specificity of trypsin?
[1 mark]
(d) What two key features of the primary specificity pocket (S1) of serine proteases
determine which P1 residue can be bound?
[2 marks]
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Section A continued. . .
17.
Name the five different biochemical classes of amino acids and name an example of
each class.
[5 marks]
18.
With the help of a diagram, name and highlight the arrangements of the five
mitochondrial transmembrane proteins that are involved in the respiratory transport
chain and ATP synthesis. Within your diagram, show how the protons move across
the inner mitochondrial membrane.
[5 marks]
19.
For the following options, match the enzyme to its preferred substrate. Only one
answer should be provided for each enzyme and each answer should be listed no
more than once.
[5 marks]
List of five enzymes:
a) Ribonucleotide reductase
b) Aspartate transcarbamoylase
c) Glutamine synthetase
d) Hexokinase
e) Pyruvate kinase
List of biological molecules:
i) Glucose
ii) dATP
iii) Lactose
iv) Glutamate
v) ADP
vi) Phosphoenolpyruvate
vii) Tryptophan
viii) 5-phosphoribosyl-1-pyrophosphate (PRPP)
ix) Aspartate
x) Phenylalanine
20.
Answer ALL parts (a), (b) and (c).
A sample of Enzyme X has been purified and biochemical studies were conducted
on it.
(a) During the purification process, as the sample became more pure in terms of its
content of Enzyme X, what would you expect to have happened to the specific
activity for this enzyme? Briefly, explain your answer.
[2 marks]
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Section A Q20 continued. . .
(b) For the purified Enzyme X, optimal activity of the enzyme was shown to require
the presence of pyruvate and NADH. What protein is likely to constitute Enzyme
X?
[1 mark]
(c) If the assays were repeated in the presence of oxamate in addition to pyruvate,
what would you expect to happen to the rate of activity of Enzyme X? Briefly,
justify your answer.
[2 marks]
END OF SECTION A
START YOUR ANSWER TO THE NEXT SECTION IN A NEW BOOKLET
SECTION B: DATA HANDLING QUESTION
Answer ALL PARTS of the question
[30 marks]
21.
(a) A series of protein samples were prepared, with an aim to use the Bradford
assay to determine the concentration of protein in each. In one sentence,
describe the principles behind the Bradford assay. In addition, suggest one
alternative approach that could be used to determine the concentration of protein
in each sample.
[4 marks]
(b) The concentration of protein in some experimental samples was measured using
the Bradford assay. A buffer was provided for the experiment, but KCl had to be
added to be at a final concentration of 0.2 M. How much solid KCl was added to
prepare 300 ml of buffer containing 0.2 M KCl? Note that the molar mass of KCl
[2 marks]
is 74.55 g.mol-1.
(c) Using a solution of bovine serum albumin (BSA) at a known concentration, a
calibration curve for a Bradford assay was prepared. Different volumes of BSA
were mixed with water so that the total volume of protein solution in each
measurement was 0.1 ml. Table 1 (on the next page) shows the absorbance
readings at 595 nm (A595) for the various amounts of protein. On the graph paper
provided, plot the amount of protein in each sample against its absorbance at
595 nm. Comment briefly on the relationship between the protein concentration
and the measured absorbance as revealed by your plot.
[6 marks]
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Section B continued. . .
Amount of
BSA
(microgram)
Absorbance
at 595 nm
0
0.000
5
0.280
10
0.590
15
0.847
20
1.132
25
1.428
30
1.595
40
1.830
50
1.915
Table 1. Bradford assay analysis of samples containing different amounts of
BSA.
(d) A solution of Protein A at an unknown concentration was analysed using the
same Bradford assay protocol. For 0.1 ml of Protein A, the A595 was 0.520. Using
the graph prepared in part (c) as your calibration curve, calculate the
[6 marks]
concentration (in mg.ml-1) of protein A.
(e) Assuming the relative molecular mass (Mr) of Protein A is 30,345, what is the
molar concentration of the sample analysed in part (d)? Give your answer in µM
to 2 decimal places.
[4 marks]
(f) A solution of Protein B at an unknown concentration was analysed using the
same Bradford assay protocol. For a mixture of 0.05 ml Protein B plus 0.05 ml of
water, the A595 was 1.195. Using the graph prepared in part (c) as your
calibration curve, calculate the concentration (in mg.ml-1) of Protein B. [4 marks]
(g) If the Bradford assay was performed on an undiluted sample of Protein B, would
the A595 measurement be higher or lower compared to that reported in part (f)?
Would the analysis of diluted or non-diluted Protein B provide a more accurate
measurement of the concentration of protein in the sample? Explain your
answer.
[4 marks]
END OF SECTION B
START YOUR ANSWER TO THE NEXT SECTION IN A NEW BOOKLET
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SECTION C: ESSAY QUESTION
Answer ONE question
[30 marks]
22.
The selective translocation of small metal ions across biological membranes is
achieved through the use of membrane proteins by either facilitated diffusion or
active transport. Describe, using one appropriate example of each mechanism, how
the selective membrane transport of sodium and potassium is achieved.
23.
Some metabolic pathways are fundamental to the growth and function of all cells.
For such central aspects of metabolism it is essential that specific molecules are
maintained at appropriate concentrations. By referring to specific types of
biomolecules that are fundamental to cell growth and function, discuss the strategies
that have evolved to allow regulation of metabolic pathways. Your answer should
include one example that highlights how a metabolic pathway is activated and one
example that highlights how a metabolic pathway is inhibited.
24.
What is the relevance of the equilibrium binding constant Kd to cell signalling initiated
by binding to cell surface receptors of ligands, such as growth factors or adrenaline?
Within your answer describe how binding of a named ligand mediates the response
of the cell.
END OF PAPER
BIO-5002A
Version 1
UNIVERSITY OF EAST ANGLIA
School of Biological Sciences
Main Series UG Examination 2015-2016
BIOCHEMISTRY
BIO-5002A
Registration Number
SECTON A:
Answer Grid (for Multiple Choice Questions only)
Place a single cross in the appropriate box
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