Download BIO-6001A - MOLECULAR ENZYMOLOGY IN BIOLOGY AND

UNIVERSITY OF EAST ANGLIA
School of Biological Sciences
Main Series UG Examination 2015-2016
MOLECULAR ENZYMOLOGY IN BIOLOGY AND MEDICINE
BIO-6001A/ BIO-3C01
Time allowed: 3 hours
Answer ALL questions in Section A and ONE question from Section B.
Write answers to EACH SECTION in a SEPARATE booklet.
The maximum number of marks available for your answers in SECTION A is 50 marks
The maximum number of marks available for your answer in SECTION B is 50 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-6001A/ BIO-3C01
Copyright of the University of East Anglia
Module Contact: Dr Andrew Hemmings, BIO
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SECTION A: SHORT ANSWER QUESTIONS
Answer ALL questions
1.
How should the terms (i) R-factor and (ii) resolution be interpreted when used to
describe the X-ray crystal structure of an enzyme?
[5 marks]
2.
Discuss briefly four considerations important in the rational design of inhibitors of a
specific protease based on the sequence of its known peptide substrate. [4 marks]
3.
You have a plasmid which has been generated for heterologous overexpression of a
gene for an enzyme of interest, in Escherichia coli. State the steps involved in a
method to introduce a single amino acid substitution in the enzyme active site.
[5 marks]
4.
Thrombin cleaves the tri-peptide substrate Gly-Val-Arg-pNA (corresponding to the
cleavage sequence of its natural substrate, fibrinogen) very poorly. However, it
cleaves the substrate Phe-Pro-Arg-pNA very efficiently. How do you account for this
apparent discrepancy?
[3 marks]
5.
Some protein inhibitors of serine proteases are proteolytically cleaved by the
enzyme, but others are not. Give three reasons that help to account for this
difference.
[3 marks]
6.
Many serine proteases are modular proteins. Give two examples of the functional
roles that the non-catalytic domains of these enzymes can play.
[4 marks]
7.
What are the two molecules that are commonly used as co-factors during the
reactions catalysed by nucleic acid ligases? What is the chemical group contained
within both molecules?
[3 marks]
8.
Briefly describe three important features of assays that have been most widely used
to detect the biochemical activity of enzymes that break or join phosphodiester bonds
in the backbone of DNA.
[3 marks]
9.
What features of DNA topoisomerases make them good targets for
chemotherapeutic agents? Give one example of an antibiotic and one of an anticancer agent that targets a topoisomerase, in each case stating which enzyme they
target.
[5 marks]
Section A continues on next page/ . . .
BIO-6001A/ BIO-3C01
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Section A continued. . .
10.
Type I DNA topoisomerases are sub-divided into two main sub-types. What are the
principle mechanistic differences between these two sub-types?
[4 marks]
11.
Name four different oxygen species that aerobic cells can be exposed to. [4 marks]
12.
Describe the three metal cofactors required by nitrogenase for nitrogen fixation.
[3 marks]
13.
While studying the kinetics of oxidation of substrates X and Y catalysed by
Cytochrome P450 3A5 you generate the following graphs. Explain what could be
happening in each case.
[4 marks]
Substrate Y
Substrate X
80
70
50
Ac vity
Ac vity
60
40
30
20
10
0
0
100
200
300
18
16
14
12
10
8
6
4
2
0
0
100
200
300
[Y] mM
[X] mM
END OF SECTION A
START YOUR ANSWER TO THE NEXT SECTION IN A NEW BOOKLET
Section B begins on next page/ . . .
TURN OVER
BIO-6001A/ BIO-3C01
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SECTION B: ESSAY QUESTION
Answer ONE question
[50 marks]
14.
Explain the strategies commonly employed by enzymes to accelerate the rates of
biochemical reactions. Illustrate your answer by reference to relevant examples.
15.
Using your knowledge of the catalytic mechanism of serine proteases, and the key
features that contribute to it, explain how the activity of these enzymes is regulated
biologically and how it can be manipulated therapeutically.
16.
DNA helicases and DNA topoisomerases perform key roles in DNA replication.
Explain what these roles are and how these enzymes carry them out. What is the
role of ATP in the reactions of helicases and topoisomerases?
END OF PAPER
BIO-6001A/ BIO-3C01
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