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Semester One 2011

Time allowed : THREE (3) hours.

Candidates are required to answer THREE (3) questions from SECTION A
(allow 45 minutes for this section)
and THREE (3) questions from SECTION B
(allow 2 hours and 15 minutes for this section).
Non-programmable calculators only are permitted.

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Candidates are required to answer
THREE (3) questions from THIS SECTION.
Allow FIFTEEN (15) minutes for each question.
All questions are of equal value.
This section is worth one quarter of the examination paper.

1. Briefly discuss the uses, advantages and disadvantages of the following

commonly-used protein fusion partners:
a) The hexahistidine (His6) tag
b) Maltose binding protein
c) Green fluorescent protein

(5 minutes)
(5 minutes)
(5 minutes)

2. Describe the properties of ribosomal DNA genes that make them appropriate for
species identification across a wide range of organisms, and why ribosomal DNA
genes have these properties.

3. You have a set of eight different human cancer cell line cultures. You want to
determine how gene expression changes in these cancer cells upon treatment
with an anti-cancer agent. Outline how you would use microarray technology to
answer this question (assuming that you have already made a microarray with all
human genes on it). Briefly discuss how the microarray signals would be

4. In one sub-discipline of synthetic biology, the aim is to assemble synthetic

components, and thereby to generate chemical systems with the properties of
living systems. Critically assess the progress towards this aim. In your answer,
consider recent experiments to expand the genetic code by using novel base
pairs, and by using four-base codons.

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Candidates are required to answer
THREE (3) questions from THIS SECTION.
Allow FORTY-FIVE (45) minutes for each question.
All questions are of equal value.
This section is worth three quarters of the examination paper.


Write an essay on the directed evolution of proteins. In your answer, outline the
key steps in one round of a directed evolution experiment. Describe some of the
methods that can be used to make randomized libraries. Discuss specific
examples in which these methods have been used to alter the properties of
proteins. What aims and/or hypotheses were these experiments addressing?

6. Choose one of the current next-generation sequencing technologies (454,

Illumina, or SOLiD) and describe in detail the process involved in determining
DNA sequences, using this technology. Starting with purified DNA, your answer
should include how to prepare this sample for sequencing, as well as the
sequencing chemistry and detection. Highlight the key differences between the
technology you have described and the other two next-generation sequencing


You are designing a new kit for cloning DNA fragments. One component of your
kit will be an alkaline phosphatase enzyme, which will be used to
dephosphorylate the cloning vector. You plan to identify a new phosphatase by
using a combination of metagenomics and phage display. You know that many
bacteria inhabit alkaline environments, and you hypothesize that these bacteria
may produce phosphatases that are suitable for commercialization.
a) Write a detailed research plan, describing your experiments to construct a
metagenomic library that is also compatible with phage display. Your plan
should include the source(s) of DNA for your metagenomic library, the
preparation of the DNA, and the cloning strategy (including the type of vector
that you will use).
(30 minutes)
b) How could you use phage display to identify active alkaline phosphatase
enzymes? Assuming that you isolate an active enzyme from your library,
what experiments would you conduct to characterize it?
(15 minutes)
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Describe the process of reconstructing and synthesizing an ancient gene. With

reference to specific examples, discuss the insight that protein resurrection is
offering into ancient palaeoenvironments, and into enzyme evolution.


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