Semester One Examinations, 2023 BIOT7018

Venue
Seat Number
Student Number | | | | | | | | |
Family Name
This exam paper must not be removed from the venue
First Name

School of Chemistry and Molecular Biosciences

Semester One Examinations, 2023
BIOT7018 Biologics
This paper is for St Lucia Campus students.

Examination Duration: 120 For Examiner Use Only

minutes Planning Time: 10 Question Mark

minutes Exam Conditions:

•This is a Closed Book examination - no written materials permitted

•No calculators permitted
•During Planning Time - Students are encouraged to review and plan
responses to the exam questions
•This examination paper will be released to the Library

Materials Permitted in the Exam Venue:

(No electronic aids are permitted e.g. laptops, phones)

None

Materials to be supplied to Students:

Additional exam materials (e.g. answer booklets, rough paper) will
be provided upon request.

1 x 14-Page Answer Booklet

Instructions to Students:
If you believe there is missing or incorrect information impacting
your ability to answer any question, please state this when writing
your answer.

Answer questions in the answer booklet provided.

Total

Page 1 of
13
Semester One Examinations, 2023 BIOT7018

THIS PAGE INTENTIONALLY LEFT BLANK

Page 2 of
13
Semester One Examinations, 2023 BIOT7018

Sarah and Angela just finished their Masters in Biotechnology at UQ. Sarah gets a job as a
consultant while Angela becomes a scientist in a Research and Development department.

Question 1 (10 marks)

Sarah is asked to consult for Parasol Corp, who are looking at developing a new treatment
for arthritis. Parasol Corp hopes to mimic the action of some approved biologic medicines
that are consistently best sellers.

a. The company has two candidate molecules (A and B). Help Sarah to classify them and
identify the IP consequences. (2 marks)

Candidate A Candidate B

Class? Originator Biologic

Molecular None Unintentional Unintentional

Differences? differences differences in
in glycosylation.
glycosylation Parasol designed
enhanced protein
binding domain from
A-virus
Patentable? Yes - expiring

b. Discuss the differences in regulatory approval between the two candidates.

(4 marks)

c. Clinically, would either candidate be considered interchangeable with the originator?

What are some of the challenges for follow on biologics to be considered
interchangeable?

(2 marks)

d. How would you advise Parasol Corp to price the two compounds relative to the
originator? Why?

(2 marks)
Questions continue over the page

Page 3 of
13
Semester One Examinations, 2023 BIOT7018

Question 2 (5 marks)

Angela is assigned to work with Amy to generate a report. Angela and Amy don’t know each
other well, and while Angela is very outgoing and opinionated, Amy is introverted and shy.
They both eagerly prepare for their first meeting and bring many ideas to their meeting.
During the meeting, Angela is very enthusiastic about her thoughts and makes plenty of
suggestions, while Amy has considerably less input and basically just nods along. Angela
thinks the meeting has gone really well. However, the next day Angela feels that Amy avoids
her. Angela tries to talk to Amy, but Amy does not make eye contact and does not reply.
Angela and Amy seem unable to move forward, while the deadline for submission of their
report approaches.

Focusing on Emotional Intelligence, explain what could have happened in this scenario.

Question 3 (10 marks)

Sarah is asked to consult for BestComp Ltd on a new project. BestComp has developed a
novel small molecule inhibitor of a cell surface receptor protein, G75F, called D1234. G75F
is expressed on tumour cells. The company is searching for a strategy to target D1234
specifically to protein G75F, in order to prevent off-target effects.

a. What antibody-based strategy can Sarah propose to BestComp and how would it work?
(1 mark)

b. There are no antibodies against G75F available. Sarah is tasked to design a strategy to
identify antibodies that bind G75F. G75F is a membrane protein with a large,
glycosylated extracellular domain. Sarah decides to use phage display to identify anti-
G75F antibodies. Describe the steps that you would take to successfully isolate
antibodies against G75F by phage display. (9 marks)

Questions continue over the page

Page 4 of
13
Semester One Examinations, 2023 BIOT7018

Question 4 (11 marks)

Angela needs to prepare an expression vector for the team project. Her supervisor gives her
the DNA sequence below and tells her to clone it in the vector below.

ATGGCACCCAAGCGATAA

a. Identify the parts of the vector a-e (which are common to any expression vector), and
indicate the function: (1 mark each, 5 marks
total)

Part a:

Part b:

Part c:

Part d:

Part e:

b. What amino acid does TAA encode? (2 marks)

c. Assuming that the intention is to express the protein in mammalian cells, using the
table below optimise the sequence accordingly. (2 marks)

M A P K R
ATG GCA GCC CCA CCC AAA AAG CGA CGT
E. coli 1.0 0.68 0.32 0.39 0.61 0.36 0.64 0.34 0.66
S. cerevisiae 1.0 0.40 0.60 0.79 0.21 0.20 0.80 0.69 0.31
C. griseus 1.0 0.65 0.35 0.42 0.58 0.88 0.12 0.24 0.76
K. lactis 1.0 0.55 0.45 0.30 0.70 0.28 0.72 0.84 0.16

Optimised DNA sequence:

d. Would the sequence provided lead to a N-linked glycosylated protein if it was

expressed in mammalian cells? (1 mark) Justify your answer. (1 mark)
Semester One Examinations, 2023 BIOT7018

Questions continue over the page

Semester One Examinations, 2023 BIOT7018

Question 5 (7 marks)

Angela’s supervisor provides her with the following sequence from a bacterial peptide and
tells her that she needs to express it in mammalian cells as a secreted peptide.

MAPKSTKCTGPNPTATSKNSTGKE*

a. Name at least 4 key steps Angela should take to obtain and engineer the DNA
sequence that will allow her to fulfil her supervisor’s request. Explain why each of these
steps is important. (4 marks, 1 mark per item)

b. Are there any potential issues with post-translational modifications in this peptide that
Angela should pay attention to? What would the issue(s) be? (3 marks)

Question 6 (5 marks)

Angela’s supervisor asks them to use a bacterial expression system to express a bacterial
protein that has a poly-His tag at the C-terminus. Describe a bioprocess that could separate
and purify the protein, considering the following parameters:

Protein Size 50 kDa, Poly His tag, pI 8.1, protein found in inclusion body.
Semester One Examinations, 2023 BIOT7018

Question 7 (20 marks)

Angela’s team is tasked to produce an scFv in yeast. The scFv binds the extracellular
domain of a cell surface receptor in B cells.
a. The scFv is secreted and is stable in the bulk phase (supernatant) for extended periods
of time. Describe a bioreactor configuration which is best suited to address a demand for
industrial-scale production of this scFv. Your response should include a mode of
operation, single use or reusable considerations, and justification for selection. (3 marks)

b. The company director is not happy with the current yield of the scFv and asks Angela’s
team to optimise the bioprocess. Name at least two different components or parameters
of the expression system and at least two components or parameters of the upstream
bioprocess you would optimise in order to achieve higher yields of the scFv. Explain how
you would optimise each of them, and why it is important to change each of those
components or parameters. (4 marks)

c. After much work, the team achieves a bioprocess generating industry standard product
titres (12 g/L). Now you are asked to find the “design space” for the process operation
parameters. What is the “design space” used for? What is the name of the approach that
focuses on the process “design space”? (3 marks)
Semester One Examinations, 2023 BIOT7018

d. Angela’s team is designing the purification strategy for the scFv. After homogenisation,
the target protein is suspended in a dense broth with a large quantity of very fine
particulate matter. What are the initial purification steps that need to be taken? The
target protein is 25 kDa in size. (5 marks)

e. Angela’s team is now tasked to design an assay to quantitatively measure the activity of
the scFv. What assay could they use? Describe the principles behind this assay.
(5 marks)
Questions continue over the page
Semester One Examinations, 2023 BIOT7018

Question 8 (6 marks)

Sarah’s company is approached by the World Health Organisation (WHO). There are signs
of an imminent outbreak of a previously unknown virus. The WHO is seeking advice in order
to make an effective vaccine.

a. What viral proteins would work as ideal targets for vaccine development and why?
(2 marks)

b. One of the WHO scientists wishes to develop an antibody therapy against the vaccine.
Would this antibody therapy be considered a vaccine? Justify your answer. (2 marks)

c. How do antibodies protect us against viruses? (2 marks)

Question 9 (4 marks)

Describe an example of a natural RNA structure that has been re-engineered into an RNA
device.
Semester One Examinations, 2023 BIOT7018

Question 10 (5 marks)

Nanomedicine design frequently includes attachment of biologic targeting ligands to

synthetic low fouling carriers with the goal of enhancing interaction with target cell
populations. While this is almost ubiquitously successful in vitro, this approach can often
result in undesired pharmacokinetics or pharmacodynamics when translated to in vivo
studies. Briefly discuss why this can be the case.

Question 11 (5 marks)

What factors determine the effectiveness of natural killer cells in combating cancer, and how
can we use this knowledge to develop better immunotherapies for cancer treatment?

Question 12 (5 marks)

One common adverse effect observed in immunotherapy is cytokine response syndrome.

Explain what this is, when is it commonly observed, and describe an approach to avoid
these adverse effects during immunotherapy research and development.
Semester One Examinations, 2023 BIOT7018

Question 13 (7 marks)

a. Describe the elements that compose the variable regions of a typical IgG antibody.
(3 marks)

b. What is the difference between a chimeric and a humanised antibody? Describe how
each of them are isolated or engineered. (2 marks each, 4 marks total)

END OF EXAMINATION