Download MEng BIOMEDICAL ENGINEERING SEMESTER TWO EXAMIN

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UNIVERSITY OF BOLTON
ENGINEERING, SPORTS AND SCIENCES
ACADEMIC GROUP
BEng (HONS)/MEng BIOMEDICAL ENGINEERING
SEMESTER TWO EXAMINATIONS 2014/15
FUNDAMENTALS OF SYSTEMS AND SYNTHETIC
BIOLOGY
MODULE NO: BME4006
Date: Wednesday 27 May 2015
INSTRUCTIONS TO CANDIDATES:
Time: 10.00 am - 1.00 pm
Candidates are advised that the
examiners
attach
importance
to
legibility of writing and clarity of
expression. YOU ARE STRONGLY
ADVISED TO PLAN YOUR ANSWERS
There are THREE sections.
Answer ALL questions from Section A
and Section B.
Answer ONE question from Section C.
Write all answers in answer booklet.
Marks for parts of questions are shown
in brackets.
This examination paper carries a total
of 100 marks.
All working must be shown.
A
numerical solution to a question
obtained by programming an electronic
calculator will not be accepted.
Page 2 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
SECTION A: Answer ALL questions in this section; 1 mark per question, 35
marks in total.
1. The insertion of a specific piece of ________ into a cell is known as gene cloning,
which is a naturally occurring process.
a. Bacteria
b. Plasmid vector
c. Foreign DNA
d. Any one of the above
1 mark
2. A ________ is an extra-chromosomal DNA molecule separate from the
chromosomal DNA and capable of autonomous replication.
a. Vector
b. Plasmid
c. Restriction enzyme
d. None of the above
1 mark
3. Ti plasmids are the most efficient plasmids used for transforming _______ and are
found in bacteria called Agrobacterium tumefaciens.
a. Mammalians cells
b. Yeast
c. Prokaryotes
d. Plant cells
1 mark
Please turn the page
Page 3 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
4. Insertion of a piece of DNA into a plasmid is possible only if both the circular
plasmid and the source of DNA have ________ for the same restriction enzymes.
a. Recognition sites
b. Sticky ends
c. DNA ligase
d. Endonuclease
1 mark
5. Type II class enzymes are the most commonly used for gene cloning. An example
of this enzyme is:
a. EcoRI
b. BamHI
c. HpaI
d. All of the above
1 mark
6. __________ is a mechanism evolved by bacteria to resist against invading
viruses.
a. Gene cloning
b. Restriction enzymes
c. Plasmids
d. None of the above
1 mark
7. The __________ travels along the DNA strand and assembles ribonucleotides
into a strand of RNA, according to the base pairing rule.
a. RNA polymerase
b. mRNA
c. Both a and b
d. Cloning vector
1 mark
Page 4 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
Please turn the page
8. The first step in the polymerase chain reaction (PCR) is:
a. Denaturation
b. Primer extension
c. Annealing
d. Cooling
1 mark
9. In the discovery of introns, a DNA molecule called _______________ was formed
that had the same nucleotide sequence as the gene that produced the mRNA.
a. mDNA
b. rDNA
c. sDNA
d. gDNA
e. cDNA
1 mark
10. With the completion of the human genome project, the next frontier is:
a. Nucleonics
b. Proteomics
c. Cytomics
d. Agronomics
1 mark
11. Viruses containing RNA rather than DNA are called:
a. Riboviruses
b. Immunoviruses
c. Bacteriophages
d. Rotaviruses
e. Retroviruses
1 mark
Page 5 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
Please turn the page
12. In a PCR, synthetic sequences of nucleotides are involved in:
a. Denaturing
b. Heating
c. Priming
d. Copying
e. All of the above
1 mark
13. Bacteria protect themselves from viruses by fragmenting viral DNA upon entry
with:
a. Ligases
b. Endonucleases
c. Methylases
d. Vectors
e. Probes
1 mark
14. To identify an individual by DNA analysis of their blood, investigators look for:
a. Primers
b. DNA fingerprints
c. Probes
d. Nucleosomes
e. Transgenic fragments
1 mark
Please turn the page
Page 6 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
15. Most restriction endonuclease enzymes cleave each strand of the double
stranded DNA at a specific restriction site, resulting in fragments that have overhanging ends -5’ and -3’, also called ________________.
a. Sticky ends
b. Blunt ends
c. Both a and b
d. None of the above
1 mark
16. When "sticky ends" are paired, they can be joined by:
a. Restriction enzymes
b. pSC101
c. Methylase
d. X-gal
e. DNA ligase
1 mark
17. A successful vector in genetic engineering has been the:
a. TMV plasmid
b. HLF virus
c. Vaccinia virus
d. Ti plasmid
e. Retrovirus
1 mark
Page 7 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
Please turn the page
18. A library of DNA fragments results from the use of:
a. Restriction endonucleases
b. Viruses
c. Plasmids
d. Recombinant DNA
e. DNA ligase
1 mark
19. Bacterial DNA is not cleaved by their own restriction enzymes because bacteria
add _______________ to their own DNA.
a. Nucleotides
b. Peptides
c. Methyl groups
d. Glyphosphate
e. Somototropin
1 mark
20. The piece of equipment that introduces DNA into cells via DNA-coated
microprojectiles is known as:
a. A laser
b. A DNA probe
c. A gene gun
d. An inoculating needle
1 mark
Please turn the page
Page 8 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
21. Genetic engineering has successfully transferred genes from eukaryotic cells
into:
a. Bacteria
b. Plants
c. Animals
d. All of the above
e. None of the above
1 mark
22. DNA molecules can be cut into sections by using:
a. ATP
b. Gel electrophoresis
c. Restriction endonucleases
d. Plasmids
e. A probe
1 mark
23. In genetic engineering, DNA ligase is used as:
a. A probe
b. A sealing enzyme
c. A restriction enzyme
d. A mutagen
e. None of the above
1 mark
Please turn the page
Page 9 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
24. Which of the following statements is true about developing cDNA?
a. Mature mRNA directs the formation of the DNA.
b. Mature mRNA does not contain introns.
c. DNA taken from the nucleus is used to produce the cDNA.
d. Both a and b are true.
e. None of the above are true.
1 mark
25. In the study of Science:
a. Deductive reasoning may be used, but inductive reasoning is preferred
b. Inductive reasoning may be used, but deductive reasoning is preferred
c. Only inductive reasoning is used
d. Either deductive reasoning, inductive reasoning, or both may be used
1 mark
26. A successful scientific experiment will result only in:
a. Rejection of one or more hypotheses
b. Proving a hypothesis
c. Accepting many hypotheses
d. Confirming predictions
1 mark
27. The "scientific method" involves all of the following except:
a. Imagination and insight
b. An educated guess
c. A rigid set of logical steps
d. A suspicion of what the truth might be
1 mark
Page 10 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
Please turn the page
28. Genetically identical organisms derived from a single genetic source are called:
a. Populations
b. Varieties
c. Sibling species
d. Ecotypes
e. Clones
1 mark
29. In order for a gene to be transcribed, RNA polymerase must have access to the
DNA helix and be able to bind to the gene’s:
a. Activator
b. Regulator
c. Promoter
d. Operator
e. Repressor
1 mark
30. A tobacco plant can be made to express a gene from fireflies, resulting in the
emission of light. Which of the following is the basis for this phenomenon?
a. Chloroplasts can be made to produce light if firefly proteins are injected into
plant cells.
b. Fireflies and tobacco plants share a recent common ancestor.
c. Fireflies and tobacco plants are infected by the same kinds of bacteria.
d. Transcription and translation are fundamentally similar in both fireflies and
tobacco plants.
e. Most enzymes in fireflies have the same amino acid sequence as the
enzymes in tobacco plants.
1 mark
Page 11 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
Please turn the page
31. The enzyme that is found in retroviruses and that is required for the synthesis of
DNA from RNA is:
a. DNA polymerase III
b. RNA polymerase
c. Restriction endonuclease
d. Reverse transcriptase
e. Dehydrogenase
1 mark
32. In gel electrophoresis, the rate of migration of the DNA fragments through the
agarose gel is determined by the:
a. Ratio of adenine to cytosine in the fragment
b. Presence of hydrogen bonds between base pairs
c. Length of time the electrophoresis unit is allowed to operate
d. Number of nucleotides in the fragment
e. Volume of the starting sample
1 mark
33. Which of the following is true of the dye used to stain the fragments in gel
electrophoresis?
a. It increases the contrast between the agar and the DNA fragments.
b. It must be accounted for when calculating the molecular weight of the
fragments.
c. Its charged areas interfere with the migration of the DNA.
d. It is bonded only to the sticky ends of the fragments and can directly
determine the sequence of the DNA fragments.
e. It gives a three-dimensional view of the structure of the DNA fragments.
1 mark
Page 12 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
Please turn the page
34. In gel electrophoresis, the type and density of the gel are important because:
a. They influence the rate of migration of the fragments
b. They may cause some DNA molecules to replicate
c. Some DNA nucleotides may be lost due to chemical reactions with the gel
d. Some DNA molecules may sink to the bottom and not migrate
e. Some DNA molecules may cross-link
1 mark
35. Systems biology is an approach by which biological questions are addressed
through integrating data collection activities with ________________ activities to
produce a better understanding of biological systems.
a. Computational modelling
b. Molecular genetic
c. Mathematical modelling
d. Computational and mathematical modelling
1 mark
Total 35 marks
Please turn the page
Page 13 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
SECTION B: Answer ALL questions in this section; 5 marks per question, 35
marks in total.
1. Two Matlab arrays are defined as:
P = [6,3,5,73]
Q = [5,3,2,45,3,5,2]
Choose from the following options (you may use each more than once):
a) 30, b) 5, c) 25, d) 10, e) error
to determine the results of:
(i)
(ii)
(iii)
(iv)
(v)
P(2) + Q(3)
P(3) * Q(6)
P(6) - Q(3)
Q(7) * P(3)
Q(3) + P(2)
5 marks
2. Quantity Q is modelled as a function of time T:
Q = J*T2 + T/K + L2*T
where J, K and L are constant and specific to the system.
Choose from the following options (you may use each more than once):
a) parameter, b) initial condition, c) independent variable, d) dependent variable,
e) boundary condition to classify:
(i)
(ii)
(iii)
(iv)
(v)
Q
T
J
K
L
5 marks
Page 14 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
Please turn the page
3. In Matlab, quantity A is calculated from the following code:
A = 0;
for k = 1:5
A = A + 2*k;
end
What is the value of A at the end of each iteration of the loop?
5 marks
4. Name the following steps in the modelling process:
a.
Results are calculated using a computer program.
b.
Parameter values are obtained using data from practical experiments.
c.
The conceptual model is compared against the model requirements to
ensure it does what it is supposed to.
d.
Model results are compared against equivalent experimental results.
e.
Parameters are identified which affect the variables in the system.
5 marks
5. Draw a network diagram for the following model, with labels on the arrows to
identify the parameters:
dA/dt = f - g*A + h*C
dB/dt = g*A - i*B
dC/dt = h*C + i*B – j*C
5 marks
Page 15 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
Please turn the page
6. Variable V changes with time t as:
dV/dt = a/V+b
where a = 2, b = 3, and V = 1 at t = 0.
Use Euler’s method [V(t+dt) = V(t) + dV] with a time step of 0.5 to calculate V at t =
0.5 and
t = 1.
5 marks
7. Describe what is meant by the term ‘emergent behaviour’ and provide a biological
example.
5 marks
Total 35 marks
Please turn the page
Page 16 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
SECTION C: Answer ONE question only; 30 marks.
1.
a. Do the advances in synthetic biology really represent the creation of new
life?
Please explain.
(15 marks)
b. Can the synthetic cell reproduce? If so, are its daughter cells viable?
(15 marks)
Total 30 marks
OR
2.
a. How is genetic engineering used to create bacteria capable of producing
human insulin?
(15 marks)
b. What are the main techniques of genetic engineering currently used in
biotechnology?
(15 marks)
Total 30 marks
OR
3.
a. Does the discovery of synthetic biology challenge religious notions about
the creation of life and the concept of a spirit? Please explain.
(15 marks)
b. Synthetic biology: what are the environmental and social impacts?
(15 marks)
Total 30 marks
Page 17 of 17
Engineering, Sports and Sciences Academic Group
BEng (Hons)/MEng Biomedical Engineering
Semester Two Examinations 2014/2015
Fundamentals of Systems and Synthetic Biology
Module No. BME4006
END OF QUESTIONS