[ess47] university of bolton school of engineering beng ...€¦ · beng (hons)/ meng biomedical...

[ESS47]

UNIVERSITY OF BOLTON

SCHOOL OF ENGINEERING

BEng (HONS)/MEng BIOMEDICAL ENGINEERING

SEMESTER TWO EXAMINATION 2017/18

FUNDAMENTALS OF SYSTEMS AND SYNTHETIC

BIOLOGY

MODULE NO: BME5009

Date: Thursday 24th May 2018 Time: 14:00 – 17:00 INSTRUCTIONS TO CANDIDATES: 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.

of 15 School of Engineering BEng (Hons)/ MEng Biomedical Engineering Semester Two Examination 2017/18 Fundamentals of Systems and Synthetic Biology Module No BME5009

SECTION A: Answer ALL questions in this section; 1 mark per question, 35 marks in total.

1. Systems biology can be defined as: a. The systematic study of organisms using a set of established guidelines b. The detailed study of the components of biochemical pathways, such as

receptor proteins, using simulation methods, such as molecular dynamics c. The combined study of biological systems integrating experimental and

computational methods and focussing on the interactions between components

d. The thorough study of the dynamics of the glycolysis pathway [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. Antibody

[1 mark]

3. The CRISPR-Cas9 system in bacteria is akin to our body’s ________.

a. Digestive system b. Immune system c. Circulatory system d. Respiratory system

[1 mark]

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 ligases d. Endonucleases

[1 mark]

Section A continues over the page….

PLEASE TURN THE PAGE….


Section A continued….

5. Bacterial cells are prokaryotic. Unlike a typical eukaryotic cell they ______. a. Have no membrane-bounded organelles in their cytoplasm b. Lack a plasma membrane c. Have a smaller nucleus d. Have no ribosomes e. Lack chromosomes

[1 mark]

6. __________ is a mechanism evolved by bacteria to resist against invading viruses.

a. Gene cloning b. A restriction enzyme c. A plasmid d. None of the above

[1 mark]

7. Bacteria are the "workhorses" of genetic engineering because they ________.

a. Are always homozygous b. Provide the polymerase for the polymerase chain reaction c. Reproduce very slowly and accurately d. Can readily take up plasmids containing human genes and then produce

the human proteins encoded by those genes [1 mark]

8. The first step in the polymerase chain reaction (PCR) is: a. Denaturation b. Primer extension c. Annealing d. Cooling

[1 mark]





9. The physicist Lord Kelvin (1824 – 1907), said: a. If I succeed in making a statistical model of the subject, I am studying then

it helps me to ask more questions b. If I succeed in making a mechanical model of the subject, I am studying

then I understand c. If I succeed in making a statistical model of the subject, I am studying then I

proceed with caution d. If I succeed in making a mechanical model of the subject, I am studying

then I would be believe it to be only an approximation to reality [1 mark]

10. Albert Einstein (1879 – 1955) said:

a. The supreme goal of all theory is maximise the number of irreducible basic elements without having to surrender the adequate representation of a single datum of experience

b. The supreme goal of all theory is to make the irreducible basic elements as simple and as few as possible because building a perfect model is impossible

c. The supreme goal of all theory is to make the irreducible basic elements as simple and as few as possible without having to surrender the adequate representation of a single datum of experience

d. The supreme goal of all theory is to make the irreducible basic elements as simple but as many as possible in order to ensure the adequate representation of experience

[1 mark]

11. Viruses containing RNA rather than DNA are called: a. Riboviruses b. Immunoviruses c. Bacteriophages d. Rotaviruses e. Retroviruses

[1 mark]





12. Complete this sentence: A dynamic discrete model could best be used to describe ________ .

a. The growth of a human baby b. A catastrophe c. Population change d. Why older people are more likely to become ill

[1 mark]

13. What do we mean by the term “minimal bacterial cell”? a. A bacterial cell that contains less than 5,000 genes. b. A bacterial cell that contains less than 20 chromosomes c. A bacterial cell that contains only the genes that are necessary and

sufficient to ensure continuous growth under ideal laboratory conditions. d. A bacterial cell that contains genes the size of which is less than 1,000

base pairs [1 mark]

14. Which of the following proteins have not been used in genome editing? a. ZFN b. TALENs c. CRISPR-Cas9 d. Meganucleases e. MHC

[1 mark]

15. Gene cloning refers to the: a. Production of large number of copies of the same gene being cloned b. Production of asexual progeny from a single individual or a cell c. Both a and b d. None of these

[1 mark]





16. What is the functional connection between the nucleolus, nuclear pores, and the nuclear envelope?

a. The nucleolus contains messenger RNA (mRNA), which crosses the nuclear envelope through the nuclear pores

b. Subunits of ribosomes are assembled in the nucleolus and pass through the nuclear membrane via the nuclear pores

c. The nuclear pores are connections between the nuclear membrane and the endoplasmic reticulum that permit ribosomes to assemble on the surface of the ER

d. Endoplasmic reticulum membrane is produced in the nucleolus and leaves the nucleus through the nuclear pores

e. None of the listed responses are correct [1 mark]

17. The CRISPR sequences are recognized by: a. Zinc finger domains b. TALE repeats c. Guide RNA d. Leucine zippers e. Retrovirus

[1 mark]

18. A library of DNA fragments results from the use of: a. Restriction endonucleases b. Viruses c. Plasmids d. Recombinant DNA e. DNA ligases

[1 mark]




Section A continued…. 19. Bacterial DNA is not cleaved by the bacteria’s own restriction enzymes because

they add _______________ to their own DNA. a. Nucleotides b. Peptides c. Methyl groups d. Glyphosphate e. Somototropin

[1 mark]

20. “CRISPR” is an acronym for what phrase? a. Chromatin Regularly Interspaced Short Palindromic Repeat b. Clustered Regularly Interspaced Short Palindromic Repeat c. Clustered Regularly Interspaced Short Palindromic Ribosome d. Cellular Regularly Interspaced Short Palindromic Repeat

[1 mark] 21. A nucleotide is made up of which of the following chemical components?

a. A nitrogenous base, a fatty acid, and an amino acid b. A nitrogenous base, an amino acid, and a phosphate group c. A series of nitrogenous bases, a nucleic acid backbone, and a hexose sugar d. A nitrogenous base, an amino acid, and a pentose sugar e. A nitrogenous base, a phosphate group, and a pentose sugar

[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]

24. What is Cas9 and what does it do? a. An RNA molecule that binds to target DNA via complementary base pairing b. A DNA sequence that binds the Cas9 protein c. A viral protein that disrupts bacterial membranes d. A protein enzyme that cuts both strands of DNA at sites specified by an

RNA guide [1 mark]

25. Which of the following describes a difference between DNA and RNA? a. RNA molecules consist of a single polynucleotide chain, whereas DNA

molecules consist of two polynucleotide chains organised into a double helix

b. One of their nitrogenous bases is different c. They contain different sugars d. The first and second listed responses are correct differences e. The first three listed responses all describe differences

[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] 28. What is meant by synthetic biology?

a. The synthesis of naturally occurring compounds. b. The genetic modification of microbial cells such that they produce

compounds that they would not normally produce. c. The study of how naturally occurring compounds are biosynthesised in cells d. The design and synthesis of enzymes capable of carrying out a specific

reaction in organic synthesis [1 mark]

29. Why is gene inactivation a useful technique to determine the function of a gene?

a. Gene inactivation provides information about the expression of a gene b. Gene inactivation provides information about the cellular location of a gene

product c. Gene inactivation provides information on the structure of the gene

product d. Gene inactivation provides an opportunity to identify phenotypic changes

associated with the loss of the functional gene [1 mark]

30. Which of the following is an example of RNA editing?

a. Degradation of an RNA molecule by nucleases b. Alteration of the nucleotide sequence of an RNA molecule c. Removal of introns from an RNA transcript d. Capping of the 5’ end of an RNA transcript

[1 mark]




Section A continued…. 31. Which of the following is not a possible outcome following DNA cleavage by

Cas9? a. Disruption of a gene b. Repair of a gene c. Deletion of a chromosome d. Disruption of more than one gene

[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]

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]

Section A continued over the page….



Section A continued…. 35. Taq polymerase is used in PCR because of its:

a. Low thermal stability b. High fidelity c. High speed d. High thermal stability

[1 mark]

Total 35 marks

END OF SECTION A



SECTION B: Answer ALL questions in this section; 5 marks per question, 35 marks in total.

1. Find the values of the variable TOTAL at the end of each iteration of the nested loops:

TOTAL = 0 For i = 1:2 For j = 1:2 For k = 1:3

TOTAL = TOTAL + i*j*k End End End

[5 marks]

2. Write ‘true’ or ‘false’ against each of these statements about the movement of

a blood vessel in a vein:- a. Its velocity can be negative b. Its acceleration can change over time c. Its acceleration can be negative d. Its velocity is always zero or positive e. Its acceleration is always zero or positive

[5 marks]

3. Write ‘true’ or ‘false’ against each of these statements about statistical modelling:

a. It is impossible to solve a set 3 equations in 4 unknowns b. Once assumptions about the biology are made often the statistical

models becomes simpler c. Biologists are not interested in variance d. The only type of models used in biology are probabilistic e. It is impossible to solve a set 4 equations in 3 unknowns

[5 marks]

Section B continues over the page….



Section B continued….

4. Construct a static mathematical model of the Loxodonta africana (African bush elephant) illustrated below, and use your model to estimate its volume, stating clearly all assumptions you have made.

[5 marks]

5. Given X = [3, 5, 4, 6, 8, 11, 5], Y = [2, 4, 3, 5, 7, 10, 4], �̅� = 6, �̅� = 5 and n =

7; write a Matlab code to calculate the covariance between X and Y:-

Cov (X, Y) = 1

7 ∑(𝑋 − �̅�) (Y - �̅�).

[5 marks]

Section B continues over the page….



Section B continued….

6. Crop yield (Y) over time (t) is modelled by:

Y = a + b 𝑒𝑐𝑡 where a, b and c are constants.

Interpret each of the following results:-

a. a > 0 and b = c = 0 b. a > 0, b = 1 and c < 0 c. a > 0, b = 1 and c > 0

d. a > 0, b = 1 and 𝑒𝑐𝑡= kt where k>0 e. a > 0, b = 1 and 𝑒𝑐𝑡= kt where k<0

[5 marks]

7. Give a brief (10 – 15 word) description of an application to a systems biological problem of each of the five mathematical models listed below: a. Time series b. Probabilistic c. Linear d. Non-linear e. Explanatory

[5 marks]

Total 35 marks

END OF SECTION B



SECTION C: Answer ONE question only; 30 marks.

1. Targeted genome editing using artificial nucleases has the potential to

accelerate biomedicine. Describe the CRISPR/CRISPR-associated protein 9 (Cas9) system by highlighting the strengths and weaknesses of this technology, and discuss possible biomedical applications.

[30 marks]

2. 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. What is the difference between genome editing and genetic modification? Please explain.

[15 marks]

Total 30 marks

3. Identify one biological question that could be addressed by using a mathematical model or statistical technique. a. Write a brief introduction to the topic area, then b. State clearly the problem or question of interest, and c. Describe the mathematical or statistical methodology you would propose. d. Finally, explain how your results may relate to your original question and

contribute to our further understanding, and then e. Critically discuss your work.

[30 marks]

END OF QUESTIONS

[ess47] university of bolton school of engineering beng ...€¦ · beng (hons)/ meng biomedical...

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