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Examination Candidate Number: _____________
Desk Number: _____________
University of York
Department of Biology
B. Sc Stage 2 Degree Examinations 2015 16
Cell Biology Time allowed: 1 hour and 30 minutes Total marks available for this paper: 80
This paper has three parts:
Section A: Short answer questions (30 marks) ● Answer all questions in the spaces provided on the examination paper
Section B: Problem questions (20 marks) ● Answer all questions in the spaces provided on the examination paper
Section C: Long answer question (marked out of 100, weighted 30 marks) ● Answer one of questions A or B or C or D ● Write your answer on the separate paper provided and attach it to the back of the question paper using the treasury tag provided
● The marks available for each question are indicated on the paper ● A calculator will be provided ● Candidates should ensure they have a ruler
For marker use only: 1 2 3 4 5 6 7 8 9 10
For office use only: Total as %
SECTION A: Short answer questions
Answer all questions in the spaces provided
Mark total for this section: 30
- a) What are the names of the subunits from which microfilaments and microtubules are assembled? (2 marks)
Gactin (1) alpha/beta tubulin dimers (1)
This was generally answered well.
b) How do these subunits differ from each other? (2 marks)
monomers v. dimers (1) Bind and hydrolyse ATP vs GTP (1)
This was also answered well, some answers discussed differences in the structures (marks were awarded), and some included differences between alpha and beta tubulins (in their GTP binding/hydrolysis) (marks were also awarded for this). Some answers outlined differences in the mechanisms by which the subunits assemble into their higher order structures (partial marks were awarded in such instances).
- Why do some transport vesicles carry both myosin and dynein? (1 mark)
To travel along both microfilament and microtubule tracks (1)
Some confusion between dynein (motor protein for transport along microtublues) and dynamin (GTPase involved in endocytosis) was evident, but apart from that this question was answered well marks were also awarded for answering that carrying both these motor proteins would allow a vesicle to move in both anterograde (along microfilaments) and retrograde (towards the microtubule organising centre) transport.
cells (1) ii) Fas/FasL recognition results in death receptor signalling procaspase 8 activation (DISC) (1) iii) leading to other caspase (3/7) activation (1). iv) Also Bid is cleaved to tBId which releases cytc from mitochondria and cas9 activation (1). v) All leading to apoptosis of viral infected cell (1).
- Give one example of each of the following:
i) cellcell junctions (1 mark)
tight junctions, adherens junctions, or desmosomes
ii) cellmatrix junctions (1 mark)
hemidesmosomes, focal adhesions
iii) communication junctions (1 mark)
gap junctions, synapses
Generally answered well, although some answers simply outlined where these junctions would be found. Also, some confusion between junctions and individual molecules (e.g. integrins) that facilitate cell adhesion.
- Describe four functions of proteoglycans. (4 marks)
i)
ii)
iii)
iv)
Four from: ● Structural/mechanical support (e.g. perlecan in basement membrane) ● Modify tissue hydration (e.g. aggrecan in cartilage) ● Withstand compressive force (e.g. aggrecan in cartilage). ● Regulate collagen fibril formation (e.g. decorin).
● Control signalling molecules (e.g. syndecan and FGF). ● Regulate cellcell and cellmatrix adhesion (e.g. hyaluronan and CD44).
Several very good answers, but needed to be specific (e.g. more than just “ECM”) and not overlapping/too similar to other functions. Some confusion with glycoproteins.
b) What would you expect if the experiments above were repeated with the addition of a minusend capping protein to each tube? (3 marks)
Concentration of Gactin in reaction tube
Expected change in filament length of added Factin
0.05μM Decrease (1)
1.50μM Increase (1)
0.65μM Increase (1)
Again generally answered well
c) Why was it necessary to include ATP in these experiments? (1 mark)
ATP binding is required for structural integrity of Gactin (1)
Most answers recognised that the ATPase activity of Factin is important for the phenomenom of treadmilling and/or that ATPactin has a higher affinity for neighbouring subunits than ADP actin also that ADP had to be exchanged for ATP following depolymerisation. Partial marks were awarded for these as appropriate, but good answers recognsied that ATP is required for the proper folding of Gactin (i.e. that which was in the tube prior to the addition of the Factin filament).
- Synaptic vesicles secrete their contents into the synaptic cleft by fusing with the plasma membrane of the presynaptic terminal. The number of vesicles that fuse with the presynaptic membrane can be visualised by electron microscopy whilst measuring neurotransmitter ‘quanta’ release. The strength of the neurotransmitter release can be regulated using a drug, 4aminopyridine (4AP).
Data from these type of experiments are shown in the table below.
Concentration of 4AP (M)
Average quanta measured
Number of fused vesicles observed by electron microscopy
0 180 130
105 700 800
104 1900 2100
103 4600 5300
a) Plot a graph of the number of vesicles fusing against the number of quanta released and add a line of best fit to the graph. (4 marks)
Still 2,100. (1mark) NEM would subsequently inhibit further rounds of fusion (1 mark) but not stop the first round since NEM would inhibit NSF and prevent SNARE recycling (1 mark). This was not answered correctly by most students. Credit given for recognising what NEM does but most students failed to recognise that NEM does not inhibit fusion per se but recycling so there would be one round of fusion before inhibition.
SECTION C: Long answer question
Answer one question on the separate paper provided
Remember to write your candidate number at the top of the page and indicate whether you have answered question A or B or C or D
Mark total for this section: 30
A) How, and why, is energy used to modulate proteinprotein interactions within a striated muscle cell?
Answers will outline the sliding filament model of muscle contraction where successive rounds of ATP binding, hydrolysis and product release drive repeated cycles of interaction between myosin heads and actin. Organisation of a muscle cell into sarcomeres should be described as should the thick and thin filament organisation of a sarcomere; indicating actin (thin) filaments anchored to zdisc interspersed with mysoin thick filaments. Answers should then detail the following steps of the cycle starting with myosin (in the absence of ATP) tightly bound to actin.
- ATP binding causes a conformational change in myosin which disrupts the actin binding site and dissociates the myosinactin complex.
- Hydrolysis of ATP then induces a further conformational change in myosin this restores the actin binding site and also pivots the head region back so that binding is to a region of the actin filament further back (towards the + end) than before. N.B. at the stage the hydrolysis products are trapped.
- Rebinding of the myosin head to the actin filament causes release of ADP and P i and triggers the “power stroke,” as the myosin head returns to its initial conformation, thereby sliding the actin filaments towards each other and contracting the sarcomere.
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C) Describe how posttranslational protein modifications, covalent and/or structural modifications, can regulate protein degradation?
Proteins can be modified covalently by phosphorylation, ubiquitination, sumoylation and glycosylation (hydroxylation and methylation weren’t covered).
Unfolded protein response (UPR) : The ERmembranebound chaperone protein calnexin binds to incompletely folded proteins containing one terminal glucose on Nlinked oligosaccharides, trapping the protein in the ER. Removal of the terminal glucose by a glucosidase releases the protein from calnexin. A glucosyl transferase is the crucial enzyme that determines whether the protein is folded properly or not: if the protein is still incompletely folded, the enzyme transfers a new glucose from UDPglucose to the Nlinked oligosaccharide, renewing the protein's affinity for calnexin and retaining it in the ER. The cycle repeats until the protein has folded completely. Calreticulin functions similarly, except that it is a soluble ER resident protein. Another ER chaperone, ERp57, collaborates with calnexin and calreticulin in retaining an incompletely folded protein in the ER. Misfolded soluble proteins in the ER lumen are translocated back into the cytosol, where they are deglycosylated, ubiquitylated, and degraded in proteasomes.
Ubiquitination : Proteins can be ubiquitinated (E1, E2 and E3 enzymes). Ubiquitination can lead soluble proteins being targeted to the proteosome for degradation (includes proteins from the UPR). Should mention proteosome cap proteins that bind ubiquitin. RPN10 and RPN13. Membrane bound proteins can be ubiquitinated (see receptor activation). Receptors can bind ligands giving conformational changes leading to phosphorylation. Phosphorylation can lead to receptor internalisation by endocytosis examples EGFR, the internalised receptor can be ubiquitinated which leads to binding of ESCRT complexes (ESCRT0, I, II and III) the formation of multivesicular bodies and then delivery of the endosome to the lysosome for degradation. Ubiquitinated proteins are also targeted to p62 and the autophagosome for degradation by macroautophagy via the lysosome.
Protein cleavage : Lots of scope here but the obvious choice would be programmed cell death. Death receptors and caspase activation leading to activation of other caspases and cleavage of Bid to tBid leading to cytochrome c release, caspase 9 activation and subsequently apoptosis via cell cytoskeleton and DNA cleavage. Removal of growth factors leads to dephosphorylation of Bad , cyt c release, caspase activation etc. All this forms apoptotic bodies that are phagocytosed and degraded by the lysosome.
Sumoylation: Briefly mentioned in that it can affect protein stability. There were some very good answers here. But most students talked about ubiquitination in only one aspect ie sending to proteosome without talking about ubiquitination and sending to the lysosome. Other covalent modifications, particulalry structural were rarely mentioned.
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