psl350h-m15 - Student Number Name Date of Exam Place of...

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Unformatted text preview: Student Number: Name: Date of Exam: Place of Exam: UNIVERSITY OF TORONTO Faculty of Arts and Science w AP Kl L. Final Examination 2015 Duration: 3 hours No aids allowed. Section 1: 22 multiple choice questions (44 marks) Section 2: 4 short answer questions for the whole class (46 marks) Section 3: 1 short answer question for each subgroup (10 marks) There are 11 pages. Print your name and student number on each page. Invigilators are not permitted to interpret questions to individual students. If you think that a question is ambiguous, answer it as you understand it, then make a note on your question book. If you do so, print your name and indicate the question number on this page. Name: Student number: Section 1. Multiple choice Questions (2 marks each ). Circle the correct and only answer for 91-10 based on Dr. Monnier’s lectures and 911-22 based on Dr. Gramolini’s lectures Q1: If a guidance protein is inhibitory for one type of axons: This protein will be: (A) inhibitory for all type of axons (B) inhibitory only for the axons that have the right receptor (C) never attractive (D) both A and C (E) both A and B Q2: The Rho family of GTPases is: (A) Activated by RhoGEFs (B) Directly activated by a transmembrane receptor (C) Activated by RhoGAPs (D) Activated by ROCK (E) Inhibited by RhoGDIs Q3: A protein that has been modified by a translational modification may appear: (A) The same size as the unmodified protein in Western Blot analysis (B) Larger than the unmodified protein in Western Blot analysis (C) Smaller than the unmodified protein in Western Blot analysis (D) All the above (E) Both A and C Q4: Why are CNS-axons not regenerating following injuries? (A) Because the cells present in the injured CNS are not the same as the one present in the developing CNS (B) Because the injured CNS expresses proteins that inhibit outgrth (C) Because of the lack of growth promoting proteins (D) A and B Q5: Name four inhibitory guidance proteins: (A) (B) (C) (D) Q6: To achieve very precise targeting within the developing CNS, an axon will rely on: (A)A precise space-temporal expression of receptors on their growth cone (B) A precise space-temporal expression of ligands on their growth cone (C) both A and B (D) A precise space-temporal expression of receptors in the growth cone environment (E) A precise space—temporal expression of ligands in the growth cone environment (F) both A and E Name: Student number: Q7: How does the nervous system achieve very precise patterning during development? (A) By providing a multitude of proteins that will react to specific receptor (B) By assigning only one specific function to each protein (e.g. only inhibition or only attraction) (C) By modifying the effect of one protein using posttranslational modifications (D)A and C (E) B and C Q8: To go to the cell surface a protein needs: (A) A signal peptide (B) A transmembrane domain (C) Some glycosylation (D) Both A and B (E) both B and C Q9: What is/are the modification/s that can be linked to the core protein via the —O- on the amino acid Serine: (A) Glycosylation (B) GPl-anchor (C) Phosphorylation (D) Both A and B (E) Both A and C Q10: Slit is an inhibitory guidance molecule for retinal axons. In some cases it is not repulsive on these axons. In which case/s? (A) When Slit is cleaved by a protease. (B) When Robo (the slit receptor) is not expressed by these axons? (C) When the molecular environment has been modified? (D) both A and B (E) A, B and, C Name: Student number: Q11: On a forward phase protein array, what is immobilized on the chip/substrate? (A) Antigen/analytes (B) Antibody (C) Fluorochrome (D) Peptides Q12: Trafficking of a mitochondrial protein requires which motif or modification? (A) Mannose—6-phosphate (B) di-RR targeting motif (C) KDEL targeting motif (D) Matrix targeting sequence Q13: Peroxisome proteins are produced through which mechanism? (A) ER-bound polyribosomes (B) Free polyribosomes (C) Mitochondrial bound polyribosomes (D) Nuclear associated polyribosomes Q14: Mitochondrial protein insertion into the mitochondrial membrane requires which protein interaction? (A) Binding with HSP70 (B) Binding with Tom40 (C) Binding with Translocon (D) Binding with Calreticulin Q15: Lysosomal protein targeting does NOT require which of the following? (A) CURL endosomes (B) Free polyribosomes (C) M-6-P receptors (D) R/KDEL sequence Q16: For ER protein synthesis, which of the following events are in correct sequence? (A) SRP:SRP receptor binding->translocon closed->translocon open->signal peptidase cleavage->protein folding (B) SRP:SRP receptor binding->translocon open->translocon closed->signal peptidase cleavage->protein folding (C) SRP:SRP receptor binding-> translocon open->signal peptidase cleavage->translocon closed->SRP:mRNA binding (D) SRP:SRP receptor binding-> translocon open->->protein folding -> signal peptidase cleavage ->translocon closed Q17: Of the following sequences, which are essential for ER protein retrieval? (A) di-arginine sequence (B) di—acidic sequence (C) di-alanine sequence (D) di-hydrophobic sequence Name: Student number: ' Q18: If a protein was synthesized on free ribosomes, did not contain a KDEL motif, did not contain an M6P motif, did not contain an NLS motif, did not contain a matrix motif, but contained a transmembrane sequence, where is that protein MOST likely to end up? (A) lysome (B) plasma membrane (C) cytosol (D) peroxisome Q19: 2—dimensional SDS PAGE [sodium dodecyl sulfate polyacrylgmide gel electrophoresis] separates proteins according to which chemical properties? (A) Solubility and hydrophobicity (B) Charge and size (C) Solubility and charge (D) Hydrophobicity and charge Q20: Across the entire genome in comparison to E. Coli, humans have how many isoforms per protein (E.Coli:human)? (A) 1:] (B) 1:10 (C) 1:100 (D) 10:] Q2]: How many genes are expressed in the human genome and how large is the genome? (A)2l,000 genes; 3x109 base pairs (B) 21,000 genes; 3xlO6 base pairs (C) 5,000 genes; 3x106 base pairs (D) 5,000 genes; 3xlO9 base pairs Q22: Antibody affinity chromatography would separate proteins or peptides based on what property? (A) Peptide sequence (B) Peptide mass (C) Peptide charge (D) All of the above Name: Student number: Section 2: Short answer Questions for the Whole class Q1. (Based on Dr. Monnier’s lectures) What are the three main steps that lead to the formation of retino-tectal maps? (10 marks) Name: Student number: Q2 (Based on Dr. Gramolini’s lectures) (A) In a rare human disease called “inclusion cell disease”, lysosomes are lacking most of their ordinary enzymes. Interestingly, their enzymes are found to be secreted from the cell. Based on your lectures, can you extrapolate and provide a likely molecular mechanism behind this disorder? (3 marks) (B) Compare and contrast the strengths and weaknesses of proteomics studies using (1) 2D gel assays vs (2) isotope labeling in high throughput mass spectrometry studies (3 marks) Name: Student number: Q3 (based on Dr. Cox’s lectures) You have observed a correlation with a higher rate of obesity in children who drank breast milk that was high in a novel cholesterol based molecule you have discovered and named “obestriol”. This effect was not dependent on diet. You have identified the enzyme, HSDl 1 1A as responsible for converting cholesterol into obestriol. You have generated a transgenic mouse line that expresses high systemic levels HSDl 11A and the breast milk of these transgenic mice has 10 times the level of obestriol compared to normal mice. Answer the following questions to outline an animal model based approach to investigating the effect of this molecule. (A) Your results support that high levels of breast milk obestriol alone lead to higher obesity in the offspring. Describe an experimental approach and rationale to determine if the observed effect has epigenetic changes in the offspring. Consider the epigenetic change you will measure, assay you will use and a tissue you would assay. (5 marks) (B) Having established an epigenetic change is occurring you wish to determine if there is a long-term multigenerational epigenetic effect and if both males and female can transmit this effect (Can be two separate experiments). Describe your experimental approaches and rationale. Consider your breeding strategy, and anticipated results of your experiments. (10 marks) Name: Student number: Q4 (Based on Dr. Jia’s lectures) What is the tTA? What is the TeTO? How would you use the tTA/TeTO system to achieve inducible gene expression in transgenic mice? What is the Cre? What is the loxP site? How would you use Cre/loxP system to achieve region/cell specific gene deletion in mice? Describe the advantages and disadvantages of using the tTA/TeTo and Cre/loxP system to manipulate gene expression in mice. (15 marks) Name: Student number: Section 3. Subgroup Questions (Answer only your own subgroup guestion, 10 marks) Elena Comelli: Define microRNA (2 marks) and briefly describe microRNA biosynthesis (4 marks). A study was presented in class showing that a subset of murine intestinal microRNAs are affected by the presence of the microbiota (Singh et al., 2012). Explain what are, according to the authors of this study, the possible implications of this finding for gut health (4 marks). Philippe Monnier: 1 Discuss why CNS neurons fail to regenerate after CNS injury. (10 marks) Shuzo Sugita: My lab has studied the structure vs function relationship of Muncl8-l and Muncl8-2 proteins. (1) Mutations in MunclS—l and Munc18-2 are associated with human diseases. What are these diseases, respectively? (2 mark) (2) To study the function of Munc18-l and Munc18-2 as a whole, Han et a1. (2009) generated neurosecretory PC12 cells in which Muncl8-1 and Munc18-2 are stably knocked down. Explain the consequence (phenotype) of Muncl 8-1/—2 double knockdown in PC12 cells. (3 marks) (3) Munc18-1 is believed to play three different physiological filnctions in exocytosis. What are they and which domains of MunclS—l are responsible for these functions? How did Dr. Sugita’s lab lead to such conclusions? (5 marks) Scott Heximer: Galpha subunits are molecular signaling switches regulated by their guanosine nucleotide (GDP or GTP) binding status. RGS proteins are GTPase activating proteins (GAPS) for G-protein Galpha subunits. (1) Describe how RGS proteins affect the ability of the Galpha subunit to function as a signaling switch. Use your knowledge of the GTPase cycle to answer this question. (6 marks) (2) Describe how RGS protein activity affects the duration and sensitivity of G—protein signaling in a cell. (4 marks) Richard P. Bazinet: (1) describe 2 cell types involved in neuroinflammation. For each cell type describe 1 function (2 makrs) (2) describe 2 methods to evaluate neuroinflammation in the brain (2 marks) (3) how are omega-3 fatty acids hypothesized to reduce neuroinflammation (6 marks) Jinrong Min: How does histone acetylation regulate chromatin structure and gene expression, and what are the major players (proteins) involved in this process? (10 marks) 10 Q) Name: Answer onl our own rou Student number: uestion in the s ace rovided below 10 marks 11 ...
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