2016 VJC H2 Biology Prelims Paper 2 Answers

1    VICTORIA JUNIOR COLLEGE BIOLOGY DEPARTMENT JC2 PRELIMINARY EXAMINATIONS 2017 HIGHER 2 9744/2 Propose answers 1 Fig.1 shows an electron micrograph of an organelle. There are two distinct group of vesicles (Boxes B and C) associated with this organelle. Fig. 1 (a) (i) Identify organelle A. Feature Golgi body/ golgi apparatus;; A stack of membranes with swollen ends;; (ii) Describe the differences in the role of the vesicles that fuse with the forming face and the vesicles that are formed at the maturing face. [4]  Box C: [2m]  vesicles contain proteins and/or lipids;  transported from rER and sER;  that will undergo chemical modification within the golgi body;  examples of modification: glycolysation, phosphorylation etc  Box B: [2m]  Packaging and transport fn: Vesicles containing modified products will be transported to the cell membrane;  where they fuse and release the products to the outside of the cell/via exocytosis; (b) Suggest how the lack of E3A expression can lead to a disruption in the structure and function of the Organelle A.  Lack of gene expression means that the enzyme E3A is not produced/ transcribed and translated;;  Proteins that are tagged by ubiquitin, are meant for degradation;;

2     These proteins are either damaged/abnormal/excess;;  Removal of these proteins help to maintain the normal functions of the GA (idea of);; (A: reverse argument) (c) State two characteristics, one in structur e and one in chemical property that you would expect to see in ubiquitin protein ligase. [2] Structure: globular / specific 3D configuartion Chemical ppty: solubility in water;;   2 (a) Explain the similarity in the pattern seen in both HDAC mRNA and HDAC protein. [2]  HDAC mRNA is the template for the translation /synthesis of HDAC protein;;  Decrease in mRNA concentration lead to a decrease in concentration of HDAC protein;; (b) (i) What information about the gene expression of RUNX3 can one conclude from the data at the beginning of the experiment? Explain your answer. [3] There are 2 possible answers to this question. Possible answer 1  RUNX3 gene is silenced/ down regulated;; (Note: this last mark is only awarded if student’s answer shows that there is an attempt to link RUNX3 gene expression to HDAC levels shown in Fig 2.1)  How does HDAC down regulate RUNX3 expression:  Remove acetyl groups from lysine residues of histones;  Increase positive charge of histones;  Results in negatively RUNX3 gene being more tightly coiled around histones;  Promoter less accessible to transcription factors and RNA polymerase;  Data: Highest HDAC mRNA and protein; Possible answer 2  RUNX3 gene is upregulated;; (Note: this last mark is only awarded if student’s answer shows that there is an attempt to link RUNX3 gene expression to HDAC levels shown in Fig 2.1)  How does RUNX3 upregulate HDA  RUNX3 TF binds to promoter of HDAC gene;  Recruits RNA pol or formation of transcription initiation complex for transcription;  Up regulation HDAC gene expression (idea of);  highest HDAC mRNA and protein concentration; A: RUNX3 TF act as activator (attaches to enhancer region); to allow correct positioning of TIC/ stabilise the TIC; through looping mechanism;

3    (ii) Suggest one way how your answer in (i) can affect the cell. [3] Down regulation of RUNX3:  [What is RUNX3] RUNX3 is a TSG Or TF coded by RUNX3 binds to/activates other TSG;;  [what is its function/ function of other genes] Involved in halting cell cycle/ repair DNA damage/send cells to apoptosis;;  [impact –leading to cancer]Reduced expression leads to accumulation of DNA damage/ cells not able to stop at the appropriate checkpoints/ do not undergo apoptosis, resulting in cancer;; Upregulation of RUNX3:  [What is RUNX3] RUNX3 codes for the TF for HDAC gene;  HDAC protein deacetylates/ silence TSG;;  [what is its function/ function of other genes] Involved in halting cell cycle/ repair DNA damage;;  [impact –leading to cancer]Reduced expression leads to accumulation of DNA damage/ cell cycle out of control, resulting in cancer;; (Described eg. cells not able to stop at the appropriate checkpoints, leading to uninhibited growth.)  RUNX3 is a protooncogene or codes for the TF for proto-oncogenes;;  Results in increase/upregulate expression of genes that promote cell growth and proliferation;;  [impact –leading to cancer] Increased expression leads to increase cell proliferation / cell cycle out of control, resulting in cancer;; (c) With reference to the data shown in Fig 2, suggest how Chemical K can bring about the change in the HDAC mRNA and protein. [2]  {Change} Decrease HDAC mRNA and protein;  Any one of the ways below: 1. Act as a repressor (specific TF) that binds to the silencer; 2. Prevents TIC assembly; 3. Down regulate HDAC expression Or 4. Breakdown mRNA/Decrease stability of mRNA; 5. Reduce half life; 6. Less mRNA and hence less HDAC protein being synthesised; Or 7. Cause DNA methylation of HDAC gene; 8. At CpG regions; 9. Silence the gene/ recruit histone acetylase; Or AVP (1 1/2m)

4    (d) Suggest why HDAC mRNA instead of the HDAC gene was analysed in this experiment. [2] Answers must provide reason for both HDAC mRNA and HDAc gene.  Fixed copies/ concentration of the HDAC gene (idea of);;  Gene may not be expressed/ idea of cannot study expression;;  Differential expression of the gene can be seen using the mRNA;;  Chemical K affects transcription and hence its effect can only be seen by observing changes in mRNA concentration;; 3 (a) (i) Identify substrates X and Y.[2] X: glucose; Y: lactose; (ii) Using your knowledge of gene expression in bacteria, explain how Fig. 3 supported their conclusion that the Lac operon is under dual control. [4] ● Evidence #1 – first growth phase: When glucose and lactose are both present, glucose is used preferentially (A! first/ preferred respiratory substrate) for bacteria to grow and reproduce;; ● Lac operon is under negative control and the gene coding for beta-galactosidase that breaks down lactose into glucose and galactose is not expressed;; ● Evidence #2 – second growth phase: when glucose is depleted, lac operon is active and under positive control, so expression of the gene for beta-galactosidase is upregulated;; ● Evidence #3 – Lag phase: bacterial growth levels / plateaus out: time needed for activation of CAP by cAMP when adenylyl cyclase inhibiti on is removed after glucose is depleted and cAMP levels increase/ time needed for the expression of lac operon;; (b) On Fig. 3, draw separate graphs to show the change in the concentration of the two substrates over time. Label your graphs. [2] Answer:

5    Each curve for glucose and for lactose must show:  Decreasing trend but with glucose being used first @½ m  Shape of curve to consist of plateau and linear segments @½ m  A! decreasing trend for glucose from time 0. (FYI – During the lag phase, bacteria are adapting to growth conditions, so that individual bacteria are maturing and not yet able to undergo binary fission. During the lag phase, synthesis of RNA, enzymes and other molecules occurs. As the cells are metabolising, there is some usage of glucose.) (c) Eukaryotes are structurally different from prokaryotes and hence exhibit differences in their control of gene expression. Explain two such differences. [4] Any two below (note: from perspective of eukaryotic genes):  Chromatin modelling – acetylation/deacetylation Or methylation/demethylation of CpGs in eukaryotic promoters;; to compact chromatin by wrapping high mw DNA/ large eukaryotic genome around histones to fit into space of nucleus;;  Post-transcriptional – 5’ capping and poly