VJC H3 BIO 2015 MS

1 VICTORIA JUNIOR COLLEGE BIOLOGY DEPARTMENT JC2 PRELIMINARY EXAMINATIONS 2015 Higher 3 VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE VICTORIA JUNIOR COLLEGE CANDIDATE NAME CLASS INDEX NUMBER BIOLOGY 9815/01 28 September 2015 Additional Materials: Answer Paper 2 hours 30 minutes READ THESE INSTRUCTIONS FIRST Write your CLASS/ INDEX no. and name on all the work you hand in. Write in dark blue or blue pen. You may use a soft pencil for any diagrams, graphs or rough working. Do not use any staples, paper clips, highlighters, glue or correction fluid. Section A Answer all questions. Section B Answer three out of four questions. Section C Answer the question. At the end of the examinations, 1. Fasten all your work securely; 2. Circle the number of the section B question you have answered in the grid opposite. The number of marks is given in brackets [ ] at the end of each question or part question. This paper consists of 10 printed pages, including the cover page. For Examiner’s Use Section A 1 2 3 4 5 Section B 6 7 8 9 Section C 10 Total Mark Scheme

2 Section A Answer all questions in this section. Key: (;) means ½ mark and (;;) means 1 m 1 (a) Fig.1 shows GDP in the binding site of a G protein. Fig. 1 (i) With reference to Fig. 1, describe the types of interactions between GDP and the amino acids that make up the binding site. [3] • Ionic interaction – between side chains of Lys and Arg and the phosphate group of GDP;; • Hydrogen bonds – between side chains of Asp and Glu with the ribose sugar of GDP;; • Hydrogen bond – between side chain of Tyr with the –NH2 group of guanosine/ nitrogenous base of GDP;; (ii) A mutation results in the change of the amino acid from Arg to Asp at the binding site. A similar change occurs within the protein core of G protein. Discuss the difference, if any, the effect of these mutations on the function/ activity of the protein. [4] 2 marks for binding site  Ability of GDP to bind may be lost or decreased but not totally lost;  Arg is positively charged whereas Asp is negatively charged/ Mutation results in an amino acid that is of a different charge;  This will repel the negative charge of the phosphate group which may result in misalignment of the GDP with other amino acids in the active site;  But the R group/ side group of Asp i s small and hence the effect may not be significant i.e. results in slight distortion in alignment;

3 2 marks for protein core  Buried charged amino acids tend to occur as “ion pairs” where oppositely charged amino acids interact to form the protein core which is hydrophobic;;  A change of charge would destabilise the protein as the two negatively charged amino acids will repel each other;; (b) A protein family is a group of proteins that have des cended from a common ancestor. Members of the same family typically have similar three -dimensional structures, functions and significant sequence similarity especially in the binding or catalytic sites. Many protein families belong to a protein superfamily which is the largest grouping (clade) of proteins for whi ch common ancestry can be inferred. Members belonging to the same superfamily share structural similarity but not necessarily sequence similarity. (i) Explain how it is possible for two proteins to share structural similari ty without sequence similarity. [2]  3-dimensional structure is a result of interactions between R groups of key amino acids ► result in the similar coiling and folding of the polypeptide;;  Clusters of similar aa that are responsible for structural folds ► occur as motifs (i.e. short sequences of less than 10 aa) while overall sequence homology is low;; (ii) On the other hand, proteins with similar primary sequence can differ in their 3 - dimensional configuration. Explain how this is possible. [2]  Depends on the environment the protein exists in: (i) aqueous environment favours protein to fold in such a way that the hydrophilic R groups will be outside while hydrophobic R groups will be located within the core; (ii) whereas a protein with similar primary structure but located i n a non- aqueous/ organic solvent will fold differently with hydrophobic R groups on the surface of the protein while the hydrophilic aa will be found in the interior;  Presence of prosthetic group : this may bind to specific amino acid residues resulting in them not being available for further interaction with other amino acids;; Accept: different post translational modifications (PTMs) affect 3D conformation;; [Total: 11]

4 2 The antibody immunoglobulin G (IgG) is a type of globulin protein that is found in blood or other bodily fluids of vertebra tes, and is used by the immune system to identify and neutralize foreign objects, such as bacteria and vir uses. It is produced by a type of white blood cell called a B cell. Fig. 2.1A is a schematic diagram of IgG while Fig. 2.1B shows the ribbon model of the same IgG molecule. Fig. 2.1A Fig. 2.1B (a) With reference to Fig. 2.1, explain the term “domain”. [2]  Protein domains are defined as compact, folded structures within a polypeptide chain;;  That corresponds to a certain function or binding property;;  Can fold independently to the rest of the polypeptide chain;; (b) Account for how the four IgG domains at the antigen -binding sites of the IgG molecule are different from the rest of the IgG domains, with refer ence to the function of the IgG. [3]  These four IgG domains have hypervariable loops or complementarity- determining regions (CDRs) (the other IgG domains do not have them);;  CDRs vary greatly in their amino acid sequence;;  Allow antibodies to be diverse in their specificity thus able to bind to a vast array of antigens;; (c) The IgG molecule can be broken down into smaller fragments by proteolytic enzymes such as papain, and pepsin. Treatment with papain yields two kinds of fragments, a pair of F(ab) fragments, and one Fc fragment while treatment with pepsin yields a single fragment, the F(ab’)2 but degrades the Fc region. Indicate, on Fig. 2.1B, the site(s) where papain and pepsin are likely to act on IgG.