2020 ASRJC H2 Biology Prelim P2 (Answer)

ANDERSON SERANGOON JUNIOR COLLEGE 9744/02/2020 [Turn over 2020 JC2 PRELIMINARY EXAMINATIONS CANDIDATE NAME CLASS INDEX NUMBER H2 BIOLOGY 9744/02 Paper 2 Structured Questions Candidates answer on Question Paper. No additional Materials are required 16 September 2020 2 hours READ THESE INSTRUCTIONS FIRST Write your name and class in the spaces at the top of this page. Write in dark blue or black pen. You may use a HB pencil for any diagrams or graphs. Do not use staples, paper clips, highlighters, glue or correction fluid. Answer all questions in the spaces provided on the Question Paper The use of an approved scientific calculator is expected, where appropriate. You may lose marks if you do not show your working or if you do not use appropriate units. At the end of the examination, fasten all your work securely together. The number of marks is given in brackets [ ] at the end of each question or part question. This document consists of 16 printed pages H2 ANDERSON SERANGOON JUNIOR COLLEGE HIGHER 2 For Examiner’s Use 1 / 6 2 /11 3 /10 4 /10 5 /9 6 /6 7 /9 8 /10 9 /11 10 /9 11 /9 /100

2 ANDERSON SERANGOON JUNIOR COLLEGE 9744/02/2020 [Turn over Anderson Serangoon JC H2 BIOLOGY 9744/02 Prelims 2020 Mark Scheme 1 (a) Glycine makes up approximately 30% of the total amino acid composition of collagen. Explain how glycine plays an essential role in the structure of collagen. • (glycine) amino acid with smallest/ H, R-group/ side chain; Reject glycine is a small/ smallest aa without reference to its R-group • Run along the, interior/ central, axis of the helical polypeptide/; Reject glycine/ glycine’s R-group/ project into interior • Allow the, triple helix/ three polypeptides, to be, closely associated/ tightly pack together/ AW; (accept tropocollagen/ collagen chains/ reject collagen/ collagen molecules) look for idea of three compact helices Ignore reference to alpha helices • Allow H-bonds to form between polypeptides (for strength); • Further details e.g. (hydrogen) bond forms between the amide (-C(=O)NH-) hydrogen atom of glycine in one polypeptide chain and the carbonyl oxygen atom of X in an adjacent polypeptide chain Examiner’s comments: Collagen have many level so students need to be specific to write which level are they talking about. If left vague, collagen is usually understood as the fibril or even microfiber level. [2] 1. (b) Collagen is continuously broken down in the extracellular matrix by the enzyme collagenase, which catalyses the hydrolysis of the peptide bond between the amino acids glycine and isoleucine. Describe how collagenase lowers the activation energy and increases the rate of collagen hydrolysis. • Reference to role of contact (e.g. weak /temporary bonds)/ catalytic residues/ R-groups/ amino acids at active sites; (need to describe briefly what the contact/ catalytic residues do e.g. contact residues bind to substrate/ form bonds with substrate, catalytic residues catalyse the reaction/ hydrolyse the bond) • hold substrate in a correct orientation inside its active site for hydrolysis reaction to occur ; • physical stress/ strain of the peptide bond is induced , increasing the likelihood that the bond will break ; • altering charges on substrate/ they increase reactivity of peptide bond by altering the distribution of electrons within the peptide bond OR changing the charge on the peptide bond • creating a more conducive micro-environment for substrate to react Examiner’s comments: Many students were clear that the substrate (what enter the active site) is not just collagen but specifically the peptide bond between the amino acids glycine and isoleucine. Many students wrote how the shape of the substrate being complementary to the active site, this is not suffice to describe how the activation energy is lowered just through the complementary shape, specific ideas like role of contact/ catalytic residues, physical strain being applied, charges altered are needed. [2]

3 ANDERSON SERANGOON JUNIOR COLLEGE 9744/02/2020 [Turn over (c) Collagen is a structural protein. Collagenase is an enzymatic protein. Describe two differences in the structural properties of collagen and collagenase. Features Fibrous proteins Globular proteins Structure Fibrous/ Long fibres making up its structure elongated / long / rods / filaments / ropes / strands Reject linear Folded into tertiary structure, spherical globular shape have, 3D / tertiary / shape / structure Quaternary Reject secondary tertiary reference to active site: specific / complementary (to another molecule)/ Amino acid sequence Repetitive sequence of amino acids. Actual sequences of amino acids may vary slightly between two samples of the same protein. Irregular amino acid sequences, hence there is a large variety of amino acids in a protein. (accept not repetitive) Sequence of each protein is highly specific and never varies between two samples of the same protein Length of polypeptide chain Length of chain may vary in two samples of the same protein Length always identical in two samples of the same protein Size Larger then collagenase Accept large Smaller than collagen Accept small Examiner’s comments: Many students compared the solubility between the fibrous and globular protein. Solubility is a physical property not structural property. [2] [Total: 6] 2 Taq polymerase is a thermostable DNA polymerase used in the polymerase chain reaction (PCR). It was originally extracted from a bacterium, Thermus aquatius, which is found in the hot springs of the Yellowstone National Park in the USA. (a) Describe the reaction catalysed by DNA polymerases such as Taq polymerase. • Condensation reaction/ release (formation) of water molecule • Form phosphodiester bond (not hydrogen bonds between base pairs!) • Between (3 ’OH group) of one DNA nucleotide and the (5’ phosphate group of) another DNA nucleotide (accept add DNA nucleotide) Reject between DNA bases ------- the nitrogenous bases are not involved in the formation of phosphodiester bonds [2]

4 ANDERSON SERANGOON JUNIOR COLLEGE 9744/02/2020 [Turn over Generally well -done. However there were some students who wrote excessively about the extension stage ( and even denaturation and annealing stage) of PCR reaction, this does not answer the question! Some answers were also vague, e.g. description on the semi-conservative mode of DNA replication / simply said replicate DNA/ elongate DNA strand/ add to the 3’ end of the DNA strand using a template DNA strand ---- these answers were ignored When a questions asks for the reaction catalysed by an enzyme. Please give: • Condensation/ hydrolysis reaction • Name the bond formed or broken • Name the exact functional group of the monomer involved Practise writing this for glycosidic bond/ peptide bond/ ester bond Ignore references to proofreading/ removal or RNA primers ------- these are not the main function performed by all DNA polymerases e.g. Taq polymerase has no proof-reading function/ there is no need to remove primers during PCR ---- give these points only in an essay or when more marks are given in the question (b)