2024 NJC H2 Bio P3 MS

©NJC 2024 9744/03/Preliminary Examination [Turn over H NATIONAL JUNIOR COLLEGE, SINGAPORE Senior High 2 Preliminary Examination Higher 2 CANDIDATE NAME BIOLOGY CLASS 2bi2_____ R E G I S T R A T I O N NUMBER Biology Paper 3 Long Structured and Free-response Questions Candidates answer on the Question Paper. Additional Materials: Answer Booklet 9744/03 13 September 2024 2 hours READ THESE INSTRUCTIONS FIRST Write your name, Biology class and registration number on all the work you hand in. Write in dark blue or black pen. You may use an HB for any diagrams or graphs. Do not use staples, paper clips, glue or correction fluid. Section A Answer all questions in the spaces provided on the Question Paper. Section B Answer any one question in the separate Answer Booklet. The use of an approved scientific calculator is expected, where appropriate. You may lose marks if you do not show your workings or if you do not use appropriate units. The number of marks is given in the brackets [ ] at the end of each question or part of question. For Examiner’s Use Section A 1 /30 2 /10 3 /10 Section B 4 or 5 /25 Total /75

2 ©NJC 2024 9744/03/Preliminar y Examination This document consists of 15 printed pages and 1 blank page.

3 ©NJC 2024 9744/03/Preliminary Examination [Turn over Section A Answer all the questions in this section. 1 Collagen is a key structural protein found in various tissues t hroughout the body. Its measurements can vary significantly depending on the type a nd function of the collagen. Type I collagen is the most abundant form. Fig. 1.1 shows the structure of type 1 collagen fibrils. Fig. 1.1 (a) (i) Describe the molecular structure of collagen and explain how its structure relates to its function. LO 1(o) Answer: Describe D1. Ref to repeated Gly–X–Y m o t i f + X i s o f t e n proline, Y is often hydroxyproline; D2. Ref to 1000 amino acids forming left-handed helix; D3. Ref to three polypeptide chains supercoiling to form tropocollagen; Explain [5]

4 ©NJC 2024 9744/03/Preliminar y Examination E1. Ref to glycine allowing tight-packing of helix + increasing strength of tropocollagen; E2. Ref to proline/ hydroxyproline’s bulky structure + contributing to rigidity (limit rotation of peptide chain) and hence stability of tropocollagen; E3. Ref to extensive hydrogen bonding between –NH and –C=O of peptide bonds in adjacent polypeptide chains/ adjacent tropocollagen molecules + increasing tensile strength of tendons/ cartilages; E4. Ref to covalent cross-linking between lysine at the ends of tropocollagen molecules + increasing tensile strength of/ distributing pressure across tendons/ cartilages; E5. Ref to staggered arrangement + minimising points of weaknesses; E6. Ref to microfibrils/fibrils forming fibres + increasing tensile strength increasing tensile strength of tendons/ cartilages; E7. Ref to hierarchical organisation of tropocollagen into fibrils into fibres + allowing body to form biomechanical structures of different size and nature; E8. Ref to insolubility + providing permanent scaffold for cell adhesion, etc ( i i ) Use Fig. 1.1 to calculate the number of rows of collagen molecules found in the diameter of collagen fibril, D. Assume that: ● t h e d i a m e t e r o f a c o l l a g e n m o l e c u l e i s 1 . 5 n m ● t h e l e n g t h o f h y d r o g e n b o n d b e t w e e n t w o r o w s o f c o l l a g e n m o l e cules is 3.0 Å (angstroms). Show your working clearly. Give your answer to the nearest whole number. number of rows of collagen molecules in one collagen fibril = Working involved: 1 – shows clearly how D is determined; 250nm scale bar 0.8–0.9cm D 0.3-0.4cm, therefore D = (0.3–0.4) / (0.8–0.9) x 250 = 83.3–125nm 2 – shows logical method of determining number of rows of colla gen molecules; Length of hydrogen bond = 3.0/10 = 0.3nm M1: Number of rows of collagen molecules = D/(1.5 + 0.3) M2: Number of rows of collagen molecules = (D – 1.5) /(1.5 + 0.3) +1 3 – gives final answer in whole number; Number of rows = 46–69 [3]

5 ©NJC 2024 9744/03/Preliminary Examination [Turn over (b) Osteogenesis imperfecta (OI) is a heritable disorder of connective tissues caused by abnormal synthesis or dysfunctional type I collagen. Each type 1 collagen molecule contains two COL1A1 polypeptides and one COL1A2 polypeptide. A study was carried out to examine the mutations in COL1A1 and COL1A2 genes in patients with OI. PCR was carried out to amplify the genes in segments, and the resulting PCR product was used for DNA sequencing to identify the nucleotide sequence. Fig. 1.2 shows a segment of COL1A1 gene, with the 5’ end starting at position 1. Fig. 1.2 ( i ) Describe the principle and procedure of PCR. LO 2(k) Answer: Principle: 1. ref to using temperature change to regulate separation of DNA strands, binding of primers, elongation; 2. ref to repeated 20–30 cycles producing 2–fold increase in number of products per cycle; Procedure: 3. ref to Taq polymerase + synthetic oligonucleotides/ primers + dNTPS; 4. ref to denaturation + 92 – 95 °C + 15 seconds; 5. ref to annealing + 50 – 60 °C + 30 seconds; 6. ref to extension + 70 – 72 °C + 90 seconds; 7. ref to breaking of hydrogen bond during denaturation + formation of hydrogen bond between complementary base pairs during primer annealing; 8. ref to Taq polymerase catalysing formation of phosphodiester b o n d between 3’OH end of primer/ elongating DNA and dNTP; [4] ( i i ) Use Fig. 1.2 to propose the sequence of the pair of primers used in PCR. Forward primer: 5’ 3’ Reverse primer: 5’ 3’ [2] LO 2(k) Answer: accept any correct primer between 15–30 nucleotides long Forward primer: 5’ TTT GCC CAG GCT GGA 3’ (shortest) – 5’ TTT GCC CAG GCT GGA GTG CAA TGG TGT GAT 3’ (longest) Reverse primer: 5’ AAT CCC AAC ATT TTG 3’ (shortest) – 5’ AAT CCC AAC ATT TTG GGA GGC TGA GGC AGT 3’ (longest)

6 ©NJC 2024 9744/03/Preliminar y Examination Fig. 1.3 shows the gene maps of mutations in COL1A1 and COL1A2 genes. The numbered box represents the numbered exon while each line between the boxes represents the intron between two exons. The types of mutations are represented by symbols “del”, “dup” and “>”. Fig. 1.3 ( i i i ) With reference to Fig. 1.3, explain the effect of the mutations in exons and introns on type I collagen protein. Answer: 1. ref to relevant example with “>” + nucleotide substitution; 2. ref to relevant example with “del” + nucleotide deletion / “dup” + nucleotide insertion; 3. ref to “>” exon mutations + silent mutation / missense mutation; 4. ref to impact on bonding within triple helix/ between triple helices; 5. ref to impact on post-translation modification, such as hydroxylation of proline and lysine residues in ER; 6. ref to impact on post-translation modification, such as clea vage of terminal peptide/ aggregation into collage fibrils; 7. ref to “dup”/ ‘del” exon mutations + frameshift / nonsense mutation; 8. ref to impact on synthesis of functional collagen; 9. ref to “>” exon mutations + silent mutation effect; 10. ref to any intron mutations ( COL1A1: 334-9A>G, 1615-2A>T, 2451+2T>G, 2667+1G>C, 2829+1G>A, 3262-2A>G. COL1A2: 739- 2A>G, 1252-7delT) + affect splice sites; [5]

7 ©NJC 2024 9744/03/Preliminary Examination [Turn over 11. ref to additional amino acids due to translation of intronic sequence; 12. ref to intron mutation 1503+12_14delCAC + three nucleotide deletion + no impact on protein; 13. ref to no impact because introns are not translated; Source: Ohata (2019) Osteogenesis imperfecta (OI) can also aris