A-LevelBiologyNucleic acids and protein synthesis9700/23 · May/June 2021 · Q312 Marks

HIV protease is an enzyme composed of two identical polypeptide chains. Each polypeptide chain is 99 amino acids long. During translation, the amino acids are joined by peptide bonds to form the polypeptide chain.

(a)Describe how a polypeptide of HIV protease is produced by the process of translation.[4]
(b)The synthesised polypeptide has a primary protein structure and can form a tertiary protein structure after translation. There are more bond types in the tertiary structure. Compare the peptide bond formed during translation with the types of bond made during tertiary structure formation.[3]
(c)(i)Some polypeptides are translated as part of one long polyprotein chain. After translation, enzymes cut the polyprotein into separate functioning proteins. HIV protease cuts a polyprotein that has been produced within the host cells of actively replicating HIV. The separate proteins are required in the replication of the virus. Fig. 3.1 shows how the two polypeptide chains of HIV protease form an enzyme with an active site enclosed by flaps, forming the flap region. [Figure 3.1] The flap region of HIV protease is flexible. With reference to Fig. 3.1, suggest and explain how the mechanism of action of HIV protease can be described as an induced fit.[3]
(c)(ii)Indinavir is one of the therapeutic drugs used in HIV anti-retroviral therapy (ART). It is similar to the polyprotein substrate of HIV protease. Suggest and explain how indinavir acts as a therapeutic drug.[2]

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Mark scheme

Marking points from the official mark scheme (May/June 2021). The mark or mark type is shown in brackets.

[1] any four from
[1] 1 mRNA, attaches to / associates with / AW, ribosome ; A ribosome reads mRNA
[1] 2 two codons, exposed / AW; A A and P sites / first and second binding sites, (on ribosome)
[1] 3 tRNA, qualified carries an amino acid to ribosomes / each type carries a specific amino acid / first amino acid is met/tRNA with met / tRNAmet ; ref. to ribosomes can be implied in mp 3 if mp1 gained
[1] 4 anticodon (on tRNA) binds to codon (on mRNA); I matches A complementary / base, pairing between codon and anticodon A H-bonds form between bases on codon and anticodon R if anticodon on mRNA
[1] 5 START (mRNA) codon / (mRNA) AUG first codon ;
[1] 6 second tRNA with its amino acid binds next to first tRNA / (two) amino acids are held in place close to each other by tRNA binding / AW ; A ref. to two tRNAs next to each other
[1] 7 (after peptide bond formation) first tRNA detaches / ribosome moves along one codon or process repeats / elongation occurs, until, STOP codon / polypeptide chain synthesised (and released from ribosome) ;
[1] 8 tRNA molecules, reused / leave ribosome to attach to another amino acid; must be in context of leaving after peptide bond formation
[1] 9 AVP; e.g. peptidyl transferase for peptide bond formation ref. to, 99/100/101, codons, qualified A number of bases in length of mRNA
[1] any three from
[1] similarity
[1] peptide bond and disulfide bond are covalent bonds ;
[1] differences
[1] tertiary structure bonds are between, R groups / side chains, (of different amino acids ;
[1] H bond / ionic bond / hydrophobic interaction, versus covalent peptide bond ;
[1] A tertiary structure bonds apart from disulfide are not covalent
[1] peptide bond, stronger / more thermostable, than, tertiary structure bonds / two named bonds ;
[1] peptide bond is between, carboxylic acid / COOH, and, amino / NH2, group (of the adjacent amino acid) ;
[1] AVP; detail of a tertiary structure bond e.g.
[1] hydrophobic between non-polar R groups
[1] disulfide between sulfur-containing R groups
[1] ionic between carboxyl and amino groups of R groups
[1] H bond between oxygen on —CO groups and H on either the —OH or —NH groups of R groups
[1] any three from:
[1] suggestion that
[1] 1 flap region, opens / moves, to let, substrate / polyprotein, enter or flap region, closes round / AW, substrate / polyprotein I flap region is closed
[1] 2 induced fit / HIV protease action, involves, change in shape of active site / active site moulding around substrate / AW ; I ref. to enzyme or substrate changing shape if mp1 and mp2 not gained allow one mark if stated that activity of flap region changes shape of active site or that flap region changes shape because it is the active site
[1] 3 ref. to better fit / fully complementary / AW ;
[1] 4 ref. to formation of, enzyme-substrate complex; A ESC
[1] 5 AVP; e.g. (induced fit) substrate / polyprotein, not (fully) complementary to (shape of) active site A does not (fully) fit active site / enzyme, returns to original shape on release of product change of shape (to give complementary fit), lowers activation energy / puts strain on bonds / AW
[1] any two from
[1] acts as competitive inhibitor ;
[1] binds to active site, qualified ; e.g. instead of, substrate / polyprotein to prevent, entry / binding, of, substrate / polyprotein so competes with substrate to prevent ESC formation I ref. to flap region as active site
[1] any one from
[1] will be permanent / non-reversible ;
[1] causes / induces, flap region to open to bind to active site ;
[1] no (A few / fewer) polyprotein products / polyprotein not cut, so viral replication prevented / AW ; R polyprotein not broken down