PJC H2 Chem 2012 Prelim P3 Soln

© PJC 2012 9647/03/JC2 Prelims/2012 2 Answer any four questions 1 Enzymes are biological molecules that catalyse chemical reactions . Almost all chemical reactions in a biological cell need enzymes in order to occur at rates sufficient for life. (a) Acquired Immuno -Deficiency Syndrome (AIDS) is a disease of the human immune system caused by the Human Immunodeficiency Virus (HIV). HIV- 1 Protease is an enzyme which speeds up the reproduction of HIV. In the development of anti -HIV drugs, scientists often study the amino acid sequence of the HIV -1 Protease to understand how this enzyme dis plays its biological properties in the human body. (i) A segment of the polypeptide structure of HIV -1 Protease, containing 10 amino acids, was digested using an enzyme and the following fragments were obtained. leu – asn – phe ile – gly – cys – thr – leu leu – thr – glu – ile – gly Deduce the primary structure of this segment of HIV-1 Protease. leu – thr – glu – ile – gly – cys – thr – leu – asn – phe (ii) A segment of the HIV strand acts as a substrate , which binds to the active site of the HIV -1 Protease which speeds up the reproduction of the HIV virus. The rate of this enzyme- catalysed reaction is investigated and can be represented by the following graph. Explain the difference in the rate of reaction at high and low co ncentrations of substrate. At low substrate concentration, § Rate of reaction increases linearly / reaction is first order wrt the substrate concentration as active sites of the enzyme are not fully occupied. At high substrate concentration, § Rat e of reaction is constant / rate is independent of substrate concentration / reaction is zero order wrt the substrate concentration as all active sites occupied. rate substrate concentration

© PJC 2012 9647/03/JC2 Prelims/2012 3 (iii) The structural formulae of the three most common amino acids present in the protein chain in HIV-1 Protease are shown below. CH2 C H NH2 COOH CH2 COOH CH C H NH2 COOH CH2 CH3 CH3 SH C H NH2 COOH CH2 glutamic acid (glu) leucine (leu) cysteine (cys) In how many different ways can these three amino acids be coupled by peptide bonds to form a tripeptide? Draw the structural formula of one such peptide. 3! = 6 ways CH2 C H2N C CH2 COOH O CH C H N C CH2 CH3 CH3 O SH C H N COOH CH2 H H H **Accept other correct tripeptides (iv) The side chains of these three amino acids are responsible for maintaining the tertiary structure of HIV-1 Protease. State and draw the type of side-chain interaction between two cysteine (cys) residues. State the type of reaction that is involved in the formation of the side- chain interaction.

© PJC 2012 9647/03/JC2 Prelims/2012 4 Type of reaction: oxidation (v) Since its discovery in 1981, scientists have studied the protein structure of HIV in order to prevent its transmissi on. The World Health Organisation recommends heat treatment of breast -milk prior to giving it to the child, as a way to reduce the risk of HIV transmission to the baby in sub-S aharan Africa. Explain how this treatment of breast-milk reduces the risk of HIV infection in infants. Heating leads to denaturation of protein. When temperature increases, molecular vibrations agitate the polypeptide cha ins sufficiently to overcome the weak interactions that stabilise protein conformation. (Also accept loss of 3d conformation) As the secondary and tertiary structures are broken down, it results in the loss of function of the HIV protein. [9] (b) An example of a co pper-containing enzyme is superoxide dismutase (SOD) that aids in the disproportionation of the strongly oxidising superoxide ion, O 2- to oxygen and hydrogen peroxide. Thus, they are an important antioxidant defense in nearly all cells exposed to oxygen, thereby protecting the body from harm. 2O2- + 2H+ O2 + H2O2 (i) The activity of SOD hinges on the active site Cu2+ ion. By referring to the following E ¡ data, suggest a mechanism for the catalysis of the disproportionation of O2- by SOD. You may represent the oxidised and reduced forms of the enzyme as SOD-Cu2+ and SOD-Cu+ respectively. E¡/ V O2 + e- Error! Objects cannot be created from editing field codes. O2- -0.33 O2- + e- + 2H+ Error! Objects cannot be created from editing field codes. H2O2 +0.89 SOD-Cu2+ + e- Error! Objects cannot +0.42

© PJC 2012 9647/03/JC2 Prelims/2012 5 be created from editing field codes. SOD-Cu+ Step 1: SOD-Cu2+ + O2- ® O2 + SOD-Cu+ E¡cell = +0.42 – (-0.33) = +0.75V (> 0, hence feasible) Step 2: SOD-Cu+ + O2- + 2H+ ® H2O2 + SOD-Cu2+ E¡cell = +0.89 – (+0.42) = +0.47V (> 0, hence feasible) (ii) State the type of catalysis and explain how SOD-Cu2+ can act as a catalyst. Homogenous catalysis The catalytic effect is due to the ability of Cu to have variable oxidation states. (iii) With the aid of a sketch of the Boltzmann distribution, explain how the presence of a catalyst affects the rate of reaction. When a catalyst is used in a reaction, it: · increases the rate of the reaction by providing an alternative reaction pathway with lower activation energy · increases the number of reacting particles with energy ³ Ea · increases the number of effective collisions per unit time · increases the rate of reaction. [1] diagram

© PJC 2012 9647/03/JC2 Prelims/2012 6 (iv) The secondary structure of SOD is composed mainly of beta -pleated sheets, as well as some regions of alpha-helices. Draw a diagram of the beta- pleated sheet, showing the bondin g which maintains the structure of the secondary structure of the enzyme. [11] [Total: 20] CC OO HH NN dd++dd++ dd-- dd-- EExxppaannddeedd vviieeww:: C N H R H C O C R N C O C R H N C O H H H C N H R H C O C R N C O C R H N C O H H H C H R C O N C O C R H N C O H H N H C R H Hydrogen bond

© PJC 2012 9647/03/JC2 Prelims/2012 7 2 Ginger has be en used as a natural remedy for many ailments for centuries. Researchers around the world are finding that ginger works wonders in the treatment of everything from cancer to migraines. Ginger consists of many chemicals. Vitamin C and chlorogenic acid are two of the chemicals present in ginger. (a) O O O H OH O H O H O O H OH O H O H O O H OH O H + specific controlled elimination compound A compound B compound D vitamin C O H O O H OH CH CH (i) Draw the structures of compounds formed when vitamin C reacts with hot acidified potassium dichromate(VI).

© PJC 2012 9647/03/JC2 Prelims/2012 8 O H O O H OH O H O O O (ii) Compound A undergoes elimination to produce compounds B and D. State and explain which compound is the major product. Compound B should be the major product. Alkene B is more highly substituted than alkene D. By Satyzev’ s rule, the more highly substituted alkene is the major product. OR Alkene B is a more stable product as it has an extended conjugate system (involving both alkenes and the ketone group). (iii) Determine the maximum number of stereoisomers of compound D. Draw the pair that has the same boiling point. Maximum no. of stereoisomers = 22 = 4 O H O OH OH H OH O O H O H H O H O OH OH HOH O O H O H H [4] (b) The structure of chlorogenic acid and its reaction pathway is shown below. or

© PJC 2012 9647/03/JC2