PJC H2 Chem 2012 Prelim P3 QP

Name: Index No.: CT Group: 11 PIONEER JUNIOR COLLEGE JC2 PRELIMINARY EXAMINATION HIGHER 2 CHEMISTRY 9647/03 Paper 3 Free Response 14 September 2012 2 hours Candidates answer on separate paper. Additional Materials: Answer Paper Data Booklet Cover Page READ THESE INSTRUCTIONS FIRST Write your Centre number, index number and name on all work you hand in. Write in dark blue or black pen on both sides of the paper. You may use a soft pencil for any diagrams, graphs or rough workings. Do not use staples, paper clips, highlighters, glue or correction fluid. Answer any four out of five questions. State the question number of the questions that you have attempted on the cover page provided. The question numbers should be stated in sequence. A Data Booklet is provided. You are reminded of the need for good English and clear presentation in your answers. The number of marks is given in brackets [ ] at the end of each question or part question. At the end of the examination, fasten all your work securely together. This document consists of 15 printed pages.

© 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 displays 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. (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 concentrations of substrate. 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. (iv) The side chains of these three amino acids are responsibl e 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. (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. [9]

© PJC 2012 9647/03/JC2 Prelims/2012 4 (b) An example of a copper -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- O2- -0.33 O2- + e- + 2H+ H2O2 +0.89 SOD-Cu2+ + e- SOD-Cu+ +0.42 (ii) State the type of catalysis and explain how SOD–Cu2+ can act as a catalyst. (iii) With the aid of a sketch of the Boltzmann distribution, explain how the presence of a catalyst affects the rate of reaction. (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]

© PJC 2012 9647/03/JC2 Prelims/2012 5 2 Ginger has been 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) The structure of vitamin C and its reaction pathway is shown below. O O O H OH O H O H O O H OH O H O H O O H OH CHCH2O H + specific controlled elimination compound A compound B compound D vitamin C O H O O H OH CH CH (i) Draw the structural formula of the compound formed when vitamin C reacts with hot acidified potassium dichromate(VI). (ii) Compound A undergoes elimination to produce compounds B and D. State and explain which compound is the major product. (iii) Determine the maximum number of stereoisomers of compound D. Draw the pair that has the same boiling point. [4]

© PJC 2012 9647/03/JC2 Prelims/2012 6 (b) The structure of chlorogenic acid and its reaction pathway is shown below. O OH O H OH O H O O OH OH O OH O H OH O H O OH OH O OH O H OH O H O OH OHN H2 NH2 NH2 chlorogenic acid compound F compound G step 1 step 2 step 3 (i) Compound F can be converted to compound G in two steps. Suggest reagents and conditions for steps 2 and 3. (ii) Draw the structures of compounds formed when compound G reacts with I H2, Ni(s), 200oC II NaBH4 in methanol [4] (c) Ginger also contains nutrients like m agnesium. Magnesium is a vital comp onent of a healthy human diet. Magnesium taken in the proper amount plays a role in preventing both stroke and heart attack. (i) Describe what is observed when a piece of magnesium ribbon is burnt in air. (ii) The product obtained in (i) is placed in a beaker of water containing a few drops of universal indicator. State the observation(s) and write equations for the reaction(s) that occur. [4]

© PJC 2012 9647/03/JC2 Prelims/2012 7 (d) Sketch a graph of the pH of the solution when the chlorides of the elements from sodium to phosphorus are added separately to water. Label your graph clearly. [2] (e) Hydrofluoric acid dissociates in water according to the following equation: HF(aq) H+(aq) + F-(aq) DHo dissociation The following are some enthalpy changes related to hydrogen fluoride. First electron affinity of fluorine/ kJ mol-1 -328 Standard enthalpy change of hydration of fluoride ion / kJ mol-1 -506 Standard enthalpy change of reaction, HF(aq) → HF(g) / kJ mol-1 +39 Standard enthalpy change of hydration of hydrogen ion / kJ mol-1 -1090 (i) By using the data provided and other relevant data from the Data Booklet, construct an energy cycle and calculate the standard enthalpy change of dissociation of hydrofluo