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Unformatted text preview: INTRODUCTORY BIOCHEMISTRY FINAL EXAM FALL 2005 SEMESTER PAGE - 9 ANSWERS TO FALL 2005 FINAL EXAM SECTION A MULTIPLE CHOICE QUESTIONS Detailed Solutions to Multiple Choice Questions 1. (C) C ysteine w ith !SH thiol side chain was shown as a typical reducing agent. More importantly, oxidation of cysteine to the d isulfide cystine (Cys!S !S !Cys) is a key aspect of protein structure, as the mechanism for formation of crosslinks (disulfide bridges) in proteins (e.g. re-oxidation to functional ribonuclease via d isulfide bonds). 2. (E) S erine is an amino acid component of membrane phospholipid called phosphatidylserine, which exhibits a n egatively charged h eadgroup. 3. (A) T he deamination (removal of amino !NH 2 group) of 5-carbon g lutamic acid yields 5-carbon "-ketoglutarate ("-keto acid ). This shows the close structural relationship between citric acid cycle intermediates and amino acids. 4. (A) T he Haworth ring structure of xylose has 5 carbon (i.e. p entose) with a nomeric C-1 p osition having two O atoms as "-anomer. Since C -1 is a nomeric carbon, indicating the aldehyde functional group carbon in the open chain form (i.e. a ldose). The structure shows a hemiacetal (R !O-H) for m utarotation , thus xylose is a reducing sugar. 5. (B) F MN is F lavin M ono N ucleotide which does not contain adenosine component. However, ATP, FAD, NADP + and coenzyme A are derivatives of a denosine (adenine base + 5C ribose sugar); more precisely, derivatives of nucleotide - A DP . 6. (B) N itrogenous bases (A, G, C, T and U) a bsorb UV light strongly at 260 nm. In 1930, F. L. Gates provided the first evidence showing the damage and killing of bacteria by UV irradiation at 265 nm, suggesting that nucleic acid is the genetic material. 7. (A) P urine h as a h eterocyclic double-ring structure comprising of a total of 9 atoms of C, N and H. Recall that C-1’ in (deoxy)ribose is $-glycosylic-linked to N-9 in purine bases (A or G). Six atoms with 4 carbons and 2 nitrogens are present in bigger ring (similar to pyrimidine), and three atoms with 1 carbon and 2 nitrogens are found in smaller ring. Thus, there are five C atoms and four N atoms in the purine ring system. The molecular formula of purine is C 5N 4 with 4 H atoms. Note that there are no N !N bonds (i.e. the N atoms are always separated by a t least one C atom ). 8. (B) T his is a challenging question to test understanding both of the covalent structures of the nucleic acid bases and also of the secondary structure of the double helix. An additional methyl group found in thymine can occupy space (i.e. p roject into ) in the major groove b etween the sugar-phosphate backbone of double helix structure of DNA. INTRODUCTORY BIOCHEMISTRY FINAL EXAM FALL 2005 SEMESTER PAGE - 10 9. (A) R ecall the mnemonics of some common s aturated fatty acids: let my pal stay around, w hich stands for lauric acid (C12:0), m yristic acid (C14:0), p almitic acid (C16:0), stearic acid (C18:0), and a rachidic acid (C20:0). 10. (E) A ll of the above statements are correct. 11. (A) F atty acids contain long hydrophobic hydrocarbon chain . They disperse in water and aggregate spontaneously to form s pherical micelles, with non-polar fatty acid chains buried in the core. Micelles range in size from a few molecules to thousands or more. 12. (E) T he key role of carnitine esters is to transport fatty acids across the outer and inner mitochondrial membranes. One form of carnitine acyl transferase acts at the outer mitochondrial membrane, converting the fatty acyl-CoA thioester into a fatty acyl carnitine ester. A transport protein moves this ester a cross the inner mitochondrial membrane. Once inside the matrix, the fatty acyl carnitine ester is reconverted to a fatty acyl-CoA thioester by another form of carnitine acyl transferase. The only fate of fatty acyl-Co A molecules on the mitochondrion is to undergo $-oxidation . 13. (D) B oth enoyl-CoA hydratase found in $-oxidation and fumarase in citric acid cycle catalyze hydration of an double-bond alkene (i.e. a ddition of H 2O to molecule, which is different from hydrolysis). Thus, both enzymes belongs to Class 4 - Lyase. 14. (D) Isocitrate dehydrogenase c atalyzes the oxidative decarboxylation, in which isocitrate (6C) is o xidized to "-ketoglutarate (5C) with a release of CO 2. The cofactor NAD + is r educed to NADH by accepting 2 eG + H + (i.e. o ne H G h ydride anion). 15. (B) M alonate (GOOC-CH 2-COO G) is a close structural analogue o f substrate succinate (GOOC-CH 2-CH 2-COO G). This is a classic case of competitive inhibition of succinate dehydrogenase, showing inhibitor with structural resemblance to substrate. 16. (E) A ll of the above are correct. 17. (D) D an Koshland postulated that h exokinase (first enzyme in glycolysis) undergoes structural conformational change (“induced-fit”) upon binding to substrate glucose. 18. (A) U nder anaerobic condition (i.e. n o involvement of mitochondrial processes such as citric acid cycle and electron transport chain), glycolysis takes place solely in cytoplasm . Formation of lactic acid implies the oxidation of r educed cofactor NADH by lactate dehydrogenase and the utilization of o xidized cofactor NAD + by glyceraldehyde-3-phosphate dehydrogenase. A t the first stage of glycolysis, o ne ATP is consumed in hexokinase step and one ATP is utilized by phosphofructokinase. A t INTRODUCTORY BIOCHEMISTRY FINAL EXAM FALL 2005 SEMESTER PAGE - 11 the second stage of glycolysis, 2 ATP are produced by phosphoglycerate kinase, and another 2 ATP are formed by pyruvate kinase. Thus, two net ATP are yielded. 19. (A) W olfgang Jünge proposed that the a subunit forms a channel through which H + flow back across the inner mitochondrial membrane, down their chemical potential gradient ()µ ). The a subunit contains two discrete “half-channels” for protons. One half-channel leads from the inter-membrane space side of the membrane into the a s ubunit; and the other half-channel leads from inside of the a subunit to the matrix. As a result, H + must jump from the a subunit onto the adjacent c subunit. 20. (D) T he C ori cycle is the re-synthesis of glucose, in which lactate produced from the muscle is transported via b lood circulation to the liver. 21. (C) B utter is mainly composed of s aturated fatty acids found in triacylglycerols. 22. (B) H exokinase transfers p hosphate group only, thus belongs to C lass 2 : Transferase. 23. (D) A ldolase is responsible for C !C bond cleavage, and belongs to C lass 4 : Lyase. 24. (E) T riose phosphate isomerase b elongs to C lass 5 : Isomerase, which converts the ketose p hosphate sugar (dihydroxyacetone phosphate) into a ldose p hosphate sugar (glyceraldehyde-3-phosphate) - functional group isomers. 25. (E) M utase is a particular subclass of C lass 5 : Isomerase, which rearranges the position of a group (e.g. phosphate) w ithin a m olecule (i.e. p ositional isomer). Phosphoglycerate mutase converts 3-phosphoglycerate into the positional isomer, 2-phosphoglycerate. INTRODUCTORY BIOCHEMISTRY FINAL EXAM SECTION B FALL 2005 SEMESTER PAGE - 12 SHORT-ANSWER QUESTIONS 1. John Walker solved the structure of the F 1 complex of the ATP synthase. 2. Standard Hydrogen Electrode undergoes reduction h alf-reaction (i.e. g ain of eG): 2 H + + 2 e G ÷ H 2(g) 3. (a) (b) (c) 4. Nucleo side uridine = uracil + 5C ribose sugar N-1 of uracil is covalently joined to C-1’ of ribose sugar via $-glycosylic linkage. 5. Balanced Equation: $-ketoacyl-CoA + CoASH ÷ F atty acyl-CoA (n !2) + CoA-SAc guanine heme 2,4-dinitrophenol (DNP) Explanation of Chemical Mechanism of Thiolase: Refer to Lecture Manual p.366 for detailed solutions. T his is an example of the reaction of a nucleophile with an electrophilic carbonyl $-carbon atom . The C !C bond cleavage is made possible by the r eactive $-dicarbonyl substrate (i.e. $-ketoacyl-CoA ). Briefly, the lone pair electrons from the nucleophile (CoA-S G) attack electrophilic carbonyl $-carbon to from a tetrahedral intermediate. * Y ou o nly n eed to draw the above diagram to obtain the full marks. INTRODUCTORY BIOCHEMISTRY FINAL EXAM 6. Option A : FALL 2005 SEMESTER PAGE - 13 “The role of non-covalent chemical interactions in protein tertiary structure.” Major points may include, for example: C globular proteins fold into well-defined structures (native conformations) C secondary structure elements ("-helix or $-sheet) remain largely intact as the protein folds correctly into tertiary structure C secondary structure forms locally, but tertiary structure forms globally, via longrange interactions between residues that may be distant on the primary sequence < for example, an acidic and a basic residue, distant on the primary sequence, may come together in space to form an ion pair (Coulomb interaction) in the interior of the protein < other weak interactions between residues, e.g. H -bonds, ion-dipole and dipole-dipole, will occur, and may involve peptide bond (C=O or H !N) or side-chain (e.g. amide, alcohols) functional groups C many tertiary structures are held in place by d isulfide bonds b etween cysteines, which form in specific patterns after the protein folds into its native conformation C native structure can be disrupted by heat or changes in environment, e.g. pH, ionic strength, chaotropic solutes (such as urea or guanidinium) C small changes in conformation at surface (e.g. $-turns) have large influence on overall tertiary structure C tertiary structure forms spontaneously, driven by non-covalent interactions, the native structure is the thermodynamically favoured (lowest-energy) structure C hydrophobic effect (mediated by v an der Waals interactions) results in a general “hydrophobic residues interior v s. polar residues on surface” effect INTRODUCTORY BIOCHEMISTRY FINAL EXAM 6. Option B : FALL 2005 SEMESTER PAGE - 14 “The role of non-covalent chemical interactions in the double-helix structure of DNA.” Major points may include, for example: C double helix forms spontaneously a s complementary single strands anneal C regular structure formed from irregularly shaped (large purine and small pyrimidine) bases, because the unit of structure is the b ase pair, not the base C strands are coiled about a common helix axis and cannot be separated except by unwinding from an end C there are no covalent bonds between the two complementary strands C double helix reversibly denatures (melts) into single strands, at high temperature C hydrophobic effect (mediated by v an der Waals interactions) drives bases into interior v s. polar sugar-phosphate backbone to exterior of double helix C van der Waals stacking interactions b etween adjacent bases stabilize double helix; aromatic rings of the bases are flat and almost p erpendicular to the helix axis C complementary Watson-Crick b ase-pairing o f A=T and G /C is mediated by H-bonding o f exocyclic and ring N and O atoms in specific patterns ...
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