Ollscoil na hÉireann, Gaillimh GX_____
National University of Ireland, Galway
Semester I Examinations 2007 / 2008
Exam Code(s) 2BS1, 2BO1, 2BY1 Exam(s) 2nd Science
Module Code(s) BI204 Module(s) Biomolecules in the Cell
Paper No. Repeat Paper Yes
External Examiner(s) Dr. Paul McLaughlin Internal Examiner(s) Dr. L. Byrnes, Dr. J. Donlon, Dr. L. O’Connor,
Dr. J. O’Keeffe, Dr. M. Tuohy.
Instructions: Section A (25 marks) Answer all questions. In all questions there is only ONE correct answer. Record your answers on the OPTICAL READER SHEETS.
Section B, C, D and E (25 marks/ question: 20 marks for part A of each question and 5 marks for part B) Answer 3 questions, one only from each section. Answer questions from each section on a SEPARATE answer book.
Duration 3 hours No. of Pages 12 Department(s) Biochemistry Course Co-ordinator(s) Dr. Lynn O’Connor
Other Material MCQ optical reader sheet
Answer all questions in Section A All questions carry equal marks Section A is equal to 25 marks
In all questions there is only ONE correct answer
Do not write answers on this sheet. USE OPTICAL READER SHEETS ONLY
1. What organic compound is illustrated below
A) an alcohol B) a aldehyde C) a ketone D) a carboxylic acid
2. What organic compound is illustrated below
A) a thiol B) a primary amine C) an aldehyde D) a ketone
3. Identify the organic compound illustrated below
A) a primary amine B) a secondary amine C) a tertiary amine D) a quaternary amine
4. Identify the functional group illustrated below
A) hydroxyl B) acyl C) carbonyl D) thiol
5. Identify the functional group illustrated below
A) thiol B) phosphate ester C) phosphate D) phosphoryl
6. Identify the linkage illustrated below
A) ether B) ester C) amide D) carboxylate
7. Identify the linkage illustrated below
A) phosphate ester B) phosphoanhydride C) amide D) ester
8. In a typical eukaryotic cell the pH is usually around 7.4. What is the [H+] in a typical eukaryotic cell?
A) 0.000000074 M B) 4 X 10-8 M C) 7.4 X 10-5 M D) 2.3 nM
9. Water derives all its special properties from its: A) cohesiveness and adhesiveness B) high boiling point and melting point C) polarity and hydrogen-bonding capacity D) small degree of ionization
10. A moon on Jupiter was recently shown to have a weather system of liquid methane but there is no water. Any life that might exist on this moon would be unlike that on earth because:
A) water is a solvent for many biomolecules B) water is a chemical participant in many biological reactions C) water’s attraction to itself drives hydrophobic interactions D) all of the above are true
11. Which of the following is true of hydrogen bonds? A) The attraction between the oxygen atom of a water molecule and the hydrogen
atom of another molecule constitutes a hydrogen bond B) Hydrogen bonds form as covalent bonds between positively and negatively
charged ions C) Hydrogen bonds form between nonpolar portions of biomolecules D) A and B are true
12. Which statement is true about a reaction with an equilibrium constant, Keq, equal to 1000?
A) the forward rate constant is 3 times greater than the reverse rate constant B) The forward rate constant is 1000 times greater than the reverse rate constant C) The forward rate constant is 1000 times smaller than the reverse rate constant D) The forward rate constant is 3 times smaller than the reverse rate constant
13. If it takes approximately 20kJ.mole-1to break a hydrogen bond in water, approximately what energy value is required to break a covalent O-H bond?
A) 10kJ.mole-1 B) 100kJ.mole-1 C) 200kJ.mole-1 D) 450kJ.mole-1
14. In DNA, phosphodiester bonds form with hydroxyl groups of carbons number ________ and ________ of each deoxyribose sugar.
A) 2'; 3' B) 2'; 4' C) 3'; 4' D) 3'; 5' E) 4'; 5'
15. The difference between dGMP and GMP is A) the type of phosphodiester linkage. B) one hydroxyl group. C) syn versus anti conformation. D) the occurrence in DNA or RNA.
16. The tetranucleotide AGTC (in DNA) has a free hydroxyl group on A) A. B) A, G, T, and C. C) C. D) G, T, and C.
17. It is easier to melt DNA richer in AT than GC because A) AT are smaller than GC B) there is one less hydrogen bond. C) the helix pitch is longer in AT rich regions. D) All of the above
18. Which type of RNA is the most abundant in living cells (by percent)? A) ribosomal B) messenger C) small D) transfer
19. What is the approximate diameter of a chromatin fibre? A) 3 nm B) 30 nm C) 300 nm D) 3 mm E) 30 mm
20. DNA wraps around an octamer of histones to form bead-like structures called ________. A) nucleoids B) nucleosomes C) nucleoli D) chromatids
21. Histone ________ is not part of the histone octamer, but binds to linker DNA and is responsible for higher-order chromatin structure. A) H1 B) H2 C) H3 D) H4 E) None of the above
22. Histones associate with DNA primarily through ________. A) hydrogen bonding B) hydrophobic interactions with the exposed bases in the major groove C) ionic interactions with the phosphate groups D) disulfide linkages
23. The replication of DNA is ________ because ________. A) conservative; one strand of parental DNA is retained in each daughter DNA B) conservative; each daughter molecule has two new strands copied from the parental DNA template C) semiconservative; one strand of parental DNA is retained in each daughter DNA D) semiconservative; each daughter molecule has two new strands copied from the parental DNA template
24. It takes about the same amount of time for eukaryotic chromosomes to be replicated in vivo as it does for E. coli. Why is this true? A) Eukaryotes have multiple origins of replication; E. coli has one unique origin. B) Most chromosomes are approximately the same size. C) Eukaryotic replication occurs at a faster rate, enabling replication of the larger
chromosomes in about the same amount of time. D) The replication of DNA in eukaryotes is faster due to a quicker, more accurate
repair of mismatches.
25. Okazaki fragments are ________. A) the smallest subunits of DNA polymerase III B) short stretches of DNA formed on the lagging strand C) short RNA primers needed for initiation of polymerization
D) fragments of DNA polymerase I that lack 5' → 3' exonuclease activity
26. Which proteins are responsible for the unwinding of the double-stranded DNA during replication? A) ligases B) helicases C) topoisomerases D) primases E) lyases
27. While studying the structure of a small gene that was recently sequenced during the Human Genome Project, an investigator notices that one strand of the DNA molecule contains 20 As, 25 Gs, 30 Cs and 22 Ts. How many of each base is found in the complete double-stranded molecule? A) A = 40, G = 50, C = 60, T = 44 B) A = 44, G = 60, C = 50, T = 40 C) A = 45, G = 45, C = 52, T = 52 D) A = 50, G = 47, C = 50, T = 47 E) A = 42, G = 55, C = 55, T = 42
28. In the Lineweaver-Burk plot of an enzyme reaction, the Km (Michaelis-Menten constant) is given by the A) x-intercept. B) y-intercept. C) negative reciprocal of the x-intercept. D) reciprocal of the y-intercept. E) none of the above.
29. Enzymes catalyze reactions by A) increasing entropy of a system. B) increasing substrate energy. C) altering reaction equilibria. D) lowering total energy levels of reactants. E) decreasing free energy of activation.
30. A purely competitive inhibitor of an enzyme A)increases Km without affecting Vmax. B) decreases Km without affecting Vmax. C) increases Vmax without affecting Km. D) decreases Vmax without affecting Km. E) decreases both Vmax and Km.
31. In enzyme chemistry, the 'active site' concept means that A) there is a covalent bond between enzyme and substrate. B) functional groups on the enzyme participate directly in the reaction. C) in some cases enzyme activity is a result of a specific folding of a peptide chain. D) prosthetic groups are responsible for catalysis. E) catalytic rate is proportional to the substrate concentration.
32. The reaction catalysed by chymotrypsin: A) involves hydrolysis of a peptide bond on the C-terminal side of arginyl or lysyl
residues. B) takes place at a serine residue in the active site. C) involves hydrolysis of a peptide bond on the N-terminal side of aromatic residues. D) has an optimal pH of 1.5 - 2.5. E) is activated by di-isopropylphosphofluoridate (DFP).
33. At physiological pH, which amino acid is least likely to participate in acid-base catalysis?
A) Lysine. B) Tyrosine. C) Aspartate. D) Glutamate. E) Histidine
34. In a plot of 1/v against 1/[S] for an enzyme-catalyzed reaction, the presence of a competitive inhibitor will alter the:
A) Vmax. B) intercept on the 1/V axis. C) intercept on the 1/[S] axis. D) curvature of the plot. E) the determination of Ki.
35. In non-competitive inhibition A) the apparent concentration of active enzyme molecules is reduced. B) Vmax is increased. C) the concentration of active enzyme molecules is unchanged. D) the apparent Km is increased. E) the apparent Km is decreased.
36. The reason to rewrite the Michaelis-Menten equation (such as Lineweaver and Burk did) is to
A) Show the reaction on a log scale B) form enzyme kinetic data as a hyperbolic curve. C) calculate the change in entropy. D) Form enzyme data as a linear curve. E) formulate plot having a negative slope.
37. The Michaelis constant (Km) A) is a true dissociation constant, since it does not vary from one substrate to another. B) is equal to the concentration of substrate that gives Vmax. C) has a characteristic value for any set of enzyme and substrate and is independent
of enzyme concentration. D) is a measure of the equilibrium between active and inactive enzyme molecules. E) is obtained graphically from the slope of the plot of rate vs. substrate
38. What is the biological function of lysozyme? A) It activates trypsinogen. B) It is a DNA ligase. C) It regulates lysosomal pH. D) It hydrolyses complex polysaccharides of bacterial cell walls. E) It is a polymerase.
39. The mechanism of action of lysozyme includes A) distortion of the substrate. B) acid catalysis. C) proximity effects. D) participation of a specific aspartate residue and a specific glutamate residue. E) all of the above.
40. The catalytic triad of chymotrypsin and other serine proteases consists of A) three subunits of the enzyme. B) three amino acid residues adjacent in the primary structure which act to make
serine a strong nucleophile. C) three enzymes of similar structure. D) three amino acid residues close enough in space to make serine a strong
nucleophile. E) a triplet of glutamine residues.
Answer three questions from three Sections B,C, D and E. Only one question from each Section
1. (a) Describe how the 20 natural amino acids can be grouped into classes and subclasses based on their side chain properties. Include the name and 3 letter code for at least one amino acid for each subclass and explain whether the residue is more likely to be found in the protein interior or exterior. (b)
In the structure above a. What do the R groups represent? b. Give the roman numbers identifying the α-carbons? c. Give the numbers identifying the peptide bonds? d. Why is there limited rotation about the Ccarbonyl to Namide bonds? e. Give the numbers of those bonds that allow rotation of the peptide backbone?
2. (a) Describe the process of RNA synthesis (transcription) in prokaryotic cells, explaining the roles of the promoter and RNA polymerase. (b) A 20-year-old anaemic man is found to have an abnormal form of -globin that is 172 amino acids long, rather than the 141 found in the normal protein. Give an example of a point mutation that is consistent with this abnormality and explain why.
SECTION D 3. (a) Describe three mechanisms by which molecules are transported across the
plasma membranes of animal cells.
(b) Docosahexaenoic acid, 22:6 (4,7,10,13,16,19) is the predominant fatty acyl group in the C-2 position of glycerol-3-phosphate in phosphatidylethanolamine and phosphatidylcholine in many types of fish.
(i) Write the molecular formula of docosahexaenoic acid. (ii) Classify docosahexaenoic acid as an -3, -6, or -9 fatty acid.
4. (a) Write an essay on triacylglycerols (triglycerides), illustrating your answer with appropriate diagrams.
(b)Using the table below, classify the following fatty acids as -3, -6 or neither: a. Linolenate, b. Linoleate c. Arachidonate d. Oleate
5. (a) Glycolipids, Glycoproteins and Proteoglycans are important classes of
glycoconjugates in higher eukaryotes. Give a detailed account of (i) either the structure or
composition, (ii) cellular location and (iii) biological importance of two of these
(b) Fischer and Haworth projections of galactose are shown below. Please answer the
I II III
I II III
i) Does Image I represent the D- or L-enantiomer of galactose?
ii) Is galactose an aldose or ketose?
iii) Is the ring structure shown in Images II and III a furan or pyran ring?
iv) Complete the following statement. Image II represents the -anomer and
Image III represents the -anomer.
v) Complete the missing word in the following sentence. ‘Lactose is a –linked
disaccharide of glucose and galactose.
6. (a) Giving examples to illustrate your answer, describe the structure, composition,
biological function and applications of one structural polysaccharides and one storage
(b) The structure of arabinose is shown below. Please answer the following questions
(i) How many stereoisomers are possible for this molecule (including the one shown)?
(ii) Arabinose is a 5-carbon sugar. True or False?
(iii) Arabinose is an aldose or a ketose? Ans:
(iv) The Fischer formula above represents which enantiomer of arabinose?
(v) An epimer of D-arabinose is D-ribose. True or False?