MBB 407/511 Molecular Biology and Biochemistry First Examination - October 1, 2002 Name Social Security Number This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is worth 2 points. Part II is short answer and drawing format. The first two of these questions are worth 15 pts each, and the last two are worth 10 pts each. Please write your answers to Part I here: 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25. Grade: Part I Part II II-1 II-2 II-3 II-4 Total 1
Part I. Multiple Choice. 1. The cellular process by which a DNA sequence is converted into a messenger RNA sequence is. (A) Reverse translation. (B) Transcription. (C) Reverse transcription. (D) Translation. 2. The principal function of the lysosome in eukaryotic cells is: (A) Protein synthesis. (B) Respiration. (C) Protein packaging. (D) Protein degradation. 3. The hydrophobic effect is primarily due to: (A) hydrogen-bonding between the hydrophobic group and water. (B) desolvation of hydrophobic groups in forming a "hydrophobic core", resulting in increased entropy of the system. (C) polar groups interacting in the "hydrophobic core". (D) all of the above. 4. For hydrogen bonds X-H --- Y, typical donor and acceptor atoms X and Y include: (A) O, N, or C (B) O, N, or S (C) C, N, or S (D) O, C, or S 5. A molecule which contains a hydrophilic head group and a hydrophobic tail is said to be: (A) polarized (B) amphipathic (C) orthorhombic (D) clathrate 6. It is well known that all of the common amino acids except glycine have chiral Cα atoms, and can be either L- or D-. One of the two common amino acids with a chiral Cβ atom in the side chain is: (A) Cysteine. (B) Serine. (C) Threonine. (D) Valine. 7. The ionization state of the cysteine sidechain at ph 10 is: (A) R-CH 2 -S-S-CH 2 -R' (B) R-CH 2 -SH (C) R-CH 2 -S - (D) R-CH 2 -S + 8. Given the following single strand of DNA: 5'-ATTGCACCT-3' the complementary stand of mrna which results from transcription is: (A) 3'-UAACGUGGA-5' (B) 3'-TUUCGTGGU-5' (C) 5'-UAACGUGGA-3' (D) 5'-TUUCGTGGU-3' 2
9. A-form RNA has a helical pitch of 2.8 nm / helical turn, and 11 residues per helical turn. Accordingly, the rise per residue ( Z / residue) is: (A) 2.55 nm. (B) 25.5 Å. (C) 2.55 Å (D) 0.255 Å 10. The melanocyte-stimulating hormone α-melanotropin has the folowing sequence: Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly-Lys-Pro-Val In the one-letter code of amino acids, this sequence would be: (A) STSMGHFAWGKPV (B) SYSMDHFAWGKPV (C) SYSMEHFAWGLPV (D) SYSMEHFRWGKPV 11. The right-handed α-helix is characterized by: (A) 3.6 Å / turn; 13 atoms per hydrogen-bonded loop. (B) 3.6 residues / turn; 13 atoms per hydrogen-bonded loop. (C) 3.6 residues / turn; 13 Å / turn. (D) 13 Å / turn; 3.6 atoms per hydrogen-bonded loop. 12. The helix-dipole moment can stabilize (or destabilize) the α- helical conformation by interacting with charged amino acids side chains at the N-terminal and C-terminal regions of the helical structure. Considering the distribution of charge which results from the helix dipole, would you expect: (A) positively charged amino acids at the C-terminus to destabilize the α-helix. (B) positively charged amino acids at the C-terminus to stabilize the α-helix. (C) negatively charged amino acids at the N-terminus to destabilize the α-helix. (D) negatively charged amino acids at the C-terminus to stabilize the α-helix. 13. In the absence of co-factors, hemes, and other prosthetic groups, the absorbtion spectra of proteins in the near UV range (250-300 nm) are dominated by the amino acid: (A) Phenylalanine (B) Tyrosine (C) Tryptophan (D) Hisidine 3
14. The symmetry operator which maps the low energy regions of the Ramachandran plots for an L- amino acid (e.g. L-Ala) into the corresponding low energy region of the D- amino acid (e.g. D-Ala) is: (A) φ φ, ψ ψ. (B) φ φ, ψ ψ. (C) φ φ, ψ ψ. (D) φ φ, ψ ψ. 15. For the helix-to-coil transition in DNA, it is known that H hc > 0 and S hc > 0. From this it follows that: (A) G ch < 0 at low temperatures. (B) G ch < 0 at high temperatures. (C) G ch > 0 at low temperatures. (D) G hc > 0 at high temperatures 16. Consider a fully relaxed circle of 400 bp double-stranded circular DNA of linking number L = 40, twist T = 40 turns, and writhe W = 0. By the action of topoisomerase, this circle is supercoiled into a tertiary conformation of linking number L = 36, with twist T = 40 turns. The writhe of the resulting supercoil will be: (A) W = +4 (B) W = +2 (C) W = -2 (D) W = -4 17. An amino acid with a hydrophilic side chain is: (A) Ile. (B) Leu. (C) Ala. (D) Asp. 18. For D-amino acids in synthetic polypeptides, most of the low energy regions of the Ramachandran plot have backbone dihedral angles: (A) psi > 0 (B) psi < 0. (C) phi > 0 (D) phi < 0 19. Ion exchange chromatography is a method for separating macromolecules primarilly on the basis of their: (A) Size (B) Charge (C) Hydrophobicity (D) Salt content. 20. Consider a β-bend to be defined by the phi-phi residues at the 2nd and 3rd positions in the amino acid sequence. A type-ii β-bend requires a phi,psi value on the right side (phi > 0) of the Ramachandran diagram at position 3. This implies that a type-ii β-bend has a high probability for which type of amino acid commonly found in protein sequences at position 3: (A) Pro. (B) Gly. (C) Thr. (D) Ile 4
21. A pair of homologous proteins functioning in the same biological context in two different genomes (e.g. human and mouse myoglobin) are called: (A) Orthologs (B) Structural Genomics (C) Parallelogs (D) Divergalogs 22. Consider a small protein of 100 amino acids. Next, consider that the only degrees of freedom in this protein are the 100 phi angles, the 100 psi angles, and 50 sidechain chi-1 dihedral angles. Finally, consider that each of these 250 dihedral angles can adopt 10 (and only 10) independent values. What is the number of possible conformations for this small peptide? Assuming that it takes one nanosecond to sample each of these conformations, how long would it take to sample all possible conformations? (A) 250 conformations; 250 x 10-9 sec. (B) 250 10 conformations; ~ 1 x 10 15 sec (C) 10 250 conformations; 10 241 sec (D) 13!10!; (13!10!) x 10-9 sec. 23. Assuming that this 100 amino acid protein actually folds in about 1 millisec, estimate the size of a "folding domain" -- that is the number of dihedral angles in the effective "folding unit" (sometimes called "foldons"). (A) three dihedral angles (B) six dihedral angles. (C) twelve dihedral angles (D) twenty dihedral angles 24. Highest thermal stability is generally associated with DNA sequences containing: (A) High AT : GC ratios (B) Equal AT and GC content. (C) High GC : AT ratios. (D) High polya content. 25. The pk a is a characteristic of the equilibrium between an acid (HA) and its conjugate base (A - ). This relationship is given by: (A) pk a = - ln { [HA] / [H + ][A - ] } (B) pk a = - log { [HA] / [H + ][A - ] } (C) pk a = - ln { [H + ][A - ] / [HA] } (D) pk a = - log { [H + ][A - ] / [HA] } 5
Part II. Drawings and Derivations Question II-1.(15 pts) Draw the structure of the polypeptide: Phe-Pro-Asp-Ile in its ionization state at ph 7, showing any formal charges on each atom. Label on the structure the dihedral angles φ, ψ, ω, χ 1, and χ 2 of the amino acid residue Asp. 6
Question II-2 (15 pts) Draw the structure of the RNA oligonucleotide at ph 7 5'OH-AGC-PO 4-2 3' including the phosphate backbone (with correct charges indicated), the ribose ring, and the bases. For the adenine ribose ring, label the 1', 2', 3', 4', and 5' carbons. 7
Question II-3. (10 pts) A polypeptide sequence can be determined by cutting it into overlapping fragments with proteolytic enzymes, purifying these fragments by reversed-phase chromatography, and sequencing each of these peptides using an the Edman reaction. You have been given a 12 amino acid long polypeptide which plays an key role in tumor growth. Digestion of the peptide with the enzyme trypsin (which cuts after Arg and Lys residues) yields the following three peptides plus 1 equivalent of free arginine. Asp-Gln Leu-Ile-Phe-Ala-Lys Gly-Val-Tyr-Lys Subsequent digestion with chymotrypsin (which cuts after the aromatic residues Phe, Tyr, and Trp) yields the three peptides Lys-Arg-Leu-Ile-Phe Ala-Lys-Asp-Gln Gly-Val-Tyr Based on these data, determine the sequence of this peptide. 8
Question II-4. (10 pts). Design a sequence of polypeptide containing up to 25 amino acids which is likely to form a hairpin α-helical structure (two antiparallel α-helices), with a β-bend in the center of the sequence. Show you proposed sequence using the one-letter code of amino acids, and explain the special features of your design. In your sequence be sure to include the following features to favor α-helix formatation: (i) hydrophobic periodicity; (ii) charged sidechains oriented to interact favorably with the helical dipoles; (iii) good ionic interactions between the two α-helices Also include amino acids in the β-bend at the center of the sequence which favor β-bend formation. (Hint: Gly and Pro are both poor helix formers). 9