SAMPLE_MIDTERM_F09 - Sample Midterm #1 from MCB124 NOW HEAR...

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Unformatted text preview: Sample Midterm #1 from MCB124 NOW HEAR THIS!! WARNING!!!!! ANSWERS NOT PROVIDED. These are NOT the only types of questions I will ask. You can use it as a guide but to study just this material is PERILOUS-you will be very unhappy with the result. Also BEWARE OF TRICKLY SIMILAR QUESTIONS WITH DIFFERENT ANSWERS!!! In other words LEARN THE MATERIAL NOT THE EXAM. VOCABULARY AND CONCEPTS A. Amino acid properties- match the factoid with the BEST amino acid (one-letter code). While some amino acids may have more than one match there is only a single way to get ALL of the points. Factoid ___ can act either as an acid or a base at physiological pH (~ pH 7) ___ the defining buried helical residue in coiled-coil proteins ___ side chain contains three nitrogens, most likely to interact with DNA ___ favored in turns because it only requires one main-chain H bond ___ most stablilzing to helices ___ side chain contains an amide group ___ its side chain contains phenol ___ Isosteric (same shape as) to valine ___ absorbs light maximallly at 280 nm, is a fluorophore ___ responsible for intra-chain cross-links in extra-cellular proteins ___ one-letter abbreviation for Glu, sidechain pKa is ~ ___ can most easily attain positive phi and psi bacbone torsion angles B. Match the words with the definition or property. Only one correct answer ___ secondary structure ___ bulge ___ major groove ___ tertiary interactions ___ base step ___ motif ___ B-form ___ quarternary structure ___ stacking interactions ___ beta strand ___ homologous superfamily ___ fold ___ turn ___ 4-way junction ___ topology ___ architecture a. describes multi-protein complexes b. connects two elements of secondary structure using 1-2 residues c. most common geometry of DNA d. contains almost 2 residues/turn and extends 3.2-3.4 /residue e. relative arrangement of secondary structure elements f. a short sequence associated with a fold or function g. classification of the 3-D path of a polypeptide or nucleic acid h. created when duplex segments contain consecutive mis-paired bases i. category based on protein sequence similarities j. provides protein access to the bases in DNA helices k. 3-D contacts between residues that are far apart in sequence l. result of London dispersion forces between planar bases m. pattern of connections between secondary structural elements n. two consecutive base pairs o. compact regular structures characterized by repeating backbone torsion angles and maximal backbone hydrogen bonds One letter code W R E L T C A Y H G P N Sample Midterm #1 from MCB124 p. Holliday structure (HJ) 1 STRUCTURE A. Some enzymes, like glutamine synthetase, are adenylated for regulatory purposes, which is to say they contain a 5'-phosphoadenosine (AMP, pA) attached via a phosphoryl ester to a tyrosine side chain (remember esters=hydroxy + acid-water). Draw the following adenylated tripeptide: K-Y(pA)-D (one letter code) . B. The 3' end of tRNAs contain the dinucleotide pCpA. When tRNAMet is charged, methionine is attached to the 3'-hydroxyl group via an ester linkage by methionyl tRNA synthetase. Draw this dinucleotide charged with methionine in the space provided on the next page. C. tRNAMet can be oxidatively damaged prior to protein synthesis and the oxidized Met is hydrolyzed away from the tRNA. On your diagram from (1) indicate the structure of the oxidized Met. 2 STRUCTURE Answer each question BREIFLY (1-2 sentences) A. Explain two of the physical-chemical factors that favor protein 2 structure formation B. Explain two physical-chemical factors that favor nucleic acid 2 structure formation C. Phi-Psi angles. Match the NON-IDEAL (but still reasonable) phi-psi angles (in degrees) on the right with the 2 structure on the left. The "i" and "i+1" are simply to indicate consecutive residues, and are not used to designate a specific position in secondary structure (like a beta turn). i i+1 1. 59 -119 -80 10 _______ A. beta strand 2. 65 -49 any _______ B. gamma turn 3. -130 120 -137 112 _______ C. alpha helix 4. -60 -45 -43 -70 _______ D. Type II' turn 5. Which "must" have at least one glycine? _______ 6. Which is MOST LIKELY to have a proline? _______ D. In the following questions, name the amino acid (eg. "Val6") in the primary sequence below that that answer the questions 1-4. 1 2 3 4 5 6 7 8 9 10 11 12 Gly-Pro-Asn-Leu-Glu-Val-Lys-Ile-Ala-Val-Leu-Pro 1. what residue would be closest AND on the same side of an alpha helix as Asn3? _________ 2. Which four residues would form the hydrophobic side of a beta strand in a beta sheet? ___________ ___________ ___________ ___________ 3. Which three residues would form the hydrophobic side of an amphipathic alpha helix? ___________ ___________ ___________ 4. Which two consecutive residues would most likely comprise a Type II' beta turn (see D above)? ___________ ___________ Sample Midterm #1 from MCB124 Tertiary/Quarternary structure (8 pts) Consider a protein motif that has two 6 residue beta strands and an 9 residue alpha helix (below). The strands MUST be paired and anti-parallel, AND the helix packed at a 90 angle against them as in this picture A. How many UNIQUE architectures are there for this motif (Careful!!!! 2 pts)______ B. Draw the architecture that allows for the shortest connections, and indicate ONLY that UNIQUE topology for this configuration by connecting the secondary structure elements. You MUST mark the N- and C-termini of the helix (use "N" and "C") and show the chain direction with an arrow at the ends of your connectors, pointing FROM N- to C-terminus. (4 pts) C. The above "module" can oligomerize to form an 10-stranded beta barrel. What -fold rotational symmetry would it have? ______________ What would be the answer to A) above if the strands were parallel?_______ NUCLEIC ACIDS A. 1. In the spaces above nucleic acid 2 structures named below, use lines and arrows to sketch the following nucleic acid structures (the duplex is give as an example). Arrows point 5'=>3'end. Duplex Stem-loop perfect Y-junction perfect 4-way junction 2. The following ssDNA sequence can form ONE OR MORE of the 4 above structures. Circle ALL of the ones that can be formed. 5'-GGTTGCCGAACGGCAACC B. 1. Draw the BASES in a G-T mismatched basepair as it would appear in dsDNA. Indicate the hydrogen bonds with dotted lines. Indicate the deoxyribose-phosphate with an "dR". 2. The G-T mis-pair in DNA is much less stable than either A-T or G-C basepairs? T or F 3. Based on your picture in the last answer, BRIEFLY explain why G-T basepairs do not accumulate at a high rate during DNA synthesis . 4. As it turns out, G-U mismatches can form an unusual triplex interaction in RNA tertiary structure. Draw a PLAUSIBLE base triplex and show all H-bonds (Hint: what is the third base?) ...
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