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SAMPLE_FINAL_Qs_F09

SAMPLE_FINAL_Qs_F09 - SAMPLE FINAL QUESTIONS(These are only...

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SAMPLE FINAL QUESTIONS (These are only PAST questions- they do not cover new topics!) MATCHING (35 pts) A. Amino acid properties- match the factoid with the BEST amino acid (one-letter code). There is only a single way to get ALL of the points. (15 pts) Factoid One letter code ___ can act either as an acid or a base at physiological pH (~ pH 7). C ___ the defining buried helical residue in coiled-coil proteins R ___ most likely to be found preceding the first residue in a helix D ___ basic side chain with five rotatable bonds P ___ side chain is CH 2 OH S ___ first residue in all newly translated proteins A ___ Isosteric to (same shape and size as) valine Y ___ responsible for intra-chain cross-links in extra-cellular proteins L ___ can most easily attain positive phi and psi bacbone torsion angles W ___ favored in turns because it only requires one main-chain H bond T ___ side chain most likely to interact with guanine bases in DNA N ___ aromatic side-chain, forms covalent bonds with DNA in Type IB topoisomerases M ___ absorbs light maximallly at 280 nm, is a fluorophore H ___ has the highest helical propensity G ___ sidechain contains an amide group K B. Match the words with the definition or property. Only one correct answer (20 pts) ____ protein stability a. major driving force for polypeptide compaction ____ junction b. at this, the amount of folded and unfolded states are equal ____ turn c. helix geometry that cannot be found in RNA ____ B-form d . Always unfavorable for folding ____ base step e. connects two elements of secondary structure using 1-2 residues ____ indirect readout f. sequence-specific contacts between amino acids and bases ____ motif g. bind to palindromic DNA sequences (inverted repeats) ____ tertiary interactions h. 3-D classification of polypeptide or nucleic acid ____ counterion condensation i. Binding specificity that arises from the sequence- dependence of deformations away from B-form ____ fold j. 3-D contacts between residues that are far apart in sequence ____ major groove k. result of London dispersion forces between planar bases ____ melting temperature l. energetics controlled by base-stacking interactions ____ direct readout m. compact regular structures with repeating backbone torsion angles and maximal backbone hydrogen bonds ____ Cp for folding n . proportional to surface area difference in F and U states ____ Hydrophobic effect o. describes a general advantage for binding polycations to DNA due to entropy ____DNA bends p. two consecutive basepairs ____ homodimers q. a short sequence associated with a fold or function ____ stacking interactions r. Difference in free energy between folded and unfolded states ____ chain entropy s. where three or more helical nucleic acid segments are joined ____ secondary structure t. provides protein access to the bases in DNA helices
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SAMPLE FINAL QUESTIONS (These are only PAST questions- they do not cover new topics!) Folding Concepts ( 17 pts ) In order to analyze energy differences between U and F states, it is critical to know the differences in their structural properties. Using understandable sentences or phrases (one or two dangling key words will be given NO CREDIT), DESCRIBE TWO UNIQUE
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