midterm2_key_2007

midterm2_key_2007 - Name:__£_’(¢____—_—— Last...

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Unformatted text preview: Name:__£_’(¢____—_—— Last First Short Answers oints as indicated' 40 ts total 1. a. (5 pts) Use a simple but clear drawing to illustrate the difference between a parallel and an anti-parallel B sheet§Show the hydrogen bonding patter in each. . r 5 “H,” {)m Hal 1 M N O = m:’tm7é—,« & GE (9 C 0 XV} 0% 41 -: avg/95.444 \, ,/0\ ce-N an‘tipnrnllg/j N C b. (8 pts) Give a brief defini ion an a simple sketch of the following: A. Primarystructure ‘ like Sail/Mm“ 91C mama cieir‘”; N—vmzt— Asp- Lem- my- «at», - (_ B. Secondary structure: “45””; 3a£€x:.c,b\9m} beta/(9,». 0.9M; {xiv helices! or- (ales-£94 Sejw'zvfj W M” é saw 0&2 c. TertiarytstEUCture ; m ‘FDIJIH; ail-s Shy/a polypefl'b'dg emu l “(4‘ OII‘NIOv-nsfonal Space D. Quaternary structure 3 1%. We; F‘n whirl“ $91,.ng .fiobhd SuLuan esxadek {N 430/», G J‘La’hf 6Vfi‘ha0 maéawfifi'fik (pmiefln 0,9,9 wank” P 9 ~ {Fate-.15 no Name: Last First 2. A) (4 pts) Draw the Ala-Ala-Ala tripeptide. 3 4e ’ J l) 3% / H N 11/ N V cl 21$ /€ 3 J. O 0 /\ \ N \ a z 0 9 H CH3 I H H 0 B) (6 pts) Mark the backbone bonds about which no rotation is allowed with a star, and the bonds used to generate a Ramachandran plot with an arrow and their name. Why is rotation around the starred bonds not allowed? 9 0 0 -- L l H 1- 5‘5 59'“ h’“"{_ A N\/ H //\\‘N\’H 0(aqu Lawmf. AVILW (6073) m my)”; ya 5.: muff “fig; 3. (5 pts) Derive the Michaelis-Menten equation. Start by write the mechanism that / describes the reaction that they treated. Km s r. a"? C 4 s 23 Es " E no #5?“ all/Es) W 1 ( \ (-1": ~ KMLE‘L—‘u - kg‘f 2 0 Km 1 £5550. W- [Es‘ {EST— 151:? M:- l<m \ \. ZEB" Eiéa e £551 /,. ‘\ __ K U33.) ‘ ((EEJML ~£E5\:) {gal “mewwm J Kim 3 (rr\ ‘ (77‘ /‘-. Fl: r 1. Name: ~—/ Last First 4. You accidentally mixed up two samples of the enzyme dihydrofolate reductase (DHFR). One sample had trimethoprim, an inhibitor of dihydrofolate reductase (DHFR). The other sample had no inhibitor. You label the tubes “A” and “B”. A protein quatitation shows that the two tubes contain equal amounts of the DHFR protein. You proceed to perform enzyme assays on the DHFR activities in the two tubes to try to detect the effects of inhibitor. The results for sample A are plotted below, and the results for sample B are given in the table. Use this information to answer the questions below. “IIIIIIIIIIIIIIIIII MIIIIIIIIIIIIIIIIII 'IIIIIIIIIIIFIIIIII filllllllllllflfllllll IIIIIIIIIIHIIIIIII “IIIIIIIIIIHIIIIIII 'IIIIIIIIIHIIIIIIII ., ~w mlllllllllfllllllllafilé7 <mwmmm lull-Illnllllllaal Mllllllllfllllllllll III-lllmlgaillllll MIIIIIIImEIIIIIIIII llllllfilllllllllll WIIIIIIHIIIIIIIIIII -0.6 -O.4 —02 0.0 0.2 0.4 0.6 0.8 1.0 ms (1IpM) Data for Sample B: r " . if: 9.1 a) (3 pts) Using the data provided, determine which sample is the comm] sample no, rm:— If I‘M E; fjvfi‘ containing the trimethoprim inhibitor? z... j b) (4 pts) What are the Km and me: for DHFR in the assay that does not contain trimethoprim? Include units for both values. _, ‘ "‘~T“:i:*“’“”""‘"""""-l _ ._...—......V... ,2 . q / / MI? J A! A / / > 1771419/ a? in t / 4;...42/ - / '///1=’t?f€ "I; [fl .‘ m w m A WWW Mum-WW if , ,‘r W. / v" _ fl , 1/ '17-. 5” fl " Zf/u. // '/ I Last "' First Name: d) (3 pts) You determine that the concentration of trimethoprim in the inhibited samEl§§ is 1 nM. What is the K; for methotrexate (include units)? // 47‘ /_—L - /-,/L I I f! A/ '90252\ ’/ : (1/ /( 1., :3 {6, at K; j; -— \ I / ' A _ 'J L“ » M~-~= : __/__,___f t: __ / '] : 1 4S '— -°‘f"’4~ fl 7( : * .3rr3; ;; [IA , /’>¢/J,j,¢: -// K: - “ k; x n. «a 5 A, ,r' flfl/ L g l K j y (.al’; . 3"“? L 2 3 .2 7: w (in: 4,! I ‘ L y: sJ-Ji" ’H‘ e) (2 pts) Which of the following mechanisriiE‘fifild 5e§T ill'fi'étr‘ate ffie'i'r’iteraction of methotrexate (I) with DHF R (E)? (circle one) A. B+s<~§ 133+; E+P B. E+S<—-_>.ES<—; E+P + + + 1 1 1 El +s<-—___>ESI ES] <—_> E1 +P C E+SSESSE+P @E+S<—; Es<—>E+P flaw/‘5?!“ + + l I Multiple Choice 13 pts each; 60 pts total) 1. Where CCl is the oc-carbon, N represents the amide nitrogen and Co is the carbonyl carbon of amino acids in a peptide, the peptide backbone of a protein consists of the repeated sequence: a. -Ca-N-Ca- b. —N—co-c..- figs—Newco— d. -Co-Ca-N- e. none of the above 2. Resonance in peptide bonds results in all EXCEPT: a. approximately 40% double bond (coplanar) character. b. restricted rotation in the peptide backbone at the N-COI bond and Cal-CO bond. 9. the coplanar six atoms of the peptide bond group of atoms. a COL-carbon that is out of the coplanar group of atoms. é. Co-N bond distance that is shorter than normal, but longer than C=N bonds. 3. Fibrous proteins, such as collagen, have which one of the following properties? a. Highly soluble in water. b. Their hydrophilic residues are directed into the interior of the protein. 0. Exhibit enzymatic activity. ,I‘;:;_,i"3:;§Serve structural roles in the cell. r e. Monomeric. 4. Globular proteins are usually all EXCEPT: ‘ ,_'.>l?(§:>}‘i)lnsoluble in water. " B. Roughly spherical. (j: N c. Folded so that the hydrophobic amino acids are in the interior of the we. "L Armolecule. U fZQJT-Iydrophobic side chains are exposed to the water. i e. None are true. 5. The amino acid sequence is defined as structure. c. tertiary d. quaternary c. all are true 6. (Jr—Helix and B-strand are components of structure a. primary secondary “‘ c. tertiary d. quaternary e. all are true 7. All of the information necessary for a protein to achieve its final folded structure is contained within its structure. "primary " “V” b. secondary c. tertiary d. quaternary e. all are true 8. Amino acid analysis of a protein gives: a. the sequence of the protein. number of each amino acid in the protein. ‘ ""c. the molecular weight of the protein. d. the percentage or ratio of some amino acids in the protein. e. an identification of the N—terminal and C-terrninal amino acids. 9. The amino acid sequence is NOT: a. a distinctive characteristic of a polypeptide. b. encoded by the nucleotide sequence of DNA. form of genetic information. ‘“ (1. read from N—terminal end to C-terrninal end. e. variable for proteins with the same fimction from different organisms. 10. Edman degradation will: a. determine the C-terminal amino acid by using a carboxypeptidase. b. cleave the protein into a multitude of smaller peptides. 0. compare overlapping sets of peptide fragments. A determine the N—terminal amino acid. . generate two difiemnt, but overlapping sets of peptide fragments. 11. The C-terminal residue of a polypeptide can be determined by reacting the polypeptide with: a. chymotrypsin. arboxypeptidase. c. trypsin. e. none of the above. Name: Last First 12. Most protein sequence information is now derived from: a. chemical sequencing (Edman method). b. mass spectrometry. c. mass spectrometry-mass Spectrometry. translating the nucleotide sequence of genes into codons, and thus amino 5 acid sequence. e. none of the above 13. Amino acid side chains capable of forming hydrogen bonds are usually located on the protein and form hydrogen bonds primarily with the {I'VE/surface, water solvent "Mb. interior, water solvent 0. surface, other amino acid side chains d. interior, other amino acid side chains 6. all are true 14. A Ramachandran plot shows: a. the amino acid residues which have the greatest degree of side chain rotational freedom. b. residues with sterically allowed rotational angles between R groups and or- carbons in apeptide. residues with sterically allowed rotational angles between Ca and the amide nitrogen (Ca-N) as well as between Cat and the amide carbonyl carbon (Ca-CO). d. residues with sterically allowed rotational angles about the amide nitrogen (NH) and CO. e. the sequence of amino acid residues in a—helix, B—sheet, etc. 15. Polylysine is a random coil when the pH is less than 11, while it forms an on—helix if the pH is raised to greater than 12. This is because at pH 12: a. the lysine residues are negatively charged which electrostatically stabilizes the helix. b. the positive charges on the lysine residues stabilizes the oc-helix. ‘ the lysine residues are neutral which eliminates electrostatic repulsion ’ 1 between the R groups. (1. the high concentration of OH- ions in solution reduces the electrostatic repulsion between the R-groups. e. the lysine side chain changes configuration with pH. 16. Tertiary structure is defined as: a. the sequence of amino acids. the folding of a single polypeptide chain in three-dimensional space. c. hydrogen bonding interactions between adjacent amino acid residues into helical or pleated segments. d. the way in which separate folded monomeric protein subunits associate to form oligomeric proteins. e. all are true. 17. Why does the core of most globular and membrane proteins consist almost entirely of oc-helix and B—sheets? . Hydrogen bonded structures must be kept away from water solvent. . Highly polar N-H and C=O moieties of the peptide backbone are completely hydrogen bonded in regular secondary structural elements in the hydrophobic core of the protein. c. Hydrogen bonding only occurs in the core of proteins. d. Trapped water stabilizes the helix and sheet structures. e. None are true. 18. Proteins can be unfolded (denatured) by which of the following? 3. Heat b. Detergents c. Guanidine hydrochloride d. Urea All of the above. 19. The most important conclusion from Michael Hecht’s four-helix randomization experiment (Science, 1993) is: a. All proteins fold quickly b. Any sequence can give a four-helix bundle protein @Binary patterning (polar outside, nonpolar inside) is critical to protein folding d. Serine is not tolerated on the interior of a protein e. None of the above 20. Electrostatic interactions among amino acid residues on proteins may be damped out by high concentrations of: a. water. b. organic solvents. @ salts. ~ . heat. e. all of the above. ...
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midterm2_key_2007 - Name:__£_’(¢____—_—— Last...

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