classes_spring08_153A-1ID29_080428_PracticeMidKey

classes_spring08_153A-1ID29_080428_PracticeMidKey - LAST...

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Unformatted text preview: LAST NAME 1. Consider the tetrapeptide whose sequence is ALEN. a) Calculate the net overall charge of this peptide at pH 2. (6 pts) b) Calculate the isoelectric point for this peptide. (4 pts) Show ALL your work below for credit. State both of your final answers in the box elow. b , 9'42 P Net charge at pH 2: O U ‘l’ IL . 9219? —~— -t ‘3’ I; '4 $6“ Isoelectric W“ Tr.- $59 point: t I 4!, 53* 7’ _ 69 3 .2, _ 69$ __.__ \x ‘ W :- 315' gas 6‘?” 63" so 2. A hypothetical enzyme catalyzes a reaction that is d313§ndent upon the ionization state of a primary amino grbup (-NHZ) found in the activgfie. In the enzyme’s active form, the amino group is positively charged while int @active form, the amino group is neutral. The pKa of the amino group has been gkperimentally determined to equal 8.9. Calculate the fraction (express as a percentwg if you prefer) of the enzyme molecules that would be active at pH 7.2 and writecfir final answer in the box. Show all your work for credit. (6 pts) we.“ (29“? H: Khfl' R“ °l HA” P P 02%;? “Mama: 3 0.0'ZH-Tl.cz t [M W1, enzyme gagflfl‘ m um "A = L. bf 0.07.: [Ad - "'75 78 molecules: M363“ GSA V m 3. What information is represented by a Ramachandran diagram? Circle the one best answer. (4 pts) ' depicts the values of phi and psi that are conformationally allowed in a peptide. b t depicts the values of phi and psi that are not conformationally allowed in a peptide. 0) It depicts the values of phi and psi that are most sterically hindered in a peptide. d) It depicts the secondary structure of a peptide. rt? LAST NAME 4. Circle true if the statement is true or circle false if the statement is'false. (6 pts) a) @a False: A reaction whose product has a lower ground state energy compared to 4 the substrate will have an overall negative AG. b) True or anti-parallel beta-sheet describes a structure where the beta strands are all oriente such that the N-)C directionality is the same between neighboring strands. é? V 0) True 0@ alseaa beta barrel structure is composed of twisted helices. ~59 5. A drug was designed to inhibit a certain enzyme that is linked to heart disease. A biochemist measured the dissociation constant, KD, for the drug in the presence of enzyme as a function of pH and got the following results: a) Compare the effect of low pH and high pH on the affinity of the drug for its enzyme target. (4 pts) TM‘MMW birds»?! JV? ' at Emu Pfigomd/w!’ at We - b) According to this data, will this drug» 6 more effective (a better inhibitor) under acidic or basic co ditions? (2 pts) 9‘ o Oil; to ‘6‘ . @4359 6. What volume of 0.5 M e’tic acid and 1 M NaOH is needed to make 1 L of a 100 mM acetate buffer at pH 4.5%- Assume that the pKa of acetic acid is 4.76. Write both of your final answers in the fibelow. Show all your work for credit. (10 pts) § 33$ CID" + .u + Volume of 0.5 M ®~§§ A A— I acetic acid: 0‘ Z-L. .295,» PH: Kr”, (£55 1 ‘3, ' VolumeoflM s P. at [W W gait 45.4.74, r908 [A1 6.035!» [HM 035000 was qumll Moll now: Q)” ' - 1:“ r m 40 a_ 0% @msu)<ig_: 0.07.51. at“ 0533 f? I“ . M3 '3' l0“ \ 0.2L owl-{c add LAST NAME 7. Circle true if the statement is true or circle false if the statement is false. (8 pts) gig?! False: Mad Cow disease and Creutzfeldt-Jakob disease are examples of 1 s that are associated with protein misfolding. b) True or he tertiary structure of collagen consists of a triple helix with a left— handed quaternary structure. c) True on enzyme kinetics, the steady state assumption says that the Q3}? concentration of substrate (and the concentration of product are at equilibrium with efih other. ,4? (10$ d) ru or False: An enzyme lowers the energy of a reaction’s trans1t10n stag: g" 6}. {b .- ‘ $5 \2. 8). Acetylcholinesterase catalyzes the hydrolysis of the neurofisnsmitter acetylcholine. The Km of this enzyme for its substrate is 90 uM. In a re ' on mixture containing 8 nmol/mL of acetylcholinesterase and 100 uM acetylchgh e, a velocity of 30 umol mL'1 5‘1 was observed for the'Teaction. 039‘ a) Calculate the Vmax for this amount of enzym§§ rite your answer in the box. For credit show ALL your work. (4 pts) \lu :' ‘) war 5 m if; ED {M l [S] §6v®® [S “ V,(Km+fél\ it 9&3 $2; b) Cgfi‘iflate the catalytic efficiency for acetylcholinesterase. Write your answer in the $35K For credit show ALL your work. (4 pts) G’ we“ : Symon mu}. Catalytic ? 0 M efficiency: ‘ . / 7i “My . ‘4‘ LAST NAME 9. An E. coli cell is grown at a relatively low temperature. a) Will its cellular membrane be more enriched in saturated fatty acids or unsaturated fatty acids? Briefly explain your answer (4 pts) w uan {61- L9/: MLVISwé, {a 0M mm fluid at £914) Enigma b) You devise a way to increase the concentration of exogenous: cholesterol in a mutanm E. coli’s cellular membrane. In general, what effect will this have on the fluidity ofgk mutant’s membrane at low temperatures? «15“ Mummi- W'W mcmbri/awb 39$. ‘Q 10) Below is a list of names or descriptions that may or may not mgffih the chemical structures or graphs shown below. Mark the box next to each sgafizture or graph with the letter of the name or description that best describes it. Each @he or description is used only once. nothing; are not described in the list below §ark£hese boxes with an X. S9 ON , ‘3 _ a”, Me 2. a) The product of an enzyme catalyzed reactlon thatgéfiuires the presence of two Mg ions in order for metal ion catalysis to occur 3’ b) A structural component found in a bacterial§® 1 wall c) S—adenosylmethionine .gsa d) An ionic detergent \ e) Tocopherol, a lipid oxidation-redurgb‘i cofactor D An N—acyl fatty acid derivative glfifiphingosine 5 H2 N HO\ ,Io 1\ I \> H2 ills ‘i \ N c—s—C—C—C—H O H H l V 2 2 NH2 OHOH COONa HO CH3 . HO / CH3 CH3 CH3 I [E] . Hack/\O a \’/\.~//\/I\CH3 HO OH @ CH3 CH3 / / /J\ H0 \ V,o c 0 _ ém A \p /0 Protein CH @ / \ o sci \c Hzc/ \o / ‘% E] H2 H3 _ 5 _ LAST NAME 0 HNACHQWCHS HO .._V,,/~»\ "/..e~._~.:% /,r(CH2)12CH3 W [a l 1. The three—dimensional backbone structure of a membrane protein with two transmembrane helices was determined usmg ’ NMR spectroscopy. The region that spans the membrane 18 shown; a) What is the n e of‘this motif? Xe/oo ~MLV _ b) Which amino acid seq ence do you most likely expect to find 1n either helix? Explain your answer. i) A—K-V—S-E—F-I ii) A-K—V-S-D—F—I ; e» . [We iii) A-V-V-S—D-F—I/ Meal WAwa gs @A-V-V-S-L-F—I W‘de am Mon *3“ .§‘5‘ in a W - “ix c) The peptide segment that connects e e ices is f on the outer face of the membrane. On a hydropathy plot, do you expect the§za residues to have positive or I ic negative values? Explain your answer. (peg W 0m 46"“ " {a e“ a h Lilo 91““ _ , <1) You don’t trust the NMR spectroscopy and decrde 0 use a different techimque to COW the 3D 5 cture 0 this membracge protein. What technique do you use? rm!) cme‘fioql a! $6” _ e) Name a detergent that 0 an 13$? to denature this protein. He. Sodium cit) [swiftly 12. Lysozyme is an antiege’t‘erial agent that hydrolyzes the (31 —>4 linkages in the repeating unit of Staph coccus aureus. (1,“ Wall - , . a) Give the full nam the hexose derivatives that compose the repeating unit. re" Nea l (Wm/W? 6° N, otch W b) Noncovglé‘tft interactions help sta ' ize the Structure of the bacterial cell walls. Name three dggarent fim tional groups on £1; repeating unit that are involved. \ am no t “tel @Tenicillin is more effective in fighting Staphylococcus infections. How is its action different from lysozyme? It inhibits erosslc‘nkm) PQVHdfiji/IW Q3” ...
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