Chem 135: First Midterm

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1 Chem 135: First Midterm September 30 th, 2013 Please provide all aswers i the spaces provided. You are ot allowed to use a calculator for this exam, but you may use (previously disassembled) molecular model kits. Icludig the title page, there should be 4 total questios spread over 5 pages. There is also a sixth page that should be blak. You ca use this last page for scratch paper if you eed it, but please remember to copy your aswers ito the appropriate exam questio space. Name: (1) (22 poits) (2) (10 poits) (3) (48 poits) (4) (20 poits) TTAL (100 poits)

2 1. May orgaisms produce cyclic peptides, which lack free N- ad C-termii. Suppose the followig (hypothetical) cyclic peptide has just bee discovered. The amio acid sequece, writte i the usual directio for a liear peptide aalog, is: VWSRGAEF a. Startig at the arrow, draw the side chais of this sequece o the backboe template show below. Draw the ioizable groups i their most promiet protoatio state at ph 7 (10 poits). start here HN HN HN N H b. If ay of the amide bods i the above structure are i the cis coformatio, circle them (6 poits). c. I geeral, polypeptides have the lowest degree of solubility whe they have o et charge. Cosiderig a rage of 0 to 14, which ph values would this be for the cyclic peptide (6 poits)? 2. I the space below, draw two peptide segmets cosistig of three amio acids each as they would be foud i a atiparallel beta sheet. You may abbreviate the side chais as R groups. Clearly idicate the hydroge bodig patter betwee the two strads (10 poits).

3 3. Phospholipases are a class of ezymes that cleave the ester groups of phospholipids. This ca be beeficial for digestio ad sigal trasductio mechaisms, but ca cause disruptio of the plasma membrae if left uchecked. As a example of the latter case, sake veom cotais large amouts of these ezymes to destroy the cells of the victim. P R - phospholipase A2 H 2 a. Assumig that the ezyme remais fuctioal at all ph values, would you expect the solutio ph to affect the overall thermodyamics of this reactio? Briefly explai your aswer (6 poits). H + H P R - b. Upo aalysis of a crystal structure of phospholipase A2, you fid evidece of a catalytic array cosistig of a asp residue, a his residue, two water molecules (represeted below by the atoms), ad a calcium io. However, remember that x-ray structures of proteis ormally do ot provide the locatios of the protos or the double bods. Fill these i o the followig diagram. Next, add the ester group to be hydrolyzed by the ezyme where you thik it would be located. Fially, provide a detailed, arrow pushig mechaism to show how this ezyme could hydrolyze the ester to provide the products show above. You may use R groups to abbreviate the ester structure as you see fit (12 poits). Ca 2+ N N

4 c. Suppose you geerate a versio of this ezyme i which the asp residue show above has bee replaced by a glu residue. You fid that the resultig ezyme has a 5-fold drop i k cat, but the value of K m is uchaged. What coclusio ca you make from this observatio (6 poits)? d. the axes provided below, sketch a graph for V vs. [S] for both the ormal ad the mutat ezymes. Clearly idicate which curve correspods to which ezyme (6 poits). V [S] e. Leavig the glu mutatio ad its associated drop i the value of k cat itact, is there ay way that the ezyme could be improved to achieve the same level of catalytic performace as the atural ezyme at low substrate cocetratio? What about at high substrate cocetratio (6 poits)? f. Because phospholipases cleave substrates with log hydrocarbo tails, they have a umber of o-polar amio acids i their bidig pocket. Usig the oe-letter codes, give 5 examples of amio acids that you thik would be foud i this locatio (6 poits). g. These amio acids would be expected to bid the hydrocarbo tails through the hydrophobic effect. Briefly describe the origi of this iteractio (6 poits).

4. Aquaporis are a class of proteis that allow water to pass through cell membraes, but ot protos or other ios.

I most cases, four idetical copies of these proteis assemble ito a tetramer that spas the plasma membrae, as show i a topdow view at right.

For some time, it has bee appreciated that alpha helices possess a C T large dipole momet that is idepedet of the specific side chais that are

Speculate o the specific structural aspect of the alpha helix that creates this dipole.

This brigs the positive eds of the helix dipoles together at a poit i the chael where oly oe water molecule ca pass through at a time.

5 4. Aquaporis are a class of proteis that allow water to pass through cell membraes, but ot protos or other ios. They are critical to the fuctio of may tissues i the body, icludig the kideys, the lugs, ad the eye. I most cases, four idetical copies of these proteis assemble ito a tetramer that spas the plasma membrae, as show i a topdow view at right. This provides four pores through which water ca freely pass. * * * * * = water trasport pores a. For some time, it has bee appreciated that alpha helices possess a C T large dipole momet that is idepedet of the specific side chais that are preset. The directioality of this dipole is show for a aquapori alpha helix o the right. Speculate o the specific structural aspect of the alpha helix that creates this dipole. Note that N T ad C T refer to the directioality of the polypeptide chai, but there are o free termii because this is a portio of a large protei structure (7 poits). N T b. All kow aquaporis possess two alpha helices that are orieted ed-to-ed, with their N-termial regios i direct cotact (see figure at right). This brigs the positive eds of the helix dipoles together at a poit i the chael where oly oe water molecule ca pass through at a time. This locatio is idicated by the white box i the figure. Sketch how a water molecule would be orieted i this positio as it passes through the chael. The protei wall is formed by other portios of the biomolecule, ad iteracts miimally with the water (7 poits). C T N T path of water molecules H 2 protei wall N T c. A critical feature of aquaporis is their ability to allow water to pass through, but ot protos or other catios. Briefly state how this helix-dipole gatig mechaism might achieve this selectivity (6 poits). C T H 2

6 This last page should be blak. You may use it as scratch paper, but if you do be sure to recopy your aswers ito the exam questios so that we ca grade them easily. Nothig o this page will be graded.

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