Name: __________KEY______________ 1 7.012 Exam One -- 2006 KEY Exam starts at 10:05 am and ends at 10:55 am. There are 10 pages including this cover page. Please write your name on each page. Only writing on the FRONT of every page will be graded. (You may use the backs, but only as scratch paper.) Question 1 21 pts________ Question 2 35 pts________ Question 3 14 pts________ Question 4 30 pts________ TOTAL out of 100_______Name: __________KEY______________ 2 CNHHHHHHPeptide bondsCONHCCOHR1NHCCONCHHHR2R3Protein SynthesisSide chain, uniqueto each differntamino acidIndividual amino acidsare linked through thesegroups to form the backbone of the protein.GENERIC AMINO ACID:STRUCTURES OF AMINO ACIDSCCOOHNH3R-+VALINE(val)TYROSINE(tyr)TRYPTOPHAN(trp)THREONINE(thr)SERINE(ser)PROLINE(pro)PHENYLALANINE(phe)METHIONINE(met)LYSINE(lys)LEUCINE(leu)ISOLEUCINE(ile)HISTIDINE(his)GLYCINE(gly)GLUTAMINE(glN)GLUTAMIC ACID(glu)CCOOHNH3CH2OHHHHH-+CCOOHNH3CH2-+CCOOHNH3CHOHCH3-+CCOOHNH3CH2OH-++COO-CNCH2CH2CH2HHHCCOOHNH3CH2HHHHH-+CCOOHNH3CH2CH2SCH3-+CCOOHNH3CH2CH2CH2CH2NH3+-+CCOOHNH3CH2CHCH3CH3-+CCOOHNH3CHCH3CH2CH3-++CCOOHNH3CH2CNCNHHHH-+CCOOHNH3H-+CCOOHNH3CH2CH2OCNH2-+-CCOOHNH3CH2CH2OOC-+CYSTEINE(cys)CCOOHNH3CH2SH-+ASPARTIC ACID(asp)-CCOOHNH3CH2COO-+CCOOHNH3CH2CONH2-++CCOOHNH3CH2CH2CH2NHCNH2NH2-+CCOOHNH3CHCH3CH3-+CCOOHNH3CH3-+ASPARAGINE(asN)ARGININE(arg)ALANINE(ala) at pH 7.0Name: __________KEY______________ 3 Question 1. (21 pts) You are studying a di-peptide with the sequence N-asp-ser-C. (a, 4 pts) Draw the structure of this di-peptide at pH7. O O ll ll N-terminus H3N+–C–C–N–C–C – O – C-Terminus CH2 CH2 C OH – O O (b, 4 pts) Draw the structure of this di-peptide at pH7 if it had been phosphorylated on one of its R groups. O O ll ll N-terminus H3N+–C–C–N–C–C – O – C-Terminus CH2 CH2 C O – O O P O O – H H H H – OName: __________KEY______________ 4 (c, 8 pts) If an interaction occurred between two proteins via each pair of the following amino acids, what is the strongest type of bond that would form between the amino acids of each pair? Your choices are: Hydrogen bond, ionic bond, hydrophobic effect, covalent bond, and van der Waals force. (i) Cys and cys Covalent bond. Two cysteines can form disulfide bonds togther, which are a type of covalent bond. (ii) Tyr and his Hydrogen bond or van der Waals were accepted here. (iii) Phe and arg Van der Waals. Phe is hydrophobic and arg is charged so there are no other bonds between them. (iv) Phe and val Hydrophobic. The R groups of phe and val are both non-polar hydrocarbons. (d, 5 pts) Which of these is a Hydrogen bond that is correctly drawn? Of the four options below, circle all that are correctly drawn. The series of dots ( ) indicate hydrogen bonds. The one above doesn’t work because carbon is not electronegative enough for there to be a partial charge on the C and the H that are bonded together. The one below doesn’t work because both Hs have a partial partial positive charge on them so they wouldn’t attract each other. O N H C N N H H H C C O H H H H H N H H H OName: __________KEY______________ 5 Question 2. (35 pts) You imagine that not all life forms (if you include viruses and aliens) must have double-stranded DNA molecules as their genetic material. Theoretically, a life form could have a genome made of: single-stranded DNA, single-stranded RNA, double-stranded DNA, double-stranded RNA, or a hybrid of one strand of RNA with one strand of DNA. Which type of genome is each of these life forms most likely to have? (a, 3 pts) genome = 26%G, 6%T, 26%C, 18%U, 24%A A hybrid of one strand of RNA with one strand of DNA. It must have both RNA and DNA in it because there are both Us and Ts. (b, 3 pts) genome = 15%G, 0%T, 15%C, 35%U, 35%A Double-stranded RNA. This genome has Us but not Ts, so it must be RNA, and the %Gs = the %Cs whereas the %As = the % Us. (c, 3 pts) genome = 31%G, 19%T, 19%C, 0%U, 31%A Single-stranded DNA. This genome has Ts but not Us, so it must be DNA, and the %Gs does NOT equal the %Cs and the %As does NOT equal the % Ts. In the following sequence: 5’-GCAT-3’ 3’-CGTA-5’ (d, 3 pts) Which of these nucleotides would have a free triphosphate group extending from one of the carbons of their sugar? List the nucleotides by the numbers (nt #1 – nt #8) with which they have been labeled. Nucleotides #1 and #5, because the 5’ end of each DNA strand has a triphosphate group. (e, 3 pts) Which of these nucleotides would have a free hydroxyl group extending from one of the carbons of their sugar? List the nucleotides by the numbers (nt #1 – nt #8) with which they have been labeled. Nucleotides #4 and #8, because the 3’ end of each DNA strand has an OH group. nt #1 nt #2 nt #3 nt #4 nt #5 nt #8 nt #7 nt #6Name: __________KEY______________ 6 You discover a new protein in E. coli that you believe has both a transmembrane domain and a domain that binds to DNA. Below is shown part of this protein’s sequence: N… Ala-Leu-Phe-Ala-Gly-Ile-Val-Glu-Asn-Ser-Thr-Ala-Asp-Trp-His-Arg-Lys-His-Arg…C (f, 5 pts) List the continuous set of amino acids that would be most likely be a part of the transmembrane domain. State why you chose that stretch of amino acids. Ala-Leu-Phe-Ala-Gly-Ile-Val. This stretch is a continuous stretch of non-polar hydrophobic amino acids, which are the only amino acids that can insert themselves into the hydrophobic core of the cell membrane. (g, 4 pts) You discover experimentally that your hypothesis that this protein is a transmembrane protein is not correct; it is a protein that resides in the cytoplasm. Where in the 3-dimensional structure of this protein do you think you would find the amino acids you listed in part (f)? They would be buried in the inside core of the protein, where they would be hidden from water. (h, 5 pts) List the continuous set of amino acids that would be most likely to bind and
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