7.012 Problem Set 1. i) What are two main differences between prokaryotic cells and eukaryotic cells?
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1 ame 7.01 Problem Set 1 Section Question 1 a) What are the four major types of biological molecules discussed in lecture? Give one important function of each type of biological molecule in the cell? b) Briefly answer the following questions. i) What are two main differences between prokaryotic cells and eukaryotic cells? ii) What is the difference between unicellular and multicellular organisms? iii) Are prokaryotes unicellular or multicellular? Are eukaryotes unicellular or multicellular?
2 Question 1, continued c) For the pairs of amino acids given below circle each side chain. Give the strongest type of interaction that occurs between the side chain groups of each pair. Amino Acids Interaction 3 GLYIE 3 GLUTAMIE 3 TYRSIE 3 GLUTAMI AID 3 ASPARAGIE 3 3 LYSIE d) Draw the chemical structure of the following polypeptide at p 7. cysteinealaninetyrosinephenylalanine e) In the structure that you drew above, circle a peptide bond Problem Set 1
3 Question The drug Minoxidil is used orally as an agent against hypertension and topically as a stimulant for hair growth. The structure if Minoxidil is shown. *Minoxidil is uncharged in its active state Minoxidil a) Below is a schematic of a Minoxidil binding site on a hypothetical protein. i) Draw the side chains at amino acid positions 51, 19, 134, and 167. ii) Draw Minoxidil as shown above binding in the site. Be sure to consider the interactions between Minoxidil and the side chains when orienting Minoxidil within the binding site. Glu 51 Asn 167 Val 19 Leu Problem Set 1 3
4 Question, continued b) List all the interactions that would occur between the specified amino acids and Minoxidil in the model you have proposed by filling out the table below. Amino acid Glu 51 Val 19 Leu 134 Asn 167 Interactions with Minoxidil c) To decide if your model is correct, you construct some altered versions of this protein and test whether Minoxidil still binds. Assume all other amino acids remain unchanged. The results are as follows: Protein Position 51 Position 19 Position 134 Position 167 Binds? normal Glu 51 Val 19 Leu 134 Asn 167 yes variant 1 Asp 51 Val 19 Leu 134 Asn 167 yes variant Gly 51 Val 19 Leu 134 Asn 167 yes variant 3 Gly 51 Val 19 Leu 134 Ala 167 no variant 4 Glu 51 Lys 19 Leu 134 Ala 167 no variant 5 Glu 51 Phe 19 Leu 134 Asn 167 yes f the possible orientations for Minoxidil in the binding site, only one orientation is consistent with the results above. Please check your model carefully, revise it if needed and answer the following questions. Explain in terms of your model and the likely interactions why... i) variant will bind Minoxidil but variant 3 will not bind Minoxidil. ii) variant 5 will bind Minoxidil but variant 4 will not bind Minoxidil Problem Set 1 4
5 Question 3 Growth factor receptors (shown below) are transmembrane proteins found on the cell surface. extracellular P P P P P P P P P P P P intracellular growth factor receptors a) The majority of the molecules that constitute the above membrane belong to what class of macromolecules? Explain the important qualities/properties of these molecules that allow them to form membranes Problem Set 1 5
6 Question 3, continued A smaller schematic of the growth factor receptor is shown here. = transmembrane region ] Sequence from this region shown below...phevalglyileleutrpphealalysserargglnasp... 3 b) Which stretch of amino acids in the above sequence is part of the transmembrane region of the receptor? ircle these amino acids and briefly explain your reasoning. When growth factor binds to the extracellular domain of the receptor, a conformational change occurs in the receptor. Growth factor binding causes dimerization of two adjacent receptors in the cell membrane. Upon dimerization, the intracellular domains of the receptors become activated. See schematic below. ligand ligand extracellullar ligandbinding domain Receptor 1 Receptor plasma membrane intracellular domain inactive domains active domains 7.01 Problem Set 1 6
7 Question 3, continued c) Regions of the two receptors that interact upon dimerization are drawn below. In parts (i iv) below, name the strongest type of interaction (choose from; hydrogen bond, ionic, covalent, van der Waals) that occurs between the side chains of the amino acids indicated. Receptor 1 ys36 S S ys8 Receptor Ala45 3 S ys75 Asp68 3 Lys65 Ser53 Gln1 Phe Val98 Interacting Side chains Type of interaction i) Phe50 : Val98 ii) Asp68 : Lys65 iii) ys75 : ys8 iv) Ser53 : Gln1 d) Explain how Gln1 and Val98, which are far apart in the primary sequence of the protein, can be close to each other in the region of the protein diagrammed above Problem Set 1 7
8 7.01 Problem Set 1 8
9 Question 3, continued e) Molecular interactions between the two receptors are important for dimerization. Thus, substitution of certain amino acids in the protein can affect receptor dimerization. Predict whether the receptors will or will not be able to dimerize given the substitutions (i iv) below. EXPLAI your reasoning. i) Asp68 Arg: ii) Ser53 Thr: iii) Phe50 Asn: iv) Val98 Ile: e) Substitution of one amino acid, ys75 Gly, leads to dimerization of the receptors with or without growth factor. Provide a brief explanation for this observation Problem Set 1 9
10 Question 4 The following reaction is the tenth and final step in glycolysis: pyruvate kinase Phosphoenolpyruvate ADP <> pyruvate ATP G o' = 7.5 kcal/mol a) alculate K eq for this reaction under standard conditions at 5 o, and circle the correct statement below. At equilibrium, [phosphoenolpyruvate] > [pyruvate] At equilibrium, [phosphoenolpyruvate] < [pyruvate] b) The following concentrations are found in red blood cells. alculate G for the reaction at 37 o. In which direction will this reaction proceed spontaneously? [ADP] = 10 mm [ATP] = 81 mm [phosphoenolpyruvate] = 10 mm [pyruvate] = 500 mm 7.01 Problem Set 1 10
11 Question 4, continued c) Draw the energy profile for this reaction under physiological conditions. n the diagram be sure to: 1) show relative energy levels of the reactants and the products. ) label the axes 3) label reactants and products 4) indicate the energy of activation 5) indicate G d) ow does pyruvate kinase (the enzyme that catalyzes this reaction) change the energy profile? 7.01 Problem Set 1 11
12 STRUTURES F AMI AIDS at p ALAIE (ala) 3 ARGIIE (arg) 3 ASPARAGIE (asn) 3 ASPARTI AID (asp) S 3 YSTEIE (cys) 3 GLUTAMI AID (glu) 3 GLUTAMIE (gln) 3 GLYIE (gly) 3 ISTIDIE (his) ISLEUIE (ile) 3 LEUIE (leu) LYSIE (lys) S 3 3 METIIE (met) 3 3 TREIE (thr) 3 3 TRYPTPA (trp) PEYLALAIE (phe) 3 PRLIE (pro) TYRSIE (tyr) 3 SERIE (ser) VALIE (val) Problem Set 1 1
13 For the reaction: A B K eq D with G o as its standard free energy at equilibrium: G 0 = RT ln [][D] [A][B] or: ' [][D] G 0 ' [A][B] = e RT where: if T = 5 o then RT = 0.59 kcal mol if T = 37 o then RT = 0.61 kcal mol [][ D] under any conditions: G = G RT ln 0 [A] [ B] Enzyme Kinetics: For the enzyme catalyzed reaction: k 1 S E ES k 3 E P k where: S = substrate E = enzyme P = product the reaction velocity is given by V = V max [S] K M [S] where: K M = k k 3 k 1 and: V max = k 3 [E] total 7.01 Problem Set 1 13
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