Emma Chesley Question 1 7 points Fall 2014 7 012 Problem Set 1 20 Points total Name Studies suggest that adenosine is important in sleep regulation When you are awake adenosine triphosphate degrades in a certain region of the brain to form adenosine Adenosine then binds to the adenosine receptors in the brain to induce sleepiness A receptor is a protein that binds a signaling molecule often termed a ligand and in response to this binding emits a signal usually into the cell a The structure of adenosine is shown below Draw the related structure adenosine triphosphate and label the functional groups that have been introduced in lecture The caffeine molecule found in your favorite coffee drink can also bind to the adenosine receptors Caffeine has the opposite effect of adenosineEit wakes you up Below is the structure of the caffeine molecule b Based on the structures given is caffeine more or less hydrophilic compared to adenosine Explain c A simplified model of the receptor binding pocket is shown below to highlight the interaction between the caffeine molecule with the adenosine receptor Only the side chains of the amino acids residues are given and labeled as R1 R2 and R3 Identify residues 1E3 in the receptor molecule and indicate whether they are polar or nonEpolar Caffeine is less hydrophilic because it has more non polar functional groups that adenosine 1 Name caffeine R1 R3 R2 Caffeine adenosine receptor d Think about each amino acid and the region of caffeine closest to the side chain of each amino acid List the strongest type of interaction that each amino acid can have with the caffeine molecule Consider the caffeine molecule and the amino acids to be in the same plane e Which interaction from part d is the strongest f What bonds primarily hold together a molecule g What bonds hold together multiple molecules h Compare the strengths of the bonds in f and g i What type of bond is broken when molecules are broken down into respective atoms or smaller molecules for example breaking down sugar into carbon dioxide and oxygen j What type of bond is broken during the boiling process d The strongest form of intermolecular force would be the hydrogen bonding between the amine functional group on R3 and the oxygen double bonded on caffeine molecule On R1 and R1 the force would be van der Waal s between the CH3 on the caffeine molecule e The strongest of the interactions is the hydrogen bonding f covalent bonds and ionic bonds g if the molecules are polar they are held together by hydrogen bonds If the molecules are non polar they are held together by van der Waal s forces h Covalent bonds are stronger than hydrogen bonds and signi cantly stronger than van der Waal s forces i this would be the breaking down of covalent bonds j During the boiling process hydrogen bonds are broken 2 Question 2 4 points Name Some representative macromolecules and their building blocks are shown below a Match each building block to its corresponding larger molecule by listing each pair by their numbers For each pair identify the building block and the larger molecule Note that the specific building block shown here will not necessarily be a part of the specific larger molecule in this question for example if the building block is alanine the larger molecule peptide might not contain alanine in its sequence O N NH2 O N O OH O H N O O P O O Larger molecule Paired with 7 Building block Paired with 5 P P N N N N N O O O O O O O O O O O O O OH OH HO NH2 O HO OH OH OH HO HO 2 1 3 4 5 6 7 8 HO HO HO OH OH NH HO HO HO OH OH OH OH OH H2N O O O O O O N O O H N N H P O O O O O OH Larger molecule Paired with 3 Building block Paired with 1 O O OH NH2 Building block Paired with 8 Larger molecule Paired with 8 O OH N H H N O Larger molecule Paired with 2 Building block Paired with 4 3 Question 3 4 5 points Name b Covalent bonds are used to connect building blocks into higher molecular weight chemically complex molecules Which type of covalent bond is involved in assembling the components of each of these macromolecules larger molecules Circle and label one bond for each molecule image You do not have to label all the connecting bonds one per molecule is sufficient You are studying the function of two different proteins encoded by two different viruses Viruses are small particles that carry the viral genome coated by protein and often lipids The genome for viral replication can either be DNA or RNA a Draw the structure of the building block for each kind of genetic material and mention at least three differences between ribonucleic acids and deoxyribonucleic acids You do not need to draw the base b You have isolated the genetic material from both viruses in a small sterile container and your lab protocol says that you should store the genetic material in the freezer However you forget and leave both tubes out at room temperature You come in the next morning and analyze the samples to find out that the sample from virus A is still intact but the sample from virus B has degraded Based on this information and what you know about ribonucleic acids and deoxyribonucleic acids determine the kind of genetic material for each virus and explain your observations Enzyme E1 phosphorylates substrate A to generate product B and water This enzymeEcatalyzed conversion of A to B happens as two coupled half reactions shown below Pi A EEEEEEEEEEEE B H2O ATP H2OEEEEEEEEEEEEEE ADP Pi a You know that the first reaction is endergonic while the second reaction is exergonic Draw an energy diagram for each of these half reactions b Why do you think these reactions are coupled together c Based on the information presented here what can you conclude about the rate of each these reactions What about the rate of the total reaction Virus A is less reactive therefore it is DNA Virus B is more reactive there it is RNA This is because RNA is more polar due to the additional oxygen 1 RNA is shorter than DNA 2 RNA uses sugar as the ribose where as DNA uses sugar as the deoxyribose 3 RNA is less stable than DNA These are coupled together because they show the two steps that make up the overall reaction Question 4 3 points The slow step indicates the rate of the reaction and in this case the rst step is the slow step because it is endergonic The rate of the slow step is the rate of the overall reaction 4 Question 5 1 5 points Name Go to the MITx edX site https lms mitx mit edu courses MITx 7 012 2014 Fall about and log into your 7 012X account Navigate to
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