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The exam also examines antibiotic binding to the E. coli ribosome using amino-acid side-chain properties and bond possibilities. 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Draw a structural representation of the amino acid, Aspartic acid, which has the side chain of: CH2COOH.  \nb) The molecule drawn above is a monomer found in    \nH H  \nH – C – C –H  \nH H  \nc) Below is a pentose found in RNA. On the diagram circle the hydroxyl that differs between ribonucleotides and  \ndeoxyribonucleotides.  \nOH  \nCH2  \nH  \nH  \nOH  \nO  \nOH  \nHH  \nOH  \nd) You find an organism that lives in thermal pools with temperatures as high as 160 ° F. You find that many of this organism’s proteins have a high percentage of cysteine. Briefly explain why this might be the case.  \ne) To the right is an iconic view of a phospholipid.  \n• List what atoms are found in a phospholipid molecule represented by the boxed region of this schematic. Describe the properties associated with this region.  \n• List what atoms are found in a phospholipid molecule represented by the shaded region of this schematic. Describe the properties associated with this region.  \nQuestion 1, continued  \na) Box the part that is added to a growing chain of nucleic acid.  \nb) Star the atom(s) that can form a hydrogen bond with the complementary nitrogenous base.  \nc) Circle the part of the molecule that decreases the stability of RNA as compared to DNA.  \nd) Draw an arrow to the part of this molecule that you would modify to prevent further elongation. Indicate what change you would make next to the arrow drawn.  \nQuestion 2  \nShown below is the structure of Drug 1, that binds to the E. coli ribosome. Indicate whether each circled region could possibly form ionic bonds, hydrogen bonds, or hydrophobic interactions with another molecule by filling out the table below. Fill in the table with “yes” if that type of bond is possible, “no” if it is not.  \na)  \nO H  \n| Part | Could this part form\u003Cbr>ionic bonds | Could this part form\u003Cbr>hydrogen bonds | Could this part be involved in a\u003Cbr>hydrophobic interaction |\n| --- | --- | --- | --- |\n| (i) |  |  |  |\n| (ii) |  |  |  |\n| (iii) |  |  |  |\n| (iv) |  |  |  |\n\nQuestion 2, continued,  \nA representation of the drug bound to the E. coli ribosome is shown below. Three amino acids of the ribosome that are important for binding are shown. If this drug can bind to different bacterial ribosomes, it may be useful asan antibiotic. The ability of this drug to bind to the ribosomes of two different species is examined. The drug binds to the ribosome of species 1, but does not bind to the ribosome of species 2.  \nFor your information:  \n\n| Amino acid | Side chain |\n| --- | --- |\n| Ile | CHCH3CH2CH3 |\n| Val | CHCH3CH3 |\n| Asn | CH2CONH2 |\n| Glu | CH2CH2COO– |\n| Lys | (CH2) 4 NH3+ |\n| Ser | CH2OH |\n| Leu | CH2CHCH3CH3 |\n| Arg | (CH2)3 NHC(NH2)2+ |\n\nb) The table shows the differences between the ribosomes. Given this information, complete the table indicating which would be from species 1 (drug binds) and which would be from species 2 (drug does not bind) .  \n\n| Ribosome from: | Amino acid found at |  |  |\n| --- | --- | --- | --- |\n|  | 101 | 231 | 312 |\n| E. coli | Lys | Asn | Leu |\n| Species   | Glu | Ser | Val |\n| Species   | Arg | Glu | Ile |\n\nc) What specific amino acid or amino acids prevents the ribosome from species 2 from binding Drug 1?  \nd) In terms of the specific non-covalent interactions, explain why the ribosome from species 2 will NOT bind Drug 1, but the ribosomes from E. coli and species 1 will.  \nQuestion 3  \nReaction 1) A  B, where ΔG’ = +2  \na) The energy profile for the reaction 1 is drawn on the axes below.  \n• Label A, B, and ΔG’ on the graph below.  \n• What is the value for the energy of activation?  \nCourse of reaction  \nCompare reaction 1 (above) to reactions 2 and 3 (below) .  \nReaction 2) C  D, where ΔG’ = -3, Energy of activation = +0.5 Reaction 3) E  F, where ΔG’ = +0.3, Energy of activation = +2  \nb) Which of these reactions, 1, 2, or 3 is most likely to proceed in the forward direction i","cbCait30Wsu8sr0b","https://ap.wps.com/l/cbCait30Wsu8sr0b","pdf",242796,"English","# Question 1\n## Question 1 continued\n# Question 2\n## Question 2 continued\n# Question 3\n## Question 3 continued\n# Question 4","[{\"question\":\"How is aspartic acid expected to be represented in Question 1(a)?\",\"answer\":\"A structural representation is required, specifically showing the side chain as CH2COOH.\"},{\"question\":\"What is the role of the circled or modified parts in Question 1(c)-(d) for RNA versus DNA stability?\",\"answer\":\"The hydroxyl difference between ribonucleotides and deoxyribonucleotides is targeted, and the question asks to circle the RNA-decreasing stability part compared with DNA and modify a specific molecule part to prevent further elongation.\"},{\"question\":\"How do enzyme-stabilized regions 1, 2, and 3 differ in Question 3 continued (e)?\",\"answer\":\"Region 1 is stabilized by hydrophobic interactions, region 2 by hydrogen bonds, and region 3 by ionic bonds between enzyme and substrate side chains.\"}]","Biochemistry Unit Exam - Question Practice | PDF",1790744450,18]