Attached are study guide problems that I need help with as there


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Attached are study guide problems that I need help with as there is no answer key provided for them. I have tried most but I would basically love explanations from someone who actually knows what they are talking about. I realize there are multiple questions 13 on one page and 10 on the other so I will try to be generous on rewards. If there are any questions about the questions in the attached files please let me know some of them are confusing to me. I am studying for an upcoming test so good explanations of the questions and promptness would be greatly appreciated. Thanks! Attachment 1 Attachment 2 ATTACHMENT PREVIEW Download attachment Biochem Questions1.docx Biochem Study Questions 1.Calculate Energy (E) for Lysine primary amine (+) and Phosphate (–) 10 Å apart in hexane (apolar solvent) and in water. 2. How does temperature (T) influence this system? How does salt affect the system? Hydrogen bonds with water? Hydrogen bonds between bases? VDW interactions? Use the two types of pointers: → to indicate positive (increases this process) effects; ⎯| to indicate negative/inhibitory effects (diminishes this process). 3. What would change if the dsDNA structure contained a basepair mismatch (which state dsDNA or ssDNA is more or less likely after this change)? 4. What would happen (in terms of equilibrium balance point) if the system was in a vacuum? What would happen if the normal A, G, C, T bases were replaced with completely non-polar groups with inter-locking shapes (sterically complementary, but no possibility for H-bonding)? 5. Would substitution of A, G, C and T with completely non-polar base analogs make dsDNA more or less stable? Explain your reasoning. 6.What interactions favor the denatured state RNA and that favor the stem loop form? What will be the impact on this equilibrium if a GC basepair in the stem is replaced with an AU basepair? What will be the impact on this equilibrium situation if all salt (e.g. Mg2+, Na+, Cl– ions) is removed from the system? 7. Concept Question. Suggest a class activity for 8th graders that communicates the idea that H-bonds are less important for DNA stability and that it is really van der Waals contacts that are more important. Important Questions: 1. (a) Name any three of the molecular interactions. (b) Rank these according to energy. (c) Name two non-covalent molecular interactions that are or can be repulsive. 2. (a) Calculate the electrostatic energy for a phosphate group (q = –1) hydrogen bonded with the primary amine of a lysine residue (q = +1). Assume an apolar solvent (D = 2). (Coulombs Law) (b) Is this a favorable (stable) or unfavorable (unstable) interaction? (c) Indicate two things that weaken this type of interaction as it would be found in a cell. (d) What is the common name for this situation? 3. Agree or disagree. The DNA double helix is primarily stabilized by hydrogen bonding. That is why GC rich DNA is more stable than AT rich DNA, since GC pairs have 3 hydrogen bonds while AT pairs have only 2. If you disagree, explain the flaw in logic? ATTACHMENT PREVIEW Download attachment Biochem Questions2.docx Biochem Study Questions 1.If a glutamate residue is moved from water (polar solvent) to an apolar environment, will the pKa increase, decrease or stay the same? 2. What do we know about ∆G for spontaneous reactions? 3. Concept: Is following the class on twitter @BiochemUU a spontaneous reaction? 4. Concept: Is completing extra credit problems a spontaneous reaction? 5. What would happen if the instructor contrived things so that students could only earn extra credit if they were following course on twitter? 6. Where are the instructions for protein folding stored? Tougher Questions: 1. Indicate how many protein subunits are found in each molecular assembly. For each molecular assembly list the ligand(s) that bind with components of the assembly. (e.g. substrates, protons, allosteric effectors etc.) Molecular assembly Number subunits Ligand(s) (a) myoglobin (b alpha3b

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