Molecular Biology Recommended End-of-Chapter Problems
pH 5
(Ch.3) A solution with pH 7 is 100 times more basic than a solution with a pH of what value?
no, peptides have directionality, established by the n-terminus and c-terminus. the order in which the amino acids are connected in a polypeptide confers unique properties on the polymer.
(Ch.3) Amino acids are joined by peptide bonds, the formation of which is accompanied by the loss of water. is the dipeptide alanylglycine the same as the dipeptide glycylalanine? Why or why not? (note that peptides are always written with the amino-terminal residue on the left)
the single bond oxygen is weaker than the double bond oxygen. the double bond allows the oxygens to be closer together than the single bond oxygens.
(Ch.3) Consider the 0- 0 and O=O bonds. Is the 0- 0 bond stronger or weaker? Are the oxygen atoms in the O=O bond closer together or farther apart than those in the 0 - 0 bond?
the enantiomers have the same chemical formula, so the answer in each case is yes.
(Ch.3) Do two enantiomers of a chemical have the same density? The same melting point? If the chemical is an acid, do they have the same pKa?
Activation energy is larger in the reverse direction
(Ch.3) For the reaction coordinate diagram shown below, the activation energy is larger when the reaction proceeds in which direction?
A and B are equal lengths. resonance structures by definition, represent the shared distribution of electrons between sets of bonding atoms, and hence the average bond lengths are the same.
(Ch.3) One of the two resonance structures for a formate ion is shown below. which carbon-oxygen bond, A or B, is longer?
the ring is flat/planar. the conjugated double bonds in the ring produce considerable resonance, such that all bonds in the ring have a partial double-bond character ans all lie in the same plane.
(Ch.3) The basethymine (seeFigure3-1) contains a six-membered ring. From your understanding of bond structures, is this ring flat/ planar or bent? Explain your reasoning.
D) it lowers the activation energy for a reaction.
(Ch.3) Which of the following statements about catalyst is correct? (a) it can change the equilibrium constant of a chemical (b) it speeds up the rate of the forward but not the reverse reaction (c) it is used up in the course of a reaction (d) it lowers the activation energy for a reaction
measuring rates
(Ch.3) the activation energy for a chemical reaction can be determined in which of the following ways? (a) measuring product amounts (b) measuring rates (c) calculating energy of bond-hydrolysis (d) calculating change-in-entropy values
the second law of thermodynamics, which states that in any chemical or physical process, the entropy of the universe tends to increase.
(Ch.3) which law of thermodynamics explains why living things require the input of energy to maintain their ordered structure?
(a) A1, R5, K20, R28 (b) D2, E4, D27, E29, T30 (c) C7, C23
(Ch.4) A biochemist isolates a peptide hormone with the following sequence: ADSERNCQLVILLAWLPGVKVQCALLDRET (a) which of these residues could contribute a positive charge? (assume the residues are numbered 1 through 30, left to right) (b) which resides contribute a negative charge? (c) which residues can be connected by a disulfide bond?
As an alpha helix, 210 A. as a beta strand, 490A
(Ch.4) A polypeptide chain has 140 amino acid residues. How long will the polypeptide chain be if it is entirely a-helical? How long will it be if it is one continuous beta strand?
Completely buried residues are likely to be hydrophobic: 12, F4, 16, V8, V12, L13, L18, and L19 fit this description. Highly polar residues, or at least their polar groups, are likely to be on the surface, exposed to water: Dl, K3, T5, S7, T14, R15, E16, Q17, and E20 fit this description.
(Ch.4) For the following 20-residue sequence in a protein, list five amino acid residues that are likely to be buried in the protein, inaccessible to water. Pick five that are good candidates for surface residues. DLKFTISVGAPVL TREQLLE
(a) and (d) both contain the consensus sequence for an ATP/GTP-binding site: (G/A)XXGXGK(T/S), where Xis any amino acid.
(Ch.4) Predict which of the following sequences would bind ATP (or GTP), and explain your answer. (See the How We Know section in this chapter.) (a) YLFGGTRGVGKTSIA (b) LLIQALPGMGDDARL (c) LLIFGPPGLPKTTKL (d) FINAGSQGIGKTACL