Problemset2_F2011 - MCB100A/Chem130. Fall 2010. Problem Set...

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Work through the questions highlighted in bold as relevant to Lecture 2. Hand in your answers to the questions marked with a * in class on Thursday, Sept 8, in class. True/False and Multiple Choice (1) The tertiary structure of functional RNA molecules is easily predicted True/False (2) Which of the following is not a stabilizing force for the structure and stability of double stranded nucleic acids? a) base stacking b) hydrogen bonding c) disulfide bonds d) electrostatic forces (3) H-bond acceptor, H-bond donor, H-bond acceptor, Methyl group is the pattern of potential interactions at the edge of what Watson-Crick base pair? a) A-T b) G-C c) A-A d) C-G e) T-A (4) Genomic DNA can become deformed from its normal B-form by DNA binding proteins such as the histone proteins and the TATA-box binding protein True/False (5) What non-standard base pair is most likely to form a wobble base par? a) U-U b) A-G c) A-A d) G-U e) G-G (6) Classify the following RNA structural elements as secondary or tertiary structure: (a) coaxial helices (b) pseudoknot (c) hairpin (d) junction (e) adenosine platform (e) ribose zipper (f) bulge MCB100A/Chem130. Fall 2010. Problem Set 2. Due Thursday, September 9, in class. Page 1 of 10
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(7) Fill in the blank: 1. The ______________ structure of a nucleic acid is the sequence of nucleotides in the DNA or RNA molecule 2. B-form DNA has a C2’ ________ sugar pucker 3. Hoogsteen basepairs, where the bonding interactions utilize the Watson-Crick base pairing edge on one base and the major groove edge in the other base, can be utilized to form a RNA _______ helix. 4. Metal Ions such as K + ,Na + , and Mg 2+ typically interact with the __________ group on the backbone of nucleic acids. 5. The most common orientation of the base with respect to the sugar in a nucleotide is referred to as ___. 6. Simple sugars can exist in both linear and ______ forms 7. ________ is an acetylated polymer found in the exoskeletons of insects and the cell walls of fungi (8) Classify the following amino acids as (i) non-polar (ii) polar, uncharged (iii) polar charged or (iv) aromatic: I, K, R, Y, Q, L, W (9) Which of the following factors is the single most important contribution to the stability of a protein’s folded conformation: A) sum of energies of formation of many weak interactions among the hundreds of amino acid residues in a protein B) sum of energies of formation of many weak interactions between a protein’s polar amino acids and surrounding water C) adoption of φ and ψ backbone torsion angles that are consistent with the Ramachandran diagram D) favorable free energy resulting from removal of nonpolar groups from water E) stabilizing effect of hydrogen bonds in a protein between the carbonyl group of one peptide bond and the amino group of another, as indicated by: -C=O|||H-N- *(10) In the diagram above, the planes drawn about the peptide bonds indicates which of the following: A) plane of rotation about the C α -N bond B) absence of rotation about the C-N bond because of its partial double bond character
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Problemset2_F2011 - MCB100A/Chem130. Fall 2010. Problem Set...

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