Question number [point value]
1) [5] Define the four categories of amino acid side chains in terms of their chemical/physical properties. What types of molecular interactions are the members of each of these categories likely to make? (bonds, etc.) (MLO 2.1)
2) [5] Compare and contrast the four levels of protein structure, identify a specific example of each and explain how amino acids play a role in their structure. (MLO 2.2)
3) [5] Identify and apply a motif as it relates to its role in structure/function of DNA, RNA, or proteins. (MLO 2.2)
4) [7] What features of the major groove of DNA make it especially useful for sequence-specific recognition by proteins? Give at least two examples of DNA-binding motifs that bind primarily to the major groove. Provide an example of a protein that does NOT use the major groove to recognize its target. Now assess how each accomplishes its specific binding? (MLO 2.2, 2.3)
5) [8] DNA repair proteins, such as DNA glycosylase, recognize and remove damaged nucleotides. Based on what you know about protein-DNA interactions, propose how these repair enzymes recognize mismatches or damaged bases in double-helix DNA, and predict what specific contacts are made between the DNA repair protein and the mismatched (or damaged) base. (MLO 2.4)
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