Directions: Answer these questions the best you can on a separate sheet of paper. Write all answers in your own words an appropriate vocabulary. Drawings, charts, etc. are acceptable provided you have ample explanations for them and YOU must create them. They don’t have to be pretty, just functional and clear. Any copied answers from the internet will result in a zero for the entire assignment. It will take much more than one word/one sentence answers to get full credit. You must be able to articulate and explain using the resources available and your own thoughts and considerations backed with evidence. Be sure to put the number corresponding to your answer on the paper. (ex. PS 1 # 1, Q1, etc.)

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.)

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

3) [5] Identify and apply a motif as it relates to its role in structure/function of DNA, RNA, or proteins.

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?

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.


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