第二部分：簡答題

1. How does one determine if two homolog proteins are paralogs or orthologs? 

(3) Nuclear run-on transcription can be used to measure transcription rates in vivo. Please describe how a     nuclear run-on assay     works and explain how it differs from a run-off assay.

Part II.填空題Please fill-in the blanks. 1. The ends of eukaryotic chromosomes are composed of short GC-rich repeat sequences called _____.

2. Escherichia coli base excision repair starts with the enzyme _____ clipping out the damaged base and leaving an apurinic or apyrimidinic site.

3. The Ds transposable element of Zea mays cannot transpose on its own because it lacks _____.

(a) GGACRFPWDQPGTPN

(b) SEAENDEMARAALKA

(a) Where might bends occur?

(b) Where might intrachain disulfide cross-linkages be formed?

(c) Assuming that this sequence is part of a larger globular protein, indicate the probable location (the external surface or interior of the protein) of the following amino acid residues: Asp, Ile. Explain your reasoning.

4. At pH 7.0, in what order would the following three peptides be eluted from a column filled with a cation-exchange polymer? Their amino acid compositions are:     Protein A    : Ala 5%, Glu 10%, Gly 10%, Leu 5%, Asp 10%, Arg 5%, Met 5%, Cys 5%, Tyr 5%, Phe 5%, His 5%, Val 5%, Pro 5%, Thr 5%, Ser 5%, Asn 5%, and Gln 5%.     Protein B    : Ala 5%, Glu 5%, Ser 5%, Leu 10%, Arg 10%, His 5%, Ile 10%, Phe 5%, Tyr 5%, Lys 10%, Gly 15%, Pro 5%, and Trp 10%.     Protein C    : Ala 5%, Val 5%, Gly 10%, Asp 5%, Leu 5%, Arg 5%, Ile 5%, Phe 5%, Tyr 5%, Lys 5%, Trp 5%, Ser 5%, Thr 5%, Glu 5%, Asn 5%, Pro 10%, Met 5%, and Cys 5%.