BICH 410, section 503, EXAM 2, Wednesday October 19, 1994

Please write your name on each page. Write concise answers and show your work in order to receive partial credit.

1) (10 pts) A disaccharide known as alpha,ß-trehalose is a nonreducing sugar that contains two D-glucopyranose residues. Based on this information, draw its structure.

2) (6 pts) Circle the double-stranded DNA in each pair which you predict to have the lowest melting temperature.
A) 1000 bp of 50% G+C composition in 0.1M NaCl OR 1000 bp of 60% A+T composition in 0.1M NaCl
B) 100 bp of 45% G+C composition in 1mM NaCl OR 100 bp of 45% G+C composition in 0.1M NaCl
C) 20 bp of 40% A+T composition in 0.1M NaCl OR 200 bp of 40% A+T composition in 0.1M NaCl

3) (10 pts) What is the approximate weight ratio of protein to DNA in a nucleosome (the complete repeat unit in chromatin)? The molecular weights of the histones are: H1: 21000; H2A: 14000; H2B: 14000; H3: 15000; H4: 11000. Show your reasoning.

4) (15 pts) Draw the structure of a guanine-cytosine base-pair. Clearly indicate the hydrogen bonds, but do not worry about making them straight. With an arrow, indicate the position on each base that would be used for a glycosidic bond to the deoxyribose in a nucleoside.

5) (15 pts) A) Write the linking number equation. What does each term mean?
B) How does this equation simplify for a relaxed DNA molecule?
C) Calculate the linking number for a relaxed B-form DNA molecule containing 2100 bp.
D) How would the linking number for the molecule in part C) change if DNA gyrase plus ATP were added?

6) (15 pts) From the following information, determine the sequence of an octapeptide. You must show your reasoning.
i) Amino acid analysis of one micromole of the starting octapeptide resulted in one micromole of arginine (arg), two micromoles of glycine (gly), one micromole of histidine (his), one micromole of lysine (lys), two micromoles of methionine (met), and one micromole of tryptophan (trp).
ii) Treatment of the starting octapeptide with fluorodinitrobenzene followed by complete hydrolysis resulted in only a single dinitrophenyl derivative substituted on the e-amino group of lysine.
iii) Digestion of the octapeptide with chymotrypsin resulted in an octapeptide. The amino terminal amino acid of the digested peptide was determined to be arginine.
iv) Digestion of the starting octapeptide with trypsin resulted in two tetrapeptides.
v) Treatment of the starting octapeptide with cyanogen bromide resulted in the formation of a dipeptide and a hexapeptide. The dipeptide was composed of met and his. When the hexapeptide was digested further with trypsin, a tetrapeptide, free lysine and free methionine were obtained. When the hexapeptide was digested further with chymotrypsin, a dipeptide and a tetrapeptide were obtained.

7) ( 4 pts) Name an example of a glycosaminoglycan. What charge is carried by this group of carbohydrates at neutral pH?

8) (10 pts) Chemically, how are cellulose and the amylose form of starch similar and how are they different? How is this chemical difference manifested in different physical structures of cellulose and amylose?

9) (15 pts) A question about the polymerase chain reaction (PCR)
A laboratory researcher tried to carry out a PCR amplfication of a segment of DNA but was unsuccessful. Upon discussing the protocol with a colleague, some possible errors in their technique were considered. Before trying the experiment again they come to you, the resident PCR expert, to ask your opinion.
For each statement below: i) Tell whether that step in the protocol is wrong (write "correct" or "incorrect"), and ii) Suggest a solution if you believe the protocol was erroneous.

A) 2-prime, 3-prime-dideoxynucleoside triphosphates were used in the reaction.
ii) solution?

B) The protocol used a two-step cycle, varying the temperature back-and-forth between 50 degrees C and 72 degrees C.
ii) solution?

C) Two oligodeoxynucleotide primers were used in the reaction that hybridized to opposite strands of the DNA
ii) solution?