University of California, Berkeley
July 28-30, 2009
Problem Set 6
The answer key will be posted by
Tuesday July 28
. Try to solve the problem sets always
ﬁrst without the answer key. Remember, your goal is to be able to solve biochemical problems
in the exams. If you can not solve one of the problems try to solve it together with one of
your classmates or ask your GSI during discussion section. Don’t just wait for the answer
key. The answer key should only conﬁrm that you solved the problem correctly!
Exercises and Problem Sets are for extra practice and exam preparation, and should not be
Recommended problems from the book:
Chapter 8: 1, 2, 3, 6, 8, 9, 11, 12, (15)
Chapter 24: 1, 3, 4, 5, 7, 8, 9, (14)
Chapter 25: 2, 3, 4,
A double-stranded DNA molecule contains 20% adenine. Determine the
number of cytosine bases if the DNA molecule is:
(a) 1000bp long
(b) 1cm long
Write the DNA base sequences that complement each of the following DNA strands.
a) 5’ AATCGCCCATTGCAGTTC 3’
b) 5’ CGATTGGCTTA 3’
Writhe and Twist
Starting with a closed circular DNA of 5250 base pairs with
= -0.004 (assume 10.5
bp/turn for B-DNA).
(a) Calculate the writhe (W) of this DNA.
(b) Calculate the twist (T) and linking number (L) for this DNA.
(c) Calculate the circumference of the circular DNA when W = 0.
(d) Now, if 13 base pairs have melted out, as in the initiation of the replication bubble
in E. coli, calculate the twist (T), linking number (L), and writhe (W) for the
resulting circular DNA.