Sandmeyer- Lecture 1

Question 0

How any H bonds between AT, GC?

Answer 0

2 between AT, 3 between GC

Question 1

What is a base + sugar called?

Answer 1

Nucleoside

Question 2

How is DNA stabilized?

Answer 2

1) H bonding between bases

2) base stacking - pi interactions

Question 3

How many residues per turn of B-DNA? How many degrees of turn per base?

Answer 3

~10.5 bases/turn, 36 degrees per base

Question 4

What form of DNA is R handed? What form is L handed?

Answer 4

R-handed: B DNA (predominant in vivo)

L-Handed: Z DNA

Question 5

What is the conversion from angstroms to nm?

Answer 5

1Ang= 0.1nm

Question 6

Where do most proteins interact on duplex DNA?

Answer 6

At the major groove

Question 7

What is the characteristics of positively supercoiled DNA? Negatively supercoiled DNA?

Answer 7

+ Supercoiling: fewer bases per turn than relaxed, due to overwinding

• Supercoiling: more bases per turn than relaxed, due to underwinding (predominant state of DNA in physiological prokaryotic DNA)

Question 8

As polymerase is reading DNA, what is happening to supercoiling? What enzymes are involved in ameliorating this?

Answer 8

DNA becomes more positively supercoiled (overwound)

Topoisomerases:
Type1 cleaves one strand
Type2 (eg gyrase) cleaves both strands

Question 9

Name 2 bacterial therapeutic and their targets and 3 cancer therapeutics and their targets.

Answer 9

Bacteria

1) quinolones: bacterial topoisomerase 2 in gram negatives, topoisomerase 4 in gram positive.Taken up thru porin channels
2) novobiocin: bacterial gyrase

Cancer:

1) Daunorubicin/doxorubicin: intercalate between bases, inhibit topoisomerase
2) cisplatin: cross-links DNA, inducing apoptosis
3) etoposide: chemotherapy drug, targets mammalian topoisomerase 2
4) radiation therapy- causes breaks in DNA, which generally goes unrepaired.

Question 10

Which bases pair with U?

Answer 10

A and sometimes G

Question 11

What factors affect DNA hybridization?

Answer 11

1) pH
2) salt
3) concentration
4) temperature
5) complementary strand length
6) base composition

Question 12

What the hell is an indel?

Answer 12

insertion or deletion mutation

Question 13

How does FISH work?

Answer 13

fluorescently labeled DNA probes used to hybridize specific chromosomal regions in metaphase chromosome spreads

Used in identifying chromosome number, translocations, indels