Exam Two: Ch 9 Learning Objectives

Question 1

What are the five commonly occuring nucleotides?

Answer 1

A,G,T,U,C

Question 2

In sequence abbreviation, p means __ while d means __

Answer 2

5’ phosphoryl group
deoxy

Question 3

Tm increase with ___ the mole fraction of __ __ base pairs due to greater __ energy

Answer 3

increasing; G-C; stacking

Question 4

Each nucleotide residues are linked via ___ bonds, running _prime to _ prime

Answer 4

phosphodiester
5 - 3

Question 5

What are three reasons B DNA is stable

Answer 5

base pairing, stacking ability, and ionic interactions

Question 6

Describe how base pairing contributes to B DNA stability

Answer 6

H bonding required for specifity of base paring in DNA

Question 7

Describe how stacking contributes to B DNA stability

Answer 7

results from hydrophobic interactions
G-C> A-T due to larger thermal stability

Question 8

What is the most common conformation of DNA?

Answer 8

B DNA

Question 9

Describe the strand formation in B DNA

Answer 9

2 anti-parallel, polynucleotide strands wind in a right-handed manner, a roughly 20 A diameter double helix

Question 10

Describe the planes of the nucleotide bases

Answer 10

planes are nearly perpendicular to helix axis

Question 11

Describe the structure of B-DNA relating to base and backbone

Answer 11

base occupies core; sugar-phoshate backbone winds around outside, forming major and minor grove

Question 12

T/F: each base pair has different widths

Answer 12

false; A-T and G-C are interchangeable; can replace each other without distorting the double helix