Chapter 2: The Structure of DNA

What are the five carbon sugars of DNA and RNA?

DNA = deoxyribose, RNA = RIbose

What are the nitrogenous bases?

purines: adenine and guanine, pyrimidines: cytosine, thymine (DNA), and uracil (RNA)

What is Chargaff’s Rule?

A = T, G = C, A + G = T + C

What is the percentage variation of G + C among species?

22 -73%

What are the three steps to form DNA and RNA chains?

1. a base is attached to a sugar (nucleoside)

2. a nucleoside with one or more phosphate is a nucleotide

3. nucleotides are linked by 5’ to 3’ phosphodiester bonds

How are DNA/RNA chains joined togther?

covalent bonds

covalent bonds

formed when electrons are shared and do not break; very stable

1000 bp =

1 kilobase pair (kb)

1,000,000 bp

1 megabase pair (mb)

What is used for the length of RNA and how long can they be?

nucleotides or bases are used; less than 100 to 1000s

What is used for the length of DNA and how long can they be?

the number of base pairs used; several kb to 1000s of mb

How is DNA wriiten?

5’ end (left) to 3’ end (right)

How many hydrogen bonds are between A and T?

two hydrogen bonds

How many hydrogen bonds are between G and C?

three hydrogen bonds

Why aren’t there other stable base pairs present in DNA?

they may not be able to form two or more hydrogen bonds

fidelity of DNA replication

proofreading and DNA repair mechanisms correct mistakes

How does base stacking provide chemical stability in the DNA double helix?

hydrophobic bases stack onto each other without a gap, DNA has a hydrophobic core

What is the structure of the double helix?

5’ to 3’, antiparrallel strands, major and minor grooves

What are alternative double helical structures

B-DNA, A-DNA, Z-DNA

B-DNA

the predominant form of DNA

Z-DNA

binding protein; energetically favorable and stable

base flipping

a region of Z-DNA is connected to B-DNA, when one base pair is flipped out from the DNA helix

denaturation

the melting of DNA; base stacking quenches the capacity of bases to absorb UV light

hyperchromicity

as DNA melts its absorption of UV light increases

Tm (melting temp.)

the temp at which help of the bases denaturing

renaturation

reannealing of DNA; permits hybridization

hybridization

the complementary base-pairing of strands from two different sources

cot curve

a plot of C/C0 versus C0t

What are two unusual DNA secondary structures

slipped structures and cruciforms

slipped structures

occur at tandem repeats; found upstream of regulatory regions; can lead to repeat expansion

cruciform

paired stem-loop formations; characterized in vitro for many inverted repeats in plasmid and phage

supercoiling

form a twisted, 3-D structure, less stable than relaxed DNA

What are the two types of supercoiling?

positive (left): underwound, negative (right): overwound

What can a strain present within supercoiling?

localized denaturation

topoisomerases

enzymes that introduce breaks in DNA strands and releases the strain of supercoiling

What is the significance of supercoiling in vivo?

• all DNA within prokaryotes and eukaryotes is negatively supercoiled

• some proteins induce negative supercoiling

• DNA is restrained around DNA binding proteins

What does processes does supercoiling play an important role in?

replication, transcription, and recombination