Nucleotides and DNA Structure

C483 Spring 2013

1. Purine(s) which are found mainly in both deoxyribonucleotides and ribonucleotides are A) thymine and cytosine.B) cytosine and uracil.C) cytosine.D) guanine and cytosine.E) adenine and guanine.

2. The abbreviation dGp indicates A) 5' deoxyguanylate.B) 3' deoxyguanylate.C) 3', 5' deoxyguanylate.D) 5', 3'deoxyguanylate.E) dGMP

3. Much of the stability of the double stranded helical DNA structure is the result ofA) hydrogen bonding between purines.B) the phosphodiester backbone.C) Ionic nucleobase attraction.D) the stacking interactions between base pairs.

All five histones are rich in ________ amino acid residues whose positive charges allow binding to the sugar-phosphate backbone of DNA.A) lysine and alanineB) lysine and arginineC) leucine and alanineD) leucine and arginine

Which does not apply to most bacterial DNA? A) Circular.B) Relaxed. C) Not packed into nucleosomes. D) Supercoiled.

Which best describes the structure of a nucleosome core particle?A) A histone octamer with DNA threaded through its center.B) About 50 bp of DNA associated with one histone H1 molecule.C) One nucleosome plus one histone H1 and linker DNA.D) A histone octamer wrapped approximately two times around with DNA.

Nucleic Acid Structure

• Nucleobase• Nucleoside• Nucleotide• Nucleic acid• Chromatin• Chromosome

Base Structure• Purines and

pyrimidines• Aromatic• Tautomers• H-bonding

Nucleosides• Ribonucleosides and deoxyribonucleoside• Purine = osine; pyrimidine = idine (watch cytosine)

Nucleotides• Phosphorylated on 2’, 3’, or 5’• 5’ unless noted• Draw these:– dA– ADP– ppAp– ApAp

• pA is normally called _______ or _______________

Polynucleotides

• Phosphate diesters• polyanion• directionality• 5’ 3’• Abbreviation is

pdApdGpdTpdC• tetranucleotide

Double Stranded DNA

• Chargaff’ Rule: %A =%T and %G = %C• (C + G) not necessarily equal to (A + T)

Complementary Base Pairs

Mismatching may occur with tautomers

N

N

HN

N N

N

NH

N

O

H

H

H

H

Adenine tautomer Cytosine

Antiparallel• Inaccuracy of two-

dimensional drawing: bases are perpendicular to the paper

• “ladder”• H-bonding

Helix

• Maximization of base pair stacking

• More compact• Major and minor

groove• How do we explain

major/minor grooves?

Major/Minor Groove

• Many pictures show ladder with backbone at 180o

• Actually a distorted ladder with poles closer to each other, on one side

Weak Forces Stabilize Double Helix

• Stacking interactions (vdW forces)

• Hydrogen bonding• Hydrophobic effect• Charge-charge

Denaturation

• Melting point• Melting curve• UV-absorption• cooperative

A/T Rich and G/C Rich strands

• GC rich strands harder to denature due to STACKING (not H-bonds)

• Cooperativity due to initial unstacking, which exposes bases to water, which destabilizes H-bonds, which leads to further denaturation

Supercoiling• Bacterial DNA• Closed, circular DNA• Topology and topoisomerases

Eukaryotic DNA

• Chromatin• 8000x packing ratio– Nucleosomes (10x)– 30nm chromatin fiber

(4x)– RNA/Protein scaffold

holds loops (200x condensation of DNA length

Nucleosomes

• Beads on string• Histones form octamer• Core particle

Unpacking

• Histones serve as negative supercoiling

• Histone acyltransferases (HATS)

• Necessary for expression

Chromosome

• Scaffold of RNA and protein

• 30nm fibers are looped many times

• Picture of histone-depleted chromosome: DNA strands have fallen off of scaffold

Answers

1. E2. B3. D4. B5. B6. D