DNA Structure, Bidning Proteins, and chromatin

the most common form of double standed DNA is

B DNA

B DNA forms from

hydrated DNA

BDNA is

right handed

the rise of B DNA is

3.4A

The pitch of BDNA is

36A

bases of BDNA are

oriented inward in center of the helix, perpendicular to the helix axis

bdna minor groove

lined with ribose rings coming towards you

bdna major groove

bases are accesible

RNA double helix is mostly

A form

DNA-RNA hybrids are

A-DNA

in A form the

major grove is deep and the minor groove is shallow

B-form as viewed down the axis

alpha form as viewed down the axis

b form

alpha form

water plays a crucial

role in DNA structure

B-DNA is

hydrated (roughly 30% water by weight)

A-T rich sequences have a

chain of water molecules along the DNA minor groove

alternating purine and pyridine strands can

form Z-DNA

ZDNA is a

left handed helix where pyrimidines are anti and purine are syn

ZDNA

The B form helix has a

wide and deep major groove

Becuase of the wide and deep major groove of B-helix

proteins like transcription factors that bind to specific sequences have a good opportunity to bind

The A form helix narrowness of major groove

does not allow proteins to contact the bases

in vivo it is only when DNA is

severely underwound that the Z form will appear

DNA structure appears rigid but there is lots of flexibility depdning on the

sequence

nucleotides can heavily influence the

nucelic acid structure

there are 6

covalent bonds of free roatation per nucelotide

The types of flexibility in nucelotides are

1. base rotation around X angle

2. sugar pucker

3. free roation around PO4 bonds

factors that affect double stand stability

1. base composition

2. solvent

3. cations

4. denaturants

5. temperature

base composition

G residues tend to have better stacking energy, so GC-rich DNA will have more stability.

H2O is polar, interacts well with the DNA/RNA backbone and the stacking of the base-pairs contributes to helix stability because of

hydrophobic effec

Decreasing the solvent polarity by addition of organic solvents will

destabilize the helix (mainly by decreasing the hydrophobic effect).

cations are important becuase they

neutralize the repulsive interaction between PO4 - groups in the complementary strands.

Decreasing the salt enough will

cause strand separation

urea or frmadie are agents that will

a) H-bond with the bases

b) decrease polarity of the solvent

So these will destabilize the double helix

free energy change for double helix is the sum of

enthalpy and entropy terms

Increases in temperature will result in a

delta g positve and therefore double helix is unstable

DNA can

supercoil as a way to maintain a constant twist value

DNA likes to have a helical twist of

10.5 bp/turn

if the twist of DNA underwines or overwinds the energy is

unfavorable and will try to change back to a normal twist

closed circular DNA can relieve bad twist is to

supercoil

supercoil is in which

a double helix winds around itself

the state of the DNA to which it twists is called

topology

Supercoiling is a real problem in a living cell because transcription (RNA synthesis) and DNA synthesis (replication)

ause changes in DNA twist with consequential changes in supercoiling

The cell deals with DNA twisting/supercoiling through the activity of the enzymes called

topoisomerases

topoisomerases

change topology isomers

topoisomerases work by inducing breaks in the

DNA backbone and allowing strand roation which releives the twisting

Chromatin

Organizes the 6 x 109 base pairs in 46 chromosomes in the human genome

Asn (Gln) forms two Hbonds to

A of T-A bp in the major groove

Arg forms two Hbonds to

G of C-G bp in major groove

What binding protein is this

MAFA

almost all of the DNA in a cell is packaged into

chromatin in the interphase cell and during division

1 meter of DNA must be condensed to fit into the

nucleus

Condensation begins when dna interacts with the

octamer of a histone to wrap around the core and create a nucelosome

How many types of proteins are found with dna when chromatin is isolated

2 (basic and acidic)

Basic proteins are the

histones

acidic proteins are the

non-histone chromosmal proteins that carry out transcription and reuguation tasks

nucelosomes are the first level of chromatin

organization in eukarytic organisms

interactions that stabilize nucleosomes must be

sequence indepenednt

The core structure of a nucelosome consists of a

histone octomer that self assmables with 146 BP of dna wrapped around it

a histone octomer is

2 histone molecules (h2a h2b h3 and h4)

an additional histone H1 bidns on the

outside of the DNA

modifications of histons H3 and H4 regulate

DNA accesibility

histones contain many

Arg and Lys residues to neutrilize DNA phosphate backbond negative charge

six levels are folding are needed to go from

nuceosomes to chromsomes

What is the second step of folding

nucleosomes as beads on a string

the third step of organization is

a helix of nucelosomes wids into a fiber

the fourth step of folding is

the fiber of nuceosomes loops into a loop domain

after a loop domain is formed the

buncing of loops forms a rossette around a nucelar scaffold

rosettes are stacked to form a

coil

soils are stacked to form the

chromatid

What are the two key roles of chromatin

1. storage

2. regulation of gene expression

Prokaryotes do not

have chromatin

Prokaryotes turn off genes by

bidning repressor proteins