BC 13 Chromatin Flashcards Preview

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Flashcards in BC 13 Chromatin Deck (20):
1

Nucleoside

Nucleotide

Nucleoside: Base linked to a sugar (without phosphates)

Nucleotide: nitrogenous base linked to a sugar (ribose or deoxyribose) and 1 to 3 phosphates (mono di tri)

Draw nucleotide triphosphates and deoxynucleotide triphosphates

2

positions of molecules on sugar ring

1' C- base
2' C- OH (ribose) H (deoxyribose)
3' C- OH
4' C - branch
5' C- off ring, phosphoester bond

3

linkage of DNA molecules

Phosphodiester bonds between sugars linking the 3' OH with phosphate of the 5' C of thenext nucleotide

DRAW

4

Ends

5' linked to phosphate, and 3' to an O

-3' C is the site of New nucleotide incorporation

ALWAYS BUILT IN 5' -> 3' orientation

5

Purines

Adenine and Guanine

TWO RING structure

6

pyrimidines

Cytosine and Thymine and Uracil

ONE RING structure

7

base pairs

G-C - three H bonds
A-T - two H bonds
A-U RNA only two H Bonds

Stabilize dsDNA, more H bonds

8

Transcription Check #1

correct H bonding between single stranded DNA and unincorporated ribonucleotides facilitates the addition without error

9

DNA replication Check #1

primarily determined by H bonding. Damage to a nucleotide that changes its H bonding characteristics will result in the twong nucleotide being incorporated

10

dsDNA

Right handed helix

stacked parallel in dinner plate fashion

no bulging, same length bond between all bonds

negative phosphodiesters on periphery of helix

Surface Grooves:
-Major: wide and deep
-minor: narrow and deep
-DNA binding protiens distinguish between grooves by recongnizing different patters of potential H bond donors and acceptors.

11

dsDNA stabilization

hydrogen bonding

base stacking (Van Der Waals)
-between bases on the same strand

Ionic Bonding: between negatively charged phosphate backbone and positively charged cations. Shields negative charge repulsion between groups.

12

Melting Point

Tm generally 95, higher with high GC content

13

Histones

Organize DNA, 10nm wide, beads on a string

nucleosome: DNA and histone complex every 20-80bp connected by linker DNA

H1 outside nucleosome: other 4 are inside (x2)

FURTHER CONDENSED 30nm fiber

14

Nucleosome

146 bp wraps 1.75 times 8 core histones

chromatosome includes H1(ninth) and is 165 bp

15

DNA coiling

naked DNA (transcriptionally active)

10nm Fiber beads

30nm Fiber of packed nucleosomes

LOOP domains

Condensed section

Fully condensed and transcriptionally inert

16

linker DNA

non nucleosome regions of DNA often associated with transcription factors bound to promoters

17

histone tails

stretches of amino acids at the N terminous of each histone protein that protrude from the nucleosome

more susceptible to enzymes and post trans modifications like acetylation

18

histone acetylation (lysine)

pos charged lysine residues within histone tails interact with negatively charged backbone of DNA holding it in place

acetylation of lysine residues removes the positive charge, and destabilizes this interaction.

DNA around nucleosome begins to loosen

HAT: histone acetyltransferase: LOOSEN
HDAC: histone deacetylases: remove and TIGHTEN

19

additional histone modifications

lysine residues can also undergo methylation

serine and threonine residues can undergo phosphorylation.


these modifications TYPICALLY

20

Constitutive Heterochromatin
Facultative Heterochromatin

CH: DNA sequences that are generally not transcribed (centromeres, telomeres)

FH: contains genes that are not transcribed in that particular cell but may be transcribed in others