BC 13 Chromatin

Question 1

Nucleoside

Nucleotide

Answer 1

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

Question 2

positions of molecules on sugar ring

Answer 2

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

Question 3

linkage of DNA molecules

Answer 3

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

DRAW

Question 4

Ends

Answer 4

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

-3’ C is the site of New nucleotide incorporation

ALWAYS BUILT IN 5’ -> 3’ orientation

Question 5

Purines

Answer 5

Adenine and Guanine

TWO RING structure

Question 6

pyrimidines

Answer 6

Cytosine and Thymine and Uracil

ONE RING structure

Question 7

base pairs

Answer 7

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

Stabilize dsDNA, more H bonds

Question 8

Transcription Check #1

Answer 8

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

Question 9

DNA replication Check #1

Answer 9

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

Question 10

dsDNA

Answer 10

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.

Question 11

dsDNA stabilization

Answer 11

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.

Question 12

Melting Point

Answer 12

Tm generally 95, higher with high GC content

Question 13

Histones

Answer 13

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

Question 14

Nucleosome

Answer 14

146 bp wraps 1.75 times 8 core histones

chromatosome includes H1(ninth) and is 165 bp

Question 15

DNA coiling

Answer 15

naked DNA (transcriptionally active)

10nm Fiber beads

30nm Fiber of packed nucleosomes

LOOP domains

Condensed section

Fully condensed and transcriptionally inert

Question 16

linker DNA

Answer 16

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

Question 17

histone tails

Answer 17

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

Question 18

histone acetylation (lysine)

Answer 18

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

Question 19

additional histone modifications

Answer 19

lysine residues can also undergo methylation

serine and threonine residues can undergo phosphorylation.

these modifications TYPICALLY

Question 20

Constitutive Heterochromatin

Facultative Heterochromatin

Answer 20

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