Exam 1 (Ppt 4)

Question 1

Chromatin

Answer 1

A given piece of DNA and its associated proteins. A “beads-on-string” structure.

Question 2

Chromosome

Answer 2

A “condensed version” of DNA molecule and its associated proteins.

Question 3

Histones

Answer 3

Most of the proteins bound to DNA in the eukaryotic nucleus are histones

Question 4

Nucleosomes

Answer 4

A structure formed with a regular association of DNA with histone

Question 5

Typical diff b/w Prokaryotic cells vs eukaryotic cells

Answer 5

“Prokaryotic cells typically have only complete copy of their chromosomes that is packaged into a structure called nucleoid.

The majority of eukaryotic cells are diploid, containing two copies of each chromosome. The two copies of a given chromosome are called homologs. “ Prof Ye

Question 6

Is genome size related to the complexity of the Organism?

Answer 6

Roughly but not exactly

Question 7

Why is gene density also important?

Answer 7

To determine approximate # of genes.

genome size x genome density

Prok. gene size is typically smaller than Euk but Prok. Gene density is usually higher b/c they have way less noncoding regions (a.k.a introns)

more complex organism = less gene density

Question 8

Reverse transcriptase

Answer 8

“RT produces dsDNA (cDNA).

cDNA can be made from the host cell’s mRNA, then reintegrate into the host genome (rare).” Prof Ye

Question 9

How are pseudogenes different than “normal” genes?

Answer 9

does not encode for proteins, not capable of transcription

Question 10

Major Players of composition of Human Genome

Answer 10

Repeats (46%)
Introns (30%)
Regulatory regions (16%)
Pseudogenes+ gene fragments (6%)
Genes (1.5%)

Question 11

What are the 3 imp regions of the chromosome structure

Answer 11

1) Centromeres
2) Telomeres
2) Ori (Origin of Replication)

Question 12

Centromere structure.. (things to know about it)

Answer 12

"Contains REPEATS.
Varies widely between species.
HIGHLY methylated and tightly controlled
Does NOT encode protein!
An attachment site for proteins." Prof Ye

Question 13

The Centromere is the Binding Site For the…

Answer 13

Kinetochore Complex

Question 14

Consequence of >1 or <1 Centromere

Answer 14

>1 = chromosome breakage
1 = proper chromosome segregation
<1 = random segregation

Question 15

Telomeres

Answer 15

“PROTECT THE ENDS of the DNA molecule from unraveling or degradation.
PREVENT FUSION of the ends of one chromosome with another.
Mechanical problem in replication”

Question 16

A euk chromosome is 50% protein: a majority of this is _____?

Answer 16

Histones!

non histone protiens = cohesin, condensin

Question 17

Histones are…?

Answer 17

Small proteins
Very basic (+)
20% lys + Arg
Highly conserved among euk

Question 18

Why would a plethora of positive charges be good for DNA binding?

Answer 18

Stabilization via charge association

DNA is negatively charged

Question 19

Nucleosome

Answer 19

light Nuclease Digestion reveals

~147 base pairs of DNA are wrapped around a histone octomer.

octomer + DNA = nucleosome core

core plus H1 linker = nucleosome (~ 200 bp of DNA)

Question 20

Nucleosome Assembly

Answer 20

H3▪H4 tetramer binds DNA first.

Two dimers of H2A▪H2B then bind.

DNA is wrapped around the histone core 1.65 times

Question 21

Domain Structure of the Core Histones

Answer 21

Each has a(n)

1) histone fold domain, at C term that mediate heterodimerization
2) unstructured N-terminal tail.

Note: octamerization requires DNA!

Question 22

Histone tails are..

Answer 22

cleaved by trypsin
accessible
not needed to maintain nucleosome core but they further stabilize and compact the DNA

Question 23

The tails DIRECT the wrapping of DNA around the histones in a ____-____ manner.

Answer 23

Left-Handed

Question 24

H3∙H4-DNA Interactions

Answer 24

Interacts with…
Phosphodiester bond
minor groove
bends the DNA into a shape that makes H2A-2B binding ‘relatively easy

Question 25

Histone H1

Answer 25

compacts DNA into 32 nm fiber
interacts with linker DNA
Protects more bp from nuclease digestion b/c wrapping becomes tighter
highest %lys + Arg conc = MORE BASIC than the others
mw is higher too => probably why its 1/2 as abundant as the rest

Question 26

Where does H1 Binds DNA?

Answer 26

1) Nucleosomal Core

2) linker region

Question 27

Are the TAILS required to form 30 nm fiber?

Answer 27

Histone Tails are required

H4 tail binds H2A at negatively charged amino acids of a nearby nucleosome

Question 28

What can be happening to exposed DNA regions

Answer 28

Transcription
Replication
DNA repair
Digestion