transcription and RNA processing in eukaryotes

Question 1

what are the main differences between prokaryotic and eukaryotic transcription?

Answer 1

• eukaryotes have a chromatin template whereas prokaryotes have a DNA template
• eukaryotic RNA polymerase cannot read the DNA whereas prokaryotic RNA polymerase can
• eukaryotes have 3 RNAPs whereas prokaryotes have 1

Question 2

what happens when you digest DNA with DNase and run on an agarose gel?

Answer 2

with time, bands appear smaller, but still present

DNA is wrapped around nucleosomes, and the DNase can only cut between nucleosomes

Question 3

what is a nucleosome?

Answer 3

146 bp of dsDNA in 1.65 turns around a histone core

Question 4

what interactions are present in the nucleosome?

Answer 4

electrostatic interactions

DNA is negative, histone tails are positive

Question 5

how are the helices of histones arranged?

Answer 5

so that positively charged termini are orientated toward periphery of the nucleosome, close to the DNA

Question 6

why is the interaction between histone proteins and DNA not sequence specific?

Answer 6

it is based on electrostatic interactions

Question 7

what is the role of the nucleosome?

Answer 7

prevents errant transcription

Question 8

how is euchromatin organised?

Answer 8

• less condensed
• found at chromosome arms
• contains unique sequences
• gene rich
• replicated through S phase

Question 9

how is heterochromatin organised?

Answer 9

-highly condensed
-found at centromeres and telomeres
contains repeated sequences
-gene poor

Question 10

why is histone H3 the target for chromatin modification?

Answer 10

contains a lot of positively charged lysines, which provide most of the electrostatic force connecting DNA to proteins

Question 11

what is the effect of acetylation?

Answer 11

neutralises positive charge on the lysine

Question 12

what is the effect of methylation?

Answer 12

makes the group more bulky, which can help another protein recognise it

Question 13

what can occur after trimethylation of histone h3?

Answer 13

hp1 can cause nucleosome aggregation

Question 14

how do H2A and H2B interact?

Answer 14

they form a dimer with N-terminal unstructured tails, these are rich in positively charged amino acids

Question 15

why is the interaction between protein and DNA not sequence specific?

Answer 15

based on electrostatic interactions between phosphates, which are present in all nucleic acid

Question 16

what is the general structure of histone proteins?

Answer 16

all have a long, a-helix which has additional helices above and below that cross perpendicular

Question 17

what is the advantage of the weak interactions between histone and DNA?

Answer 17

octamers may be entirely displaced from DNA to generate a nucleosome free gap, allowing for organisation of nucleosomes at the promoter to be changed.

Question 18

what are the two functional domains of core histones?

Answer 18

1) a central domain involved in histone-histone interactions

2) lysine rich terminal positioned near the exterior of the nucleosome