Module 10: V1 - V4

Question 1

What are the characteristics of DNA structure?

Answer 1

DNA is not a static molecule that always sits with a perfect helix with 10.5 bp per full turn
usually under tension (over or under wound) and supercoils then form

Question 2

Is most cellular DNA underwound or overwound? What is this regulated by?

Answer 2

underwound

the cell

Question 3

When is DNA strained?

Answer 3

when it is underwound resulting in there being fewer turns than before e.g. 8 -> 7

Question 4

When is DNA relaxed?

Answer 4

when it is overwound resulting in there being more turns than before e.g. 7 -> 8

Question 5

What is the purpose of supercoiling?

Answer 5

relieves tension in the DNA when it is underwound and allows the strands to be separated a little bit more easily during transcription and DNA replication

Question 6

Which proteins relieve tension during DNA strand separation?

Answer 6

topoisomerases

Question 7

How is supercoiling observed on an agarose gel?

Answer 7

relaxed circular DNA travels much slower, while tightly supercoiled circular DNA travels much faster

Question 8

How does different amounts of time circular DNA has been treated with topoisomerase affect its movement on an agarose gel?

Answer 8

the longer circular DNA has been treated with topoisomerase, the shorter the distance it will travel on the gel

Question 9

What are the two types of topoisomerase?

Answer 9

type I and type II

Question 10

How do type I topoisomerases relieve tension?

Answer 10

active-site Tyr cleaves a phosphodiester bond in one DNA strand -> the unbroken DNA strand passes through the break in the first (enzyme open) -> broken strand is religated (enzyme closed)

Question 11

How do type II topoisomerases relieve tension?

Answer 11

the multisubunit enzyme binds a segment of a DNA molecule -> the second segment of the same DNA molecule is bound at the N gate and trapped, the first segment is cleaved on both strands -> the second DNA segment is passed through the break -> the broken DNA is religated, and the second DNA segment is released through the C gate

Question 12

What is DNA protected by?

Answer 12

DNA is always protected in the cell by being bound by proteins
together the DNA and the proteins are called chromatin

Question 13

How many histones are 2 loops of DNA wrapped around?

Answer 13

8 histones in each core

Question 14

2 loops of DNA wrapped around 8 histones =

Answer 14

a nucleosome

Question 15

What does the nucleosome represent?

Answer 15

the first level of compaction ~7 fold

Question 16

What are characteristics of histones?

Answer 16

small basic proteins, 5 major classes, they are highly conserved across species

Question 17

Where is histone H1? What is the role of histone H1?

Answer 17

on the outside of the nucleosome and acts like a clip as it keeps the DNA closed and stabilises the whole nucleosome

Question 18

What is the significance of histone tails?

Answer 18

protrude from the nucleosome and are highly disordered
this is where histones can be modified
some of the amino acid tails can interact with the tails of the neighbouring chromosome

Question 19

What is the purpose of modifications that occur on the histone tails and on the body of the histones as well?

Answer 19

alter the structure and packing of the chromatin

and the access to the DNA of DNA binding proteins

Question 20

What is the purpose of the ‘histone code’?

Answer 20

marks the DNA for specific biological processes

Question 21

What is the role of lysine acetylation?

Answer 21

allow for the opening and closing of chromatin which allows for DNA transcription or closes down transcription

Question 22

Which enzymes acetylate DNA and makes it less condensed?

Answer 22

histone acetyl transferases

Question 23

Which enzymes remove acetyl groups from DNA and make it more condensed?

Answer 23

histone deacetylases

Question 24

What is chromatin remodelling

Answer 24

changes in the accessibility of DNA to enzymes that carry out transcription or replication
these changes are mediated by chromatin remodelling complex

Question 25

What determines chromatin remodelling?

Answer 25

the histone code

Question 26

When are chromosomes most condensed?

Answer 26

during mitosis

Question 27

What is the first level of compaction?

Answer 27

histones and DNA = nucleosomes
‘beads on a string’
~7 fold compaction
active DNA

Question 28

What is the second level of compaction?

Answer 28

nucleosome plus one histone H1, wrapped into another coil
30 nm fibre
~100 fold compaction
inaccessible DNA

Question 29

What forms the foundation of the chromosome?

Answer 29

chromosomal protein scaffold

Question 30

How are chromosomes activated in the nucleus?

Answer 30

active regions exist in the nucleus where the chromosome can be looped into to turn on gene expression

Question 31

What is the purpose of cytosine methylation?

Answer 31

occurs on CG dinucleotides, usually when they occur in an extended region known as a CpG island
CpG islands are usually found in promoters and regulate transcription levels

Question 32

How does DNA methylation affect the expression of a gene?

Answer 32

represses the expression of a gene

Question 33

Which enzymes can methylate CpG islands?

Answer 33

DNA methyltransferases which are directed to specific areas of the DNA by DNA specific binding proteins

Question 34

What is the role of maintenance DNA methyltransferases?

Answer 34

recognises and methylates the unmethylated side of a replicated DNA strand

Question 35

What is an epigenetic change?

Answer 35

no change to DNA sequence
are maintained in the cell, but can be altered by signals
inherited from cell to cell