Genome structure

Question 1

In what direction is a DNA strand by convention?

Answer 1

Sequence is 5’ to 3’ by convention

Question 2

How does DNA exist in its 3D form?

Answer 2

• There are two antiparallel strands of DNA
• The bases are stacked
• There are two grooves ‘major and minor’

Question 3

How many grooves does DNA have?

Answer 3

2 grooves -Major -Minor

Question 4

How is DNA packaged?

Answer 4

DNA double helix–>Nucleosomes(Beads on string)–>Chromatin fibre –>Loops of chromatin fiber–>Metaphase chromosome

Question 5

What is the function of histones?

Answer 5

Basic protein that bind DNA

Question 6

How many histones form a nucleosome?

Answer 6

8 histones form a nucleosome

Question 7

Which histone binds the linker DNA?

Answer 7

Histone 1 binds the linker DNA

Question 8

Why do chromosomes come in different shapes? What are the three different types of chromosomes?

Answer 8

Chromosomes come in different shapes due to position of centromere

• Metacentric
• Submetacentric - small arms
• Acrocentric - satellite arms

Question 9

What does the primary DNA sequence encode?

Answer 9

Primary DNA sequence encodes all the gene products necessary for an organism

Question 10

What does the primary DNA sequence also contain a large number of?

Answer 10

Primary DNA sequence also includes a large number of regulatory signals

Question 11

What is the definition of the exome?

Answer 11

Sum of all gene sequences

Question 12

Definition of a gene

Answer 12

All of the DNA that is transcribed into RNA plus all of the cis-linked(local) control regions that are required to ensure quantitatively appropriate tissue-specific expression of the final protein

Question 13

What do intergenic regions contain?

Answer 13

Contain sequences of no known function like:

• Repetitive DNA
• Endogenous retrovirus
• Pseudogenes

Question 14

What do genes often cluster in? What does this allow?

Answer 14

• Genes often cluster in families e.g globin gene cluster
• Allows for co-ordinated gene regulation
• May just reflect evolutionary history

Question 15

What does clustering of genes into families allow?

Answer 15

Allows for coordinate gene regulation

Question 16

What does the promoter recruit and to where?

Answer 16

Promoter recruits RNA polymerase to DNA template

Question 17

In what orientation does RNA polymerase bind and what direction does it only move in?

Answer 17

RNA polymerase binds asymmetrically and can only move from 5’ to 3’ direction

Question 18

What are UTR’s a part of?

Answer 18

UTR’s are a part of the exons

Question 19

Why is a TATA box needed?

Answer 19

Needed to recruit general transcription factors and RNA polymerase

Question 20

Why is a regulatory element needed?

Answer 20

Needed to regulate recruitment of RNA polymerase

Question 21

What does RNA polymerase 1 do?

Answer 21

Needed to transcribe rRNA genes

Question 22

What does RNA polymerase 2 do?

Answer 22

Needed to transcribe mRNA

Question 23

What does RNA polymerase 3 do?

Answer 23

Needed to transcribe tRNA and other small RNA’s

Question 24

Process of transcription

Answer 24

1) RNA polymerase recruited (open complex)
2) DNA helix locally unwound (open complex)
3) RNA synthesis begins
4) Elongation
5) Termination
6) RNA Polymerase dissociates

Question 25

What happens to mRNA after transcription?

Answer 25

mRNA is extensively modified after transcription:

1.Capped at 5’ end using 7-methylguanosine - makes resistant to digestion within the cell and nucleus which would degrade the message, transcription will continue to completion

2.Polyadenylated at 3’ end - cleavage factors bind and signal for cleavage to occur, poly A polymerase adds A bases to 3’ end

3.Removal of introns

Question 26

When is the 5’ cap added and why?

Answer 26

After RNA polymerase begins transcription, a methylated cap is added to prevent digestion

Question 27

What is 3’ poly A tail formed by?

Answer 27

Formed by: 1.Removal of G/U rich region by clevage factors 2.Polyadenylate polymerase adds many A bases forming poly A tail preventing degradation

Question 28

What is splicing?

Answer 28

Splicing is removal of introns by spliceosome and by joining of exons

Question 29

What is alternative splicing?

Answer 29

Exons can be skipped or added so different isoforms of protein can be produced from the same gene

Question 30

How have pseudogenes lost their function?

Answer 30

Genes which are partially inactivated due to the loss or gain of a sequence which disrupts their correct transcription/ and or translation.

Processed pseudogenes have no promoter or exons as they are copied from mRNA by retrotransposition

Question 31

List some regulatory regions in a gene and their function

Answer 31

- ENHANCERS = upregulate gene expression - short sequences that can be in the gene or many kilobases distant. They are targets for transcription factors (activators)

- SILENCERS = down regulate gene expression. They are also position-independant and are targets for transcription factors (repressors)

- INSULATORS = short sequences that prevent enhancers/ silencers influencing other genes