Genome Structure

Question 1

DNA is

Answer 1

Deoxyribonucleic acid

Question 2

What type of molecule is DNA?

Answer 2

Macromolecule consisting of a linear strand of nucleotides

Nucleotide

Question 3

What the difference between deoxyribose sugar and ribose sugar

Answer 3

Deoxyribose doesn’t have the 2’- hydroxy group

Question 4

What charge is the phosphate group?

Answer 4

Negative charge

Question 5

DNA in 3D

Answer 5

2 groves (major and minor)
2 antiparallel strands
bases stacked

Question 6

How to pack DNA

Answer 6

Histones

Question 7

Histones

Answer 7

Basic (positively charged) proteins that bind DNA
8 Histones form a nucleosome
Histone 1 binds the linker DNA

Question 8

DNA packing

Answer 8

DNA double strand helix -> Nucleosomes -> chromatin -> loops of chromatin fiber -> metaphase chromosome

Question 9

How many chromosomes in a human?

Answer 9

23 pairs (human karyotype)

Question 10

What do gene contain?

Answer 10

CAAT box
TATA box 
Transcription initiation 
Translation initiation 
Translation termination 
Transcription termination

Question 11

The exome

Answer 11

• The exome is made up of gene sequences

Question 12

What is a gene?

Answer 12

Gene promoter, the coding sequences, stop codon

Question 13

Globin gene size

Answer 13

1.8 kb

Question 14

Dystrophin gene size

Answer 14

2.4 Mb

Question 15

Gene clusters

Answer 15

An example of clusters globin clusters

• allows for co-ordinated gene regulation
• may just reflect evolutionary history

Question 16

Introns within a gene

Answer 16

• Vary in number from 0 to at least 311
• Vary in size - 30 bp to 1 Mbp
• Some introns contain other genes

Question 17

What do promoters do?

Answer 17

Recruit RNA polymerase

Question 18

Regulation of RNA synthesis

Answer 18

Regulation occurs via transcription factors

Question 19

Enhancers

Answer 19

Upregulate gene expression – they are short sequences that can be in the gene or many kilobases distant. They are targets for transcription factors (activators).

Question 20

Silencers

Answer 20

Downregulate gene expression. They are also position-independent and are also targets for transcription factors (repressors).

Question 21

Insulators

Answer 21

Short sequences that act to prevent enhancers/silencers influencing other genes

Question 22

Transcription

Answer 22

Catalysed by RNA Polymerase II
• Transcribes in 5’ to 3’ direction
• Transcribes everything after the transcription start site (exons and introns)
• mRNA is post-transcriptionally modified

Question 23

RNA polymerase 2

Answer 23

Recognise promoters efficiently with the assistance of many other transcription factors

Question 24

Post transcriptional modification of mRNA

Answer 24

• Capped at 5’ end
• Spliced - introns removed
• Polyadenylated at 3’ end

Question 25

5' cap

Answer 25

After 25-30nts are synthesised, a methylated cap is added to the 5’ end by three enzyme activities: • RNA 5’-triphosphatase • Guanylyltransferase • N7G-methyltransferase

Question 26

What other enzyme is needed for 5' capping?

Answer 26

The first two activities are carried out by a bifunctional capping enzyme (CE) RNA Pol II is also required

Question 27

What is the TREX complex?

Answer 27

Transcription-EXport. | mRNA alsohas the 5' cap, poly A tail and exon junction complexes.

Question 28

3' Poly A tail

Answer 28

- CPSF recognise the PAS and acts on cleavage site. - CSTF recognises GU-rich downstram elements - PAP is requited and adds multiple A bases after cleavage site - PAB is Poly A Binding protein. Other proteins appear to be required for this process - CFlm and simplekin

Question 29

CPSF

Answer 29

Cleavage and Polyadenylation Stimulating Factor

Question 30

PAS

Answer 30

Polyadenylation Signal

Question 31

CSTF

Answer 31

Cleavage Stimulating Factor

Question 32

DSE

Answer 32

Downstream Elements

Question 33

PAP

Answer 33

Poly-A polymerase

Question 34

PAB

Answer 34

Poly A binding protein

Question 35

CFlm

Answer 35

Cleavage Factor lm

Question 36

Alternative splicing

Answer 36

Produces different proteins due to exon splicing

Question 37

Isoform

Answer 37

Variations of proteins from the same gene