Genome Structure

Question 1

What is a genome?

Answer 1

A complete set of genes or genetic material present in a cell or organism.

Question 2

What is DNA?

Answer 2

• Deoxyribonucleic acid.
• A macromolecule consisting of a linear strand of nucleotides.
• Single linear strands bind to complementary strands to form double-stranded DNA.

Question 3

Why is DNA have a deoxyribose sugar?

Answer 3

It does not have the 2’-hydroxyl group of ribose

Question 4

In which direction does DNA run?

Answer 4

Strands are antiparallel and run in opposite directions.

Question 5

What are the two grooves of DNA? What are they used for?

Answer 5

Major and minor

Enzymes and DNA binding proteins can access these grooves

Question 6

Describe the genome packing problem

Answer 6

• There is about 2m of DNA in a nucleated cell.
• 37.2 trillion cells in the body
• That is 7.44 x 10(13) metres of DNA
• How is it fit into the cell as the cell is 50 micrometres in diameter.

Question 7

Describe DNA packing

Answer 7

• DNA is wrapped around histones forming a nucleosome
• Wrapped further to form a chromatin fibre
• Forms extended sections of chromosomes
• Forms loop of chromatin fibres
• Form chromosomes

Question 8

What are histones?

Answer 8

Basic proteins that bind DNA.

Question 9

How many histones form a nucleosome?

Answer 9

8

Question 10

What is the role of histone 1?

Answer 10

Binds the linker DNA

Question 11

What is the name of the chromosome based on?

Answer 11

Based on where the centromere is located

• Metacentric
• Submetacentric = small arms
• Acrocentric = “satellite arms”

Question 12

Function of the primary DNA sequence

Answer 12

• Encodes all the gene products necessary for an organism
• Includes a large number of regulatory signals
• Does not all have an assigned function yet

Question 13

What is the exome?

Answer 13

The sum of all gene sequences.
Some defintions just use the coding sequences - about 37 mbp
Some definitions use the whole sequences - about 60 mbp

Question 14

What is a gene?

Answer 14

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 15

What is cis-linked control regions?

Answer 15

The regions physically close to the exons on the DNA strand.

Question 16

Trans-regulatory region locations

Answer 16

Can be on different chromosomes

Question 17

What do all nucleated somatic cells contain?

Answer 17

The same genome

• Human genome size - 3Gbp
• Contains 19-20000 genes
• Less than 2% of DNA is gene

Question 18

How is the genome organised?

Answer 18

• Genes often vary in size
• Intergenic regions contain sequences of no known function such as repetitie DNA, endogenous retroviruses, pseudogenes.
• There is no correlation between genome size and organism complexity.

Question 19

What are genes sorted into often?

Answer 19

Genes are often in cluster families e.g. globin clusters

Question 20

Why are genes in clusters?

Answer 20

To allow for co-ordination gene regulation

May just reflect evolutionary history

Question 21

What percentage of the genome is the intergenic region?

Answer 21

about 98%

Question 22

Role of promoters in transcription

Answer 22

Recruit RNA polymerase to the DNA template

Question 23

Where do the promoters lie?

Answer 23

Outside the transcribed region in DNA

Question 24

What does RNA polymerase do?

Answer 24

It binds asymmetrically and can only move 5’ to 3’.

Question 25

What is the basic structure of a gene?

Answer 25

``` 5' - Promoter region: CAAT box, TATA box - Transcriotion initiation (ATG) (Exon 1) - Exon - Intron - Exon - Intron... subsequently - Translation termination 3' ```

Question 26

Describe two types of eukaryotic promoter

Answer 26

- Regulatory element: needed to regulate recruitment of RNA polymerase - TATA box: needed to recruit general transcription factors and RNA polymerase

Question 27

What does transcription involve?

Answer 27

Local unwinding of the DNA template

Question 28

What are the three eukaryotic RNA polymerases and their functions?

Answer 28

RNA polymerase I - needed to transcribe rRNA genes RNA polymerase II - needed to transcribe mRNA RNA polymerase III - needed to transcribe tRNA and other small RNAs

Question 29

Summarise the process of transcription

Answer 29

- RNA polymerase recruited - DNA helix locally unwound to open complex - RNA synthesis begins - Elongation - Termination - RNA polymerase dissociates

Question 30

Introns in genes

Answer 30

- Vary in number - Vary in size - Some introns contian other genes

Question 31

What are 3 other regulatory regions?

Answer 31

- Enhancers - Silencers - Insulators

Question 32

What do enhancers do?

Answer 32

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 33

What do silencers do?

Answer 33

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

Question 34

What are insulators?

Answer 34

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

Question 35

How is mRNA modified after transcription?

Answer 35

- Capped at 5' end - Polyadenylated at 3' end - Splicing

Question 36

Why does capping occur?

Answer 36

A cap is added to the 5' end. This makes it resistant to digestion by enzymes within the cell and nucleus which would degrade the message.

Question 37

Why does polyadenylation occur?

Answer 37

Protects the 3' end from degradation and helps target them for transportation out of the nucleus via nuclear pore.

Question 38

What is splicing?

Answer 38

Intervening sequences (introns are removed)

Question 39

What are the possible splicing patterns?

Answer 39

- Exon skipping/inclusion - Alternative 3' splice sites - Alternative 5' splice sites - Mutually exclusive exons - Intron retention

Question 40

Describe how splicing works

Answer 40

- 150 proteins make up the spliceosome and brings the ends of the exons together - Removes the introns inbetween the adjacent exons - Lariat-like structure (introns) are degraded.

Question 41

What is alternative splicing and what does it form?

Answer 41

Alternative splicing is when exons are skipped or added so variations of a protein can be produced from the same gene.

Question 42

What is an isoform?

Answer 42

Variation of a protein from the same gene

Question 43

What happens to the mRNA after splicing?

Answer 43

These mRNA are marked for nuclear export.

Question 44

What recognises the polyadenylation signal?

Answer 44

Cleavage and polyadenylation stimulating factor (CPSF)

Question 45

What does the cleavage stimulating factor (CSTF) do?

Answer 45

It recognises GU-rich downstream elements

Question 46

What does poly-A polymerase (PAP) do?

Answer 46

It is recruited and adds multiple A bases after cleavage sites.

Question 47

Summarise the formation of mRNA

Answer 47

1. RNA polymerase binds to recognition sequence on DNA strand 2. Elongation 3. Termination 4. Capping, polyadenylation and splicing 5. Nuclear export via nuclear pore

Question 48

How is nuclear DNA organised in somatic cells?

Answer 48

In domains

Question 49

How are domains identifed?

Answer 49

Identified using Hi-C (detects sequences in close proximity) and high-throughput microscopy

Question 50

What does the identification of domains involve?

Answer 50

It involves CTCF protein and cohesin protein complex, as well as transcription machinery.

Question 51

What are pseudogenes?

Answer 51

These are genes that have been at least partially inactivated by the loss or gain of sequence that disrupt their correct transcription and/or translation.

Question 52

Give an example of a pseudogene

Answer 52

Glucocerebrosidase has an adjacent pseudogene that only differs in the coding region by one 55bp detection and a few single base changes.

Question 53

What do processed pseudogenes not have and why?

Answer 53

They do not have a promoter or exons as they are copied from mRNA by retrotransposition.