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Genomics > Genome Structure > Flashcards

Genome Structure Flashcards

1
Q

Describe the basic structure of DNA

A

• DNA is deoxyribonucleic acid
• It is a macromolecule consisting of a linear strand of nucleotides
• Single linear strands bind to complementary strands to form double-stranded DNA
Two antiparallel strands of DNA
Bases “stacked”
Two grooves
• Major
• Minor

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2
Q

Describe the charge of a DNA molecule

A

Negatively charged because of the phosphates

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3
Q

What type of molecule is a single strand of DNA

A

linear macromolecule

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4
Q

How many base pairs is the human genome and how many genes are there in a human?

A
  • Human genome is 3 x 109 base pairs – 3Gbp

* It contains ~20 000 genes.

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5
Q

What is the main issue with DNA?

A

DNA is very lengthy:

There is around 2m of DNA in a nucleated cell
• 37.2 trillion cells in your body
• That is 7.44x1013 metres of DNA

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6
Q

So how do we fit DNA into nucleated cells?

A

The solution is Histones

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7
Q

Describe the charge of histones

How many histones form a nucleosome?

What binds the linker DNA

A

Basic positively charged that binds to negative DNA

Eight histones 2x(H2A+H2B+H3+H4) form the nucleosome

Histone 1

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8
Q

Have a look at the image of X-ray crystallography of DNA around histones

A

On image

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9
Q

What are the phases of DNA packing?

A
  1. DNA double helix
  2. Nucleosomes
  3. Chromatin fibre
  4. Extended section of chromosome
  5. Loops of chromatin fibre
  6. Metaphase chromosome
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10
Q

Descirbe the structure of a chromosome

A

On image

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11
Q

What is a human karotype and what does it show?

A
  • Stained chromosomes, nucleus in metaphase

* Banding patterns

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12
Q

Define genome (3)

A
  • The primary DNA sequence encodes all the gene products necessary for a human
  • The primary DNA sequence also includes a large number of regulatory signals
  • Much of the DNA sequence does not have an assigned function as yet
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13
Q

Define exon (there are two)

A

• The exome is made up of gene sequences
Coding regions of DNA
• Some definitions use all of the coding sequences (~37 Mbp – 1.2% of genome)
• Some definitions use all of the gene sequences (~60Mbp – 2% of genome)

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14
Q

Define gene and describe the structure of a gene

A
  • 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
  • It is NOT just the bits that encode the final protein, regulation of the gene is very important.

On image

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15
Q

Where are the size of the genes globin and dystrophin ?

A

globin = 1.8kb, dystrophin = 2.4Mb

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16
Q

What are intergenic regions?

A

Intergenic regions contain sequences of no known function, such as repetitive DNA, endogenous retroviruses, pseudogenes. They may contain many regulatory elements.

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17
Q

How do genes tend to exist and what does this allow?

A

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

  • allows for co-ordinated gene regulation
  • may just reflect evolutionary history
18
Q

What is an intron?

How many are there and what is the size of them?

A

Non-coding regions of DNA

  • Vary in number – from 0 to at least 311
  • Vary in size - 30bp to 1Mbp
19
Q

Describe the structure of a gene

A

On image

20
Q

What are the two major regions that the promoter region contains and what are there functions?

A
  1. Regulatory region - needed to regulate the recruitment of RNA polymerase 2
  2. TATA box - needed to recruit general transcription factors and RNA polymerase
21
Q

3 general functions of the promoter region

A
  • Promoters recruit RNA polymerase to a DNA template
  • RNA polymerase binds asymmetrically and can only move 5’ to 3’
  • Regulation occurs via transcription factors
22
Q

What are the purpose of enhancers?

A

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

23
Q

What are the purpose of silencers?

A

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

24
Q

What are insulators?

A

• Insulators are short sequences that act to prevent enhancers/silencers influencing other genes

25
Q

What is transcription catalysed by?

In what direction does it catalyse the reaction?

Does it trascribe coding AND non-coding regions?

A
  • Messenger RNA synthesis (transcription) is 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
26
Q

What is the purpose of RNA polymerase 2 and look at its structure?

A

RNA polymerase II recognises promoters efficiently with the assistance of many other transcription factors

27
Q

What are the 7 stages of transcription?

A
  1. DNA
  2. RNA polymerase recruited (closed complex)
  3. DNA helix is locally unwound (open complex)
  4. RNA synthesis begins
  5. Elongation
  6. Termination
  7. RNA polymerase dissociates
28
Q

What does transcription produce?

What does post-transcriptional modification produce?

A

pre-mRNA

mRNA

29
Q

What 3 process form post-transcriptional modification?

A
  • Capped at 5’ end
  • Spliced - introns removed
  • Polyadenylated at 3’ end
30
Q

Describe how a 5’ capped is formed?

Whats the purpose of the 5’ cap?

A

After 25-30nts are synthesised, a methylated cap is added to the 5’ end by three enzyme activities:
• RNA 5’-triphosphatase
• Guanylyltransferase
• N7G-methyltransferase
The first two activities are carried out by a bifunctional capping enzyme (CE)
RNA Pol II is also required

Makes it resistant to digestion by enzymes within the cell

31
Q

How is the 3’ Poly A tail formed?

What’s the purpose?

A

CPSF (Cleavage and Polyadenylation Stimulating Factor) recognises the PAS (Polyadenylation signal) and acts on cleavage site
• CSTF (Cleavage Stimulating Factor) recognises GU-rich Downstream Elements (DSE)
• PAP (Poly-A polymerase) is recruited and adds multiple A bases after cleavage site
• PAB is Poly-A Binding Protein. Other proteins appear to be required for this process – CFIm (Cleavage Factor Im), CFIIm and Simplekin

  • The 3’ poly A tail
    o Around 250 As are added
    o Protects the end from degradation
    o Also help target messages out of the nucleus
32
Q

Describe the process of splicing

What is it?

What catalyses it?

What happens in the process?

A

Splicing of introns (removal of introns)
• The spliceosome catalyses this reaction
• The spliceosome (150 proteins) catalyses the OH group to the P group
• This frees up the Oh group, linked to phosphate
• 2’ to 5’ linkage
• Its then spliced out and is known as the lariat

33
Q

What happens after splicing?

A

splicing targets mRNAs for nuclear export:

Once they are spliced, TRanscription-Export (recruited by Exon Junction Complex) which helps to export this mRNA out of the nucleus. This allows targeting of the MRNA to the ER.

34
Q

Give an outline of the whole process

A

On image

35
Q

What is Alternative splicing?

A
  • We can choose to splice out different exons as well as introns and so can produce new proteins as a result.
  • We can skip or even add exons to produce variations of a protein from the same gene (isoforms)
36
Q

How do we get protein variation?

A

On image

37
Q

How is DNA organised in somatic cells and how is it identified?

What did it involve and require?

A
  • In somatic cells the nuclear DNA is arranged non-randomly
  • Organisation has been identified using Hi-C (detects genomic DNA sequences in close proximity) and high-throughput microscopy
  • Involves CTCF protein and Cohesin protein complex, as well as transcription machinery
38
Q

What are the 2 compartments that the genome is found in?

A
  • Compartment A – transcriptionally active with active histone modifications
  • Compartment B – transcriptionally repressed with repressive histone modifications

These are interspersed throughout the 2D sequence but the same compartment types are brought close together in the 3D genome

39
Q

What are Topologically-Associated Domains (TADs)?

What are they separated by?

A
  • Individual compartments are made up of several non-interacting sub-compartments
  • These are Topologically-Associated Domains (TADs)
  • They are usually separated by the Transcriptional Repressor CTCF protein
40
Q

Have a look at transcriptional control and genome structure (3D)

A

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Genomics (17 decks)

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