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Genomics > Genome Structure > Flashcards

Genome Structure Flashcards

1
Q

What is a genome?

A

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

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2
Q

What is DNA?

A
  • Deoxyribonucleic acid.
  • A macromolecule consisting of a linear strand of nucleotides.
  • Single linear strands bind to complementary strands to form double-stranded DNA.
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3
Q

Why is DNA have a deoxyribose sugar?

A

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

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4
Q

In which direction does DNA run?

A

Strands are antiparallel and run in opposite directions.

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5
Q

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

A

Major and minor

Enzymes and DNA binding proteins can access these grooves

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6
Q

Describe the genome packing problem

A
  • 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.
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7
Q

Describe DNA packing

A
  • 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
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8
Q

What are histones?

A

Basic proteins that bind DNA.

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9
Q

How many histones form a nucleosome?

A

8

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10
Q

What is the role of histone 1?

A

Binds the linker DNA

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11
Q

What is the name of the chromosome based on?

A

Based on where the centromere is located

  • Metacentric
  • Submetacentric = small arms
  • Acrocentric = “satellite arms”
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12
Q

Function of the primary DNA sequence

A
  • Encodes all the gene products necessary for an organism
  • Includes a large number of regulatory signals
  • Does not all have an assigned function yet
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13
Q

What is the exome?

A

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

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14
Q

What is 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.

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15
Q

What is cis-linked control regions?

A

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

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16
Q

Trans-regulatory region locations

A

Can be on different chromosomes

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17
Q

What do all nucleated somatic cells contain?

A

The same genome

  • Human genome size - 3Gbp
  • Contains 19-20000 genes
  • Less than 2% of DNA is gene
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18
Q

How is the genome organised?

A
  • 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.
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19
Q

What are genes sorted into often?

A

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

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20
Q

Why are genes in clusters?

A

To allow for co-ordination gene regulation

May just reflect evolutionary history

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21
Q

What percentage of the genome is the intergenic region?

A

about 98%

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22
Q

Role of promoters in transcription

A

Recruit RNA polymerase to the DNA template

23
Q

Where do the promoters lie?

A

Outside the transcribed region in DNA

24
Q

What does RNA polymerase do?

A

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

25
Q

What is the basic structure of a gene?

A 
5' 
- Promoter region: CAAT box, TATA box 
- Transcriotion initiation (ATG) (Exon 1) 
- Exon  
- Intron 
- Exon 
- Intron... subsequently 
- Translation termination 
3'
26
Q

Describe two types of eukaryotic promoter

A
  • Regulatory element: needed to regulate recruitment of RNA polymerase
  • TATA box: needed to recruit general transcription factors and RNA polymerase
27
Q

What does transcription involve?

A

Local unwinding of the DNA template

28
Q

What are the three eukaryotic RNA polymerases and their functions?

A

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

29
Q

Summarise the process of transcription

A
  • RNA polymerase recruited
  • DNA helix locally unwound to open complex
  • RNA synthesis begins
  • Elongation
  • Termination
  • RNA polymerase dissociates
30
Q

Introns in genes

A
  • Vary in number
  • Vary in size
  • Some introns contian other genes
31
Q

What are 3 other regulatory regions?

A
  • Enhancers
  • Silencers
  • Insulators
32
Q

What do enhancers do?

A

Upregulate gene expression

  • They are short sequences that can be in the gene or many kilobases distant.
  • They are targets for transcription factors (activators)
33
Q

What do silencers do?

A
  • They downregulate gene expression.
  • They are also position-independent
  • They are also targets for transcription factors (repressors)
34
Q

What are insulators?

A

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

35
Q

How is mRNA modified after transcription?

A
  • Capped at 5’ end
  • Polyadenylated at 3’ end
  • Splicing
36
Q

Why does capping occur?

A

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.

37
Q

Why does polyadenylation occur?

A

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

38
Q

What is splicing?

A

Intervening sequences (introns are removed)

39
Q

What are the possible splicing patterns?

A
  • Exon skipping/inclusion
  • Alternative 3’ splice sites
  • Alternative 5’ splice sites
  • Mutually exclusive exons
  • Intron retention
40
Q

Describe how splicing works

A
  • 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.
41
Q

What is alternative splicing and what does it form?

A

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

42
Q

What is an isoform?

A

Variation of a protein from the same gene

43
Q

What happens to the mRNA after splicing?

A

These mRNA are marked for nuclear export.

44
Q

What recognises the polyadenylation signal?

A

Cleavage and polyadenylation stimulating factor (CPSF)

45
Q

What does the cleavage stimulating factor (CSTF) do?

A

It recognises GU-rich downstream elements

46
Q

What does poly-A polymerase (PAP) do?

A

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

47
Q

Summarise the formation of mRNA

A
  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
48
Q

How is nuclear DNA organised in somatic cells?

A

In domains

49
Q

How are domains identifed?

A

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

50
Q

What does the identification of domains involve?

A

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

51
Q

What are pseudogenes?

A

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.

52
Q

Give an example of a pseudogene

A

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

53
Q

What do processed pseudogenes not have and why?

A

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

Genomics (19 decks)

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