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Genomics SGUL Sem 3 > Genome structure > Flashcards

Genome structure Flashcards

1
Q

What are the bases like in 3D DNA?

A

Stacked

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2
Q

How much DNA is in a nucleated cell?

A

2m

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3
Q

How wide is the average cell?

A

50 micrometers

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4
Q

What are the 6 levels of DNA packing?

A
  1. DNA helix
  2. Nucleosomes
  3. Chromatin Fibres
  4. Chromatin loops
  5. Loops of condensed chromatin
  6. Chromosome
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5
Q

What are histones?

A

Basic +ve proteins that bind DNA

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6
Q

How many histones form the nucleosome?

A

8
2x(H2A, H2B, H3, H4)

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7
Q

What histone binds Linker DNA?

A

Histone 1

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8
Q

What is linker DNA?

A

Piece of DNA that is between nucleosomes

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9
Q

What is an acrocentric chromosome?

A

They don’t have the short arms

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10
Q

What does the primary DNA sequence encode?

A

All the gene products necessary for an organism
Regulatory signals

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11
Q

What is the exome?

A

Sum of all the gene sequences includes a large number of regulatory signals- non coding

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12
Q

What do the two definitions of the exome include?

A

Coding sequences whole gene sequences

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13
Q

What is a gene?

A

All of the DNA that is transcribed into RNA. 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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14
Q

What is the size of the human genome?

A

Up to 2 Giga base pairs

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15
Q

What % of the DNA is genes?

A

Less than 2%

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16
Q

What is the general trend linking genes and organism complexity?

A

The more genes the more complex

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17
Q

Why does the number of genes not necessarily correlate to complexity?

A

A marbled lungfish has 130Gbp. Paris Japonica (flower) has 149Gbp (biggest genome)

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18
Q

What is an example of gene size variation?

A

Globin gene 1.8kb dystrophin gene 2.4mb

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19
Q

What do intergenic regions or pseudogenes contain?

A
  1. Remnants of retroviruses
  2. Contain sequences of no known function
  3. May contain many regulatory elements
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20
Q

How do genes often cluster and give an example?

A

In families, Globin clusters

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21
Q

What does gene clustering allow for?

A

Co-ordinate gene regulation
Reflect evolutionary history

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22
Q

What is the transcription unit divided into?

A

Exons and Introns

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23
Q

Where are introns found?

A

Between exons 30bp to 1Mbp

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24
Q

What does the promoter do?

A

Recruits RNA polymerase to a DNA template

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

25
Q

How does RNA polymerase bind and in what direction does it go?

A

Asymmetrically from 5’ to 3’

26
Q

What are 2 regulatory signals?

A

CAAT and TATA

27
Q

What are the 5 components of a gene?

A

Exons and introns
Regulatory signals CAAT and TATA
Signals that allow to start transcription and translation
Signals to stop transcription and translation
3’ and 5’ UTR

28
Q

What is the TATA box for?

A

Recruit general transcription factors and RNA polymerase

29
Q

How many polymerases are there in eukaryotes and what are they?

A

RNA pol I, RNA pol II and RNA pol III

30
Q

What are the RNA polymerases for in eukaryotes?

A

RNA pol I → transcribe rRNA genes
RNA pol II → transcribe mRNA
RNA pol III → Transcribe tRNA and other small RNAs

31
Q

What do co-factors do?

A

Regulate how much and when transcription is occurring

32
Q

What are the steps for transcription?

A

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

33
Q

What do some introns contain?

A

Other genes

34
Q

What are enhancers?

A

Short sequences that can be in the gene or many Kb distant.

Targets for transcription factors that activate expression

35
Q

What do enhancers do?

A

Up regulate gene expression

36
Q

What are silencers?

A

Targets for transcription factors (repressors)
Position independent

37
Q

What do silencers do?

A

Down regulate gene expression, position-independent and are also targets for transcription factors (repressors)

38
Q

What are insulators?

A

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

39
Q

How is eukaryotic mRNA modified after transcription?

A
  1. Capped at 5’ end
  2. Polyadenylated at 3’ end
  3. Introns are removed
40
Q

When and why is the 5’ cap added?

A

After RNA polymerase begins transcription, so the mRNA looks like the 5’ end of the message. also to protect it from nuclease activities

41
Q

What are the two termination signals?

A

AAUAAA and G/U rich region

42
Q

What happens when the termination signal is reached?

A

G/U rich region and everything after it is removed

Polyadenylate polymerase adds lots of As to the end of the sequence

43
Q

Why is polyadenylation required?

A

Protects the end from degradation and targets it to leave the nucleus

44
Q

How does splicing work?

A
  1. Protein complex called a spliceosome
  2. Brings the ends of the exons together and removes the intron in-between, joins exons together
  3. Lariat is degraded
45
Q

What is alternative splicing?

A

Exons can be skipped or added so variations of proteins (isoforms) can be made from the same gene

46
Q

What targets mRNA for nuclear export?

A

TREX is bound to the cap. It is enhanced by the exon junction complex

47
Q

What are pseudogenes?

A

Genes that have been at least partially inactivated by loss or gain of sequence that disrupt their transcription or translation

48
Q

What is an example of a pseudogene?

A

Glucocerebrosidase has an adjacent pseudogene

It differs in the coding region by one 55bp deletion

49
Q

How are pseudogenes copied from mRNA?

A

Retrotransposition

50
Q

What proteins do not have introns in their mRNA?

A

Histones

51
Q

What enzymes are involved in 5’ Cap?

A

RNA 5’-triphosphatase
Guanylyltransferase
N7G-methyltransferase

52
Q

What are the 1st two activities carried out by in Capping?

A

A bifunctional capping enzyme (CE)

53
Q

What is the role of CPSF?

A

Cleavage and Polyadenylation Stimulating Factor) recognises the PAS (Polyadenylation signal) and acts on cleavage site at about 20bps

54
Q

What is the CSTF?

A

Cleavage Stimulating Factor) recognises GU-rich Downstream Elements (DSE) and helps recruit PAP. PAP (Poly-A polymerase) is recruited and adds multiple A bases after cleavage site

55
Q

What are other proteins required for Poly A?

A

CFIm (Cleavage Factor Im), CFIIm and Simplekin. They stabilise the process

56
Q

What can compartments be separated into?

A

Compartment A – transcriptionally active with active histone modifications

Compartment B – transcriptionally repressed with repressive histone modifications

57
Q

What are TADs?

A

Individual compartments are made up of several non-interacting sub-compartments

Usually separated by the Transcriptional Repressor CTCF protein

58
Q

What is 3D transcriptional control involving CTCF?

A

Bidirectionally along DNA extrudes the chromatin fibre and generates chromatin loops when it pauses at CTCF binding sites

Genomics SGUL Sem 3 (21 decks)

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