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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
How does RNA polymerase bind and in what direction does it go?
Asymmetrically from 5' to 3'
26
What are 2 regulatory signals?
CAAT and TATA
27
What are the 5 components of a gene?
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
What is the TATA box for?
Recruit general transcription factors and RNA polymerase
29
How many polymerases are there in eukaryotes and what are they?
RNA pol I, RNA pol II and RNA pol III
30
What are the RNA polymerases for in eukaryotes?
RNA pol I → transcribe rRNA genes RNA pol II → transcribe mRNA RNA pol III → Transcribe tRNA and other small RNAs
31
What do co-factors do?
Regulate how much and when transcription is occurring
32
What are the steps for transcription?
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
What do some introns contain?
Other genes
34
What are enhancers?
Short sequences that can be in the gene or many Kb distant. Targets for transcription factors that activate expression
35
What do enhancers do?
Up regulate gene expression
36
What are silencers?
Targets for transcription factors (repressors) Position independent
37
What do silencers do?
Down regulate gene expression, position-independent and are also targets for transcription factors (repressors)
38
What are insulators?
Short sequences that act to prevent enhancers/silencers influencing other genes
39
How is eukaryotic mRNA modified after transcription?
1. Capped at 5' end 2. Polyadenylated at 3' end 3. Introns are removed
40
When and why is the 5' cap added?
After RNA polymerase begins transcription, so the mRNA looks like the 5’ end of the message. also to protect it from nuclease activities
41
What are the two termination signals?
AAUAAA and G/U rich region
42
What happens when the termination signal is reached?
G/U rich region and everything after it is removed Polyadenylate polymerase adds lots of As to the end of the sequence
43
Why is polyadenylation required?
Protects the end from degradation and targets it to leave the nucleus
44
How does splicing work?
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
What is alternative splicing?
Exons can be skipped or added so variations of proteins (isoforms) can be made from the same gene
46
What targets mRNA for nuclear export?
TREX is bound to the cap. It is enhanced by the exon junction complex
47
What are pseudogenes?
Genes that have been at least partially inactivated by loss or gain of sequence that disrupt their transcription or translation
48
What is an example of a pseudogene?
Glucocerebrosidase has an adjacent pseudogene It differs in the coding region by one 55bp deletion
49
How are pseudogenes copied from mRNA?
Retrotransposition
50
What proteins do not have introns in their mRNA?
Histones
51
What enzymes are involved in 5' Cap?
RNA 5’-triphosphatase Guanylyltransferase N7G-methyltransferase
52
What are the 1st two activities carried out by in Capping?
A bifunctional capping enzyme (CE)
53
What is the role of CPSF?
Cleavage and Polyadenylation Stimulating Factor) recognises the PAS (Polyadenylation signal) and acts on cleavage site at about 20bps
54
What is the CSTF?
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
What are other proteins required for Poly A?
CFIm (Cleavage Factor Im), CFIIm and Simplekin. They stabilise the process
56
What can compartments be separated into?
Compartment A – transcriptionally active with active histone modifications Compartment B – transcriptionally repressed with repressive histone modifications
57
What are TADs?
Individual compartments are made up of several non-interacting sub-compartments Usually separated by the Transcriptional Repressor CTCF protein
58
What is 3D transcriptional control involving CTCF?
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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