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Genomics > 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

→ DNA helix
→ Nucleosomes

→ Chromatin Fibres
→ Chromatin loops
→ Loops of condensed chromatin
→ 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

→ 2A, 2B, 3, 4

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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

→ Upto 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

→ Remnants of retroviruses
→contain sequences of no known function
→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

→ 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

→ 5’ to 3’

26
Q

What are 2 regulatory signals?

A

→ CAAT

→ 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

→ 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

→ upregulate gene expression

36
Q

What are silencers?

A

→ Targets for transcription factors (repressors)

→ position independent

37
Q

What do silencers do?

A

→ Downregulate 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

→ Capped at 5’ end
→ Polyadenylated at 3’ end

→ 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

→ 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

→ Protein complex called a spliceosome
→ brings the ends of the exons together and removes the intron inbetween

→ joins exons together
→ 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 fiber and generates chromatin loops when it pauses at CTCF binding sites.

Genomics (21 decks)

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