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Genomics > Genome Structure > Flashcards

Genome Structure Flashcards

1
Q

how many base pairs is the human genome

A

3 x 10^9

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2
Q

is genome size strongly related to complexity of an organism?

A

no

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3
Q

what are the problems related to DNA length

A

2m of DNA in a nucleated cell

average cell is 50um

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4
Q

how do we overcome the problem with DNA length in our cells?

A

histone proteins which are basic positively charged proteins that bind DNA

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5
Q

what are the different levels of DNA packaging

A 
DNA double helix
nucleosomes
chromatin fibre 
extended section of chromosome 
loops of chromatin fibre 
metaphase chromosome
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6
Q

what does the primary DNA do?

A

encodes all the gene products necessary for a human

includes many regulatory signals

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7
Q

what is the exome

A

made up of gene sequences

some use all coding sequences or whole gene sequence

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8
Q

what is a gene

A

all the DNA that is transcribed into RNA and all the cis-linked control regions required to ensure quantitatively appropriate tissue specific expression of the final protein

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9
Q

describe the gene structure

A

98% of the genome
contain sequence of no known function, repetitive DNA, endogenous retroviruses, pseudogenes
cluster into families

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10
Q

describe introns in genes

A

vary in number 0-311

vary in size 30bp-1Mbp

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11
Q

describe the structure of a gene

A

coding regions/exons
introns
promoter at 5’ end
Transcriptor factor binding sites

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12
Q

what is the promoter

A

recruit RNA polymerase to a DNA template

RNA p binds asymmetrically and only moves 5’-3’

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13
Q

what are enhancers

A

up-regulate gene expression, short sequences that can be in the gene or many kilo bases distant.
targets for transcription factors

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14
Q

what are silencers?

A

down regulate gene expression

position independent and targets for TFs

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15
Q

what are insulators?

A

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

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16
Q

7 steps of transcription

A
  1. promoter and transcription unit region
  2. RNA polymerase recruited
  3. DNA helix locally unwound
  4. RNA synthesis begins
  5. elongation of strand
  6. termination
  7. RNA polymerase dissociates
17
Q

post-transcriptional modification of mRNA

A

capped at 5’ end
spliced = introns removed
polyadenylated at 3’ end

18
Q

3 enzymes involved in 5’ cap

A

RNA 5’ triphosphatase
guanylyl transferase
N7G- methyltransferase

19
Q

what do spliceosomes do

A

help remove introns

20
Q

what is a lariat

A

the joining of two axons, intron spliced out

21
Q

what is the TREX complex

A

transcription export complex

22
Q

what is CPSF

A

cleavage and polyadenylation simulating factor

recognises Polyadenylation signal and acts on cleavage site

23
Q

what is CSTF

A

cleavage stimulating factor

recognises GU rich downstream elements

24
Q

what is PAP

A

poly A polymerase

recruited and adds multiple A bases after cleavage site

25
Q

what is PAB

A

poly B binding protein

cleavage factor Im, CFIIm, simpleton

26
Q

the purpose of splicing?

A

allows variations of a proteins to be produced from the same gene

27
Q

how is DNA arranged in somatic cells

A

non-randomly

28
Q

how has organisation of DNA been identified

A

Hi-c (detects genomic DNA sequences in proximity)

high-throughput microscopy

29
Q

genomes can be separated into compartments.

describe compartment A and B

A

A = transcriptionally active with active histone modifications

B= transcriptionally repressed with repressive histone modifications

30
Q

what are TADs

A

topologically associated domains
- individual compartments made up of several non-interacting sub-compartments

usually separated by transcriptional repressor CTCF protein

31
Q

what is 3D transcription control

A

loop extrusion model for enhancer control of transcription

Genomics (20 decks)

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