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Genomics > Genome Structure > Flashcards

Genome Structure Flashcards

1
Q

DNA is

A

Deoxyribonucleic acid

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2
Q

What type of molecule is DNA?

A

Macromolecule consisting of a linear strand of nucleotides

Nucleotide

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3
Q

What the difference between deoxyribose sugar and ribose sugar

A

Deoxyribose doesn’t have the 2’- hydroxy group

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4
Q

What charge is the phosphate group?

A

Negative charge

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5
Q

DNA in 3D

A

2 groves (major and minor)
2 antiparallel strands
bases stacked

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6
Q

How to pack DNA

A

Histones

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7
Q

Histones

A

Basic (positively charged) proteins that bind DNA
8 Histones form a nucleosome
Histone 1 binds the linker DNA

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8
Q

DNA packing

A

DNA double strand helix -> Nucleosomes -> chromatin -> loops of chromatin fiber -> metaphase chromosome

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9
Q

How many chromosomes in a human?

A

23 pairs (human karyotype)

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10
Q

What do gene contain?

A 
CAAT box
TATA box 
Transcription initiation 
Translation initiation 
Translation termination 
Transcription termination
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11
Q

The exome

A

• The exome is made up of gene sequences

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12
Q

What is a gene?

A

Gene promoter, the coding sequences, stop codon

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13
Q

Globin gene size

A

1.8 kb

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14
Q

Dystrophin gene size

A

2.4 Mb

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15
Q

Gene clusters

A

An example of clusters globin clusters

  • allows for co-ordinated gene regulation
  • may just reflect evolutionary history
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16
Q

Introns within a gene

A
  • Vary in number from 0 to at least 311
  • Vary in size - 30 bp to 1 Mbp
  • Some introns contain other genes
17
Q

What do promoters do?

A

Recruit RNA polymerase

18
Q

Regulation of RNA synthesis

A

Regulation occurs via transcription factors

19
Q

Enhancers

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).

20
Q

Silencers

A

Downregulate gene expression. They are also position-independent and are also targets for transcription factors (repressors).

21
Q

Insulators

A

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

22
Q

Transcription

A

Catalysed by RNA Polymerase II
• Transcribes in 5’ to 3’ direction
• Transcribes everything after the transcription start site (exons and introns)
• mRNA is post-transcriptionally modified

23
Q

RNA polymerase 2

A

Recognise promoters efficiently with the assistance of many other transcription factors

24
Q

Post transcriptional modification of mRNA

A
  • Capped at 5’ end
  • Spliced - introns removed
  • Polyadenylated at 3’ end
25
Q

5’ cap

A

After 25-30nts are synthesised, a methylated cap is added to the 5’ end by three enzyme activities:
• RNA 5’-triphosphatase
• Guanylyltransferase
• N7G-methyltransferase

26
Q

What other enzyme is needed for 5’ capping?

A

The first two activities are carried out by a bifunctional capping enzyme (CE)
RNA Pol II is also required

27
Q

What is the TREX complex?

A

Transcription-EXport.

mRNA alsohas the 5’ cap, poly A tail and exon junction complexes.

28
Q

3’ Poly A tail

A
  • CPSF recognise the PAS and acts on cleavage site.
  • CSTF recognises GU-rich downstram elements
  • PAP is requited and adds multiple A bases after cleavage site
  • PAB is Poly A Binding protein. Other proteins appear to be required for this process - CFlm and simplekin
29
Q

CPSF

A

Cleavage and Polyadenylation Stimulating Factor

30
Q

PAS

A

Polyadenylation Signal

31
Q

CSTF

A

Cleavage Stimulating Factor

32
Q

DSE

A

Downstream Elements

33
Q

PAP

A

Poly-A polymerase

34
Q

PAB

A

Poly A binding protein

35
Q

CFlm

A

Cleavage Factor lm

36
Q

Alternative splicing

A

Produces different proteins due to exon splicing

37
Q

Isoform

A

Variations of proteins from the same gene

Genomics (19 decks)

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