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SGUL - Genomics > Genome Structure > Flashcards

Genome Structure Flashcards

1
Q

What is the DNA?
What is it composed of?

A
  • DNA is a deoxyribonucleic acid
  • It is a macromolecule consisting of a linear strand of nucleotides
  • The single linear strands bind to it’s complementary strands forming a double stranded DNA
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2
Q

What is the Nucleotide made up of?

A
  • A sugar molecule
  • Nitrogenous base
  • Phosphate group
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3
Q

Describe the single stranded DNA

A
  • The Nucleotides attach to eachother from the Carbon 3 of one molecule to the Carbon 5 of another molecule
  • 5’ and 3’ carbons are indicated
  • The sequence is 5’ -> 3’ by convention
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4
Q

Describe the DNA in three dimensions

A
  • Has 2 anti parallel strands of DNA
  • The bases are stacked
  • Has two grooves = Major/minor
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5
Q

How big is the human genome?

A

The human genome is about 3 x 10^9 base pairs - 3Gbp

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6
Q

How many genes does the human genome contain?

A

Contains about 20 000 genes

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7
Q

Describe the trend in genes in regards to the human genome

A
  • The simpler the organism, the fewer genes they have. For e.g. flies have 10 000, yeast have 4000, bacteria 1000
  • However the genome size is not always strongly related to the complexity of the organism
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8
Q

What is the problem with DNA in the body?

A
  • The body has about 2 meters of DNA in a nucleated cell with about 37.2 trillion cells in the body.
  • That’s about 7.44 x 10^13 meters of DNA
  • The average cell is 50 ùm in diameter so how does the DNA fit
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9
Q

How is this problem resolved?

A
  • Solved through a type of protein called Histone proteins
  • They’re basic positively charged proteins that bind DNA
  • Eight histones 2x(H2A+H2B+H3+H4) form the nucleosome
  • Histone 1 binds to the linker DNA
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10
Q

Describe the Chromosome structure

A
  • The metacentric has a short arm and long arm
  • The Submetacentric has a centromere (At centre), Telomeres at the bottom ends and chromatids at the top ends
  • The acrocentric has Satellites on the centromeres
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11
Q

Describe the primary DNA sequence

A
  • The primary DNA sequence encodes all the gene products necessary for a human
  • Also includes a large number of regulatory signals
  • Much of the DNA sequence does not have an assigned function as yet
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12
Q

Describe the Exome

A
  • The exome is made up of gene sequences
  • Some definitions use all the coding sequences ( -37 Mbp about 1.2% of genome)
  • Some definitions use all of the gene sequences (~60Mbp – 2% of genome)
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13
Q

What is a gene?

A
  • The gene is all of the DNA that’s transcribed into RNA including the Cis linked regions
  • Cis linked regions ensure quantitatively appropriate tissue specific expression of the final protein
  • It is not just the bits that encode the final protein, Regulation of the gene is very important
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14
Q

Describe the gene structure (View diagram on slide)

A

Has a 2 gene region at the start of the gene followed by the inter gene region followed by another gene region. (These genes can often be very different in size)

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15
Q

Describe the interagency region

A

Intervened regions contain sequences which have no known functions such as repetitive DNA, endogenous retroviruses, pseudo genes. They can contain many regulatory elements.

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16
Q

Gene Structure. Describe the composition of the gene itself.

A

Genes often cluster in families
- Allows for co-ordinated gene regulation
- May just reflect evolutionary history

17
Q

Describe the introns present in genes

A
  • Vary in number (from 0 - 311)
  • Vary in size (30bp - 1Mbp)
  • Some introns contain other genes
18
Q

What is the role of introns in a gene?

A

Introns can increase transcription levels by affecting the rate of transcription, nuclear export, and transcript stability.

19
Q

Describe the promoter region

A
  • Promoters recruit DNA polymerase to a DNA template
  • RNA polymerase binds asymmetrically and can only move in the 5’ to 3’ direction
  • Regulation occurs via transcription factors
20
Q

Describe the Other Regulatory Regions - Enhancers

A

Enhancers up-regulate gene expression
- They’re short sequences that can be in the gene or many kilo bases distant.
- They’re targets for transcription factors (Activators)

21
Q

Describe the Other Regulatory Regions - Silencers

A

Silencers down-regulate gene expression.
- They’re position independent
- They’re also targets for transcription factors (repressors)

22
Q

Describe the Other Regulatory Regions - Insulators

A

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

23
Q

Describe Transcription - Messenger RNA synthesis

A
  • Catalysed by RNA polymerase II
  • Transcribes in the 5’ to 3’ direction
  • Transcribes everything after the transcription start site
  • mRNA is post transcriptionally modified
24
Q

What is the function of RNA polymerase II?

A

Recognises promoters efficiently with the assistance of many other transcription factors

25
Q

Outline the steps of Transcription

A

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

26
Q

What are the 3 types of Post Transcriptional Modifications?

A

Capping
Splicing
Polyadenylation

27
Q

Where does the Post-transcriptional modifications occur?

A
  • Capping - at the 3’ end
  • Splicing - Introns removed
  • Polyadenylation - at the 3’ end
28
Q

Describe the 5’ Cap

A

After 25-30 nts are synthesised, a methylated cap is added to the 5’ end by 3 enzyme activities:
- RNA 5’ - triphosphatase
- Guanylyltransferase
- N7G-methyltransferase
The first 2 activities is carried out by a bifunctional capping enzyme. RNA Pol II is also required

29
Q

Describe the 3’ poly A tail

A

1 - CPSF (Cleavage and Polyadenylation Stimulating Factor) recognises the PAS (Polyadenylation signal) and acts on cleavage site
2 - CSTF (Cleavage Stimulating Factor) recognises GU-rich Downstream Elements (DSE)
3 - PAP (Poly-A polymerase) is recruited and adds multiple A bases after cleavage site
4 - PAB is Poly-A Binding Protein. Other proteins appear to be required for this process – CFIm (Cleavage Factor Im), CFIIm and Simpleki

30
Q

What is the point of Splicing?

A

Splicing makes genes more “modular,” allowing new combinations of exons to be created during evolution.

31
Q

What is alternative splicing?

A

Where Exons are skipped or added so many variations of a protein can be produced from the same gene

32
Q

Describe the 3D genome structure

A
  • Most of the time, DNA is not organised into chromosomes
  • In somatic cells, The nuclear DNA is arranged non randomly
  • Organisation has been identified using Hi-C (detects genomic DNA sequences in close proximity) and high-throughput microscopy
  • Involves CTCF protein and Cohesin protein complex, as well as transcription machinery
33
Q

How are the Compartments of the genome organised?

A

The genome can be separated into 2 compartments
- Compartment A: Transcriptionally active with active Histone modifications
- Compartment B:Transcriptionally repressed with repressive Histone modifications

These are interspersed throughout the 2D sequence but the same compartment types are brought close together in the 3D genome

34
Q

Describe the TOPOLOGICALLY-ASSOCIATED DOMAINS (TADs)

A
  • Individual compartments are made up of several non interacting sub compartments (TADs)
  • They’re usually separated by transcriptional repress or CTFC protein

SGUL - Genomics (21 decks)

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