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genomics notes > genome structure > Flashcards

genome structure Flashcards

1
Q

what is DNA?

A
  • DNA is deoxynucleic acid
  • macromolecule consisting of linear strand of nucleotides
  • single linear strands bind to complementary strands to form double stranded DNA.
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2
Q

What are constitutes of DNA?

A
  • nitrogenous base
  • ribose sugar
  • phosphate group
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3
Q

which direction is DNA transcribes?

A
  • 5’ to 3’

- DNA polymerase only works in 5’ to 3’ direction.

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4
Q

Which bases are purines and which are pyrimidines?

A
  • purines = G, A,
  • pyrimidines = C, T, U
    uracil replaces thymine so its also a pyrimidine
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5
Q

How many hydrogen bonds do AT and CG have?

A
  • AT = 2 H bonds

- CG = 3 H bonds

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6
Q

What are features of 3D structure of DNA?

A
  • 2 antiparallel strands
  • bases are stacked
  • 2 grooves = major groove and minor groove
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7
Q

outline human genome variation.

A
  • 3x10^9 base pairs - 3Gbp
  • about 20, 000 genes
  • normally smaller organisms have fewer genes BUT this is not always the case
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8
Q

How does 2 meter of DNA fit in 50 micrometer diameter cell?

A
  • histones and DNA packaging in coils.
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9
Q

what are histones?

A
  • basic (-ve charged) proteins that bind to DNA.
  • 10 nm molecules
  • 146 bp of DNA wind around the histone core octomer.
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10
Q

How many histones form nucleosome?

A
  • 8 histones

- 2x (H2A) , (H2B) , (H3), (H4) .

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11
Q

Which histone binds to the linker DNA?

A
  • histone 1 binds to the linker DNA
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12
Q

What are the 6 stages of DNA packaging?

A
  1. DNA double helix
  2. nucleosome
  3. chromatin fibre
  4. extended section of chromosome
  5. loops of chromatin fibre
  6. metaphase chromosome (densest form)
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13
Q

What are 3 chromosome structures?

A
  1. metacentric : equal long and short arm.
  2. submetacentric : long long arms and short short arms
  3. acrocentric : no short arm at all.
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14
Q

What are the 2 main features of chromosome?

A
  1. centromere = holds the chromatin arms in place at the centre
  2. telomeres = ends to the chromatin, prevents eroding of genetic material.
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15
Q

What is human karyotype?

A
  • process of pairing and ordering all chromosomes of an organism shows bonding patterns, size differences etc.
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16
Q

What is a genome?

A
  • The primary DNA sequence encodes all the gene products necessary for a human
  • primary DNA sequence also includes a large number of regulatory signals
  • much of the DNA sequence does not have an assigned function yet.
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17
Q

What is an exome?

A
  • regions of the gene that encode for protein

- 1- 2% of the genome is exome.

18
Q

How do we define genome?

A
  • All of the DNA that is transcribed into RNA plus all of the cis- linked (local) control regions that are required to ensure quantitatively appropriate tissue - specific expression of the final protein.
19
Q

What are intergenic regions and what do they contain?

A
  • DNA sequences , endogenous retroviruses, pseudogenes etc.
  • regions between genes.
  • 98% of the genome
20
Q

What do gene clusters reflect?

A
  • allows for co-ordinated gene regulation

- may just reflect evolutionary history

21
Q

What is the purpose of introns?

A
  • used in splicing to form a variety of exons

- used in evolution to form new genes

22
Q

What is the function of the promoter?

A
  • promoters recruit RNA polymerase to a DNA template
  • RNA polymerase binds asymmetrically to the promoter and can only move 5’ to 3’
  • regulation occurs via transcription factors.
23
Q

What are the different structures that make up a gene?

A
  1. promotor
  2. transcription unit
    • initiation
    • exon
    • intorns
    • termination
24
Q

What is the function of enhancers?

A
  • upregulate gene expression (activators)
  • they are short sequences that can be in the gene or many kilobases distant.
  • they are targets for transcription factors
25
Q

What is the function of silencers?

A
  • downregulate gene expression (repressors)

- they are also position - independent and are also targets for transcription factors

26
Q

What is the function of insulators?

A
  • short sequences that act to prevent enhancers/ silencers influencing other gene
27
Q

What is transcription?

A
  • process of copying DNA sequence to RNA.
28
Q

What catalyses the synthesis of messenger RNA?

A
  • RNA polymerase II

- RNA polymerase II recognises promoter efficiently with assistance of many other transcription factors.

29
Q

What direction does RNA polymerase II transcribe in?

A
  • 5’ to 3’ direction

- transcribes everything after the transcription start site (exon and introns)

30
Q

Describe the steps of transcription.

A
  1. RNA polymerase recruited (closed complex).
  2. DNA helicase locally unwound.
  3. RNA synthesis occurs
  4. Elongation
  5. termination
  6. RNA polymerase dissociates.
31
Q

What are 3 post transcriptional modifications?

A
  1. capping
  2. splicing
  3. polyadenylation
32
Q

Describe the process of capping.

A
  1. after 25- 30 nts synthesised a methylated cap is added to the 5’ end by 3 enzyme activities
  2. 5’ to 5’ triphosphate bridge added by RNA 5’ triphosphatase.
  3. guanosine added by guanylytransferase
  4. which is methylated by N7G- methyltransferase at position 7
33
Q

What are the 3 enzymes involved in capping?

A
  1. RNA 5’ triphosphatase
  2. guanyltransferase
  3. N7G- methyltransferase
34
Q

Describe the process of splicing.

A
  • process of removing introns, using spliceosomes.
    1. spliceosome catalyses the connection of one exon to another.
    2. creates a 2’ - 5’ linkage
    3. intron is a lariat structure (loop)
35
Q

Why is splicing important?

A
  • splicing allows target mRNAs for nuclear export
36
Q

Describe polyadenylation.

A
  • addition of poly A tail in the 3’ .
    1. CPSF(cleavage and polyadenylation stimulating factors) recognises the PAS (poladynlation signal) and acts on cleavage site.
    2. CSTF (cleavage stimulating factor) recognises GU- rich down stream element (DSE)
    3. PAP (poly A polymerase) is recruited and adds multiple A bases after cleavage site.
37
Q

Describe translation.

A
  • once mRNA is exported from nucleus into cytoplasm via nuclear pore
  • ribosome picks it up and starts translating the mRNA -> protein
38
Q

What is the point of alternative splicing?

A
  • splicing is the process of removing introns
  • alternative splicing: splicosomes cuts at different length of the DNA sequence making a variety of exons
  • variety of exons = variety of proteins (isoforms) from the same gene.
39
Q

What 2 compartments can genome be separated into?

A
  • compartment A : transcriptionally active histone modification
  • Compartment B:
    transcriptionally repressed with repressive histone modification

(same compartments brought together in 3D structure)

40
Q

What are topologically - associated domains (TADs)

A
  • individual compartments made up of several non- interacting sub - compartments
  • TADs are usually separated by the transcriptional repressor CTCF protein.
41
Q

What is cohesion regulated chromatin loop extrusion?

A
  • separating parts of DNA

- enhancer and promoter close together = strong transcription and translation and vice versa.

42
Q

What different colours in 3D structure show active and inactive genes?

A
  • regions of chromosomes where genes are active are BLUE.

- regions which are inactive are YELLOW

genomics notes (18 decks)

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