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Medical genetics > Organisation of the Genome > Flashcards

Organisation of the Genome Flashcards

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Biology 101 flashcards USMLE® Step 1 flashcards
1
Q

What forms the human genome

A

3 billion base pairs spread over 23 pairs of linear chromosomes (51Mbp-245Mbp)

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2
Q

Size of mitochondrial genome

A

16,569bp, circular DNA

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3
Q

What percentage of the human genome encodes for proteins

A

~1%

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4
Q

Size of E. coli genome

A

4.6Mbp, 4288 protein-encoding genes

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5
Q

Size of mouse genome

A

2,800Mbp, ~23,000 protein encoding genes

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6
Q

C-value paradox

A

Human genome is smaller than mudpuppy genome, but human genome has a greater percentage of protein encoding genes

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7
Q

Explain DNA Melt-Reassociation

A

Denatured ssDNA fragments -> rapid reassociation -> highly repeated reannealed dsDNA fragments

Denatured ssDNA fragments -> intermediate reassociation -> moderately repeated reannealed dsDNA fragments

Denatured ssDNA fragments -> slow reassociation -> Unique reannealed dsDNA fragments

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8
Q

Eukaryotic DNA sequence organisation

A

Single copy

Gene families

Tandem gene arrays

Intermediate repeat (transposable elements)

Simple sequence repetitive DNA

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9
Q

Single copy DNA in genome

A
  • Forms ~25% of genome but exons only 1%
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10
Q

Size of average gene

A

27kb with 9 exons

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11
Q

Smallest gene

A

SRY on Y chromosome

0.9kb formed from 1 exon which is 850bp

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12
Q

Larger genes

A

DMD

Encodes for dystrophin

2400kb formed from 79 exons which are 180bp - introns are 30,770bp

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13
Q

Non-protein-coding single copy DNA

A

24% of genome is intron

15% of genome is single copy but not a part of a protein-coding gene

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14
Q

Function of single-copy non-coding DNA

A
  • Most of this part is functional - over 80% has ≥1 biochemical activity
  • Majority can be transcribed

22,219 non-coding genes

rRNAs, tRNAs, snRNAs

miRNAs - involved in gene regualtion (2,588 identified)

long non-coding (lnc)RNAs (14,727) - some known to be functional, e.g. Xist
Target regulatory proteins
Disease markers eg. DD3/PCA3 (prostate cancer)
Possible causative agents in disease (BACE1)

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15
Q

Human gene families

A

a-globins - 4 genes

b-globins - 5 genes

Actin - 15 genes

Keratin type 1 - 19 genes

b-tubulin - 19 genes

a-tubulin - 10 genes

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16
Q

What are tandemly arrayed genes (TAGs)

A
  • Gene clusters created by tandem duplications
  • One gene duplicated, copy next to original
  • Can encode large numbers of genes at a time (2-100’s)
  • 14-17% of human, mouse and rat coding genomes
17
Q

Tandem clusters of rRNA encoding genes

A

Human embryo has 5-10 million ribosomes

Cell number doubles within 24 hours

Single RNA gene may not be able to provide enough RNA, but tandem repeats allows sufficient RNA production

18
Q

What are the different eukaryotic transposable elements

A

Retrotransposons (retroposons):
Transpose via an RNA intermediate
Viral: retrovirus like e.g endogenous retroviruses or LINE like e.g. LINE1 and LINE2
Non-viral: SINEs or processed pseudogenes

DNA-DNA transposable elements:
Transpose directly from DNA to DNA
Similar to bacterial transposons - Not active in human genome

19
Q

What are eukaryotic transposable elements important for

A

Genome evolution - Source of regulatory elements, site of recombination. Insertions can cause disease

20
Q

Viral retrotransposons

A

Gag - Group antigens (viral core structure, RNA binding)
Pol - reverse transcriptase
Env - Envelope protein

21
Q

LINE-1 element

A

> 500,000 copies in human genome
1-6kb in length
Only 40-50 active

Open reading frames:
ORF1:1137bp - homology to gag
ORF2: 3900bp - homology to pol

No LTRs

22
Q

Timing and tissue specificity of L1 transposition

A
  • Mostly repressed (methylation)
  • Demethylation and increased transposition in tumours

Germ cells (many unique new insertions)

Early embryos (somatic cells)

Neural progenitor cells during childhood
 Each human is a unique mosaic

23
Q

What percentage of the human genome has transposable element composition

A

~30%

24
Q

Non-viral elements

A

SINEs (13% of genome)
- Genomic copies of small RNAs
- Mostly belong to Alu family (7SL RNA)
- also copies of snRNAs and tRNAs

Processed pseudogenes (genomic copies of mRNAs)

25
Q

What are Alu sequences

A

150-300bp

1 million copies, 10% of genome

Found in other vertebrates

Occur every 6kb

Transcribed to give RNA

Transpose using LINE reverse transcriptase

Sites of recombination (hotspots)

Insertions cause inherited disease

26
Q

SVAs: SINE-VNTR-Alu

A

non-autonomous hominid-specific

retrotransposons

Don’t exist in Old World monkeys

Several subtypes

Can be transcribed

Mobilize by LINE L1 retrotransposase

Associated with disease in humans

27
Q

Highly repetitive DNA: Tandem repeat DNA

A

simple sequence repeat DNA

~8% of genome

Repeat length 2-200bp

Total array length up to 5 x 10^6 bp (alphoid DNA)

Short tandem repeats

Minisatellite and microsatellite DNAs

28
Q

Short tandem repeats

A

5% of genome

Repeat unit length 1-6 bp

Total array length up to 100bp

Length variations can affect gene expression is some hereditary diseases e.g. HD, autism, schizophrenia

Maybe by directly (weakly) binding transcription factors – STRs are enriched in (some) TF binding regions

29
Q

What do short tandem repeats influence?

A

Transcription factor protein binding at core gene regulatory sequences

Binding of TFs to STRs is weaker than to core regulatory sequences but stronger than it is to genomic sequences

30
Q

Minisatellites

A

Repeat unit length 15-100bp

0.5-30kbp

Array length variable - Variable number tandem repeats (VNTRs) or short tandem repeats

Can be used in paternity and forensics

31
Q

Microsatellites

A

2-5bp - Repeat unit length

60-200bp - Total array length

Array length variable - Variable number tandem repeats (VNTRs) or short tandem repeats

Can be used in paternity and forensics

Medical genetics (5 decks)

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