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BIOL312 Medical Genetics > Lecture 1: Organisation of the human genome > Flashcards

Lecture 1: Organisation of the human genome Flashcards

- Overview of human genome - Introduction to the different classes of DNA - Intron/Exon structure of genes - Impact of transposable elements - Analysis of repetitive DNA

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1
Q

Describe the human genome

A

3 billion base pairs spread over 23 pairs of linear chromosomes

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2
Q

How does the mitochondrial genome differ?

A

Circular DNA of around 16,500 thousand base pairs

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3
Q

Which cells will have more mitochondrial DNA?

A

Energy demanding cells (E.g. muscle, nerve cells)

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4
Q

Approximately what percentage of the human genome codes for proteins?

A

1%

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5
Q

What is the C-value paradox?

A

Refers to the observation that the observation that there is not a correlation between organism complexity and the genome size in eukaryotes

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6
Q

Why does genome size not correlate with organism complexity?

A

The presence of junk (non-protein coding) DNA makes up a significant amount of the eukaryotic genome

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7
Q

What is DNA Melt-Reassociation?

A

The genome of an organism is heated to denature the double stranded bonds and fragmented, then cooled and measured with a spectrophotometer
- SS DNA and DS DNA have different absorbance maxima
- the time taken for the SS DNA to reanneal is recorded
- SSDNA that rapidly becomes DS DNA again = highly repeated sequence
- intermediate time = moderately repeated
- slow time = unique sequences (E.g. exons)

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8
Q

What are the 5 types of eukaryotic DNA sequence organisation?

A
  • Single copy
  • Gene families
  • Tandem gene arrays (TAGs)
  • Intermediate repeats (Transposable elements)
  • Simple sequence repetitive DNA
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9
Q

Define exon

A

Regions of genes that encode for proteins or give rise to rRNA or tRNA

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10
Q

What percentage of the genome is intron?

A

24%

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11
Q

What percentage of the genome is single copy but not part of a protein coding gene?

A

15%

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12
Q

What is the function of non-protein-coding single copy DNA?

A

1) Structural RNAs (rRNA, tRNA, snRNA - involved in splicing)
2) microRNAs (miRNA) incorporated into silencing complexes to prevent translation of target mRNA)
3) long-non-coding RNAs (lncRNA)

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13
Q

What are gene families and how do they arise?

A

a number of related genes generally found close to each other that show sequence homology
- arise by gene duplication and sequence diversion driven by mutation

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14
Q

Give an example of a gene family?

A

Globin genes (alpha-globin gene family comprised of 4 genes, and beta-globin gene family comprised of 5 genes)

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15
Q

What are pseudo genes in the globin gene families?

A

Pseudogenes are genes that have been mutated and subsequently rendered inactive.

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16
Q

What are TAGs?

A

Tandemly arrayed genes are gene clusters created by tandem duplications (single copy of gene is duplicated adjacent to the original) that can encode large numbers of genes at one time

17
Q

What is the purpose of TAGs?

A

allows for faster transcription (E.g. tandem clusters of rRNA encoding genes are important in embryonic development where there is rapid cell division and expansion that a single RNA gene may not provide sufficient RNA)

18
Q

What are transposable elements?

A

Intermediate repetitive DNA sequences that can replicate themselves within genomes independently of the host cell DNA and move location throughout the genome

19
Q

What are the two main types of eukaryotic transposable elements?

A
  1. Retrotransposons that transpose via an RNA intermediate
  2. DNA-DNA transposable elements that transpose directly from DNA to DNA
20
Q

What are the two main types of retrotransposons giving two examples belonging to each group?

A

Viral Retrotransposon, including:
1. retrovirus-like retrotransposons (E.g. HERVs that were once exogenous retrovirus but has become fixed in out DNA and now inherited)
2. LINE-like (LINE1, LINE2)

Non-viral retrotransposon, including:
1. SINEs
2. processed pseudogenes

21
Q

Describe the structure and transposition of retrovirus-like viral retrotransposons

A

Note: Retroviral-like retrotransposons come from endogenous retroviruses (HERVs) present in the genome

Retroviral-like retrotransposons are LTR-transposons that have long terminal repeats (LTRs) with promoter enhancer elements flanking coding regions (gag, pol, int, env)

Integrated into genome as a provirus. Cellular transcription machinery transcribes provirus, reverse transcriptase produces cDNA, integrase integrates the cDNA into the genome at random position.

22
Q

Describe the structure and transposition of LINE viral retrotransposons

A

LINE retrotransposons are non-LTR-transposons with 2 open reading frames (ORF1 which has homology to gag and ORF2, which has homology to pol)

23
Q

What is the most numerous LINE family in the human genome?

A

LINE-1 (L1)

24
Q

True or False: all human genome LINEs are mobile?

A

False: only a small subset of the the full-length LINE-1 repeats are capable of transposition (the majority of LINEs are truncated resulting in loss of transposition)

25
Q

What is the most common non-viral retrotransposon SINE family?

A

Alu family

26
Q

True or false: SINEs are autonomous retrotransposons?

A

False: they are non-autonomous and require reverse transcriptase supplied by neighbouring LINE or retrovirus-like transposon.

27
Q

Why are LINEs and retrovirus-like transposons said to be autonomous?

A

They encode reverse transcriptase so can transpose independently.

28
Q

What are SVAs?

A

SINE-VNTR-Alu’s are non-viral retrotransposons that are non-autonomous

29
Q

How are SVAs associated with disease in humans?

A

SVA insertion polymorphism causes gene disruption that leads to disease

30
Q

What is the length of a tandem repeat DNA unit?

A

2-200 bp

31
Q

Where is most of the simple sequence tandem repeat DNA found?

A

in the heterochromatin - particularly in telomeres and centromeres of chromosomes

32
Q

What are two examples of types of tandem repeat DNA?

A

Short tandem repeats (STRs)
Minisatellite/microsatellite DNA

33
Q

How may STRs affect gene expression?

A

May weakly bind transcription factors - transcription factor binds more strongly to STR adjacent to core regulatory sequence than to random genomic sequences = concentrates transcription factors close to the core regulatory sequence to enhance binding and increase gene expression

34
Q

True or false: minisatellites/microsatellites can be VNTRs or STRs?

A

True - depending on the array length

35
Q

What are the main uses of minisatellites/microsatellites?

A

DNA fingerprinting in:
- paternity analysis
- forensic analysis
- gene mapping

BIOL312 Medical Genetics (10 decks)

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