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Genomics > The Mitochondrial Genome > Flashcards

The Mitochondrial Genome Flashcards

1
Q

What are the features of the mitochondrial genome?

A 
Double stranded circular molecule 
Heavy and light strand
Multi copy gene
37 genes
No introns
D loops is a non-coding region where replication and transcription are initiated
Maternally inherited so no recombination
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2
Q

What numbers and types of genes make up the 37 mitochondrial genes?

A

13 OXPHOS protein subunits
22 transfer RNAs
2 ribosomal RNAs

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3
Q

What do the OXPHOS proteins consist of?

A

5 enzyme complexes (CI-CV)

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4
Q

What is special about the OXPHOS complex II?

A

It’s the only entirely nuclear coded subunit

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5
Q

What does the non-coding mtDNA region contain?

A

Regulatory sequences for replication and transcription

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6
Q

Where does mtDNA replication start?

A

The origin of the heavy strand

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7
Q

Where does mtDNA transcription start?

A

Heavy strand and light strand promoters

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8
Q

What is mtDNA packaged into?

A

Nucleoids

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9
Q

How many copies of mtDNA do you get per nucleoid?

A

One or two copies

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10
Q

What does transcription factor A act as in mtDNA?

A

A histone protein

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11
Q

What are the exceptions to the universal genetic code?

A

AUA codes for methionine in mtDNA and isoleucine in nuclear DNA
UGA codes for tryptophan in mtDNA and is a stop codon in nuclear DNA
AGA and AGG are stop codons in mtDNA not argenine

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12
Q

What are mtDNA variants called?

A

Haplogroups

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13
Q

Why is the human mtDNA genotype specifically split into haplogroups?

A

MtDNA is maternally inherited so no recombination occurs

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14
Q

Does the mitochondria need both mtDNA and nuclear DNA to function?

A

Yes

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15
Q

How many OXPHOS proteins does the mtDNA encode?

A

13

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16
Q

What is the mtDNA polymerase called?

A

Polymerase gamma

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17
Q

What are the subunits of Polymerase gamma?

A

One catalytic subunit (A) and two accessory subunits (B)

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18
Q

What does the Polymerase gamma catalytic subunit contain and what does it do?

A

Contains 3’-5’ exonucelase domains to proofread newly synthesised DNA

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19
Q

What do the Polymerase gamma accessory subunits contain and what do they do?

A

Enhance interactions with the DNA template and increases activity and processing of the polymerase gamma A

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20
Q

What is the mtDNA helicase called?

A

TWINKLE

21
Q

How many subunits is TWINKLE made up of?

A

Six

22
Q

What does the mitochondrial single stranded binding protein do?

A

Binds to single stranded DNA

23
Q

Why does mitochondrial single stranded binding protein bind to single stranded DNA?

A

Protects against nucleuses, prevents secondary structure formation and enhances mtDNA synthesis by stimulating TWINKLE helicase activity

24
Q

What is the strand displacement model of mtDNA replication?

A

Parental heavy strand displaced and coated with MtSSBP
TWINKLE helicase unwinds MtDNA
Mitochondrial RNA polymerase synthesise RNA primer using the light strand as a template
Polymerase gamma uses RNA primer to replicate DNA at the OH

25
Q

What are the steps in mtDNA light strand replication?

A

Stem loop structure formed
MtRNA polymerase synthesises RNA primer using the heavy strand as a template
Polymerase gamma uses RNA primer to replicate the light strand DNA

26
Q

What does segregation of mtDNA daughter molecules need?

A

Topoisomerase IIIa

27
Q

What is the most common form of mitochondrial disease?

A

OXPHOS disorders

28
Q

What does LHON stand for?

A

Leber’s hereditary optic neuroretinopathy

29
Q

What does KSS stand for?

A

Kearns-Sayre syndrome

30
Q

What does MELAS stand for?

A

Mitochondrial Encephalopathy, Lactic Acidosis, and Stroke-like episodes

31
Q

What does MERRF stand for?

A

Myoclonus epilepsy red ragged fibres

32
Q

What does NARP stand for?

A

Neurogenic muscle weakness, ataxia, and retinitis pigmentosa

33
Q

What does MINGIE stand for?

A

Mitochondrial myopathy neuropathy gastrointestinal disease encephalopathy

34
Q

What are the hallmarks of mitochondrial disease?

A 
Abnormal bilateral leisions in the basal ganglia of the brain
Gamori staining
Hypertrophic cardiomyopathy 
Pseudo-intestinal obstruction 
Sideroblast anaemia
Enlargement of eye vessels
35
Q

What is gamori staining?

A

Clusters of red signal in the muscle fibres

36
Q

How do you diagnose a mitochondrial disease?

A

Clinical signs
Blood and tissue histochemical and analyse measurements
Neuro imaging
Enzymatic assays of OXPHOS in tissue samples and cultured cells
DNA analysis

37
Q

What are some clinical features of mitochondrial disease?

A

Most have a neurological component and are progressive

38
Q

What types of muscle histology studies are there?

A 
Haematoxylon and eosin
Gomori trichrome
SDH
Cox 
Combined cox/SDH
39
Q

What is homoplasmy?

A

One type of mtDNA in a cell

40
Q

What is heteroplasmy?

A

One or more mutant mtDNAs in a cell

41
Q

What do heteroplasmy levels determine?

A

Disease manifestation

42
Q

What % heteroplasmy causes disease manifestation?

A

80%

43
Q

What do heteroplasmic mutations mean for the inheritance of mutant load?

A

Random

44
Q

What do homoplasmic mutations mean for the inheritance of mutant load?

A

Cause the female carriers to transmit to all children

45
Q

How can you identify mtDNA mutations?

A

Off target reads using WES

46
Q

What do mutations in the mtDNA replication machinery cause?

A

Secondary mutations in mtDNA

47
Q

What do dominant mutations in TWINKLE cause?

A

MtDNA deletions and late-onset mitochondrial myopathy

48
Q

What are your options for embryos with mtDNA mutations?

A

Oocyte donation
Prenatal diagnosis
Preimplantation genetic diagnosis
Mitochondrial replacement therapy

49
Q

What is the most common form of mitochondrial disease?

A

OXPHOS disorders

Genomics (16 decks)

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