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Genomics SGUL Sem 3 > Mitochondrial Genome > Flashcards

Mitochondrial Genome Flashcards

1
Q

What are the 4 functions of mitochondria?

multicopy genome-

A

→ Produce ATP
→ Haem synthesis
→ Neurotransmitter synthesis
→ Nucleotide synthesis

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2
Q

What does mitochondrial DNA look like?

A

Double stranded circular molecule

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3
Q

What does mitochondrial DNA consist of?

A

Heavy and light strand

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4
Q

How many genes does a mitochondria have?

A

37

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5
Q

What are the mitochondrial genes for?

A

→ 13 oxidative phosphorylation protein subunits
→ 22 tRNAs
→ 2 ribosomal RNAs

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6
Q

Does a mitochondria have introns?

A

No

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7
Q

What is a D loop?

A

A non coding region where replication and transcription are initiated

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8
Q

How are mitochondria inherited?

A

Maternally with no recombination

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9
Q

Which of the OXPHOS proteins is not coded for by mitochondria?

A

→ Succinate dehydrogenase
→ Complex 2

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10
Q

How is mtDNA packaged?

A

Nucleoids

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11
Q

How are nucleoids arranged?

A

One or two copies of mtDNA per nucleoid

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12
Q

What acts as a histone protein in mitochondria?

A

TFAM (transcription factor A)

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13
Q

Where does mtDNA replication start?

A

Origin of heavy strand (Oh)

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14
Q

Where does mtDNA transcription start?

A

Heavy strand promoter and light strand promoter

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15
Q

What are the exceptions to the universal genetic code in mitochondria?

A

→ AUA and AUG code for methionine (isoleucine in nuclear DNA)
→ UGA codes for tryptophan (stop codon in nuclear DNA)
→ AGA and AGG are stop codons ( arginine in nuclear DNA)

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16
Q

What are the haplogroups of mtDNA?

A

→ M
→ N
→ H
→ L0-L3

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17
Q

What is the most common haplogroup in Europe?

A

H

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18
Q

Why can mtDNA subdivide humans into discrete haplogroups?

A

It does not recombine

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19
Q

Describe the origin of mitochondria

A

1) A primitive eukaryotic cell ingested bacteria
2) The bacteria helped the cell become more complex
3) All bacterial DNA transferred to nucleus
4) Remnant of DNA is mtDNA

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20
Q

Where do the proteins for replication, transcription and translation come from?

A

They are encoded by nuclear genes and imported into the mitochondria

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21
Q

What are the 4 requirements for replicating mtDNA?

A

→ Polymerase gamma (POLG) - mtDNA polymerase
→ TWINKLE - mtDNA helicase - unwinds DNA
→ Single stranded binding protein (SSBP) - keeps DNA unwound
→ TFAM - packages and protects mtDNA

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22
Q

What is the composition of polymerase gamma?

A

→ Heterotrimer
→ One catalytic subunit (POLyA)
→ Two accessory subunits (POLyB)

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23
Q

What does POLyA contain?

A

3’ to 5’ exonucleases domain to proofread newly synthesized DNA

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24
Q

What is the function of POLyB?

A

Enhances interactions with DNA template and increases activity and processivity of POLyA

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25
What type of structure is TWINKLE?
Hexamer
26
What is the function of TWINKLE?
Unwinds double stranded mtDNA to allow replication by POLy
27
What are the 4 functions of mtSSBP?
→ Binds to ssDNA → Protects against nucleases → Prevents secondary structure formation → Enhances mtDNA synthesis by stimulating TWINKLE helicase
28
What is the main model of mtDNA replication?
Strand displacement model
29
What kind of model is the displacement model?
→ asynchronous → two models are not replicated at the same time
30
Describe the strand displacement model
1) heavy strand is displaced and coated with mtSSP 2) TWINKLE helicase unwinds mtDNA 3) mtRNA polymerase synthesizes RNA primer using the light strand as a template 4) POLY uses the RNA primer to replicate DNA at OH 5) heavy strand replication passes Ol 6) stem loop structure is formed on the heavy strand preventing mtSSBP binding 7) this allows POLRMT to bind using the heavy strand as a template 8) POLy uses RNA primer to replicate the light strand DNA at Ol
31
What is used to separate the two strands?
TOP3A
32
Why are mtDNA strands named heavy and light?
It is richer in guanine bases and paired with cytosine which has single ring
33
What types of cells might have higher copies of mtDNA?
Cells that need a lot of energy
34
When is a disease defined as rare?
When it affects less than 1:2000 individuals
35
What do mitochondrial diseases affect?
Highly metabolic organs that are abundant in mitochondria
36
What is Pearson syndrome?
Pancreatic dysfunction
37
What is the most common mitochondrial disease presentation?
Leigh syndrome
38
What is LHON?
Lebers hereditary optic neuroretinopathy
39
What is KSS?
Kearns Sayre Syndrome
40
What is MELAS?
Mitochondrial encephalomyopathy lactic acidosis stroke like episodes
41
What is MERRF?
Myoclonus epilepsy red ragged fibres
42
What is NARP?
Neurogenic muscle weakness ataxia retinitis pigmentosa
43
How does mitochondrial disease manifest?
Through the maternal line
44
What is homoplasmy?
One variant of mtDNA
45
What is heteroplasmy?
Two variants of mtDNA
46
What is the amount of mutation required for disease manifestation?
>80%
47
How are three parent embryos formed?
→ Healthy nuclear DNA is removed from patients egg cell (1) → (2) patients nuclear DNA is transplanted into donor egg with healthy mitochondrial DNA → Reconstructed egg is fertilised and implanted into patient
48
What kind of mitochondrial mutations are there?
TWINKLE or POLy can be mutated
49
What is different about complex II?
The only one with is entirely nuclear encoded succinate dehydrogenase
50
What are the histochemical staining of muscle?
→ Gomori trichrome red- ragged fibres. Accumulation is response to OXPHOS defect → SDH (Complex II) proliferation → COX (Complex IV)
51
What does high resolution respirometry measure?
Oxygen consumption
52
What is shown in electron micrography of muscle mitochondria?
Paracrystalline inclusions (PCI) thought to be accumulated creatine kinase
53
What other effects does OXPHOS defects have on mitochondria?
Result in overall architecture of the mitochondria
54
What are the variable penetrance shown in homoplasmic mutations in LHON?
50% males affected 10% females affected
55
What happens during differentiation in primary oocytes?
Reduction in the amount of mitochondria as well as asymmetric division of the mitochondria
56
Why is NGS used for sequencing mtDNA?
→ Increased reliability and sensitivity → More accurate detection of low level heteroplasmy → Detect SNVs, single or multiple deletions, duplications
57
Why is whole exome genome sequencing reliable for mtDNA mutation identification?
with NGS the entire length of mtDNA is covered with several hundred short-reads.
58
What do mutations in mtDNA replication replication cause?
→ Secondary mutations in mtDNA → mtDNA deletions → mtDNA depletion → Occurs in post-mitotic tissues
59
What are examples of post mitotic tissues?
Brain Muscle Heart Liver
60
What do dominant mutations in TWINKLE cause?
mtDNA deletions and late-onset mitochondrial myopathy
61
What are the features of mitochondrial myopathy?
→ Multiple mtDNA deletions in muscle, brain and heart → Progressive external ophthalmoplegia (PEO), muscle weakness, exercise intolerance → No cure and lack of treatments → Lack of biomarkers for diganosis and as outcome measures in clinical trials → Reasons for tissue-specificity unknown
62
What is mitochondrial replacement therapy?
→ Involves using an egg from an egg donor → Nucleus of the egg is removed and replaced with the nuclear DNA from the woman who has mitochondrial DNA mutations → Egg is then fertilised with the father’s sperm in the embryology lab. → If it grows into an embryo for transfer during IVF treatment, the embryo would be free of mitochondrial disease

Genomics SGUL Sem 3 (21 decks)

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