The Mitochondrial Genome Flashcards
What are some of the lesser known functions of the mitochondria?
- Haem synthesis
- Neurotransmitter synthesis, e.g. glutamate
- Nucleotide synthesis - Produces purine intermediates which are required for DNA synthesis
- Produces reactive Oxygen species (via oxidative phosphorylation) - reactive oxygen species are important for cell signalling
Why is it that mitochondria are said to be important in innate immunity?
- Nn the surface of mitochondria there’s the mitochondrial antiviral-signalling complex which is important for producing inflammation
What are some of the features of the mitochondrial genome?
- Mitochondrial DNA (mtDNA) is a double stranded circular molecule
- mtDNA is really small
- Consists of a heavy and a light strand
- Multicopy genome (10-100,000 copies per cell) - in contrast to the human genome which only has 2 copies per cell (diploid genome)
- Contains 37 genes
- Maternally inherited
- Doesn’t contain introns
What is the difference between the heavy and light strands that mean they are given those names?
- Heavy strand contains a large amount of guanine nucleotides while light strand contains a large amount of cytosine.
- Guanine is a purine base which is a double ring instead of a single ring like cytosine which means guanine is heavier than cytosine
- Fact that heavy strand contains more guanine means it’s more dense than light strand which is why it’s called the heavy strand.
What do the 37 genes within the mitochondrial genome encode for?
- 13 encode for oxidative phosphorylation protein subunits
- 22 encode for transfer RNAs (tRNAs)
- 2 encode for ribosomal RNAs (rRNAs)
Mitochondrial DNA contains a non-coding region what structures are present within this non-coding region?
- Heavy and light strand promoters
- Origin of the heavy strand
- 7S DNA
- D-loop
What is the D-loop (displacement loop)?
- Replicated segment of the heavy strand that’s hydrogen bonded to the light strand
- It forms when replication of heavy strand is arrested/stopped temporarily
In which part of the non-coding region of the mitochondrial genome does mtDNA replication start?
starts in Origin of heavy strand (OH)
In which part of the non-coding region of the mitochondrial genome does transcription start?
Transcription starts at Heavy strand promoter (HSP) and Light strand promoter (LSP)
How is mitochondrial DNA packaged so that it can fit inside the mitochondria?
- mtDNA is packaged into structures called nucleoids
- There are one or two copies of mtDNA per nucleoid
- Transcription factor A (TFAM) acts as a histone protein - mtDNA wraps around the TFAM to form the nucleoid structure
Some triplet codons code for different amino acids in mitochondrial DNA compared to nuclear DNA, give some examples where this is the case.
- AUA codes for methionine - AUA codes for isoleucine in nuclear DNA
- UGA codes for tryptophan - Codes for stop codon in nuclear DNA
- AGA and AGG are stop codons - Code for arginine in nuclear DNA
What is a mitochondrial haplogroup?
- A haplogroup created by differences in mitochondrial DNA
What characteristics of mitochondrial DNA mean that mitochondrial DNA haplogroups developed over time?
- mtDNA is maternally inherited which means that all the different mitochondrial genes are inherited from one parent in groups
- mtDNA doesn’t recombine which means that as mutations within the mtDNA acquired over time, the mutations weren’t able to be repaired and were maintained within the population
What are the first 4 mitochondrial DNA haplogroups and when did they develop?
- L0-L3 haplogroups developed in sub-Saharan Africa 130,000 - 200,000 years ago
What other haplogroups developed from the L3 haplogroup?
- Haplogroups M and N then arose from L3 around 65,000 – 70,000 years ago
Mitochondrial DNA produces 13 proteins used in oxidative phosphorylation, what role do these proteins have in the process of oxidative phosphorylation?
- Oxidative phosphorylation requires five enzyme complexes
- mtDNA encodes for some of the subunits that make up every complex involved in oxidative phosphorylation apart from complex II.
There are over 100 different proteins involved in oxidative phosphorylation but only 13 of those are encoded for by genes in the mtDNA in the mitochondria. Where are the rest of the genes that encode for these proteins and what does it mean for the proteins that they aren’t produced in the mitochondria?
- The rest of the proteins involved are encoded for by genes within nuclear DNA
- This means that when these proteins are produced they have to migrate from the cytoplasm to the mitochondria.
To make the 13 mitochondrial proteins involved in oxidative phosphorylation mtDNA genes must be replicated, transcribed and translated. The proteins required for these processes aren’t produced in the mitochondria. Where are they produced and what does it mean for these proteins?
- The genes that encode for these proteins are found within nuclear DNA
- This means that just like the majority of proteins involved in Oxidative phosphorylation, these nuclear proteins have to migrate to the mitochondria from the cytoplasm.
What are the main enzymes involved in mitochondrial DNA replication?
- Mitochondrial DNA polymerase (Polγ)
- Twinkle helicase - mtDNA helicase, unwinds DNA for replication
- Single stranded binding protein 1 (SSBP1)
- Transcription factor A (TFAM) - packages and protects mtDNA
What are some properties of the mitochondrial DNA polymerase?
- Heterotrimer protein - consists of 3 different subunits
- One catalytic subunit (POLγA)
- Two accessory subunits (POLγB)
What role do the POLγA and POLγB subunits play in the activity of mitochondrial DNA polymerase?
- POLγA contains a 3’ – 5’ exonuclease domain to proofread newly synthesized DNA
- POLγB enhances interactions with DNA template and increases activity and processivity of POLγA.
What is the processivity of an enzyme?
An enzyme’s ability to catalyze consecutive reactions without releasing its substrate
What is the function of the mitochondrial DNA helicase (TWINKLE) in mtDNA replication?
- Unwinds double stranded mtDNA template to allow replication by the mitochondrial DNA polymerase
What is the function of the mitochondrial single stranded binding protein (mtSSBP)?
Binds to single stranded mtDNA formed once the duplex has been unwound and has a number of different functions including:
- Protecting single stranded mtDNA against nucleases
- Preventing secondary structures forming from single stranded mtDNA
- Enhancing mtDNA synthesis by interacting with TWINKLE helicase and stimulating its activity
