Mitochondria Flashcards
How many membranes does mitochondria have?
2 - outer and inner
Where are ATP synthases located?
inner membrane
What is the equivalent to the cytoplasm in the mitochondria?
mitochondrial matrix
The majority of proteins for mitochondria are encoded in ____
nuclear genome
The mitochondria has ____ that code for itself
its own genome
there are enzymes in the matrix that are involved in breakdown of what?
food products
What is mitochondria known for?
ATP production - power plant
ATP production is what kind of respiration?
Aerobic
The number of mitochondria in a cell varies depending on what?
That cells energy needs.
What kinds of cells have a lot of ATP?
neurons and muscle
What is significant about the outer membrane of mitochondria?
It is permeable to ions
What is significant about the inner membrane of mitochondria?
It is impermeable to ions
What protein contributes to the impermeability of the inner membrane?
cardiolipin
What is between the inner and outer membrane in mitochondria?
intermembranous space
The matrix encodes for its own _____
ribosomes
Where does actual ATP production occur?
matrix
What important reactions happen in the mitochondria inner membrane?
ETC, ATP synthesis (the actual production of ATP occurs in matrix)
Oxidative metabolism is the production of ____
ATP
What important synthesis happens in outer membrane of mitochondria?
Cardiolipin synthesis
Where are TCA cycle enzymes located?
matrix of mitochondria
What allows for the free diffusion of ions in outer membrane of mitochondria?
Porins
Where do transmembrane proteins cross in mitochondria?
Outer & inner membrane
Where is peptidoglycan located in mitochondria?
intermembranous space
What is a double phospholipid?
Has four fatty acid tails
A cardiolipid is a ____
phospholipid
Where is cardiolipid made?
Mitochondria
Key words: cardiolipin synthesis, SIDS, high mortality in infants are what disease?
Barth syndrome
Defect in cardiolipin is the cause of what disease?
Barth syndrome
What is the mode of inheritance for barth syndrome?
x-linked
Characteristics: SIDS, cardiomyopathy, generalized muscle weakness, chronic fatigue, neutropenia are what disease?
Barth syndrome
What is neutropenia?
abnormally low concentration of neutrophils in blood
What is the mechanism for Barth syndrome?
defect in cardiolipid -cardiolipid helps create impermeability of inner membrane in mitochondria → lack of structure & permeability → inefficient ATP synthesis → chronic fatigue
Where does glycolysis take place?
cytoplasm
What does glycolysis become?
pyruvate
Without oxygen, pyruvate goes through what?
fermentation
With oxygen, pyruvate goes through what reaction?
oxidative phosphorylation
What is pyruvate broken down to in mitochondria?
Acetyl CoA
How is the first proton pumped into the intermembranous space in the ETC?
NADH has a high energy electron, complex I has higher affinity for electron than NADH, with the coupling of electron a proton is released into inter membranous space
How many complexes are there in the ETC?
4
Each time an electron is passed from one carrier to the next in the ETC, what happens?
a proton is pumped into intermembranous space
Why are protons pumped into intermembranous space in ETC?
to create a proton gradient, want a much higher concentration of protons outside of matrix
How can protons enter into matrix of mitochondria?
ATP synthase
How is acetyl CoA metabolised?
By TCA, reduces NAD+ to NADH
What is used to pass high energy electrons to first complex in ETC?
NADH
When proton enters the cell through ATP synthase, what allows that process to create ATP?
mechanical energy rotates enzyme and uses that energy to couple ADP and inorganic phosphate to make ATP
Once ATP is made in mitochondria, what happens to it?
It is exported to cytoplasm for use
Why is it called oxidative phosphorylation?
oxidation: generating high energy electrons
phosphorylation: the electrons are used to couple ADP to inorganic phosphate to create ATP
What is the gradient across the inner and intermembrane space called?
electrochemical proton gradient
Why is it called the electrochemical proton gradient?
Chemical: the intermembrous space has lower pH b/c of all the protons
electro: charge is more positive in intermembrous space
What drives ATP synthesis?
Electrochemical proton gradient
What does the proton couple with at the end of the ETC?
Oxygen - makes water
Where is the proton carrier located in ATP synthase?
transmembrane
Where is the head located in ATP synthase?
matrix
What does the head do in ATP synthase?
binds ADP to inorganic phosphate, it does this via rotation and conformation change
How does the head attach ADP to inorganic phosphate (Pi) in ATP synthase?
rotation and conformational change
What does ATP synthase do?
couples oxidation to phosphorylation
What assists ATP in leaving the mitochondria and going to the cytoplasm?
mitochondrial gradient (there is different pH and voltage gradient)
What does the TCA cycle create?
CO2 & NADH
How do the concentrations of ions in cytoplasm and intermembranous space of mitochondria compare?
They are similar
Protons fall down ______ ______ through ATP synthase, making ATP
electrochemical gradient
What is the exception to the way mitochondria make ATP?
thermogenesis - brown fat
What do the TCA and ETC produce in brown fat?
heat
What does UCP stand for?
uncoupling protein
What is another name for uncoupling protein?
thermogenin
What does thermogenin do?
It uncouples oxidation from phosphorylation to make heat
it allows protons to “leak “ from cytoplasm to matrix
Electrons have a very high affinity for what?
Oxygen
What happens when an electron reacts with oxygen?
Free radical (reactive oxygen species)
There is high probability of what bad thing happening in mitochondria?
free radicals being created
What does ROS stand for?
reactive oxygen species
ROS is very damaging to what?
ETC, protein, DNA, RNA
Why is ROS in mitochondria so dangerous compared to say, a ROS in nucleus?
mitochondrial genome does not have repair mechanisms that are in place in nucleus
Mutations in mitochondrial genes will affect what?
ETC
Explain how ROS can lead to snowball affect
More ROS leads to more damage of DNA, ETC, etc. the more damaged the DNA & ETC is, the more ROS is created, and the cycle continues
What is the function of superoxide dismutase?
It converts ROS to hydrogen peroxide
What is the function of glutathione peroxidase?
converts hydrogen peroxide to water
What does SOD2 stand for?
superoxide dismutase
What does GPX stand for?
glutathione peroxidase
Describe the extrinsic pathway for apoptosis
Cell: death receptor → death ligand binds death receptor → recruits proteins → activate caspase →activates more caspases →digest cell→ scramblase inhibitor broken down → scramblase puts phosphotidyl serine on outside
Describe the intrinsic pathway for apoptosis in mitochondria
DNA damage → opening of pores in outer membrane of mitochondria → cytochrome C leaks to cytoplasm → cytochrome C combines w/ cytosolic protein Apaf1 → activates caspases → cell death
What is caspase important for?
apoptosis
Bcl-2 is a family of proteins that control what?
control pore formation in mitochondria
What do pro-apoptotic bcl-2 proteins do?
promote pore formation in mitochondria
Pore formation in mitochondria promotes what?
apoptosis
What do anti-apoptocic bcl-2 proteins do?
inhibit the pro-apoptotic bcl-2 proteins, which stop apoptosis
BAX & BAD are examples of what?
pro-apoptotic bcl-2 proteins
What does Bcl-2 inhibit?
BAX
Bcl-2 is what kind of protein?
anti-apoptotic
Cytochrome C in cytosol activates what for apoptosis?
caspase cascade
How do mitochondria replicate/divide?
lengthen and then go through fission (similar to bacteria)
Explain the bottleneck affect in mitochondria
There are lots of mitochondria, but only a few are taken to create an egg. The egg could have all normal cells, all mutant cells, or any combination. Depending on the mitochondria in the egg, and then how that replicates, will determine if child will express disease
What is heteroplasmy?
Variability of mitochondrial diseases. can’t say recessive or dominnat b/c of all the mitochondria in cell.
What is homoplasmy?
All mitochondria are the same - can be wild type or mutant (almost all homoplasmy mutants will die)
How does mitotic segregation affect the way wild type and mutant mitochondria divide and affect a child?
Certain cells can end up having way more mutant mitochondria than others, and certain tissues can be more affected than others
What cells are most affected by mitochondrial inheritance?
muscle & neuron
What does mRNA have to have to enter mitochondria?
mitochondrial signal sequence
Where are mRNA that are destined to mitochondria folded?
In mitochondria
What is the purpose of Hsp70?
Prevents mitochondrial protein from folding in cytoplasm
Where are Hsp70 proteins located?
In cytoplasm and matrix of mitochondria. They have different functions in both locations. in cytoplasm prevents folding of protein, in mitochondria it helps fold protein
What is TOM?
A protein in outer membrane of mitochondria that Hsp70 will bind to
What happens once Hsp70 binds to TOM?
the unfolded protein travels across membrane, signal sequence is removed by protease, protein spontaneously folds or is helped by Hsp60
What does TOM stand for?
translocase of outer membrane
What helps protein fold in mitochondria?
Hsp60
How many proteins are encoded for in mitochondria?
13
How many total genes are in mitochondrial DNA?
37
How many tRNA genes are in mitochondrial DNA?
22
How many rRNA genes are in mitochondrial DNA?
2
What are the two strands of the mitochondrial genome called?
H-strand & L-strand
H-strand is rich in what?
G
L-strand is rich in what?
C
How many genes are encoded for in H strand?
12 of the protein - coding genes
How many genes are encoded for in L-strand?
1 protein coding gene (and some tRNA)
What controls the replication and transcription of mitochondrial DNA?
D loop
What does D loop stand for?
Displacement Loop
How many origins of replication are there no the mitochondrial genome?
2
How are mitochondrial strands transcribed?
polycistronically (at the same time)
Which is the heavy mitochondrial strand?
H-strand
Which is the light mitochondrial strand?
L-strand
What is the promoter for the heavy strand?
HSP
What is the promoter for the light strand?
LSP
How are the promoter regions for the two mitochondrial strands related to each other?
H promoter (Oh) is at twelve o clock, L promoter (OL) is at 8 o clock
Which complex in ox phos pathway contains only nuclear-encoded proteins?
Complex II
Complex I contains how many genes encoded for by mitochondria?
7
Complex III contains how many genes encoded for by mitochondria?
1
Complex IV contains how many genes encoded for by mitochondria?
3
Complex V contains how many genes encoded for by mitochondria?
2
What surrounds every protein coding gene in mitochondrial genome?
tRNA coding genes
What is one purpose of tRNA coding genes in mitochondrial genome?
Act as spacers b/w different genes
Which complexes in mitochondria carry out oxidative phosphorylation?
I, III, IV
Replication occurs _____ for mitochondrial DNA (symmetric or not?)
Asymmetrically
To complete replication, mtDNA has its own ____ and ____
polymerase and helicase
One cell may contain how many mtDNA genomes?
thousands
Are there okazaki fragments in mtDNA replication?
no
What is the dedicated helicase for mtDNA called?
Twinkle
How many mitochondrial DNA polymerase are there?
1
What is the name of the mitochondrial DNA polymerase?
DNA polymerase gamma
What is the function of DNA polymerase gamma?
mostly replication, some repair
What does the PLOG gene encode?
Catalytic subunit
Mutations in PLOG are associated with what?
reduced levels of mtDNA and/or mutations in the mtDNA
What is Ophtalmoplegia?
Weakness or paralysis of muscles that move the eye
Key words: bilateral ptosis, mtDNA depletion/deletion, polymerase gamma are what disease?
Progressive External Ophtalmoplegia (PEO)
PEO stands for what?
Progressive External Ophtalmoplegia (PEO)
Characteristics: Bilateral ptosis – progressive weakening of external eye muscles, proximal muscle weakness and wasting, exercise intolerance are what disease?
PEO - Progressive External Opthalmoplegia
What is the most common mode of inheritance for PEO?
Autosomal dominant, but can be autosomal recessive
How many genes are involved in PEO disease?
5
If PLOG or TWINKLE is the mutated in PEO disease, what is the mode of inheritance?
AD
What is the mechanism for PEO?
mtDNA depletion or large deletion - usually is large deletion
What two proteins may affected by mutations in PEO?
Twinkle & PLOG
What kind of mutation is more damaging to the mtDNA and will have more sever clinical outcomes?
Missense mutations
What is the name of a nucleoside used to treat HIV?
AZT
Describe AZT
A nucleoside used to treat HIV. It is thymidine analogue - has thymidine without hydroxyl group at 3’ and with a bunch of nitrogens at 2’
What is Zidovudine?
Another name for AZT - drug used to treat HIV
What is the mechanism AZT/Zidovudine works?
It doesn’t affect DNA Pol delta (in nucleus) but DNA Pol gamma (in mitochondria) is inhibited. B/c it is attached to methylated thymine, thymine will insert itself onto mtDNA and cause deletion of DNA. It protects against HIV because it competes with dTTP for incorporation into DNA by viral reverse transcriptase
What is myopathy?
disease of muscle
What is a side effect of AZT?
Myopathy
What are the names of the two promoters in control region of mtDNA?
HSP & LSP
What processes the giant transcripts from mitochondria?
RNA endonuclease
What does RNA endonuclease recognize in the mitochondria to excise certain genes?
It recognizes secondary structure in tRNA of the giant transcripts
mRNAs in mitochondria are ______ but not _____
poly adenylated but not capped
How does protein synthesis in mitochondria resemble that of bacteria?
It starts with N-formyl methionine
Which has more repeats, nuclear or mitochondrial DNA?
nuclear
How many tRNAs are involved in mitochondrial translation?
22
Explain the difference b/w tRNA in mitochondria and the rest of the cell
There is more wobble in tRNA in mitochondria, there is less tRNA available to recognize all the codons
What is the exception to the universal genetic code? Give example
Mitochondria codons do not code for the same thing as codons for everything else. Ex: UGA is usually stop codon, in mitochondria it codes for Trp
What is the size of the nuclear genome compared to mitochondrial?
Nuclear: 3 billion bp
Mitochondrial: 16 thousand bp
Are there introns in mitochondrial DNA?
No
Compare the % of coding DNA in nuclear genome vs. mitochondrial
Nuclear: 3%
Mitochondrial: 93%
What is the mutation rate of mitochondrial DNA? Why?
10x faster than in nuclear DNA. b/c of oxygen radicals formed after ox/phos
Mitochondrial DNA is very variable, meaning it is _____
polymorphic
Why is mtDNA so polymorphic?
the high mutation rate
The variations in mtDNA are mostly what?
SNP’s (single nucleotide polymorphism) & small deletions/insertions
What are the 3 major types of mutations in mtDNA?
deletions or duplications
point mutations in tRNA
Missense mutations in coding regions
What do most mtDNA mutations affect
ox/phos - ultimately ATP production
Describe a ragged red muscle fibers
It has defective mitochondria, so more mitochondria are produced. If you biopsy and stain with certain dye, it will look ragged and stain red, it has a lot more mitochondria.
What is the threshold hypothesis for mtDNA disorders?
the proportion of mutated mtDNA molecules must exceed a certain threshold before clinical consequences
Mitochondrial diseases often exhibit what?
reduced penetrance
The _____ of consequence of mitochondrial mutations correlates with _____ of mutated molecules
severity, proportion
People can survive giant mutations in mtDNA but not if it’s ______
homoplasmic
Giant deletions are usually inherited how?
Spontaneously - not passed down
A giant deletion is easy to detect using what method?
southern blot
How will a giant deletion present on a southern blot compared to a normal mitochondrial DNA?
normal will have one blot. Mutated will have 3, because of the deletion. They will be thicker b/c there is more mitochondria b/c cell is compensating for it not working well
The ____/______ of bottleneck with oocytes can cause very different levels of heteroplasmy in children
restriction/ampmlification
key words: no bone marrow involvement, late onset, ragged red fibers are what disease?
Kearns-Sayre Syndrome (KSS)
KSS stands for?
Kearns-Sayre Syndrome
Characteristics: late onset, typical ragged red fibers (>80% mutated mtDNA), PEO, retinopathy, cerebellar ataxia, heart block are what disease?
Kearns-Sayre Syndrome
What is the mode of inheritance for KSS?
mitochondrial
What is the mechanism for KSS?
giant mtDNA deletion
What does MELAS stand for?
Mitochondrial Encephalomyopathy, Lactic Acidosis and Stroke-like episodes
What is mutated in MELAS?
leucine tRNA
Key words: tRNALeu, short, stroke, diabetes are what disease?
MELAS
Characteristics: short stature, stroke-like episodes (vomiting, headaches, visual disturbances), diabetes, sensorineural hearing loss are what disease?
MELAS
MELAS is always what?
heteroplasmic
key words: tRNALys, ragged red fibers, epilepsy are what disease?
MERRF
characteristics progressive myoclonic epilepsy and seizures are what disease?
MERRF
MERRF stands for?
Myoclous Epilepsy and Ragged Red Fibers
MERRF is always
heteroplasmic
What is the mutated gene in MERRF?
lysine tRNA
What does LHON stand for?
Leber’s Hereditary Optic Neuropathy
What is the only mitochondrial disease that might be homoplasmic?
LHON
What kind of gene mutation is in LHON?
missense
key words: mutated Complex I gene, optic nerve damage, homoplasmy, bilateral vision failure are what disease?
LHON
characteristics: subacute painless bilateral visual failure, male:female 4:1 (X-chromosome penetrance), ~24 years old are what disease?
LHON
What complex is affected in LHON?
Complex 1
key words: ATPase 6 gene, ataxia, retinopathy, pigmentation, Leigh Syndrome Note: Maternally inherited Leigh Syndrome is a more severe form with a larger portion of mutated mtDNA are what disease?
NARP
characteristics: late childhood or adult onset peripheral neuropathy, ataxia, pigmentary retinopathy are what disease?
NARP
NARP is always
heteroplasmic
What does NARP stand for?
Neurogenic muscle weakness, Ataxia, and Retinitis Pigmentosa
What kind of mutation is in NARP?
missense
what gene is mutated in NARP?
ATPase 6 gene of Complex V
NARP is a ____variation of Leigh syndrome
milder
Describe 3 parent babies
mother with affect mtDNA can have unaffected children, nuclear genome of affected zygote transferred to another zygote from unaffected donor.
