T4 Flashcards
How is a translocated polypeptide released from TIM23 complex?
Through action of ATPase.
Describe the translocation of mitochondrial protein from the cytosol to the matrix.
- Binding of N-terminal signal sequence to TOM complex receptor
- Stripping of cytosolic Hsp70 from protein
- Binding of signal sequence to TIM23
- Translocation of protein by mitochondrial Hsp70 and electrophoresis
- Cleavage of signal sequence
How are mitochondrial proteins integrated into the outer/inner mitochondrial membrane?
In the outer by the SAM complex (aids in insertion and folding). OXA complex aids in mitochondria native protein insertion in inner membrane.
How is peptide folding inhibited in the intramembranous space?
By chaperones.
Outline the four mechanisms of translocated protein recognition/sig.seq. release inside mitochondria by integral protein complexes.
- Recognition by inner membrane integral protein complex of N-terminal signal sequence and then hydrophobic sequence (stops translocation in intermembraneous space).
- Recognition by TIM23 complex of signal sequence and then cleavage sequence/second signal sequence. Recognition of 2nd sig.seq. by OXA complex (also mitochondria native peptides) and translocation to intermembranous space.
- Binding to inner membrane complex and release by 2nd signal peptidase.
- Internal sig.seq. recognised by TOM complex (running through of peptide), binding of chaperones and transport to TIM22 (yes, 22).
What structures allow proteins to traverse inner resp. outer mitochondrial membrane?
Porins in outer membrane, metabolite-specific transporters in inner.
Does the mitochondria export protein into the cytosol at any point?
Normally no, protein transport is unidirectional, from cytosol to mitochondrion. However, during apoptosis protein transport may take place in the opposite direction.
awhre is the mitochondrial gneome located?
In the matrix.
How does mitochondrial protein synthesis resemble that of bacteria?
- Both start with N-formyl methionine
2. Also mitochondrial ribosomes are sensitive to antibacterial antibiotics
How is mitochondrion number and shape in a cell controlled?
Through fission and fusion, mediated by GTPase dependent enzymes.
When does mitochondrion genome replication take place?
Throughout the cell cycle.
What determines what mitochondrial DNA molecules are to be replicated?
Random selection. However regulated during constant conditions to ensure “constant amount of organelle DNA”.
Is the majority of mitochondrial protein coded by mitoDNA or by nuclear DNA?
Nuclear.
Ehat does the human mitoDN encode for?
“2 ribosomal RNAs, 22 tRNAs and 13 different polypeptide chains”
What are nucleoids?
Multiple structures containing mitoDNA, attached to the inner membrane. A simple circle.
What is the endosymbiont hypothesis and how is it supported?
The theory of an anaerobic cell engulfing an aerobic one in order to cope with the oxygen rich environment, and the subsequent gene transfer from the aerobic organism (mitoc.) to the anaerobic host (nucleus). Similar gene transfers have been observed in modern time.
What features distinguish mitochondrial genome?
- Dense gene packing (very few non-coding nucleotides)
- Relaxed codon usage (many tRNAs recognize any of four nucleotides in position 3)
- Variant genetic coding (4/64 codons code different proteins than the nuclear genome)
In what form is the mitochondrial genome?
Circular, non histone-bound.
How is the mitochondrial genome transcribed?
Symmetric transcription of both strands, starting from the same promotor region and progressing in opposite direction produces 2 giant RNAs.
How are the mitoRNA transcripts processed?
1: extensive nucleade cleavage produces 2 rRNAs, most tRNAs and ca 10 poly-A RNAs
2: 8 tRNAs and 1 small poly-A RNA
What is the function of the non-coding part of the genome of the mitochondria?
Complimentary sequences to coding parts on opposite strand.
What defines mitochondrial substitue for mRNA?
poly-A-containing RNA (and lack of 5’cap).
Are human mitochondrial mRNAs spliced?
No.
What is mitotic segregation in mitocDNA inheritance?
Mitochondrial genome in haploid cell isn’t inherited 50/50 from each parent cell but is instead enriched over time (inheritance of more of one type/mitotic enriching), to produce individual cells with predominantly one type of mitochondrial genome vs. the other.
What does cytoplasmic inheritance entail?
All daughter cells (of diploid cell) contain the same mitochondrial genome.
Through what mechanism is the mitochondrial genome inherited in humans?
Through maternal inheritance.
What is the basis for maternal inheritance?
The greater contribution of cytoplasm to the zygote from the egg cell (vs. the sperm cell).
Are all the copies of mitchondrial genome inherited from the mother (in humans)?
No. One or two may be from the father/sperm cell.
Why are muscles and nerves most susceptible to mitochondrial disease?
Due to their greater need of ATP.
What might be the mechanism for eruption of mitochondrial disease (ex. MERRF)?
Mutation in one tRNA gene and inheritance of a threshhold amount to a cell and later, tissue.
Some mitochondrial proteins perform several steps of the urea cycle. Where are these proteins encoded?
Nucleus.
Why might mitochondrion function differ in persons with the same mitochondrial genome?
Nucleus encoded protein makes up most of mitochondrial proteome.
What is the role of cardiolipin in mitochondria?
Constitute 20% of inner membrane. Derived from ER phosphatidylserine, as are most lipid molecules of the mitochondria.
Describe the structure of cardiolipin.
Fatty glycerol with 2 phosphate groups and 2+2 fatty acid groups.
Why is it important for the mitochondrion to contain superoxide dismutase (MnSOD) and glutathione peroxidase enzymes?
Because 90% of cellular O_2 ^- is produced in mitochondrion.
How is the abundance of ROS detected in mitochondrion?
mitoDNA contains a ten-fold higher amount of oxidized nucleotides compared to nuclear DNA.
Describe the “viscious cycle” hypothesis.
The hypothesis of oxidized mitoDNA becoming progressively defective and ultimately resulting so many mutations that somatic cell protein synthesis is affected, resulting in aging.
Mitochondrial and cytosolic proteins with the sanr function: autologuous or homologuous?
Usually autologuous.
Name two genes always contained in mitoDNA.
Cox1 and Cob.
Are all inherited mitochondria of the zygote from the mother?
Yes/no. Mitochondria are also inherited from the father but subsequently destroyed, prior to mitosis of zygote (?).
What’s the main form of energy production of foeti?
Glycolysis. Thus mitochondrial defects seldom arise before birth.
What gene deficit occurs with aging?
COX
What does mitochondrial genome instability refer to?
Multiple deletions.
Define apoptosis.
Programmed cell death.
awhat are the characteristic morphological changes of a cell during apoptosis?
Shrinkage, condensing, collapse of cytoskeleton, disassembly of nuclear envelope and condensing/breaking up of chromatin.
What’s an apoptotic body?
A ‘blebbed’ off part (vesicle) of the apoptotic cell with chemically altered surface for macrophage recognition.
Why is the surface of an apoptotic body chemically different to a normal plasma membrane (2 reasons)?
In order to aid macrophagic recognition and prevent spillage of cell content.
How does cell necrosis differe from apoptosis?
In necrosis cell contents are released in an uncontrolled manner onto neighbouring cells, eliciting an inflammatory response.
What role does apoptosis play in the developing foetus?
Selective destruction of tissue in order to form ex. fingers and toes.
Give an example of the quality control aspect of apoptosis in humans.
Destruction of developing T- and B-cells that are not functioning correctly.
How does apoptosis work as part of a tissue size regulating system?
Removes cells in unnaturally enlarged tissue (ex. liver affected by phenobarbital).
How is apoptosis evisent in neutrophil production?
Vast quantities of neutrophils die in the bone marrow as part of maintenance of a supply of short-lived neutrophils.
Through what function may a DNA-defective cell, unable of reparation of the genome, inhibit itself from becoming cancerous?
Apoptosis.
How can apoptotic cells be marked?
With the TUNEL technique (massive quantity of cleaved DNA makes for many DNA-fragment ends that can be marked).
What pattern can be discerned in gel-electrophoresis of apoptosed cells?
The ladder pattern.
What chemical change occurs in the apoptotic cells plasma membrane?
Phodphatidylserine is translocated to the outer layer (vs. normally only found on the inner leaflet). ‘Don’t eat me’-signal is removed.
What difference does phagocytosis of a cell with a phosphatidylserine-rich outer surface make for a macrophage?
Inhibits the inflammatory response usually elicited (release of cytokines etc.).
What is cytochrome c in the cytosol evidence of?
Apoptosis.
How does the cell membrane potential change in an apoptotic cell vs. a non-apoptotic one.
Membrane potential (electrical) decreases.
Describe the proteolytic caspase cascade during apoptosis.
- Two inactive procaspases are cleaved into prodomains, large and small subunits (heterodimers).
- The two ‘large+small subunits’ tetramerize into active initiator caspace (fortress configuration).
- Active initiator caspaces activate many molecules of executioner caspaces.
What’s a caspase?
A protease with cysteine at its active site that cleaves target proteins at “specific aspartic acids”.
What are the target proteins for caspace?
Nuclear lamina proteins, endonuclease (activates it), components of cytoskeleton and cell-to-cell adhesion compelxes.
What part of the mechanism of apoptosis makes it irreversible?
Exceeding threshold value of caspace cascade.
Is the same caspace used in all tissues?
No, there are many different ones, coded for by different genes. Some code for initiator caspaces, some for executioner caspaces for example.
How is the caspace cascade activated?
Procaspaces have a prodomain containing CARD (caspace recruitment domain) which enables assembly into activation complexes upon signal regeption.
Name two signaling pathways that can initiate apoptosis.
The extrinsic pathway and the intrinsic pathway.
Describe the extrinsic pathway of apoptosis.
- Killer lymphocyte with Fas ligand binds to Fas death receptor on cell (both are trimers).
- Cytosolic domain of Fas recruits adaptor protein FADD (Fas-associated death domain) via death domain of each protein.
- Trimer complex binds initiator procaspase wia death effector domain on both forming DISC (death inducing signaling complex)
- Complex forms active initiator caspace.
What’s the difference between the extrinsic and intrinsic pathway of apoptosis?
Activation signal coming from outside or inside the cell.
What’s the mechanism behind the intrinsic pathway of apoptosis?
Activation of caspace cascade due to release of intermembrane mitochondrial proteins due to lack of nutrients/oxygen, DNA damage or extracellular survival signals.
Describe the function of cytochrome c in the intrinsic pathway of apoptosis.
Binds to Apaf1 (apoptotic protease activating factor-1), causing oligomerization and formation of a wheel-like heptamer called an apoptosome.
What does an apoptosome do?
It retains initiator procaspace-9 proteins and activates them.
What’s the function of Bcl2 proteins?
They regulate the intrinsic pathway of apoptosis.
Do Bcl2 activate or supress the intrinsic pathway of apoptosis?
Both.
How do Bcl2 proteins regulate each others’ function?
Through binding to each other (inactivation of each) and forming a heterodimer.
Which are the pro-apoptotic Bcl2 proteins?
BH123 and BH-3 subfamilies.
What role does the Bcl2-subfamily BH123 play in intrinsic pathway activation in apoptosis?
It forms octamers, inducing release of cytochrome c from the mitochobdria.
Name the two main BH123 proteins. Are they pro- or anti-apoptotic?
Bak and Bax. Pro-apoptotic.
What’s the main function of the BH3-only subfamily of Bcl2 proteins.
“To promote apoptosis /…/ by inhibiting anti-apoptotic Bcl2 proteins”.
What’s the role of BH3-only proteins?
They connect apoptotic stimuli with the intrinsic pathway of apoptosis.
How does the p53 tumour supressor protein activate intrinsic apoptosis?
It activates transcription of BH3-only proteins.
Whre are the anti-apoptotic Bcl2 proteins found?
On the surface of mitochondria.
What protein links they extrinsic and the intrinsic apoptotic pathways, and how does it do it?
Bid. tBID (truncated BID) binds anti-apoptotic Bcl2 proteins on mitochondria, inhibiting their function.
Where do IAPs reside?
In the cytosol.
What do all IAPs (inhibitor od apoptosis) have in common?
They contain “one or more BIR (baculovirus IAP repeat) domains”.
How are IAPs de-activated?
Anti-IAP proteins released from mitochondrial intermembrane space bind to the BIR-domain.
What results from the lack of survival signals from neighbouring cells?
Intrinsic pathway of apoptosis activated through production/activation of pro-apoptotic BH3-only proteins (they override Bcl2 proteins).
Through what three mechanisms can extracellular survival factors inhibit apoptosis?
- Increasing production of anti-apoptotic Bcl2 proteins.
- Inactivation through phosphorylation of Bad (BH3-only Bcl2 pro-apoptotic protein) by Akt.
- (in drosophilia) inactivation of anti-IAP Hid.
Where can inactivated genes of Fas and Fad lrad to disease?
In spleen and lymph glands (thymus), leading to autoID.
From where is the Bcl2 name derived?
B-cell lymphoma. Bcl2 was discovered in this disease where IAP Bcl2 was overproduced.
What blocks IAP?
anti-IAPs, Smack/Diablo
How many times does the mtDNA replicate during a cell cycle?
Once.
What caspaces are initiator cadpaces?
8- and 10- for inner, somethig. something for extrinsic
