Mitochondria Flashcards
What does it mean for mitochondria to have a monophyletic origin?
A single event. Alpha-proetobacterial origins. A gram negative bacteria became the mito.
Describe gene expression in mito as compared to its ancestry.
Mitochondria has a conservation of bacteria-like translation system and bacteriophahe-like DNA and RNA polymerase
What are the hypotheses for mitochondrial endosymbiotic evolution?
- archezoan scenario
- symbiogenesis scenario
Describe the archezoan scenario.
anaerobic archaeon cell engulfs aerobic bacterium. After engulfment causes bacterium loses second membrane. There is not much evidence for this hypothesis.
Describe the symbiogenesis scenario for mitochondria evolution.
symbiotic association of hydrogen-dependent anaerobic archaebacterium with eubacterium that was able to respire but generated molecular hydrogen as a waste product of anaerobic heterotrophic metabolism. This hypothesis is most commonly accepted.
Describe the diversity of mitochondrial DNA in unicellular eukaryotes.
- ranges vastly in size
- smallest size is in plasmodium, malaria parasite
- kinetoplastid parasites have maxicircle and minicircle mtDNA
- some anaerobic protists have no mtDNA at all, just mitoplasts to make FeS clusters only
Describe human mtDNA
- contains tRNA genes
- contains rRNA genes
- has protein coding genes (13) for NADH dehydrogenase, cytochrome oxidase, NADH dehydrogenase, ATP synthase, and cytochrome b
Largest and smallest mtDNA?
largest: rickettsia bacterium
smalles: plasmodium
Describe this slide
A. kinetoplastid parasite. red area is the mitochondria spread throughout the cell. Within the mito are thousands of little circle structures surrounding a chain of DNA
C. the mini circles all aligned around the DNA forms a kDNA disc. Each mini circle kDNA will replicate on its own in the kinetoflagellar zone of the mitochondria. Proteins in the antipodal sites of the mito then help to process and reassemble to circles into the kDNA disc
Describe this figure.
transcript-edited NADH dehydrogenase gene from kinetoplast parasite mtDNA
- red = uracil nucleotides added post-transcriptionally
- * = deletion of uracil nucleotides post-transcriptionally
- kDNA minicircles code for guide RNAs that position the insertion or deletion of uracil nucleotides (targeting is similar to CRISPR)
Describe the dynamic nature of mitochondria membranes.
The mito membrane is not static as it appears in textbooks. In fact, the membranes are constantly forming and cristae are rearranging.
Describe this figure.
- mitochondria can be fused together to form larger organelles
- mito can be cut by fission to form smaller organelles
- mito can move and be transcported through the cell on microtubules to locations where they are most needed
- mito can be degraded by mitophagy if they incur damage (mitophagy defects are seen in Parkinson’s be mutations in Parkin gene)
- mito biogenesis can take place to generate mito in large numbers
Only 13 proteins are encoded in human mtDNA. Where do the rest of the mito proteins come from?
They are encoded by nuclear DNA.
How does mitochondria vary between tissue types?
size, shape, amount per cell. The mito arrangement in different cell types all differs drastically (e.g. cardiac muscle versus sperm cell tail)
Where in the mito are mtDNA, ribosomes, and RNA held?
in the matrix
Describe the surface area of cristae.
It is much, much larger than that of the outer membrane because it is full of folds and invaginations.
Why does the mitochondria have such high complexity?
Because of all the reactions that must take place in the mito, it is highly complex. The high complexity is also energetically expensive to maintain.
Describe mitochondrial energy economics in the context of this figure.
Protons will flow down their electrochemical gradient through the alpha and beta subunits in the plasma membrane of ATP synthase, causing the gamma stalk and the C-subunits to begin turning. The number of C-subunits determines the number of protons needed flow through the inner membrane into the matrix to turn the apparatus 360 degrees to produce 3 ATP. Therefore:
- animals have 8 c-subunits, so require 8 protons
- other eukaryotes likes plants have 10-13 subunits, and require 10-13 protons to make 3 ATP. This is therefore less efficient and less advantageous than the setup that animals have
Describe the two components of the electrochemical gradient in mitochondria (delta uH+)
- electropotential gradient (delta psi) -200 mV. This component contributes most to the elctrochemical gradient and the inflow of protons across the inner membrane
- pH gradient: the delta pH varies from 0.4 to 0.6 U (the matrix is more basic than the inner membrane space)
The proton motive force for protons acros the membrane is a combination of the proton motive forces for each of these components.
Why is this depiction of the ETC in mitochondria not accurate?
The proteins involved in the ETC (many of which are transported in from the cytosol) are present in supramolecular structures. Supercomplexes are more economical
- first shown is the solid state model
- second shown is the random collision model (least likely)
- the last is the plasticity model, where the supracomplexes are random associations
How is the curvature of the cristae membrane achieved?
ATP synthase monomers are arranged at 45 degrees from other monomers, which forces the cristae membrane to curve. Deep invaginations form that cause ETC supercomplexes to be concentrated in cristae membranes, and therefore proton gradients are more concentrated, allowing the ATP synthase to work more effiiently.
Discuss this figure.
When ATP in the matrix is low and ADP + P is high (phosphate also gets in by proton gradient) then ATP synthase will make ATP. If the ATP levels are high and ADP + P is low, the ATP synthase can go in the reverse direction and act as an ATPase. This can help regenerate the proton gradient to get more ADP and Pi into the matrix. The same carrier protein moves ATP out of the matrix and ADP into th matrix.
Describe the role of mitochondria in thermogenesis.
- brown fat is needed to produce non-shivering heat in newborns and hibernating animals (and is in high frequency in lean individuals)
- when the body senses cold, the BAR receptor is triggered which causes cAMP secondary messenger to activate PKA and induce B-oxidation of FFA in the mito, which helps to make the electrochemical gradient across the inner mito membrane.
- in the large number of mitochondria, uncoupling protein I (UCPI), expressed at high levels in brown fat, uncouples the ETC from ATP production, causing the proton gradient to dissipate and heat to be let off. (protons will flow through UCPI)
Describe calcium intake into the mitochondria after release from the ER/SR
A uniporter is responsible for bringing Ca2+ into the mito.
- Ca2+ can diffuse readily from the cytosol, past the outer mito membrane and into the intermembrane space
- MCU proteins form a channel in the inner membrane of the mitochondria.
- When Ca2+ is low in the intermembrane space and not bound to MICU1 and MICU2, the two proteins occlude the channel
- when Ca2+ is high in the intermembrane space, it binds to MICU1 and MICU2, causing them to move out of the way of the channel so Ca2+ can readily enter the mito matrix.
- Ca2+ influx then regulates players of the TCA cycle
Discuss this figure.
Biogenesis of FeS clusters in the mitochondria and their uses in the cell.
- in mito, ISC (iron sulfur cluster) assembly machinery assembles FeS clusters onto apo proteins to form holoproteins. These mitochondria resident enzymes are involved in respiration, TA cycle, and lipoate synthesis.
- in cytoplasm, CIA (cytoplasm iron sulfer cluster assembly) machinery adds FeS clusters to cytoplasmic apo proteins. These holo enzymes are involved in protein translation, tRNA modification, and iron regulation. Some of these holo enzymes enter the nucleus.
- in the nucleus, holo enzymes function in DNA replication, DNA repair, and chromosome segregation
**iron homeostasis is very important due to its toxicity!
Describe the activities taking place in quiescent vs proliferating eukaryotic cells.
- when not proliferating, the cell is generating some pyruvate and the mitochondria is mainly just doing oxphos.
- when the cell is proliferating, a ton of pyruvate is being made via glycolysis converted to acetyl-coA for use as precursors for macromolecule biogenesis. TCA cycle goes overtime, using acetyl-coA to make lots of intermediates for things. Thus, lactic acid fermentation is being done to recycle NAD for glycolysis. This occurs even when O2 is present, because the intermediates of the TCA cycle or NADH/FADH2 that would go off to the ETC and oxphos are busy doing other things. This is very similar to what happens in cancer with the Warburg effect.
Describe the role of Gln-dependent anaplerosis.
Proliferating cells are using a lot of Gln in addition to pyruvate to feed the TCA cycle, so that other intermediates like pyruvate to become more available for biosynthesis.
