Mitochondria and Chloroplasts (Unit 5) Flashcards
Describe the journey an electron takes through the ETC
Electrons from NADH enter Complex 1 while those from FADH enter Complex 2, both then go to Ubiquinone which gives them to complex 3 Then, they go to Cyt C and finally Complex 4 where 4 of them + 4H+ s are added to O2 to become 2 waters
Give the names for the following:
Complex 1
Q
Complex 2
Complex 3
Complex 4
NADH Dehydrogenase
Coenzyme Q
Succinate Dehydrogenase
CytC reductase
CytC oxidase (COX)
Describe the journey an electron takes inside COX
Enters Copper atoms through CytC
Goes to heme a
Goes to heme a3 which clamps oxygen until it has taken in 4 electrons (to avoid superoxide O2-formation)
*Cyanide or azide may take this oxygen binding spot
What is a prosthetic group?
A group tightly bound to a protein
What is an apoprotein?
A protein without its prosthetic group
Which complex does not pump H+ in the ETC?
Complex 2
Why are prosthetic groups in the ETC often transition metals?
Because these guys have multiple oxidation states with closely spaced redox potentials for easy electron transfer
Name the 4 electron carriers in the ETC
Cytochromes
FeS clusters
CytC
Ubiquinone
Describe the 4 electron carriers
-Cyt
-CytC
-Ubiquinone
-FeS clusters
-Porphyrin heme + apocCyt with same prosthetic groups as heme (Fe3+) and chlrophyll (Mg2+)
-aqueous heme that moves 1 e at a time
-lipid-soluble coenzyme Q move up to two e at a time
-Flavin and copper atoms at pros. groups
What is the basic principle behind ATPase function?
The coupling of H+ movement to allosteric changes in the protein that result in ATP synthesis or hydrolysis depending on the ratio of ATP:ADP
How is electron movement coupled to H+ pumping?
Electrons cause allosteric changes in the H+ pumps which allow them to line up ionic/polar side chains to create a H+ wire.
The wire moves H+s much faster than H20 (where it is already quite mobile due to H-bonding network)
What is the mitochondrial proton gradient created by the ETC?
More H+ is moved to the IMM against its gradient
What is delta G?
What does it do?
The free energy change for a reaction
It determines whether or not a reaction will happen
What does it depend on?
What is favorable G?
Depends on:
-standard free energy change: Based on the chemicals
-[ ] of the chemicals
(thus if [ ] are equal, it will just be the standard free energy change)
Favorable G is large and negative
What is the reason why ATP hydrolysis has such a highly negative delta G
(and thus is very easy)?
Because the [ATP] is much higher than that of ADP or Pi
The mitochondria maintains this difference
Does ATP sythase only make ATP?
NO! It can also hydrolyze ATP and pump H+ back into IMS ex: in Lysosomes
What is the proper name for ATP synthase? Can you describe the molecule?
F1F0ATPase
Really big
Contains rotor and stator
What does the F0 part of ATP synthase do?
Creates a hydrophillic path for H+ to move down its gradient back into the matrix. This energectically favoured move gets coupled to ATP generation via allosteric changes in the protein as it spins the turbine
What determines the direction of ATP synthase?
The balance between the steepness of the H+ electrochemical graident and the local delta G for ATP
What does F1 in ATP synthase do?
Make the ATP in the matrix
What do uncoupling agents do? what are they?
Why do we have them?
Lipid soluable ionophores that Disconnect e- transfer from ATP synthesis by dissipating the H+
Doing this DEC the efficiency of cellular respiration thus more O2 is needed to move more e- and more energy gets lost as heat
What do cristae do? Where are the proteins found on them?
Trap H+ so it doesn’t leave thru the OMM
ATP synthase form long dimer rows and stick out like lolipops into the matrix to help with curvature while the H+ pumps exist on either side of them
how is mtDNA inherited?
in plants + animals: Uniparental
in humans: Maternally (but some lit suggests there may be some small incidence of paternal inheritance)
This is because the egg contributes a lot more cytoplasm than sperm does to the zygote
Also Sperms lose mtDNA as they mature and ferilized egg works to destroy it once they come together
Is mito essential for life?
NO! there is one eukaryote (a protozoa) that was determined to have suffered a mito loss
What is OXPHOS
oxidative phosphorylation
uses O2 to make ATP
What is the name of the energy-making mechanism used by mito and chloro?
Chemiosmotic coupling
Is mito static?
No its shape is always changing as it divides and fuses (depending on the cell type)
How do we live-cell image mito?
MitoTracker Red is a fluoresecnet dye that mito takes up given that it has a potential across its inner membrane
What are reponsible for the distribution and orientation of mito in the cell?
MTs but dynamin (a large GTPase) does the actual work
Does dynamin have GEF or GAP?
No! bc it is a large GTPase
Where do we find mito?
Where there are high amounts of ATP
what is MAM?
Mito-associated membrane
A part of ER that is physically connected to mito
-thought to allow for lipid exchange
-ER tubules are thought to help determine future mito divsion sites
What is the only double membraned organelle
mito
What are the 5 functional mito spaces
OMS: porins, TOMs, pro-apop proteins
IMS: Same proteins as cytosol so no ECG between them
IMM: Transporters, OXPHOS machinery and TIMs [crista and innerboundary membrnae]
Matrix: Metabolic enzymes for oxidizing food
Are cristae always connected to the IMM?
No! sometimes they can pinch off and form their own organelles
What is the part of the inner membrane parallel to the OMM called?
The interboundary membrane
H+ move through wires, but how do e- move in the ETC?
Via prosthetic groups on proteins
What fuels ATP production during starvation
Amino acids (using OXPHOS)
How do cells relying on glycolysis speed it up?
they remove excess NADH from the cytosol (and put it in the mito)
What can the cytosol make with citrate?
fatty acids and sterols
What are the 2 main things mito gives to the cytosol when it is not making ATP?
Carbon skeletons and reducing power
ex: Citrate can make C (carbon) and NADPH (has reducing power)
How do mito buffer redox potential in the cytosol?
Cytosol needs supply of NAD+ to do glycolysis and make NADH.
Mito turns NADH back into NAD+ and gives it back to the cytosol
(this exchange is done with metabollite shuttle systems bc IMM is not permeable to NADH)
What is the FeS cluster? Where is it?
Proteins involved in redox rxns
In mito
Aside from making ATP, being the site of FeS cluster, buffering the redox potential of the cytosol, and providing the cytosol with Carbon skeletons and reducing power, what does mito do?
-site of biogenesis for heme (Ex: protoheme in Hb, Mb, Cyt P450s)
-part of urea cycle
-makes lipids ex: cardiolipin
-helps with Ca2+ buffering
What is cardiolipin?
Two-headed, four-tailed lipid found in IMM
How does the energy level and redox potential of an e- change as it goes through the ETC?
Both drop
Why doesn’t the conversion of H2 and O2 to make water create an explosion?
Because we store the energy instead of wasting it as heat
What 2 gradients represent the PMF?
pH (lower in IMS) and Voltage (more + in IMS)
Hence why the pumps move H+ against its gradient
What is redox potential? What does it mean if its high or low?
A measure of electron affinity. It is the voltage difference between your redox pair and the arbitraily determined standard redox pair.
If its high, your electron affinity is high (and your energy level is high?)
I have a low redox pair and a high redox pair, where will e- move from/to
From the low to the high
Give an example of a high and a low redox pair
High: O2:H20
Low: NADH:NAD+
what lipid is COX associated with
cardiolipin
How would you describe COX binding site?
binuclear
What is COX made of?
3 Copper atoms
2 Heme A
1 Mg
1 Zn
Which genome makes COX?
Both!
What is stroma?
Chloro version of the matrix
What extra space does chloro have? why?
The thalakoid space
Because it has a third membrane
Why doesn’t chloro need crista?
It already has a huge pH gradient from the thalakoid spcae (its ph is 5.5 vs 8 in stroma) and so it doens’t need to create spaces of locally low pH
How does ATP synthase differ in chloro from mito?
What is the supercomplex in the ETC? What does it do? What does it require?
A complex of complexes 1,3, and 4.
It helps transfer e- in the cristae membrane in a more efficient way while also reducing the risk of potential redox side rxns
It requires cardiolipin
What does cardiolipin do and what shape does it have?
Associates with OXPHOS and ATP transport proteins
Supports membrane curvature of crista
cone shape
What makes mito unique?
It is a double-membraned oraganelle
It is inherited almost exclusively maternally instead of following Mendelian genetics
-It has very unique DNA (there are 4 reasons for this)
What are the unique features of mt DNA?
Relaxed Codon Usage (22 vs 33 tRNAs)
Doesn’t follow universal stop: Most animals mtDNA have UGA as TRP instead of STOP like normal
INC mutation rate: 10X greater than nDNA and not tied to cell divison, also crude repair pathways and exposed to ROS
Dense Gene Packing: no introns (in ppl)
What is heteroplasmy and why does it happen?
When a cell or mito has different mtDNA populations
Happens because cells can have multiple mitos and mitos can have multiple mtDNAs
What can cause heteroplasmy and threshold effects?
Random segregation during cytokenesis
What are thershold effects?
When a given mutant load has different effect on different tissues due to heteroplasmy or the fact that some tissues (ex: muscle) have a ton of mito
What do nuclear DNA proteins do in the mito?
Transcription
Translation
Repair
Packaging
(all of which are specific to the mito)
Also works with mtDNA to create the OXPHOS protein complexes
is mtDNA packaged with histones?
No! it has other proteins that associate with it
Are mito proteins ever used anywhere other than in the mito?
Almost never!
Describe the mito genome
only 37 genes
-13 proteins
-22 tRNAs (for punctuation - separates the protein genes)
-2 rRNAs
What do mtDNA proteins do?
Form subunits for the Respiratory chain complexes
What is mito replication called and why do they do it
How does it work?
Fission
-to respond to metabolic needs
-to populate daughter cells
Mito grows and then divides using dynamin (assebly constriction then hydrolysis’ constriction)
who controls mito dynamics?
What are mito dynamics?
GTPases in inner and outer membranes
Dynanmin and Opa1
They move around and change shape alot
What is horizontal gene transfer
What 3 things does it require?
the movement of genes from the mito to the nucl
-Adaptation to nucl. transciption and translation machinery
-movement through the cytoplasm
-mito signal sequence
Why do we do horizontal gene transfer?
Why do we still have mtDNA?
-mito genome is expensive and needs a lot of nucl proteins to achive
-it might be harder for super hydrophobic proteins (like some of the ETC complex subunits) to transport to the mito via the cytoplasm
What is vertical gene transfer?
Parent to offspring
