Lecture #3 - Mitochondria and Peroxisomes Flashcards
Use of Organelles/cell compartments
Organelles/cell compartments provide :
1. Create specialization (Ex. Energy production)
- Example – Mitocondria is specialized for making ATP
2. Concentration of Activities in a cell (Ex. TCA cycle)
- Example - Mitochondria = concentrates TCA and Oxidative Phosphorylation
3. Sequestering of toxic metabolites (EX. ROS h2o2)
4. Make Microenvirnments (Ex. Membrane potential across membrane ; Ion or pH gradients across membrane)
Issues with organelles
Organelles pose probelms for the cell :
1. How to control organelle number and shape
2. How to transport small molecules in and out
- Need to transport small molecules in and out of organelles because they have membranes (need transporters)
3. How to assmble organelles with proteins and lipids
4. How to control location + movement + inheritance of organelles during cell division
Mitocondria membranes
Mitocondria = have 2 memebranes
- Outer membrane (Smooth)
- Inner membrane
- Inner membrane = folds into Cristae –> Cristae = increases the surface area to accommodate the many protein complexes (Ex. Oxidaive phosphorylation machinery + transporters)
Between the membranes = have inter membrane space
Insider the inner membrane = matrix (has mtDNA)
EM section of mitocondria
Image – EM image of mitocondria
- Shows inner and outter memebrane
- Small dots = ribosomes (Ribosomes = make proteins in the matrix of the mitocondria)
3D reconstruction of serial EM images (tomoagraphy) of mitocondria
Image – 3D view of mitocondria using EM tomography
- EM tomography = cuts serial sections of mitocondria and reconstitutes sections into 3D image
- Blue = Outer membrane ; Yellow = inner membrane
- See 3D of inner membrane –> shows the inner membrane is sheet structures NOT tubules
Number of mitocondria per cell
Each cell has hundreds of mitocondria
- Have 2 copies of nuclear genome in 1 cell BUT have >100 copies of mtDNA in 1 cell
Image:
- Red = Mitocondira ; Green = Nuclear DNA ; Yellow = mtDNA
- See many mitocondria in cell + see nuclear DNA + see many copies of mtDNA in cell cell
Functions of mitochondria
- Energy production (synthesize ATP)
- Major function of mitocondria = synthesize energy in the form of ATP
- Metabolsim
- Heat generation (Control body temperatureby generating heat)
- Involved in Signaling
- Intracellular Ca+ signaling (suing Ca) and ROS (ROS can be a signlaing molecule)
- Apoptosis (programmed cell death)
OVERALL – means mitocondria are essential organelles
Mitocondria metabolsism
- Some lipid syntehsis (made in mitochondria)
- Heme and Fe-S cluster synthesis
- Heme and Fe-S cluster = part of enzymes in cells
- Fatty acid metabolsim (making energy)
- Some Amino Acid metabolism
- Urea degredtion
How do you make ATP using mitochondria?
Answer – Mitocondira make energy by burning what you eat
- Get energy from burning (oxidizing) the substrates used for ATP synthesis –> make ATP
Mitocondria burns Sugars + proteins + fats AND using oxygen to extract energy from these molecules –> then make ATP
- In process of making ATP turn O2 –> CO2
Mitocondria ATP production (process)
- Sugars or fats or proteins undergo TCA cycle in the matrix
- TCA cycle produces high energy compounds (NADH and FADH2)
- NADH and FADH2 = made in the matrix with TCA cycle - NADH and FADH2 are used in ETC (proton pumps)
- ETC will make an electrochemical gradient across the inner mitochondrial memebrane
- F1/Fo ATPase (ATP synthase ; aka complex 5) will use the gradeint to make ATP
Use of NADH and FADH2
NADH and FADH2 = used to make membrane potential – creates an electrochemical gradient across the inner membrane using proton pumps
- Proton pumps - pump protons from the matrix to the intermembrane space
- When pumping the H+ - pumping H+ against their natural concetration of protons (pumping from low to high)
- Creating form of energy by mitocodnira
F1/Fo ATPase
F1/Fo ATPase (ATP synthase ; aka complex 5) will use the gradeint to make ATP
- H+ gradient = energy created by the mitocondria
After the gradient is made – H+ will flow down the gradient back into the matrix using ATP synthase
- When the proton goes into the matrix –> ATP synthase uses the energy to generate ATP
H+ potential across the inner membrane us used for many other things
Byproduct of electron transport
ROS is a bypoduct of electron transport
- Because using Oxygen to make ATP = make ROS as a byproduct
- ROS = toxic
ROS needs to be taken care of with enzymes that will detoxify ROS
Mitochondria and disease
Since mitocondria are essnetial – if have defects in mitocondrial function -> get many types of human disease
Genrally mitochondrial diseases often first/primarily affect tissues with high energy (ATP) demands:
1. Skelatal and msucle disorders
2. Cardiomyopathies (affcets heart)
3. Metabolic Disorders (Ex. Diabetes)
- Liver and adipocutes are affceted in metabolism disorders
4. Neurodegernative disorders (Ex. Parkinsones + many types of blindness + ataxia and dystonia)
- Nuerons = high energy demand = get neurological disorders
Mitocondria + Cancer
Mitochondria play a role in tumorgenisis
Some types of cancer are associated with defects in mitochondrial activity
Example – Mutations in complex 2 cause pheochromocytoma (neuroendocrine tumor)
Mitocondria + Aging
Mitochondria may be the primary cause of aging
Decline in mitochondrial function may contribute to the aging process in the body
Use of the proton gradient
Product gradinet can be used to make ATP BUT it can also be used to trasnport moecules into the matrix
Examples:
1. Can import ADP and phosphate into matrix
2. Once make ATP –> ATP can be transported out
Mitocondria have many transporters to control metabolism –> THE TRANSPORT IS DRIVEN BY THE H+ GRADIENT
Carriers in Inner membrane
Since the mitocondria Inner membrane is imperbale (even to H+) –> many special carriers are needed to transport small molecules in and out of the matrix
Many carriers use the inner membrane potential:
1. Voltage gradient drives ADP-ATP exchange
2. pH gradient drives pyruvate import
3. pH gradient drives phosphate import
H+ gradient
H+ gradients = form of energy the mitocondria makes using the ETC
Answer – ALL OF THE ABOVE (mitocondria like most organelles do many things for the cell and are thus essential)
Compartments of the mitochondria
Compartments of the mitochondria – Have 4 compartments and 2 membranes
- Outer membrane
- Inner membrane
- Intermembrane Space
- Matrix
General method for isolating mitocondira and other organelles
General method for isolating mitochondria and other organelles = subcellular fractionation
- Break up cells or tissue mechanically (homogenize) –> now have the cytosol + organelles
- Use differential centrifugation –> spin down organelles based on size + density
- Low speed centrifuging = get big structure (ex. Nucleus)
- Increase the speed = get pellet with mitocondria + lysosomes + peroxisomes (intermeduate size density structures
- Spin at higher speed = get pellete with smaller structures (Ex. ER)
- If use ultra centrifugation = get pellete with protein complexes (Ex. Get ribosomes)
Using this people have isolated the mitocondria to study structure and function
Subceullar Fractionation on Mitocondria
Mitochondria = can be isolated by subcellular fractionation (aka differential centrifugation)
Mitochondria can be further fraction into outer membrane or inner membrane or inter membrane space or matrix
- Can study the compartments by separating them from isolated mitochondria
Mitocondrial Outer membrane
Outer membrane = has big pores = makes membrane permeable to small molecules and ions
- Phosphates + ATP + ADP = can go through the outer membrane BUT need to be transported across the inner membrane with transporters because the inner membrane is impermeable to these molecules
Pore in outer membrane
Porin creates pores in the outer membrane
Pore = allows small molecules (Ex. ATP + ADP + phosphates + sugars) to freely diffuse in/out across the outer membrane (don’t need a specific transporter)
- EXCEPTION = need trasnpoorters for proteins
Porin = type of beta barel protein
- Beta barel protein = also found in bacterial membrane (found in bacteria membrane + mitochondria membrane = links mitocondria and bacteria in orgin)
Mitocondria Intermembrane Space
Intermebrane space = between the the outer and inner membrane
Intermembrane space has very few proteins but does have Cytochrome C
Cytochrome C
Cytochrome C –> protein in the ETC machinery (moves between complexes 3 and 4)
Cyt C = controls life AND death of cells
- Life - Cyc C normally functions as a protein SU of ETC complex 4 –> part of the Oxydative Phosphorylation machinery that creates the H+ gradient and actually creates ATP = importnt for cells to live
- Death – when cells decide to die through apoptosis –> Cyt C is released from complex 4 and goes to the cytosol -> in the Cytosol Cyt C binds to regulator of apoptosis and induces apoptosis = cell dies
Depending on the condition of the cells Cyt C will function in ATP production or cell death
Mitocondrial Inner Membrane
Inner membrane has Oxidative Phosphorylation machinery
- Inner membrane Cardiolipin –> important for mitocondria function
Inner membrane = has big membrane area because of Cristae –> Area allows for a lot of transporters + oxidative phsophorylation machinery
Where is the ETC found
ETC complex (Oxidatative phosphorylation machinery) - found on the inner membrane
Mitocondria inner membrane carries the machinery for oxidative phosphorylation (ATP production)
5 complexes (made of of many proteins)
ATP synthase
Complex 5 = ATP synthase –> uses the gradient to create ATP from ADP and phosphate
- Once ATP is made (it will be in the matrix) –> ATP is transported to the intermembrane spoace and to the cytosol (goes to the cytosol through porins in the outer membrane)
Complex 1-4 = used to generate H+ gradient by pumping protons from the matrix to the intermembrabe space (Pumps H+ using NADH and FADH2 as teh energy source (because pumping against the gradient))
- Transporters transport ATP and ADP through the inner membrane using the H+ gradient
Mitocondria matrix
Matrix = inside inner membrane
Matrix has mtDNA
TCA cycle = happens in the matrix (has the enzymes for the TCA cycle)
- TCA = uses pyruvate as primary sugar source to create higher energy compounds (high energy compouds = makes NADH and FADH2) –> NADH and FADH2 = used to create proton gradient in ETC
- Pyruvate = sugar produced in glycolysis
mtDNA vs. nuclear DNA
mtDNA is different from nuclear DNA
- mtDNA uses different codons
- Example – Nuclear DNA uses AUA as isoleucine BUT mtDNA uses AUA for methionin
- Patterns are similar to the pattern of codons found in bacteria (Again suggest the link between mitochondria and and bacteria)
- Structure of mtDNA is different from nuclear DNA (Nuclear DNA = linear ; mtDNA is circular (similar to bacteria) )
What does mtDNA code for
mtDNA has 13 protein coding genes
- ALL genes code for SU for different ETC complexes
- Different species have different numbers of genes in mtDNA
MtDNA also codes for rRNA and rTNA for protein syntehsis for genes encoded in mtDNA (Have translation in matrix)
Mutation rate of mtDNA
mtDNA tends to have more mutations at an increased rate compared to nuclear DNA
Have more mutations because mtDNA have more ROS that can damage the DNA in the mitocondria AND because mitochondria have less efficient repair mechanisms for DNA damage
Diseases + mtDNA
Many diseases are caused by mutations in mtDNA (many diseases affect the mitochondria because of mutations in mtDNA)
Example:
1 . 1 – Leber’s hereditary optic neuropathy (LHON)
- Mutations in genes ND1,4, and 6 (SU in complex 1)
2. Myoclonic epilepsy with Ragged Red fiberes (affects muscles)
- Mutate the tRNA = creates defects in protein synthesis in the mitocondria
3. 3 – Neuropathy, ataxia, and retinitus pigmentosa (affects nervous system)
- Mutations in compelx 5 (ATP synthase)
These are types of disease caused by mtDNA defects BUT many mitochondria proteins are ALSO encoded in the nuclear genome (mutations in nuclear genoms encoding mitocondrial proteins can also lead to mitocondrial diseases)
mtDNA inheritnace
Have specific pattern of inheritance of mtDNA because mtDNA is only inherited in the oocyte (inherited from the mom)
- Get from mom because mitocondria and mtDNA are degraded once fertiization and fusion between the oocyte and sperm happens –> only maintain the mtDNA and mitocondira derived from the oocyte
- MEANS mutations in oocyte can be inherited BUT mutation in mtDNA in sperm is not = have a maternal inheritance pattern
Pedigre – shows 4 chidlren ate affected –> Son – does not pass to offspring BUT the daughteer can pass to offspring
2nd factor for mtDNA associated disease
2nd factor for mtDNA associated disease = mtDNA associated diseases are not 100% penetrance
- Not 100% penetrance because have lots of mtDNA (100s) in each cell –> depending on the ratio of mutant DNA to WT mtDNA the symptoms/outcomes can be different
Ex – even of the mom is affected –> the ratio between mutant mtDNA and WT mtDNA can chnage in each individual
- Each tissue can have diffrent ratio + the ratio can chnage over time
- MEANs not all offspring will have the disease even though the mom has a mutation (depending on the amount of mutant mtDNA you may or may not have the symptims)
Mouse model of mtDNA inheritance
Found that need over 60% of the mitocdonria to be mutated to see defected –> shows that the WT copy of mtDNA can be dominant
- Explains why there is heterogeneity in inheritance of mitocondrial diseases
Answer – False –> Cells often contain more than one type of mtDNA (called heteroplasmy). So, the ratio of mutated mtDNA to wild-type dictates whether you will have disease or not. Note, the ratio can change in different individuals, in different tissues of the same individual, and over time!