Mitochondria

Similarities between eukaryotic and prokaryotic cells

both have cell membrane, cytoplasm, and DNA

Differences between eukaryotic and prokaryotic cells

-Prokaryotes don’t have mitochondria, nucleus, chloroplasts

-Eukaryotes are more advances and have organelles

Mitochondria and Chloroplasts similarities

both involved in converting energy from one form to another

-both only present in eukaryotic cells

-both have multiple layers of membranes filled with enzymes

Similarities between mitochondria/chloroplasts to bacteria

-Contain their own DNA, have the ability to replicate and make RNA/protein

-Their DNAS are circular and its sequence resembles that of bacteria

-The DNA lacks histones/ribosomes (like in bacteria)

-Mitochondria and Chloroplasts undergo fission (which is how bacteria divide)

How is mitochondria inherited

Maternally inherited

What does mitochondria do

cellular respiration (produces chemical energy (ATP) from food)

What is mitochondria comprised of

outer membrane, inner membrane (has lots of folding), matrix, intermembrane space

How does mitochondria adapt to meet energy demand

-Size depends on the cell and its energy demand

-Mostly located in the cytosol where energy demand is highest

-Number of mitochondria increase with increasing energy demand

Additional functions of mitochondria

Calcium regulation, cell death, antiviral actions, regulation of stem cells

What’s mitochrondria fission

The process by which mitochondria divides (similar to bacteria)

What is mitochondrial fusion

Mitochondria fuse together so that damaged and healthy mitochrondria and mix

What are cristae and what do they do

They are inner membrane folds that increase surface area which allows for more ATP to be produced by the ETC

What do porins do and where are they found

Found in the outer membrane and they allow passage of water, pyruvate, and other small molecules into the intermembrane space

Does inner membrane have porins and why

No, because it has proteins of ETC, ATP Synthase, and pumps to move soluted in and out of the matrix

Is the inner membrane permeable and why

IMpermeable because of its unique lipid composition

What does the matrix contain a lot of and what are they used for

Contains lots of proteins making it viscous and they are used in the citric acid cycle to generate ATP

What does matrix contain in addition to proteins

DNA and ribosomes (MT has about 37 genes but around 1000 proteins that are synthesized by nuclear DNA)

What lipids are a part of mitochondria

Phosphatidylcholine and Cardiolipin

Where does mitochondria get its lipids

the ER

What is outer membrane lipid composition similar to

Plasma membrane

What happens to some of the imported lipids in mitochondria

It gets converted to cardiolipin

Whats cardiolipin

A phospholipid with 4 hydrophobic tails which helps make inner membrane impermeable

How much cardiolipin in inner and outer membranes

Makes up 20% of lipid in the inner membrane, None in outer membrane

What is mitochondrial fussion stimulated by

energy demand/stress

What does mitochondial fission do

generates new organelles and facilitates quality control

Mitochondrial encephalomytopathy with lactic acidosis and stroke-like episodes (MELAS)

caused by mutations in several mitochondrial genes

affects brain and muscles

Myoclonic epilepsy with ragged-red fibers (MERRF)

caused by mutations in several mitochondrial genes

affects brain and muscles

Leigh syndrome

caused by mutations in several mitochondrial genes

affects brain and spinal cord

Kearns Sayre syndrome

caused by deletions/rearrangements in mtDNA

Affects brain, spinal cord, eyes, and muscles

Alpers syndrome

caused by mutations in the POLG gene (polymerase gamma), which functions to replicate/maintain mtDNA

affects brain, spinal cord, and muscles

Aging related diseases like ALS, Alzheimer’s, cancer metabolic disorders, loss of muscle function

caused by epigenetic modifications (mutations/methylation changes) that alter expression of MT genes, ATP production, and calcium storage

What do high-energy electrons from NADH and FADH2 do

drive oxidative phosphorylation of ADP → ATP

Inner mitochondria membrane role in oxidative phosphorylation

Acts as an energy device that converts the high energy of electrons stored in NADH and FADH into phosphate bond of ATP

What does oxidative phosphorylation involve

consumption of O2 and additions of a phosphate group to ADP to form ATP

Where does ETC take place

inner membrane

How do NADH and FADH2 transfer electrons to ETC

through oxidizing other molecules

What do electrons pass through in the ETC and what happens when they pass

They pass through a series of electron acceptor/donor molecules that form the chain.

Electrons fall to successively lower energy states as they pass through the chain

What is the energy released from electrons passing through the chain used for

It drives H+ ions (protons) across the membrane into the intermembrane space from the matrix

What does driving protons across the membrane do

generates a transmembrane gradient of protons that serve as a source of energy for phosphorylation of ADP to generate ATP

What happens at the end of the electron transport chain

electrons are added to O2 molecules, which combines with H+ to produce H2O

How does ETC begin

the remove of a hydride ion (a hydrogen atom w/extra electron) from NADH or FADH2

What happens to hydride ion when it is removed from NADH or FADH2

Enters ETC and the NADH dehydrogenase complex where it is converted into a proton and 2 high-energy electrons

What does removal of high-energy electrons from NADH and FADH2 do

Creates NAD+ and FAD which can be reduced again in the citric acid cycle

What does NADH dehydrogenase complex do

catalyzes the reaction of hydride ion (H-) into a proton and 2 electrons

Ubiquionone

a small hydrophobic molecule in the bilayer that carries electrons/donates them (doesn’t generate protons)

Cytochrome C

carry electrons/donates them (doesn’t generate protons)

What are the 3 complexes in ETC (in order)

(1) NADH dehydrogenase complex (2) Cytochrome c reductase complex (3) cytochrome c oxidase complex)

What do all 3 complexes in ETC have

Each possesses metal ions and chemical groups that form a pathway for electrons through the enzyme

LEO goes GER

Lose electron → oxidation

Gain electron → reduction

What does oxidized ubiquinone do

Receives electrons from the NADH dehydrogenase complex (or directly from FADH2) and then picks up protons from the aqueous enviornment

What does reduced ubiquinone do

Passes electrons and protons to the cytochrome c reductase complex

What does cytochrome c reductase complex do

pumps protons into the intermembrane space and passes on the electrons to cytochrome c

Why might certain cells have abundant inner membranes

Because they are more active and may need more energy (like muscle cells)

What’s the total electrochemical gradient of H+ across the IMM

-large force due to membrane potential

-small force due to H+ concentration gradient

what’s proton-motive force

the role of membrane potential + pH gradient that adds to the driving force pulling H+ across the membrane (low pH to high pH) = electrochemical gradient

Essential requirements for harnessing ATP energy

(1) membrane containing a series of electron carriers (ETC), a pump protein, and ATP synthase

(2) pump harnesses energy of electron trasnfer to pump protons and creates proton gradient across membrane

(3) source of high-energy electrons (e-) derived from the oxidation of food

What does the proton gradient do

Serves as an energy store and is used to drive the synthesis of ATP by the ATP synthase

Stage 1 of chemiosmosis

High-energy electron passing through proton pump drives proton across IMM AGAISNT its gradient

Concentration of proton gradient created by proton pumping in the intermembrane versus matrix

High concentration of protons in the intermembrane space (pH = 7.2) than the matrix (pH = 7.9)

Stage 2 of chemiosmosis

Electrochemical H+ gradient drives protons through ATP synthase which phosphorylates ADP to ATP

Whats Chemiosmotic coupling

ATP production (chemi) is brought about by transport across a membrane (osmosis)

Batteries and chemical reactions

Chemiosmotic mechanisms allow cell to harness energy of electron transfer in the same way energy stored in batteries can be harnessed to do smth

Energy of electrons from NADH

enough to pump protons across IMM at 3 places

Energy of electrons from FADH2

donated to ubiquinone and have enough energy to pump protons across IMM at 2 places

How does proton gradient lead to generation of ATP

ATP synthase forms pathway for protons across the IMM and the protons pumped through ATP synthase by the electrochemical proton gradient provide energy to phosphorylate ADP to ATP

What is ATP synthase composed of

head portion (F1 ATPase) and transmembrane H+ carrier (F0 Rotor) → both are multi-subunit complexes

How much ATP can ATP synthase produce per second

100 (3 molecules of ATP per revolution)

What does it mean if ATP synthase is a reversible coupling device

ATP can convert energy of electrochemical proton gradient into chemical-bond energy, and vice versa meaning that it can (1) synthesize ATP w/H+ gradient or (2) pump protons against electrochemical gradient by hydrolyzing ATP to make ADP depending on which direction the rotation goes

Steps in which ATP synthase converts mechanical energy to chemical energy

(1) Proton flow to the stroma turns the rotor

(2) ATP synthase head has 3 subunits that each consist of an alpha and beta subunit, where ADP + Pi bind to an active site

(3) Rotation of the central stalk changes the conformation of the proteins in the head → phosphorylates ADP to ATP

(4) ATP is released, and the process is repeated

If IMM is impermeable, how are molecules transported in/out of the matrix

pumps and transporters

How does pyruvate/protons enter matrix

Symport

How do phosphate and protons enter matrix

symport

How does ADP enter the matrix and ATP exit

antiport

What drives the import of pyruvate and Pi

electrochemical gradient of H+

What does pump out of ATP and pump in of ADP (ADP-ATP exchange) depend on

voltage gradient across membrane (membrane potential)

The ADP-ATP exhcange moves on negative charge out of the mitochondrion

Can you separate proton generation from ATP production

Yes, with uncoupling agents which are H+ carriers that can insert into the IMM

How does uncoupling occur naturally in some specialized fat cells (brown fat cells)

Most of the energy from oxidation is dissipated as heat rather than converted to ATP

What’s special of IMM of brown fat cells

contain special transport protein that allows protons to move across (important in protecting sensitive areas of newborns from the cold)

What do uncoupling agents do

prevent ATP from being made

what’s 2, 4-dinitrophenol (DNP)

an uncoupling agent that causes the inner membrane to be permeable to protons, allowing H+ flow into mitochondrion without passing thru ATP synthase → ATP is not made

Use of DNP for weight loss

Highly toxic, small amounts were given, effective in melting away pounds (especially loss of fat reserves), patients had elevated temps and sweated a lot during treatment

With each of the 3 respiratory enzyme complexes, where do electrons mainly move

between metal atoms that are tightly bound to the proteins

What carries electrons between different complexes

electron carriers which are molecules that diffuse along the lipid bilayer

Quinones

only electron carriers in ETC that function without being tightly bound to a protein

How does long hydrophobic tail affect ubiquinone

It confines ubiquinone to the membrane

Where is cytochrome c held

Held loosely on the outer face of the inner membrane by ionic interaction

How many amino acids does cytochrome c contain

just over 100

What makes up cytochrome c

a iron atom in the bound heme group can carry a single electron

What does heme group in hemoglobin do

reversibly binds O2 rather than electron

How can you demonstrate proton gradients power ATP production

When bacteriorhodopsin is added to artificial vesicle, protein generates proton gradient in response to light

What happens in artificial vesicles containing both bacteriorhodopsin and ATP synthase

proton gradient drives formation of ATP

What happens if theres either only bacteriorhodopsin or only ATP synthase

No ATP generated

What happens in uncoupling agent is also there with bacteriorhodopsin and ATP synthase

uncoupling agent abolishes gradient and stops ATP synthesis

How does proton go from one side to another

NADH dehydrogenase complex picks up proton from one side of membrane when it accepts eelctron from NADH, and then it releases the proton to the other side of the membrane when it donates the electron to ubiquinone

What is cytochrome oxidase

protein complex that receives electrons from cytochrome c and donates it to O2

What is cytochrome oxidase composed of

Subunits I and II

What is present at active site of cytochrome oxidase where O2 is bound i

Cytochrome oxidase contains complex of a heme iron atom juxtaposed with tightly bound copper atom

How can conformational change in a protein pump driven by an energetically favorable reaction cause H+ pumping

Proteins, like NADH dehydrogenase or cytochrome oxidase, are driven through a cycle of 3 conformations (A, B, C)

A and B have a high affinity for H+, so it picks H+ up

C has low affinity for H+, so it releases H+

The transition from B to C is energetically unfavorable and needs to be coupled to a favorable reaction (aka electron transport)