cell 10

Glycolysis

Stage 1 of aerobic respiration, in the cytosol: a 6-carbon sugar is split and oxidized into two 3-carbon molecules

Pyruvate oxidation

Stage 2 of aerobic respiration, in the mitochondrial matrix: each 3-carbon end product of glycolysis loses one carbon as CO₂ and becomes the 2-carbon acetyl CoA

Citric acid cycle

Stage 3 of aerobic respiration, in the mitochondrial matrix: acetyl CoA is completely oxidized to CO₂

Electron transport

Stage 4 of aerobic respiration, in the inner mitochondrial membrane: electrons pass from NADH/FADH₂ to O₂ while protons are pumped out of the matrix

Oxidative phosphorylation

Stage 5 of aerobic respiration: protons flow back into the matrix through ATP synthase, and that flow drives ATP production

It continuously reoxidizes NADH and other reduced coenzymes (regenerating NAD⁺ and FAD)

Besides letting pyruvate be fully oxidized to CO₂, what does having O₂ as the terminal electron acceptor do that keeps the earlier pathways running?

Outer mitochondrial membrane

Mitochondrial membrane that is freely permeable to small molecules, so the space it borders is chemically similar to the cytosol

Porins

Channels in the outer mitochondrial membrane that let solutes up to about 5000 daltons pass through

About 75% protein by weight

Composition of the inner mitochondrial membrane, reflecting its many transporters, ETC complexes and ATP synthase

It contains no cholesterol

Feature of the inner mitochondrial membrane's lipid makeup that makes it very fluid

Cristae

Infoldings of the inner mitochondrial membrane that increase surface area for electron transport; cells with high metabolic activity have more of them

Lamellar (flat, layered) or tubular

The two arrangements that the infoldings of the inner mitochondrial membrane can adopt

Crista junctions

Small openings linking the inner-membrane infoldings to the inner boundary membrane, limiting exchange so the infoldings act as semi-separate spaces

Intracristal space

The space inside an infolding of the inner mitochondrial membrane; a local region where pumped protons can accumulate

Transit sequence

Targeting signal on the N-terminus of a nuclear-encoded polypeptide that directs it to the mitochondrion

N-terminus

End of a polypeptide where the mitochondrial targeting signal is located

TOM (translocase of the outer membrane)

Protein-import complex in the outer mitochondrial membrane that forms a channel and carries the receptor that first recognizes an incoming polypeptide

TIM (translocase of the inner membrane)

Protein-import complex forming the channel through the inner mitochondrial membrane into the matrix

Transit sequence receptor

Component of the outer-membrane import complex that recognizes and binds the targeting signal of an incoming polypeptide

Chaperone proteins (Hsp70, Hsp60)

Proteins that keep a polypeptide headed for the mitochondrion unfolded for transport and then help it fold afterward

Transit peptidase

Enzyme in the mitochondrial matrix that cuts off the targeting signal from an imported polypeptide once it arrives

Cytosolic Hsp70 binds the new polypeptide and keeps it unfolded

Step 1 of importing a nuclear-encoded protein into the mitochondrial matrix (Figure 10.4)

The transit sequence binds the TOM receptor

Step 2 of importing a nuclear-encoded protein into the mitochondrial matrix (Figure 10.4)

Hsp70 is released (ATP hydrolyzed) as the chain threads through the TOM and TIM pores

Step 3 of importing a nuclear-encoded protein into the mitochondrial matrix (Figure 10.4)

Transit peptidase removes the transit sequence as soon as it reaches the matrix

Step 4 of importing a nuclear-encoded protein into the mitochondrial matrix (Figure 10.4)

Mitochondrial Hsp70 binds and releases the chain as it enters (using ATP), pulling it in

Step 5 of importing a nuclear-encoded protein into the mitochondrial matrix (Figure 10.4)

Mitochondrial Hsp60 helps the polypeptide fold into its final shape

Step 6 (final step) of importing a nuclear-encoded protein into the mitochondrial matrix (Figure 10.4)

Cytosolic Hsp70

Chaperone that keeps a mitochondrial protein unfolded before import

Mitochondrial Hsp70

Chaperone that binds a polypeptide as it enters the mitochondrial matrix

Hsp60

Chaperone that helps an imported mitochondrial protein fold at the end of import

ATP synthase

The combined FoF1 complex (membrane-embedded Fo plus knob-like F1) that makes most of the ATP in mitochondria and bacteria

Tricarboxylic acid (TCA) cycle and Krebs cycle

Two other names for the citric acid cycle

Pyruvate + CoA–SH + NAD⁺ → acetyl CoA + CO₂ + NADH

Overall reaction catalyzed by the pyruvate dehydrogenase complex (PDH) in the matrix, an oxidative decarboxylation

Pantothenic acid

B vitamin contained in coenzyme A

Sulfhydryl (–SH) group

Group on coenzyme A that links to acetate through a high-energy thioester bond, making CoA a good acetate carrier

Acetyl CoA (2C) + oxaloacetate (4C) → citrate (6C)

Citric acid cycle step CAC-1 (reaction, with carbon counts)

Citrate → isocitrate

Citric acid cycle step CAC-2 (reaction)

Isocitrate → (oxalosuccinate) → α-ketoglutarate (5C)

Citric acid cycle step CAC-3, the first oxidative decarboxylation (reaction)

α-ketoglutarate → succinyl CoA (4C)

Citric acid cycle step CAC-4, the second oxidative decarboxylation (reaction)

Succinyl CoA → succinate

Citric acid cycle step CAC-5, the only step that directly makes GTP/ATP (reaction)

Succinate → fumarate

Citric acid cycle step CAC-6, where electrons go to FAD (reaction)

Fumarate + H₂O → malate

Citric acid cycle step CAC-7, a hydration (reaction)

Malate → oxaloacetate

Citric acid cycle step CAC-8, which regenerates the 4-carbon starting acceptor (reaction)

FAD

Lower-energy electron acceptor used at CAC-6 because oxidizing succinate doesn't release enough energy to reduce NAD⁺

Two electrons and two protons

What FAD accepts in order to become FADH₂

Less ATP than NADH, because its electrons enter the ETC at a lower-energy point

How the ATP yield of FADH₂ electrons compares to NADH electrons, and why

Products inhibit, substrates activate

General logic of citric acid cycle regulation

Slow down

What high NADH, ATP or acetyl CoA signals to the citric acid cycle ("energy is plentiful")

Speed up

What high NAD⁺, ADP or AMP signals to the citric acid cycle ("energy is needed")

Covalent modification (phosphorylation)

Second layer of control on PDH beyond allosteric regulation, needed because PDH decides how much acetyl CoA enters the citric acid cycle

PDH kinase

Enzyme that adds a phosphate to PDH, inactivating it when the [ATP]/[ADP] ratio is high

PDH phosphatase

Enzyme that removes the phosphate from PDH, activating it when the [ATP]/[ADP] ratio is low

Inactive (off)

State of PDH when it is phosphorylated

Citric acid cycle

Main route for aerobic energy metabolism of fats and proteins, not just sugar

Peptidases

Enzymes that finish digesting the small peptides left after proteolysis

Endopeptidases

Peptide-digesting enzymes that cut internal peptide bonds

Exopeptidases

Peptide-digesting enzymes that remove amino acids one at a time from the ends of a peptide

Amphibolic

Term for a pathway, like the citric acid cycle, that serves both breakdown (catabolism) and synthesis (anabolism)

Flavoproteins, iron-sulfur proteins, cytochromes, copper-containing cytochromes, coenzyme Q

The five kinds of electron carriers in the electron transport chain

Flavoproteins and coenzyme Q

The only ETC carriers that move protons as well as electrons

Iron-sulfur proteins and cytochromes

ETC carriers that move electrons only, no protons

It picks up protons on the matrix side, diffuses across the membrane, and releases them on the other side

How coenzyme Q contributes to proton pumping

4

Protons pumped per electron pair by Complex I (NADH → CoQ)

0

Protons pumped per electron pair by Complex II (succinate → FADH₂ → CoQ)

4 (via the Q cycle)

Protons pumped per electron pair by Complex III (CoQH₂ → cytochrome c)

2

Protons pumped per electron pair by Complex IV (cytochrome c → O₂)

Its electrons enter at CoQ and bypass Complex I, so 6 protons are pumped instead of 10

Why FADH₂ gives less ATP than NADH (in terms of the respiratory complexes)

Cyanide and azide

Poisons lethal to aerobic cells because they bind the Fe-Cu center of Complex IV (cytochrome c oxidase) and block electron flow to oxygen

Superoxide (O₂⁻) and hydrogen peroxide (H₂O₂)

Reactive oxygen species formed when Complexes I and III leak electrons directly to O₂, reducing it only partially

They damage cells and contribute to aging

Effects of the reactive oxygen species formed by partial reduction of O₂ at Complexes I and III

Mobile (they diffuse within the inner membrane)

Property of the respiratory complexes shown by freeze-fracture studies in an electric field

Glycolysis, pyruvate oxidation and the citric acid cycle

Pathways during which coenzymes are reduced, before they are reoxidized by passing electrons to O₂

Electrochemical proton gradient

What the energy released by passing electrons from reduced coenzymes to O₂ is used to build, which in turn drives ATP synthesis

Oxidative phosphorylation

ATP synthesis driven by a proton gradient that is linked to oxygen-dependent electron transport

Chemiosmotic model (Peter Mitchell, 1961)

Model, and who proposed it and when, explaining how electron transport is coupled to ATP synthesis

Chemiosmotic model

States that electron transport pumps protons across a membrane, creating an electrochemical potential (not a high-energy chemical intermediate) that links electron transport to ATP formation

Membrane potential

The "electro" component of the proton gradient: a charge difference across the membrane

Concentration difference (pH difference)

The "chemo" component of the proton gradient

An artificial pH gradient makes ATP with no electron transport

Most direct evidence for the chemiosmotic model, showing the gradient alone is sufficient

10 protons

Number pumped when 2 electrons pass from NADH to O₂

6 protons

Number pumped when 2 electrons pass from FADH₂ to O₂

3 ATP

Traditional ATP yield per NADH used in the slides

2 ATP

Traditional ATP yield per FADH₂ used in the slides

Submitochondrial particles

Small vesicles Racker made by breaking up mitochondria, which could still carry out both electron transport and ATP synthesis

Shaking or protease treatment, then centrifugation

How Racker stripped the F₁ knobs off and separated them from the membranes

Electron transport, but not ATP synthesis

What Racker's stripped membranes (F₁ removed) could still do

Hydrolyze ATP (ATPase activity)

The only activity Racker's isolated F₁ particles showed; they could neither transport electrons nor make ATP

An enzyme catalyzes a reaction in both directions

Why an ATPase is a candidate ATP synthase

Both electron transport and ATP synthesis were restored

Result when Racker added isolated F₁ particles back to the stripped membranes

Coupling factor

Name given to F₁ after Racker's reconstitution experiments showed it restores ATP synthesis

Fo

Part of ATP synthase embedded in the inner membrane

F₁

Part of ATP synthase that projects into the matrix

10 c subunits (c₁₀ ring)

Subunits of Fo that rotate like a gear, 1/10 of a turn per proton

α₃β₃ catalytic ring

Part of F₁ where ATP is actually made

1 γ + 1 ε

F₁ subunits that rotate, forming the central stalk fixed to the c ring

c₁₀ ring + γ + ε

The rotor of ATP synthase (the parts that move)

a + b₂ + δ + α₃β₃

The stator of ATP synthase (the parts that stay put)

γ subunit

The subunit that actually rotates inside the catalytic ring of ATP synthase

2 ATP + 2 NADH (4–6 ATP from coenzymes) = 6–8 ATP

Glycolysis contribution to the ATP tally per glucose (range depends on the shuttle carrying cytosolic NADH electrons in)

2 NADH = 6 ATP

Pyruvate → acetyl CoA (×2) contribution to the ATP tally per glucose