Cell Bio Exam 2 - Cellular Energetics Part 2

net equation for glycolysis

glucose + 2ADP + 2Pi + 2 NAD+

yields

2pyruvate + 2ATP + 2NADH + 2H+ + H20

2 ATP is net yield per glucose

where does glycolysis occur

cytoplasm

where does pyruvate oxidation occur

mito matrix

where does the CAC occur

mito matrix

where does ETC occur

inner mitochondrial membrane

stage one of aerobic oxidation - entry into mitochondria

• Glucose (in cytosol):

  • Converted to pyruvate via glycolysis.

• Fatty acids (in cytosol):

  • Activated to fatty acyl-CoA.

• Transport into mitochondria:

  • Outer membrane is porous due to mitochondrial porins.

  • Inner membrane requires specific transport proteins:

    • Pyruvate transport protein (yellow oval).

    • Fatty acid transport/carnitine shuttle system (blue oval).

  • Fatty acyl groups are temporarily transferred to carnitine → transported across inner membrane → reattached to CoA inside the matrix.

stage two of aerobic oxidation - Conversion to Acetyl-CoA & Citric Acid Cycle

• Pyruvate oxidation:

  • Pyruvate → acetyl-CoA + NADH + CO₂.

• Fatty acyl-CoA oxidation (β-oxidation):

  • Removes 2 carbons per cycle → acetyl-CoA, FADH₂, NADH.

• Citric Acid Cycle (TCA):

  • Acetyl-CoA fully oxidized.

  • Generates: NADH, FADH₂, GTP, CO₂.

stage three of aerobic oxidation - Electron Transport Chain (ETC)

• Location: Inner mitochondrial membrane.

• Process:

  • Electrons from NADH enter at Complex I → passed to Complex III → then to oxygen at Complex IV.

  • Electrons from FADH₂ (via succinate dehydrogenase, Complex II) → feed into Complex III (bypassing Complex I).

  • Protons (H⁺) are pumped from the matrix into the intermembrane space, creating the proton-motive force.

• End result: Oxygen is reduced to H₂O.

stage four of aerobic oxidation - ATP Synthesis (Oxidative Phosphorylation)

• ATP synthase (F₀F₁ complex):

  • Uses the proton-motive force to phosphorylate ADP → ATP.

• Transport across inner membrane:

  • Antiporters import ADP + Pi into the matrix.

  • Export ATP and hydroxyl groups out.

• NADH shuttles:

  • Cytosolic NADH cannot cross the inner membrane.

  • Special shuttle systems move its electrons into the matrix (e.g., malate-aspartate shuttle).

• Gas exchange:

  • O₂ diffuses in (final electron acceptor).

  • CO₂ diffuses out (from pyruvate oxidation & TCA cycle).

pyruvate dehydrogenase complex

bridge from glycolysis to CAC in aerobic conditions

otherwise pyruvate is fermented

• Pyruvate is actively transported into the mitochondria where it is decarboxylated:

  • Acetyl group transferred to coenzyme A → acetyl CoA  

  • NADH + H⁺ produced during process

  • Acetyl CoA  into Citric Acid cycle

  • CO₂ released

where does PDC occur

euk - mito

back and arc - cytosol

very exergonic process

CAC

completely oxidizes the 2-carbon acetyl group from acetyl-CoA to CO₂

9 steps + PDC

enzymes of cac

occur in mito matrix

one in inner mitomembrane - succinate dehydorgenase

4 redox reactions in CAC

3 - NAD+ reduced to NADH+H+ (steps 4,5,9)

1 - FAD reduced to FADH2 (step 7)

1 GTP generating reaction

• Step 5 (redox + formation of succinyl-CoA):
  α-Ketoglutarate is oxidatively decarboxylated to succinyl-CoA (high-energy thioester).

  • Enzyme: α-ketoglutarate dehydrogenase complex

  • Makes NADH and a high-energy CoA-thioester bond.

• Step 6 (use of that high energy):
  Succinyl-CoA is hydrolyzed; the energy released is used to attach Pi_ii​ to GDP → GTP.

  • Enzyme: Succinyl-CoA synthetase

  • This is the one and only GTP-producing step.

net equation from pyruvate through citric acid cycle

So per pyruvate: (1 + 3) NADH = 4 NADH, 1 FADH₂, 1 GTP, 3 CO₂.

• Pyruvate dehydrogenase (link step):
  Pyruvate → Acetyl-CoA + NADH + CO₂

• Citric Acid Cycle (per acetyl-CoA):
  3 NADH + 1 FADH₂ + 1 GTP + 2 CO₂

citric acid cycle yield

• The purpose of the Citric Acid cycle is not to yield large quantities of ATP.

• The Citric Acid cycle produces high energy carrier molecules (NADH and FADH₂) that will be used in subsequent steps during oxidative phosphorylation to produce ATP.

glycolysis and CAC overview

1. Glycolysis: glucose → use 2 atp and splits into 2 pyruvate (3c each); this yields 1 NADH and 2 ATP per pyruvate

2. Pyruvate decarb - pyruvate (3C)  conv to acetyl Coa (2C) by PDC; this yields 1 NADH and loses 1 CO2

3. CAC - 1 gtp, 3 NADH, 1 FADH2, loses 2 CO2

Energy generated by each pair of e transferred

• About 3 ATPs per pair from NADH generated in the mitochondria

• About 2 ATPs per pair FADH₂ generated in the mitochondria

• About 2 ATPs per pair shuttled from cytoplasmic NADH to mitochondrion using the glycerol-3-phosphate shuttle (brain)

• About 3 ATPs per pair shuttled from cytoplasmic NADH to mitochondrion using the malate-aspartate shuttle (heart and liver)

NADH shuttles

• Glycerol-3-phosphate shuttle (GPS) requires an energy cost; cytosolic NADH from glycolysis enters the respiratory chain as FADH2 in complex II

• Malate-aspartate shuttle (MAS) requires no additional energy cost; cytosolic NADH from glycolysis enters respiratory chain as NADH in complex I

malate aspartate shuttle

no energy cost bc it doesn't physically move nadh

It transfers the electrons from cytosolic NADH to matrix NAD⁺, regenerating cytosolic NAD⁺ so glycolysis can continue and supplying NADH for the electron transport chain.

• The inner mitochondrial membrane is impermeable to NADH/NAD⁺.

• The shuttle moves the reducing power (electrons) of cytosolic NADH into the matrix, so they can enter the electron-transport chain.

• Net effect:

  • Cytosolic NADH → NAD⁺

  • Matrix NAD⁺ → NADH

malate aspartate shuttle steps

Step 1 – Reduction of oxaloacetate in cytosol

• Enzyme: Cytosolic malate dehydrogenase

Step 2 – Malate import / α-ketoglutarate export

• Transporter: Malate–α-ketoglutarate antiporter (blue)

• Action: Malate enters the matrix as α-ketoglutarate leaves to the cytosol.

Step 3 – Re-oxidation of malate in matrix

• Enzyme: Mitochondrial malate dehydrogenase

Step 4 – Convert oxaloacetate → aspartate

• Enzyme: Transaminase in matrix
  (OAA can’t cross the inner membrane, but aspartate can.)

Step 5 – Aspartate export / glutamate import

• Transporter: Aspartate–glutamate antiporter (red)

• Action: Aspartate goes to cytosol; glutamate comes into matrix.

Step 6 – Regenerate oxaloacetate in cytosol

• Enzyme: Cytosolic transaminase
  (Completes the cycle and regenerates OAA for Step 1.)

CAC role of AA

can be used as source for ATP production - catabolic

can be produced- precursors made by CAC - anabolic

fats

highly reduced; lots of C and A

• Significant source of energy

• Stored as triglycerides 

• Fatty acids removed from glycerol and CoA attached to carboxyl end before beta ox

  • Occurs in cytoplasm

beta oxidation

breaks fatty acids → acetyl-CoA for CAC

2 carbon units removed from carboxyl end w each turn

major electron-carrying components of etc

1. Flavoproteins (FMN and FAD), which contain a nucleic acid derivative of riboflavin

2. Iron-sulfur proteins (Fe-S)

3. Heme (Iron Fe²⁺ metal cofactor)

4. Copper ions (Cu²⁺)

5. Ubiquinone (Coenzyme Q)

organization of etc

• Complex I – NADH:ubiquinone oxidoreductase

• Complex II – Succinate dehydrogenase

• Complex III – Cytochrome bc₁ complex

• Complex IV – Cytochrome c oxidase

complex 1

Accepts electrons from NADH → passes to Coenzyme Q (Q), pumps H⁺

complex 2

Accepts electrons from succinate (FADH₂) → passes to Q, no H⁺ pumping

complex 3

Transfers electrons from QH₂ to cytochrome c, pumps H⁺

complex 4

Transfers electrons from cytochrome c to O₂ → H₂O, pumps H⁺

Coupled proton pumping

Complexes I, III, IV pump H⁺ into the intermembrane space, generating the proton-motive force for ATP synthase.

The ETC is arranged

so electrons flow NADH → FMN/Fe–S → Q → cytochromes → O₂, following increasing redox potential. This downhill energy flow powers proton pumping and ultimately ATP synthesis.

three big free energy drops in etc

• Complexes I, III, and IV.

• At each, electrons flow to a more electronegative carrier, the carrier picks up H⁺ when reduced, and releases H⁺ when oxidized — protons are supplied from the matrix water.

• This is how electron flow is coupled to proton pumping and ATP production.

etc proton pumping

establishes proton gradient

establishes membrane potential (voltage diff) 

combination of these makes proton motive force

ATP synthase uses pmf to pull protons back in to make ATP.

skipping complexes

electrons can enter the electron-transport chain at different points depending on the source of reducing power

skipping c1

Happens whenever electrons come from FADH₂ rather than NADH:

skipping c2

Most common when electrons start as NADH

more normal, energy yielding route

electron affinity

decreases as we move down etc

substrate level phosphorylation

Direct energy input into ATP synthesis by transfer of a high energy phosphate bond to ADP to make ATP.

Mechanism of ATP synthesis by glycolysis and the Citric Acidcycle.

oxidative phosphorylation

Indirect energy input into ATP synthesis.  Direct energy input into rotational catalysis but no transfer of a high energy phosphate bond.  ADP + Pi phosphorylates in a spontaneous, energetically favorable manner. Mechanism of ATP synthesis by chemiosmosis powered from the electron transport chain. 

machinery for ATP formation

binding chain mechanism

• F₀ = proton channel in the inner membrane; cring

• F₁ = catalytic head in the matrix making ATP; binding chain

ATP synthase is molecular motor

machinery for ATP formation steps

1. proton enters c ring

2. arg210 displaced

3. adjacent proton exits

4. cring rotates

5. repeat

binding chain mech for ATP formation

• binding-change mechanism happens in the F₁ catalytic β subunits, not in the c-ring.

• As the c-ring turns (driven by proton flow), it rotates the central γ shaft.

• The rotating γ shaft forces the β subunits of F₁ to cycle through three conformations

O

open

releases ATP, binds ADP + Pi

L

loose

holds ADP + Pi

T

tight

catalyzes formation of ATP from ADP + Pi

Each 120° rotation of γ converts one β subunit from O → L → T and releases one ATP.

pmf plays role in

• ATP/ADP Translocator (adenine nucleotide translocase)

  • Exchanges matrix ATP⁴⁻ for cytosolic ADP³⁻.

  • Driven mostly by the membrane potential (ΔΨ): the matrix is negative, so export of more negatively charged ATP is favored if ΔΨ is intact.

• Phosphate (Pi) Transport

  • H₂PO₄⁻/H⁺ symporter uses the proton gradient: a proton moves down its gradient with Pi to pull phosphate into the matrix for ATP synthesis.

• Calcium Uptake

  • Mitochondrial Ca²⁺ uniporter depends on the negative matrix potential (ΔΨ); Ca²⁺ is pulled in by the electrical gradient.

• Protein Import into the Matrix

  • Preproteins cross via the TIM/TOM complexes.

  • PMF (especially ΔΨ) helps draw the positively charged presequences of proteins through the inner membrane.

pmf and respiration

“respiratory control” or “acceptor control.”

• The availability of ADP (which lets protons re-enter and make ATP) is the main signal:

  • High ADP → ATP synthase turns faster → PMF drops → ETC speeds up.

  • Low ADP (high ATP) → PMF builds → ETC slows.

Allosteric regulation of cytochrome c oxidase (Complex IV)

biochemical feedback loop: when ATP is plentiful, Complex IV slows electron flow even before the PMF gets extremely high; when ADP appears, the enzyme is more active.

if only glycolysis happened

2 atp 2 Nadh

complete oxidation but w glycerol 3 phosphate shuttle

36 atp

complete oxidation but w malate aspartate shuttle

38 atp

prok cells

38 ATP bc they don't need no shuttle ah