Mitochondria, Chloroplasts, and Peroxisomes

How does Mitochondria generate energy?

breakdown of lipids and carbohydrates

How do chloroplasts generate ATP?

sunlight energy

Chloroplasts reduce power to synthesize carbohydrates from what molecules?

CO2 and H2O

Gibbs Free Energy

ability of work a system can do

Coupled Reactions

reactions that work together to drive energetically unfavorable processes. (A+C><B+D)

ATP

Adenosine 5’-triphosphate stores free energy in cells

Bonds between the Phosphates in ATP are?

High energy bonds

Mitochondria Structure

Double Membrane, Intermembrane space, Cristae, Matrix

Chloroplast vs Mitochondria Equivalent Spaces

• Stroma ↔ Matrix
  Both are the “main interior” where metabolic cycles occur.

• Thylakoid lumen ↔ Mitochondrial intermembrane space
  Both are proton‑accumulating spaces used to power ATP synthase.

• Outer/inner membranes match up
  Both organelles have a double membrane from their bacterial origins.

Mitochondrial Double Membrane System

Inner Membrane: Electron Transport Chain (ADP→ATP)

Both: Impermeable to ions, separated by inner membrane space

Outer Membrane: Has porins to facilitate passages, transporters and other proteins

Mitochondria Energy Production

Oxidative carboxylation of Glucose and Fatty Acids

The Citric Acid Cycle (TCA/Krebs Cycle)

Oxidative Phosphorylation

Energy yielding reactions (G<0)

within the cell are coupled to ATP Synthesis

Energy requiring reactions (G>0)

Are coupled to ATP hydrolysis

The complete oxidative breakdown of glucose to CO2 and H20 yields a large amount of free energy

Delta G= -686 kcal/mol

Glycolysis in the first stage

-In cytosol (nothing to do w/ mitochondria)

-Net yield= 2ATP, pyruvate, and 2NADH

-NAD+ (electron aceptor) converted to NADH

Glycolysis

What goes in

• Glucose

• 2 ATP (investment)

• 2 NAD⁺

What comes out

• 2 pyruvate

• 4 ATP (net gain of 2 ATP)

• 2 NADH

Where does it go from there

• Pyruvate → mitochondria for the citric acid cycle (if oxygen is present)

• Pyruvate → lactate in anaerobic conditions

• NADH → electron transport chain (aerobic)

Pyruvate

What goes in

• Pyruvate (from glycolysis)

What comes out

• With oxygen:

  • Acetyl‑CoA

  • CO₂

  • NADH

Where does it go from there

• Acetyl‑CoA → citric acid cycle in the mitochondria

• NADH → electron transport chain (aerobic)

Citric Acid Cycle Yield

Per pyruvate (glucose molecule):

1 ATP

3NADH

1 FADH2

How many pyruvate do you get per glucose?

Two pyruvate molecules are produced per molecule of glucose during glycolysis.

Where is Fatty Acid Oxidation reaction taking place?

Mitochondria Matrix

Fatty Acid Oxidation

CoA-SH directly interacts with fatty acid

Each Cycle yeilds:

1 Acetyl-CoA

1 FADH2

1 NADH

ATP Production via Oxidative Phosphorylation

Stage 1: Generation of a proton gradient by electron transfer through the electron transport chain.

Stage 2: ATP synthesis by proton flow down its gradient though ATP synthase

ADP+P=

ATP

Energy for adding the phosphate to ADP comes from:

proton gradient

Both chemical (H+ gradient) and electric gradients go from

High positively charged to low positively charged

ATP is produced in

Matrix

Where is the electron transport chain located ?

Inner membrane of Mitochondria

Chemiosmotic Coupling

What goes in

• NADH & FADH₂ (electron donors)

• O₂ (final electron acceptor)

• Protons pumped across membrane

• ADP + Pi

What comes out

• Proton gradient (H⁺ gradient)

• ATP (via ATP synthase)

• H₂O

• Regenerated NAD⁺ & FAD

Where it goes from there

• ATP → used for cellular work

• NAD⁺ & FAD → return to glycolysis / pyruvate oxidation / TCA cycle

• H₂O → stays in the matrix

Complex I (ETC)

• Accepts electrons from NADH

• Transfers those electrons into the ETC

• Pumps protons (H⁺) from the matrix to the intermembrane space

• Helps create the proton gradient that drives ATP synthase

Complex II (ETC)

• Accepts electrons from FADH₂

• Passes electrons into the ETC (but does NOT pump protons)

• Contributes to the proton gradient indirectly

Complex III (ETC)

• Accepts electrons from Complex I & II (via ubiquinone)

• Pumps protons (H⁺) into the intermembrane space

• Passes electrons to cytochrome c

Complex IV (ETC)

• Accepts electrons from cytochrome c

• Transfers electrons to O₂, forming H₂O

• Pumps protons (H⁺)

• Final step that strengthens the proton gradient for ATP synthase

ATP Synthase (Complex V) (ETC)

What it does

• Uses the proton gradient created by Complexes I–IV

• Lets protons flow back into the matrix through its channel

• Converts ADP + Pi → ATP

Why it matters

• Makes the majority of ATP in aerobic respiration

Things needed to know about Electron Transport Chain

-Electrons are transferred to complex III by Coenzyme Q (ubiquinone)

-Cytochrome c then carries electrons to complex IV (cytochrome oxidase) where they are transferred to O2

What is the result of the Electron Transport Chain (ETC)

-ATP

-H2O

Electrochemical Gradient

High proton concentration

(+)charge intermembrane (low proton concentration)

(-)charge matrix moves through ATP synthesis

ATP synthesis

-ATP is generated as protons move

-1 place to move through (ATP synthesis Complex)

ATP synthase consists of two components

1: Fo: where protons pass from intermembrane to matrix

2: F1: (spins) Adding P onto ADP to get ATP

what is the conformational change happening in ATP synthesis?

F1 turning allowing P and ADP molecules to alight in grooves to be added to make ATP which is then released.

What kind of ribosomes would mitochondrial genes be translated on?

Free ribosomes

Proteins encoded by nuclear genes include:

-Complex II

-RNA pol

-DNA pol

Mitochondrial Genomes

-Circular (prokaryotes)

Mitochondrial Genome Genes

-Making tRNAs

-Making Ribosomes- rRNA

-Complex I, III, IV proteins

-ATP synthase

proteins encoated by nuclear genes include

– Complex two

– RNA polymerase

– DNA polymerase

The outer mitochondrial membrane

Highly permeable to small molecules

porins

Proteins and membrane allowing molecules in and out (transporters)

The composition of the inner membrane space is similar to what

cytosol

what cannot easily flow through the outer membrane?

Protons

pre-sequence dependent import

– Proteins are targeted to matrix (have to get through two membranes)

– pre-sequences buying to receptors on the mitochondria (outer membrane)

– Proteins are then transferred to another complex in the inner membrane( from tom to tim)

where does chaperones bind for pre-sequence dependent import?

cytosol

Confirmational change of chaperones

What:

Chaperones (e.g., Hsp70) change shape when ATP is used during mitochondrial protein import.

Why:

This helps pull the protein into the mitochondria and prevents it from folding too early.

Result:

The protein is successfully imported and can function in mitochondrial ATP production.

what happens to proteins when ATP is hydrolyzed?

Confirmational change:

What:

When ATP is hydrolyzed, the chaperone undergoes a conformational change and tightly binds the protein.

Why:

This stabilizes the unfolded protein and helps move it through the mitochondrial membrane.

Result:

The protein is pulled further into the mitochondria for proper import and folding.

protein translocation

– Driven by electrochemical gradient

– Proteins must be unfolded

– pre-sequences are cleaved by matrix processing peptides

– Polypeptide is bound by other HSP 70 chaperones

pre-sequence independent translocation (no pre sequence)