Module 1: Mitochondria, Respiration, Chloroplast

Mitochondrion

• site of aerobic respiration

• produces most of the cell’s ATP via ETC and oxidative phosphorylation

• uses glucose and fatty acids as fuel

• abundant in high energy cells

Mitochondria Organization

1. Outer Mitochondrial Membrane

   • contains porins

   • allows free passage of all molecules

2. Inner Mitochondrial Membrane

   • folded into cristae which increases surface area

   • contains the ETC and ATP synthesis for ATP production

Anaerobic Fermentation

• occurs without oxygen

• no ETC

• low ATP yield

• partial breakdown of glucose

Aerobic Respiration

• requires oxygen

• involves complete oxidation of glucose via glycolysis and ETC

• high ATP yield

• more efficient at producing energy

Cellular Respiration

• process where electrons flow through membranes to external electron acceptor

• this results in complete oxidation of substrates and ATP production

• requires co-enzymes like FAD, coenzyme Q

Types of Cellular Respiration

1. Aerobic Respiration

   • oxygen is the terminal electron acceptor

   • oxygen is reduced to water

   • yields high amounts of ATP

2. Anaerobic Respiration

   • used by bacteria and archaea

   • uses non-oxygen electron acceptors

   • yields less ATP than aerobic respiration

Aerobic Respiration vs Fermentation

Aerobic Respiration:

• occurs in mitochondria (eukaryotes), plasma membrane and cytoplasm (prokaryotes)

• oxygen is final electron acceptor in ETC

• allows re-oxidation of NADH and FADH2

• produces 36-38 ATP per glucose

• highly efficient

Fermentation:

• occurs in the cytoplasm

• does not use oxygen or the ETC

• relies only on glycolysis → 2 ATP per glucose

• produces waste product like lactate or ethanol

Key Functions of the Mitchondria

1. Citric Acid Cycle (Krebs Cycle)

   • oxidizes glucose derived molecules

   • produces NADH and FADH2 for ETC

2. ETC

   • transfers electrons to oxygen, forming water

   • builds proton gradient across the inner mitochondrial membrane

3. Oxidative Phosphorylation

   • ATP synthase uses the proton gradient to synthesize ATP

     • support for the endosymbiotic theory: double membrane, circular DNA, bacterial-like ribosomes

     • found in all aerobic eukaryotic cells

Mitochondrial Structure

• traditionally viewed as numerous, oval shaped organelles, based on electron microscopy

• EM only captures thin slices, misrepresenting larger structures

• Hoffman and Avers proposed that these profiles may be parts of a single, branched, interconnected mitochondrion

• modern evidence supports that mitochondria can form dynamic networks, not just isolated units

Internal Structure of Mitochondria

• inner membrane encloses the mitochondrial matrix

• matrix is site of key metabolic pathways: krebs cycle and fatty acid oxidation

• contains: circular mitochondrial DNA and ribosomes

• while mitochondrial DNA encodes some RNAs and proteins, most mitochondrial proteins are made from nuclear DNA and imported into the organelle

Mitochondrial Membranes and Compartments

1. Outer Mitochondrial Membrane

   • contains porins (protein channels)

   • freely permeable to small solutes, ions and metabolites

   • makes the inter-membrane space chemically similar to the cytosol

2. Intermembrane Space

   • space between the inner and outer membrane

   • contains proteins involved in ETC, apoptosis and metabolite exchange

   • similar to cytosol due to porins, but includes selectively transported proteins

3. Inner Mitochondrial Membrane

   • impermeable to most solutes

   • requires specific transport proteins

   • 75% protein by weight

   • critical for solute transport and ETC

   2 regions of IMM:

   • Inner Boundary Membrane:

     • faces the inter membrane space

     • contains transporters for metabolite and ion exchange between cytosol and matrix

   • Cristae:

     • deep infoldings into the matrix

     • increases surface area for maximum ATP production

     • house ETC complex, ATP synthase and oxidative phosphorylation

Mitochondrial Matrix

• semifluid matrix

• site of metabolic processes

Contains:

• mitochondrial DNA: encodes few mitochondrial proteins

• ribosomes: protein synthesis

- Most mitochondrial proteins are encoded by nuclear DNA, synthesized in the cytoplasm, and imported into the mitochondria

Cristae

• increases surface area of inner mitochondrial membrane

• tubular and stacked structure for optimal efficiency

• maximizes space for ETC complexes and ATP synthase

• creates intracristal spaces where hydrogen ions accumulate during ETC

• connected to inner boundary membrane via crista junctions (small openings that regulate molecule flow)

• cristaes are more densely packed in high energy cells

Nuclei and mitochondria are similar in that they both ___. 

1. Have double membranes

2. Contain DNA

3. Contain ribosomal RNA molecules

4. Contain proteins

5. All of the above

1. All of the above

Where do mitochondrial functions occur?

• found on cristae, infolding of the mitochondrial membrane

• cells with high energy needs contain larger number of mitochondria

• mitochondria cluster in regions where ATP demand is highest, ensuring efficient energy supply

Localization of Major Functions

Glycolysis

• cytoplasm (outside mitochondria)

Pyruvate Oxidation

• mitochondrial matrix

Citric Acid Cycle

• mitochondrial matrix

Fatty Acid/Amino Acid Catabolism

• mitochondrial matrix

ETC

• inner mitochondrial membrane

ATP Synthesis

• inner mitochondrial membrane

Stages of Cellular Respiration

Stage 1 – Glycolysis (Cytoplasm):

• Glucose → 2 Pyruvate

• Produces: 2 ATP (net), 2 NADH

Stage 2 – Pyruvate Oxidation (Matrix):

• Pyruvate → Acetyl-CoA + CO₂ + NADH

Stage 3 – Citric Acid Cycle (Matrix):

• Acetyl-CoA → CO₂, NADH, FADH₂, small amount of ATP (or GTP)

Stage 4 – Electron Transport Chain (Inner Membrane):

• NADH & FADH₂ transfer electrons → O₂ (final acceptor)

• Protons (H⁺) are pumped into the intermembrane space

Stage 5 – ATP Synthesis via Proton Gradient (Inner Membrane):

• ATP synthase uses the proton motive force to convert ADP + Pi → ATP

ATP Generation During Respiration

• the key connection between ETC and ATP synthase is the electrochemical proton gradient

• this gradient is known as proton motive force (PMF)

• protons are actively pumped across the inner mitochondrial membrane into the inter-membrane space

FoF₁ ATP Synthase Complex

F1 Complex:

• located in the mitochondrial matrix

• contains catalytic sites where ATP is synthesized

• connected to Fo by a protein stalk

Fo Complex:

• embedded in the inner mitochondrial matrix

• forms a proton channel

• allows hydrogen ions to re enter the matrix own their gradient

How it Works:

• proton flow through Fo causes rotation and conformational change in F1

• this mechanical energy is used to synthesize ATP from ADP and Pi

During aerobic respiration starting with glucose, which chemical would be the greatest surprise to produce?

1. Pyruvate

2. Adenine

3. ATP

4. NADH

5. Acetyl CoA

1. Adenine

Chloroplasts

• plastids found in plant cells

• large sized and shape varies

• photosynthetic organelle

• composed of outer membrane and 2 inner membranes separated by inter membrane space

• the inner membrane encloses the stroma, gel like matrix

• thylakoid is flat, saclike structures found in stroma

• they enclose a single continuous compartment, thylakoid lumen

• grana are thylakoids arranged in stacks

• Chromoplasts:

  • pigment containing plastids, responsible for the coloration of flowers, fruits and other plant parts

• Amyloplast:

  • specialized for storage of starches

Photosynthesis

the conversion of light energy to chemical energy and
its subsequent use in synthesis of organic molecules

Phototrophs

organisms that convert solar energy into chemical energy as ATP and reduced coenzymes

Two Biochemical Processes in Photosynthesis

1. Energy Transduction Reactions

   • light reactions

   • light energy is captured and converted into chemical energy

2. Carbon Assimilation Reactions

   • carbon fixation reactions

   • carbohydrates are formed from co2 and h2o

3 Stages of Calvin Cycle

1. Carboxylation:

   • of ribulose-1,5-biphosphate and generation of two 3-phosphoglycerate molecules

2. Reduction:

   • of 3-phosphoglycerate into glyceraldehyde-3-phosphate

3. Regeneration:

   • of original acceptor to allow continued carbon assimilation

Energy Transduction Reactions

1A. LIGHT HARVESTING

• Light energy is captured by chlorophyll in photosystems (PSII and PSI) in the thylakoid membrane.

• Photoexcitation: A photon excites an electron in chlorophyll → electron is transferred to the electron transport system (ETS).

• Photosystems include:

  • Chlorophyll

  • Accessory pigments

  • Chlorophyll-binding proteins

  • ETS proteins

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1B. NADPH Synthesis (Photoreduction)

• Electrons flow: PSII → cytochrome b6f → PSI → ferredoxin → NADP⁺

• Final product: NADPH

  • NADPH is used in anabolic processes (e.g., carbon fixation).

• Proton gradient is created as electrons flow → protons pumped into the thylakoid lumen.

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1C. ATP Synthesis (Photophosphorylation)

• Proton gradient powers ATP synthase (CF₀CF₁ complex).

• Location: Thylakoid membrane

• Protons flow back into the stroma via ATP synthase → ATP is produced.

• ATP is essential for the Calvin cycle (carbon fixation).

Carbon Assimilation Reactions

These reactions occur after the light-dependent reactions and are responsible for:

• Fixing carbon dioxide (CO₂) into organic molecules using the ATP and NADPH produced during light reactions.

• Occur in the stroma of chloroplasts.

• Do not require light directly, so they are often called light-independent reactions or the Calvin Cycle.

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Key Purpose:

• Convert inorganic CO₂ → organic carbon compounds, ultimately forming:

  • Glucose

  • Sucrose – the main transport sugar in most plants

  • Starch – the main storage carbohydrate in plants

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2A. The Calvin Cycle

• Main cycle for carbon fixation in plants

• Occurs in the stroma of chloroplasts

• Requires ATP and NADPH from the light reactions

• Begins with CO₂ entering the leaf through stomata

• CO₂ diffuses into mesophyll cells and reaches the stroma

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Summary of Calvin Cycle Reactions:

1. Carbon Fixation – CO₂ is attached to a 5-carbon sugar (RuBP)

2. Reduction – ATP and NADPH reduce the fixed carbon to G3P

3. Regeneration – RuBP is regenerated to continue the cycle