Unit 3: Mitochondria, Ribosomes and Peroxisomes

1. Mitochondria: Structure and Function

Mitochondria (singular: mitochondrion) are famously known as the "powerhouses" of the cell. They are the primary sites of ATP synthesis through cellular respiration.

Structure

Mitochondria have a unique double-membrane structure:

• Outer Membrane: A smooth membrane that is permeable to small molecules and ions.
• Intermembrane Space: The narrow region between the outer and inner membranes. H⁺ ions (protons) are pumped here during electron transport.
• Inner Membrane: A highly folded membrane. The folds are called cristae. This folding vastly increases the surface area.
  • Function of Cristae: The inner membrane is embedded with the proteins of the Electron Transport Chain (ETC) and the enzyme ATP synthase. This is where oxidative phosphorylation occurs.
• Matrix: The gel-like substance filling the innermost compartment. The matrix contains:
  • Mitochondrial DNA (mtDNA)
  • 70S Ribosomes
  • Enzymes for the Krebs Cycle (Citric Acid Cycle).

Function

The primary function is Cellular Respiration, the process of converting glucose and oxygen into ATP (energy).

1. Glycolysis (in cytoplasm): Glucose -> Pyruvate.
2. Krebs Cycle (in mitochondrial matrix): Pyruvate is fully oxidized to CO₂, producing high-energy electron carriers (NADH and FADH₂).
3. Oxidative Phosphorylation (on inner membrane/cristae):
   • Electron Transport Chain (ETC): Electrons from NADH and FADH₂ are passed down a chain of proteins, releasing energy. This energy is used to pump H⁺ ions into the intermembrane space.
   • Chemiosmosis: The H⁺ ions flow back into the matrix down their gradient, passing through ATP synthase. This flow powers ATP synthase, which generates large amounts of ATP from ADP and Pi.

2. Mitochondria: Semi-autonomous Nature

Mitochondria (along with chloroplasts in plants) are described as "semi-autonomous" because they retain some features of an independent organism.

They are "semi" (partially) autonomous, not fully, because they still depend on the cell's nucleus for most of their proteins.

Evidence for Semi-autonomy:

• Own DNA: They possess their own circular DNA (mtDNA), similar to a prokaryotic chromosome. This DNA codes for some mitochondrial proteins and RNAs.
• Own Ribosomes: They have their own 70S ribosomes (prokaryotic type), which are different from the 80S ribosomes in the cell's cytoplasm.
• Own Protein Synthesis: They can synthesize some of their own proteins using their mtDNA and 70S ribosomes.
• Self-Replication: They can grow and reproduce independently of the cell's division (mitosis/meiosis). They replicate by binary fission, just like bacteria.

3. Endosymbiotic Hypothesis

This theory, championed by Lynn Margulis, explains the origin of mitochondria and chloroplasts in eukaryotic cells. It provides a reason for their semi-autonomous nature.

Endosymbiotic Hypothesis: This theory proposes that mitochondria evolved from an aerobic prokaryote (bacterium) that was engulfed by a larger ancestral host cell (an early eukaryote). Instead of being digested, the bacterium formed a symbiotic relationship (an endosymbiosis) with the host.

The Process:

1. Engulfment: A large anaerobic host cell engulfed a small, aerobic bacterium.
2. Symbiosis: The host cell provided the bacterium with protection and nutrients. The bacterium, being aerobic, efficiently produced ATP (energy) for the host cell, which was a huge advantage in an increasingly oxygen-rich world.
3. Evolution: Over millions of years, the bacterium became the mitochondrion, and the host cell became the ancestor of all eukaryotic cells.

Evidence Supporting the Hypothesis:

This is a classic exam question. The evidence is simply the list of semi-autonomous features that resemble a prokaryote:

• Double Membrane: The inner membrane was the bacterium's original plasma membrane, and the outer membrane was derived from the host cell's vacuole membrane during engulfment.
• 70S Ribosomes: Identical in size and structure to prokaryotic ribosomes.
• Circular DNA: The mtDNA is circular and lacks histone proteins, just like a bacterial chromosome.
• Binary Fission: Mitochondria replicate by binary fission, the same method used by bacteria.

4. Ribosomes: Types, Structure, and Functions

Ribosomes are the "protein factories" of the cell. They are non-membranous organelles responsible for protein synthesis (translation).

Structure

• Ribosomes are composed of two main components: ribosomal RNA (rRNA) and proteins.
• They consist of two subunits: a Large Subunit and a Small Subunit. These subunits only come together during protein synthesis.

Types

Ribosome size is measured in Svedberg units (S), which measure sedimentation rate (not size or mass, which is why 50S + 30S does not equal 80S).

• Prokaryotic Ribosomes: 70S
  • Found in: Bacteria, Archaea, and also in the mitochondria and chloroplasts of eukaryotes.
  • Subunits: 50S (large) + 30S (small).
• Eukaryotic Ribosomes: 80S
  • Found in: The cytoplasm and on the Rough ER of eukaryotic cells.
  • Subunits: 60S (large) + 40S (small).

Functions

1. Translation: The primary function. The ribosome reads the genetic code on a messenger RNA (mRNA) molecule.
2. Peptide Bond Formation: The large subunit (specifically, the rRNA acting as a "ribozyme") catalyzes the formation of peptide bonds between amino acids, linking them into a polypeptide chain.
3. Binding Sites: The ribosome has binding sites for mRNA and transfer RNA (tRNA), which brings the correct amino acids.

5. Peroxisomes: Structure and Function

Peroxisomes are small, single-membrane-bound metabolic organelles.

Structure

• Small, spherical vesicles enclosed by a single membrane.
• Contain a dense, crystalline core of oxidative enzymes.
• They are not part of the endomembrane system (they don't bud from the Golgi) and are thought to replicate by budding/fission.

Function

Peroxisomes are involved in various oxidative reactions, primarily for detoxification and fatty acid breakdown.

1. Breakdown of Fatty Acids: They perform beta-oxidation of very-long-chain fatty acids, breaking them down into smaller molecules that can be sent to the mitochondria for fuel.
2. Detoxification: They contain enzymes (oxidases) that neutralize harmful substances (toxins) by transferring hydrogen from the toxins to oxygen, producing hydrogen peroxide (H₂O₂) as a byproduct.
   (e.g., R-H₂ + O₂ → R + H₂O₂)
3. Neutralizing Hydrogen Peroxide: H₂O₂ is itself toxic. Peroxisomes contain a high concentration of the enzyme catalase, which immediately breaks down the H₂O₂ into harmless water and oxygen.
   (2H₂O₂ → 2H₂O + O₂)
4. Example: Abundant in liver cells, where they detoxify alcohol and other harmful compounds.