VCE Biology Unit 3 Notes

VCE Biology Unit 3, Area of Study 1: How Cells Maintain Life

Section 1: The Blueprint of Life: From DNA to Protein

This section provides a comprehensive exploration of the molecules and processes that convert genetic information into functional proteins, forming the absolute foundation of molecular biology.

1.1 The Information Molecules: A Comparative Analysis of DNA and RNA

At the heart of cellular function are nucleic acids, macromolecules that encode and transmit the instructions for life. The two primary types, DNA and RNA, work in a coordinated fashion to ensure the faithful synthesis of proteins.

1.1.1 DNA (Deoxyribonucleic Acid): The Master Blueprint

Deoxyribonucleic acid, or DNA, is the molecule of inheritance. It contains the complete set of genetic instructions—the genome—required for the development, functioning, and reproduction of all known living organisms.

Structure and Composition: DNA is a polymer composed of repeating monomer units called nucleotides. Each DNA nucleotide consists of three components: a five-carbon deoxyribose sugar, a phosphate group, and one of four nitrogenous bases. The molecule is famously structured as a double helix, with two polynucleotide strands running antiparallel to each other, meaning they are oriented in opposite directions. The sugar and phosphate groups of adjacent nucleotides are linked by strong covalent phosphodiester bonds, forming a stable sugar-phosphate backbone for each strand.
Nitrogenous Bases: The four bases in DNA are categorised into two groups based on their chemical structure. Adenine (A) and Guanine (G) are purines, which have a double-ring structure. Cytosine (C) and Thymine (T) are pyrimidines, which have a single-ring structure.
Complementary Base Pairing: The two strands of the double helix are held together by weaker hydrogen bonds formed between specific base pairs. Adenine always pairs with Thymine via two hydrogen bonds, while Guanine always pairs with Cytosine via three hydrogen bonds. This strict A-T and G-C pairing rule is known as complementary base pairing and is fundamental to DNA’s ability to replicate and be transcribed accurately.

1.1.2 RNA (Ribonucleic Acid): The Versatile Messenger and Worker

Ribonucleic acid, or RNA, is a more transient and versatile nucleic acid that acts as the essential intermediary between the DNA blueprint and the protein-synthesis machinery of the cell.

Structure and Composition: Like DNA, RNA is a polymer of nucleotides. However, an RNA nucleotide contains a ribose sugar instead of deoxyribose, and it is typically a single-stranded molecule.
Nitrogenous Bases: RNA contains Adenine, Guanine, and Cytosine, but it uses Uracil (U), another pyrimidine, in place of Thymine. During transcription, Adenine in the DNA template pairs with Uracil in the forming RNA strand.

1.1.3 The Three Main Forms of RNA

RNA exists in several forms, each with a specialised role in the process of gene expression. The three main types are:

Messenger RNA (mRNA): This is a linear RNA molecule that serves as a temporary copy of a gene. It is synthesised during transcription in the nucleus (of eukaryotes) and carries the genetic “message” out to the ribosomes in the cytoplasm, where it dictates the amino acid sequence of a protein.
Transfer RNA (tRNA): This molecule functions as a molecular adaptor. It has a unique, folded three-dimensional structure often described as a “cloverleaf”. At one end, it has a three-base anticodon that is complementary to a specific mRNA codon. At the other end, it carries the corresponding amino acid. The role of tRNA is to read the mRNA codons and deliver the correct amino acids to the ribosome for incorporation into the growing polypeptide chain.
Ribosomal RNA (rRNA): This is the most abundant type of RNA and is a primary structural and catalytic component of ribosomes. Within the ribosome, rRNA helps to correctly position the mRNA and tRNA molecules and catalyses the formation of peptide bonds that link the amino acids together.

The distinct structural features of DNA and RNA are not arbitrary; they are intrinsically linked to their different biological roles. DNA’s double-helix structure and the chemical nature of its deoxyribose sugar make it exceptionally stable and resistant to degradation. This stability is paramount for its function as a permanent, reliable, long-term archive of an organism’s entire genetic blueprint, which must be preserved with high fidelity across generations. In contrast, RNA’s single-stranded nature and the presence of the more reactive ribose sugar make it less stable and more susceptible to being broken down. This transient quality is advantageous for its role as a temporary, disposable “work order.” The cell requires these messages to be short-lived so that it can dynamically control protein production in response to changing needs, preventing the wasteful or harmful accumulation of proteins that are no longer required. This fundamental principle—that molecular structure dictates biological function—is a recurring theme throughout biology.

1.2 Anatomy of a Gene and The Genetic Code

A gene is not merely a continuous stretch of protein-coding DNA. It is a complex functional unit comprising both coding and non-coding regulatory sequences that work in concert to control its expression.

1.2.1 The Structure of a Gene

Promoter: This is a specific, non-coding DNA sequence located upstream (at the 5′ end) of the gene’s coding region. It functions as the recognition and binding site for the enzyme RNA polymerase, thereby initiating the process of transcription. It effectively acts as the gene’s “on” switch. In eukaryotic promoters, a common sequence element is the TATA box.
Operator: This is a short segment of DNA that serves as a binding site for a repressor protein. In prokaryotic systems like the trp operon, the operator is typically located near or overlapping the promoter. When a repressor protein is bound to the operator, it physically blocks RNA polymerase from transcribing the gene, acting as a regulatory “off” switch.
Exons and Introns: Eukaryotic genes have a fragmented structure. Exons are the expressed sequences; they contain the information that is ultimately translated into a protein. Introns are intervening, non-coding sequences that are found between the exons. While introns are transcribed along with exons into a primary RNA transcript (pre-mRNA), they are removed during a later processing step and are not part of the final, mature mRNA that is translated. Prokaryotic genes are typically continuous and lack introns.

1.2.2 The Genetic Code

The genetic code is the set of rules the cell uses to translate the information encoded in the nucleotide sequence of an mRNA molecule into the amino acid sequence of a protein. It has several key properties:

Triplet Code: The code is read in non-overlapping groups of three consecutive bases, known as codons. Each codon specifies either a particular amino acid or a signal to stop translation.
Degenerate (or Redundant): There are 4³=64 possible codons but only 20 common amino acids are used in protein synthesis. This means that most amino acids are specified by more than one codon.
Unambiguous: The code is not ambiguous. While an amino acid may have multiple codons, each individual codon specifies only one particular amino acid.
Universal: The genetic code is virtually identical in all known forms of life, from bacteria and archaea to plants and animals. This universality is powerful evidence for the common ancestry of all life on Earth.

The degeneracy of the genetic code is not a flaw but a highly evolved feature that provides a crucial buffer against the potentially damaging effects of mutations. Furthermore, the existence of introns and exons in eukaryotes is the foundation for a mechanism of profound importance called alternative splicing. By combining different sets of exons from the same pre-mRNA transcript, a single gene can generate multiple, distinct mature mRNA molecules. Each of these mRNAs is then translated into a different protein isoform, each with a potentially unique function. This process is a primary driver of organismal complexity.

1.3 The Central Dogma in Action: Gene Expression

Gene expression is the process by which the genetic information stored in DNA is used to synthesise a functional gene product, such as a protein. This fundamental process, often summarised as the “central dogma” of molecular biology, occurs in a series of discrete steps.

1.3.1 Step 1: Transcription (in the Nucleus of Eukaryotes)

Transcription is the synthesis of an RNA molecule from a DNA template.

Initiation: The process begins when the enzyme RNA polymerase binds to the promoter region of a gene. This binding causes the DNA double helix in that region to unwind and the two strands to separate.
Elongation: RNA polymerase moves along the template strand and synthesises a complementary molecule of pre-mRNA in the 5′ to 3′ direction by adding free RNA nucleotides.
Termination: RNA polymerase continues until it reaches a termination sequence. This signal causes the polymerase to detach from the DNA, releasing the newly synthesised pre-mRNA transcript.

1.3.2 Step 2: RNA Processing (Post-transcriptional Modification in Eukaryotes)

In eukaryotic cells, the initial pre-mRNA transcript must undergo several modifications within the nucleus to become a mature mRNA molecule.

Capping: A modified guanine nucleotide, called a 5′ methylguanosine cap, is added to the 5′ end of the pre-mRNA. This cap protects the mRNA from degradation and acts as a recognition signal for the ribosome.
Polyadenylation: A long chain of 50-250 adenine nucleotides, known as the poly-A tail, is added to the 3′ end. This tail increases stability and facilitates export from the nucleus.
Splicing: A large molecular complex called a spliceosome removes non-coding introns and joins the remaining exons together to form a continuous coding sequence.

1.3.3 Step 3: Translation (at the Ribosome in the Cytoplasm)

Translation is the process of protein synthesis, where the genetic information encoded in the mature mRNA is used to build a polypeptide chain.

Initiation: The mRNA binds to a ribosome, which scans for the START codon (almost always AUG). An initiator tRNA molecule carrying Methionine binds to the start codon.
Elongation: The ribosome moves along the mRNA one codon at a time. For each codon, a specific tRNA delivers the corresponding amino acid. The ribosome catalyses the formation of a peptide bond between the amino acids.
Termination: Elongation continues until the ribosome encounters a STOP codon (UAA, UAG, or UGA). Release factors bind to the stop codon, causing the completed polypeptide chain to be released.

The physical separation of transcription (nucleus) and translation (cytoplasm) in eukaryotes is what necessitates and permits RNA processing. This separation is a key evolutionary milestone that allows for complex gene regulation mechanisms like alternative splicing, paving the way for the generation of a vastly more complex proteome and the evolution of multicellular organisms.

1.4 Controlling the Flow: Gene Regulation via the trp Operon

Cells must precisely control which proteins are synthesised and when. In prokaryotes, a common method of regulation involves operons.

1.4.1 The Operon Model

An operon is a cluster of genes with related functions that are transcribed together as a single mRNA molecule and are controlled by a single promoter and operator region. This allows for coordinated gene expression.

1.4.2 The trp Operon: A Repressible System

The trp operon in E. coli is a classic example of a repressible operon, meaning it is usually “on” but can be turned “off”. It contains five structural genes for synthesising the amino acid tryptophan.

Components: Structural Genes (trpE, D, C, B, A), Promoter, Operator, and a Regulatory Gene (trpR) that codes for a repressor protein in an inactive state.
Scenario 1: Tryptophan is ABSENT (Operon is ON): The repressor protein is inactive and cannot bind to the operator. RNA polymerase is free to transcribe the structural genes, and the cell produces enzymes to synthesise its own tryptophan.
Scenario 2: Tryptophan is PRESENT (Operon is OFF): Tryptophan acts as a corepressor, binding to the repressor protein and activating it. The active repressor-tryptophan complex binds to the operator, physically blocking RNA polymerase and preventing transcription. The pathway is switched off.

The trp operon is a quintessential example of a negative feedback loop. The end product (tryptophan) inhibits the expression of the genes responsible for its own production. This self-regulating mechanism allows the bacterium to maintain homeostasis with remarkable efficiency.

1.5 The Architecture of Function: Protein Structure

Proteins’ incredible range of functions is a direct consequence of their complex and specific three-dimensional structures, which are built up in a hierarchical manner.

1.5.1 Amino Acids: The Monomers

The fundamental building blocks of all proteins are amino acids. Each has a central carbon atom bonded to an amino group (–NH₂), a carboxyl group (–COOH), a hydrogen atom (–H), and a variable R-group (or side chain). The R-group’s unique chemical nature determines the amino acid’s properties.

1.5.2 The Hierarchical Levels of Protein Structure

Primary (1°) Structure: The unique, linear sequence of amino acids in a polypeptide chain, joined by covalent peptide bonds. This sequence is determined by the gene.
Secondary (2°) Structure: Initial, localised folding of the polypeptide chain into regular, repeating patterns due to hydrogen bonds in the backbone. Common structures are the α-helix and the β-pleated sheet.
Tertiary (3°) Structure: The overall, complex, and specific three-dimensional shape of a single polypeptide chain, driven by interactions between the R-groups (hydrogen bonds, ionic bonds, hydrophobic interactions, disulfide bridges). This structure is critical for function.
Quaternary (4°) Structure: Applies only to proteins with two or more polypeptide chains (subunits). It describes how these subunits are arranged and interact to form a single, functional protein complex (e.g., haemoglobin).

The primary structure is the ultimate determinant of the protein’s final shape. A change in a single amino acid can have catastrophic effects. For example, in sickle-cell anaemia, a single amino acid substitution in haemoglobin alters its tertiary and quaternary structure, causing the protein to clump and distort red blood cells into a “sickle” shape. This provides a powerful link between a change in a gene, a change in protein structure, and a resulting disease state.

1.6 The Proteome and its Diversity

While the genome is an organism’s complete set of genetic instructions, the proteome is the entire set of proteins expressed by a cell, tissue, or organism at a particular time and under specific conditions.

1.6.1 The Dynamic Nature of the Proteome

An organism’s genome is relatively static, but its proteome is highly dynamic and variable. The set of proteins in a cell changes based on its developmental stage, function, and response to environmental signals. For example, a muscle cell and a pancreatic cell have the same genome but vastly different proteomes.

1.6.2 The Functional Diversity of Proteins

Proteins are the “workhorses” of the cell, with diverse functions:

Enzymes: Biological catalysts (e.g., amylase, DNA polymerase).
Structural Proteins: Provide support and shape (e.g., keratin, collagen).
Transport Proteins: Carry substances (e.g., haemoglobin).
Hormones: Chemical messengers (e.g., insulin).
Immunological Proteins: Part of the immune system (e.g., antibodies).
Contractile Proteins: Responsible for movement (e.g., actin, myosin).

1.7 The Cellular Export System: The Protein Secretory Pathway

Proteins destined for export from the cell (secretion), insertion into membranes, or delivery to specific organelles follow a specialised endomembrane system known as the protein secretory pathway.

Rough Endoplasmic Reticulum (RER): Synthesis begins on a ribosome attached to the RER. The polypeptide is threaded into the RER lumen, where it folds and may undergo glycosylation (addition of carbohydrate chains).
Transport Vesicles: The protein is enclosed in a transport vesicle that buds off from the RER.
Golgi Apparatus (Golgi Complex): The vesicle fuses with the cis face of the Golgi. The protein moves through the Golgi stack, undergoing further modification, sorting, and packaging.
Secretory Vesicles and Exocytosis: At the trans face, the finished protein is packaged into a secretory vesicle. This vesicle moves to the plasma membrane and fuses with it, releasing the protein outside the cell in a process called exocytosis.

The protein secretory pathway is a masterful example of compartmentalisation in eukaryotic cells. By confining proteins within the endomembrane system, the cell creates specialised environments for modification and ensures orderly transport, preventing cellular chaos. Failures in this pathway can lead to diseases like cystic fibrosis.

VCE Biology Unit 3, Area of Study 2: Biochemical Pathway Regulation

Within every living cell, a constant and highly organised series of chemical reactions occurs, collectively known as metabolism. This intricate network of reactions is the very essence of life, responsible for converting energy, building complex structures, and breaking down waste. Metabolism is broadly divided into two types of processes.

Anabolic pathways are those that construct complex molecules from simpler ones, a process that requires an input of energy and is therefore described as endergonic.
Catabolic pathways involve the breakdown of complex molecules into simpler units, a process that releases energy and is thus described as exergonic.

These metabolic processes are organised into highly regulated, multi-step sequences called biochemical pathways. In these pathways, the product of one chemical reaction becomes the starting material, or substrate, for the next reaction in the sequence. Each step is catalysed by a specific enzyme, allowing the cell to precisely manage the flow of matter and energy through the entire pathway.

Section 1: The Engines of Life: Enzymes and Their Function

At the heart of every biochemical pathway are enzymes, the master regulators and facilitators of cellular chemistry. Without these remarkable molecules, the reactions necessary to sustain life would occur too slowly to be of any use.

1.1 The Nature of Enzymes as Biological Catalysts

Enzymes are typically large, globular proteins that function as biological catalysts. A catalyst is a substance that significantly increases the rate of a chemical reaction without being chemically altered or consumed in the process. Within the enzyme’s complex structure is a specific region known as the active site. The active site is a small pocket or cleft with a shape and chemical environment that is precisely complementary to the molecule(s) it acts upon, which are called the substrates.

1.2 The Energy Hurdle: Activation Energy

For any chemical reaction to proceed, the reactant molecules must first overcome an energy barrier. This initial energy investment, required to break existing chemical bonds and initiate the reaction, is called the activation energy (E_a). The primary function of an enzyme is to lower the activation energy required for the reaction to begin. By binding to the substrate, the enzyme stabilises the transition state, effectively reducing the height of the energy hill and dramatically accelerating the reaction rate.

1.3 The Modern View: The Induced-Fit Model of Enzyme Action

The currently accepted model is the induced-fit model. This model posits that the active site is not rigid but flexible. The initial binding of the substrate induces a subtle change in the three-dimensional shape (conformation) of the enzyme’s active site. This conformational change allows the active site to mould around the substrate, creating a more precise and stronger binding arrangement. This induced fit places physical strain on the substrate molecule, weakening its chemical bonds and making it more reactive, thus lowering the activation energy.

1.4 Factors Affecting Enzyme Activity

Temperature: As temperature increases, reaction rate increases up to an optimal temperature. Beyond this point, high temperatures disrupt the bonds maintaining the enzyme’s tertiary structure, causing it to denature—a permanent change to the active site that renders it non-functional.
pH: Each enzyme has an optimal pH. Deviations from this optimum can alter the charges on amino acids in the active site, disrupting substrate binding. Extreme pH changes can cause irreversible denaturation.
Substrate and Enzyme Concentration: Increasing substrate concentration increases the reaction rate until the enzyme becomes saturated (all active sites are occupied). At this point, the rate reaches its maximum velocity (V_max) and is limited by how fast the enzyme can process the substrate.

1.5 Regulating the Engines: Enzyme Inhibition

Cells control enzyme activity primarily through inhibition.

Competitive Inhibition: A competitive inhibitor is a molecule with a structure similar to the substrate. It binds to the active site, physically blocking the substrate. This type of inhibition can be overcome by increasing the substrate concentration.
Non-competitive Inhibition: A non-competitive inhibitor binds to a different location on the enzyme called an allosteric site. This binding changes the overall shape of the enzyme, altering the active site so it can no longer bind the substrate. This cannot be overcome by adding more substrate.

This mechanism is fundamental to cellular regulation through feedback inhibition. In this system, the final product of a pathway acts as a non-competitive inhibitor for an enzyme that functions early in the pathway. When the product concentration is high, it shuts down its own production line, preventing wasteful overproduction and maintaining homeostasis.

Section 2: The Currency and Couriers: Coenzymes

Enzymes often require assistance from small, non-protein helper molecules. Coenzymes act as critical shuttles, transferring energy and chemical groups between reactions.

2.1 Defining Cofactors and Coenzymes

A cofactor is a broad term for any non-protein chemical compound or ion required for an enzyme’s activity. Coenzymes are a specific subset of cofactors; they are organic, non-protein molecules that bind temporarily to an enzyme to assist in a reaction, often acting as carriers. Many are synthesised from vitamins.

2.2 The Coenzyme Cycle: Transferring Energy and Electrons

Coenzymes are continuously cycled between a high-energy, loaded state and a low-energy, unloaded state.

ATP (Adenosine Triphosphate): The universal energy currency. When hydrolysed to ADP (Adenosine Diphosphate) and inorganic phosphate (P_i), it releases energy to power cellular processes.
NADH and FADH₂: Central to cellular respiration. Their unloaded forms, NAD⁺ and FAD, accept high-energy electrons and protons during the breakdown of glucose to become “loaded” into NADH and FADH₂. They then transport this energy to the electron transport chain.
NADPH: The primary electron carrier in photosynthesis. Its unloaded form, NADP⁺, accepts high-energy electrons during the light-dependent reactions to become loaded into NADPH, which provides the reducing power for the Calvin cycle.

Table 1: Key Coenzymes in Metabolism
Coenzyme	Unloaded Form	Loaded Form	Primary Process
Adenosine Triphosphate	ADP + P_i	ATP	Universal energy currency for all cellular processes
Nicotinamide Adenine Dinucleotide	NAD⁺	NADH	Cellular Respiration (electron carrier)
Flavin Adenine Dinucleotide	FAD	FADH₂	Cellular Respiration (electron carrier)
Nicotinamide Adenine Dinucleotide Phosphate	NADP⁺	NADPH	Photosynthesis (electron carrier)

Section 3: The Photosynthesis Pathway: Building with Light

Photosynthesis is the quintessential anabolic pathway that converts light energy into chemical energy stored in the bonds of glucose. It is the foundation of nearly all ecosystems on Earth.

3.1 The Factory Floor: Chloroplast Structure and Function

In eukaryotes, photosynthesis occurs in the chloroplast. Its structure is perfectly adapted to its function.

Double Membrane: Encloses the chloroplast. Its presence, along with circular DNA and ribosomes, is evidence for the endosymbiotic theory.
Thylakoids and Grana: Thylakoids are flattened membranous sacs containing chlorophyll and the machinery for the light-dependent reactions. They are often arranged in stacks called grana, which increases the surface area for light absorption.
Stroma: The dense, fluid-filled space surrounding the grana. It contains the enzymes (like RuBisCO) for the light-independent reactions.

3.2 Stage 1: The Light-Dependent Reactions (in the Thylakoid Membranes)

This stage converts light energy into chemical energy (ATP and NADPH).

Inputs: Light Energy, Water (H₂O), ADP + P_i, NADP⁺
Process:
1. Light energy is absorbed by chlorophyll, exciting electrons.
2. Light energy splits water (photolysis) into electrons, protons (H⁺), and oxygen gas (O₂).
3. High-energy electrons are passed along an electron transport chain (ETC).
4. Energy from the ETC is used to pump protons into the thylakoid lumen, creating a proton gradient.
5. Protons flow back into the stroma through ATP synthase, driving the synthesis of ATP.
6. At the end of the chain, electrons and protons are accepted by NADP⁺ to form NADPH.
Outputs: Oxygen (O₂), ATP, NADPH

3.3 Stage 2: The Light-Independent Reactions / Calvin Cycle (in the Stroma)

This cyclical pathway uses the chemical energy from ATP and NADPH to fix inorganic CO₂ into organic molecules.

Inputs: Carbon Dioxide (CO₂), ATP, NADPH
Process (Calvin Cycle):
1. Carbon Fixation: The enzyme RuBisCO attaches one molecule of CO₂ to a five-carbon sugar (RuBP).
2. Reduction: Energy from ATP and electrons from NADPH are used to convert the resulting molecules into a three-carbon sugar (G3P).
3. Regeneration: For every six G3P molecules created, one exits the cycle to synthesise glucose and other organic compounds. The other five are used to regenerate the starting RuBP, a process that requires more ATP.
Outputs: Glucose (C₆H₁₂O₆), ADP + P_i, NADP⁺

3.4 The RuBisCO Dilemma and Plant Adaptations

The enzyme RuBisCO is inefficient and can bind to O₂ instead of CO₂, initiating a wasteful process called photorespiration. This is worse in hot, dry conditions when plants close their stomata. Some plants have evolved adaptations to overcome this.

C4 Plant Adaptation: Plants like maize use a highly efficient enzyme (PEP carboxylase) to initially fix CO₂ in outer cells. This fixed carbon is then transported to deeper cells where it releases the CO₂, creating a high concentration around RuBisCO and preventing photorespiration. This is a spatial separation of processes.
CAM Plant Adaptation: Desert plants like cacti use a temporal separation. They open their stomata at night to fix CO₂ into organic acids. During the day, with stomata closed, these acids release CO₂ for the Calvin cycle, ensuring a high concentration around RuBisCO while conserving water.

3.5 Factors Affecting the Rate of Photosynthesis

The rate is determined by the factor in shortest supply (Law of Limiting Factors).

Light Intensity: Rate increases with intensity until a plateau is reached (light saturation point).
Carbon Dioxide Concentration: Rate increases with concentration until limited by another factor.
Temperature: Rate increases to an optimum, then rapidly declines as enzymes denature.
Water Availability: Lack of water causes stomata to close, which severely limits CO₂ intake, reducing the overall rate.

Table 2: Summary of Photosynthesis Stages
Feature	Light-Dependent Stage	Light-Independent Stage (Calvin Cycle)
Location in Chloroplast	Thylakoid membranes (in the grana)	Stroma
Overall Purpose	To convert light energy into chemical energy	To use chemical energy to synthesise organic compounds from inorganic CO₂
Inputs	Light energy, Water (H₂O), ADP + P_i, NADP⁺	Carbon Dioxide (CO₂), ATP, NADPH
Outputs	Oxygen (O₂), ATP, NADPH	Glucose (C₆H₁₂O₆), ADP + P_i, NADP⁺
Energy Conversion	Light energy is converted to chemical energy (ATP, NADPH)	Chemical energy (ATP, NADPH) is used to form chemical energy stored in glucose

Section 4: The Cellular Respiration Pathway: Releasing Chemical Energy

Cellular respiration is the primary catabolic pathway that breaks down organic molecules, such as glucose, to release their stored chemical energy and capture it in the form of ATP.

4.1 The Powerhouse: Mitochondrion Structure and Function

In eukaryotes, aerobic respiration occurs in the mitochondrion.

Double Membrane: An outer membrane and a highly folded inner membrane.
Cristae: The extensive folds of the inner membrane, which increase surface area for the electron transport chain and ATP synthase.
Intermembrane Space: The narrow space between the membranes where protons are pumped to create a gradient.
Matrix: The innermost compartment containing enzymes for the Krebs cycle, mitochondrial DNA, and ribosomes.

4.2 Stage 1: Glycolysis (in the Cytosol)

Glycolysis (“sugar splitting”) is a universal, anaerobic pathway that occurs in the cytosol.

Purpose: To begin the breakdown of glucose and produce a small amount of ATP and loaded coenzymes.
Inputs: 1 Glucose, 2 ATP, 2 NAD⁺
Outputs: 2 Pyruvate, 4 ATP, 2 NADH
Net ATP Yield: 2 ATP

4.3 Stage 2: The Krebs Cycle / Citric Acid Cycle (in the Mitochondrial Matrix)

If oxygen is present, pyruvate enters the mitochondrial matrix for the Krebs cycle.

Purpose: To complete the oxidation of glucose, releasing CO₂ and harvesting high-energy electrons in NADH and FADH₂.
Link Reaction: Before the cycle, each pyruvate is converted to Acetyl-CoA, producing CO₂ and NADH.
Inputs (per glucose): 2 Acetyl-CoA, 6 NAD⁺, 2 FAD, 2 ADP + P_i
Outputs (per glucose): 4 CO₂, 6 NADH, 2 FADH₂, 2 ATP
ATP Yield: 2 ATP

4.4 Stage 3: The Electron Transport Chain and Oxidative Phosphorylation (on the Cristae)

This final, aerobic stage produces the vast majority of ATP.

Purpose: To use the energy from electrons carried by NADH and FADH₂ to generate a large amount of ATP.
Inputs: 10 NADH, 2 FADH₂, Oxygen (O₂), ADP + P_i
Process (Oxidative Phosphorylation):
1. NADH and FADH₂ donate high-energy electrons to the ETC.
2. As electrons move down the chain, released energy is used to pump protons (H⁺) from the matrix to the intermembrane space, creating a proton motive force.
3. Protons flow back into the matrix through ATP synthase, driving the synthesis of a large quantity of ATP.
4. At the end of the chain, oxygen acts as the final electron acceptor, combining with electrons and protons to form water (H₂O).
Outputs: Water (H₂O), ~32-34 ATP, NAD⁺, FAD
ATP Yield: ~32-34 ATP

4.5 Life Without Oxygen: Anaerobic Fermentation (in the Cytosol)

In the absence of oxygen, the ETC halts. Fermentation’s sole purpose is to regenerate NAD⁺ from NADH, allowing glycolysis to continue producing its small yield of 2 ATP. It produces no additional ATP itself.

Lactic Acid Fermentation (in Animals): Pyruvate accepts electrons from NADH to form lactic acid. This regenerates NAD⁺.
Ethanol (Alcoholic) Fermentation (in Yeast and Plants): Pyruvate is converted to ethanol and CO₂, regenerating NAD⁺ in the process. This is the basis of baking and brewing.

4.6 Factors Affecting the Rate of Cellular Respiration

Temperature: Rate increases to an optimum, then falls sharply as enzymes denature.
Glucose Availability: Rate increases with glucose concentration until enzymes become saturated or another factor is limiting.
Oxygen Concentration: Essential for aerobic respiration. At low concentrations, the overall rate is limited. As oxygen increases, the rate increases until it plateaus.

Table 3: Summary of Aerobic Respiration Stages
Stage	Location	Inputs (per glucose)	Outputs (per glucose)	ATP Yield (per glucose)
Glycolysis	Cytosol	1 Glucose, 2 ATP, 2 NAD⁺	2 Pyruvate, 4 ATP, 2 NADH	2 (net)
Krebs Cycle	Mitochondrial Matrix	2 Acetyl-CoA, 6 NAD⁺, 2 FAD, 2 ADP + P_i	4 CO₂, 6 NADH, 2 FADH₂, 2 ATP	2
Electron Transport Chain	Inner Mitochondrial Membrane (Cristae)	10 NADH, 2 FADH₂, O₂, ADP + P_i	H₂O, ATP, NAD⁺, FAD	~32-34
Total				~36-38

Section 5: Synthesis and Comparison: The Cycle of Life

Photosynthesis and cellular respiration are the two pillars of energy and matter cycling in the biosphere. While one captures energy and builds organic matter, the other releases that energy and breaks organic matter down.

5.1 A Complementary Relationship

At a fundamental level, photosynthesis and cellular respiration are reverse processes:

Photosynthesis: 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂ (requires light energy)
Cellular Respiration: C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + Energy (ATP)

This reveals a beautiful symmetry. The products of one are the reactants of the other, forming the basis of the carbon and oxygen cycles on Earth. Energy flows in one direction: from sunlight, captured by photosynthesis, and then released as ATP by respiration to power life.

5.2 Direct Comparison of Key Features

Table 4: Comparative Analysis of Photosynthesis and Aerobic Respiration
Feature	Photosynthesis	Aerobic Respiration
Overall Purpose	Energy capture and storage; synthesis of organic molecules.	Energy release; breakdown of organic molecules to produce ATP.
Overall Equation	6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂	C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O
Type of Pathway	Anabolic (builds up)	Catabolic (breaks down)
Energy Requirement	Endergonic (requires light energy)	Exergonic (releases energy)
Organelle	Chloroplast	Mitochondrion and Cytosol
Primary Coenzymes	NADPH	NADH and FADH₂
Final Electron Acceptor	NADP⁺ (in light-dependent reactions)	Oxygen (O₂)

VCE Biology Unit 3 Detailed Plain Notes