Metabolism, Enzyme Function, Cellular Respiration, and Photosynthesis: Study Notes for General Biology

Metabolism: Enzyme Structure and Function

Conservation of Mass Principle

The conservation of mass principle states that matter cannot be created or destroyed in a chemical reaction. In biological systems, this means that the total mass of reactants equals the total mass of products.

• Key Point: All atoms present in the reactants must be accounted for in the products.

• Example: In cellular respiration, the carbon atoms in glucose are found in the carbon dioxide produced.

Gibbs Free Energy Definition

Gibbs free energy (G) is a thermodynamic quantity that indicates the amount of energy available to do work in a system at constant temperature and pressure.

• Formula: $\Delta G = \Delta H - T\Delta S$

• Key Point: A negative $\Delta G$ indicates a spontaneous reaction.

Catabolic vs. Anabolic Reactions

Metabolic reactions are classified as either catabolic (breaking down molecules to release energy) or anabolic (building complex molecules from simpler ones).

• Catabolic: Example: Cellular respiration breaks down glucose.

• Anabolic: Example: Photosynthesis synthesizes glucose from CO2 and H2O.

Graphical Representation of Free Energy

Free energy diagrams show the energy changes during a reaction, including activation energy and the difference between reactants and products.

• Key Point: The peak represents the activation energy barrier.

Enzymes

Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.

• Function/Purpose: Increase reaction rates without being consumed.

• Induced Fit Model: The enzyme changes shape to better fit the substrate upon binding.

• Active Site:

  • Purpose: Region where substrate binds and reaction occurs.

  • Bond Types: Hydrogen bonds, ionic bonds, and van der Waals interactions help substrate binding.

  • Specificity: Enzymes are highly specific for their substrates.

• Effect of Substrate Saturation: At high substrate concentrations, enzyme activity plateaus (Vmax).

• Reaction Rate Graphs:

  • Competitive inhibition: Inhibitor competes with substrate for active site.

  • Noncompetitive inhibition: Inhibitor binds elsewhere, changing enzyme shape.

  • Allosteric inhibition: Inhibitor binds to a site other than the active site, affecting enzyme activity.

• Collision Theory: Reactants must collide with sufficient energy and proper orientation.

• Denaturation: Loss of enzyme structure due to factors like heat, pH, or chemicals, resulting in loss of function.

• Inhibitors:

  • Irreversible: Permanently inactivate enzymes.

  • Reversible: Can be competitive or noncompetitive.

• Methods of Assaying Enzyme Activity: Use of colorimetric, spectrophotometric, or radiometric assays.

Definition of Cofactors, Coenzymes, and Prosthetic Groups

Cofactors are non-protein chemical compounds required for enzyme activity. Coenzymes are organic cofactors (e.g., NAD+). Prosthetic groups are tightly bound cofactors.

ATP: Why is it Needed?

ATP (Adenosine Triphosphate) is the primary energy currency of the cell, used to power cellular processes.

ATP Phosphorylation and Energy Coupling

ATP phosphorylation refers to the addition of a phosphate group to ADP to form ATP, coupling energy-releasing reactions to energy-requiring ones.

• Phosphorylation Definition: Transfer of a phosphate group to a molecule.

Basic Metabolism and Aerobic Respiration

Energy and Matter

Cells transform energy and matter through metabolic cycles. Some cycles regenerate intermediates, while others do not.

• Types of Potential Energy: Chemical, electrical, mechanical.

• ATP: Main energy carrier in cells.

Aerobic Cellular Respiration

Aerobic respiration is the process by which cells convert glucose and oxygen into ATP, CO2, and H2O.

• Purpose/Definition: To produce ATP using oxygen.

• Know Equation: $\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{ATP}$

• Flow of Energy:

  • Glucose contains the most energy.

  • Energy is released as glucose is oxidized.

• NAD+ and FAD: Electron carriers that transport electrons during respiration.

• Stages of Respiration:

  1. Glycolysis:

     • Energy investment phase: ATP is used.

     • Energy payoff phase: ATP is produced.

     • Production of NADH.

     • Does not require oxygen.

  2. Pyruvate Oxidation: Pyruvate is converted to Acetyl-CoA.

  3. Krebs Cycle (Citric Acid Cycle): Acetyl-CoA is oxidized, producing NADH, FADH2, and CO2.

  4. Oxidative Phosphorylation:

     • Electron transport chain (ETC) and chemiosmosis.

     • ATP synthesis driven by proton gradient.

Difference Between Substrate-Level and Oxidative Phosphorylation

• Substrate-level phosphorylation: Direct transfer of phosphate to ADP.

• Oxidative phosphorylation: ATP synthesis powered by electron transport chain and chemiosmosis.

Components of Mitochondria

• Matrix: Site of Krebs cycle.

• Inner membrane: Location of ETC.

• Intermembrane space: Accumulates protons for chemiosmosis.

Anaerobic Respiration

Occurs when oxygen is absent; cells use alternative electron acceptors or fermentation.

• Alcohol Fermentation: Converts pyruvate to ethanol and CO2.

• Lactic Acid Fermentation: Converts pyruvate to lactic acid.

Photosynthesis

Purpose/Definition

Photosynthesis is the process by which plants, algae, and some bacteria convert light energy into chemical energy stored in glucose.

• Equation: $6\text{CO}_2 + 12\text{H}_2\text{O} + \text{light energy} \rightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 + 6\text{H}_2\text{O}$

Energy Transformation

Light energy is transformed into chemical energy in the form of glucose.

CO2 and Water in Plants

• CO2 Entry: Through stomata in leaves.

• Water Entry: Through roots and transported via xylem.

Chloroplast Structure

• Site of Photosynthesis: Contains thylakoid membranes and stroma.

Photosynthesis Stages

• Light Reactions:

  • Occurs in thylakoid membranes.

  • Uses visible light (400-700 nm).

  • Produces ATP and NADPH.

• Calvin Cycle:

  • Occurs in stroma.

  • Uses ATP and NADPH to fix CO2 into glucose.

  • Key enzyme: Rubisco.

Photosystems I and II

• Photosystem II (PSII): P680 chlorophyll.

• Photosystem I (PSI): P700 chlorophyll.

• Function: Absorb light and transfer electrons through ETC.

Electron Transport Chain (ETC) in Photosynthesis

• Components: Series of proteins embedded in thylakoid membrane.

• Function: Transfer electrons and pump protons to create a gradient for ATP synthesis.

ATP Synthesis and Chemiosmosis

• ATP Synthase: Enzyme that synthesizes ATP using proton gradient.

• Chemiosmosis: Movement of protons across membrane to drive ATP production.

Calvin Cycle Steps

• Step 1: Carbon Fixation

  • CO2 is attached to RuBP by Rubisco.

• Step 2: Reduction

  • ATP and NADPH are used to reduce 3-PGA to G3P.

• Step 3: Regeneration of RuBP

  • Some G3P is used to regenerate RuBP.

Relationship Between Photosynthesis and Respiration

Photosynthesis stores energy in glucose, while respiration releases energy from glucose.

HTML Table: Comparison of Catabolic and Anabolic Pathways

Pathway	Function	Example
Catabolic	Breaks down molecules, releases energy	Cellular respiration
Anabolic	Builds complex molecules, requires energy	Photosynthesis

HTML Table: Photosystems Comparison

Photosystem	Chlorophyll Type	Function
PSII	P680	Initial electron donor, splits water
PSI	P700	Final electron acceptor, produces NADPH

HTML Table: Cellular Respiration Stages

Stage	Main Events	Location
Glycolysis	Glucose to pyruvate, ATP and NADH produced	Cytoplasm
Pyruvate Oxidation	Pyruvate to Acetyl-CoA, NADH produced	Mitochondrial matrix
Krebs Cycle	Acetyl-CoA oxidized, CO2, NADH, FADH2 produced	Mitochondrial matrix
Oxidative Phosphorylation	Electron transport, ATP synthesis	Inner mitochondrial membrane

Additional info: Some details, such as the specific steps of glycolysis and the Calvin cycle, were expanded for clarity and completeness.