Metabolism Study Notes microbiology

METABOLISM

Overview

  • Metabolism is a broad field that encompasses all chemical reactions occurring within living organisms.
  • Key aspects include the conversion of chemical energy from nutrients into usable forms and the disposal of waste products.

Chemical Energy Sources

  • Types of Chemical Energy:
    • Carbohydrates
    • Fats
    • Proteins
    • Other molecules

ATP (Adenosine Triphosphate)

  • Body's Energy Currency:
    • ATP stores and transfers energy within cells, facilitating various biochemical processes.

Chemical Wastes

  • Primary waste products from metabolism include:
    • Carbon Dioxide
    • Water
    • Heat (also a byproduct of metabolic processes)

Basic Chemical Reactions Underlying Metabolism

Types of Metabolic Reactions

  • Catabolism and Anabolism:
    • Catabolic Pathways:
    • Break larger molecules into smaller products.
    • Exergonic Reactions: Release energy.
    • Anabolic Pathways:
    • Synthesize large molecules from smaller products.
    • Endergonic Reactions: Require more energy than they release.

Metabolism Composition

  • Figure 5.1 illustrates that metabolism is composed of catabolic and anabolic reactions, with energy being lost as heat and nutrients being converted into ATP.

Oxidation and Reduction Reactions

Electron Transfer

  • Oxidation: Loss of electrons from an electron donor.
  • Reduction: Gain of electrons by an electron acceptor.
  • These reactions always occur simultaneously, known as redox reactions.
  • Electron Carriers: Transport electrons often in the form of hydrogen atoms, including:
    • NAD+ (Nicotinamide Adenine Dinucleotide)
    • NADP+ (Nicotinamide Adenine Dinucleotide Phosphate)
    • FAD (Flavin Adenine Dinucleotide)

ATP Production and Energy Storage

  • Energy is released from nutrients and stored in high-energy phosphate bonds of ATP.
  • Phosphorylation: The process where inorganic phosphate is added to a substrate to form ATP from ADP.
  • Types of Phosphorylation:
    • Substrate-Level Phosphorylation
    • Oxidative Phosphorylation
    • Photophosphorylation
  • Anabolic pathways utilize ATP energy by breaking phosphate bonds.

The Role of Enzymes in Metabolism

Enzyme Functionality

  • Enzymes: Biological catalysts that increase the likelihood of reactions occurring by lowering the activation energy required.

Enzyme Classification

  • Enzymes are categorized based on their mode of action into six groups:
    • Hydrolases: Catalyze hydrolysis reactions (e.g., Lipase breaks down lipids).
    • Isomerases: Rearrange the atoms within a molecule (e.g., Phosphoglucoisomerase).
    • Ligases/Polymerases: Join two or more substrates together (e.g., Acetyl-CoA synthetase).
    • Lyases: Split a chemical into smaller parts without using water (e.g., Fructose-1,6-bisphosphate aldolase).
    • Oxidoreductases: Transfer electrons or hydrogen atoms (e.g., Lactic acid dehydrogenase).
    • Transferases: Move functional groups between molecules (e.g., Hexokinase).

Enzyme Structure

  • Many protein enzymes are complete in themselves.
  • Apoenzymes: Inactive without nonprotein cofactors (inorganic ions or organic coenzymes).
  • Binding of an apoenzyme and its cofactor results in a holoenzyme, which is active.
  • Some enzymes are made of RNA, known as ribozymes.

Enzyme Activity

Influencing Factors

  • Factors affecting enzyme activity:
    • Temperature
    • pH
    • Concentrations of enzymes and substrates
    • Presence of inhibitors

Control of Enzymatic Activity

  • Activators: Some enzymes require cofactors that bind to sites other than the active site to become functional.
  • Inhibitors: Substances that block enzyme activity:
    • Competitive Inhibitors: Compete with substrates for the active site.
    • Noncompetitive Inhibitors: Bind to allosteric sites, distorting the active site.
  • Feedback Inhibition: A type of regulation where the final product of a metabolic pathway inhibits an earlier step to prevent overproduction.

Carbohydrate Catabolism

Energy Production

  • Carbohydrates as Energy Sources: Many organisms primarily oxidize carbohydrates for energy. The most common carbohydrate used is glucose.
  • Processes for Glucose Catabolism:
    • Cellular Respiration
    • Fermentation

Glycolysis

  • Location: Occurs in the cytoplasm of most cells.
  • Process: Splitting of six-carbon glucose into two three-carbon sugar molecules, pyruvic acid.
  • Substrate-Level Phosphorylation: Direct transfer of phosphate leading to a net gain of:
    • 2 ATP molecules
    • 2 NADH molecules
    • 1 precursor metabolite (pyruvic acid)

Stages of Glycolysis

  • Three Stages (Total steps: 10):
    1. Energy-Investment Stage: Requires ATP.
    2. Lysis Stage: Cleavage of fructose 1,6-bisphosphate.
    3. Energy-Conserving Stage: Produces ATP and NADH.

Cellular Respiration

Synthesis of Acetyl-CoA

  • Results in producing:
    • 2 molecules of Acetyl-CoA
    • 2 molecules of CO2
    • 2 molecules of NADH

Krebs Cycle

  • Occurs in the matrix of mitochondria in eukaryotes or cytoplasm in prokaryotes.
  • Generates energy from the oxidation of Acetyl-CoA through:
    • Anabolic reactions
    • Isomerization
    • Redox reactions
    • Decarboxylations
    • Substrate-level phosphorylation
    • Hydration

Electron Transport Chain (ETC)

  • Major ATP production through a series of redox reactions.
  • Located in the inner mitochondrial membrane of eukaryotes and in prokaryotic cytoplasmic membranes.

Final Steps of Cellular Respiration

  • Aerobic and anaerobic respiration. Oxygen serves as final electron acceptor in aerobic respiration, whereas other molecules serve this function in anaerobic respiration.
  • Chemiosmosis: Protons flow back through ATP synthase, generating ATP from ADP through oxidative phosphorylation, leading to a total of approximately 34 ATP produced from a single glucose molecule.

Metabolic Diversity

Alternative Pathways

  • Entner-Doudoroff Pathway: An alternative catabolic pathway found in some bacteria that produces less ATP than the EMP pathway.
  • Pentose Phosphate Pathway: An alternative to glycolysis, producing precursor metabolites and NADPH, important for the synthesis of nucleotides and fatty acids.

Fermentation

  • A process for energy production when oxygen is not present, allowing regeneration of NAD+ through partial oxidation of sugars.

Other Catabolic Pathways

Lipids and Proteins

  • Lipids and proteins also serve as energy sources and can be converted into precursor metabolites that enter glycolysis or Krebs cycle.

PHOTOSYNTHESIS

Overview

  • Photosynthesis is the process by which many organisms synthesize organic molecules from inorganic carbon dioxide using light energy.

Structures and Chemicals Involved

  • Chlorophylls: Pigment molecules essential for capturing light energy, with structural similarities to cytochrome molecules in the ETC.
  • Photosystems: Structures that contain chlorophyll and other pigments to capture light energy, organized in thylakoid membranes within chloroplasts (in eukaryotes).

Light-Dependent Reactions

  • Involve the transfer of electrons down an electron transport chain to create ATP through photophosphorylation.

Light-Independent Reactions

  • Utilize ATP and NADPH from light-dependent reactions, primarily through the Calvin-Benson cycle, which includes three steps:
    1. Fixation of CO2
    2. Reduction
    3. Regeneration of RuBP