Microbial Metabolism: Catabolism and Anabolism

• Metabolism is the collection of controlled biochemical reactions within a microbe.
• The ultimate function of metabolism is to reproduce the organism.
• Every cell acquires nutrients.
• Metabolism requires energy from light or catabolism of nutrients.
• Energy is stored in adenosine triphosphate (ATP).
• Cells catabolize nutrients to form precursor metabolites.
• Precursor metabolites, energy from ATP, and enzymes are used in anabolic reactions.
• Enzymes plus ATP form macromolecules.
• Cells grow by assembling macromolecules.
• Cells reproduce once they have doubled in size.

Catabolism and Anabolism

• Catabolism and anabolism are the two major classes of metabolic reactions.
• Catabolic pathways break larger molecules into smaller products and are exergonic, releasing energy.
• Anabolic pathways synthesize large molecules from the smaller products of catabolism and are endergonic, requiring more energy than they release.

Oxidation and Reduction Reactions

• Oxidation-reduction reactions involve the transfer of electrons from an electron donor to an electron acceptor.
• Reactions always occur simultaneously.
• Cells use electron carriers to carry electrons, often in H atoms.
• Three important electron carriers are nicotinamide adenine dinucleotide (NAD+), nicotinamide adenine dinucleotide phosphate (NADP+), and flavin adenine dinucleotide (FAD).
  • NAD+ is derived from Niacin, Vitamin B3
  • FAD is derived from Riboflavin, Vitamin B2

ATP Production and Energy Storage

• Organisms release energy from nutrients, which can be concentrated and stored in high-energy phosphate bonds (ATP).
• Phosphorylation involves adding inorganic phosphate to a substrate.
• Cells phosphorylate adenosine diphosphate (ADP) to ATP in three ways: substrate-level phosphorylation in cytoplasm, oxidative phosphorylation in mitochondria, and photophosphorylation in chloroplasts.
• Anabolic pathways require the application of ATP and the breaking of a phosphate bond

The Roles of Enzymes in Metabolism

• Enzymes are organic catalysts that increase the likelihood of a reaction.
• Enzymes are classified into six categories based on mode of action: hydrolases, isomerases, ligases or polymerases, lyases, oxidoreductases, and transferases.
  • Most enzyme names end in -ase.
• Many protein enzymes are complete in themselves.
• Apoenzymes are inactive if not bound to nonprotein cofactors (inorganic ions or coenzymes).
  • An example of a coenzyme is NAD+.
• Binding of an apoenzyme and its cofactor(s) yields a holoenzyme.
• Some enzymes are RNA molecules called ribozymes.
• Enzyme activity is influenced by temperature, pH, enzyme and substrate concentrations, and presence of inhibitors.
• Some enzymes are activated when a cofactor binds to a site other than the active site.
• Inhibitors block an enzyme's activity, including competitive and noncompetitive inhibitors.
• Feedback inhibition controls the action of some enzymes.

Carbohydrate Catabolism

• Many organisms oxidize carbohydrates as a primary energy source for anabolic reactions.
• Glucose is the most common carbohydrate used
• Cellular respiration and fermentation are two processes that catabolize glucose.
• Glycolysis occurs in the cytoplasm of most cells and involves splitting of a six-carbon glucose into two three-carbon sugar molecules.
  • 1 glucose turns into 2 pyruvate (aka pyruvic acid)
• Substrate-level phosphorylation is a direct transfer of phosphate between two substrates.
• Glycolysis produces 4 ATP (2 net ATP), 2 NADH (NAD+ is an important electron carrier), and 2 pyruvate (3-carbon molecules that will be further oxidized).
• Glycolysis is divided into three stages involving 10 total steps: energy-investment stage (2 ATP invested), lysis stage (glucose split into 2 precursor molecules called glyceraldehyde-3-phosphate), and energy-conserving stage (aka payoff phase).

Cellular Respiration

• Resultant pyruvic acid is completely oxidized to produce ATP by a series of redox reactions
• The three stages of cellular respiration are synthesis of acetyl-CoA, Krebs cycle (aka Citric Acid Cycle, aka Tricarboxylic Acid Cycle), and final series of redox reaction (electron transport chain).
• Synthesis of acetyl-CoA results in two molecules of acetyl-CoA, two molecules of CO2, and two molecules of NADH.
• The Krebs cycle sees great energy amounts remain in bonds of acetyl-CoA, that is then transferred to NAD+ and FAD coenzymes
• The Krebs cycle occurs in cytosol of prokaryotes, and in the matrix of mitochondria in eukaryotes.
• The Krebs cycle involves six types of reactions: anabolism (of citric acid), isomerization, redox reactions, decarboxylations, substrate-level phosphorylation, and hydration.
• The Krebs cycle results in two molecules of ATP, two molecules of FADH2 (another important electron carrier), six molecules of NADH, and four molecules of CO2.
• The greatest ATP production occurs within the electron transport chain (ETC), through redox reactions.
• Electrons are transferred from one carrier molecule to another ending with a final electron acceptor.
• The energy from electrons is used to pump protons (H+) across the membrane, initiating the proton gradient.
• The ETC happens in the inner mitochondrial of eukaryotes, and in the cytoplasmic membrane of prokaryotes.
• Carrier molecules in the ETC include flavoproteins, ubiquinones, metal-containing proteins, and cytochromes.
• Aerobic respiration occurs with oxygen acting as the final electron acceptor.
• Anaerobic respiration occurs with other molecules acting as the final electron acceptor.
• Chemiosmosis is used to create ATP through of electrochemical gradients
• Cells employ energy from redox reactions of ETC to create proton gradient.
• Protons flow down electrochemical gradient through ATP synthases that phosphorylate ADP to ATP.
• Oxidative phosphorylation is the creation of a proton gradient is created by oxidation of components of ETC
• Approximately 34 ATP molecules form from one molecule of glucose

Metabolic Diversity

• The Entner-Doudoroff (ED) pathway is substituted for the EMP pathway by some bacteria, occuring only in prokaryotes.
  • The ED Pathway produces one ATP, NADH, and NADPH.
• The Pentose phosphate pathway is an alternative of Glycolysis but is less energy efficient.
  • The Pentose phosphate pathway produces precursor matabolites and NADPH
  • DNA nucleotides, steroids, and fatty acids are then created

Fermentation

• Sometimes cells cannot completely oxidize glucose by cellular respiration because conditions are anaerobic.
• Fermentation pathways provide cells with an alternative source of NAD+
• Those pathways involve the partial oxidation of sugar (or other metabolites) releasing energy using an organic molecule from within the cell as final electron acceptor.
• Fermentation takes place under anaerobic conditions
• Fermentation involves the recycling of +NAD and consecutive rounds of Glycolysis
• This produces pyruvate which then turns into either latic acid or ethanol

Carbohydrate Catabolism

• Lipids and proteins contain energy in their chemical bonds.
  • The two energy sources then turn into precursor metabolites
  • The metabolites serve as substates in Glycolysis and the Kebs cycles

Photosynthesis

• Many organisms synthesize their own organic molecules from inorganic carbon dioxide
• Most of these organisms capture light energy and use it to synthesize carbohydrates from CO2 and H₂O.
• Photosynthesis takes place in the chloroplast, which contains the thylakoid space and the stroma.
• Light-dependent reactions occur within the thylakoid space and the light-independent reactions occur in the stroma.
• Chlorophylls are important to organisms that capture light energy with pigment molecules
  • structurally simular to cytochrome molecules in ETC
  • Structural differences cause absorption at different wavelengths.
• Arrangement of molecules of chlorophyll and other pigments form light-harvesting matrices known as thylakoids
  • In prokaryotes—invagination of cytoplasmic membrane
  • In eukaryotes-formed from inner membrane of chloroplasts
  • Arranged in stacks called grana
• Stroma is the space between the outer membrane of grana and thylakoid membrane.
• Photosystems absorb light energy and use redox reactions to store energy in the form of ATP and NADPH.
• Light-dependent reactions depend on light energy.
• Electrons moving down the chain, pumps protons across the membrane
  • Photophosphorylation uses proton motive force to generate ATP
  • Photophosphorylation can be cyclic or noncyclic.
• Light-independent reactions synthesize glucose from carbon dioxide and water.
  • Carbon Fixation created by the Calvin-Benson cycle

Other Anabolic Pathways

• Anabolic reactions are synthesis reactions requiring energy and a source of precursor metabolites.
• Energy is derived from ATP from catabolic reactions
• Many anabolic pathways are simply the reverse of catabolic pathways.
• Reactions that can proceed in either direction are amphibolic.

Integration and Regulation of Metabolic Function

• Cells synthesize or degrade channel and transport proteins to regulate the input of building blocks.
• Cells often synthesize enzymes only when a substrate is available.
• Cells catabolize the more energy-efficient choice when multiple energy sources are available.
• Eukaryotic cells isolate enzymes of different metabolic pathways within membrane-bounded organelles.
• Allosteric sites on enzymes control enzyme activity.
• Feedback inhibition slows/stops anabolic pathways when product is in abundance.
• Two Types of Regulatory Mechanisms:
  • Cells regulate the amount and timing the protein enzyme is expressed
  • Cells can control amounts of the proteins expressed.
  • Amphibolic pathways regulated by cells that require coenzymes for pathway operation

Microbial metabolism involves controlled biochemical reactions essential for reproduction. Cells acquire nutrients and utilize energy from light or nutrient catabolism, stored as ATP. Catabolic pathways break down molecules, releasing energy, while anabolic pathways synthesize molecules, requiring energy.