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LECTURES IN MICROBIOLOGY Microbial Metabolism Sofronio Agustin Professor LESSON 6
Lesson 6 Topics • Metabolism • Energy • Pathways • Biosynthesis
Metabolism • Catabolism • Anabolism • Enzymes
Catabolism • Breakdown of complex organic molecules in order to extract energy and form simpler end products. • Enzymes are involved.
Enzymes • Function • Structure • Enzyme-substrate interaction • Cofactors • Action • Regulation
Enzyme Structure • Simple enzyme - primarily protein • Conjugated enzyme - protein and nonprotein • Three-dimensional features: • Specificity -”lock-and-key” • Active site or catalytic site
Conjugated Enzymes Conjugated enzymes contain a metallic cofactor, coenzyme, or both in order for it to function as a catalyst.
Active Site Specific active sites are folded regions of the protein molecule and contain specific amino acids in its microenvironment.
Enzyme-Substrate Interaction • Substrates specifically bind to the active sites on the enzyme: -“lock-and-key” style -Induced fit • Once the reaction is complete, the product is released and the enzyme reused.
Lock-and-Key Model Specificity of enzyme-substrate reactions and induced fit.
Coenzymes • Function as transient carriers • Alter a substrate by removing a chemical group from it and adding it to another. • Ex. NAD, FAD and CoA
Coenzyme Activity • Carrier function of coenzymes • A coenzyme transfers chemical groups from one substrate to another.
Enzyme Action • Exoenzymes • Endoenzymes • Constitutive • Induction or repression • Types of reactions
Enzyme Location Exoenzymes are inactive while inside the cell, but upon release from the cell they become active. Endoenzymes remain in the cell and are always active.
Constitutive and Regulated Enzymes • Constitutive enzymes are present in constant amounts. • Regulated enzymes are either induced or repressed.
Types of Reactions • Condensation • Hydrolysis • Transfer reactions
Synthesis and Hydrolysis Condensation reactions are associated with anabolic reactions, and hydrolysis reactions are associated with catabolic reactions.
Transfer Reactions • Transfer of electrons from one substrate to another. Ex: Oxidoreductase - oxidation-reduction reactions. • Transfer of functional groups from one molecule to another. Ex: Aminotransferases - transfer of amino group.
Sample Enzymes Examples of enzymes, their substrates, and their reactions.
Regulation • Metabolic pathways • Direct control • Genetic control
Patterns of Metabolism • Metabolic pathways follow stepwise patterns. • These are regulated by enzymes that catalyze these reactions.
Enzyme Control Mechanisms Competitive inhibition and noncompetitive inhibition are forms of direct control (regulation) of the enzyme action.
Genetic Control • Repression - end products stop the expression of genes that encode for proteins (enzymes) which are responsible for metabolic reactions. • Induction - substrate initiates and enhances the expression of genes for proteins (enzymes) that drive metabolic reactions.
Repression Repression as a type of genetic control of enzyme synthesis
Bioenergetics • Cell energetics - Exergonic reactions - Endergonic reactions • Redox reaction • Electron carriers • Adenosine Triphosphate (ATP)
Energy Machinery of the Cell The general scheme associated with metabolism of organic molecules, the redox reaction, and the capture of energy in the form of ATP.
Redox Reaction • Oxidation - removal or loss of electrons • Reduction - addition or gain of electrons • These are coupled reactions • Biological redox reactions involve transfer of electrons and protons (hydrogens) = dehydrogenation • Dehydrogenases - catalyze these reactions
Electron Carriers • Electron carriers - transfer electrons (and protons) from donor to acceptor molecules. • Coenzymes: Ex: Nicotinamide adenine dinucleotide (NAD) • Respiratory chain (ETC) carriers: Ex: Cytochromes (protein+porphyrin)
Adenosine Triphosphate • Temporary energy repository (“cellular battery”) • Breaking of pyrophosphates bonds will release free energy for cellular work. • Three part molecule: • Nitrogen base - Adenine • Pentose sugar - Ribose) • Chain of three phosphate groups
Energy Capture • The phosphate groups capture the energy derived from metabolism as pyrophosphate bonds within the ATP molecule. • ATP and its partner compounds ADP and AMP.
Phosphorylation • ATP can be used to phosphorylate an organic molecule such as glucose during catabolism. • Phosphorylation -catalyzed by phosphorylases (e.g. hexokinase)
Substrate-level Phosphorylation • ATP can be synthesized by substrate-level phosphorylation. • A phosphate group from an intermediate is transferred to ADP to regenerate ATP.
Catabolic Pathways • Embden-Meyerhoff-Parnas (EMP) Pathway or Glycolysis • Kreb’s or Tricarboxylic Acid (TCA) Cycle • Electron Transport or Respiratory Chain • Alternate pathways • Fermentation
Glucose Metabolism • Overview of the location, flow, end-products of cellular (aerobic) respiration. • Glucose is catabolized to harness energy.
Cellular Respiration • Glycolysis • Kreb’s Cycle • Electron Transport Chain
Glycolysis • Glucose (6-carbon sugar) splits into two pyruvates (3-carbon molecules). • Glucose is oxidized and coenzyme NAD is reduced to NADH. • Energy investment phase: - Phosphorylation of intermediates using 2 ATP molecules • Energy yielding phase: - Substrate-level-phosphorylation of ADP to produce 4 ATPs.
Kreb’s Cycle • Each pyruvic acid is processed to enter the Kreb’s Cycle as Acetyl CoA. • CO2 is generated -decarboxylation reactions. • Coenzymes NAD and FAD are reduced to NADH and FADH2 • Net yield of two ATPs per molecule of glucose.
Electron Transport Chain • NADH and FADH2 from glycolysis and Kreb’s Cycle donate electrons to the electron carriers (ETC). • Membrane bound carriers transfer electrons by redox reactions. • Oxygen (final electron acceptor) completes the terminal step.
Electron Transport Chain The Electron Transport Chain and Chemiosmosis driven by the Proton Motive Force
Location of ETC • Eukaryotes - Inner Mitochondrial Membrane • Prokaryotes- Cytoplasmic Membrane
ATP Yield • Glycolysis - 2 • Kreb’s Cycle - 2 • ETC- 34 Total Yield: 38 • NADH yield - 2 in Glycolysis 8 in Kreb’s Cycle • FADH2 yield- 2 in Kreb’s Cycle
Anaerobic Respiration • Similar to aerobic respiration, except nitrate or nitrite is the final electron acceptor
Fermentation • Glycolysis only • NADH from glycolysis is used to reduce the glucose • Organic compounds as the final electron acceptors (not O2) • Low ATP yields per glucose molecule compared to cellular respiration
Fermentation • Chemistry of fermentation: • Production of ethyl alcohol or lactic acid and release of CO2
Types of Fermenters • Facultative anaerobes • Fermentation in the absence of oxygen • Respiration in the presence of oxygen Ex. Escherichia coli • Strict fermenters • No respiration Ex. yeast
Fermentation Products • Alcoholic fermentation • Acidic fermentation • Mixed acid fermentation