microbiology miniworkshop - aalborg...
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Microbial Metabolism
The Metabolism of Microbes
metabolism – all chemical reactions and physical workings of a cell
Two types of chemical reactions:
• anabolism – biosynthesis; process that forms larger macromolecules from smaller molecules; requires energy input
• catabolism – degradative; breaks the bonds of larger
molecules forming smaller molecules; releases energy
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Microbial Metabolism
Enzymes -> Catalysators
Enzymes are biological catalysts that increase the rate of a chemical reaction by lowering the energy of activation. (no not interfere with the equilibrium of reaction)
The enzyme is not permanently altered in the reaction.
Enzyme promotes a reaction by serving as a physical site for specific substrate molecules to position.
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Microbial Metabolism
Enzyme Structure
Simple enzymes – consist of protein alone
Conjugated enzymes or holoenzymes – contain protein and nonprotein molecules• apoenzyme –protein portion
• cofactors – nonprotein portion
metallic cofactors – iron, copper, magnesium
coenzymes -organic molecules (Acetyl-CoA) – vitamins
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Microbial Metabolism
Enzymes: Specificity and the Active Site
Exhibits primary, secondary, tertiary, and some, quaternary structure
Site for substrate binding is active site, or catalytic site
A temporary enzyme-substrate union occurs when substrate moves into active site – induced fit
Appropriate reaction occurs; product is formed and released
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Microbial Metabolism
Enzymes: Enzyme – Substrate Reactions
ES complex ->
transition state
Induced fit -> enzyme adapts slightly -> more precise binding
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Microbial Metabolism
Enzymes: Location and Regularity of Enzyme Action
Exoenzymes – transported extracellularly, where they break down large food molecules or harmful chemicals
• cellulase, amylase, penicillinase
endoenzymes – retained intracellularly and function there
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Microbial Metabolism
Enzymes: Location and Regularity of Enzyme Action
Constitutive enzymes – always present, always produced in equal amounts or at equal rates, regardless of amount of substrate
• enzymes involved in glucose metabolism
Regulated enzymes – not constantly present; production is turned on (induced) or turned off (repressed) in response to changes in concentration of the substrate
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Microbial MetabolismEnzymes: Synthesis and Hydrolysis Reactions
Synthesis or condensation reactions – anabolic reactions to form covalent bonds between smaller substrate molecules, require ATP, release one molecule of water for each bond formed
Hydrolysis reactions– catabolic reactions that break down substrates into small molecules; requires the input of water to break bonds
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Microbial MetabolismEnzymes: Transfer Reactions
Oxidation-reduction reactions – transfer of electrons• compound that loses electrons – oxidized
• compound that gains electrons – reduced
Aminotransferases – convert one type of amino acid to another by transferring an amino group
Phosphotransferases – transfer phosphate groups, involved in energy transfer
Methyltransferases – move methyl groups from one molecule to another
Decarboxylases – remove carbon dioxide from organic acids
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Microbial Metabolism
Enzymes: Sensitivity to their Environment
Temperature
pH
Osmotic pressure
Organism’s habitat
-> Changes induce instability
Denaturation: non-covalent bonds are broken
-> loss of structure and function
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Microbial Metabolism
Metabolic Pathways
Sequence of metabolic reactions that proceed in a systematic, highly regulated manner –metabolic pathways
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Microbial Metabolism
Control of Enzyme Activity
Competitive inhibition – substance that resembles normal substrate competes with substrate for active site
Noncompetitive inhibition – enzymes are regulated by the binding of molecules other than the substrate on the active site
• feedback inhibition – concentration of product at the end of a pathway blocks the action of a key enzyme
• feedback repression – inhibits at the genetic level by controlling synthesis of key enzymes
-> enzyme induction – enzymes are made only when suitable substrates are present
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Microbial Metabolism
Control of Enzyme Activity
-> enzyme induction/repression – enzymes are made only when suitable substrates are present
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Microbial Metabolism
The Pursuit and Utilization of Energy
Energy – the capacity to do work or to cause change
The ultimate source of energy is the sun (with the exception of certain chemoautotrophs).
-> in the cell : Energy = chemical Energy (ATP)
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Microbial MetabolismThe Pursuit and Utilization of Energy: Cell Energetics
Cells manage energy in the form of chemical reactions that make or break bonds and transfer electrons.
Endergonic reactions – consume energy
Exergonic reactions – release energy
Energy present in chemical bonds of nutrients are trapped by specialized enzyme systems as the bonds of the nutrients are broken.
Energy released is temporarily stored in high energy phosphate molecules (ATP). The energy of these molecules is used in endergonic cell reactions.
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Microbial Metabolism
The Pursuit and Utilization of Energy: -> Biological Oxidation and Reduction
Redox reactions - always occur in pairs
There is an electron donor (reduced) and electron acceptor (oxidized) which constitute a redox pair.
Process salvages electrons and their energy
Released energy can be captured to phosphorylate ADP (-> ATP) or another compound.
Electron and Proton Carriers:
Repeatedly accept and release electrons and hydrogen to facilitate the transfer of redox energy
Most carriers are coenzymes:
NAD, FAD, NADP, coenzyme A and compounds of the respiratory chain
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Microbial Metabolism
The Pursuit and Utilization of Energy: -> Biological Oxidation and Reduction
Reduction of NAD+
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Microbial Metabolism
The Pursuit and Utilization of Energy: -> Adenosine Triphosphate: ATP
Three part molecule consisting of:
• adenine – a nitrogenous base
• ribose – a 5-carbon sugar
• 3 phosphate groups
ATP utilization and replenishment is a constant cycle in active cells.
Removal of the terminal phosphate
releases energy.
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Microbial Metabolism
The Pursuit and Utilization of Energy: -> Formation of ATP
ATP can be formed by three different mechanisms:
Substrate-level phosphorylation – transfer of phosphate group from a phosphorylated compound (substrate) directly to ADP
Oxidative phosphorylation – series of redox reactions occurring during respiratory pathway
Photophosphorylation – ATP is formed utilizing the energy of sunlight
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Microbial Metabolism
Pathways of Bioenergetics
Bioenergetics – study of the mechanisms of cellular energy release and use
Includes catabolic and anabolic reactions
Primary catabolism of fuels (glucose) proceeds through a series of three coupled pathways:
• glycolysis
• tricarboxylic acid cycle, Kreb’s cycle
• respiratory chain, electron transport
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Microbial Metabolism
Metabolic Strategies
Nutrient processing is varied, yet in many cases is based on three catabolic pathways that convert glucose to CO2 and gives off energy (ATP).
Aerobic respiration – glycolysis, the TCA cycle, respiratory chain; O2 final electron acceptor
Anaerobic respiration - glycolysis, the TCA cycle, respiratory chain; molecular oxygen is not final electron acceptor
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Microbial Metabolism
Metabolic Strategies: Aerobic Respiration
Series or enzyme-catalyzed reactions in which electrons are transferred from fuel molecules (glucose) to oxygen as a final electron acceptor
Glycolysis – glucose (6C) is oxidized and split into 2 molecules of pyruvic acid (3C)
TCA – processes pyruvic acid and generates 3 CO2 molecules and NADH + FADH2
Electron transport chain – accepts electrons NADH and FADH2; generates energy through sequential redox reactions called oxidative phosphorylation -> generates ATP
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Microbial Metabolism
Metabolic Strategies: Aerobic RespirationElectron Transport and Oxidative Phosphorylation
Final processing of electrons and hydrogen and the major generator of ATP
Chain of redox carriers that receive electrons from reduced NADH and FADH2 (from TCA cycle)
ETS shuttles electrons down the chain, energy is released and subsequently captured and used by ATP synthase complexes to produce ATP. – oxidative phosphorylation
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Microbial Metabolism
Metabolic Strategies: Aerobic RespirationElectron Transport and Oxidative Phosphorylation
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Microbial Metabolism
Metabolic Strategies: Aerobic RespirationThe Formation of ATP and Chemiosmosis
Chemiosmosis – as the electron transport carriers shuttle electrons, they actively pump hydrogen ions (protons) across the membrane setting up agradient of hydrogen ions -proton motive force.
Hydrogen ions diffuse back through the ATP synthasecomplex causing it to rotate, causing a 3-dimensional change resulting in the production of ATP.
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Microbial Metabolism
Metabolic Strategies: Aerobic RespirationThe Formation of ATP and Chemiosmosis
1 mol glucose -> aerobic 38 mol ATP
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Microbial Metabolism
Metabolic Strategies: Aerobic RespirationThe Terminal Step
Oxygen accepts 2 electrons from the ETS and then picks up 2 hydrogen ions from the solution to form a molecule of water. Oxygen is the final electron acceptor.
2H+ + 2e- + ½O2 → H2O
-> in anaerobic respiration: different electron acceptors !!!
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Microbial Metabolism
Metabolic Strategies: Anaerobic Respiration
Functions like aerobic respiration except it utilizes oxygen containing ions, rather than free oxygen, as the final electron acceptor (facultative anaerob: E. coli, Pseudomonas, Bacillus,…)
• Nitrate (NO3-) and nitrite (NO2
-)
Most obligate anaerobes use the H+ generated during glycolysis
and TCA to reduce some compound other than O2.
Methanogens: reduce CO2 -> CH4
Sulfate Bacteria: reduce SO42- -> H2S
Some bacteria use metals or organic compounds as H+ acceptor
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Microbial Metabolism
Metabolic Strategies: Fermentation
Incomplete oxidation of glucose or other carbohydrates in the absence of oxygen
Uses organic compounds as terminal electron acceptors
Yields a small amount of ATP
Production of Ethanol by yeasts acting on glucose
Formation of acid, gas and other products by the action of various bacteria on pyruvic acid
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Microbial Metabolism
Metabolic Strategies: Fermentation
Products of different microorganisms growing under anaerobic conditions
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Microbial Metabolism
Biosynthesis and the Crossing Pathways of Metabolism
Many pathways of metabolism are bi-directional or amphibolic.
Catabolic pathways contain molecular intermediates (metabolites) that can be diverted into anabolic pathways.• pyruvic acid can be converted into amino acids through
amination• amino acids can be converted into energy sources
through deamination• glyceraldehyde-3-phosphate can be converted into
precursors for amino acids, carbohydrates and fats
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