Download pdf - Microbiology Miniworkshop - Aalborg Universitethomes.nano.aau.dk/fp/microbio/microbiology-miniworkshop 3.pdf · 4 Microbial Metabolism Enzymes -> Catalysators Enzymesare biological

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Microbiology Miniworkshop

3rd lecture: Chapter 8

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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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The Metabolism of Microbes

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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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Enzymes -> Catalysators

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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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Co-factors

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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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Enzymes: Enzyme – Substrate Reactions

ES complex ->

transition state

Induced fit -> enzyme adapts slightly -> more precise binding

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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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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:

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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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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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Metabolic Pathways

Sequence of metabolic reactions that proceed in a systematic, highly regulated manner –metabolic pathways

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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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-> enzyme induction/repression – enzymes are made only when suitable substrates are present

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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 MetabolismThe Pursuit and Utilization of Energy: Cell’s Energy Machine

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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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The Pursuit and Utilization of Energy: -> Biological Oxidation and Reduction

Reduction of NAD+

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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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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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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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Pathways of Bioenergetics

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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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Metabolic Strategies

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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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Metabolic Strategies: Aerobic Respiration

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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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Metabolic Strategies: Aerobic RespirationElectron Transport and Oxidative Phosphorylation

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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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Metabolic Strategies: Aerobic RespirationThe Formation of ATP and Chemiosmosis

1 mol glucose -> aerobic 38 mol ATP

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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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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

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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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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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Metabolic Strategies: Fermentation

Products of different microorganisms growing under anaerobic conditions

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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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