start here_ch05_lecture

Lecture prepared by Mindy Miller-Kittrell, University of Tennessee, Knoxville

M I C R O B I O L O G YWITH DISEASES BY BODY SYSTEM SECOND EDITION

Chapter 5 Microbial Metabolism

Basic Chemical Reactions Underlying Metabolism

• Metabolism– Collection of controlled biochemical reactions that take place

within cells of an organism– Ultimate function of metabolism is to reproduce the organism

• Metabolic Processes Guided by Eight Elementary Statements– Every cell acquires nutrients– Metabolism requires energy from light or from 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

Animation: Microbial Metabolism: Metabolism: OverviewAnimation: Microbial Metabolism: Metabolism: Overview

• Catabolism and Anabolism– Two major classes of metabolic reactions– Catabolic pathways break larger molecules into smaller

products; they are exergonic (release energy)– Anabolic pathways synthesize large molecules from the smaller

products of catabolism; they are endergonic (require more energy than they release)

[INSERT FIGURE 5.1]

• Oxidation and Reduction Reactions– Transfer of electrons from molecule that donates an electron to a

molecule that accepts an electron– Reactions always occur simultaneously– Cells use electron carrier molecules to carry electrons (often in H

atoms)– Three important electron carriers

– Nicotinamide adenine dinucleotide (NAD+)– Nicotinamide adenine dinucleotide phosphate (NADP+) – Flavine adenine dinucleotide (FAD) → FADH2

[INSERT FIGURE 5.2]

Animation: Microbial Metabolism: Oxidation-Reduction ReactionsAnimation: Microbial Metabolism: Oxidation-Reduction Reactions

• ATP Production and Energy Storage– Organisms release energy from nutrients; can be concentrated and stored in

high-energy phosphate bonds of ATP– Phosphorylation – organic phosphate is added to substrate– Cells phosphorylate ADP to ATP in three ways

– Substrate-level phosphorylation– Oxidative phosphorylation– Photophosphorylation

– Anabolic pathways use some energy of ATP by breaking a phosphate bond

• The Roles of Enzymes in Metabolism– Naming and classifying enzymes

– Enzymes are organic catalysts – increase the likelihood of a reaction but are not permanently changed

– Six categories of enzymes based on mode of action– Hydrolases– Isomerases– Ligases or polymerases– Lyases– Oxidoreductases– Transferases

[INSERT TABLE 5.1]

Animation: Microbial Metabolism: Enzymes: OverviewAnimation: Microbial Metabolism: Enzymes: Overview

• The Roles of Enzymes in Metabolism– Makeup of enzymes

– Many protein enzymes are complete in themselves– Others are composed of protein portions (apoenzymes) that

are inactive if not bound to non-protein cofactors (inorganic ions or coenzymes)

– Binding of apoenzyme and its cofactor(s) yields holoenzyme– Some are RNA molecules called ribozymes

[INSERT FIGURE 5.3]

[INSERT TABLE 5.2]

[INSERT FIGURE 5.4]

[INSERT FIGURE 5.5]

[INSERT FIGURE 5.6]

Animation: Microbial Metabolism: Enzymes: Steps in a ReactionAnimation: Microbial Metabolism: Enzymes: Steps in a Reaction

• The Roles of Enzymes in Metabolism– Enzyme activity

– Many factors influence the rate of enzymatic reactions– Temperature– pH– Enzyme and substrate concentrations– Presence of inhibitors

– Inhibitors– Substances that block an enzyme’s active site– Do not denature enzymes– Three types

[INSERT FIGURE 5.7]

[INSERT FIGURE 5.8]

[INSERT FIGURE 5.9]

Animation: Microbial Metabolism: Enzymes: Competitive InhibitionAnimation: Microbial Metabolism: Enzymes: Competitive Inhibition

[INSERT FIGURE 5.10]

Animation: Microbial Metabolism: Enzymes: Noncompetitive InhibitionAnimation: Microbial Metabolism: Enzymes: Noncompetitive Inhibition

Carbohydrate Catabolism

• Many organisms oxidize carbohydrates as the primary energy source for anabolic reactions

• Glucose most common carbohydrates used• Glucose catabolized by

– Cellular respiration – Fermentation

• Glycolysis– Occurs in cytoplasm of most cells– Involves splitting of a six-carbon glucose into two three-carbon

sugar molecules– Direct transfer of phosphate between two substrates occurs four

times – substrate = level phosphorylation– Net gain of two ATP molecules, two molecules of NADH, and

precursor metabolite pyruvic acid

Animation: Microbial Metabolism: Glycolysis: OverviewAnimation: Microbial Metabolism: Glycolysis: Overview

• Glycolysis– Divided into three stages involving ten total steps

– Energy-investment stage– Lysis stage– Energy-conserving stage

Animation: Microbial Metabolism: Glycolysis: StepsAnimation: Microbial Metabolism: Glycolysis: Steps

• Alternatives to Glycolysis– Yield fewer molecules of ATP than glycolysis– Reduce coenzymes and yield different metabolites needed in

anabolic pathways– Two pathways

– Pentose phosphate pathway – net gain of two molecules of NADPH, one molecule of ATP, and five-carbon precursor metabolites

– Entner-Doudoroff pathway – net gain of two molecules of NADPH, one molecule of ATP, and precursor metabolites

• Continuation of Cellular Respiration– Resultant pyruvic acid completely oxidized to produce ATP by a

series of redox reactions– Three stages of cellular respiration

1. Synthesis of acetyl-CoA2. Krebs cycle3. Final series of redox reactions (electron transport chain)

• Continuation of Cellular Respiration– Synthesis of acetyl-CoA

– Results in– Two molecules of acetyl-CoA– Two molecules of CO2

– Two molecules of NADH

• Continuation of Cellular Respiration– The Krebs cycle

– Great amount of energy remains in bonds of acetyl-CoA– The Krebs cycle transfers much of this energy to coenzymes

NAD+ and FAD– Occurs in cytoplasm of prokaryotes and in matrix of

mitochondria in eukaryotes

– Six types of reactions in Krebs cycle– Anabolism of citric acid– Isomerization reactions– Hydration reaction– Redox reactions– Decarboxylations– Substrate-level phosphorylation

Animation: Microbial Metabolism: Krebs Cycle—OverviewAnimation: Microbial Metabolism: Krebs Cycle—Overview

Animation: Microbial Metabolism: Krebs Cycle— StepsAnimation: Microbial Metabolism: Krebs Cycle— Steps

– Results in– Two molecules of ATP– Two molecules of FADH2

– Six molecules of NADH– Four molecules of CO2

• Continuation of Cellular Respiration– Electron transport

– Most significant production of ATP occurs through stepwise release of energy from series of redox reactions known as an electron transport chain (ETC)

– Consists of series of membrane-bound carrier molecules that pass electrons from one to another and ultimately to final electron acceptor

– Energy from electrons used to pump protons (H+) across the membrane, establishing a proton gradient

– Located in cristae of eukaryotes and in cytoplasmic membrane of prokaryotes

Animation: Microbial Metabolism: Electron Transport Chain: OverviewAnimation: Microbial Metabolism: Electron Transport Chain: Overview

• Continuation of Cellular Respiration– Electron transport

– Four categories of carrier molecules– Flavoproteins– Ubiquinones– Metal-containing proteins– Cytochromes

– Some organisms can vary their carrier molecules under different environmental conditions

– In aerobic respiration oxygen serves as final electron acceptor to yield water

– In anaerobic respiration molecules other than oxygen serve as final electron acceptor

Animation: Microbial Metabolism: Electron Transport Chain: The ProcessAnimation: Microbial Metabolism: Electron Transport Chain: The Process

Animation: Microbial Metabolism: Electron Transport Chain: Animation: Microbial Metabolism: Electron Transport Chain: Factors Affecting ATP YieldFactors Affecting ATP Yield

• Continuation of Cellular Respiration

– Chemiosmosis– Membrane maintains electrochemical gradient by keeping one or more

chemicals in higher concentration on one side– Cells use energy released in redox reactions of ETC to create proton

gradient, which has potential energy known as proton motive force– Protons, propelled by proton motive force, flow down electrochemical

gradient through ATP synthases (protein channels) that phosphorylate ADP to ATP

– Called oxidative phosphorylation because proton gradient created by oxidation of components of ETC

– Total of ~34 ATP molecules formed from one molecule of glucose

[INSERT TABLE 5.3]

• Fermentation– Sometimes cells cannot completely oxidize glucose by cellular

respiration– Cells require constant source of NAD+ that cannot be obtained by

simply using glycolysis and the Krebs cycle– In respiration, electron transport regenerates NAD+ from NADH

– Fermentation pathways provide cells with alternate source of NAD+

– Partial oxidation of sugar (or other metabolites) to release energy using an organic molecule from within the cell as an electron acceptor

[INSERT TABLE 5.4]

Animation: Microbial Metabolism: FermentationAnimation: Microbial Metabolism: Fermentation

Other Catabolic Pathways

• Lipid Catabolism• Protein Catabolism

Photosynthesis

• Every food chain begins with anabolic pathways in organisms that synthesize their own organic molecules from inorganic carbon dioxide

• Most of these organisms capture light energy from the sun and use it to drive the synthesis of carbohydrates from CO2 and H2O by a process called photosynthesis

Photosynthesis

Animation: Microbial Metabolism: Photosynthesis: Overview Animation: Microbial Metabolism: Photosynthesis: Overview

Photosynthesis

• Chemicals and Structures– Chlorophylls

– Most important of organisms that capture light energy with pigment molecules

– Composed of hydrocarbon tail attached to light-absorbing active site centered around magnesium ion

– Active sites structurally similar to cytochrome molecules in ETC

– Vary slightly in lengths and structures of hydrocarbon tails and in atoms that extend from active site

– They subsequently absorb light of different wavelengths

Photosynthesis

• Chemicals and Structures– Cells arrange molecules of chlorophyll and other pigments in

protein matrix to form light-harvesting matrices called photosystems

– Embedded in cellular membranes called thylakoids– In prokaryotes – invagination of cytoplasmic membrane– In eukaryotes – formed from infoldings of inner membrane of

chloroplasts– Arranged in stacks called grana– Stroma is space between outer membrane of grana and

thylakoid membrane

Photosynthesis

• Chemicals and Structures– Two types of photosystems

– Photosystem I (PS I)– Photosystem II (PS II)

– Photosystems absorb light energy and use redox reactions to store energy in the form of ATP and NADPH

– Classified as light-dependent reactions because they depend on light energy

– Light-independent reactions synthesize glucose from carbon dioxide and water

Photosynthesis

• Light-Dependent Reactions– As electrons move down the chain, their energy is used to pump

protons across the membrane– Photophosphorylation uses proton motive force to generate ATP– Photophosphorylation can be cyclic or noncyclic

Photosynthesis

Animation: Microbial Metabolism: Photosynthesis: Animation: Microbial Metabolism: Photosynthesis: Cyclic PhotophosphorylationCyclic Photophosphorylation

Photosynthesis

Animation: Microbial Metabolism: Photosynthesis: Animation: Microbial Metabolism: Photosynthesis: Noncyclic PhotophosphorylationNoncyclic Photophosphorylation

Photosynthesis

[INSERT TABLE 5.5]

Photosynthesis

• Light-Independent Reactions– Do not require light directly, but use ATP and NADPH generated

by light-dependent reactions– Key reaction is carbon fixation by Calvin-Benson cycle

– For every three molecules of CO2 that enter the cycle, one molecule of glyceraldehyde 3-phosphate leaves

– For every two molecules of glyceraldehyde 3-phosphate, one molecule of glucose 6-phosphate is anabolically synthesized by glycolysis

Photosynthesis

Animation: Microbial Metabolism: Photosynthesis: Animation: Microbial Metabolism: Photosynthesis: Light-Independent ReactionsLight-Independent Reactions

Other Anabolic Pathways

• Anabolic reactions are synthesis reactions requiring energy and a source of metabolites

• Energy derived from ATP from catabolic reactions• Glycolysis, the Krebs cycle, and the pentose phosphate pathway

provide twelve basic precursor metabolites from which all macromolecules and cellular structures are made

• Many anabolic pathways are the reversal of the catabolic pathways– Reactions that can proceed in either direction are amphibolic

[INSERT TABLE 5.6]

Integration and Regulation of Metabolic Function

• Cells synthesize or degrade channel and transport proteins• Cells often synthesize enzymes needed to catabolize a particular

substrate only when that substrate is available• If two energy sources are available, cells catabolize the more energy

efficient of the two first.• Cells synthesize the metabolites they need, but typically cease synthesis

if metabolite is available

• Eukaryotic cells keep metabolic processes from interfering with each other by isolating particular enzyme within membrane-bounded organelles

• Cells use allosteric sites on enzymes to control the activity of enzymes

• Feedback inhibition slows or stops anabolic pathways when product is in abundance

• Cells regulate amphibolic pathways that use the same substrate by requiring different coenzymes for each pathway

• Two types of regulatory mechanisms– Control of gene expression

– Cells control amount and timing of protein (enzyme) production– Control of metabolic expression

– Cells control activity of proteins (enzymes) once produced

Animation: Microbial Metabolism: Metabolism: The Big PictureAnimation: Microbial Metabolism: Metabolism: The Big Picture

start here_ch05_lecture

basic chemical reactions

microbial metabolism

metabolism animation

metabolism catabolism

nutrients metabolism

metabolism oxidation

metabolism naming

electron reactions

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