Chapter 5, part AMicrobial Metabolism

Life fundamental feature: growth (metabolism)reproduction (heritable genetic information)

Organic compounds in life organismsCarbohydrates sugarsLipids fatty acids Proteins amino acids Nucleic acids - nucleotidesVitaminsChemical reactions involve the making or breaking of bonds between atoms.A change in chemical energy occurs during a chemical reaction.Endergonic reactions absorb energy.Synthesis reactionExergonic reactions release energy.Decomposition Reactions

CarbonEnergyWhat do all organisms need?

Metabolism is the sum of all chemical reactions that occur in living organisms to maintain life. Catabolism is breakdown and the energy-releasing processes.Provides energy and building blocks for anabolism.Anabolism is biosynthesis and the energy-using processesUses energy and building blocks to build large moleculesRole of ATP in Coupling Reactions

Nutritional ( metabolic) types of organisms Trophe = nutritionSources of energy Chemotrophs: Bond energy is released from a chemical compound Phototrophs: Light is absorbed in photo receptors and transformed into chemical energy.Sources of carbonAutotrophs: Carbon dioxide (CO2) is used as source of carbon Heterotrophs: Organic compounds are metabolized to get carbon for growth and development.

The collision theory states that chemical reactions can occur when atoms, ions, and molecules collide. Reaction rate:Activation energy - needed to disrupt electronic configurations.Frequency of collisions depends on concentration of the atoms and molecules

Reaction rate can be increased by:Increasing temperature or pressure.Lowering the activation energy - CatalystsEnzymes - biological catalysts

Chemical reactions - Collision theory

EnzymesLike all catalysts, enzymes work by lowering the activation energy for a reaction, thus dramatically increasing the rate of the reaction

Enzymatic reactions Substrates - The material or substance on which an enzyme acts (The molecules at the beginning of the process) EnzymeProducts - The molecules at the end the reaction

EnzymesEnzymes are biomolecules that catalyze ( increase the rates of) chemical reactions. Almost all enzymes are proteins.

RNA molecules called ribozymes are capable of performing specific biochemical reactions Peptidyl transferase is catalysed by the rRNA component of the large ribosomal subunit.Although most ribozymes are quite rare in the cell, their roles are sometimes essential to life

EnzymesLike all proteins, enzymes are made as long, linear chains of amino acids Each unique amino acid sequence (peptide) produces a specific structure (a three-dimensional product) , which has unique properties. Active site

The structure and chemical properties of the active site allow the recognition and binding of the substrate

Figure 5.2

EnzymesEnzyme-substrate complex - Substrates bind to the active site of the enzyme Bind through hydrogen bonds, hydrophobic interactions, temporary covalent bonds (van der waals) or a combination of all of these The active site modifies the reaction mechanism in order to decrease the activation energy of the reaction. The product is usually unstable in the active site, it is released and returns the enzyme to its initial unbound state. The turnover number is generally 1-10,000 molecules per second.

Enzymes are not used up in that reactionE + S ES EP E + P

EnzymesFigure 5.3Apoenzyme: proteinInactive

Cofactor: Nonprotein componentNAD+, (NADH)NADP+, (NADPH)FADCoenzyme: Organic cofactorVitaminsCoenzyme AHoloenzyme: Apoenzyme + cofactorActive

Factors Influencing Enzyme Activity1. Effect of Substrate Concentration on Enzyme ActivitySubstrate Product1 + Product2[E][S][P1][P2]* Point of saturation

Figure 5.5bFactors Influencing Enzyme Activity3. Effect of pH on Enzyme Activity2. Effect of Temperature on Enzyme ActivityEnzymes can be denatured by temperature and pH* Optimal temperature* Optimal pH

Inhibitors of Enzyme Activity1. Competitive inhibition competition for the active siteFigure 5.7a, b

Inhibitors of Enzyme Activity2. Noncompetitive inhibitionFigure 5.7a, c

Feedback inhibition of biochemical pathwaysThe term feedback inhibition refers to a situation in which the substances at the end of a long series of reactions inhibits a reaction at the begining of the series of reactions. Figure 5.8

A metabolic pathway is a sequence of chemical reactions occurring within a cell In each pathway, a principal chemical is modified by chemical reactions.

Enzymes catalyze these reactions often require dietary minerals, vitamins, and other cofactors in order to function proper

Metabolic pathways are determined by enzymes.Enzymes are encoded by genes.Metabolic Pathways

Starting moleculeE1E2E3intermediate Bend productintermediate A

EnzymesEnzymes are usually very specific as to which reactions they catalyze and the substrates that are involved in these reactions Enzyme Classification Oxidoreductase: Oxidation-reduction reactionsTransferase: Transfer functional groupsHydrolase: HydrolysisLyase: Removal of atoms without hydrolysisIsomerase: Rearrangement of atomsLigase: Joining of molecules, uses ATP

Oxidation is the removal of electrons.Reduction is the gain of electrons.Redox reaction is an oxidation reaction paired with a reduction reaction.Oxidation-ReductionFigure 5.9

In biological systems, the electrons are often associated with hydrogen atoms. Transfer of electrons or hydrogen atoms from one molecule (hydrogen or electron donor) to another (the acceptor) Biological oxidations are often dehydrogenations.Oxidation-ReductionFigure 5.10

Energy production - CatabolismCells use biological oxidation-reduction reactions in catabolism to breakdown organic compoundsRelease energy associated with the electrons that form bonds between their atoms

(substrate) (products)Energy released during certain metabolic reactions can be trapped to form ATPAddition of PO4- a to a molecule is called phosphorylation ATP is generated by the phosphorylation of ADP.

( C6H12O6) CO2 + H2O + energyhighly reduced compounds (with many hydrogen atoms)highly oxidized compounds

Generate ATP serves as a convenient energy carrier

During substrate-level phosphorylation, a high-energy from an intermediate in catabolism is added to ADP.

During oxidative phosphorylation, energy is released as electrons are passed to a series of electron acceptors (an electron transport chain) and finally to O2 or another inorganic compound.

During photophosphorylation, energy from light is trapped by chlorophyll, and electrons are passed through a series of electron acceptors. The electron transfer releases energy used for the synthesis of ATP.

The Generation of ATP

Catabolism Metabolic Pathways +ATP+ATP+ATP123

Most of a cells energy is produced from the oxidation of carbohydrates.Glycolysis - the most common pathway for the oxidation of glucose. Glucose is the most commonly used carbohydrate.One glucose molecule.End-product - Pyruvic acid 2 ATP and 2 NADH moleculesare produced Alternatives to GlycolysisThe pentose phosphate pathwayUsed to metabolize five-carbon sugars;One ATP and 12 NADPH molecules are produced from one glucose molecule.The Entner-Doudoroff pathway One ATP and two NADPH molecules from one glucose molecule. Does not involve glycolysisPseudomonas, Rhizobium, Agrobacterium

Carbohydrate Catabolism

GlycolysisPreparatory stage Energy-Conserving Stage2 Glucose-3-phosphate oxidized to 2 Pyruvic acid4 ATP produced2 NADH producedFigure 5.12.21,3-diphosphoglyceric acid3-phosphoglyceric acid2-phosphoglyceric acidPhosphoenolpyruvic acid(PEP)6789102 molecules Pyruvic acid2 ATPs are usedGlucose is split to form 2 Glucose-3-phosphate 1 molecule Glucose1 Glucose + 2 ATP + 2 ADP + 2 PO4 + 2 NAD+ 2 pyruvic acid + 4 ATP + 2 NADH + 2H+

substrate-level phosphorylation,

The two major types of glucose catabolism are:Respiration, in which glucose is completely broken downTo CO2 and H2O - aerobic respirationTo NO2, N2 , H2S, CH4 and H2O anaerobic respiration

Fermentation, in which glucose is partially broken down (organic molecule)Carbohydrate Catabolism

Pyruvic acid (from glycolysis) is oxidized and decarboyxlatedRespiration - Intermediate StepFigure 5.13.12 Pyruvic acid2 NADH

Respiration - Krebs CycleFigure 5.13.2 Oxidation of acetyl CoA produces NADH and FADH22 Acetyl CoA6 NADH2 FADH2

Respiration - The Electron Transport ChainA series of carrier molecules that are, in turn, oxidized and reduced as electrons are passed down the chain.

Energy released can be used to produce ATP by chemiosmosis

10 NADH2 FADH2

ChemiosmosisProtons being pumped across the membrane generate a proton motive force as electrons move through a series of acceptors or carriers.Energy produced from movement of the protons back across the membrane is used by ATP synthase to make ATP from ADP .Electron carriers are located: In eukaryotes in the inner mitochondrial membrane; In prokaryotesin the plasma membrane.

oxidative phosphorylation

Figure 5.17

ATP produced from complete oxidation of 1 glucose using aerobic respiration 36 ATPs are produced in eukaryotes.

PathwayBy substrate-level phosphorylationBy oxidative phosphorylationFrom NADHFrom FADHGlycolysis260Intermediate step06Krebs cycle2184Total4304

RespirationAerobic respiration The final electron acceptor in the electron transport chain is molecular oxygen (O2).Product - H2OAnaerobic respiration The final electron acceptor in the electron transport chain is not O2. .

Electron acceptorProductsNO3 (nitrate ion )NO2 (nitrite ion) , N2 O or N2 + H2OSO42 (sulfate ion) H2S + H2OCO32 (carbonate ion) CH4 + H2O

Respiration

PathwayEukaryoteProkaryoteGlycolysisCytoplasmCytoplasmIntermediate stepCytoplasmCytoplasmKrebs cycleMitochondrial matrixCytoplasmETCMitochondrial inner membranePlasma membrane

Learning objectivesDefine metabolism, and describe the fundamental differences between anabolism and catabolism.Identify the role of ATP as an intermediate between catabolism and anabolism.Identify the components of an enzyme.Describe the mechanism of enzymatic action.List the factors that influence enzymatic activity.Explain what is meant by oxidationreduction.List and provide examples of three types of phosphorylation reactions that generate ATP.Explain the overall function of biochemical pathways.Describe the chemical reactions of glycolysis.Explain the products of the Krebs cycle.Describe the chemiosmosis model for ATP generation.Compare and contrast aerobic and anaerobic respiration.

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