chapter 10 lecture notes - youngstown state...

BIOL 3702: Chapter 10 AY 2015-2016

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Slide No. 1

BIOL 3702: Chapter 10

Introduction to Metabolism

BIOL 3702: Microbiology (2015)Portions Copyright © The McGraw-Hill Companies, Inc. and Copyright © C. R. Cooper, Jr.

Metabolism

u Metabolism is the sum total of all the chemical reactions occurring in a cell

u Two major parts of metabolism:vCatabolism

Ø Large, more complex molecules are broken down into smaller, simpler molecules with the release of energy

Ø Fueling reactionsØ Energy-conserving reactions Ø Provide ready source or reducing power (electrons)Ø Generate precursors for biosynthesis

Slide No. 2BIOL 3702: Microbiology (2015)Portions Copyright © The McGraw-Hill Companies, Inc. and Copyright © C. R. Cooper, Jr.

Metabolism (cont.)

vAnabolismØ The synthesis of complex organic molecules from simpler ones

Ø Requires energy from fueling reactions


http://antranik.org/anabolic-and-cat aboli c-reactions/

Energy and Work

u Energy - the ability to do worku Living organisms carry out three essential types of work using energy:vChemical - synthesis of complex biological molecules

vTransport - uptake of nutrients, elimination of wastes, and maintenance of internal ion balances

vMechanical - change the physical location of organisms, cells, or internal structures


Energy and Work (cont.)

u Biological energy comes from two main sourcesvPhotosynthesis - process which uses the ultimate source of energy, visible light

vAerobic respiration - breakdown of complex molecules with oxygen as the terminal electron acceptor

vAnaerobic respiration and fermentation also contribute to energy production



u Much of the energy from these processes is transferred to the structure of adenosine 5’-triphosphate (ATP) which drives work

Slide No. 6

Figure 10.5


BIOL 3702: Chapter 10 AY 2015-2016

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u ATP is a high-energy molecule and serves as the energy currency of the cell

u ATP’s energy is “stored” in the covalent bonds of its two terminal phosphate groupsvTo form the bonds, energy is requiredvTo break the bonds, energy is released

Slide No. 7BIOL 3702: Microbiology (2015)Portions Copyright © The McGraw-Hill Companies, Inc. and Copyright © C. R. Cooper, Jr. Slide No. 8

Figure 10.3a



u Exergonic breakdown of ATP is coupled with endergonic reactions to make them more favorable

Slide No. 9

Figure 10.4


Oxidation-Reduction Reactions

u Many metabolic processes involve oxidation-reduction (“redox”) reactions (electron transfers)

u Electron carriers are often used to transfer electrons from an electron donor to an electron acceptor

Slide No. 10BIOL 3702: Microbiology (2015) Portions Copyright © The McGraw-Hill Companies, Inc. and Copyright © C. R. Cooper, Jr.

Oxidation-Reduction Reactions (cont.)

u Transfer of electrons from a donor to an acceptorvCan result in energy release, which can be conserved and used to form ATP

vThe more electrons a molecule has, the more energy rich it is


Oxidation-Reduction Reactions (cont.)

u Redox reactions can be considered two half reactionsvOne is electron donating (oxidizing reaction)vOne is electron accepting reaction (reducing reaction)

vAcceptor and donor are conjugate redox pairØ Acceptor + e-Ø Donor - e-


BIOL 3702: Chapter 10 AY 2015-2016

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Electron Transport Chain

u Electron carriers are often organized into an electron transport chain (ETC)vLocation

Ø Plasma membranes of chemoorganotrophs in bacteria and archaeal cells

Ø Internal mitochondrial membranes in eukaryotic cellsvExamples of electron carriers include NAD, NADP, and others

vFirst carrier is reduced and electrons moved to the next carrier and so on

Slide No. 13BIOL 3702: Microbiology (2015)Portions Copyright © The McGraw-Hill Companies, Inc. and Copyright © C. R. Cooper, Jr. Slide No. 14BIOL 3702: Microbiology (2015)

Portions Copyright © The McGraw-Hill Companies, Inc. and Copyright © C. R. Cooper, Jr.

Figure 10.7

Electron Transport Chain (cont.)

u Some common electron carrier molecules important in metabolism:vNicotinamide adenine dinucleotide

Ø Oxidized form - NAD+Ø Reduced form - NADH

vNicotinamide adenine dinucleotide phosphateØ Oxidized form - NADP+Ø Reduced form - NADPH



To view this video, go to Chapter 10 Animations of Prescott's Microbiology Companion Site (9th ed.) located at the following URL: http://highered .mhe du cati on. com/si tes /0 073 40 24 00 /st ude nt _vie w0/i nd ex. ht ml

Slide No. 17

Figure 10.8


Electron Transport Chain (cont.)

vFlavin adenine dinucleotideØ Oxidized form - FAD+Ø Reduced form - FADH

vOthers involved in many respiratory electron chainsØ Coenzyme Q (ubiquinone)Ø Various cytochromesØ Nonheme iron proteins, e.g., ferredoxin


BIOL 3702: Chapter 10 AY 2015-2016

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Slide No. 19

Figure 10.9

BIOL 3702: Microbiology (2015)Portions Copyright © The McGraw-Hill Companies, Inc. and Copyright © C. R. Cooper, Jr. Slide No. 20

Figure 10.10






Enzymes

u Enzymes are protein catalysts having great specificity for a particular reaction and its reactantsvCatalyst increases the rate of a reaction without being permanently altered itself

vReacting molecules are termed substratesvThe resulting molecules of a reaction are termed products


(Source: Black 1999)


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Enzymes (cont.)

u Most enzymes are pure proteins whereas others are a mixture of proteins and other substances

u Holoenzyme - complete enzyme consisting of the apoenzyme and its cofactorvApoenzyme - protein portionvCofactor - non-protein portion

Ø Firmly attached - prosthetic groupØ Loosely attached - coenzyme




Enzymes (cont.)

u Six classes of enzymes [Table 10.3]


Enzymes (cont.)

u Mechanism of actionvEnzymes increase reaction rates without altering equilibrium constants

v In simplest terms, enzymes lower a reaction’s activation energy - amount of energy required for reacting molecules to reach the transition state


Slide No. 29

Figure 10.15


Enzymes (cont.)

vActivation energy is lowered through bringing reactants into close proximity with one another and in the proper orientationØ Active (catalytic) site - special location on the enzyme where substrates bind

Ø Enzyme-substrate complex is formed as a result of this binding


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Slide No. 31



Enzymes (cont.)

vEnzymes use two models to perform this functionØ Lock-and-key model - rigid and specific sites

Ø Induced fit model -wraps around substrate(s)

Slide No. 32

Lock-and-key model


Slide No. 33

Induce fit model

BIOL 3702: Microbiology (2015)Portions Copyright © The McGraw-Hill Companies, Inc. and Copyright © C. R. Cooper, Jr. Slide No. 34

Induce fit model


Figure 10.16

Enzymes (cont.)

u Factors that affect enzyme activity:vSubstrate concentration

Ø Low concentrations - slow reactionsØ Higher concentrations - increase reaction rates until saturation is achieved

vpH and temperatureØ Enzymes have pH and temperature optima at which they have maximum activity (often reflects their environmental habitat)

Ø Very high pH levels or temperature leads to denaturation of the enzyme, i.e., destruction of the peptide structure



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Enzymes (cont.)

u Enzyme Inhibition - activity can be stopped by two distinct mechanisms:vCompetitive inhibition - a molecule closely resembling the true substrate competes with it for binding at the active site

vNoncompetitive inhibition - a molecule binds to the enzyme at some other portion other than the active site, inducing a conformational (shape) change to the enzyme rendering it inactive or less active


Competitive Inhibition

Figure 9.18


Slide No. 39

Non-competitive Inhibition



Enzymes (cont.)

u Thomas Cech and Sidney Altman discovered that some RNA molecules also can catalyze reactionsvCatalyze peptide bond formationvSelf-splicingv Involved in self-replication


Metabolic Regulation

u Microbes must coordinate metabolism to conserve energy and resources, as well as to maintain metabolic balance

u Carbon flow is regulated in three ways:vControlling the number of enzyme molecules present

vMetabolic channeling - localization of enzymes and metabolites

vPost-translational control of enzyme activity -stimulating or inhibiting enzymatic function


Metabolic Regulation (cont.)

u Metabolic channelingvMicrobes utilize compartmentation to segregate particular enzymes and metabolites into different organelles or cell structures to regulate metabolismØ Provides simultaneous, but separate operation and regulation of similar pathways

Ø Coordinates pathways via transport of metabolites and cofactors between cellular compartments

vChanneling may occur in compartments


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u Post-translational control of enzyme activity regulates many metabolic pathways using several different mechanisms:vAllosteric regulationvCovalent modificationvFeedback inhibition[each of these mechanisms is described in further detail on the following slides]



vAllosteric regulationØ Activity of regulatory enzymes, known as allostericenzymes, altered by a small molecules (effector[modulator] molecule)

Ø Effector binds to a site (regulatory site) separate from the catalytic site changing the enzyme’s shape and either§ Substrate affinity, or§ Velocity of the reaction


Slide No. 45

Figure 10.19



vCovalent modification Ø Some of these same enzymes are allosteric, thereby adding a second level of regulation and giving the enzyme more dynamic properties

Ø Also, regulation of enzymes that catalyze the covalent modification can occur, further adding another layer of regulation to a metabolic pathway



Figure 10.20


vFeedback inhibitionØ Reversible inhibition of a key regulatory enzyme (pacemaker) in a pathway that usually catalyzes the slowest or rate-limiting reaction

Ø Typically regulated by the end-product of the pathway in a process known as feedback (end product) inhibition

Slide No. 48

Figure 10.21


BIOL 3702: Chapter 10 AY 2015-2016

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