metabolism biol 3702: chapter 10 introduction to...

BIOL 3702: Chapter 10 AY 2015-2016

Dr. Cooper 1

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: v Catabolism

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

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

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

Metabolism (cont.)

v Anabolism Ø The synthesis of complex organic molecules from

simpler ones Ø Requires energy from fueling reactions


http://antranik.org/anabolic-and-catabolic-reactions/

Energy and Work

u Energy - the ability to do work u Living organisms carry out three essential

types of work using energy: v Chemical - synthesis of complex biological

molecules v Transport - uptake of nutrients, elimination of

wastes, and maintenance of internal ion balances

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


Energy and Work (cont.)

u Biological energy comes from two main sources v Photosynthesis - process which uses the

ultimate source of energy, visible light v Aerobic respiration - breakdown of complex

molecules with oxygen as the terminal electron acceptor

v Anaerobic 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 groups v To form the bonds, energy is required v To break the bonds, energy is released

Slide No. 7 BIOL 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


Oxidation-Reduction Reactions (cont.)

u Transfer of electrons from a donor to an acceptor v Can result in energy release, which can be

conserved and used to form ATP v The more electrons a molecule has, the more

energy rich it is


Oxidation-Reduction Reactions (cont.)

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

reaction) v Acceptor and donor are conjugate redox pair

Ø 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) v Location

Ø Plasma membranes of chemoorganotrophs in bacteria and archaeal cells

Ø  Internal mitochondrial membranes in eukaryotic cells v Examples of electron carriers include NAD,

NADP, and others v First carrier is reduced and electrons moved to

the next carrier and so on

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

Ø Oxidized form - NAD+ Ø Reduced form - NADH

v Nicotinamide adenine dinucleotide phosphate Ø 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.mheducation.com/sites/0073402400/student_view0/index.html

Slide No. 17

Figure 10.8


Electron Transport Chain (cont.)

v Flavin adenine dinucleotide Ø Oxidized form - FAD+ Ø Reduced form - FADH

v Others involved in many respiratory electron chains Ø Coenzyme Q (ubiquinone) Ø Various cytochromes Ø 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 reactants v Catalyst increases the rate of a reaction without

being permanently altered itself v Reacting molecules are termed substrates v The resulting molecules of a reaction are termed

products


(Source: Black 1999)


BIOL 3702: Chapter 10 AY 2015-2016

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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 cofactor v Apoenzyme - protein portion v Cofactor - non-protein portion

Ø Firmly attached - prosthetic group Ø Loosely attached - coenzyme




Enzymes (cont.)

u Six classes of enzymes [Table 10.3]


Enzymes (cont.)

u Mechanism of action v Enzymes 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.)

v Activation energy is lowered through bringing reactants into close proximity with one another and in the proper orientation Ø 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.)

v Enzymes use two models to perform this function Ø 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: v Substrate concentration

Ø Low concentrations - slow reactions Ø Higher concentrations - increase reaction rates until

saturation is achieved v pH and temperature

Ø 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



BIOL 3702: Chapter 10 AY 2015-2016

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Enzymes (cont.)

u Enzyme Inhibition - activity can be stopped by two distinct mechanisms: v Competitive inhibition - a molecule closely

resembling the true substrate competes with it for binding at the active site

v Noncompetitive 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 reactions v Catalyze peptide bond formation v Self-splicing v 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: v Controlling the number of enzyme molecules

present v Metabolic channeling - localization of enzymes

and metabolites v Post-translational control of enzyme activity -

stimulating or inhibiting enzymatic function Slide No. 41 BIOL 3702: Microbiology (2015)


Metabolic Regulation (cont.)

u Metabolic channeling v Microbes utilize compartmentation to segregate

particular enzymes and metabolites into different organelles or cell structures to regulate metabolism Ø Provides simultaneous, but separate operation and

regulation of similar pathways Ø Coordinates pathways via transport of metabolites

and cofactors between cellular compartments v Channeling may occur in compartments


BIOL 3702: Chapter 10 AY 2015-2016

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u Post-translational control of enzyme activity regulates many metabolic pathways using several different mechanisms: v Allosteric regulation v Covalent modification v Feedback inhibition [each of these mechanisms is described in further detail on the following slides]



v Allosteric regulation Ø Activity of regulatory enzymes, known as allosteric

enzymes, 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



v Covalent 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


v Feedback inhibition Ø 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


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