Essential Concepts of Essential Concepts of MetabolismMetabolism

Chapter 5Chapter 5

Microbiology 130Microbiology 130

Metabolism: An OverviewMetabolism: An Overview

Metabolism-Metabolism-

AnabolismAnabolism

Catabolism-Catabolism-

- electron transfer- electron transfer

Oxydation-Oxydation-

Reduction-Reduction-

How do microbes obtain energy?How do microbes obtain energy?Autotrophs- self feeders, use CO2 to Autotrophs- self feeders, use CO2 to sysnthesis sysnthesis organic compoundsorganic compounds

- Photoautotrophs- use sunlight for - Photoautotrophs- use sunlight for energyenergy

- Chemoautotrophs- use inorganics such as - Chemoautotrophs- use inorganics such as sulfides and nitrites for energysulfides and nitrites for energy

Heterotrophs- other feeders, use organic Heterotrophs- other feeders, use organic molecules,molecules,

- Photoheterotrophs-obtain chemical energy - Photoheterotrophs-obtain chemical energy from from lightlight

- Chemoheterotrophs- obtain energy from - Chemoheterotrophs- obtain energy from ready ready made organic compoundsmade organic compounds

What Is Energy?What Is Energy?Capacity to do workCapacity to do work

Forms of energyForms of energy– Potential energy, Potential energy, – Kinetic energyKinetic energy– Chemical energyChemical energy– What Can Cells Do With Energy?What Can Cells Do With Energy?

Cells use energy for:Cells use energy for:

– Chemical workChemical work

– Mechanical workMechanical work

– Electrochemical workElectrochemical work

One-Way Flow of EnergyOne-Way Flow of EnergyThe sun is life’s primary energy sourceThe sun is life’s primary energy source

Producers trap energy from the sun Producers trap energy from the sun and convert it into chemical bond and convert it into chemical bond energyenergy

AllAll organisms use the energy stored in organisms use the energy stored in the bonds of organic compounds to do the bonds of organic compounds to do work work

Endergonic ReactionsEndergonic Reactions

Energy input Energy input

requiredrequired

Product has more Product has more

energy than energy than

starting substancesstarting substances

glucose, a high energy product

ENERGY IN

low energy starting substances

6

+ 6O2

6

66

Exergonic ReactionsExergonic ReactionsEnergy is Energy is releasedreleased

Products have Products have less energy less energy than starting than starting substancesubstance

glucose, a high energy starting substance

+ 6O2

6 6

low energy products

ENERGY OUT

The Role of ATPThe Role of ATP

Cells “earn” ATP in exergonic reactionsCells “earn” ATP in exergonic reactions

Cells “spend” ATP in endergonic reactionsCells “spend” ATP in endergonic reactions

base

sugar

three phosphate

groups

ATP/ADP CycleATP/ADP Cycle

When adenosine triphosphate (ATP) When adenosine triphosphate (ATP) gives up a phosphate group, adenosine gives up a phosphate group, adenosine diphosphate (ADP) formsdiphosphate (ADP) forms

ATP can re-form when ADP binds to ATP can re-form when ADP binds to inorganic phosphate or to a phosphate inorganic phosphate or to a phosphate group that was split from a different group that was split from a different moleculemolecule

Regenerating ATP by this ATP/ADP cycle Regenerating ATP by this ATP/ADP cycle helps drive most metabolic reactionshelps drive most metabolic reactions

Participants in Participants in Metabolic ReactionsMetabolic Reactions

Energy carriersEnergy carriers

EnzymesEnzymes

CofactorsCofactors

Transport proteinsTransport proteins

ReactantsReactants

IntermediatesIntermediates

ProductsProducts

Chemical EquilibriumChemical Equilibrium

At equilibrium, the energy in the At equilibrium, the energy in the reactants equals that in the productsreactants equals that in the products

Product and reactant molecules Product and reactant molecules usually differ in energy contentusually differ in energy content

Therefore, at equilibrium, the Therefore, at equilibrium, the amount of reactant almost never amount of reactant almost never equals the amount of product equals the amount of product

Chemical EquilibriumChemical Equilibrium

Redox ReactionsRedox Reactions

Cells release energy efficiently by Cells release energy efficiently by electron transfers, or oxidation-electron transfers, or oxidation-reduction reactions (“redox” reduction reactions (“redox” reactions)reactions)One molecule gives up electrons (is One molecule gives up electrons (is oxidized) and another gains them oxidized) and another gains them (is reduced)(is reduced)Hydrogen atoms are commonly Hydrogen atoms are commonly released at the same time, thus released at the same time, thus becoming Hbecoming H++

Electron Transfer ChainsElectron Transfer Chains

Arrangement of enzymes, Arrangement of enzymes,

coenzymes, at cell membranecoenzymes, at cell membrane

As one molecule is oxidized, next is As one molecule is oxidized, next is

reduced reduced

Function in aerobic respiration and Function in aerobic respiration and

photosynthesisphotosynthesis

Uncontrolled vs. Controlled Uncontrolled vs. Controlled Energy ReleaseEnergy Release

H2 1/2 O2

Explosive release of energy asheat that cannot be harnessedfor cellular work

H2O

H2

2H+ 2e-

Energy input splits hydrogenInto protons (H+) and electrons

Somereleased energy isharnessedfor cellular work (e.g., making ATP)

2H+

H2O

1/2 O2

2e-

1/2 O2

Electrons transferred through electron transfer chain

Spent electrons and free oxygen form water.

Metabolic PathwaysMetabolic Pathways

Defined as enzyme-Defined as enzyme-mediated sequences mediated sequences of reactions in cellsof reactions in cells– Biosynthetic (anabolic) Biosynthetic (anabolic)

– – ex: ex:

photosynthesisphotosynthesis– Degradative (catabolic) Degradative (catabolic)

– – ex: aerobic ex: aerobic

respirationrespiration

ENERGY IN ENERGY IN

organiccompounds,

oxygen

photosynthesis

aerobic respiration

ENERGY OUT

carbondioxide,

water

Enzyme Structure Enzyme Structure and Functionand Function

Enzymes are catalytic moleculesEnzymes are catalytic molecules

They speed the rate at which reactions They speed the rate at which reactions approach equilibriumapproach equilibrium

Four Features of EnzymesFour Features of Enzymes

1) Enzymes do not make anything 1) Enzymes do not make anything happen that could not happen on its happen that could not happen on its own. They just make it happen own. They just make it happen much faster.much faster.

2) Reactions do not alter or use up 2) Reactions do not alter or use up enzyme molecules.enzyme molecules.

Four Features of EnzymesFour Features of Enzymes

3) The same enzyme usually works for 3) The same enzyme usually works for

both the forward and reverse both the forward and reverse reactions.reactions.

4) Each type of enzyme recognizes and 4) Each type of enzyme recognizes and binds to only certain substrates.binds to only certain substrates.

Activation EnergyActivation Energy

For a reaction to For a reaction to occur, an energy occur, an energy barrier must be barrier must be surmountedsurmounted

Enzymes make Enzymes make the energy the energy barrier smallerbarrier smaller

activation energywithout enzyme

activation energywith enzyme

energyreleased

by thereaction

products

starting substance

How Catalase WorksHow Catalase Works

Induced-Fit ModelInduced-Fit Model

Substrate molecules are brought Substrate molecules are brought togethertogether

Substrates are oriented in ways Substrates are oriented in ways that favor reactionthat favor reaction

Active sites may promote acid-Active sites may promote acid-base reactionsbase reactions

Active sites may shut out waterActive sites may shut out water

Factors Influencing Factors Influencing Enzyme ActivityEnzyme Activity

Temperature Temperature

pHpH

Salt concentrationSalt concentration

Allosteric regulatorsAllosteric regulators

Coenzymes and cofactorsCoenzymes and cofactors

Enzyme Helpers Enzyme Helpers

CofactorsCofactors– CoenzymesCoenzymes

NADNAD++, NADP, NADP++, FAD, FAD

Accept electrons and hydrogen ions; transfer Accept electrons and hydrogen ions; transfer them within cellthem within cell

Derived from vitaminsDerived from vitamins

– Metal ionsMetal ionsFerrous iron in cytochromesFerrous iron in cytochromes

Allosteric ActivationAllosteric Activation

allosteric activator

vacantallosteric binding site

active site altered, can bind substrate

active site cannot bind substrate

enzyme active site

Allosteric InhibitionAllosteric Inhibition

allosteric inhibitor

allosteric binding site vacant; active site can bind substrate

active site altered, can’t bind substrate

Feedback InhibitionFeedback Inhibition

enzyme 2 enzyme 3 enzyme 4 enzyme 5

enzyme 1

SUBSTRATE

END PRODUCT

(tryptophan)

A cellular change, caused by a specific activity, shuts down the activity that brought it about

Effect of TemperatureEffect of Temperature

Small increase in Small increase in temperature temperature increases molecular increases molecular collisions, reaction collisions, reaction ratesratesHigh temperatures High temperatures disrupt bonds and disrupt bonds and destroy the shape of destroy the shape of active site active site

Effect of pHEffect of pH

Producing the Universal Currency Producing the Universal Currency of Life of Life

All energy-releasing pathways All energy-releasing pathways – require characteristic starting materialsrequire characteristic starting materials

– yield predictable products and by-yield predictable products and by-

products products

– produce ATP produce ATP

Main Types of Main Types of Energy-Releasing PathwaysEnergy-Releasing Pathways

Anaerobic pathwaysAnaerobic pathways

Evolved firstEvolved firstDon’t require oxygenDon’t require oxygenStart with glycolysis in cytoplasmStart with glycolysis in cytoplasmCompleted in cytoplasmCompleted in cytoplasm

Aerobic pathwaysAerobic pathways

Evolved laterEvolved laterRequire oxygenRequire oxygenStart with glycolysis in cytoplasmStart with glycolysis in cytoplasmCompleted in mitochondriaCompleted in mitochondria

Energy-Releasing PathwaysEnergy-Releasing Pathways

Main Pathways Start Main Pathways Start with Glycolysiswith Glycolysis

Glycolysis occurs in cytoplasmGlycolysis occurs in cytoplasm

Reactions are catalyzed by enzymesReactions are catalyzed by enzymes

GlucoseGlucose 2 Pyruvate2 Pyruvate

(six carbons) (six carbons) (three (three carbons)carbons)

The Role of CoenzymesThe Role of Coenzymes

NADNAD++ and FAD accept electrons and and FAD accept electrons and hydrogen from intermediates during hydrogen from intermediates during the first two stagesthe first two stagesWhen reduced, they are NADH and When reduced, they are NADH and FADHFADH22

In the third stage, these coenzymes In the third stage, these coenzymes deliver the electrons and hydrogen to deliver the electrons and hydrogen to the transfer chainthe transfer chain

Anaerobic Pathways Anaerobic Pathways

Do not use oxygenDo not use oxygen

Produce less ATP than aerobic pathwaysProduce less ATP than aerobic pathways

Two types of fermentation pathwaysTwo types of fermentation pathways

– Alcoholic fermentationAlcoholic fermentation

– Lactate fermentationLactate fermentation

Fermentation PathwaysFermentation PathwaysBegin with glycolysisBegin with glycolysis

Do not break glucose down completely to Do not break glucose down completely to

carbon dioxide and watercarbon dioxide and water

Yield only the 2 ATP from glycolysisYield only the 2 ATP from glycolysis

Steps that follow glycolysis serve only to Steps that follow glycolysis serve only to

regenerate NADregenerate NAD++

Alcoholic FermentationAlcoholic Fermentation

C6H12O6

ATP

ATPNADH

2 acetaldehyde

electrons, hydrogen from NADH

2 NAD+

2

2 ADP

2 pyruvate

2

4

energy output

energy input

glycolysis

ethanol formation

2 ATP net

2 ethanol

2 H2O

2 CO2

YeastsYeasts

Single-celled fungiSingle-celled fungi

Carry out alcoholic fermentationCarry out alcoholic fermentation

Saccharomyces cerevisiaeSaccharomyces cerevisiae– Baker’s yeastBaker’s yeast– Carbon dioxide makes bread dough rise Carbon dioxide makes bread dough rise

Saccharomyces ellipsoideusSaccharomyces ellipsoideus– Used to make beer and wineUsed to make beer and wine

Lactate FermentationLactate Fermentation

Carried out by certain bacteriaCarried out by certain bacteria

Electron transfer chain is in bacterial Electron transfer chain is in bacterial plasma membrane plasma membrane

Final electron acceptor is compound Final electron acceptor is compound from environment (such as nitrate), from environment (such as nitrate), notnot oxygen oxygen

ATP yield is lowATP yield is low

Lactate FermentationLactate Fermentation

C6H12O6

ATP

ATPNADH

2 lactate

electrons, hydrogen from NADH

2 NAD+

2

2 ADP

2 pyruvate

2

4

energy output

energy input

glycolysis

lactate formation

2 ATP net

Carbohydrate Breakdown Carbohydrate Breakdown and Storageand Storage

Glucose is absorbed into bloodGlucose is absorbed into blood

Pancreas releases insulinPancreas releases insulin

Insulin stimulates glucose uptake by cellsInsulin stimulates glucose uptake by cells

Cells convert glucose to glucose-6-Cells convert glucose to glucose-6-

phosphatephosphate

This traps glucose in cytoplasm where it This traps glucose in cytoplasm where it

can be used for glycolysiscan be used for glycolysis

Glycolysis Occurs Glycolysis Occurs in Two Stages in Two Stages

Energy-requiring stepsEnergy-requiring steps

– ATP energy activates glucose and its six-ATP energy activates glucose and its six-

carbon derivativescarbon derivatives

Energy-releasing stepsEnergy-releasing steps

– The products of the first part are split into The products of the first part are split into

three-carbon pyruvate moleculesthree-carbon pyruvate molecules

– ATP and NADH formATP and NADH form

Energy-Requiring StepsEnergy-Requiring Steps

ATP

ATP

2 ATP invested

ENERGY-REQUIRING STEPSOF GLYCOLYSIS

glucose

ADP

ADP

P

P

P

P

glucose–6–phosphate

fructose–6–phosphate

fructose–1,6–bisphosphate DHAP

Energy-Releasing StepsEnergy-Releasing Steps

ATP

PGAL PGAL

ATP

NADH NADH

ATP ATP

2 ATP invested

ENERGY-RELEASING STEPS OF GLYCOLYSIS

2 ATP invested

NAD+

Pi

NAD+

Pi

3-phosphoglycerate 3-phosphoglycerate

2-phosphoglycerate 2-phosphoglycerate

PEP PEP

ADP ADP

1,3-bisphosphoglycerate 1,3-bisphosphoglycerateP P P P

P P

P P

P P

pyruvate pyruvate

to second set of reactions

substrate-level phosphorylation

substrate-level phosphorylation

H2O H2O

ADP ADP

Net Energy Yield Net Energy Yield from Glycolysisfrom Glycolysis

Energy requiring steps:Energy requiring steps: 2 ATP invested2 ATP invested

Energy releasing steps:Energy releasing steps:2 NADH formed 2 NADH formed 4 ATP formed4 ATP formed

Net yield is 2 ATP and 2 NADHNet yield is 2 ATP and 2 NADH

Overview of Aerobic RespirationOverview of Aerobic Respiration

Overview of Aerobic RespirationOverview of Aerobic Respiration

CC66HH12120066 + 6O + 6O22 6CO6CO22 + 6H + 6H2200 glucose oxygen carbon waterglucose oxygen carbon water

dioxide dioxide

Overview of Aerobic RespirationOverview of Aerobic Respirationcytoplasm

mitochondrion

GLYCOLYSIS

ELECTRON TRANSPORT

PHOSPHORYLATION

KrebsCycle ATP

ATP

energy input to start reactions

2 CO2

4 CO2

2

32

water

2 NADH

8 NADH

2 FADH2

2 NADH2 pyruvate

e- + H+

e- + oxygen

(2 ATP net)

glucose

TYPICAL ENERGY YIELD: 36 ATP

e-

e- + H+

e- + H+

ATP

H+

e- + H+

ATP2

Second-Stage ReactionsSecond-Stage ReactionsOccur in the mitochondriaOccur in the mitochondria

Pyruvate is broken down to carbon dioxidePyruvate is broken down to carbon dioxide

More ATP is formedMore ATP is formed

More coenzymes are reduced More coenzymes are reduced

Two Parts of Second StageTwo Parts of Second Stage

Preparatory reactionsPreparatory reactions– Pyruvate is oxidized into two-carbon Pyruvate is oxidized into two-carbon

acetyl units and carbon dioxideacetyl units and carbon dioxide– NADNAD++ is reduced is reduced

Krebs cycleKrebs cycle– The acetyl units are oxidized to carbon The acetyl units are oxidized to carbon

dioxidedioxide– NADNAD+ + and FAD are reducedand FAD are reduced

Preparatory ReactionsPreparatory Reactions

pyruvate + coenzyme A + NADpyruvate + coenzyme A + NAD++

acetyl-CoA + NADH + COacetyl-CoA + NADH + CO22

One of the carbons from pyruvate is released in One of the carbons from pyruvate is released in COCO22

Two carbons are attached to coenzyme A and Two carbons are attached to coenzyme A and continue on to the Krebs cyclecontinue on to the Krebs cycle

Using GlycogenUsing Glycogen

When blood levels of glucose decline, When blood levels of glucose decline,

pancreas releases glucagonpancreas releases glucagon

Glucagon stimulates liver cells to convert Glucagon stimulates liver cells to convert

glycogen back to glucose and to release it glycogen back to glucose and to release it

to the bloodto the blood

(Muscle cells do not release their stored (Muscle cells do not release their stored

glycogen)glycogen)

Energy ReservesEnergy Reserves

Glycogen makes up only about 1 percent Glycogen makes up only about 1 percent

of the body’s energy reservesof the body’s energy reserves

Proteins make up 21 percent of energy Proteins make up 21 percent of energy

reservesreserves

Fat makes up the bulk of reserves (78 Fat makes up the bulk of reserves (78

percent)percent)

Energy from FatsEnergy from Fats

Most stored fats are triglyceridesMost stored fats are triglycerides

Triglycerides are broken down to glycerol and fatty acids Triglycerides are broken down to glycerol and fatty acids

Glycerol is converted to PGAL, an intermediate of glycolysisGlycerol is converted to PGAL, an intermediate of glycolysis

Fatty acids are broken down and converted to acetyl-CoA, Fatty acids are broken down and converted to acetyl-CoA,

which enters Krebs cyclewhich enters Krebs cycle

Energy from ProteinsEnergy from Proteins

Proteins are broken down to amino acidsProteins are broken down to amino acids

Amino acids are broken apartAmino acids are broken apart

Amino group is removed, ammonia forms, Amino group is removed, ammonia forms,

is converted to urea and excretedis converted to urea and excreted

Carbon backbones can enter the Krebs Carbon backbones can enter the Krebs

cycle or its preparatory reactionscycle or its preparatory reactions

Reaction SitesReaction Sites

FOOD

fats glycogen complex carbohydrates proteins

simple sugars(e.g., glucose) amino acids

glucose-6-phosphate

carbon backbones

NH3

urea

ATP

(2 ATP net)

PGAL

glycolysisATP2

glycerolfatty acids

NADH pyruvate

Acetyl-CoA

NADH CO2

KrebsCycle

NADH,FADH2

CO2

ATP

ATPATP

many ATP

fatsH+

e– + oxygen

e–

4

ATP2

Evolution of Metabolic PathwaysEvolution of Metabolic Pathways

When life originated, atmosphere had little When life originated, atmosphere had little oxygenoxygen

Earliest organisms used anaerobic pathwaysEarliest organisms used anaerobic pathways

Later, noncyclic pathway of photosynthesis Later, noncyclic pathway of photosynthesis

increased atmospheric oxygenincreased atmospheric oxygen

Cells arose that used oxygen as final Cells arose that used oxygen as final

acceptor in electron transferacceptor in electron transfer

Processes Are Processes Are LinkedLinked

Aerobic RespirationAerobic Respiration

ReactantsReactants

– Sugar Sugar

– OxygenOxygen

ProductsProducts

– Carbon dioxideCarbon dioxide

– WaterWaterPhotosynthesisPhotosynthesis

ReactantsReactants

– Carbon dioxideCarbon dioxide

– WaterWater

ProductsProducts

– Sugar Sugar

– OxygenOxygen

Life Is System Life Is System of Prolonging Orderof Prolonging Order

PowPowered by energy inputs from sun, life ered by energy inputs from sun, life continues onward through reproductioncontinues onward through reproduction

Following instructions in DNA, energy and Following instructions in DNA, energy and

materials can be organized, generation materials can be organized, generation

after generationafter generation

With death, molecules are released and With death, molecules are released and

may be cycled as raw material for next may be cycled as raw material for next

generation generation