Metabolism• Metabolism in bacteria is similar to that in

eukaryotes.• Some bacterial enzymes (especially metabolic enzymes,

like oxidase) can be interchanged with human enzymes in laboratory experiments.

• However, bacteria also have unique enzymes that allow them to adapt to many niches.

• How do horses and cows digest cellulose?• How do bacteria live at the depths of the ocean?

– They have special enzymes which have been adapted for specific environments.

•Metabolism: pertains to all chemical reactions and physical workings of the cell

•Anabolism: -synthesis of molecules, requires the input of energy

•Catabolism:-breaks the bonds of larger molecules, releases energy

Metabolism

3

All Catabolic reactions involve electron transfer

• Electron transfer:– allows energy to be captured in high-energy bonds in ATP and similar

molceules.– Directly related to oxidation & reduction (remember those redox

reactions from chemistry?)• Oxidation=loss of electrons• Reduction=gain of electrons

• Imagine A=organic molecule like glucose

• Imagine B=NAD+ coenzyme, an electron carrier

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Rel

ati

ve

co

mp

lex

ity

of

mo

lec

ule

s

ANABOLISM

ANABOLISM

ANABOLISM

Nutrientsfrom outsideor frominternalpathways

Glycolysis

Krebs cycle

Respiratorychain

Fermentation

Yields energy Uses energy Uses energy Uses energy

Some assemblyreactions occurspontaneously

Complex lipids

RNA + DNA

Peptidoglycan

Proteins

Amino acids

Sugars

Nucleotides

Fatty acidsGlyceraldehyde-3-P

Acetyl CoA

Pyruvate

CATABOLISM

Glu

PheLys

Ala

ValGlucose

Precursormolecules

Macromolecules

Bacterialcell

Buildingblocks

Simplified Model of Metabolism

5

• In order for bonds to be FORMED or BROKEN, there has to be a minimal amount of energy available. This minimal amount of energy is termed “activation energy.”

How do chemical reactions take place?

How do chemical reactions take place?• Activation energy can be in the form of temperature or

pressure, etc. to increase the number of particle collisions.

• Paradoxically, the temperature and pressure that humans and bacteria would require for their chemical reactions would KILL them!

• How do we solve this problem?• ENZYMES!! • Enzymes reduce the amount of activation energy needed

for chemical reactions and speed them up so that life can continue.

Enzymes

• Enzymes have specific active sites that bind to specific substrates. • Bond formed between the substrate and enzyme are weak and easily reversible• Enzyme are fast!

- the number of substrate molecules converted per enzyme per second- Catalase reacts several million times per second- lactate dehydrogenase reacts a thousand times per second

Specific active sites arise due to the folding of the protein

9

Enzyme-substrate interactions

• Substrates specifically bind to the active sites on the enzyme– “lock-and-key”– Induced fit

• Once the reaction is complete, the product is released and the enzyme reused

Lock-and-key model

Induced fit model

Enzyme-Substrate Reactions

•The need of microorganisms for trace elements arises from their roles as cofactors for enzymes

-iron, copper, magnesium, manganese, zinc, cobalt, selenium, etc.

•Participate in precise functions between the enzyme and substrate

-help bring the active site and substrate close together

-participate directly in chemical reactions with the enzyme-substrate complex

Cofactors

Metalliccofactor

-organic compounds that work in conjunction with an enzyme

-general function is to remove a chemical group from one substrate molecule and add it to another substrate molecule

-carry and transfer hydrogen atoms, electrons, carbon dioxide, and amino groups

-many derived from vitamins

Coenzymes

Coenzyme

Apoenzyme

• The main enzyme portion is a globular protein called an apoenzyme

Example of how a coenzyme transfers chemical groups from one substrate to another

Constitutive enzymes: always present in relatively constant amounts regardless of the amount of substrate

Regulation of Enzymes

Regulated enzymes: production is turned on (induced) or turned off (repressed) in responses to changes in concentration of the substrate

Regulation of Enzymes

One type of genetic control of enzyme synthesisRegulation of Enzymes

•If E. coli is inoculated with only lactose, it will produce the enzyme lactase to hydrolyze the lactose into glucose and galactose

•If E. coli is inoculated with only sucrose, it will cease to synthesizing lactase and begin synthesizing sucrase

•Benefits:• Allows the organism to utilize a

variety of nutrients• Prevents wasting energy by

making enzymes for a substrate that is not present

Enzyme Induction in E. coli

•Activity of enzymes influenced by the cell’s environment• Natural temperature, pH, osmotic pressure• Denaturation: weak bonds that maintain the native shape of

the enzyme are broken

Regulation of Enzyme Function

Competitive inhibition-inhibits enzyme activity

by supplying a molecule that resembles the enzyme’s normal substrate

-“mimic” occupies the active site, preventing the actual substrate from binding

Inhibition of Enzymes

Noncompetitive inhibition

Noncompetitive inhibitors bind to an “allosteric” or “other” site on the enzyme, not the active site.

Inhibition of Enzymes

•Often occur in a multistep series or pathway, with each step catalyzed by an enzyme

•Product of one reaction is often the reactant (substrate) for the next, forming a linear chain or reaction

Metabolic Pathways

A

B

C

D

E

Linear

Example:Glycolysis

Many pathways have braches that provide alternate methods for nutrient processing

Metabolic Pathways

O2

O

O1

M

N

P

Q

R

M

A

B

C

N

X

Y

Z

Branched

Convergent

Example:Amino acidsynthesis

Divergent

Other pathways have a cyclic form, in which the starting molecule is regenerated to initiate another turn of the cycle

Metabolic Pathways

U

V

W

X

Z

Y

Cyclic

T input

KrebsCycle

S product

Metabolic pathways do not stand alone; they are interconnected and merge at many sites

Metabolic Pathways

CA

TA

BO

LIS

MA

NA

BO

LIS

M

Gly

coly

sis

Beta oxidationDeamination

GLUCOSE

Metabolicpathways

Simplepathways

Pyruvic acid

Acetyl coenzymeA

KrebsCycle

NH3 H2O

CO2

Building block

Macromolecule

Cellstructure

Membranesstorage

Cell wallstorage

Enzymes/Membranes

Chromosomes

Lipids/Fats

Starch/CelluloseProteins

Nucleicacids

Fatty acidsCarbohydratesAmino acidsNucleotides

•Oxidation: loss of electrons

•Reduction: gain of electrons

•Oxidoreductases: enzymes that remove electrons from one substrate and add them to another

-their coenzyme carriers are nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD)

Oxidation and Reduction

-+

Na 2 8 7Cl2 8 1

Oxidizing agentaccepts electrons.

Reducing agentgives up electrons.

Na 2 8 2 8 8Cl

Oxidizedcation

Reducedanion

Energy present in the electron acceptor can be captured to phosphorylate to ADP to store energy in ATP

Oxidation and Reduction

•Three-part molecule-nitrogen base

(adenine)-5-carbon sugar (ribose)-chain of three

phosphate groups bonded to ribose

-phosphate groups are bulky and carry negative charges, causing a strain between the last two phosphates making it very volatile

N

NN

N N

H H

H

H

O

HHH H

O

O

O

O

P O

O

H

HPP

Adenine

AdenosineAdenosine

Diphosphate(ADP)

AdenosineTriphosphate

(ATP)

HO

OH OH OH

OH

Ribose

OHBond that releasesenergy when broken

Adenosine Triphosphate- ATP

ATP can be used to phosphorylate an organic molecule

Ex. Phosphorylation of glucose to activate its catabolism

ATP and Phosphorylation

Electron carriers resemble shuttles that load and unload, electrons and hydrogens to facilitate transfer of redox energy

electrons availablein NADH and FADH2

H+

P

P

P

P

H++NAD+ NAD H

Reduced Nicotinamide

From substrate

Oxidized Nicotinamide

Adenine

Ribose

NH2

2H2e:

H

C

C C

C C

O

CH

NH2

H

C

C C

C C

O

C

N N

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Electron Carriers: Cell’s Reducing Power

Fermentation

ANAEROBIC RESPIRATION FERMENTATION

ATP ATP

AEROBIC RESPIRATION

CO2

NAD H

ATP

CO2

NAD H

ATP

NAD HCO2

ATPFADH2

Using organiccompounds as

electron acceptor

Electron Transport System Electron Transport System

Alcohols, acids

2 ATPs2–36 ATPs36–38 ATPsMaximum net yield

Yields variableamount ofenergy

Yields 2 GTPs

Yields 2 ATPs

CO2

NAD H

ATP

NAD H

FADH2 ATP

CO2

KrebsCycle

KrebsCycle

Using O2 as electron acceptor Using non- O2 compound as electron acceptor

(So42–, NO3–, CO3

2–)

Gly

co

lys

is

Gly

co

lys

is

Gly

co

lys

is

Overview of the Three Main Catabolic Pathways

-a series of reactions that converts glucose to CO2 and allows the cell to recover significant amounts of energy

-Complete breakdown of pyruvic acid into inorganicmolecules

-relies on free oxygen as the final electron

-characteristic of many bacteria, fungi, protozoa, and animals

Aerobic Respiration: Overview

ATP

Electron Transport System

36–38 ATPsMaximum net yield

CO2

NAD H

ATP

NAD H

FADH2 ATP

CO2

KrebsCycle

Using O2 as electron acceptor

Gly

co

lys

is

GlucoseGlucose

-uses NO3-, SO4

2-, CO33-, and other

oxidized compounds as final electron acceptors

-Like aerobic respiration there is a complete breakdown of pyruvic acid into inorganic molecules

-Unlike aerobic respiration, anaerobic respiration does not use all of the steps in the Kreb’s cycle.

-characteristic of bacteria that require or tolerate anaerobic conditions

Anaerobic Respiration: Overview

ATP

CO2

NAD H

ATP

NAD HCO2

ATPFADH2

Electron Transport System

2–36 ATPsMaximum net yield

KrebsCycle

Using non- O2 compound as electron acceptor

(So42–, NO3–, CO3

2–)

Gly

co

lys

is

GlucoseGlucose

• Unlike aerobic and anaerobic respiration pyruvic acid is not a completely broken down into inorganicmolecules

• Pyruvic acid is partially broken down

into organic compounds that are the final electron acceptors. Ex. lactic acid, ethanol…

• oxygen is not required

Fermentation: Overview

Fermentation

CO2

NAD H

ATP

Using organiccompounds as

electron acceptor

Alcohols, acids

2 ATPsMaximum net yield

Gly

co

lys

is

GlucoseGlucose

• Oxidation of glucose into pyruvate, which yields energy in the pathways that follow

• Occurs in cytoplasm of both eukaryotes and prokaryotes- Does this go against the Endosymbiotic theory?

Table 7.2

One reaction breaks fructose-1,6-diphosphateinto two 3-carbon molecules.

Five reactions convert each 3 carbon moleculeinto the 3C pyruvate.

Pyruvate is a molecule that is uniquely suited for chemicalreactions that will produce reducing power (which willeventually produce ATP).

C C C C C C

Fructose-1, 6-diphosphate

C C C C C C

C C CC C C

C C CC C C

Glycolysis

Energy Lost or Gained

Uses 2 ATPs

Overview Details

Three reactions alter and rearrange the6-C glucose molecule into 6-C fructose-1,6diphosphate.

Yields 4 ATPs and 2 NADHs

Total Energy Yield: 2 ATPs and2 NADHs

Glucose

Pyruvate Pyruvate

Glycolysis

Table 7.3

Each acetyl CoA yields 1 GTP, 3 NADHs,1 FADH, and 2 CO2 molecules.

Total Yield per 2 acetyl CoAs:CO2: 4 In the course of seven more

reactions, citrate is manipulatedto yield energy and CO2 andoxaloacetate is regenerated.

Intermediate molecules on thewheel can be shunted into othermetabolic pathways as well.

In the first reaction, acetyl CoAdonates 2Cs to the 4C moleculeoxaloacetate to form 6C citrate.

C C C

Energy: 2 GTPs, 6 NADHs, 2 FADHs

Pyruvate

CC CC CC

Details

The Krebs Cycle

Energy Lost or Gained Overview

Pyruvate

The 3C pyruvate is converted to2C acetyl CoA in one reaction.

Otherintermediates GTP

CO2

CO2

Yields:3 NADHs1 FADH2

Citrate

Oxaloacetate

Acetyl CoA

Remember: Thishappens twice for

each glucosemolecule that

enters glycolysis.

One CO2 is liberated and one NADH isformed.

C C C C

C C C C C C

C CC

The Krebs Cycle• Produces 2 ATP for each molecule of glucose• Purpose is to produce NADH and FADH2 to be fed into the ETC• Occurs in the cytoplasm of bacteria and in the mitochondrial matrix

of eukaryotes

Table 7.4 The Respiratory (Electron Transport) Chain

Anaerobicrespirers

Aerobicrespirers

CytoplasmH2O NO2

– HS–

O2

H+

CellmembraneWith ETS

Cell wall

H+

H+

H+

H+

H+

H+

H+

H+

H+

H+

H+

H+

H+

H+

Cytochromes

NAD H

ATPADP

ATPsynthase

NO3–

SO42–

Electron Transport Chain

•A chain of special redox carriers that receives reduced carriers (NADH, FADH2) generated by glycolysis and the Krebs cycle

-passes them in a sequential and orderly fashion from one to the next

-highly energetic-allows the transport of hydrogen ions outside of the

membrane-in the final step of the process, oxygen accepts electrons

and hydrogen, forming water-Electron transport carriers and enzymes are embedded in

the cell membrane in prokaryotes and on the inner mitochondrial membrane in eukaryotes

Electron Transport Chain

•Released energy from electron carriers in the electron transport chain is channeled through ATP synthase

•Oxidative phosphorylation: the coupling of ATP synthesis to electron transport

-each NADH that enters the electron transport chain can give rise to 3 ATPs

-Electrons from FADH2 enter the electron transport chain at a later point and have less energy to release, so only 2 ATPs result

Electron Transport Chain

-electrons from cytochrome c, and H+ from solution react with oxygen to form water

2H+ + 2e- + ½ O2 H20

Final Electron Acceptor: Aerobic Respiration

•Most eukaryotes have a fully functioning cytochrome system

•Bacteria exhibit wide-ranging variations in this system-some lack one or more redox steps

-several have alternative electron transport schemes

-lack of cytochrome c oxidase is useful in differentiating among certain genera of bacteria (we will do this with MM)

Final Electron Acceptor: Aerobic Respiration

•Utilizes oxygen-containing ions, rather than free oxygen, as the final electron acceptor

Ex. Nitrate reductase

NO3- + NADH NO2

- + H2O + NAD+

•Nitrate reductase catalyzes the removal of oxygen from nitrate, leaving nitrite and water as products

Final Electron Acceptor: Anaerobic Respiration

Table 7.5

Pyruvic acid from glycolysis can itself become the electronacceptor.

Pyruvic acid can also be enzymatically altered and then serve asthe electron acceptor.

The NADs are recycled to reenter glycolysis.

The organic molecules that became reduced in their role aselectron acceptors are extremely varied, and often yield usefulproducts such as ethyl alcohol, lactic acid, propionic acid,butanol, and others.

C C

O

H

H

H

H

CC C

H

H

H

H

O

C C

H

H

H

H

H

C C C

Lactic acid

OH

OH

NAD+

Ethyl alcohol

OH

Acetaldehyde

CO2

Pyruvic acid

Remember: Thishappens twice for

each glucosemolecule that

enters glycolysis.

Fermentation

NAD H NAD H

Fermentation-the incomplete oxidation of glucose or other carbohydrates in

the absence of oxygen

-uses organic compounds as the terminal electron acceptors

-Yields 2 ATPs per molecule of glucose

-Used by organisms that do not have an electron transport chain

-Other organisms repress the production of electron transport chain proteins when oxygen is lacking in their environment

to revert to fermentation

-Many bacteria grow as fast as they would in the presence of oxygen due to an increase in the rate of glycolysis

•Permits independence from molecular oxygen-allows colonization of anaerobic environments-enables adaptation to variations in oxygen availability-provides a means for growth when oxygen levels are too low

for aerobic respiration

Fermentation

•Bacteria and ruminant cattle-digest cellulose through fermentation

-hydrolyze cellulose to glucose

-ferment glucose to organic acids which are absorbed as the bovine’s principal energy source

Fermentation

Final Electron Acceptor: Fermentation

-Uses organic compounds as the terminal

electron acceptors

•Products:•Alcoholic beverages:

ethanol and CO2

•Solvents: acetone, butanol

•Organic acids: lactic acid, acetic acid

•Vitamins, antibiotics, and hormones

•The Frugality of the Cell-cells have systems for

careful management of carbon compounds

-catabolic pathways contain strategic molecular intermediates (metabolites) that can be diverted into anabolic pathways

-a given molecule can serve multiple purposes; maximum benefit can be derived from all nutrients and metabolites of the cell pool

The Crossing Pathways of Metabolism

Gly

coly

sis

Beta oxidationDeamination

GLUCOSE

Metabolicpathways

Simplepathways

Pyruvic acid

Acetyl coenzymeA

KrebsCycle

NH3 H2O

CO2

Building block

Macromolecule

Cellstructure

Membranesstorage

Cell wallstorage

Enzymes/Membranes

Chromosomes

Lipids/Fats

Starch/CelluloseProteins

Nucleicacids

Fatty acidsCarbohydratesAmino acidsNucleotides