microbial metabolism: the chemical crossroads of life · microbial metabolism: the chemical...

Microbial Metabolism: The Chemical Crossroads of Life

Microbiology: A Systems Approach

Chapter 8, pages 198 to 231 1

Microbial

Metabolism:

The Chemical

Crossroads

of Life

Chapter 8

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

Metabolism

Glucose

Rela

tiv

e c

om

ple

xit

y o

f m

ole

cu

les

+

Macromolecules

Nutrients from

outside or from

internal pathways

Pyruvate

Acetyl CoA

Glyceraldehyde-3-P

Amino acids

Sugars

Nucleotides

Fatty acids

Proteins

Peptidoglycan

RNA + DNA

Complex lipids

Glycolysis

Krebs cycle

Respiratory chain

Fermentation

Yields energy

Building

blocks

Precursor

molecules

ATP

NADH

Uses energy Uses energy




8.1 The Metabolism of Microbes

• Metabolism: All chemical reactions and physical workings of the cell

• Functions of metabolism

• Assembles smaller molecules into larger macromolecules needed for the cell

• Degrades macromolecules and yields energy

• Energy is conserved in the form of ATP or heat

Metabolism

• Anabolism (biosynthesis):

process that results in

synthesis of cell molecules

and structures

• usually requires energy input

• Catabolism: breakdown

of bonds of larger

molecules into smaller

molecules

• often release energy




Enzymes

• Enzymes are catalysts

• Catalysts - chemicals that increase

the rate of a chemical reaction

without becoming part of the products

or being consumed in the reaction

How do Enzymes Work?

• Energy of activation: the amount of energy which must be overcome for a reaction to proceed.

• Act as a physical site where the reactant molecules (substrates) can be positioned for various interactions




Enzyme Structure

• Most are protein

• Can be classified as simple or conjugated

• Simple enzymes- consist of protein alone

• Conjugated enzymes (haloenzyme) - contain protein and nonprotein molecules

• Protein (now called the apoenzyme) and one or more cofactors

• Cofactors are either organic molecules (coenzymes) or inorganic elements (metal ions)

Conjugated Enzyme Structure




Apoenzymes: Specificity and the Active

Site • Exhibits levels of molecular complexity called the primary,

secondary, tertiary, and quaternary organization

• The actual site where the substrate binds is a crevice or

groove called the active site or catalytic site

Enzyme-Substrate Interactions

• For a reaction to take place, a temporary enzyme-

substrate union must occur at the active site

• “Lock-and-key” fit

• The bonds are weak and easily reversible




Cofactors: Supporting the Work of

Enzymes • Metallic cofactors

• Include Fe, Cu, Mg, Mn, Zn, Co, Se

• Activate enzymes, help bring the active site and substrate close together, and participate directly in chemical reactions with the enzyme-substrate complex

• Coenzymes

• Organic compounds that work in conjunction with an apoenzyme to perform a necessary alteration of a substrate

• Removes a chemical group from one substrate molecule and adds it to another substrate

• Vitamins: one of the most important components of coenzymes

Classification of Enzyme Functions

• Site of action

• Type of action

• Substrate




Location and Regularity of Enzyme

Action

• Either inside or outside

of the cell

• Exoenzymes break

down molecules

outside of the cell

• Endoenzymes break

down molecules inside

of the cell

Rate of Enzyme Production

• Constitutive enzymes:

always present and in

relatively constant

amounts

• Regulated enzymes:

production is either

induced or repressed in

response to a change in

concentration of the

substrate




Synthesis and Hydrolysis Reactions

Transfer Reactions by Enzymes

• Oxidation-reduction reactions

• A compound loses electrons (oxidized)

• A compound receives electrons (reduced)

• Other enzymes that play a role in necessary molecular conversions by directing the transfer of functional groups:

• Aminotransferases

• Phosphotransferases

• Methyltranferases

• Decarboxylases




The Role of Microbial Enzymes in

Disease

• Many pathogens secrete unique exoenzymes

• Help them avoid host defenses or promote

multiplication in tissues

• These exoenzymes are called virulence factors

or toxins

The Sensitivity of Enzymes to Their

Environment • Enzyme activity is highly influenced by the cell’s

environment

• Enzymes generally operate only under the natural temperature, pH, and osmotic pressure of an organism’s habitat

• When enzymes subjected to changes in normal conditions, they become chemically unstable (labile)

• Denaturation: the weak bonds that maintain the native shape of the apoenzyme are broken




Direct Controls on the Action of

Enzymes

• Competitive inhibition: The cell supplies a molecule that resembles the enzyme’s normal substrate, which then occupies and blocks the enzyme’s active site

• Noncompetitive inhibition: The enzyme has two binding sites- the active site and the regulatory site; a regulator molecule binds to the regulatory site providing a negative feedback mechanism

Control Mechanisms for Enzymes




Controls on Enzyme Synthesis

• Enzyme repression: decrease enzyme expression

• Enzyme induction: increase enzyme expression

8.2 The Pursuit and Utilization of

Energy

• Energy in Cells

• Exergonic reaction: a reaction that releases

energy as it goes forward

• Endergonic reaction: a reaction that is driven

forward with the addition of energy




Cell Energy Production

A Closer Look at Biological Oxidation

and Reduction

• Biological systems often extract energy through redox reactions

• Redox reactions always occur in pairs- an electron donor paired with an electron acceptor

• Electron donor (reduced) + electron acceptor (oxidized) Electron donor (oxidized) + electron acceptor (reduced)

• The energy in the electron acceptor can be captured to phosphorylate ADP or some other compound, storing the energy in a high-energy molecule like ATP




Oxidation/Reduction

• Oxidation is losing electrons

• Reduction is gaining electrons

• Oxidation is always linked to reduction

2 8 1 2 8 2 8 7 2 8 8

1 2

Reduced

anion

Cl Na Cl Na

Reducing agent

gives up electrons.

Oxidizing agent

accepts electrons.

Oxidized

cation

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

Electron Carriers

• Repeatedly accept and

release electrons and

hydrogens

• Most carriers are

coenzymes that transfer

both electrons and

hydrogens

• Some transfer electrons

only

• Most common carrier-

NAD (nicotinamide

adenine dinucleotide)




Adenosine Triphosphate

The Metabolic Role of ATP

• When used in a chemical reaction, must be replaced

• Ongoing cycle

• Adding a phosphate to ADP replenishes ATP but it requires an input of energy

• In heterotrophs, this energy comes from certain steps of catabolic pathways




Substrate Level Phosphorylation

• ATP can be used to drive reactions

Glucose + ATP Glucose-6-phosphate + ADP

• Some compounds can be used to make ATP

Phosphoenolpyruvate + ADP pyruvate +

ATP

• This is called substrate level phosphorylation

8.3 The Pathways

• Metabolism uses enzymes to catalyze reactions that break down (catabolize) organic molecules to materials that cells can then use to build (anabolize) larger, more complex molecules.

• Reducing power and energy are needed in large quantities for the anabolic parts of metabolism; they are produced during the catabolic part of metabolism.

• Pathway- a series of biochemical reactions




Catabolism: Getting Materials and

Energy

• Glucose is often the nutrient catabolized

• Three major pathways

• Aerobic respiration: series of reactions that convert glucose to CO2 and allows the cell to recover significant amounts of energy; requires oxygen

• Fermentation: Use only glycolysis to incompletely oxidize glucose

• Anaerobic respiration: Does not use molecular oxygen as the final electron acceptor

Glucose Metabolism




Aerobic Respiration

• Series of enzyme-catalyzed reactions

• Electrons are transferred from fuel molecules to oxygen as a final electron acceptor

• Principal energy-yielding scheme for aerobic heterotrophs

• Provides both ATP and metabolic intermediates for many other pathways in the cell

• Glucose is the starting compound

• Glycolysis enzymatically converts glucose through several steps into pyruvic acid

Glycolysis

Second phosphorylation

Dihydroxyacetone

phosphate

(DHAP)

NAD

Glucose

Glyceraldehyde-3

phosphate

Diphosphoglyceric

acid

Split of F-1,6-P; subsequent

reactions in duplicate

Substrate-level

phosphorylation

3-phosphoglyceric

acid

2-phosphoglycericacid

Substrate-level

phosphorylation

Phosphoenolyruvicacid

Pyruvicacid

ATP

Glyceraldehyde-3-P

(G-3-P)

To

ele

ctro

n tra

ns

po

rt

First phosphorylation

To

ele

ctr

on

tra

ns

po

rt

NAD

NADH

Goes to Goes to

Krebs cycle or fermentation Krebs cycle or fermentation

Fructose-6-phosphate

Glucose-6-phosphate

Fructose-1,6-diphosphate

(F-1,6-P)

ATP

ADP

ATP

ADP

ATP

ADP

ATP

ADP

AEROBIC RESPIRATION ANAEROBIC RESPIRATION FERMENTATION

Glycolysis Glycolysis Glycolysis

Glucose Glucose

CO2 CO2 CO2

ATP

NADH NADH

ATP

Acetyl CoA Acetyl CoA Fermentation

FADH2 FADH2

Lactic acid Acetaldehyde

Ethanol

Krebs Krebs

NADH NADH

ATP ATP

CO2 CO2

Electrons Electrons Or other alcohols,

acids, gases

An organic molecule is final

electron acceptor (pyruvate,

acetaldehyde, etc.).

ATP produced � 2 ATP produced � 2 to 36 ATP produced �

38

No oxygen electron acceptors

(examples: SO4 2-, NO3

-, CO32-)

O2 is final electron

acceptor.

Electron transport

Electron transport

ATP

PO4

PO4

PO4 PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4 PO4

PO4

PO4

PO4 PO4

PO4

PO4

C C C C C C

C C C C C C

C C C C C C

C C C C C C

C C C C C C

C C C C C C

C C C C C C

C C C C C C

NADH

C C C C C C

C C C C C C

C C C C C C

1

2

3

4

5

6

7

8

9





Pyruvic Acid- A Central Metabolite

• Pyruvic acid from glycolysis serves an important position

in several pathways

• Different organisms handle it in different ways

• In strictly aerobic organisms and some anaerobes,

pyruvic acid enters the Krebs cycle

The Krebs Cycle: A Carbon and Energy

Wheel

• Pyruvic acid is energy-rich, but its hydrogens

need to be transferred to oxygen

• Takes place in the cytoplasm of bacteria and in

the mitochondrial matrix in eukaryotes

• Produces reduced coenzymes NADH and

FADH2, 2 ATPs for each glucose molecule




Krebs Cycle

The Respiratory Chain: Electron

Transport and Oxidative Phosphorylation

• The final “processing mill” for electrons and

hydrogen ions

• The major generator of ATP

• A chain of special redox carriers that receives

electrons from reduced carriers (NADH and

FADH2) and passes them in a sequential and

orderly fashion from one redox molecule to the

next.




Electron Transport System

H

H

H H

H

H H

H

H

H

H

H

H

H H

H

H

H

H

H

Cell wall

Cytochromes

Cytoplasm

Cell membrane

with ETS

ATP

ADP

ATP synthase


• NADH oxidized

• Electrons pass

through membrane

carriers

• Carriers are called

“cytochromes”

• Protons pumped out

• Protons pass through

ATP synthase to form

ATP

The Terminal Step

• Oxygen accepts the electrons

• Catalyzed by cytochrome aa3 (cytochrome oxidase)

• 2 H+ + 2 e- + 1/2O2 H2O

• Most eukaryotic aerobes have a fully functioning cytochrome system

• Bacteria exhibit wide-ranging variations which can be used to differentiate among certain genera of bacteria




ATP Yield from Aerobic Respiration

Anaerobic Respiration

• Functions like the aerobic cytochrome system

except it utilizes oxygen-containing ions rather

than free oxygen as the final electron acceptor

• The nitrate and nitrite reduction systems are best

known, using the enzyme nitrate reductase

• Denitrification: when enzymes can further

reduce nitrite to nitric oxide, nitrous oxide, and

nitrogen gas- important in recycling nitrogen in

the biosphere




Fermentation

• The incomplete oxidation of glucose or other carbohydrates in the absence of oxygen

• Uses organic compounds as the terminal electron acceptors and yields a small amount of ATP

• Many bacteria can grow as fast using fermentation as they would in the presence of oxygen

• This is made possible by an increase in the rate of glycolysis

• Permits independence from molecular oxygen

Products of Fermentation in

Microorganisms

• Products of Fermentation in Microorganisms

• Alcoholic beverages

• Organic acids

• Dairy products

• Vitamins, antibiotics, and even hormones

• Two general categories

• Alcoholic fermentation

• Acidic fermentation




Fermentation Pathways

Alcoholic Fermentation Products

• Occurs in yeast or bacterial species that have

metabolic pathways for converting pyruvic acid to

ethanol

• Products: ethanol and CO2




Acidic Fermentation Products

• Extremely varied pathways

• Lactic acid bacteria ferment pyruvate and reduce

it to lactic acid

• Heterolactic fermentation- when glucose is

fermented to a mixture of lactic acid, acetic acid,

and carbon dioxide

• Mixed acid fermentation- produces a

combination of acetic, lactic, succinic, and formic

acids and lowers the pH of a medium to about

4.0

8.4 Biosynthesis and the Crossing

Pathways of Metabolism

• The Frugality of the Cell- Waste Not, Want Not

• Most catabolic pathways contain strategic

molecular intermediates (metabolites) that can be

diverted into anabolic pathways

• Amphibolism: the property of a system to

integrate catabolic and anabolic pathways to

improve cell efficiency

• Principal sites of amphibolic interaction occur

during glycolysis and the Krebs cycle




Amphibolic Metabolism

Amphibolic Sources of Cellular Building

Blocks

• Pyruvate also provides intermediates for amino acids and can serve as the starting point in glucose synthesis from metabolic intermediates (gluconeogenesis)

• The acetyl group that starts the Krebs cycle can be fed into a number of synthetic pathways

• Fats can be degraded to acetyl through beta oxidation

• Two metabolites of carbohydrate catabolism that the Krebs cycle produces are essential intermediates in the synthesis of amino acids

• Oxaloacetic acid

• Α-ketoglutaric acid

• Occurs through amination

• Amino acids and carbohydrates can be interchanged through transamination




Amino Acid Formation

Anabolism: Formation of

Macromolecules

• Monosaccharides, amino acids, fatty acids, nitrogen bases, and vitamins come from two possible sources

• Enter the cell from outside as nutrients

• Can be synthesized through various cellular pathways

• Carbohydrate Biosynthesis

• Several alternative pathways

• Amino Acids, Protein Synthesis, and Nucleic Acid Synthesis

• Some organisms can synthesize all 20 amino acids

• Other organisms (especially animals) must acquire the essential ones from their diets




Assembly of the Cell

• When anabolism produces enough

macromolecules to serve two cells

• When DNA replication produces duplicate copies

of the cell’s genetic material

• Then the cell undergoes binary fission

8.5 It All Starts with Light

• Photosynthesis

• Proceeds in two

phases

• Light-dependent

reactions

• Light-

independent

reactions

Glucose

NADPH

ATP

Chloroplast

H2O

O2

CO2

2H + e–





Light-Dependent Reactions

• Solar energy delivered in discrete energy packets called photons

• Light strikes photosynthetic pigments

• Some wavelengths are absorbed

• Some pass through

• Some are reflected

• Light is absorbed through photosynthetic pigments

• Chlorophylls (green)

• Carotenoids (yellow, orange, or red)

• Phycobilins (red or blue-green)

Light-Dependent Reactions

• Bacterial chlorophylls

• Contain a photocenter- a magnesium atom held in the center of a complex ringed molecule called a porphyrin

• Harvest the energy of photons and converts it to electron energy

• Accessory photosynthetic pigments trap light energy and shuttle it to chlorophyll




Photosynthesis

Light-Independent Reactions

• Occur in the chloroplast stroma or the cytoplasm

of cyanobacteria

• Use energy produced by the light phase to

synthesize glucose by means of the Calvin cycle




Calvin Cycle

• Fix carbon dioxide

• Autotrophs

• Reverse of glycolysis

• 6 CO2 Glucose

P P

P P

P P

P P

P P

P

P

P

P

H

H

3-phosphoglyceric

acid

Splitting

ATP × 2

ADP

1,3-bisphosphoglyceric acid

NADPH × 2

NADP+

Glyceraldehyde-3-

phosphate

Glucose

ADP

ATP

Seriesof7-carbon

and5-carbon

Intermediates

Ribulose-1,5-bisphosphate

5-carbon

Fructoseintermediates

6-carbon

intermediate

Calvin Cycle

CO2


Other Mechanisms of

Photosynthesis • Oxygenic (oxygen-releasing) photosynthesis that occurs

in plants, algae, and cyanobacteria- dominant type on earth

• Other photosynthesizers such as green and purple bacteria

• Possess bacteriochlorophyll

• More versatile in capturing light

• Only have a cyclic photosystem I

• These bacteria use H2, H2S, or elemental sulfur rather than H2O as a source of electrons and reducing power

• They are anoxygenic (non-oxygen-producing); many are strict anaerobes

microbial metabolism: the chemical crossroads of life · microbial metabolism: the chemical...

Documents