Chapter 7: Microbial Metabolism-

the Chemical Crossroads of Life

Rediet G., General Microbiology

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

• Anabolism: also called biosynthesis- any process that results in

synthesis of cell molecules and structures (usually requires energy input)
• Catabolism: the breakdown of bonds of larger molecules into smaller
molecules (often release energy)
• Functions of metabolism

– Assembles smaller molecules into larger macromolecules needed for

the cell
– Degrades macromolecules into smaller molecules and yields energy

– Energy is conserved in the form of ATP or heat

 Enzymes

• Catalyze the chemical reactions of life

• Enzymes: an example of catalysts, chemicals that increase

the rate of a chemical reaction without becoming part of the

products or being consumed in the reaction

Rediet G., General Microbiology
 How do Enzymes Work?
• Energy of activation: the amount of energy which must be
overcome for a reaction to proceed Can be achieved by:
– Increasing thermal energy to increase molecular velocity

– Increasing the concentration of reactants to increase the rate of

molecular collisions
– Adding a catalyst

• An enzyme promotes a reaction by serving as a physical site upon

which the reactant molecules (substrates) can be positioned for
various interactions
Rediet G., General Microbiology
 Enzyme Structure
• Most- protein

• Can be classified as simple or conjugated

– Simple enzymes consist of protein alone

– Conjugated enzymes contain protein and non-protein molecules

• A conjugated enzyme (haloenzyme) is a combination of a

protein (now called the apoenzyme) and one or more
cofactors
• Cofactors are either organic molecules (coenzymes) or
inorganic elements (metal ions)

Rediet G., General Microbiology

 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

Rediet G., General Microbiology

Rediet G., General Microbiology
 Enzyme-Substrate Interactions

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

union must occur at the active site. (Called an enzyme-
substrate complex.)
• “Lock-and-key” fit

• The bonds are weak and easily reversible

Rediet G., General Microbiology

 Rediet G., General Microbiology
Figure 8.4
 Cofactors: Supporting the Work of Enzymes

• Metallic cofactors
– Include Fe, Cu, Mg, Mn, Zn, Co, Se
– Metals 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
Rediet G., General Microbiology
 Classification of Enzyme Functions

• Site of action
• Type of action
• Substrate

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 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

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 Rediet G., General Microbiology
Figure 8.5
 Transfer Reactions by Enzymes
• Oxidation-reduction reactions

– A compound loses electrons (oxidized)

– A compound receives electrons (reduced)

– Common in the cell

– Important components- oxidoreductases

• Other enzymes that play a role in necessary molecular conversions by directing

the transfer of functional groups:
– Aminotransferases

– Phosphotransferases

– Methyltranferases

– Decarboxylases

Rediet G., General Microbiology

 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

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 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 are 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

Rediet G., General Microbiology

 Regulation of Enzymatic Activity and Metabolic
Pathways

• Metabolic Pathways

– Metabolic reactions usually occur in a multiseries step or

pathway
– Each step is catalyzed by an enzyme

– Every pathway has one or more enzyme pacemakers that

set the rate of a pathway’s progression

Rediet G., General Microbiology

Rediet G., General Microbiology
 Rate of Enzyme Production

• Enzymes are not all produced in the cell in equal amounts or at

equal rates
– Constitutive enzymes: production is continuous and in
relatively constant amounts
– Regulated enzymes: production is either induced or
repressed in response to a change in concentration of the
substrate

Rediet G., General Microbiology

 Control of Enzyme Activity

• Direct control of enzyme activity (constitutive enzymes)

• Regulation of enzyme synthesis (regulated enzymes)

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 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

Rediet G., General Microbiology

 Rediet G., General Microbiology
Figure 8.9
 Controls on Enzyme Synthesis

• Enzymes eventually must be replaced

• Enzyme repression: stops further synthesis of an enzyme

somewhere along its pathway
• Enzyme induction: The inverse of enzyme repression

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 Regulated Enzymes

• Inducible enzymes- break down complex substrates into simpler

products; eg. lactose to glucose;
– enzymes are only synthesized (induced) when excess substrate is present.
Otherwise the enzymes are not synthesized.

• Repressible enzymes- synthesize products such as tryptophan

when the product is not available in nutrient sources. Presence of
excess product represses enzyme production.

Rediet G., General Microbiology

Rediet G., General Microbiology
Rediet G., General Microbiology
 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

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Rediet G., General Microbiology
 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 and electron acceptor

– Redox pair

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

(oxidized) + electron acceptor (reduced)
• This process leaves the previously reduced compound with less energy than the
now oxidized one
• The energy in the electron acceptor can be captured to phosphorylate to ADP or
some other compound, storing the energy in a high-energy molecule like ATP

Rediet G., General Microbiology

 Electron Carriers: Molecular Shuttles

• Electron carriers repeatedly accept and release electrons

and hydrogens
• Facilitate the transfer of redox energy

• Most carriers are coenzymes that transfer both electrons

and hydrogens
• Some transfer electrns only

• Most common carrier- NAD

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Rediet G., General Microbiology
 Adenosine Triphosphate: Metabolic Money
• ATP
• Can be earned, banked, saved, spent, and exchanged
• A temporary energy repository
• The Molecular Structure of ATP
– Three-part molecule
• Nitrogen base (adenine)
• 5-carbon sugar (ribose)
• Chain of three phosphate groups
– The high energy originates in the orientation of the phosphate
groups
– Breaking the bonds between two successive phosphates of
ATP yields ADP
– ADP can then be converted to AMP
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Rediet G., General Microbiology
 The Metabolic Role of ATP
• Primary energy currency of the cell

• 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

• Some ATP molecules are formed through substrate-level phosphorylation

– ATP is formed by a transfer of a phosphate group from a phosphorylated

compound (substrate) directly to ADP
 Phosphorylation

• Oxidative phosphorylation

– Series of redox reactions occurring during the final phase

of the respiratory pathway
• Photophosphorylation

– ATP is formed through a series of sunlight-driven reactions

in phototrophic organisms

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 The Pathways

• Pathway- a series of biochemical reactions

• Metabolism uses enzymes to catalyze reactions that break down

(catabolize) organic molecules to materials (precursor molecules)

that cells can then use to build (anabolize) larger, more complex

molecules that are particularly suited to them.

• Reducing power and energy are needed in large quantities for the

anabolic parts of metabolism;

• they are produced during the catabolic part of metabolism.

Rediet G., General Microbiology
 Catabolism: Getting Materials and Energy

• Frequently the nutrient needed is glucose

• Most common pathway to break down glucose is glycolysis

• Three major pathways

– Respiration: series of reactions that convert glucose to

CO2 and allows the cell to recover significant amounts of

energy

Rediet G., General Microbiology

– Aerobic respiration: When oxygen is used as the final
electron acceptor at the end of the respiration scheme to
produce H2O.

– Anaerobic respiration: Does not use molecular oxygen as

the final electron acceptor, but uses nitrogen or compounds
of nitrogen or sulfur or compounds of sulfur, or other
inorganic substances and the final electron acceptor.
– Fermentation: when facultative and aerotolerant
anaerobes use only the glycolysis scheme to incompletely
oxidize glucose
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 Catabolism of Macromolecules
• Carbohydrates:

– Some monosaccharides may require

•Nucleic Acids
interconversion to glucose or other sugar
intermediate. Ribose sugar to PPP
– C5 & C4 sugars to PPP.
Purines and Pyrimidines to
• Proteins:

– Amino acid deamination and transamination.

component amino acids.
– Mostly enter pathways as carboxylic acid •Lipids
intermediates.
Glycerol and fatty acids
Fatty acids to acetyl-CoA
via β-oxidation.

Rediet G., General Microbiology

 Catabolism of Glucose

Glycolosis: Both R & F; ends in pyruvate; ATP via substrate level

phosphorylation (SLP).

Respiration: pyruvate oxidized by Krebs Cycle (ATP by SLP);

Electron Transport Chain & Chemiosmosis (ATP via oxidative
phosphorylation); terminal electron acceptor (O2 or other like NO3-).

Fermentation: Lack of respiration; pyruvate is reduced to another

organic; little ATP yield by SLP.

Rediet G., General Microbiology

 Catabolism:
• Hydrolysis of complex (polymeric) organics

• Breakdown of Glucose (6C) to Pyruvate (3C)

– Glycolytic Pathway (Embden-Meyerhof)

– Pentose Phosphate Pathway (PPP)

– Entner-Doudoroff Pathway (E-DP)

• Fate of Pyruvate

– Fermentation

– Krebs Cycle (Tricarboxylic Acid, i.e. Citric Acid)

• Electron Transport Chain & Oxidative Phosphorylation

– Aerobic Respiration

– Anaerobic Respiration

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 Glucose → Pyruvate via Glycolysis
Six Carbon (Investment)
Stage:
Hexose phosphorylation and
cleavage to two
Glyceraldehyde-3-Phosphates.
Five enzymatic reactions in this
stage; three are reversible.
Enzyme #1: Hexokinase (-
G6P) & Enzyme #3:
Phosphofructokinase (+ AMP; -
ATP; - Citrate) are regulated
enzymes.
Requires an investment of 2
ATP to “prime” the reaction. Glycolysis
 Glucose → Pyruvate via Glycolysis
Three Carbon (Yield) Stage:
•Two glyceraldehyde-3-phosphates
can pass per glucose.
•Five more enzymatic reactions for a
total of ten in Glycolysis. Four at
this stage are reversible.
•Enzyme #10: Pyruvate Kinase
(+ F1,6BP; - ATP) is regulated.
•As the carbon becomes oxidized the
phosphate bonds elevate in their
energy potential.
•Two steps involve SLP for ATP.
•Total of 4 ATP yield here, minus 2
ATP invested earlier = 2 ATP for all
Glucose → Pyruvate via E-DP

•Two stage linear pathway like Glycolysis; First stage unique; second

stage identical.

•KDPG the unique intermediate.

•Yields 1 ATP, 1 NADH, 1NADPH.

•Note one pyruvate is generated at each stage of the pathway.

•Found in some Gram negative bacteria instead of Glycolysis

(Rhizobium, Agrobacterium, Azotobacter, Pseudomonas)

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(KDPG)
 Glucose → Pyruvate via PPP

•Found in most bacteria.

•Can produce pentoses (5C) from hexoses (6C) via oxidative

decarboxylation, which forms NADPH. Source of ribose for
nucleosides.

•Other unique sugars are produced (4C, 7C); source of erythrose for
aromatic amino acids (Phe, Tyr, Trp)

•G3P enters Gycolysis to produce ATP and pyruvate.

Rediet G., General Microbiology

 Overview
 The pentose phosphate pathway is also
called Hexose Monophosphate Shunt or
Phosphogluconate Pathway.
 It is an alternate route for the oxidation
of glucose without direct consumption
or generation of ATP.
 It takes place entirely in the cytoplasm.

Rediet G., General Microbiology

Importance of pentose phosphate pathway :
 Generation of NADPH
- mainly used for reductive synthesis
of fatty acids, cholesterol and
steroid hormones.
- hydroxylation reaction in
metabolism of phenylalanine and
tryptophan.
- production of reduced glutathione
in erythrocytes and other cells.

 Production of ribose residues

- used for nucleotide, nucleic acid ,
and coenzyme biosynthesis

 Serves as an entry into Glycolysis

for both 5‐carbon & 6‐carbon sugars.
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 The PPP is divided into two phases
 Oxidative non-reversible phase
-generates NAPDH
-Glucose 6-p undergoes dehydrogenation and decarboxylation to give a pentose,
ribulose 5-p, which is converted to its isomer, D-ribose 5-p.
-Overall equation of 1st phase:
Glucose 6-p + 2 NADP++ H2O  ribose 5-p + CO2 + 2 NADPH + 2 H+

 Non-oxidative reversible phase

-ribose 5‐P is converted back to Glucose 6-p by a series of reactions involving
especially two enzymes
1. Transketolase :Transfer of the 2‐C fragment
2. Transaldolase :Transfer of the 3‐C fragment

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 Regulatory enzyme

5 carbon atoms

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 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

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•Lack of any respiration accumulates NADH.

•Without NAD+, Glycolysis or E-DP won’t proceed, i.e. no source of

ATP

•Fermentation pathways couple NADH oxidation and pyruvate

reduction, or reduction of another endogenous organic.

•Permits some ATP production; slow growth.

•Many species specific types.

Rediet G., General Microbiology
Rediet G., General Microbiology
Rediet G., General Microbiology
 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

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 Alcoholic Fermentation Products

• Occurs in yeast or bacterial species that have metabolic

pathways for converting pyruvic acid to ethanol

• Products: ethanol and CO2

Rediet G., General Microbiology

 Rediet G., General Microbiology
Figure 8.20
 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
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 Krebs (TCA) Cycle
•Respiration allows pyruvate to be
completely oxidize to CO2.
•First oxidative decarboxylation converts
pyruvate to Acetyl-CoA by the multi-
enzyme Pyruvate Dehydrogenase
Complex – highly regulated “pacemaker”.
•Acetyl-CoA (2C) forms citric acid (6C)
by condensation with oxaloacetate (4C).

•During the next 7 cyclic steps:

•Two additional decarboxylations.
•1 ATP by SLP.
•3 NADH & 1 FADH2 produced.
•Back to 1 oxaloacetate
 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

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Rediet G., General Microbiology
Rediet G., General Microbiology
 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

Rediet G., General Microbiology

 Significance of Krebs Cycle
1. Intermediate compounds used for the synthesis of biomolecules like
amino acids, nucleotides, chlorophyll, cytochromes and fats etc.

2. Intermediate like succinyl CoA takes part in the formation of

chlorophyll.

3. Amino Acids are formed from α- Ketoglutaric acid, pyruvic acids and
oxaloacetic acid.

4. releases plenty of energy (ATP) required for various metabolic

activities of cell.

5. carbon skeleton are got, which are used in process of growth and for
maintaining the cells.

Rediet G., General Microbiology

 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

Rediet G., General Microbiology

 Catabolism of Noncarboyhdrate Compounds
• Polysaccharides can easily be broken down into their component sugars
which can enter glycolysis
• Microbes can break down lipids and proteins to produce precursor
metabolites and energy
– Lipases break apart fats into fatty acids and glycerol
• The glycerol is then converted to DHAP(dihydroxyacetone phosphate)

• DHAP can enter step 4 of glycolysis

• The fatty acid component goes through beta oxidation

• Can yield a large amount of energy (oxidation of a 6-carbon fatty

acid yields 50 ATPs)

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– Proteases break proteins down to their amino acid

components

• Amino groups are then removed by deamination

• Results in a carbon compound which can be converted

to one of several intermediates of either glycolysis or

the Krebs cycle

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Rediet G., General Microbiology
 Β-Oxidation of Fatty Acids

The spiral pathway of fatty acid synthesis is nearly the reverse of this.
Rediet G., General Microbiology
 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

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Rediet G., General Microbiology
 Amphibolic Sources of Cellular Building Blocks

• Glyceraldehyde-3-phosphate can be diverted away from

glycolysis and converted into precursors for amino acid,
carbohydrate, and triglyceride synthesis
• 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
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• 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

transanimation

Rediet G., General Microbiology

 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 Rediet G., General Microbiology
 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

Rediet G., General Microbiology