LECTURE PRESENTATIONS

For BROCK BIOLOGY OF MICROORGANISMS, THIRTEENTH EDITION

Michael T. Madigan, John M. Martinko, David A. Stahl, David P. Clark

Chapter 4
Nutrition, Culture,
Lectures by
John Zamora
and Metabolism of
Middle Tennessee State University
Microorganisms
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I. Nutrition, Culture, and Metabolism
of Microorganisms
4.1 Nutrition and Cell Chemistry
4.2 Culture Media

4.3 Laboratory Culture

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4.1 Nutrition and Cell Chemistry
Metabolism
The sum total of all chemical reactions that occur
in a cell
Catabolic reactions (catabolism)
Energy-releasing metabolic reactions
Anabolic reactions (anabolism)
Energy-requiring metabolic reactions
Most knowledge of microbial metabolism is
based on study of laboratory cultures

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4.1 Nutrition and Cell Chemistry
Nutrients
Supply of monomers (or precursors of)
required by cells for growth
Macronutrients
Nutrients required in large amounts
Micronutrients
Nutrients required in trace amount

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4.1 Nutrition and Cell Chemistry
Carbon
Required by all cells
Typical bacterial cell ~50% carbon (by dry weight)
Major element in all classes of macromolecules
Heterotrophs use organic carbon
Autotrophs use inorganic carbon

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4.1 Nutrition and Cell Chemistry
Nitrogen
Typical bacterial cell ~12% nitrogen
(by dry weight)
Key element in proteins, nucleic acids, and
many more cell constituents

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4.1 Nutrition and Cell Chemistry
Other Macronutrients
Phosphorus (P)
Synthesis of nucleic acids and phospholipids
Sulfur (S)
Sulfur-containing amino acids (cysteine and
methionine)
Vitamins (e.g., thiamine, biotin, lipoic acid) and
coenzyme A
Potassium (K)
Required by enzymes for activity

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4.1 Nutrition and Cell Chemistry
Other Macronutrients (contd)
Magnesium (Mg)
Stabilizes ribosomes, membranes, and
nucleic acids
Also required for many enzymes
Calcium (Ca)
Helps stabilize cell walls in microbes
Plays key role in heat stability of endospores
Sodium (Na)
Required by some microbes (e.g., marine
microbes)

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4.1 Nutrition and Cell Chemistry
Iron
Key component of cytochromes and FeS
proteins involved in electron transport
Under anoxic conditions, generally ferrous
(Fe2+) form; soluble
Under oxic conditions: generally ferric
(Fe3+) form; exists as insoluble minerals
Cells produce siderophores (iron-binding
agents) to obtain iron from insoluble mineral
form (Figure 4.2)

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4.1 Nutrition and Cell Chemistry
Growth Factors
Organic compounds required in small
amounts by certain organisms
Examples: vitamins, amino acids, purines,
pyrimidines
Vitamins
Most commonly required growth factors
Most function as coenyzmes

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4.2 Culture Media
Culture Media
Nutrient solutions used to grow microbes in
the laboratory
Two broad classes
Defined media: precise chemical composition
is known
Complex media: composed of digests of
chemically undefined substances (e.g., yeast
and meat extracts)

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4.2 Culture Media
Selective Media
Contains compounds that selectively inhibit
growth of some microbes but not others
Differential Media
Contains an indicator, usually a dye, that
detects particular chemical reactions
occurring during growth

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4.2 Culture Media
For successful cultivation of a microbe, it is
important to know the nutritional requirements
and supply them in proper form and
proportions in a culture medium

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4.3 Laboratory Culture
Pure culture: culture containing only a single kind
of microbe
Contaminants: unwanted organisms in a culture
Cells can be grown in liquid or solid culture media
Solid media are prepared by addition of a gelling
agent (agar or gelatin)
When grown on solid media, cells form isolated
masses (colonies)

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4.3 Laboratory Culture
Pure culture technique
Streak plate (Figure 4.5)
Pour plate
Spread plate

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Figure 4.5

Isolated colonies Confluent growth at

at end of streak beginning of streak

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4.4 Bioenergetics
Energy is defined in units of kilojoules (kJ), a
measure of heat energy
In any chemical reaction, some energy is lost
as heat
Free energy (G): energy released that is
available to do work
The change in free energy during a reaction is
referred to as G0

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4.4 Bioenergetics
Reactions with a negative G0 release free
energy (exergonic)
Reactions with a positive G0 require
energy (endergonic)
To calculate free-energy yield of a reaction,
we need to know the free energy of formation
(Gf0; the energy released or required during
formation of a given molecule from the
elements)

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4.5 Catalysis and Enzymes
Free-energy calculations do not provide
information on reaction rates
Activation energy: energy required to bring all
molecules in a chemical reaction into the
reactive state (Figure 4.6)
A catalysis is usually required to breach
activation energy barrier

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Figure 4.6

Activation
energy
no enzyme
Free energy

Substrates Activation
(A + B) energy with
enzyme
G0 = Gf0(C + D)
Gf0(A + B)

Products (C + D)

Progress of the reaction

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4.5 Catalysis and Enzymes
Catalyst: substance that
Lowers the activation energy of a reaction
Increases reaction rate
Does not affect energetics or equilibrium of a
reaction

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4.5 Catalysis and Enzymes
Enzymes
Biological catalysts
Typically proteins (some RNAs)
Highly specific
Generally larger than substrate
Typically rely on weak bonds
Examples: hydrogen bonds, van der Waals
forces, hydrophobic interactions
Active site: region of enzyme that binds
substrate

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4.5 Catalysis and Enzymes
Enzymes (contd)
Increase the rate of chemical reactions by 108 to
1020 times the spontaneous rate
Enzyme catalysis: E + S ES E+P
(Figure 4.7)
Catalysis dependent on
Substrate binding
Position of substrate relative to catalytically active
amino acids in active site

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Figure 4.7

Substrate Products

Active site

Free lysozyme Enzyme-substrate Free lysozyme

complex

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4.5 Catalysis and Enzymes
Many enzymes contain small nonprotein molecules
that participate in catalysis but are not substrates
Prosthetic groups
Bind tightly to enzymes
Usually bind covalently and permanently
(e.g., heme group in cytochromes)
Coenzymes
Loosely bound to enzymes
Most are derivatives of vitamins
(e.g., NAD+/NADH)

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III. OxidationReduction and Energy-
Rich Compounds
4.6 Electron Donors and Electron Acceptors
4.7 Energy-Rich Compounds and Energy
Storage

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4.6 Electron Donors and Electron
Acceptors
Energy from oxidationreduction (redox)
reactions is used in synthesis of energy-rich
compounds (e.g., ATP)
Redox reactions occur in pairs (two half
reactions; Figure 4.8)
Electron donor: the substance oxidized in a
redox reaction
Electron acceptor: the substance reduced in a
redox reaction

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4.6 Electron Donors and Electron
Acceptors
Redox reactions usually involve reactions
between intermediates (carriers)
Electron carriers are divided into two classes
Prosthetic groups (attached to enzymes)
Coenzymes (diffusible)
Examples: NAD+, NADP (Figure 4.10 )

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Figure 4.10

NAD NADH H
Nicotinamide

NAD/ NADH
Adenine E0 0.32V

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4.6 Electron Donors and Electron
Acceptors
NAD+ and NADH facilitate redox reactions
without being consumed; they are recycled
(Figure 4.11)

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Figure 4.11 NAD reduction
Enzyme I reacts with electron donor and
oxidized form of coenzyme, NAD

Enzyme
NAD Active substrate
binding site complex
site

Enzyme I

NAD Electron donor NADH

(substrate)

Electron
Electron donor
acceptor oxidized
reduced NADH (product)
(product) binding Active
site site

Enzyme II Electron
NADH oxidation acceptor
Enzyme (substrate)
Enzyme II reacts with electron
acceptor and reduced form
substrate
of coenzyme, NADH complex

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4.7 Energy-Rich Compounds and
Energy Storage
Chemical energy released in redox reactions
is primarily stored in certain phosphorylated
compounds (Figure 4.12)
ATP; the prime energy currency
Phosphoenolpyruvate
Glucose 6-phosphate
Chemical energy also stored in coenzyme A

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Figure 4.12

Ester
bond
Anhydride bonds
Ester bond

Anhydride bond

Phosphoenolpyruvate Adenosine triphosphate (ATP) (ATP) Glucose 6-phosphate

Thioester Anhydride
bond bond

Acetyl Coenzyme A
Acetyl-CoA Acetyl phosphate

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4.7 Energy-Rich Compounds and
Energy Storage
Long-term energy storage involves insoluble
polymers that can be oxidized to generate ATP
Examples in prokaryotes
Glycogen
Poly--hydroxybutyrate and other
polyhydroxyalkanoates
Elemental sulfur
Examples in eukaryotes
Starch
Lipids (simple fats)
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IV. Essentials of Catabolism
4.8 Glycolysis
4.9 Respiration and Electron Carriers
4.10 The Proton Motive Force
4.11 The Citric Acid Cycle
4.12 Catabolic Diversity

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4.8 Glycolysis
Two reaction series are linked to energy
conservation in chemoorganotrophs:
fermentation and respiration (Figure 4.13)
Differ in mechanism of ATP synthesis
Fermentation: substrate-level phosphorylation;
ATP directly synthesized from an energy-rich
intermediate
Respiration: oxidative phosphorylation; ATP
produced from proton motive force formed by
transport of electrons

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Figure 4.13
Energy-rich
Intermediates intermediates

Substrate-level phosphorylation

Energized
membrane

Less energized
membrane

Oxidative phosphorylation
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4.8 Glycolysis
Fermented substance is both an electron donor
and an electron acceptor
Glycolysis (Embden-Meyerhof pathway): a
common pathway for catabolism of glucose
(Figure 4.14)
Anaerobic process
Three stages

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Figure 4.14
Stage I

Glucose
Stage II

Pyruvate

2 lactate
Stage III 2 Pyruvate
2 ethanol 2 CO2

Intermediates 1,3-Bisphosphoglycerate Enzymes Phosphoglycerokinase

Glucose 6-P 3-P-Glycerate Hexokinase Phosphoglyceromutase
Fructose 6-P 2-P-Glycerate Isomerase Enolase
Fructose 1,6-P Phosphoenolpyruvate Phosphofructokinase Pyruvate kinase
Dihydroxyacetone-P Aldolase Lactate dehydrogenase
Glyceraldehyde-3-P Triosephosphate isomerase Pyruvate decarboxylase
Energetics Glyceraldehyde-3-P Alcohol dehydrogenase
Yeast dehydrogenase

Lactic acid bacteria

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4.8 Glycolysis
Glycolysis
Glucose consumed
Two ATPs produced
Fermentation products generated
Some harnessed by humans for consumption

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4.9 Respiration and Electron Carriers
Aerobic Respiration
Oxidation using O2 as the terminal electron
acceptor
Higher ATP yield than fermentations
ATP produced at the expense of the proton
motive force, which is generated by electron
transport

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4.9 Respiration and Electron Carriers
Electron Transport Systems
Membrane associated
Mediate transfer of electrons
Conserve some of the energy released during
transfer and use it to synthesize ATP
Many oxidationreduction enzymes are involved in
electron transport (e.g., NADH dehydrogenases,
flavoproteins, ironsulfur proteins, cytochromes)

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4.9 Respiration and Electron Carriers
NADH dehydrogenases: proteins bound to
inside surface of cytoplasmic membrane;
active site binds NADH and accepts 2
electrons and 2 protons that are passed to
flavoproteins
Flavoproteins: contains flavin prosthetic
group (e.g., FMN, FAD) that accepts 2
electrons and 2 protons but only donates the
electrons to the next protein in the chain
(Figure 4.15)

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Figure 4.15

Isoalloxazine ring

Ribitol
Oxidized
Reduced

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4.9 Respiration and Electron Carriers
Cytochromes
Proteins that contain heme prosthetic groups
(Figure 4.16)
Accept and donate a single electron via the
iron atom in heme

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Figure 4.16 Porphyrin
ring

Pyrrole

Heme (a porphyrin)
Protein

Histidine-N N-Histidine

Cysteine-S
S-Cysteine

Amino acid Amino acid

Cytochrome

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4.9 Respiration and Electron Carriers
IronSulfur Proteins
Contain clusters of iron and sulfur (Figure 4.17)
Example: ferredoxin
Reduction potentials vary depending on number
and position of Fe and S atoms
Carry electrons

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Figure 4.17
Cysteine Cysteine

Cysteine Cysteine

Cysteine

Cysteine
Cysteine

Cysteine

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4.9 Respiration and Electron Carriers
Quinones
Hydrophobic non-protein-containing
molecules that participate in electron
transport (Figure 4.18)
Accept electrons and protons but pass along
electrons only

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Figure 4.18

Oxidized

Reduced

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4.10 The Proton Motive Force
Electron transport system oriented in
cytoplasmic membrane so that electrons are
separated from protons (Figure 4.19)

Electron carriers arranged in membrane in order

of their reduction potential

The final carrier in the chain donates the

electrons and protons to the terminal electron
acceptor

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Figure 4.19 E0(V)

0.22

0.0 Complex II
Q Succinate
cycle
ENVIRONMENT

Fumarate

0.1
CYTOPLASM

0.36

0.39

E0(V)
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4.10 The Proton Motive Force
During electron transfer, several protons are
released on outside of the membrane
Protons originate from NADH and the
dissociation of water
Results in generation of pH gradient and an
electrochemical potential across the
membrane (the proton motive force)
The inside becomes electrically negative and
alkaline
The outside becomes electrically positive and
acidic
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4.10 The Proton Motive Force
Complex I (NADH:quinone oxidoreductase)
NADH donates e to FAD
FADH donates e to quinone

Complex II (succinate dehydrogenase complex)

Bypasses Complex I
Feeds e and H+ from FADH directly to
quinone pool

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4.10 The Proton Motive Force
Complex III (cytochrome bc1 complex)
Transfers e from quinones to cytochrome c
Cytochrome c shuttles e to cytochromes a
and a3
Complex IV (cytochromes a and a3)
Terminal oxidase; reduces O2 to H2O

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4.10 The Proton Motive Force
ATP synthase (ATPase): complex that converts
proton motive force into ATP; two components
(Figure 4.20)
F1: multiprotein extramembrane complex, faces
cytoplasm
Fo: proton-conducting intramembrane channel
Reversible; dissipates proton motive force

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Figure 4.20

F1
F1

In In
b2
b2

a c a

Membrane Fo
Fo
c12 Out Out

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4.11 The Citric Acid Cycle
Citric acid cycle (CAC): pathway through
which pyruvate is completely oxidized to CO2
(Figure 4.21a)
Initial steps (glucose to pyruvate) same as
glycolysis
Per glucose molecule, 6 CO2 molecules
released and NADH and FADH generated
Plays a key role in catabolism and
biosynthesis
Energetics advantage to aerobic respiration
(Figure 4.21b)

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Figure 4.21a Pyruvate (three carbons)

C2
Acetyl-CoA C4
C5
C6

Oxalacetate2 Citrate3

Aconitate3
Malate2

Isocitrate3

Fumarate2

Succinate2
-Ketoglutarate2

Succinyl-CoA

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Figure 4.21b

Energetics Balance Sheet for Aerobic Respiration

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4.11 The Citric Acid Cycle
The citric acid cycle generates many compounds
available for biosynthetic purposes
-Ketoglutarate and oxalacetate (OAA):
precursors of several amino acids; OAA also
converted to phosphoenolpyruvate, a precursor
of glucose
Succinyl-CoA: required for synthesis of
cytochromes, chlorophyll, and other tetrapyrrole
compounds
Acetyl-CoA: necessary for fatty acid biosynthesis

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4.12 Catabolic Diversity
Microorganisms demonstrate a wide range of
mechanisms for generating energy (Figure 4.22)
Fermentation
Aerobic respiration
Anaerobic respiration
Chemolithotrophy
Phototrophy

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Figure 4.22 Fermentation Carbon flow
Organic compound
Carbon flow in
respirations Electron transport/
generation of pmf Biosynthesis

Aerobic respiration
Electron
acceptors
Chemotrophs Anaerobic respiration
Chemoorganotrophy

Electron transport/
generation of pmf Biosynthesis

Electron Aerobic respiration

acceptors
Anaerobic respiration
Chemolithotrophy

Light
Photoheterotrophy Photoautotrophy

Organic e
Phototrophs

compound donor
Electron
transport

Generation of pmf
and reducing power

Biosynthesis Biosynthesis

Phototrophy
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4.12 Catabolic Diversity
Anaerobic Respiration
The use of electron acceptors other than
oxygen
Examples include nitrate (NO3), ferric iron
(Fe3+), sulfate (SO42), carbonate (CO32),
certain organic compounds
Less energy released compared to aerobic
respiration
Dependent on electron transport, generation
of a proton motive force, and ATPase activity

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4.12 Catabolic Diversity
Chemolithotrophy
Uses inorganic chemicals as electron donors
Examples include hydrogen sulfide (H2S), hydrogen
gas (H2), ferrous iron (Fe2+), ammonia (NH3)
Typically aerobic
Begins with oxidation of inorganic electron donor
Uses electron transport chain and proton motive
force
Autotrophic; uses CO2 as carbon source

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4.12 Catabolic Diversity
Phototrophy: uses light as energy source
Photophosphorylation: light-mediated ATP
synthesis
Photoautotrophs: use ATP for assimilation of
CO2 for biosynthesis
Photoheterotrophs: use ATP for assimilation
of organic carbon for biosynthesis

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V. Essentials of Anabolism
4.13 Biosynthesis of Sugars and Polysaccharides
4.14 Biosynthesis of Amino Acids and
Nucleotides
4.15 Biosynthesis of Fatty Acids and Lipids
4.16 Regulating the Activity of Biosynthetic
Enzymes

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4.13 Biosynthesis of Sugars and
Polysaccharides
Prokaryotic polysaccharides are synthesized
from activated glucose (Figure 4.23a)
Adenosine diphosphoglucose (ADPG)
Precursor for glycogen biosynthesis
Uridine diphosphoglucose (UDPG)
Precursor of some glucose derivatives
needed for biosynthesis of important
polysaccharides
Examples: N-acetylglucosamine,
N-acetylmuramic acid

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Figure 4.23a

Glucose

Uridine diphosphoglucose (UDPG)

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4.13 Biosynthesis of Sugars and
Polysaccharides
Gluconeogenesis (Figure 4.23b)
Synthesis of glucose from phosphoenolpyruvate
Phosphoenolpyruvate can be synthesized from
oxalacetate

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Figure 4.23b

C2, C3, C4, C5, Compounds

Citric acid cycle

Oxalacetate

Phosphoenolpyruvate CO2

Reversal of glycolysis

Glucose-6-P

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4.13 Biosynthesis of Sugars and
Polysaccharides
Pentoses are formed by the removal of one
carbon atom from a hexose (Figure 4.23c)

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Figure 4.23c

Glucose-6-P

Ribulose-5-P CO2

Ribose-5-P

Ribonucleotides Ribonucleotides
NADPH Ribonucleotide reductase

RNA Deoxyribonucleotides DNA

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4.14 Biosynthesis of Amino Acids and
Nucleotides
Biosynthesis of amino acids and nucleotides often
involves long, multistep pathways
Amino acid biosynthesis
Carbon skeletons come from intermediates of
glycolysis or citric acid cycle (Figure 4.24)
Ammonia is incorporated by glutamine
dehydrogenase or glutamine synthetase
(Figure 4.25)
Amino group transferred by transaminase and
synthase

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Figure 4.24
Glutamate family
Proline
-Ketoglutarate Glutamine
Arginine
Citric acid cycle Aspartate family
Asparagine
Oxalacetate Lysine
Methionine
Threonine
Isoleucine

Alanine family
Pyruvate Valine
Leucine
Glycolysis Serine family
3-Phosphoglycerate Glycine
Cysteine
Phospho-
enolpyruvate Aromatic family
Phenylalanine
Chorismate Tyrosine
Erythrose-4-P Tryptophan
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Figure 4.25

Glutamate
dehydrogenase

Glutamine
synthetase

Transaminase

Glutamate
synthase

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4.14 Biosynthesis of Amino Acids and
Nucleotides
Purine and pyrimidine biosyntheses are complex
Purines (Figure 4.26)
Adenine and guanine
Inosinic acid intermediate
Pyrimidines
Thymine, cytosine, and uracil
Orotic acid intermediate

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Figure 4.26
Amino group CO2 Glycine
of aspartate

Formyl
group
(from folic
acid)
Amide nitrogen
of glutamine Ribose-5-P
Purine skeleton Inosinic acid
Purine biosynthesis

Aspartic acid
NH3

CO2
Orotic acid Uridylate
Pyrimidine biosynthesis
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4.15 Biosynthesis of Fatty Acids
and Lipids
Fatty acids are biosynthesized two carbons at a
time (Figure 4.27)
Acyl carrier protein (ACP) involved
ACP holds the growing fatty acid as it is being
synthesized

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Figure 4.27

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4.15 Biosynthesis of Fatty Acids
and Lipids
In Bacteria and Eukarya, the final assembly of
lipids involves addition of fatty acids to
glycerol
In Archaea, lipids contain phytanyl side
chains instead of fatty acids
Phytanyl biosynthesis is distinct from that of
fatty acids

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4.16 Regulating the Activity of Biosynthetic
Enzymes
Two major modes of enzyme regulation
Amount
Regulation at the gene level
Activity
Temporary inactivation of the protein through
changes in enzyme structure

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4.16 Regulating the Activity of Biosynthetic
Enzymes
Feedback Inhibition: mechanism for turning off the
reactions in a biosynthetic pathway (Figure 4.28)
End product of the pathway binds to the first
enzyme in the pathway, thus inhibiting its activity
The inhibited enzyme is an allosteric enzyme
(Figure 4.29)
Two binding sites: active and allosteric
Reversible reaction

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Figure 4.28

Starting substrate
The allosteric
enzyme
Enzyme A

Intermediate I
Enzyme B
Intermediate II Feedback
inhibition
Enzyme C
Intermediate III
Enzyme D

End product
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Figure 4.29
End product
(allosteric effector)

Allosteric site Active site

Enzyme
Substrate
INHIBITION: ACTIVITY:
Substrate cannot Enzyme reaction
bind; enzyme proceeds
reaction inhibited

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4.16 Regulating the Activity of Biosynthetic
Enzymes
Some pathways controlled by feedback
inhibition use isoenzymes
Isoenzymes
Different enzymes that catalyze the same
reaction but are subject to different regulatory
controls (Figure 4.30)

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Figure 4.30

Phosphoenol- Erythrose Initial

pyruvate 4-phosphate substrates

DAHP synthases
(isoenzymes 1, 2, 3)
DAHP

Chorismate

Tyrosine Tryptophan Final

Phenylalanine products
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4.16 Regulating the Activity of Biosynthetic
Enzymes
Biosynthetic enzymes can also be regulated by
covalent modifications
Regulation involves a small molecule attached to
or removed from the protein (Figure 4.31)
Results in conformational change that inhibits
activity
Common modifiers include adenosine
monophosphate (AMP), adenosine diphosphate
(ADP), inorganic phosphate (PO42), methyl
groups (CH3)
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