Microbial Metabolisam

Microbial Metabolism: The Chemical
Crossroads of Life
Microbiology: A Systems Approach
Microbial
Metabolism:
The Chemical
Crossroads
of Life
Chapter 8
Copyright The McGraw-Hill Companies, Inc) Permission required for reproduction or display.
Metabolism
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
Relative complexity of molecules
Glycolysis
Krebs cycle
Respiratory chain
Fermentation
Macromolecules
Building
blocks
Glucose
Precursor
molecules
+
ATP
NADH
Yields energy
Chapter 8, pages 198 to 231
Uses energy
Uses energy

Crossroads of Life
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
Catabolism: breakdown
of bonds of larger
molecules into smaller
molecules
usually requires energy input
often release energy

Crossroads of Life
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

Crossroads of Life
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

Crossroads of Life
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 enzymesubstrate union must occur at the active site
Lock-and-key fit
The bonds are weak and easily reversible

Crossroads of Life
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

Crossroads of Life
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

Crossroads of Life
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

Crossroads of Life
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 cells
environment
Enzymes generally operate only under the natural
temperature, pH, and osmotic pressure of an
organisms 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

Crossroads of Life
Direct Controls on the Action of

Enzymes
Competitive inhibition: The cell supplies a
molecule that resembles the enzymes normal
substrate, which then occupies and blocks the
enzymes 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
10

Crossroads of Life
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
11

Crossroads of Life
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
12

Crossroads of Life
Oxidation/Reduction
Oxidation is losing electrons
Reduction is gaining electrons
Oxidation is always linked to reduction
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Na
281
Reducing agent
gives up electrons.
Cl
287
Oxidizing agent
accepts electrons.
Na
Oxidized
cation
28
Cl
288
Reduced
anion
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 carrierNAD (nicotinamide
adenine dinucleotide)
13

Crossroads of Life
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
14

Crossroads of Life
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
15

Crossroads of Life
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
16

Crossroads of Life
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
AEROBIC RESPIRATION ANAEROBIC RESPIRATION FERMENTATION
Glycolysis
Glycolysis
Glycolysis
Glucose
Glucose
ATP
ATP
NADH
NADH
CO2
CO2
CO2
Acetyl CoA
Fermentation
Acetyl CoA
C C C
Glucose
FADH 2
FADH2
Krebs
CO2
NADH
Krebs
CO2
Acetaldeh yd e
Lactic acid
NADH
ATP
First phosphorylation
Ethanol
ATP
ATP
1
ADP
Or other alcohols,
acids, gases
Electrons
Electrons
Electron transport
Electron transport
O2 is final electron
acceptor.
ATP produced
38
No oxygen electron acceptors

(examples: SO4 2-, NO3-, CO32-)
ATP produced
2 to 36
An organic molecule is final

electron acceptor (pyruvate,
acetaldehyd e, etc.).
ATP produced
PO4
C C C
C C
C C C
C C
Second phosphorylation
Glucose-6-phosphate
PO4
Fructose-6-phosphate
ATP
3
ADP
PO4
PO4
C
Dihydroxyacetone
phosphate
(DHAP)
Fructose-1,6-diphosphate
(F-1,6-P)
Split of F-1,6-P; subsequent

reactions in duplicate
PO4
C
Glyceraldehyde-3
phosphate
C C PO4
C PO4
C C C
To electron transport
NAD
Glyceraldehyde-3-P
(G-3-P)
PO4
NAD
NADH
NADH
PO4 C C C
Diphosphoglyceric
acid
Substrate-level
phosphorylation
PO4
ADP
ATP
C C C
PO4 C C
PO4
C C C
PO4
ADP
ATP
3-phosphoglyceric
acid
PO4
To electron transport
7
PO4
PO4
C C C
2-phosphoglycericacid
C C
8
PO4
C
Phosphoenolyruvicacid
C
C C
Substrate-level
phosphorylation
ATP
C
ATP
C C
Goes to
Krebs cycle or fermentation
PO4
Pyruvicacid
Goes to
Krebs cycle or fermentation
17

Crossroads of Life
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
18

Crossroads of Life
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.
19

Crossroads of Life
Electron Transport System

NADH oxidized
Electrons pass
through membrane
carriers
Carriers are called
cytochromes
Cell wall
H
H
H
H
H
H
H
Protons pumped out
H
H
Cytochromes
H
H
Protons pass through

ATP synthase to form
ATP
Cytoplasm
ATP synthase
Cell membrane
with ETS
ADP
H
H
H
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
20

Crossroads of Life
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
21

Crossroads of Life
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
22

Crossroads of Life
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
23

Crossroads of Life
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
24

Crossroads of Life
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
-ketoglutaric acid
Occurs through amination
Amino acids and carbohydrates can be interchanged through

transamination
25

Crossroads of Life
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
26

Crossroads of Life
Assembly of the Cell

When anabolism produces enough
macromolecules to serve two cells
When DNA replication produces duplicate copies
of the cells genetic material
Then the cell undergoes binary fission
8.5 It All Starts with Light

Photosynthesis
Proceeds in two
phases
Light-dependent
reactions
Lightindependent
reactions
Glucose
H2O
ATP
2H + e
NADPH
O2
Chloroplast
CO2
27

Crossroads of Life
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
28

Crossroads of Life
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
29

Crossroads of Life
Calvin Cycle
CO2
Fix carbon dioxide

Reverse of glycolysis
Splitting
6-carbon
intermediate
P
Autotrophs
3-phosphoglyceric
acid
Ribulose-1,5-bisphosphate
5-carbon
ADP
Calvin Cycle
ATP 2
ADP
ATP
6 CO2 Glucose
P
Seriesof7-carbon
and5-carbon
Intermediates
P
1,3-bisphosphoglyceric acid
P
H
P
H
NADPH 2
NADP+
Glyceraldehyde-3phosphate
Glucose
Fructoseintermediates
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
30

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Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

Relative complexity of molecules

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

8.1 The Metabolism of Microbes

usually requires energy input

often release energy

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

How do Enzymes Work?

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

Conjugated Enzyme Structure

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

Apoenzymes: Specificity and the Active

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

Cofactors: Supporting the Work of

Classification of Enzyme Functions

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

Location and Regularity of Enzyme

Rate of Enzyme Production

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

Synthesis and Hydrolysis Reactions

Transfer Reactions by Enzymes

Other enzymes that play a role in necessary

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

The Role of Microbial Enzymes in

The Sensitivity of Enzymes to Their

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

Direct Controls on the Action of

Control Mechanisms for Enzymes

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

Controls on Enzyme Synthesis

8.2 The Pursuit and Utilization of

Exergonic reaction: a reaction that releases

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

Cell Energy Production

A Closer Look at Biological Oxidation

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach

Chapter 8, pages 198 to 231

Microbial Metabolism: The Chemical

Microbiology: A Systems Approach