2012 Pearson Education Inc.

Lecture prepared by Mindy Miller-Kittrell

North Carolina State University
Chapter 5
Microbial
Metabolism
Basic Chemical Reactions Underlying Metabolism
Metabolism
Collection of controlled biochemical reactions
that take place within a microbe
Ultimate function of metabolism is to
reproduce the organism
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Basic Chemical Reactions Underlying Metabolism
Metabolic Processes Guided by Eight Elementary
Statements
Every cell acquires nutrients
Metabolism requires energy from light or from
catabolism of nutrients
Energy is stored in adenosine triphosphate (ATP)
Cells catabolize nutrients to form precursor
metabolites
Precursor metabolites, energy from ATP, and
enzymes are used in anabolic reactions
Enzymes plus ATP form macromolecules
Cells grow by assembling macromolecules
Cells reproduce once they have doubled in size
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Basic Chemical Reactions Underlying Metabolism
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ANIMATION Metabolism: Overview
Basic Chemical Reactions Underlying Metabolism
Catabolism and Anabolism
Two major classes of metabolic reactions
Catabolic pathways
Break larger molecules into smaller products
Exergonic
Anabolic pathways
Synthesize large molecules from the products
of catabolism
Endergonic
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Figure 5.1 Metabolism
Energy lost
as heat
Nutrients
Energy
stored
Energy
used
Energy lost
as heat
Precursor
molecules
Larger building
blocks
Energy storage
(carbohydrates,
lipids, etc.)
Macromolecules
Cellular
processes
(cell growth,
cell division,
etc.)
Cellular structures
(membranes,
ribosomes, etc.)
ANABOLISM
Basic Chemical Reactions Underlying Metabolism
Oxidation and Reduction Reactions
Electron transfer from an electron donor to an
electron acceptor
Reactions always occur simultaneously
Cells use electron carriers to carry electrons
(often in H atoms)
Three important electron carriers
Nicotinamide adenine dinucleotide (NAD
+
)
Nicotinamide adenine dinucleotide phosphate
(NADP
+
)
Flavine adenine dinucleotide (FAD) FADH
2

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Figure 5.2 Oxidation-reduction, or redox, reactions
Electron
donor
Electron
acceptor
Oxidation
Reduction
Oxidized
donor
Reduced
acceptor
Basic Chemical Reactions Underlying Metabolism
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ANIMATION Oxidation-Reduction Reactions
Basic Chemical Reactions Underlying Metabolism
ATP Production and Energy Storage
Organisms release energy from nutrients
Stored in high-energy phosphate bonds (ATP)
Phosphorylation organic phosphate is added to
substrate
Cells phosphorylate ADP to ATP in three ways
Substrate-level phosphorylation
Oxidative phosphorylation
Photophosphorylation
Anabolic pathways use some energy by breaking
phosphate bonds
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Basic Chemical Reactions Underlying Metabolism
The Roles of Enzymes in Metabolism
Enzymes are organic catalysts
Increase likelihood of a reaction
Six categories of enzymes based on mode of
action
Hydrolases
Isomerases
Ligases or polymerases
Lyases
Oxidoreductases
Transferases
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Basic Chemical Reactions Underlying Metabolism
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ANIMATION Enzymes: Overview
Basic Chemical Reactions Underlying Metabolism
The Roles of Enzymes in Metabolism
Makeup of enzymes
Many protein enzymes are complete in
themselves
Apoenzymes are inactive if not bound to
nonprotein cofactors
Binding of apoenzyme and its cofactor(s)
yields holoenzyme
Some are RNA molecules called ribozymes
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Figure 5.3 Makeup of a protein enzyme
Inorganic cofactor Active site
Holoenzyme
Coenzyme
(organic
cofactor)
Apoenzyme (protein)
Basic Chemical Reactions Underlying Metabolism
The Roles of Enzymes in Metabolism
Enzyme activity
Enzymes lower the activation energy
Enzyme-substrate specificity
Active site complementary to shape of the
substrate
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Figure 5.4 Effect of enzymes on chemical reactions
Reactants
E
n
e
r
g
y

Progress of reaction
Products
Activation energy
without enzyme
Activation energy
with enzyme
Figure 5.5 Enzymes fitted to substrates-overview
Figure 5.6 The process of enzymatic activity
(Fructose 1,6-bisphosphate)
Substrate
Enzyme
Enzyme-
substrate
complex
Products
(Fructose 1,6-
bisphosphate
aldolase)
Glyceraldehyde-3P Dihydroxyacetone-P
Basic Chemical Reactions Underlying Metabolism
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ANIMATION Enzymes: Steps in a Reaction
Basic Chemical Reactions Underlying Metabolism
The Roles of Enzymes in Metabolism
Enzyme activity
Many factors influence the rate of enzymatic
reactions
Temperature
pH
Enzyme and substrate concentrations
Presence of inhibitors
Inhibitors
Substances that block an enzymes active site
Do not denature enzymes
Three types
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Figure 5.7 Effects of temperature, pH, and substrate concentration on enzyme activity-overview
Figure 5.8 Denaturation of protein enzymes
Functional protein Denatured protein
Figure 5.9 Competitive inhibition of enzyme activity-overview
Basic Chemical Reactions Underlying Metabolism
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ANIMATION Enzymes-Substrate Interaction:
Competitive Inhibition
Figure 5.10 Allosteric control of enzyme activity-overview
Basic Chemical Reactions Underlying Metabolism
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ANIMATION Enzyme-Substrate Interaction:
Noncompetitive Inhibition
Figure 5.11 Feedback inhibition
Feedback
inhibition
Bound
end-product
(allosteric
inhibitor)
Substrate
Enzyme 1
Allosteric
site
Intermediate A
Intermediate B
Enzyme 2
Enzyme 3
End-product
Pathway
shuts down
Pathway
operates
Carbohydrate Catabolism
Carbohydrate Catabolism
Many organisms oxidize carbohydrates as
primary energy source for anabolic reactions
Glucose most common carbohydrate used
Glucose catabolized by two processes:
cellular respiration and fermentation
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Figure 5.12 Summary of glucose catabolism
Acetyl-CoA
Pyruvic acid
(or derivative)
Formation of
fermentation
end-products
2 Pyruvic acid
Glucose
G
L
Y
C
O
L
Y
S
I
S
Respiration Fermentation
KREBS
CYCLE
Electrons
Carbohydrate Catabolism
Glycolysis
Occurs in cytoplasm of most cells
Involves splitting of a six-carbon glucose into two
three-carbon sugar molecules
Substrate-level phosphorylation: direct transfer of
phosphate between two substrates
Net gain of two ATP molecules, two molecules of
NADH, and precursor metabolite pyruvic acid
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Carbohydrate Catabolism
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ANIMATION Glycolysis: Overview
Carbohydrate Catabolism
Glycolysis
Divided into three stages involving 10 total
steps
Energy-investment stage
Lysis stage
Energy-conserving stage
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Figure 5.13 Glycolysis-overview
Carbohydrate Catabolism
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ANIMATION Glycolysis: Steps
Figure 5.14 Example of substrate-level phosphorylation
Holoenzyme
Phosphoenolpyruvate (PEP) Pyruvic acid
Phosphorylation
Carbohydrate Catabolism
Cellular Respiration
Resultant pyruvic acid completely oxidized to
produce ATP by series of redox reactions
Three stages of cellular respiration
1. Synthesis of acetyl-CoA
2. Krebs cycle
3. Final series of redox reactions
(electron transport chain)
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Figure 5.15 Formation of acetyl-CoA
Pyruvic acid
Decarboxylation
Acetate
Coenzyme A
Acetyl-coenzyme A
(acetyl-CoA)
Respiration Fermentation
Carbohydrate Catabolism
Cellular Respiration
Synthesis of acetyl-CoA
Results in
Two molecules of acetyl-CoA
Two molecules of CO
2

Two molecules of NADH
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Carbohydrate Catabolism
Cellular Respiration
The Krebs cycle
Great amount of energy remains in bonds of
acetyl-CoA
Transfers much of this energy to coenzymes
NAD
+
and FAD
Occurs in cytosol of prokaryotes and in matrix
of mitochondria in eukaryotes
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Carbohydrate Catabolism
Cellular Respiration
The Krebs cycle
Six types of reactions in Krebs cycle
Anabolism of citric acid
Isomerization reactions
Hydration reaction
Redox reactions
Decarboxylations
Substrate-level phosphorylation
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Figure 5.16 The Krebs cycle
Fermentation Respiration
Acetyl-CoA
Oxaloacetic acid
Malic acid
Fumaric acid
Succinic acid
Succinyl-CoA
-Ketoglutaric acid
Isocitric acid
KREBS
CYCLE
Citric acid
OOH
OOH
OOH
OOH
OOH
HOO
OOH
OOH
OOH
OOH
OOH
OOH
OOH
OOH
OOH
OOH
OOH
Carbohydrate Catabolism
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ANIMATION Krebs Cycle: Overview
Carbohydrate Catabolism
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ANIMATION Krebs Cycle: Steps
Carbohydrate Catabolism
Cellular Respiration
The Krebs cycle
Results in
Two molecules of ATP
Two molecules of FADH
2

Six molecules of NADH
Four molecules of CO
2
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Carbohydrate Catabolism
Cellular Respiration
Electron transport
Most significant ATP production occurs from
electron transport chain (ETC)
Carrier molecules pass electrons from one to
another to final electron acceptor
Energy from electrons used to pump protons (H
+
)
across the membrane, establishing a proton
gradient
Located in cristae of eukaryotes and in cytoplasmic
membrane of prokaryotes
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Figure 5.17 An electron transport chain
Path of
electrons
FMN
Oxidized
Reduced
Reduced
Oxidized
FeS
Oxidized
Oxidized
Reduced
Reduced
CoQ
Cyt
Cyt
Cyt
Reduced
Reduced
Oxidized
Oxidized
Final electron
acceptor
2
2
2
2
Fermentation Respiration
Carbohydrate Catabolism
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ANIMATION Electron Transport Chain: Overview
Carbohydrate Catabolism
Cellular Respiration
Electron transport
Four categories of carrier molecules
Flavoproteins
Ubiquinones
Metal-containing proteins
Cytochromes
Aerobic respiration: oxygen serves as final electron
acceptor
Anaerobic respiration: molecule other than oxygen
serves as final electron acceptor
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Figure 5.18 One possible arrangement of an electron transport chain
Bacterium
Exterior
Cytoplasmic
membrane
Cytoplasm
Intermembrane
space
Matrix
Mitochondrion
Exterior of prokaryote
or intermembrane space
of mitochondrion
FMN
Phospholipid
membrane
NADH
from glycolysis,
Krebs cycle,
pentose phosphate
pathway, and
Entner-Doudoroff
pathway
FADH
2

from
Krebs cycle
Ubiquinone
Cytoplasm of prokaryote
or matrix of mitochondrion
Cyt c
2

Cyt b
Cyt c
Cyt a
Cyt a
3
ATP synthase

Carbohydrate Catabolism
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ANIMATION Electron Transport Chain: Process
Carbohydrate Catabolism
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ANIMATION Electron Transport Chain:
Factors Affecting ATP Yield
Carbohydrate Catabolism
Cellular Respiration
Chemiosmosis
Use of electrochemical gradients to generate ATP
Create proton gradient from energy released in
redox reactions of ETC
Protons flow down electrochemical gradient through
ATP synthases that phosphorylate ADP to ATP
Called oxidative phosphorylation because proton
gradient created by oxidation of components of ETC
~34 ATP molecules formed from one molecule of
glucose
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Carbohydrate Catabolism
Alternatives to Glycolysis
Yield fewer molecules of ATP than glycolysis
Reduce coenzymes and yield different
metabolites needed in anabolic pathways
Two pathways
Pentose phosphate pathway
Entner-Doudoroff pathway
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Figure 5.19 Pentose phosphate pathway
Glucose
Glucose 6-phosphate
Glucose 6-phosphogluconic acid
Pentose phosphate
sugars
Ribulose t-phosphate
Xylulose 5-phosphate Ribose 5-phosphate
Sedoheptulose 7-phosphate Glyceraldehyde 3-phosphate (G3P)
Erythrose 4-phosphate
Erythrose 6-phosphate
Glucose 6-phosphate
Glyceraldehyde 3-phosphate (G3P)
To synthesis
of amino acids
To step 1 of glycolysis
or reenter pentose
phosphate pathway
To step 6 of
glycolysis
To step 2 of
glycolysis
To step 6 of
glycolysis
To synthesis of
nucleotides
To Calvin-Benson cycle
of photosynthesis
To anabolic reactions
requiring electron donors
Figure 5.20 Entner-Douoroff pathway
Glucose
Glucose 6-phosphate
6-Phosphogluconic acid
2-Keto-3-deoxy-
6-phosphogluconic acid
Glyceraldehyde 3-phosphate (G3P)
Steps 610
of glycolysis
Pyruvic acid
Pyruvic acid
To Kerb cycle
or fermentation
Carbohydrate Catabolism
Fermentation
Sometimes cells cannot completely oxidize
glucose by cellular respiration
Cells require constant source of NAD
+

Cannot be obtained simply using glycolysis and
Krebs cycle
Fermentation pathways provide cells with source
of NAD
+

Partial oxidation of sugar or other metabolites to
release energy
Uses organic molecule within cell as final electron
acceptor
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Figure 5.21 Fermentation
Respiration Fermentation
Pyruvic acid
Lactic acid Acetaldehyde
Ethanol
Figure 5.22 Representative fermentation products and the organisms that produce them
Glucose
Pyruvic acid
Organisms
Fermentation
Fermentation
products
CO
2
, propionic acid Lactic acid CO
2
, ethanol Acetone, isopropanol
Swiss cheese Cheddar cheese,
yogurt, soy sauce
Wine, beer Nail polis remover,
rubbing alcohol
Propionibacterium
Aspergillus
Lactobacillus
Streptococcus
Saccharomyces Clostridium
Carbohydrate Catabolism
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ANIMATION Fermentation
Other Catabolic Pathways
Lipid Catabolism
Protein Catabolism
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Figure 5.23 Catabolism of a fat molecule-overview
Figure 5.24 Protein catabolism
Polypeptide
Proteases
Extracellular fluid
Amino acids
Cytoplasmic
membrane
Cytoplasm
Deamination
To Krebs cycle
Photosynthesis
Many organisms synthesize organic
molecules from inorganic carbon
dioxide
Capture light energy and use it to
synthesize carbohydrates from CO
2
and
H
2
O by a process called photosynthesis
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Photosynthesis
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ANIMATION Photosynthesis: Overview
Photosynthesis
Chemicals and Structures
Chlorophylls
Important to organisms that capture light energy
with pigment molecules
Composed of hydrocarbon tail attached to light-
absorbing active site centered on magnesium ion
Active sites similar to cytochrome molecules in ETC
Structural differences cause absorption at different
wavelengths
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Photosynthesis
Chemicals and Structures
Photosystems
Arrangement of molecules of chlorophyll and other
pigments to form light-harvesting matrices
Embedded in cellular membranes called thylakoids
In prokaryotes invagination of cytoplasmic
membrane
In eukaryotes formed from inner membrane of
chloroplasts
Arranged in stacks called grana
Stroma is space between outer membrane of
grana and thylakoid membrane
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Figure 5.25 Photosynthetic structures in a prokaryote-overview
Photosynthesis
Chemicals and Structures
Two types of photosystems
Photosystem I (PS I)
Photosystem II (PS II)
Photosystems absorb light energy and use
redox reactions to store energy in the form of
ATP and NADPH
Light-dependent reactions depend on light
energy
Light-independent reactions synthesize glucose
from carbon dioxide and water
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Photosynthesis
Light-Dependent Reactions
As electrons move down the chain, their
energy is used to pump protons across the
membrane
Photophosphorylation uses proton motive
force to generate ATP
Photophosphorylation can be cyclic or
noncyclic
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Figure 5.26 Reaction center of a photosystem
Light
Acceptor
Reaction
center
Reaction
center chlorophyll
Possible path of
energy transfer
Photosystem I
Figure 5.27 Light-dependent reactions of photosynthesis: Cyclic and noncyclic phosphorylation-overview
Photosynthesis
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ANIMATION Photosynthesis: Light Reaction:
Cyclic Photophosphorylation
Photosynthesis
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ANIMATION Photosynthesis: Light Reaction:
Noncyclic Photophosphorylation
Photosynthesis
Light-Independent Reactions
Do not require light directly
Use ATP and NADPH generated by light-
dependent reactions
Key reaction is carbon fixation by Calvin-Benson
cycle
Three steps
Fixation of CO
2
Reduction
Regeneration of RuBP
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Figure 5.28 Simplified diagram of the Calvin-Benson cycle
CALVIN-BENSON
CYCLE
Ribulose bisphosphate
(RuBP)
3-Phosphoglyceric acid
G3P
6
3
3
3 O
2

3
5
1
6
6
6
6
6
6
6
1,3-Bisphosphoglyceric acid
Glyceraldehyde 3-phosphate
(G3P)
Glucose 6-phosphate
G3P G3P
Glucose
From the
Calvin-Benson
cycle or
glycolysis
From light-
dependent
reactions of
photosynthesis
or catabolic
pathways
Photosynthesis
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ANIMATION Photosynthesis: Light-Independent
Reaction
Other Anabolic Pathways
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Anabolic reactions are synthesis reactions
requiring energy and a source of metabolites
Energy derived from ATP from catabolic reactions
Many anabolic pathways are the reverse of
catabolic pathways
Reactions that can proceed in either direction are
amphibolic

Figure 5.29 Role of gluconeogenesis in the biosynthesis of complex carbohydrates
Glucose
Starch, celluose Glycogen Peptidoglycan
Glycerol
(from fat)
Fatty acids
(from fat)
Amino acids
(from protein)
CALVIN-
BENSON
CYCLE
Glucose 6-phosphate
Fructose 6-phosphate
Fructose 1,6-bisphosphate
G3P DHAP
2
2
Oxaloacetic acid
Pyruvic acid
Acetyl-CoA
O
2

G
L
U
C
O
N
E
O
G
E
N
E
S
I
S
Figure 5.30 Biosynthesis of fat, a lipid
Fats
Glycerol
Fatty acids
DHAP
CALVIN-
BENSON
CYCLE
Glyceraldehyde 3-phosphate
(G3P)
Glycolysis
Acetyl-CoA
Reverse of beta-oxidation
Figure 5.31 Synthesis of amino acids via amination and transamination-overview
Figure 5.32 Biosynthesis of nucleotides
DNA and RNA
Pyrimidine nucleotides Purine nucleotides
PABA
Folic acid
(vitamin
in humans)
Photosynthesis
Aspartic acid
(from Krebs
cycle)
Glutamine (derived
from glutamic acid
from Krebs cycle)
Glucose 6-phosphate
PENTOSE
PHOSPHATE
PATHWAY
Ribose 5-phosphate
Glycolysis Phosphoglyceric acid Glycine
Integration and Regulation of Metabolic Function
Cells synthesize or degrade channel and
transport proteins
Cells often synthesize enzymes needed to
catabolize a substrate only when substrate is
available
If two energy sources are available, cells
catabolize the more energy-efficient of the
two first
Cells synthesize metabolites they need, cease
synthesis if metabolite is available
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Integration and Regulation of Metabolic Function
Eukaryotic cells isolate enzymes of different
metabolic pathways within membrane-
bounded organelles
Cells use allosteric sites on enzymes to
control activity of enzymes
Feedback inhibition slows/stops anabolic
pathways when product is in abundance
Cells regulate amphibolic pathways by
requiring different coenzymes for each
pathway
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Integration and Regulation of Metabolic Function
Two types of regulatory mechanisms
Control of gene expression
Cells control amount and timing of protein
(enzyme) production
Control of metabolic expression
Cells control activity of proteins (enzymes)
once produced
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Figure 5.33 Integration of cellular metabolism (shown in an aerobic organism)
Proteins
METABOLIC PATHWAYS FOR THE POLYMERIZATION OF MACROMOLECULES
Nucleic acids
Amino acids Other sugars Nucleotides
Lipids Polysaccharides
PENTOSE
PHOSPHATE
PATHWAY
ATP AND
PRECURSOR
METABOLIC
PATHWAYS
GLYCOLYSIS GLUCONEOGENESIS
Fructose 1,6-bisphosphate
Glucose
Glucose 6-phosphate
Glyceraldehyde 3-phosphate (G3P) Glycerol
Fatty acids
3-Phosphoglyceric acid
Pyruvic acid
Acetyl-CoA
NH
3

O
2

KREBS
CYCLE
CALVIN-
BENSON
CYCLE
Photosynthetic
organisms
INTERMEDIATE
METABOLIC
PATHWAYS
KEY:
Catabolic pathway
Anabolic pathway
Light
Integration and Regulation of Metabolic Function
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ANIMATION Metabolism: The Big Picture