Metabolism involves catabolic reactions that break down molecules and anabolic reactions that build them up. Catabolic pathways are exergonic and release energy, while anabolic pathways are endergonic and require energy. Central to metabolism are oxidation-reduction reactions in which electrons are transferred between molecules. Cells harness this redox energy to produce ATP through substrate-level phosphorylation, oxidative phosphorylation, or photophosphorylation. Enzymes catalyze metabolic reactions and allow organisms to precisely regulate biochemical pathways. Anaerobic organisms can perform oxidation using electron acceptors other than oxygen such as during fermentation.

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Chapter 5

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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 Statements
• Every cell acquires nutrients
• Metabolism requires energy from light or 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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Metabolism: Overview

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Basic Chemical Reactions Underlying
Metabolism
• Catabolism and Anabolism
• Two major classes of metabolic reactions
• Catabolic pathways
• Break larger molecules into smaller products
• Exergonic (release energy)
• Anabolic pathways
• Synthesize large molecules from the smaller products of
catabolism
• Endergonic (require more energy than they release)

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Figure 5.1 Metabolism is composed of catabolic and anabolic reactions.

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Basic Chemical Reactions Underlying
Metabolism
• Oxidation and Reduction Reactions
• Transfer of electrons 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+)
• Flavin adenine dinucleotide (FAD)

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Figure 5.2 Oxidation-reduction, or redox, reactions.

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Oxidation-Reduction Reactions

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Basic Chemical Reactions Underlying
Metabolism
• ATP Production and Energy Storage
• Organisms release energy from nutrients
• Can be concentrated and stored in high-energy
phosphate bonds (ATP)
• Phosphorylation – inorganic phosphate is added to substrate
• Cells phosphorylate ADP to ATP in three ways
• Substrate-level phosphorylation
• Oxidative phosphorylation
• Photophosphorylation
• Anabolic pathways use some energy of ATP by breaking a
phosphate bond

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Basic Chemical Reactions Underlying
Metabolism
• The Roles of Enzymes in Metabolism
• Enzymes are organic catalysts
• Increase likelihood of a reaction

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Enzymes: Overview

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Basic Chemical Reactions Underlying
Metabolism
• The Roles of Enzymes in Metabolism
• Naming and classifying enzymes
• 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
• The Roles of Enzymes in Metabolism
• The makeup of enzymes
• Many protein enzymes are complete in themselves
• Apoenzymes are inactive if not bound to nonprotein
cofactors (inorganic ions or coenzymes)
• 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 holoenzyme.
Inorganic cofactor Active site
Coenzyme
(organic
cofactor)
Apoenzyme (protein)
Holoenzyme

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Figure 5.4 The effect of enzymes on chemical reactions.
Reactants
Activation energy
without enzyme
Activation energy
with enzyme
Products

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Figure 5.5 Enzymes fitted to substrates.
Active sites similar
to substrate's
shape
Substrate
Enzyme Enzyme-substrate complex;
active sites become exact
shape of substrate

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1
Enzyme-
substrate
complex
Enzyme
(Fructose-1,6-
bisphosphate
aldolase)
Substrate
(Fructose 1,6-bisphosphate)
Dihydroxyacetone-P
Glyceraldehyde-3P
Products
2
3
4
Figure 5.6 The process of enzymatic activity.

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Enzymes: Steps in a Reaction

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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 block an enzyme's active site
• Do not denature enzymes
• Three types

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Figure 5.7 Representative effects of temperature, pH, and substrate concentration on enzyme activity.

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Figure 5.8 Denaturation of protein enzymes.

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Competitive
inhibitor
Substrate
Enzyme
Reversible
competitive
inhibitor
Substrate
Increase in
substrate
concentration
Enzyme
Figure 5.9 Competitive inhibition of enzyme activity.

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Enzymes: Competitive Inhibition

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Active site Enzyme
Allosteric site
Allosteric (noncompetitive) inhibition
Distorted,
nonfunctional
active site
Allosteric
inhibitor
Distorted active site
Substrate
Active site becomes
functional
Allosteric activator
Allosteric site
Allosteric activation
Substrate
Figure 5.10 Allosteric control of enzyme activity.

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Enzyme-Substrate Interaction: Noncompetitive
Inhibition

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Figure 5.11 Feedback inhibition.
Substrate
Pathway
shuts down
Bound
end-product
(allosteric
inhibitor)
Enzyme 1
Allosteric
site
Pathway
operates
Feedback
inhibition Intermediate A
Enzyme 2
Intermediate B
End-product
Enzyme 3

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Basic Chemical Reactions Underlying
Metabolism
• Tell Me Why
• How can oxidation take place in an anaerobic
environment, that is, without oxygen?

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Carbohydrate Catabolism
• Many organisms oxidize carbohydrates as primary
energy source for anabolic reactions
• Glucose is most common carbohydrate used
• Glucose is catabolized by two processes
• Cellular respiration
• Fermentation

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Glucose
2 Pyruvic acid
Electrons
KREBS
CYCLE
Acetyl-CoA
Final electron
acceptor
Formation of
fermentation
end-products
Pyruvic acid
(or derivative)
G
L
Y
C
O
L
Y
S
I
S
Fermentation
Respiration
Figure 5.12 Summary of glucose catabolism.

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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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Glycolysis: Overview

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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.

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Glycolysis: Steps

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Figure 5.14 Example of substrate-level phosphorylation.
Phosphoenolpyruvate (PEP)
Holoenzyme
Pyruvic acid
Phosphorylation

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Carbohydrate Catabolism
• Cellular Respiration
• Resultant pyruvic acid is 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 reaction
(electron transport chain)

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Figure 5.15 Formation of acetyl-CoA.

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Carbohydrate Catabolism
• Cellular Respiration
• Synthesis of acetyl-CoA
• Results in
• Two molecules of acetyl-CoA
• Two molecules of CO2
• 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
• Redox reactions
• Decarboxylations
• Substrate-level phosphorylation
• Hydration reaction

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Figure 5.16 The Krebs cycle.

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Krebs Cycle: Overview

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Krebs Cycle: Steps

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Carbohydrate Catabolism
• Cellular Respiration
• The Krebs cycle
• Results in
• Two molecules of ATP
• Two molecules of FADH2
• Six molecules of NADH
• Four molecules of CO2

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Carbohydrate Catabolism
• Cellular Respiration
• Electron transport
• Most significant production of ATP occurs from series of
redox reactions known as an electron transport chain
(ETC)
• Series of carrier molecules that pass electrons from one to
another to final electron acceptor
• Energy from electrons is 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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Respiration Fermentation
Path of
electrons
Final electron
acceptor
Figure 5.17 An electron transport chain.

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Electron Transport Chain: Overview

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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
Intermembrane
space
Matrix
Mitochondrion
Cytoplasm
Phospholipid
membrane
NADH
from glycolysis,
Krebs cycle,
pentose phosphate
pathway, and
Entner-Doudoroff
pathway
FADH2
from
Krebs cycle
Cytoplasm of prokaryote
or matrix of mitochondrion
Exterior of prokaryote
or intermembrane space
of mitochondrion
Ubiquinone
FMN
NADH FADH2
NAD+ Cyt c1
ATP synthase
Cyt b
H+
H+
2
1
e–
e–
e–
e–
H+ H+
e–
e–
e–
e–
e–
e–
Cyt c Cyt a
Cyt a3
H+
H+
e–
e–
H+
H+
4
H+
H+
H+
H+
ADP
3
H2O
ATP
P
+
1/2 O2
H+
H+
FAD +
+
H+

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Electron Transport Chain: The Process

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Electron Transport Chain: Factors Affecting
ATP Yield

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Carbohydrate Catabolism
• Cellular Respiration
• Chemiosmosis
• Use of ion gradients to generate ATP
• Cells use energy released in redox reactions of ETC to
create proton gradient
• Protons flow down electrochemical gradient through ATP
synthases that phosphorylate ADP to ATP
• Called oxidative phosphorylation because proton gradient
is created by oxidation of components of ETC
• Total of ~34 ATP molecules formed from one molecule of
glucose

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Carbohydrate Catabolism
• Alternatives to Glycolysis
• Yield fewer molecules of ATP than does 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 The pentose phosphate pathway.

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Figure 5.20 Entner-Doudoroff pathway.
Glucose
Glucose 6-phosphate
6-Phosphogluconic acid
2-Keto-3-deoxy-
6-phosphogluconic acid
Glyceraldehyde 3-phosphate (G3P)
Pyruvic acid
Pyruvic acid
To Krebs cycle
or fermentation
Steps 6–10
of glycolysis

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Carbohydrate Catabolism
• Fermentation
• Sometimes cells cannot completely oxidize glucose by
cellular respiration
• Cells require constant source of NAD+
• Cannot be obtained simply by using glycolysis and Krebs
cycle
• Fermentation pathways provide cells with alternative source
of NAD+
• Partial oxidation of sugar (or other metabolites) to release
energy using an organic molecule from within the cell as
final electron acceptor

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Figure 5.21 Fermentation.

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Figure 5.22 Representative fermentation products and the organisms that produce them.

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Fermentation

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Carbohydrate Catabolism
• Tell Me Why
• Why do electrons carried by NADH allow for production
of 50% more ATP molecules than do electrons carried
by FADH2?

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Other Catabolic Pathways
• Lipids and proteins contain energy in their
chemical bonds
• Can be converted into precursor metabolites
• Serve as substrates in glycolysis and the Krebs cycle

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Figure 5.23 Catabolism of a fat molecule.
Fatty acid chains
Glycerol
Lipase
3
Glycerol
+
Fatty acids
Hydrolysis
DHAP
To step 5
glycolysis
Fatty acid
To electron
transport chain
Acetyl-CoA
To Krebs cycle
Shorter fatty acid
Beta-oxidation

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Extracellular fluid
Protease
s
Polypeptide
Amino
acids
Cytoplasmic
membrane
Cytoplasm
Deamination
To Krebs
cycle
Figure 5.24 Protein catabolism.

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Other Catabolic Pathways
• Tell Me Why
• Why does catabolism of amino acids for energy result in
ammonia and other nitrogenous wastes?

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Photosynthesis
• Many organisms synthesize their own organic
molecules from inorganic carbon dioxide
• Most of these organisms capture light energy and
use it to synthesize carbohydrates from CO2 and
H2O by a process called photosynthesis

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Photosynthesis: Overview

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Metabolism

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Photosynthesis
• Chemicals and Structures
• Chlorophylls
• Type of pigment molecule that photosynthetic organisms
use to capture light energy
• Composed of hydrocarbon tail attached to light-absorbing
active site centered on magnesium ion
• Active sites are structurally 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 granum and
thylakoid membrane

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Figure 5.25 Photosynthetic structures in a prokaryote.
Photosystem embedded
in membrane (sectioned) Chlorophyll
Thylakoid
membrane
Active
site
Tail
(carbon
chain)
Thylakoid

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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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Acceptor
Light
Reaction
center chlorophyll
Possible path of
energy transfer
Photosystem:
reaction center
Figure 5.26 Reaction center of a photosystem.

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Exterior of prokaryote
or thylakoid space of chloroplast
Cyclic photophosphorylation
Cytochromes
Cu
Photosystem I
Fe
Reaction center
Light
Cytoplasm of
prokaryote
or stroma of
chloroplast
ATP synthase
Membrane of
prokaryote or
of thylakoid in
chloroplast
Membrane of
prokaryote or
of thylakoid in
chloroplast
ATP synthase
Photosystem I
Cytochromes
Fe
Light
Cytoplasm of
prokaryote
or stroma of
chloroplast
Light
Quinone
Reaction
center
Reaction
center
Cu
Noncyclic photophosphorylation
Exterior of prokaryote
or thylakoid space
of chloroplast
To
Calvin-Benson
cycle
NADPase
Photosystem II
Figure 5.27 The light-dependent reactions of photosynthesis: Cyclic and noncyclic photophosphorylation.

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Photosynthesis: Light Reaction: Cyclic
Photophosphorylation

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Photosynthesis: Light Reaction: Noncyclic
Photophosphorylation

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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 CO2
• Reduction
• Regeneration of RuBP

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Figure 5.28 Simplified diagram of the Calvin-Benson cycle.

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Photosynthesis: Light-Independent Reaction

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Photosynthesis
• Tell Me Why
• An uninformed student describes the Calvin-Benson
cycle as "cellular respiration in reverse." Why is this
student incorrect?

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Other Anabolic Pathways
• Anabolic reactions are synthesis reactions
requiring energy and a source of precursor
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

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Figure 5.29 The role of gluconeogenesis in the biosynthesis of complex carbohydrates.

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Figure 5.30 Biosynthesis of fat, a lipid.

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Figure 5.31 Examples of the synthesis of amino acids via amination and transamination.

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Figure 5.32 The biosynthesis of nucleotides.

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Other Anabolic Pathways
• Tell Me Why
• Why is nitrogen required for the production of amino
acids by amination?

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Integration and Regulation of Metabolic
Function
• Cells synthesize or degrade channel and transport
proteins
• Cells often synthesize enzymes only when
substrate is available
• Cells catabolize the more energy-efficient choice if
two energy sources are available
• 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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Integration and Regulation of Metabolic
Function
• Tell Me Why
• Why is feedback inhibition necessary for controlling
anabolic pathways?

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Figure 5.33 Integration of cellular metabolism (shown in an aerobic organism).

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Metabolism: The Big Picture

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Important topics
• Chloroplast
– Structure
– Function
• Photosynthesis vs. Calvin-Benson cycle
• Gluconeogenesis
• ETC (Electron Transport Chain)