Chapter 5:
Microbial Metabolism
Microbial Metabolism
Metabolism refers to all chemical reactions that occur
within a living a living organism.
These chemical reactions are generally of two types:
 Catabolic: Degradative reactions that release energy by
breaking down large, complex molecules into smaller ones.
Often involve hydrolysis, breaking bonds with water.
 Anabolic: Biosynthetic reactions that build large
complex molecules from simpler ones.
Require energy and often involve dehydration synthesis.
Coupling of Anabolic and Catabolic Reactions
 Catabolic
reactions provide the energy needed to
drive anabolic reactions.
 ATP stores energy from catabolic reactions and
releases it to drive anabolic reactions.
 Catabolic reactions are often coupled to ATP
synthesis:
ADP + Pi + Energy -----------> ATP
 Anabolic reactions are often coupled to ATP
hydrolysis:
ATP ----------->
ADP + Pi + Energy
 Efficiency: Only part of the energy released in
catabolism is available for work, the rest is lost
as heat. Energy transformations are inefficient.
Anabolic and Catabolic Reactions are
Linked by ATP in Living Organisms
Enzymes
 Protein
molecules that catalyze chemical
reactions.
 Enzymes are highly specific and usually catalyze
only one or a few closely related reactions.
Sucrase
Sucrose + H2O ----------->
(substrate)
 Enzymes
Glucose + Fructose
(products)
are extremely efficient. Speed up
reaction up to 10 billion times more than without
enzyme.
 Turnover number: Number of substrate
molecules an enzyme molecule converts to
product each second. Ranges from 1 to 500,000.
Enzymes (Continued)
 The
rate of a chemical reaction depends on
temperature, pressure, substrate
concentration, pH, and several other factors in
the cell.
 Energy
of activation: The amount of energy
required to trigger a chemical reaction.
 Enzymes
speed up chemical reactions by
decreasing their energy of activation without
increasing the temperature or pressure inside
the cell.
Example: Bring reactants together, create
stress on a bond, etc.
Enzymes Lower the Energy of
Activation of a Chemical Reaction
Naming Enzymes
 Enzyme
 There
names typically end in -ase.
are six classes of enzymes
1. Oxidoreductases: Catalyze oxidation-reduction
reactions. Include dehydrogenases and oxidases.
2. Transferases: Transfer functional groups (amino,
phosphate, etc).
3. Hydrolases: Hydrolysis, break bonds by adding
water.
4. Lyases: Remove groups of atoms without hydrolysis.
5. Isomerases: Rearrange atoms within a molecule.
6. Ligases: Join two molecules, usually with energy
provided by ATP hydrolysis.
Enzyme Components
 Some
enzymes consist of protein only.
 Others
have a protein portion (apoenzyme) and a
nonprotein component (cofactor).
Holoenzyme = Apoenzyme + Cofactor
cofactors may be a metal ion (Mg2+ ,
Ca2+, etc.) or an organic molecule (coenzyme).
Many coenzymes are derived from vitamins.
 Enzyme
Examples:
 NAD+:
Nicotinamide adenine dinucleotide
 NADP+:
Nicotinamide adenine dinucleotide phosphate
are both cofactors derived from niacin (B vitamin).
 Coenzyme
A is derived from panthotenic acid.
Components of a Holoenzyme
Mechanism of Enzymatic Action
Surface of enzyme contains an active site that
binds specifically to the substrate.
1. An enzyme-substrate complex forms.
2. Substrate molecule is transformed by:
 Rearrangement
 Breakdown
of existing atoms
of substrate molecule
 Combination
with another substrate molecule
3. Products of reaction no longer fit the active
site and are released.
4. Unchanged enzyme is free to bind to more
substrate molecules.
Mechanism of Enzymatic Action
Factors Affecting Enzymatic Action
Enzymes are protein molecules and their threedimensional shape is essential for their function.
The shape of the active site must not be altered so
that it can bind specifically to the substrate.
Several factors can affects enzyme activity:
 Temperature: Most enzymes have an optimal
temperature. At low temperatures most reactions
proceed slowly due to slow particle movement. At very
high temperatures reactions slow down because the
enzyme is denatured.
Denaturation: Loss of three-dimensional protein
structure. Involves breakage of H and noncovalent
bonds.
Denaturation of a Protein Abolishes its
Activity
Factors that Affect Enzyme Activity: pH,
Temperature, and Substrate Concentration
Factors Affecting Enzymatic Action
 pH:
Most enzymes have an optimum pH. Above
or below this value activity slows down. Extreme
changes in pH cause denaturation.
 Substrate concentration: Enzyme acts at
maximum rate at high substrate concentration.
Saturation point: Substrate concentration at
which enzyme is acting at maximum rate possible.
 Inhibitors: Inhibit enzyme activity. Two types:
 Competitive
inhibitors: Bind to enzyme active site.
Example: Sulfa drugs, AZT.
 Noncompetitive
inhibitors: Bind to an allosteric site.
Example: Cyanide, fluoride.
Competitive versus Noncompetitive
Enzyme Inhibitors
Factors Affecting Enzymatic Action
 Feedback
Inhibition: Also known as end-product
inhibition.
Some allosteric inhibitors stop cell from making
more of a product than it needs.
The end product of a series of reactions, inhibits
the activity of an earlier enzyme.
Enzyme 1
Enzyme 2
Enzyme 3
A --------> B -------> C --------> D
Enzyme 1 is inhibited by product D.
Feedback inhibition is used to regulate ATP, amino
acid, nucleotide, and vitamin synthesis by the cell.
Feedback Inhibition of an Enzymatic
Pathway
Ribozymes
 Catalytic
RNA molecules
 Have active sites that bind to substrates
 Discovered in 1982
 Act on RNA substrates by cutting and splicing
them.
Energy Production
Oxidation-Reduction or Redox Reactions:
Reactions in which both oxidation and
reduction occur.
Oxidation: Removal of electrons or H atoms
Addition of oxygen
Associated with loss of energy
Reduction: Gain of electrons or H atoms
Loss of oxygen
Associated with gain of energy
Examples: Aerobic respiration & photosynthesis
are redox processes.
Oxidation-Reduction Reactions
Aerobic Respiration is a Redox Reaction
C6H12O6 + 6 O2 -----> 6 CO2 + 6 H2O + ATP
Glucose oxygen oxidized reduced
ATP Production
Some of the energy released in oxidation-reduction
processes is trapped as ATP; the rest is lost as
heat.
Phosphorylation reaction:
ADP + Energy + P ---------> ATP
There are three different mechanisms of ATP
phosphorylation in living organisms:
1. Substrate-Level Phosphorylation:
 Direct
transfer of phosphate from phosphorylated
compound to ADP.
 Simple process that does not require intact membranes.
 Generates a small amount of energy during aerobic
respiration.
Two Mechanisms of ATP Synthesis:
Oxidative and Substrate Level Phosphorylation
2. Oxidative Phosphorylation:
 Involves
electron transport chain, in which electrons
are transferred from organic compounds to electron
carriers (NAD+ or FAD) to a final electron acceptor
(O2 or other inorganic compounds).
 Occurs on membranes (plasma membrane of
procaryotes or inner mitochondrial membrane of
eucaryotes).
 ATP is generated through chemiosmosis.
 Generates most of the ATP in aerobic respiration.
3. Photophosphorylation:
Occurs in photosynthetic cells only.
 Convert solar energy into chemical energy (ATP and
NADPH).
 Also involves an electron transport chain.

Carbohydrate Catabolism
 Most
microorganisms use glucose or other
carbohydrates as their primary source of energy.
 Lipids
and proteins are also used as energy
sources.
Two general processes are used to obtain energy
from glucose: cellular respiration and
fermentation.
Carbohydrate Catabolism
I. Cellular respiration:
 ATP generating
process in which food molecules
are oxidized.
 Requires
 Final
an electron transport chain.
electron acceptor is an inorganic molecule:
 Aerobic
respiration final electron acceptor is oxygen.
Much more efficient process.
 Anaerobic
respiration final electron acceptor is
another inorganic molecule. Energetically inefficient
process.
II. Fermentation:
 Releases
energy from sugars or other organic
molecules.
 Does not require oxygen, but may occur in its presence.
 Does not require an electron transport chain.
 Final electron acceptor is organic molecule.
 Inefficient: Produces a small amount of ATP for each
molecule of food.
 End-products are energy rich organic compounds:
 Lactic acid
 Alcohol
Aerobic Respiration versus Fermentation
Cellular Respiration
I. Aerobic Respiration
C6H12O6 + 6 O2 -----> 6 CO2 + 6H2O + ATP
Glucose oxygen oxidized reduced
 Most
energy efficient catabolic process.
 Oxygen
is final electron acceptor.
Aerobic Respiration occurs in three stages:
1. Glycolysis
2. Kreb’s Cycle
3. Electron Transport & Chemiosmosis
Three Stages of Aerobic Respiration
Cellular Respiration
I. Stages of Aerobic Respiration
1. Glycolysis: “Splitting of sugar”.
 Glucose
(6 C) is split and oxidized to two molecules of
pyruvic acid (3C).
 Most organisms can carry out this process.
 Does not require oxygen.
Net yield per glucose molecule:


2 ATP (substrate level phosphorylation)
2 NADH
In Glycolysis Glucose is Split into Two
Molecules of Pyruvic Acid
Cellular Respiration
I. Stages of Aerobic Respiration
2. Krebs Cycle (Citric Acid Cycle):
 Before
cycle can start, pyruvic acid (3C) loses one carbon
(as CO2) to become acetyl CoA (2C).
 Acetyl CoA (2C) joins oxaloacetic acid (4C) to form citric
acid (6C).
 Cycle of 8 oxidation-reduction reactions that transfer
energy to electron carrier molecules (coenzymes NAD+
and FAD).
 2 molecules of carbon dioxide are lost during each cycle.
 Oxaloacetic acid is regenerated in final step.
Net yield per glucose molecule:



2 ATP (substrate level phosphorylation)
8 NADH
2 FADH2
Pyruvic Acid is Converted to Acetyl
CoA Before the Kreb’s Cycle Starts
Notice that carbon dioxide is lost.
Kreb’s Cycle: Two Carbons In & Two Out
Cellular Respiration
I. Stages of Aerobic Respiration
3. Electron Transport Chain and Chemiosmosis:
 Electrons
from NADH and FADH2 are released to
chain of electron carriers.
 Electron carriers are on cell membrane (plasma
membrane of bacteria or inner mitochondrial
membrane in eucaryotes).
 Final electron acceptor is oxygen.
 A proton gradient is generated across membrane as
electrons flow down chain.
 ATP is made by ATP synthase (chemiosmosis) as
protons flow down concentration gradient.
Net ATP yield:


2 FADH2 generate 2 ATPs each:
10 NADH generate 3 ATPs each:
4 ATP
30 ATP
Electron Transport Chain in Aerobic Respiration:
Oxygen is Final Electron Acceptor
Chemiosmosis in Aerobic Respiration:
ATP Synthesis Requires Intact Membranes
Summary of Aerobic Respiration in Procaryotes
Total Yield from Aerobic Respiration of 1
Glucose molecule: 36-38 molecules of ATP
In procaryotes:
C6H12O6 + 6 O2-----> 6 CO2 + 6 H2O + 38 ATP
In eucaryotes:
C6H12O6 + 6 O2 -----> 6 CO2 + 6 H2O + 36 ATP
Yield is lower in eucaryotes because transport of
pyruvic acid into mitochondria requires energy.
Cellular Respiration
II. Anaerobic Respiration
 Final
electron acceptor is not oxygen.
 Instead it is an inorganic molecule:
(NO3-): Pseudomonas and Bacillus. Reduced
to nitrite (NO2-):, nitrous oxide, or nitrogen gas.
 Sulfate (SO42-): Desulfovibrio. Reduced to hydrogen
sulfide (H2S).
 Carbonate (CO32-): Reduced to methane.
 Nitrate
 Inefficient
(2 ATPs per glucose molecule).
 Only
part of the Krebs cycle operates without oxygen.
 Not all carriers in electron transport chain participate.
 Anaerobes
tend to grow more slowly than aerobes.
Fermentation
 Releases
energy from sugars or other organic molecules.
 Does not require oxygen, but may occur in its presence.
 Does not require Krebs cycle or an electron transport
chain.
 Final electron acceptor is organic molecule.
 Inefficient. Produces a small amount of ATP for each
molecule of food. (1 or 2 ATPs)
 End-products may be lactic acid, alcohol, or other energy
rich organic compounds.
 Lactic Acid Fermentation: Carried out by
Lactobacillus and Streptococcus. Can result in food
spoilage. Used to make yogurt, sauerkraut, and pickles.
 Alcohol Fermentation: Carried out by yeasts and
bacteria.
Fermentation is Less Efficient Than Aerobic Respiration
Alcohol and Lactic Acid Fermentation
Fermentation: Generates Various Energy Rich,
Organic End-Products
Catabolism of Various Organic Food Molecules
Photosynthesis
6 CO2 + 6 H2O + Light -----> C6H12O6 + 6 O2
Light Dependent Reactions
 Light
energy is trapped by chlorophyll.
 Water is split into oxygen and hydrogen.
 NADP+ is reduced to NADPH.
 ATP is made.
Light
 Do
Independent Reactions
not require light.
 CO2 from air is fixed and used to make sugar.
 Sugar is synthesized, using ATP and NADPH.
Metabolic Diversity
Living organisms can be classified based on
where they obtain their energy and carbon.
Energy Source
 Phototrophs:
Light is primary energy source.
 Chemotrophs: Oxidation of chemical compounds.
Carbon Source
 Autotrophs:
Carbon dioxide.
 Heterotrophs: Organic carbon source.
Four Groups Based on Metabolic Diversity
1. Chemoheterotrophs:
 Energy
source: Organic compounds.
 Carbon source: Organic compounds.

Examples: Most bacteria, all protozoans, all fungi, and all animals.
2. Chemoautotrophs:
 Energy
source: Inorganic compounds (H2S, NH3, S, H2, Fe2+, etc.)
 Carbon source: Carbon dioxide.

Examples: Iron, sulfur, hydrogen, and nitrifying bacteria.
3. Photoheterotrophs:
 Energy
source: Light.
 Carbon source: Organic compounds.

Examples: Purple and green nonsulfur bacteria.
4. Photoautotrophs:
 Energy
source: Light.
 Carbon source: Carbon dioxide.

Examples: Plants, algae, photosynthetic bacteria
Organisms Are Classified Based on Their
Metabolic Requirements