Microbial

Metabolism
 Simplified Model of Metabolism

ANABOLISM Bacterial
Glu cell

Phe ANABOLISM
L ys
Relative complexity of molecules

Ala Macromolecules

CATABOLISM
Val
Glucose ANABOLISM
Proteins
Building
blocks Peptidoglycan
Nutrients
from Precursor RNA + DNA
molecules Amino acids
outside
Glycolysis Complex lipids
or from Sugars
internal Pyruvate
pathways Krebs cycle
Nucleotides
Respiratory Acetyl CoA
chain Fatty acids
Glyceraldehyde-3-P
Some assembly
Fermentation reactions occur
spontaneously

Yields energy Uses energy Uses energy Uses energy

Enzymes: Catalyzing the Chemical Reactions of
Life
•Enzymes
-are catalysts that increase the rate of chemical
reactions without becoming part of the
products or being consumed in the reaction

-substrates: reactant molecules acted on by

an enzyme

-Have unique active site on the enzyme that fits

only the substrate
Enzyme Structure
•Simple enzymes consist of protein alone

•Conjugated enzymes contain protein and nonprotein

molecules
-sometimes referred to as a holoenzyme

-apoenzyme: protein portion of a conjugated

enzyme

-cofactors: inorganic elements (metal ions)

-coenzymes: organic cofactor molecules

 Conjugated Enzyme Structure

Coenzyme Coenzyme

Metallic
cofactor

Metallic
Apoenzymes cofactor
Enzyme-Substrate Interactions
•A temporary enzyme-substrate union must occur at the
active site
-fit is so specific that it is described as a “lock-
and-key” fit

•Bond formed between the substrate and enzyme are

weak and easily reversible

•Once the enzyme-substrate complex has formed, an

appropriate reaction occurs on the substrate, often with
the aid of a cofactor

•Product is formed

•Enzyme is free to interact with another substrate

 Enzyme-Substrate Reactions

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Substrates

Products

Enzyme (E) ES complex E

Does
not fit

(a) (b) (c)

Cofactors: Supporting the Work of Enzymes
•The need of microorganisms for trace elements arises
from their roles as cofactors for enzymes
-iron, copper, magnesium, manganese, zinc,
cobalt, selenium, etc.

•Participate in precise functions between the enzyme

and substrate
-help bring the active site and substrate close
together

-participate directly in chemical reactions with

the enzyme-substrate complex
Cofactors: Supporting the Work of Enzymes
(cont’d)
•Coenzymes
-organic compounds that work in conjunction
with an apoenzyme

-general function is to remove a chemical

group from one substrate molecule and add it to
another substrate molecule

-carry and transfer hydrogen atoms, electrons,

carbon dioxide, and amino groups

-many derived from vitamins

Classification of Enzyme Functions
•Enzymes are classified and named according to
characteristics such as site of action, type of action,
and substrate
-prefix or stem word derived from a certain
characteristic, usually the substrate acted upon or
type of reaction catalyzed

-ending –ase
Classification of Enzyme Functions (cont’d)
•Six classes of enzymes based on general biochemical
reaction
-oxidoreductases: transfer electrons from one
substrate to another, dehydrogenases transfer a
hydrogen from one compound to another

-transferases: transfer functional groups from

one substrate to another

-hydrolases: cleave bonds on molecules with

the addition of water
Classification of Enzyme Functions (cont’d)
•Six classes of enzymes based on general biochemical
reaction (cont’d)
-lyases: add groups to or remove groups from
double-bonded substrates

-isomerases: change a substrate into its

isomeric form

-ligases: catalyze the formation of bonds with

the input of ATP and the removal of water
Classification of Enzyme Functions (cont’d)
•Each enzyme also assigned a common name that
indicates the specific reaction it catalyzes
-carbohydrase: digests a carbohydrate substrate

-amylase: acts on starch

-maltase: digests maltose

-proteinase, protease, peptidase: hydrolyzes the

peptide bonds of a protein

-lipase: digests fats

-deoxyribonuclease (DNase): digests DNA

-synthetase or polymerase: bonds many small molecules

together
Regulation of Enzyme Function

Constitutive enzymes: Always present in relatively constant

amounts regardless of the amount of substrate

Regulated enzymes: production is turned on (induced) or

turned off (repressed) in responses to changes in
concentration of the substrate
Regulation of Enzyme Function (cont’d)
Activity of enzymes influenced by the cell’s environment
-natural temperature, pH, osmotic pressure
-changes in the normal conditions causes
enzymes to be unstable or labile

•Denaturation
-weak bonds that maintain the native shape of
the apoenzyme are broken
-this causes disruption of the enzyme’s shape
-prevents the substrate from attaching to the
active site
Metabolic Pathways
•Often occur in a multistep series or pathway, with each
step catalyzed by an enzyme
•Product of one reaction is often the reactant
(substrate) for the next, forming a linear chain or
reaction
•Many pathways have branches that provide alternate
methods for nutrient processing
•Others have a cyclic form, in which the starting
molecule is regenerated to initiate another turn of the
cycle
•Do not stand alone; interconnected and merge at many
sites
 Patterns of Metabolism

Multienzyme Systems

Linear Cyclic Branched

Divergent Convergent
A
M A X
U
B

V T input N B Y
C S product Z
Krebs
W O P
Cycle C Z
D Y
X
O1 Q M Example:
E Amino acid
synthesis
O2 R N
Example:
Glycolysis
Direct Controls on the Action of Enzymes
•Competitive inhibition
-inhibits enzyme activity by supplying a
molecule that resembles the enzyme’s normal
substrate
-“mimic” occupies the active site, preventing
the actual substrate from binding
•Noncompetitive inhibition
-enzymes have two binding sites: the active site
and a regulatory site
-molecules bind to the regulatory site
-slows down enzymatic activity once a certain
concentration of product is reached
Two Common Control Mechanisms for Enzymes
Competitive Inhibition Noncompetitive Inhibition

Normal Competitive Substrate

substrate inhibitor with
similar shape
Active site
Both molecules
compete for
the active site.
Enzyme

Enzyme
Regulatory site

Regulatory
molecule
(product)

Reaction proceeds. Reaction is blocked Reaction proceeds. Reaction is blocked because

because competitive binding of regulatory molecule
inhibitor is incapable in regulatory site changes
of becoming a product. conformation of active site so
Product that substrate cannot enter.
Controls on Enzyme Synthesis
•Enzymes do not last indefinitely; some wear out, some
are degraded deliberately, and some are diluted with
each cell division
•Replacement of enzymes can be regulated according to
cell demand
•Enzyme repression: genetic apparatus responsible for
replacing enzymes is repressed
-response time is longer than for feedback
inhibition
•Enzyme induction: enzymes appear (are induced) only
when suitable substrates are present
Enzyme Induction in E. coli
•If E. coli is inoculated into a medium containing only
lactose, it will produce the enzyme lactase to hydrolyze
it into glucose and galactose

•If E. coli is subsequently inoculated into a medium

containing only sucrose, it will cease to synthesizing
lactase and begin synthesizing sucrase

•Allows the organism to utilize a variety of nutrients,

and prevents it from wasting energy by making enzymes
for which no substrates are present
 Concept Check

Which of the following mechanisms of enzyme control

blocks a reaction catalyzed by an enzyme, by the binding
of a product to a regulatory site on the enzyme?

A. enzyme repression
B. competitive inhibition
C. enzyme induction
D. noncompetitive inhibition
E. None of the choices is correct.
 Learning Outcomes: Section 7.2
6. Name the chemical in which energy is stored in cells.

7. Create a general diagram of a redox reaction.

8. Identify electron carriers used by cells.

Energy in Cells
•Energy is managed in the form of chemical reactions
that involve the making and breaking of bonds and the
transfer of electrons

•Exergonic reactions release energy, making it available

for cellular work

•Endergonic reactions are driven forward with the

addition of energy

•Exergonic and endergonic reactions are often coupled

so that released energy is immediately put to work
Oxidation and Reduction
•Oxidation: loss of electrons
-when a compound loses electrons, it is oxidized

•Reduction: gain of electrons

-when a compound gains electrons, it is reduced

•Oxidation-reduction (redox) reactions are common in

the cell and are indispensable to the required energy
transformations
Oxidation and Reduction (cont’d)
•Oxidoreductases: enzymes that remove electrons
from one substrate and add them to another
-their coenzyme carriers are nicotinamide
adenine dinucleotide (NAD) and flavin adenine
dinucleotide (FAD)

•Redox pair: an electron donor and an electron acceptor

involved in a redox reaction
Oxidation and Reduction (cont’d)
•Energy present in the electron acceptor can be
captured to phosphorylate (add an inorganic
phosphate) to ADP or to some other compound to store
energy in ATP

•The cell does not handle electrons as discrete entities

but rather as parts of an atom such as hydrogen
(consisting of a single electron and a single proton)

•Dehydrogenation: the removal of hydrogen during a

redox reaction
Electron Carriers: Molecular Shuttles
•Electron carriers resemble shuttles that are alternately loaded and unloaded,
repeatedly accepting and releasing electrons and hydrogens to facilitate transfer of
redox energy

NAD+ NAD H + H+

From substrate
Oxidized Nicotinamide Reduced Nicotinamide

H H H H+
C 2H C
C C C NH2 C C C NH2
2e:
C C O C C O
N N

Adenine

P Ribose P

P P
ATP: Metabolic Money
•Three-part molecule
-nitrogen base (adenine) Adenosine
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Adenosine
Triphosphate Diphosphate Adenosine
(ATP) (ADP)
-5-carbon sugar (ribose) H H
Adenine
N

-chain of three phosphate N

N

groups bonded to ribose H

H
N N

-phosphate groups are OH OH OH

H

bulky and carry negative HO P O P O P O H

charges, causing a strain O O O

O

between the last two H H

H H
phosphates Bond that releases
energy when broken OH OH

Ribose
-the removal of the terminal
phosphate releases
energy
 PRACTICE QUESTIONS
 Name three basic catabolic pathways, and give an estimate of
how much ATP each of them yields.

 Write a summary statement describing glycolysis.

 Describe the Krebs cycle.

 Discuss the significance of the electron transport system.

 Point out how anaerobic respiration differs from aerobic

respiration.

 Provide a summary of fermentation.

Catabolism
•Metabolism uses enzymes to catabolize organic
molecules to precursor molecules that cells then use to
anabolize larger, more complex molecules
•Reducing power: electrons available in NADH and
FADH2
•Energy: stored in the bonds of ATP
-both are needed in large quantities for anabolic
metabolism
-both are produced during catabolism
 Overview of the Three Main Catabolic Pathways

AEROBIC RESPIRATION ANAEROBIC RESPIRATION FERMENTATION

Glycolysis

Glycolysis
Glycolysis
NAD H NAD H NAD H
CO2 CO2 CO2

Yields 2 ATPs ATP ATP ATP

NAD H Krebs NAD H Krebs

Cycle CO2 Cycle CO2

FADH2 FADH2
Yields 2 GTPs ATP ATP

Fermentation
Electron Transport System Electron Transport System
Using organic
compounds as
Using O2 as electron acceptor Using non- O2 compound as electron acceptor electron acceptor
(So42–, NO3–, CO32–)
Yields variable
amount of
energy ATP ATP
Alcohols, acids

Maximum net yield 36–38 ATPs 2–36 ATPs 2 ATPs

Getting Materials and Energy
•Nutrient processing in bacteria is extremely varied, but
in most cases the nutrient is glucose
•Aerobic respiration
-a series of reactions that converts glucose to
CO2 and allows the cell to recover significant
amounts of energy
-utilizes glycolysis, the Krebs cycle, and the
electron transport chain
-relies on free oxygen as the final electron and
hydrogen acceptor
-characteristic of many bacteria, fungi, protozoa,
and animals
Getting Materials and Energy (cont’d)
•Anaerobic respiration
-used by strictly anaerobic organisms and those who
are able to metabolize with or without oxygen
-involves glycolysis, the Krebs cycle, and the electron
transport chain
-uses NO3-, SO42-, CO33-, and other oxidized
compounds as final electron acceptors
•Fermentation
-incomplete oxidation of glucose
-oxygen is not required
-organic compounds are final electron acceptors
Glycolysis
•Turns glucose into pyruvate, which yields energy in the pathways that
follow
Glycolysis
Energy Lost or Gained Overview Details
Glucose
Uses 2 ATPs
C C C C C C
Three reactions alter and rearrange the
6-C glucose molecule into 6-C fructose-1,6
diphosphate.
Fructose-1, 6-diphosphate

C C C C C C

One reaction breaks fructose-1,6-diphosphate

into two 3-carbon molecules.
C C C C C C

Yields 4 ATPs and 2 NADHs Pyruvate Pyruvate Five reactions convert each 3 carbon molecule
into the 3C pyruvate.
C C C C C C

Total Energy Yield: 2 ATPs and Pyruvate is a molecule that is uniquely suited for chemical
2 NADHs reactions that will produce reducing power (which will
eventually produce ATP).
The Krebs Cycle (Citric Acid Cycle):
A Carbon and Energy Wheel
•After glycolysis, pyruvic acid is still energy-rich
•cytoplasm of bacteria and mitochondrial matrix of eukaryotes
-a cyclical metabolic pathway that begins with acetyl CoA,
which joins with oxaloacetic acid, and then
participates in seven other additional transformations
-transfers the energy stored in acetyl CoA to NAD+ and
FAD by reducing them (transferring hydrogen ions to
them)
-NADH and FADH2 carry electrons to the electron
transport chain
-2 ATPs are produced for each molecule of glucose
through phosphorylation
 The Krebs Cycle

The Krebs Cycle

Energy Lost or Gained Overview Details

One CO2 is liberated and one NADH is The 3C pyruvate is converted to

formed. 2C acetyl CoA in one reaction.
Pyruvate Pyruvate

C C C C C C

Remember: This
happens twice for
Each acetyl CoA yields 1 GTP, 3 NADHs, Acetyl CoA each glucose In the first reaction, acetyl CoA
1 FADH, and 2 CO2 molecules. molecule that donates 2Cs to the 4C molecule
Oxaloacetate C C enters glycolysis.
oxaloacetate to form 6C citrate.
Total Yield per 2 acetyl CoAs: C C C C
CO2: 4 Citrate In the course of seven more
Yields: reactions, citrate is manipulated
Energy: 2 GTPs, 6 NADHs, 2 FADHs 3 NADHs C C C C C C to yield energy and CO2 and
1 FADH2
oxaloacetate is regenerated.
CO2
CO2
Intermediate molecules on the
wheel can be shunted into other
Other
metabolic pathways as well.
intermediates GTP
The Respiratory Chain: Electron Transport
•A chain of special redox carriers that receives reduced
carriers (NADH, FADH2) generated by glycolysis and the
Krebs cycle
-passes them in a sequential and orderly
fashion from one to the next
-highly energetic
-allows the transport of hydrogen ions outside
of the membrane
-in the final step of the process, oxygen accepts
electrons and hydrogen, forming water
The Respiratory Chain: Electron Transport (cont’d)
•Principal compounds in the electron transport chain:
-NADH dehydrogenase
-flavoproteins
-coenzyme Q (ubiquinone)
-cytochromes
•Cytochromes contain a tightly bound metal ion in their
center that is actively involved in accepting electrons and
donating them to the next carrier in the series
 The Respiratory (Electron Transport) Chain
The Respiratory (Electron Transport) Chain
Reduced carriers (NADH, FADH) transfer electrons and H+ to first
electron carrier in chain: NADH dehydrogenase.
These are then sequentially transferred to the next four to six
carriers with progressively more positive reduction potentials.
The carriers are called cytochromes. The number of carriers varies,
depending on the bacterium.

Simultaneous with the reduction of the electron carriers,

protons are moved to the outside of the membrane, creating a
concentration gradient (more protons outside than inside the
cell). The extracellular space becomes more positively charged
and more acidic than the intracellular space. This condition
H+ creates the proton motive force, by which protons flow down the
H+ concentration gradient through the ATP synthase embedded in the
H+ membrane. This results in the conversion of ADP to ATP.
H+
ATP
H+ synthase
Cell wall
H+
H+

H+

ADP ATP
H+

H+
Cell H+ H+ Once inside the cytoplasm, protons combine with O2 to
membrane H+
form water (in aerobic respirers [left]), and with a variety of
With ETS Cytochromes H+
H+
O-containing compounds to produce more reduced compounds.

NAD H O2
SO42–
NO3– Aerobic respiration yields a maximum of 3 ATPs per
oxidized NADH and 2 ATPs per oxidized FADH.

H2O NO2– HS–

Cytoplasm Anaerobic respiration yields less per NADH and FADH.

Aerobic Anaerobic
respirers respirers
The Electron Transport Chain (cont’d)
•Electron transport carriers and enzymes are embedded in the cell
membrane in prokaryotes and on the inner mitochondrial membrane
in eukaryotes

Intermembrane
H+ ions space
Cristae
The Electron Chain (cont’d)
•Released energy from electron carriers in the electron
transport chain is channeled through ATP synthase
• Oxidative phosphorylation: the coupling of ATP
synthesis to electron transport
- each NADH that enters the electron transport chain
can give rise to 3 ATPs

- Electrons from FADH2 enter the electron transport

chain at a later point and have less energy to release,
so only 2 ATPs result
The Terminal Step
•Aerobic respiration
-catalyzed by cytochrome aa3, also known as
cytochrome oxidase

-adapted to receive electrons from cytochrome

c, pick up hydrogens from solution, and react
with oxygen to form water

2H+ + 2e- + ½ O2  H20

The Terminal Step (cont’d)

•Most eukaryotes have a fully functioning cytochrome

system

•Bacteria exhibit wide-ranging variations in this system

-some lack one or more redox steps

-several have alternative electron transport

schemes

-lack of cytochrome c oxidase is useful in

differentiating among certain genera of bacteria
The Terminal Step (cont’d)
•A potential side reaction of the respiratory chain is the
incomplete reduction of oxygen to the superoxide ion
(O2-) and hydrogen peroxide (H2O2)

•Aerobes produce enzymes to deal with these toxic

oxygen products
-superoxide dismutase
-catalase
-Streptococcus lacks these enzymes but still
grows well in oxygen due to the production of
peroxidase
The Terminal Step (cont’d)
•Anaerobic Respiration
-the terminal step utilizes oxygen-containing
ions, rather than free oxygen, as the final electron
acceptor

Nitrate reductase

NO3- + NADH NO2- + H2O + NAD+

•Nitrate reductase catalyzes the removal of oxygen from

nitrate, leaving nitrite and water as products
Anaerobic Respiration (cont’d)
•Denitrification
-some species of Pseudomonas and Bacillus
possess enzymes that can further reduce nitrite
to nitric oxide (NO), nitrous oxide (N2O), and
even nitrogen gas (N2)
-important step in recycling nitrogen in the
biosphere
•Other oxygen-containing nutrients reduced
anaerobically by various bacteria are carbonates and
sulfates
•None of the anaerobic pathways produce as much ATP
as aerobic respiration
After Pyruvic Acid II: Fermentation
•Fermentation
-the incomplete oxidation of glucose or other
carbohydrates in the absence of oxygen
-uses organic compounds as the terminal
electron acceptors
-yields a small amount of ATP
-used by organisms that do not have an electron
transport chain
-other organisms revert to fermentation when
oxygen is lacking
Fermentation (cont’d)
•Only yields 2 ATPs per molecule of glucose

•Many bacteria grow as fast as they would in the

presence of oxygen due to an increase in the rate of
glycolysis
•Permits independence from molecular oxygen
-allows colonization of anaerobic environments
-enables adaptation to variations in oxygen
availability
-provides a means for growth when oxygen
levels are too low for aerobic respiration
Fermentation (cont’d)
•Bacteria and ruminant cattle
-digest cellulose through fermentation
-hydrolyze cellulose to glucose
-ferment glucose to organic acids which are absorbed
as the bovine’s principal energy source

•Human muscle cells

-undergo a form of fermentation that permits short
periods of activity after the oxygen supply has been
depleted
-convert pyruvic acid to lactic acid, allowing
anaerobic production of ATP
-accumulated lactic acid causes muscle fatigue
 Fermentation

Fermentation

C C C Pyruvic acid from glycolysis can itself become the electron

acceptor.
Pyruvic acid
CO2
Remember: This
happens twice for
H
each glucose Pyruvic acid can also be enzymatically altered and then serve as
molecule that
H C C H the electron acceptor.
enters glycolysis.

H O The NADs are recycled to reenter glycolysis.

Acetaldehyde
NAD H NAD H The organic molecules that became reduced in their role as
electron acceptors are extremely varied, and often yield useful
H H H OH products such as ethyl alcohol, lactic acid, propionic acid,
O butanol, and others.
NAD +

H C C OH H C C C
OH
H H H H
Ethyl alcohol Lactic acid
Products of Fermentation in Microorganisms
•Alcoholic beverages: ethanol and CO2

•Solvents: acetone, butanol

•Organic acids: lactic acid, acetic acid

•Vitamins, antibiotics, and hormones

•Large-scale industrial syntheses by microorganisms

often utilize entirely different fermentation
mechanisms for the production of antibiotics,
hormones, vitamins, and amino acids
Catabolism of Noncarbohydrate Compounds
•Complex polysaccharides broken into component
sugars, which can enter glycolysis

•Lipids broken down by lipases

-glycerol converted to dihydroxyacetone
phosphate, which can enter midway into
glycolysis

-fatty acids undergo beta oxidation, whose

products can enter the Krebs cycle as acetyl CoA
Catabolism of Noncarbohydrate Compounds
(cont’d)
•Proteins are broken down into amino acids by
proteases
-amino groups are removed through
deamination

-remaining carbon compounds are converted

into Krebs cycle intermediates or decarboxylated
Anabolism:
Formation of Macromolecules
•Two possible sources for monosaccharides, amino
acids, fatty acids, nitrogenous bases, and vitamins
-enter the cell from the outside as nutrients

-can be synthesized through various cellular

pathways
Anabolism:
Formation of Macromolecules (cont’d)
•The degree to which an organism can synthesize its
own building blocks is genetically determined and varies
from group to group
-autotrophs only require CO2 as a carbon
source and a few minerals to synthesize all cell
substances

-some heterotrophs such as E. coli can

synthesize all cellular substances from a few
minerals and one organic carbon source such as
glucose