MICROBIAL METABOLISM

AAAT, PharmD.
Learning Objectives

A. Distinguish among metabolism, anabolism, and

catabolism
B. Compare and contrast the three types of ATP
phosphorylation
C. Describe how temperature, pH, substrate
concentration, and competitive and noncompetitive
inhibition affect enzyme activity.
D. Contrast electron transport in aerobic and
anaerobic respiration
E. Describe fermentation and contrast it with
respiration
F. Describe other catabolic pathways
Basic Chemical Reactions
Underlying Metabolism
Metabolism
• Collection of controlled biochemical reactions that take
place within a microbe

• to reproduce the organism

• Sum of ALL chemical reactions in a living organism that
provide energy and create substances to sustain life.
Metabolic Processes Guided by
Eight Elementary Statements

1. Every cell acquires nutrients.

1. Metabolism requires energy from light or catabolism of nutrients.

1. Energy is stored in adenosine triphosphate (ATP).

1. Cells catabolize nutrients to form precursor metabolites.

Metabolic Processes Guided by
Eight Elementary Statements

5. Precursor metabolites, energy from ATP, and enzymes are

used in anabolic reactions.

5. Enzymes plus ATP form macromolecules in polymerization rxns.

5. Cells grow by assembling macromolecules

5. Cells reproduce once they have doubled in size.

Catabolism and Anabolism

• Catabolic pathways
• “Breakdown”
• Break larger molecules into smaller products
• Exergonic (release energy)
• Some of which can be a precursor metabolite of
Anabolism.

• Anabolic pathways
• Synthesize large molecules from the smaller products of
catabolism
• “Building”
• Endergonic (require more energy than they release)
Figure 5.1 Metabolism is composed of catabolic and anabolic reactions.

Energy lost
as heat

Energy lost
Energy
as heat
used
ATP
Energy
stored ANABOLISM
Larger building
Precursor
blocks
molecules

ADP Macromolecules

Energy storage
Nutrients (carbohydrates,
lipids, etc.) Cellular structures
Cellular (membranes,
processes ribosomes, etc.)
(cell growth,
cell division,
etc.)
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)
• Oxidation - removal of electrons
• Reduction - Gain of Electrons
• Redox Reaction - an oxidation reaction paired with a
reduction reaction
Figure 5.2 Oxidation-reduction, or redox, reactions.

Reduction
Electron Oxidized
donor donor
e– e–

Electron Reduced
acceptor acceptor
Oxidation

OIL RIG:
oxidation involves loss;
reduction involves gain.
Oxidation and Reduction Reactions
• Three important electron carriers:

• Nicotinamide adenine dinucleotide (NAD+)

• Nicotinamide adenine dinucleotide phosphate

(NADP+)

• Flavin adenine dinucleotide (FAD)

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
• For example, cells phosphorylate adenosine diphosphate (ADP), which has
two phosphate groups, to form adenosine triphosphate (ATP), which has
three phosphate groups.
ATP Production and Energy Storage
• Cells phosphorylate adenosine diphosphate (ADP) to ATP
in three ways:

• Substrate-level phosphorylation
• involves the transfer of phosphate to ADP from another
phosphorylated organic compound
• Oxidative phosphorylation
• in which energy from redox reactions of respiration is used to
attach inorganic phosphate to ADP
• Photophosphorylation
• which light energy is used to phosphorylate ADP with inorganic
phosphate
• Anabolic pathways use some energy of ATP by breaking a phosphate bond
The Roles of Enzymes in Metabolism

• Chemical reactions of life depend on catalysts,

which are chemicals that increase the likelihood
of a reaction but are not permanently changed
in the process.

• Enzymes are organic catalysts

• Increase likelihood of a reaction
Naming and Classifying Enzymes
• Six categories of enzymes based on mode of action:
• Hydrolases
• Isomerases
• Ligases or polymerases
• Lyases
• Oxidoreductases
• Transferases
Enzyme Activity

• Many factors influence the rate of enzymatic reactions:

• Temperature
• The optimum temperature for the enzymes in the
human body is 37°C.
• Enzymes in those microor ganisms is also 37°C.
• hyperthermophiles, organisms that grow best at
temperatures above 80°C
• pH
• Changing the pH provides a way to control the growth
of unwanted microorganisms by denaturing their
proteins
• For example, vinegar (acetic acid, pH 3.0) acts as a
preservative in dill pickles, and ammonia (pH 11.5)
can be used as a disinfectant
Figure 5.5 Enzymes fitted to substrates.

Substrate

Active sites similar

to substrate's
shape

Enzyme Substrate binding induces an

enzyme's active site to more
closely match the shape of
the substrate (induced fit)
Enzyme Activity
• Many factors influence the rate of enzymatic reactions:
• Enzyme and substrate concentrations
• As substrate concentration increases, enzymatic activity increases as
more and more enzyme active sites bind more and more substrate
molecules.
• Presence of inhibitors
• Competitive - are shaped such that they fit into an enzyme’s active
site and thus prevent the normal substrate from binding.
• can bind permanently or reversibly to an active site.

• Noncompetitive - do not bind to the active site but instead prevent

enzymatic activity by binding to an allosteric site.
• Binding at an allosteric site alters the shape of the active site so that
substrate cannot be bound
Figure 5.6 The process of enzymatic activity.
Substrate
(Fructose 1,6-bisphosphate)

Enzyme
(Fructose-1,6-
bisphosphate
aldolase)

Enzyme-
substrat
e
complex

Glyceraldehyde-3P Dihydroxyacetone-P

Product
s
Figure 5.10 Competitive inhibition of enzyme activity.

Substrate
Competitive
inhibitor

Enzyme

Substrate
Reversible
competitive
inhibitor

Increase in
substrate
concentration
Enzyme
• An example of competitive inhibition is the action of sulfanilamide, which has a
shape similar to that of para-aminobenzoic acid (PABA).
• Sulfanilamide has great affinity for the active site of an enzyme required in the
conversion of PABA into folic acid, which is essential for DNA synthesis.
• As a result, it prevents synthesis of folic acid. Sulfanilamide effectively inhibits
bacteria that make folic acid.
Enzyme Activity
• Inhibitors:
• Substances that block an enzyme's activity
• Include competitive and noncompetitive inhibitors

• Feedback inhibition controls the action of some

enzymes
Figure 5.11 Noncompetitive inhibition at an allosteric site.

Distorted active site

Active site Enzyme (enzymatic activity is
reduced or stopped)

Allosteric site
Allosteric
inhibitor
Noncompetitive inhibition at an allosteric
site
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
• Fermentation
Figure 5.13 Summary of glucose catabolism.

Respiration Fermentation
G Glucose
L
Y
C
O
L
Y
S
I
S

2 Pyruvic acid Pyruvic acid

(or derivative)

Formation of
fermentation
Acetyl-CoA end-products

EL
EC
TR
KREBS ON
CYCLE TR
AN
SP
OR
T
CH
AI
N

Electrons
Final electron
acceptor
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
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 reaction (electron transport
chain)
Figure 5.16 Formation of acetyl-CoA.

Respiration Fermentation

Pyruvic acid

Decarboxylation

Acetate

Coenzyme A

Acetyl-coenzyme A
(acetyl-CoA)
Cellular Respiration
Synthesis of Acetyl-CoA
• Results in:
• Two molecules of acetyl-CoA
• Two molecules of CO2
• Two molecules of NADH
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
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
Figure 5.17 The Krebs cycle.
Respiration Fermentation

H3 C C CoA
Acetyl-CoA

CoA

C OOH
NADH C HOO C
1 C
C
NAD+ C OOH HOO C C
Oxaloacetic acid C
HOO C
8
Citric acid
2
C OOH
C
C C OOH
C OOH C
Malic acid C C OOH
C
C OOH
Isocitric acid
7
KREBS
H2 o
CYCLE

NAD+
C OOH 3
C NADH + C O2
C
HOO C
Fumaric acid
NAD+ C OOH
CoA C
C
6 C
FADH2
C OOH
4 α-Ketoglutaric acid
C OOH CoA C OOH
FAD
C C
C 5 C
C OOH C
Succinic acid NADH + C O2
CoA
GTP GDP Succinyl-CoA

ADP ATP
Cellular Respiration
The Krebs Cycle
• Results in:
• Two molecules of ATP
• Two molecules of FADH2
• Six molecules of NADH
• Four molecules of CO2
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
Cellular Respiration
Electron Transport

• Energy from electrons used to pump protons (H+) across

the membrane, establishing a proton gradient

• Located in inner mitochondrial membrane of eukaryotes

and in cytoplasmic membrane of prokaryotes
Figure 5.18 One possible electron transport chain.

Respiration Fermentation

NADH

Oxidized
2 H+

NAD+ FMN
e– Reduced

Reduced FeS
Path of Oxidized
electrons AT 2 H+
P Oxidized CoQ
Reduced
FADH2
Reduced Cyt
Oxidized
FA AT 2 H+
D P Oxidized Cyt
Reduced

Reduced
Cyt
Final electron
AT acceptor
P Oxidized 2 H+

AT
P
Reduced
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
Figure 5.19 One possible arrangement of an electron transport chain.
Prokaryote

Exterior

Cytoplasmic
membrane

Cytoplasm

+ + +
+
Exterior H+ + Exterior
+ + +
H+ + +
FMN + + + +
+ +
2 Ubiquinone + +
+ H+ H+ +
Cyt b H+ + +
H+ +
Cytoplasmic Cyt a3
membrane e– + + H+ +
Cyt c Cyt a
1 e– + H+ +
e–
e–
e–
e–
– e– e–
–
–
NADH + H+ FADH e–
–
2
e– 4
– –
– NAD+ FA Cyt c1 –
NADH from + H+
– FADH2 D H+ ATP
glycolysis and H+ – – –
from – e– synthase
Krebs cycle – H+ H+
Krebs cycle – – H+
– e–
– –
– – –
–
Cytoplasm 1
2
O2 – ADP + P

H2O
ATP
Table 5.3 Summary of Ideal Prokaryotic Aerobic Respiration of One Molecule of Glucose
Pentose Phosphate Pathway
• Alternative to glycolysis

• Less energy efficient than glycolysis

• Produces precursor metabolites and NADPH

• Used to make DNA nucleotides, steroids, fatty acids
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

alternate 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
Figure 5.20 Examples of fermentation.

Respiration Fermentation

O O
CH3 C C OH
Pyruvic acid

NADH
NAD+ C O2
OH O O
CH3 CH C OH CH3 C H
Lactic acid Acetaldehyde
NADH
NAD+

CH3 CH2 OH
Ethanol
Table 5.4 Comparison of Aerobic Respiration, Anaerobic Respiration, and Fermentation
Figure 5.21 Representative fermentation products and the organisms that produce them.

Glucose
NAD+

NADH

Pyruvic acid

Aspergillus
Representive Propionibacterium Lactobacillus Saccharomyces Clostridium NADH
microbes Streptococcus

Fermentation

CO2, propionic Lactic acid CO2, ethanol Acetone, NAD+

acid isopropanol

Fermentation
products

Nail polish
Swiss cheese Cheddar cheese, Wine, beer remover,
yogurt, soy sauce rubbing alcohol
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
Figure 5.23 Protein catabolism.

H H O R H H O R H H O R

… N C C N C C N C C N C C N C C N C C … Polypeptide

R H H O R H H O R H H O

H2O Proteases

Extracellular fluid

H H O R H H O

H N C C OH H N C C OH H N C C OH Amino acids

R H H O R

Cytoplasmic
membrane H2O Deamination

NH2
2H
Cytoplasm
R

C C OH To Krebs cycle

O O
Table 5.6 The 12 Precursor Metabolites