Microbial Metabolism

(Chapter 5)

Metabolism = sum of all chemical reactions in

a living organism:
- Catabolic reactions: break complex organic
compounds into simper ones, usually via
hydrolysis, usually exergonic
- Anabolic reactions: build complex molecules
from simpler ones, usually via dehydration
synthesis, usually endergonic
*Catabolic reactions provide the energy (ATP)
and building blocks to drive anabolic
reactions (cell growth and repair)
(handout)

Lecture Materials
for
Amy Warenda Czura, Ph.D.
Suffolk County Community College
Eastern Campus
Primary Source for figures and content:
Tortora, G.J. Microbiology An Introduction 8th, 9th, 10th ed. San Francisco: Pearson
Benjamin Cummings, 2004, 2007, 2010.

Metabolic pathway = series of steps to

perform a chemical reaction in living
organisms, requires a new enzyme at each
step
Pathways used by an organism depend on
enzymes encoded by the DNA: what types
of reactions any one organism can perform
is determined by its genetic makeup
Enzymes
- biological catalysts, catalytic proteins
- speed up reactions by lowering activation
energy, orient molecules to favor reaction

- can increase reaction rates up to 10 billion X

faster than random collisions allow
Turnover number = maximum number of
substrate molecules an enzyme converts to
product each second,
different for different enzymes
Each enzyme has a unique 3D shape: it will
bind only its specific substrate(s) at the
active site and catalyze only one specific
reaction resulting in particular product(s)

All cellular reactions performed by enzymes:

cells require thousands of different enzymes
all encoded by the DNA to carry out all
reactions required for life
The majority of proteins in a cell are enzymes

Amy Warenda Czura, Ph.D.

SCCC BIO244 Chapter 5 Lecture Notes

Enzyme Nomenclature
-most end in - ase
-6 classes based on type of reaction:
1. Oxidoreductase
oxidation/reduction reactions
2. Transferase
transfer functional groups
3. Hydrolase
hydrolysis
4. Lyase
removal of atoms without hydrolysis
5. Isomerase
rearrangement of atoms in a molecule
6. Ligase
joining of two molecules
- typically named for reaction catalyzed and
substrate acted upon:
e.g. DNA ligase: functions to join two pieces
of DNA together

Enzyme Components:

Most enzymes have two parts:

1. Apoenzyme = protein part, inactive by itself
2. Cofactor = non-protein part, usually a metal
ion, turns the apoenzyme on
Coenzyme = organic cofactor
apoenzyme + cofactor = holoenzyme
(whole active enzyme)
Metal ion cofactors form a bridge between
enzyme and substrate to facilitate the
reaction

Coenzymes accept/donate atoms or carry

electrons to transfer to other molecules

Two most important coenzymes:

- NAD+
(nicotinamide adenine dinucleotide)
Carries electrons in catabolic reactions
- NADP+
(nicotinamide adenine dinucleotide phosphate)
Carries electrons in anabolic reactions
Both are derived from the B vitamin nicotinic
acid

Mechanism of Enzyme Action

(on handout)

1. The substrate contacts the active site

2. The enzyme-substrate complex is formed.
3. The substrate molecule is altered
atoms are rearranged,
or the substrate is broken into smaller parts,
or the substrate is combined with another molecule
4. Product(s) is/are released from the active site.
5. The enzyme is unchanged and can catalyze a new reaction.

Each enzyme acts on only one substrate, but

any one substrate can be acted upon by
multiple enzymes
Amy Warenda Czura, Ph.D.

SCCC BIO244 Chapter 5 Lecture Notes

Enzymes must be controlled to maintain

homeostasis: two ways to control:
1. level of synthesis (amount produced)
2. level of activity (control cofactors, restrict
access to substrate)
Factors that influence enzyme activity:
1. Temperature
! temp = ! reaction rate
until denaturation
-Enzymes have an optimal
temperature = temp at
which the enzyme
catalyzes the reaction at
its maximum rate
-above this they become denatured
denatured = unfolded, enzyme no longer fits
substrate, cannot catalyze the reaction

2. pH
-enzymes have an optimal
pH that favors the native
conformation (correct
folding)
-pH that is too acidic or too
basic will denature the enzyme
3. Substrate concentration
! substrate conc = ! rxn rate
saturation
until saturation
-each enzyme has a
maximum turnover
number = top speed for
converting substrate into
product
-at saturation, the active site is always full: the
enzyme works at maximum speed
-addition of more substrate beyond the
saturation point will not increase the
reaction rate

4. Inhibitors
inhibitor = a substance that
blocks enzyme function
Three types:
A. Competitive inhibitors
-block the active site
-same shape as the substrate
-competes for the active site
thus blocking enzyme
reaction with the substrate
-some bind permanently thus
killing the enzyme =
irreversible competitive inhibitor
-some bind reversibly and just
slow the reaction rate =
reversible competitive inhibitor

-binding of inhibitor to the allosteric site

causes a shape change in the whole enzyme
such that substrate no longer fits in the
active site = allosteric inhibition

-a reversible allosteric inhibitor will slow the

reaction rate
-an irreversible allosteric inhibitor will kill the
enzyme permanently
C. Enzyme poisons
-bind up metal ion cofactors thus preventing
formation of the holoenzyme

B. Noncompetitive inhibitors
-does not bind the active site
-binds elsewhere
= the allosteric site
Amy Warenda Czura, Ph.D.

SCCC BIO244 Chapter 5 Lecture Notes

Usually there are many steps in a metabolic

pathway to convert substrate to final
product
Each step requires a different enzyme

Energy Production In A Cell

(notes on typed handout)

Feedback inhibition / End product inhibition:

-the product controls its own rate of formation
-occurs when the final
product can inhibit one
of the enzymes in the
pathway
-when product
accumulates, the
pathway is shut
down to prevent
over-production
-common to
anabolic pathways
-usually functions
by reversible
allosteric inhibition of the first enzyme

Metabolism overview
play Metabolism.mpg

Decarboxylation

Glycolysis

Amy Warenda Czura, Ph.D.

Krebs Cycle

SCCC BIO244 Chapter 5 Lecture Notes

Electron Transport Chain

Summary of aerobic respiration

Fermentation

Amy Warenda Czura, Ph.D.

Catabolism of organics for energy production

SCCC BIO244 Chapter 5 Lecture Notes

Photosynthesis: light-dependent reactions

Light-independent reactions

e.g. green and purple non-sulfur bacteria

e.g. plants, algae, cyanobacteria

Biochemical tests
-each organism produces a unique set of
enzymes that determine what type of
metabolic reactions it can carry out
-often a microbe can be identified based on the
substrates it can metabolize and the
products it generates
e.g. Escherichia and Enterobacter both
catabolize glucose but Escherichia will
produce mixed acids and Enterobacter
will produce butanediol (neutral)
Escherichia can ferment lactose into
acid plus gas, Salmonella cannot
ferment lactose
-results from lab assays can be compared to
known metabolic profiles (in Bergeys
Manual) to identify unknowns

Summary of energy production

In the environment, often one organisms

waste serves as anothers fuel

Amy Warenda Czura, Ph.D.

SCCC BIO244 Chapter 5 Lecture Notes

Metabolic Diversity
Organisms classified by nutritional patterns:
Energy source:
Phototrophs = light
Chemotrophs = redox rxns
Carbon source:
Autotrophs = carbon dioxide
Heterotrophs = organic molecules
(handout)

Photoautotrophs
-light for energy
(non-cyclic photophosphorylation)
-CO2 for carbon
(Calvin-Benson cycle)
-e.g. most photosynthetic bacteria, algae,
plants
- can be:
Oxygenic: H from H2O used to reduce
CO2 producing O2 as waste e.g.
Cyanobacteria, algae, plants
Anoxygenic: no O2 produced, other
molecules like H2S used to reduce CO2
e.g. green and purple sulfur bacteria
Photoheterotrophs
-light for energy
(cyclic photophosphorylation)
- organics for carbon (respiration)
- e.g. green and purple non-sulfur bacteria
- always anoxygenic

Chemoautotrophs
- electrons from inorganics for energy (redox)
- CO2 for carbon (Calvin-Benson cycle)
- compounds used for oxidative
phosphorylation: H2S, S, NH3, NO2-, H2,
Fe2+, CO
(electron acceptor in respiration)
- e.g. Few bacteria, e.g. Pseudomonas

energy production = catabolic reactions to

generate ATP
biosynthesis = anabolic reactions use ATP and
building blocks to generate new organic
molecules
Biosynthesis
Autotrophs: fix CO2 via Calvin-Benson cycle
Heterotrophs: need organics to supply Carbon

Chemoheterotrophs
- electrons from H in organics for energy
(redox reactions)
- C from same organics for carbon
(respiration)
- compounds used for oxidative
phosphorylation: O2, organics, inorganics
- classified based on source of organics:
saprophytes - dead organics
parasites - nutrients from living host
- e.g. most bacteria, all fungi, all protozoa, all
animals (including humans)
Amy Warenda Czura, Ph.D.

Polysaccharide Biosynthesis
- catabolism/hydrolysis of carbohydrates,
lipids and amino acids can provide carbon
for glucose synthesis
-glucose is bonded into polysaccharides via
dehydration synthesis with ATP
- carbs used for: glycocalyx, cell walls,
complex molecules (e.g. glycoproteins),
and energy storage

SCCC BIO244 Chapter 5 Lecture Notes

Lipid Biosynthesis
-many different lipids, different structures
-e.g. triglyceride (fat) = glycerol + 3 fatty
acids
- glycerol derived from a 3-carbon glycolysis
intermediate
- fatty acids = hydrocarbon chains, built by
linking acetyl molecules (via dehydration
synthesis with ATP)

Amino Acid and Protein Biosynthesis

- protein = peptide bonded amino acids
- some organisms must ingest amino acids
- some synthesize them from glucose and
inorganic salts or Krebs cycle
intermediates (amination)
-some perform amino acid conversion
(transamination)

- amino acids are peptide bonded together via

dehydration synthesis with ATP
- polypeptides self-fold into the native
conformation of the protein
- proteins used for: enzymes (metabolism,
regulation), transport, structure

- lipids used for: cell membranes, cell walls,

energy storage, parts of complex
molecules

Nucleic Acid Biosynthesis

(nucleotides for DNA and RNA synthesis)
A, G = purines, double ring structure
T, C, U = pyrimidines, single ring structure
- ring structures generated from amino acids:
aspartic acid, glycine, and glutamine
- ring attached to sugar and phosphate to
create nucleotide
Nucleotide = pentose sugar + phosphate +
base (purine or pyrimidine)
Nucleotides are bonded via dehydration
synthesis with ATP to form DNA and
RNA
-DNA & RNA used for information storage

Amy Warenda Czura, Ph.D.

Integration of Metabolism
Amphibolic pathways - can function in both
anabolic and catabolic reactions
- e.g. Krebs Cycle:
catabolism - ATP production
anabolism - intermediates used to
synthesize amino acids

SCCC BIO244 Chapter 5 Lecture Notes