Download Microbiology: A Systems Approach

LECTURES IN
MICROBIOLOGY
Microbial Metabolism
LESSON 6
Sofronio Agustin
Professor
Lesson 6 Topics
 Metabolism
 Energy
 Pathways
 Biosynthesis
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Metabolism
 Catabolism
 Anabolism
 Enzymes
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Catabolism
Breakdown of complex organic
molecules in order to extract
energy and form simpler end
products.
Enzymes are involved.
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Metabolism Model
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Enzymes
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Function
Structure
Enzyme-substrate interaction
Cofactors
Action
Regulation
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Enzyme Structure
Simple enzyme - primarily protein
Conjugated enzyme
- protein and nonprotein
Three-dimensional features:
Specificity -”lock-and-key”
Active site or catalytic site
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Conjugated Enzymes
Conjugated enzymes contain a metallic cofactor, coenzyme,
or both in order for it to function as a catalyst.
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Active Site
Specific active sites are folded regions of the protein molecule
and contain specific amino acids in its microenvironment.
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Enzyme-Substrate Interaction
Substrates specifically bind to the active
sites on the enzyme:
-“lock-and-key” style
-Induced fit
Once the reaction is complete, the product
is released and the enzyme reused.
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Lock-and-Key Model
Specificity of enzyme-substrate reactions and induced fit.
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Coenzymes
 Function as transient carriers
 Alter a substrate by removing a
chemical group from it and adding it
to another.
 Ex. NAD, FAD and CoA
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Coenzyme Activity
Carrier function of
coenzymes
A coenzyme
transfers
chemical groups from
one substrate to
another.
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Enzyme Action
Exoenzymes
Endoenzymes
Constitutive
Induction or repression
Types of reactions
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Enzyme Location
Exoenzymes are inactive while inside the cell, but upon
release from the cell they become active.
Endoenzymes remain in the cell and are always active.
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Constitutive and Regulated Enzymes
Constitutive enzymes are
present in constant amounts.
Regulated enzymes are either
induced or repressed.
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Types of Reactions
 Condensation
 Hydrolysis
 Transfer reactions
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Synthesis and Hydrolysis
Condensation reactions are associated with anabolic reactions,
and hydrolysis reactions are associated with catabolic reactions.
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Transfer Reactions
Transfer of electrons from one substrate to
another.
Ex: Oxidoreductase - oxidationreduction
reactions.
Transfer of functional groups from one molecule
to another.
Ex:
Aminotransferases - transfer of
amino group.
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Sample Enzymes
Examples of enzymes, their substrates, and their reactions.
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Regulation
Metabolic pathways
Direct control
Genetic control
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Patterns of Metabolism
Metabolic pathways
follow stepwise
patterns.
These are regulated
by enzymes that
catalyze these
reactions.
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Enzyme Control Mechanisms
Competitive inhibition and noncompetitive inhibition are
forms of direct control (regulation) of the enzyme action.
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Genetic Control
Repression - end products stop the expression
of genes that encode for proteins (enzymes) which
are responsible for metabolic reactions.
Induction - substrate initiates and enhances the
expression of genes for proteins (enzymes) that
drive metabolic reactions.
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Repression
Repression as a type of genetic control of enzyme synthesis
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Enzyme Characteristics
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Bioenergetics
 Cell energetics
- Exergonic reactions
- Endergonic reactions
 Redox reaction
 Electron carriers
 Adenosine Triphosphate (ATP)
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Energy Machinery of the Cell
The general scheme associated with metabolism of organic molecules,
the redox reaction, and the capture of energy in the form of ATP.
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Redox Reaction
Oxidation - removal or loss of electrons
Reduction - addition or gain of electrons
These are coupled reactions
Biological redox reactions involve transfer of
electrons and protons (hydrogens) =
dehydrogenation
Dehydrogenases - catalyze these reactions
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Electron Carriers
Electron carriers - transfer electrons (and
protons) from donor to acceptor molecules.
Coenzymes:
Ex: Nicotinamide adenine dinucleotide
(NAD)
Respiratory chain (ETC) carriers:
Ex: Cytochromes (protein+porphyrin)
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Adenosine Triphosphate
Temporary energy repository (“cellular battery”)
Breaking of pyrophosphates bonds will release
free energy for cellular work.
Three part molecule:
Nitrogen base - Adenine
Pentose sugar - Ribose)
Chain of three phosphate groups
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Energy Capture
The phosphate groups
capture the energy
derived from metabolism
as pyrophosphate bonds
within the ATP molecule.
ATP and its partner
compounds ADP and
AMP.
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Phosphorylation
ATP can be used
to phosphorylate
an organic
molecule such as
glucose during
catabolism.
Phosphorylation catalyzed by
phosphorylases
(e.g. hexokinase)
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Substrate-level Phosphorylation
ATP can be synthesized by substrate-level
phosphorylation.
A phosphate group from an intermediate is
transferred to ADP to regenerate ATP.
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Catabolic Pathways
Embden-Meyerhoff-Parnas (EMP) Pathway
or Glycolysis
Kreb’s or Tricarboxylic Acid (TCA) Cycle
Electron Transport or Respiratory Chain
Alternate pathways
Fermentation
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Glucose Metabolism
Overview of the
location, flow, endproducts of cellular
(aerobic)
respiration.
Glucose is
catabolized to
harness energy.
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Cellular Respiration
Glycolysis
Kreb’s Cycle
Electron Transport Chain
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Glycolysis
Glucose (6-carbon sugar) splits into two
pyruvates (3-carbon molecules).
Glucose is oxidized and coenzyme NAD is
reduced to NADH.
Energy investment phase:
- Phosphorylation of intermediates using
2 ATP molecules
Energy yielding phase:
- Substrate-level-phosphorylation of
ADP to produce 4 ATPs.
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Glycolytic Steps
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Kreb’s Cycle
 Each pyruvic acid is processed to enter
the Kreb’s Cycle as Acetyl CoA.
 CO2 is generated -decarboxylation

reactions.
Coenzymes NAD and FAD are reduced to
NADH and FADH2
 Net yield of two ATPs per molecule of
glucose.
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Steps in Kreb’s Cycle
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Electron Transport Chain
•NADH and FADH2 from glycolysis and
Kreb’s Cycle donate electrons to the electron
carriers (ETC).
•Membrane bound carriers transfer electrons
by redox reactions.
•Oxygen (final electron acceptor) completes
the terminal step.
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Electron Transport Chain
The Electron Transport Chain and Chemiosmosis driven by the
Proton Motive Force
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Location of ETC
 Eukaryotes - Inner Mitochondrial
Membrane
 Prokaryotes- Cytoplasmic Membrane
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ATP Yield
Glycolysis 2
Kreb’s Cycle - 2
ETC34
Total Yield:
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NADH yield FADH2 yield-
2 in Glycolysis
8 in Kreb’s Cycle
2 in Kreb’s Cycle
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Anaerobic Respiration
Similar to aerobic respiration,
except nitrate or nitrite is the
final electron acceptor
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Fermentation
Glycolysis only
NADH from glycolysis is used to reduce
the glucose
Organic compounds as the final
electron acceptors (not O2)
Low ATP yields per glucose molecule
compared to cellular respiration
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Fermentation
Chemistry of
fermentation:
Production of
ethyl alcohol or
lactic acid and
release of CO2
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Types of Fermenters
Facultative anaerobes
Fermentation in the absence of oxygen
Respiration in the presence of oxygen
Ex. Escherichia coli
Strict fermenters
No respiration
Ex. yeast
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Fermentation Products
 Alcoholic fermentation
 Acidic fermentation
 Mixed acid fermentation
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Mixed Acid Fermentation
Mixed acid fermentation and related products synthesized from pyruvate
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Biosynthesis
Amphibolic
Gluconeogenesis
Beta oxidation
Amination
Transamination
Deamination
Macromolecules
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Amphibolic Synthesis
Integration of the catabolic and anabolic
pathways (Coupled Reactions)
Intermediates serve multiple purposes
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Amphibolic Synthesis
Intermediates
serve as
precursors to
synthesize
amino acids,
carbohydrates
and lipids.
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Gluconeogenesis
Pyruvate (intermediate) is converted back to
glucose
Occurs when the glucose supply is low
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Beta Oxidation
Metabolism of fats into acetyl, which can
then enter the Kreb’s cycle as acetyl CoA.
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Amino Acid Synthesis
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Macromolecules
Cellular building blocks:
Monosaccharides
Amino acids
Fatty acids
Nitrogen bases
Vitamins
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