Chapter 5
Microbial Metabolism
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Catabolic and Anabolic Reactions
Metabolism: The sum of the chemical reactions in an
organism
Chemical reactions are divided into two classes:
Catabolism
Also called degradation
Breakdown of complex molecules into simpler/smaller
ones
Release energy (exergonic)
Anabolism
Also called biosynthesis
Building of complex molecules from simpler/smaller
ones
Consumes energy (endergonic)
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What Makes Catabolic and Anabolic
Reactions occur?
Chemical reactions occur when chemical bonds are
formed or broken
Chemical reactions occur with help of enzymes
Most enzymes are proteins!
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What are Enzymes?
Biological catalysts
Speed up chemical reaction
Are NOT used up in the reaction
Are NOT changed in the reaction
Specific for a chemical reaction (enzyme and substrate are
complementary in shape)
Sometimes enzymes require cofactors or coenzymes for activation
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How do Enzymes Speed up Chemical
Reactions?
Reaction rate can be increased by:
enzymes (catalysts)
They lower activation energy
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Cofactors and Coenzymes Help
Enzymes to Speed up Chemical
Reaction
Cofactors:
Help catalyze a reaction by forming a bridge between an
enzyme and its substrate
NAD+
NADP+
FAD
Ions
Coenzymes:
Organic molecules such as vitamins
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Enzyme Classification
Enzymes are very specific
Names of enzymes usually end in ase
Oxidoreductase: Oxidation-reduction reactions
Transferase: Transfer functional groups
Hydrolase: Hydrolysis
Isomerase: Rearrangement of atoms
Ligase: Joining of molecules
Ribozyme:
An example of enzyme that is not a protein!
Unique type of RNA molecule that plays important role
in protein synthesis
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Factors Influencing Enzyme Activity
1. Temperature
2. pH
3. Substrate concentration
4. Inhibitors
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Factors Influencing Enzyme Activity
1. Temperature
2. pH
Temperature and pH can denature proteins
Figure 5.6
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Effect of Temperature on Enzyme
Activity
Figure 5.5a
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Effect of pH on Enzyme activity
Figure 5.5b
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Factors Influencing Enzyme Activity
3. Substrate concentration
Substrate is a
molecule on which
the enzyme works
( it will either help to
break down the
substrate or build
the substrate
As substrate
concentration
increases, chemical
reaction occurs
faster until all
available enzymes
become saturated
with stubstrates
Figure 5.5c
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Factors Influencing Enzyme Activity
4. Inhibitors
Enzyme inhibitors:
Competitive vs. Noncompetitive
Binds the active site of the enzyme Do not bind the active site of the enzyme
Does not undergo reaction to form product Interacts with another part of the enzyme
Some bind irreversibly, others bind reversibly Causes active site to change its shape
Overcome by increasing the substrate concentration Can be reversible or irreversible
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Enzyme Inhibitors: Feedback Inhibition
Noncompetitive inhibitors play important role in feedback inhibition
(end product inhibition)
Mechanism that stops the cell from making more of a substance than it needs
It usually inhibits one of first enzymes in the pathway
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Oxidation-Reduction Reactions
Oxidation: Removal of electrons (e-) from an atom
or molecule
Reduction: Gain of electrons (e-) from an atom or
molecule
Oxidation and reduction reactions are coupled
Redox reaction: An oxidation reaction paired with a
reduction reaction
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Oxidation-Reduction Reactions
In biological systems, electrons are often associated with
hydrogen atoms
Figure 5.10
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Chemical Reaction that Generates ATP
ATP is generated by the phosphorylation of ADP
ATP can be generated through:
Substrate level phosphorylation
Oxidative phosphorylation
Photophosphorylation
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Substrate-Level Phosphorylation
ATP is synthesized by phosphorylation (transfer of
P) of ADP
High energy is directly transferred
P comes from phosphorylated substrate
Ex: fructose-1,6-biphosphate
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Oxidative Phosphorylation
Electors are transferred from one electron carrier to
the next
Energy is released
Some of this energy is used to make ATP
(chemiosmosis)
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Photophosphorylation
Occurs only in photosynthetic cells
Light + water + CO2 = energy (ATP), sugars, O2
Light causes chlorophyll to give up electrons. Energy
released from transfer of electrons (oxidation) of
chlorophyll through a system of carrier molecules is
used to generate ATP.
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Chemical Reaction: ATP synthesis
through carbohydrate Catabolism
The breakdown of carbohydrates to release energy
Three steps that all together will generate about 38
ATP molecules per cycle:
Glycolysis
Krebs cycle
Electron transport chain
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Glycolysis
The oxidation (break down) of glucose to pyruvic
acid produces ATP (through substrate level
phosphorylation) and NADH
Figure 5.11
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Glycolysis (Part 1)
2 ATP are used to
phosphorylate glucose
Glucose split to form 2
glucose-3-phosphate
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Glycolysis (Part 2)
2 glucose-3-phosphate are oxidized
to 2 pyruvic acid
End product of glycolysis:
4 ATP produced
Gain net is only 2 ATP
2 NADH produced
2 pyruvic acid molecules
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Alternatives to Glycolysis
Many bacteria have another pathway in addition to glycolysis for the
oxidation of glucose:
Pentose phosphate pathway
Operates simultaneously with glycolysis
Breaks down glucose and five-carbon sugars
Generates intermediate pentoses used in synthesis of:
Nucleic acid, glucose, amino acids
Net gain of 1 ATP molecule
Entner-Doudoroff pathway
Can metabolize glucose without glycolysis or pentose phosphate
pathway
Net gain of 1 ATP molecule
Found in some gram negative bacteria
Generally not found in gram positive bacteria
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Intermediate Step (Before Krebs cycle)
Pyruvic acid (from glycolysis) cannot enter Krebs
cycle directly
Therefore it is oxidized and decarboyxlated to form Acetyl
CoA
End product: 2 NADH and 2 Acetyl CoA
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Krebs Cycle
Oxidation of acetyl CoA produces 2ATP, 6 NADH and 2 FADH2
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The Electron Transport Chain
NADH and FADH2 enter ETC, they become oxidized
(NAD, FAD) as other electron acceptors become
reduced
Energy released to produce ATP by chemiosmosis
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Total ATP production form cellular
respiration
Single NADH stores enough energy to make 3 ATP
Single FADH2 stores enough energy to make 2 ATP
How do we get 38 ATP molecules at the end?
Glycolysis:
2ATP ----------> 2
2NADH -> 2x3= 6
Preparation step:
2NADH -> 2x3= 6
Krebs cycle:
2ATP ----------> 2
6NADH -> 6x3=18
2FADH2 ->2x2= 4
Total 38 ATP
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Carbohydrate Catabolism comparison
Pathway Eukaryote Prokaryote
Glycolysis Cytoplasm Cytoplasm
Intermediate step Cytoplasm Cytoplasm
Krebs cycle Mitochondrial matrix Cytoplasm
ETC Mitochondrial inner membrane Plasma membrane
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Respiration Reaction that Produces
ATP
Two types:
Aerobic respiration: The final electron acceptor in the
electron transport chain is molecular oxygen (O2).
Yields about 38 ATP
38 ATP molecules are produced from
Glycolysis+Intermediate step+Kreb Cycle+ETC
Anaerobic respiration: The final electron acceptor in the
electron transport chain is inorganic substance.
Yields less energy than aerobic respiration because only
part of the Krebs cycles operates under anaerobic
conditions.
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Fermentation (anaerobic respiration)
After glucose has been broken down into pyruvic
acid, it can be further broken down into an organic
product
Does not require oxygen
Does not use the Krebs cycle or ETC
Uses an organic molecule as the final electron acceptor
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Fermentation
Alcohol fermentation: Produces ethanol + CO2
Glucose is converted into 2 pyruvic acids (glycolysis)
2ATP are generated
2 pyruvic acids converted to ethanol and CO2
Lactic acid fermentation: Produces lactic acid
Glucose is converted into 2 pyruvic acids (glycolysis)
2ATP are generated
2 pyruvic acids are reduced by 2 NADH to form 2 lactic
acids
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End-Products of Fermentation
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A Fermentation Test
Fermentation is carried out by a number of bacteria and yeast
Simple test is used to determine whether bacteria can perform fermentation
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Types of Fermentation
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Chemical Reaction: Lipid and Protein
catabolism
Glucose is the main energy-supplying carbohydrate
BUT, microbes can also use lipids and proteins as energy
source
Microbes produce Microbes produce
extracellular enzymes extracellular enzyme
called protease and called lipase that
peptidase that breaks fats into
break proteins into fatty acids and
amino acids glycerol
Amino acids are then Each component is
deaminated (amino then metabolized and
group is removed), enters Krebs cycle to
decarboxylated (carboxyl produce ATP
group is removed) or
desulfurated (sulfur group
is removed)
in order to enters
Krebs cycle to produce ATP
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Biochemical tests and bacterial
identification
Biochemical testing is frequently used to identify
bacteria and yeasts because different species
produce different enzymes
Such biochemical tests are designed to detect presence of
specific enzymes
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Biochemical Test
Lysine
decarboxylase
Figure 5.22
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Biochemical Test
Desulfurylation
Figure 5.24
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Biochemical Test
Urease
Urea NH3 + CO2
Clinical Focus Figure B
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Photosynthesis
Oxygenic:
6 CO2 + 12 H2O + Light energy
C6H12O6 + 6 H2O + 6 O2
Anoxygenic:
6 CO2 + 12 H2S + Light energy
C6H12O6 + 6 H2O + 12 S
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Photosynthesis
Light dependent reaction
Water splits into H+, e-, and oxygen
Sun energy excited e-, which then move through ETC
Conversion of ADP to ATP, and NAD+ to NADPH (energy rich carrier
of electorsn) occurs
Light independent reaction
ATP and NADPH are used to reduce carbon dioxide into sugars
(carbon fixation)
Cyanobacteria, algae and green plants perform photosynthesis
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Photosynthesis Compared
Table 5.6
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Metabolic diversity among organisms
Microbes can be classified metabolically according
to their nutritional requirement
Source of energy and carbon
Classification:
Phototrophs
Chemotrophs
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Chemotrophs
Chemo-autotrophs
Use chemical reaction for energy
Use carbon dioxide as source of carbon
Chemo-heterotrophs
Use chemical reaction for energy
Use organic compounds as a source of carbon
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Phototrophs
Photo-autotrophs:
Use light as source of energy
Use carbon dioxide as source of carbon
Photo-heterotrophs:
Use light as source of energy
Cannot convert carbon dioxide into sugar
Use alcohols, fatty acids as a source of carbon
Anoxygenic
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Metabolic Diversity among Organisms
Nutritional Type Energy Source Carbon Source Example
Photoautotroph Light CO2 Oxygenic:
Cyanobacteria plants
Anoxygenic: Green,
purple bacteria
Photoheterotroph Light Organic Green, purple nonsulfur
compounds bacteria
Chemoautotroph Chemical CO2 Iron-oxidizing bacteria
Chemoheterotroph Chemical Organic Fermentative bacteria
compounds Animals, protozoa,
fungi, bacteria.
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