Microbial Metabolism

Catabolic and Anabolic

Reactions
 The energy-producing reactions within cells
generally involve the breakdown of
complex organic compounds to simpler
compounds. These reactions release energy
and are called catabolic reactions.
 Anabolic reactions are those that consume
energy while synthesizing compounds.
 ATP produced by catabolic reactions
provides the energy for anabolic reactions.
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Anabolic and catabolic reactions are
Metabolism – sum of all the
chemical reactions within a living
organism
 2. Anabolism ( Anabolic )
• the building of complex organic molecules from simpler ones
• requires ENERGY
 1. Catabolism ( Catabolic )
• breakdown of complex organic molecules into simpler compounds
releases ENERGY
 An anabolic reaction
Energy

Catabolic and Anabolic

Reactions
ATP ADP + Pi

Energy

A catabolic reaction

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 Enzymes lower the amount of
activation energy needed for a reaction.
Enzymes Lower Activation
Energy Supplied
Energy Activation energy
without enzyme

Activation energy
with enzyme
Energy Released

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Anabolism
Anabolism provides the substances needed for cellular
growth and repair
Dehydration synthesis
• type of anabolic process
• used to make polysaccharides, triglycerides, and
proteins
• produces water
Anabolism
Catabolism
Catabolism breaks down larger molecules into smaller ones

Hydrolysis
• a catabolic process
• used to decompose carbohydrates, lipids, and proteins
• water is used
• reverse of dehydration synthesis
Catabolism
ENZYMES
Biological catalysts; specific; not used up in
that reaction
A metabolic pathway is a sequence of
enzymatically catalyzed chemical reactions
in a cell.
Metabolic pathways are determined by
enzymes, which are encoded by genes.
 Enzymes

 Catalysts are substances that speed up chemical

reactions. Organic catalysts (contain carbon) are
called enzymes.
 Enzymes are specific for one particular reaction or
group of related reactions.
 Many reactions cannot occur without the correct
enzyme present.
 They are often named by adding “ASE" to the name
of the substrate. Example: Dehydrogenases are
enzymes that remove hydrogen.

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Enzyme Components
2 Parts
1. Apoenzyme - protein portion
2. Coenzyme (cofactor) - non-protein

Holoenzyme - whole enzyme

Enzyme Specificity can be explained
by the Lock and Key Theory

E + S -----> ES ------> E + P
Naming of Enzymes - most are
named by adding “ase” to the substrate
 Sucrose Sucrase
 Lipids Lipase
 DNA DNase
 Proteins Protease
 removes a Hydrogen Dehydrogenase
 removes a phosphate phosphotase
Naming of Enzymes
 Grouped based on type of reaction they
catalyze
 1. Oxidoreductases oxidation & reduction
 2. Hydrolases hydrolysis
 3. Ligases synthesis
Enzymes - catalysts that speed up and
direct chemical reactions
 A. Enzymes are substrate specific
• Lipases Lipids
• Sucrases Sucrose
• Ureases Urea
• Proteases Proteins
• DNases DNA
Co-Enzymes and Co-Factors
Some enzymes require another organic molecule or substance
to be present before they can function. These organic
molecules or substances are called Co-enzymes or Co-
factors. Co-enzymes are organic molecules (usually
vitamins) and co-factors are inorganic substance
(minerals). This is one of the reasons it is so important to
eat a well balanced diet. For example, Vitamin K is
necessary for the enzyme responsible for blood clot
formation. A lack of vitamin K leads to easy bruising and
prolonged bleeding when injuries occur. Calcium is a co-
factor which is required by several enzymes for their
activation.
Coenzymes
 Many are derived from vitamins

 1. Niacin
• NAD (Nicotinamide adenine dinucleotide)
 2. Riboflavin
• FAD (Flavin adenine dinucleotide)
 3. Pantothenic Acid
• CoEnzyme A
 Lecture 2

 factors

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 Rate of Reaction

 Reactions with enzymes are up to 10 billion times

faster than those without enzymes.
 Enzymes typically react with between 1 and 10,000
molecules per second. Fast enzymes catalyze up to
500,000 molecules per second.
 Substrate concentration, enzyme concentration,
Temperature, and pH affect the rate of enzyme
reactions.

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 Environmental Factors Which Affect
Enzyme Activity
Since enzymes are protein any environmental
change that can affect their structure affects their
activity.
All protein shape determine their function.
Their structure is due primarily to hydrogen
bonding at the various levels.
If any thing disrupts or interferes with the
hydrogen bonding the protein’s level of
structure begins to breakdown and the protein
“unravels” or “unfolds” and becomes non-
functional.

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  Denaturing is the destruction of a protein’s function
due to the breakdown or loss of its structure.
Denaturing is an irreversible process (ex. egg
albumin before and after cooking) Any
environmental factor that has an effect of hydrogen
bonding can denature proteins. Temperature and
pH both effect hydrogen bonding and can denature
proteins. Therefore they would have a definite effect
on enzyme activity.

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Factors that Influence Enzymatic
Activity

Denaturation of an Active Protein

Environmental Factors Which Affect
Enzyme Activity: Temperature
All enzymes have an
optimum temperature at
which they work best. If
you observe the enzyme’s
activity below the specific
temperature it will
steadily increase until it
reaches the optimum.
After the optimum Depending on the species, the
temperature is reached range of optimum activity is very
the enzymes activity broad. Above is a comparison of
drops dramatically due to human enzyme activity with that of
denaturing. bacteria found in hot springs and
oceanic vents.

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Environmental Factors Which Affect
Enzyme Activity: pH
All enzymes have an In the human body’s digestive tract
optimum pH at which there are variations in pH from area
to area. The stomach’s juices’ pH
they work best. If the is around 2 (acidic), the enzyme pepsin
found in the gastric juices has
pH falls below or optimum activity at a pH of 2. The small
intestine’s juice’s pH is around 8 (basic).
rises above the The enzyme trypsin found in the small intestine’s
juices has optimum activity at a pH of 8.
optimum value,
enzymatic activity
decreases
as a result of
denaturing.

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Environmental Factors Which Affect
Enzyme Activity: Substrate Concentration
The concentration of substrate also has an affect on the rate of enzyme
activity. If the concentration of substrate is increased while the
concentration of enzyme is constant, the level of enzyme activity
will increase until a point of saturation is reached. At this point
there are no enzymes available to react with excess substrate and the
rate of the reaction stabilizes. No matter if you continue to add
substrate, the reaction rate will not increase!

Point of Saturation, all active

sites are filled with substrate.
Rate of Reaction

Increasing Substrate Concentration

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 Substrate Concentration
 At lower concentrations, the active sites on most of the enzyme
molecules are not filled because there is not much substrate. Higher
concentrations cause more collisions between the molecules. With
more molecules and collisions, enzymes are more likely to encounter
molecules of reactant.
 The maximum velocity of a reaction is reached when the active sites
are almost continuously filled. Increased substrate concentration after
this point will not increase the rate. Reaction rate therefore increases
as substrate concentration is increased but it levels off.

Enzyme
Rate of Reaction

Active Site is
Saturated

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 Enzyme Concentration
 If there is insufficient enzyme present, the reaction will
not proceed as fast as it otherwise would because there is
not enough enzyme for all of the reactant molecules.
 As the amount of enzyme is increased, the rate of reaction
increases. If there are more enzyme molecules than are
needed, adding additional enzyme will not increase the
rate. Reaction rate therefore increases as enzyme
concentration increases but then it levels off.

Even when adding

Rate of Reaction

more enzymes, there

isn’t any more
available substrate to
create product at a
Enzyme Concentration
faster rate
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 Effect of Temperature on Enzyme
Activity
Rate of Reaction

30 40 50
Temperature

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Increasing the temperature causes
Effect of Temperature on Enzyme
more collisions between substrate
and enzyme molecules. The rate of
Activity
reaction therefore increases as
temperature increases.
Rate of Reaction

30 40 50
Temperature

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 Effect of Temperature on Enzyme
Activity Enzymes denature when
the temperature gets too
high. The rate of reaction
Rate of Reaction

decreases as the enzyme

becomes nonfunctional.

30 40 50
Temperature
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 Temperature
 Higher temperature causes more collisions between the atoms,
ions, molecules, etc. It therefore increases the rate of a reaction
– “Turnover Rate”. More collisions increase the likelihood that
substrate will collide with the active site of the enzyme.
 Above a certain temperature, activity begins to decline because
the enzyme begins to denature (unfold).
 The rate of chemical reactions therefore increases with
temperature but then decreases.
Rate of Reaction

30 40 50
Temperature
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 Denaturation
 If the hydrogen bonds within an enzyme are broken, the
enzyme may unfold or take on a different shape. The enzyme
is denatured.
 A denatured enzyme will not function properly because the
shape of the active site has changed.
 If the denaturation is not severe, the enzyme may regain its
original shape and become functional.
 The following will cause denaturation:
– Heat
– Changes in pH
– Heavy-metal ions (lead, arsenic, mercury)
– Alcohol
– UV radiation
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 Effect of pH on Enzyme Activity
Each enzyme has its own optimum pH.
Rate of Reaction
Pepsin Trypsin

2 3 4 5 6 7 8 9

pH

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 pH

 Each enzyme has an optimal pH. Pepsin, an enzyme found in the

stomach, functions best at a low pH. Trypsin, found in the intestine,
functions best at a neutral pH.
 A change in pH can alter the ionization of the R groups of the amino
acids. When the charges on the amino acids change, hydrogen bonding
within the protein molecule change and the molecule changes shape.
The new shape may not be effective.
 The diagram shows that pepsin functions best in an acid environment.
This makes sense because pepsin is an enzyme that is normally found in
the stomach where the pH is low due to the presence of hydrochloric
acid. Trypsin is found in the duodenum (small intestine), and therefore,
its optimum pH is in the neutral range to match the pH of the
Rate of Reaction

duodenum. Pepsin Trypsin

2 3 4 5 6 7 8 9

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 upto 35

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Inhibitors can effect enzymatic activity
1. Competitive Inhibitors
2. Noncompetitive Inhibitors
 Inhibitors
Competitive vs Noncompetitive –
inhibitors allosteric
inhibitors

Fig 5.7
Competitive Inhibitors -compete for
the active site
 1. Penicillin
• competes for the active site on the enzyme
involved in the synthesis of the pentaglycine
crossbridge
 2. Sulfanilamide (Sulfa Drugs)
• competes for the active site on the enzyme that
converts PABA into Folic Acid
• Folic Acid - required for the synthesis of DNA and
RNA

Selective Toxicity
Energy Production
 1. Oxidation
• refers to the loss of Hydrogens and or electrons
 2. Reduction
• the gain of Hydrogens and or electrons
Carbohydrate Catabolism
 Microorganisms oxidize carbohydrates as
their primary source of energy
 Glucose - most common energy source
 Energy obtained from Glucose by:
• Respiration
• Fermentation
Cellular Respiration
Occurs in three series of reactions
1. Glycolysis
2. Citric acid cycle
3. Electron transport chain
Produces
• carbon dioxide
• water
• ATP (chemical energy)
• heat
Includes
• anaerobic reactions (without O2) - produce little ATP
• aerobic reactions (requires O2) - produce most ATP
ATP Molecules
• each ATP molecule has three parts:
• an adenine molecule
• a ribose molecule
• three phosphate molecules in a chain
• third phosphate attached by high-energy bond
• when the bond is broken, energy is transferred
• when the bond is broken, ATP becomes ADP
• ADP becomes ATP through phosphorylation
• phosphorylation requires energy released from cellular respiration
Aerobic Cellular Respiration
 Electrons released by oxidation are passed
down an Electron Transport System with
oxygen being the Final Electron Acceptor

 General Equation:

 Glucose + oxygen----> Carbon dioxide + water


 ATP
Chemical Equation
 C6H12O6 + 6 O2 -------> 6 CO2 + 6 H2O

 38 ADP + 38 P 38 ATP
Aerobic Cellular Respiration
 4 subpathways

 1. Glycolysis
 2. Transition Reaction
 3. Kreb’s Cycle
 4. Electron Transport System
 Steps of Respiration
•
1. glycolysis

Coenzyme Junction
2. Citric acid cycle

3. ETC

4. Chemiosmosis
What Carries the Electrons?

 NAD+
(nicotinadenine
dinucleotide) acts as
the energy carrier
 NAD+ is a coenzyme
 It’s Reduced to
NADH when it
picks up two
electrons and one
hydrogen ion

Copyright Cmassengale
1. Glycolysis (splitting of sugar)

 Oxidation of Glucose into 2 molecules of

Pyruvic acid
 Embden-Meyerhof Pathway

 End Products of Glycolysis:

• 2 Pyruvic acid
• 2 NADH2 Nicotinamide adenine dinucleotide -
• 2 ATP Adenosine triphosphate
 Glycolysis (sugar-breaking)

• series of ten reactions

• breaks down glucose into 2 pyruvic acids
• occurs in cytosol
• anaerobic phase of cellular respiration
• yields two ATP molecules per glucose

Summarized by three main events

1. phosphorylation
2. splitting
3. production of NADH and ATP
 Glycolysis
Event 1 - Phosphorylation
• two phosphates
added to glucose
• requires ATP

Event 2 – Splitting (cleavage)

• 6-carbon glucose split
into two 3-carbon
molecules
 Glycolysis
Event 3 – Production of NADH and
ATP
• hydrogen atoms are released
• hydrogen atoms bind to NAD+ to
produce NADH
• NADH delivers hydrogen atoms
to electron transport chain if
oxygen is available
• ADP is phosphorylated to
become ATP
• two molecules of pyruvic acid
are produced
 Anaerobic Reactions (Absence of
Oxygen)
If oxygen is not available -
• electron transport chain
cannot accept NADH
• pyruvic acid is converted
to lactic acid
• glycolysis is inhibited
• ATP production declines
Aerobic Reactions (Presence of
Oxygen)
If oxygen is available –
• pyruvic acid is used
to produce acetyl CoA
• citric acid cycle
begins
• electron transport
chain functions
• carbon dioxide and
water are formed
• 36 molecules of ATP
produced per glucose
molecule
2. Transition Reaction
 Connects Glycolysis to Krebs Cycle

 End Products:
• 2 Acetyl CoEnzyme A
• 2 CO2
• 2 NADH2
3. Krebs Cycle (Citric Acid Cycle)

 Series of chemical reactions that begin and

end with citric acid
Products:
• 2 ATP
• 6 NADH2 nicotinamide adenosine
dinucleotide
• 2 FADH2 flavin adenine dinucleotide
• 4 CO2
 Citric Acid Cycle
• begins when acetyl CoA
combines with oxaloacetic
acid to produce citric acid
• citric acid is changed into
oxaloacetic acid through a
series of reactions
• cycle repeats as long as
pyruvic acid and oxygen are
available
• for each citric acid
molecule:
• one ATP is produced
• eight hydrogen atoms
are transferred to NAD+
and FAD
• two CO2 produced
4. Electron Transport System
 Occurs within the cell membrane of Bacteria

 Chemiosomotic Model of Mitchell

• 34 ATP
Total ATP production for the
complete oxidation of 1 molecule
of glucose in Aerobic Respiration
 ATP
 Glycolysis 2
 Transition Reaction 0
 Krebs Cycle 2
 E.T.S. 34

 Total 38 ATP
Anaerobic Respiration
 Electrons released by oxidation are passed
down an E.T.S., but oxygen is not the final
electron acceptor

 Nitrate (NO3-) ----> Nitrite (NO2-)

 Sulfate (SO24-) ----> Hydrogen Sulfide (H2S)
 Carbonate (CO24-) -----> Methane (CH4)
Fermentation
 Anaerobic process that does not use the
E.T.S. Usually involves the incomplete
oxidation of a carbohydrate which then
becomes the final electron acceptor.

 Glycolysis - plus an additional step

Fermentation may result in numerous
end products

1. Type of organism
2. Original substrate
3. Enzymes that are present and active
1. Lactic Acid Fermenation
 Only 2 ATP
 End Product - Lactic Acid
 Food Spoilage
 Food Production
• Yogurt - Milk
• Pickles - Cucumbers
• Sauerkraut - Cabbage
 2 Genera:
• Streptococcus
• Lactobacillus
2. Alcohol Fermentation
 Only 2 ATP
 End products:
• alcohol
• CO2
 Alcoholic Beverages
 Bread dough to rise

 Saccharomyces cerevisiae (Yeast)

3. Mixed - Acid Fermentation
 Only 2 ATP
 End products - “FALSE”

 Escherichia coli and other enterics

Propionic Acid Fermentation
 Only 2 ATP
 End Products:
• Propionic acid
• CO2

 Propionibacterium sp.
Fermentation End Products
End
Lipid Catabolism
Protein Catabolism
Photosynthesis - conversion of light
energy from the sun into chemical energy
 Chemical energy is used to reduce CO2 to
sugar (CH2O)
 Carbon Fixation - recycling of carbon in the
environment (Life as we known is dependant on this)

 Photosynthesis
• Green Plants
• Algae
• Cyanobacteria
Chemical Equation

 6 CO2 + 6 H2O + sunlight -----> C6H12O6 + 6 O2

 2 Parts:
• 1. Light Reaction
• 2. Dark Reaction
Light Reaction
 Non-Cyclic Photophosphorylation
• O2
• ATP
• NADPH2

 Light Reaction (simplified)

2. Dark Reaction