Microbiology- a clinical approach by Anthony
Strelkauskas et al. 2010
Chapter 3: : Essentials of metabolism
http://www.wired.com/news/images/full/5thplace_f.j
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It is important to have a basic understanding of metabolism
because it governs the survival and growth of
microorganisms.
The growth of microorganisms can have a direct effect on
infectious disease.
Good metabolic function makes pathogens more successful
at causing disease.
Understanding microbial growth will allow finding effective
ways to inhibit microbial growth.
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Metabolism is:
◦ A series of chemical processes that go on in living organisms.
◦ Used to obtain energy.
◦ Linked to growth
Carbon and energy are required for growth.
The body has two processes to obtain carbon:
◦ Autotrophy : carbon from inorganic substances
◦ Heterotrophy: carbon from other organic molecules
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Energy can be gained in two major ways
◦ Phototrophy : from sun light (phototroph)
◦ Chemotrophy: through chemical reactions involving the break
down of organic molecules
 Nearly all infectious organisms are chemoheterotrophs.
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Metabolism is broken
down into two parts:
◦ Catabolism – molecules are
broken down through
metabolic processes to
release the energy stored in
their chemical bonds.
◦ Anabolism – metabolic
processes in which the
energy derived from
catabolism is used to build
large organic molecules from
smaller ones.
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Both processes involve
electron transfer and
oxidation and reduction
reactions.
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An oxidation reaction is a chemical reaction in
which an atom, ion or molecule loses one or more
electrons.
A reduction reaction is a chemical reaction in
which an atom, ion or molecule gains one or more
electrons.
Oxidation and reduction reactions always occur
together.
◦ The combination of an oxidation reaction and a reduction
reaction are jointly referred to as redox reactions.
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When a substance is oxidized, it loses electrons.
When a substance is reduced, it gains electrons
Note: loss of hydrogen = oxidation; gain of hydrogen = reduction
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In metabolism, respiration occurs at the
cellular level and is not the same as breathing
(respiration at the macroscopic level).
Cellular respiration describes catabolic
processes and is divided into:
◦ Aerobic respiration – metabolism that uses oxygen
◦ Anaerobic respiration– metabolism that does not use
oxygen
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Technically: respiration always involves an
electron transport chain
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Metabolic reactions occur in series of chemical
reactions called pathways.
◦ The following is an example of a pathway. A is the
initial substrate and E is the final product of the
pathway, with B, C, and D being intermediates.
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A
B
C
D
E
Each step in the pathway is mediated or
facilitated by a specific enzyme.
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Enzymes are proteins that act as catalysts for
metabolic reactions, making the reaction go
faster.
Each enzyme is specific for a reaction.
Enzymes are found in all living organisms and
most cells contain hundreds of types which are
constantly being manufactured and replaced.
Enzymes work by lowering the energy of
activation.
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Reduce activation energy for a chemical reaction
Reaction occurs faster
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Enzymes have specific three
dimensional shapes: if the shape
changes, activity is inhibited.
The shape of the molecule provides
a distinctive site called the active
site. It is here that:
◦ The substrate fits into the enzyme and
the reaction occurs.
◦ The enzyme and substrate interact to
form the enzyme-substrate complex.
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The electrical charges found at the
active site are also important.
Enzymes are generally highly
specific.
◦ A given enzyme catalyzes only one type
of reaction.
◦ Most enzymes react with only one
particular substrate.
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Some enzymes work on more than one
substrate but in these cases the enzymes
always work in a particular type of reaction.
◦ Proteases: degrade proteins
◦ Lipases: cleave lipids
◦ Nucleases: cleave nucleic acids
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Many enzymes can catalyze a
reaction only if other substances
are present at the active site.
◦ These enzymes are referred to as
apoenzymes.
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Co-factors are helper substances
that are inorganic ions such as
magnesium, zinc, or manganese.
Coenzymes are helper substances
that are non-protein organic
molecules.
Co-factors or coenzymes bind to
the active site and change the
shape of the active site so the
substrate now fits.
They can also be used as carrier
molecules.
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Two coenzyme carrier molecules frequently
encountered in biological reactions are:
◦ NAD+ = nicotinamide adenine dinucleotide NADH (reduced
form)
◦ FAD = flavin adenine dinucleotide  FADH2 (reduced form)
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Both are vitamins
The electrons carry the energy
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Targeted enzyme inhibition takes place in
three ways:
◦ Competitive inhibition
◦ Allosteric inhibition
◦ Feedback inhibition
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The inhibitor molecule is similar in structure to the substrate
and competes with the substrate to bind to the active site.
When the inhibitor has bound to the active site, the substrate
cannot bind.
The binding of the competitor is reversible and dependent upon
the relative numbers of inhibitor molecules and substrate
molecules present.
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This activity also involves inhibitor molecules but they do not block
the active site.
Inhibitor molecules bind to a part of the enzyme away from the
active site: the allosteric site.
This binding changes the shape of the active site in such a way
that it can no longer fit properly with the substrate.
The binding of some allosteric inhibitors is reversible*.
*Note: lead and mercury irreversibly inhibit enzymes.
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Feedback inhibition is used in many of the metabolic pathways
found in the cell.
The final product in a pathway accumulates and begins to bind to
and inactivate the enzyme that catalyzes the first reaction of
the pathway.
It is reversible and, when the level of end product decreases,
the inhibition stops and the pathway begins to function again.
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pH
◦ Influences charges in the enzyme molecule
◦ Very low or very high pH denatures the enzyme
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Temperature
◦ Slight increases increase activity, decreases inhibit
the activity
◦ Extreme high temperatures break hydrogen bonding
and denature enzymes
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Concentration of the substrate, enzyme,
product
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Enzymes are proteins that work in metabolism by
lowering the energy of activation.
These proteins have a specific three dimensional
shape and complex with the substrate they act
upon at a place that is called active site.
Enzymes are highly specific and in some cases
require cofactors and coenzymes to function.
Enzyme function can be regulated by competitive
inhibition, allosteric, or feed back inhibition.
Temperature, pH, and the concentration of
substrate all affect the function of enzymes.
Catabolism is the process
in which
During a reduction
reaction a substance
A. Molecules are broken
down
B. Molecules are
transformed into more
essential components
C. Molecules are built up
D. Energy id decreased
A. Gains an electron and
becomes more positively
charged
B. Loses an electron and
becomes more
negatively charged
C. Gains an electron and
becomes more
negatively charged
D. Loses an electron and
becomes positively
charged
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Catabolic processes in metabolism cause the
breakdown of large organic molecules into
smaller ones.
These are called fueling reactions because they
cause a release of energy.
There are three important pathways by which
most organisms release energy from nutrient
molecules:
◦ Glycolysis
◦ Krebs cycle
◦ Electron transport chain
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The catabolic pathway is used by most organisms.
The best example of this pathway is glucose breakdown.
The process itself is a series of chemical reactions and
involves substrate phosphorylation.
The reactions occur in the cytoplasm and do not require
oxygen.
◦ 1 molecule glucose + 2 ATP  2 molecules pyruvate and 4 ATP
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Four ATP molecules are produced in glycolysis
◦ The first steps of the pathway consume two ATP molecules.
◦ The net gain is 2ATP molecules/ molecule glucose.
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ATP is a high energy carrier
◦ ADP + Pi + energy
ATP
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Glycolysis can lead to
further pathways.
◦ Krebs cycle and cellular
respiration with electron
transport chain(aerobic)
◦ Fermentation (anaerobic)
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The Krebs cycle is also known as the tricarboxylic
acid (TCA) cycle or the citric acid cycle.
It is an aerobic catabolic pathway seen in aerobic
cellular respiration.
Continues from glycolysis
Pyruvate is further metabolized in this process.
◦ modified with coenzyme A to produce Acetyl-CoA
Involves electron and hydrogen shuffling, release
of carbon as CO2
NADH and FADH2 are produced and sent to the
electron transport chain
Through the electron transport chain ATP is
generated.
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The electron transport chain is a sequence of
molecules.
◦ In eukaryotes, they are found in the inner
mitochondrial membrane.
◦ In prokaryotes, they are organized in the plasma
membrane
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Electrons are transferred to a final electron
acceptor.
◦ In aerobic respiration, the final acceptor is oxygen.
◦ In anaerobic respiration, the final acceptor is an
inorganic oxygen-containing molecule.
Accumulation of H+ across the membrane
+
-
In prokaryotes the electron transport chain is located on the cell membrane.
Note: Cytochrome oxidase C is detected
in diagnostic assays for Pseudomonas
aeruginosa.
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As electrons are transferred along the electron transport
chain, protons (H+) are pumped out of the cell (or across
inner mitochondrial membrane) .
This causes the proton concentration outside the cell to
be higher than inside the cell, causing a concentration
gradient and a charge gradient to form.
Specialized membrane proteins allow protons to re-enter
the cell.
◦ Energy is released as protons re-enter the cell.
◦ This energy is used to bind phosphate to ADP, making the highenergy molecule ATP.
 36 molecules of ATP/1 molecule glucose
◦ The difference in proton concentration in this process is called
the proton motive force.
◦ Important for active transport and flagella movement
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Fermentation is the enzymatic breakdown of
carbohydrates that have been produced by
glycolysis.
The final electron acceptor is an organic
molecule.
This process does not require oxygen and
typically occurs in the absence of oxygen.
Fermentation does not increase the yield of
ATP from what it is after glycolysis (2
molecules of ATP/ 1 glucose molecule).
Different microorganisms use different
fermentation pathways with varying end
products.
No gas, also used in muscle cells
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Anabolic reactions are classified as biosynthetic
reactions because they are used to synthesize all the
biological molecules needed by the cells of living
organisms.
Biosynthetic reactions form the network of pathways
that produce the components required by the cell for
growth and survival.
These reactions are fueled by the energy stored in
high-energy bonds in ATP.
Production of carbohydrates, amino acids, lipids, nucleic
acids.
These pathways are inhibited by some antibiotics:
sulfonamide, trimethoprim
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Metabolism is the chemical process that
provides or stores energy for the organism.
Metabolism can be broken down into two
parts: catabolism (breaking down molecules)
and anabolism (building up molecules).
Oxidation and reduction reactions involve the
transfer of electrons.
Nearly all chemical processes of the cell
consist of a series of chemical reactions
known as a pathway.
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Enzymes are proteins that speed up chemical
reactions by lowering the energy of
activation.
Enzymes work on the basis of their threedimensional shape. They are specific and in
some cases require cofactors or coenzymes
to function.
Temperature, pH, and concentration of
substrate all affect enzyme function.
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When oxygen is involved, catabolism occurs
through glycolysis, the Krebs cycle, and
electron transport.
Aerobic metabolism requires oxygen and
yields 38 ATP molecules from the breakdown
of one molecule of glucose.
Breakdown of one molecule of glucose without
oxygen via fermentation (anaerobic
metabolism) yields only 2 molecules of ATP.
During competitive
inhibition of enzyme
function
The final electron
acceptor in aerobic
respiration is
A. The product competes
with the substrate for
the action site
B. ATP competes with the
substrate for the
active site
C. A molecule can compete
with the substrate for
the active site
D. Any molecule can
compete with the
substrate for the
active site
A. Water
B. Oxygen
C. Hydrogen
D. Both A and B