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Introduction to
Metabolism

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 Microbial Metabolism and Its
Importance
• Metabolism is the total of all chemical
reactions in the cell and is divided into two
parts
– catabolism
– anabolism

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 Catabolism
• fueling reactions
• energy-conserving reactions
• provide ready source or reducing power (electrons)
• generate precursors for biosynthesis
Anabolism
• the synthesis of complex organic molecules from
simpler ones
• requires energy from fueling reactions

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 Microbial Cells Must Do Work
• Chemical work
– synthesis of complex molecules
• Transport work
– take up of nutrients, elimination of wastes, and
maintenance of ion balances
• Mechanical work
– cell motility and movement of structures within
cells

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 The Laws of Thermodynamics
• Thermodynamics
– a science that analyzes energy changes in a
collection of matter called a system (e.g., a
cell)
– all other matter in the universe is called the
surroundings

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First Law of Thermodynamics
• Energy can be neither created nor destroyed
• Total energy in universe remains constant
– However, energy may be redistributed either
within a system or between the system and its
surroundings
Second Law of Thermodynamics
• Entropy
– amount of disorder in a system
• Physical and chemical processes proceed in
such a way that the disorder of the universe
increases to the maximum possible 8
 Energy Units
• Calorie (cal)
– amount of heat energy needed to raise 1 gram
of water from 14.5 to 15.5°C
• Joules (J)
– units of work capable of being done by a unit
of energy
– 1 cal of heat is equivalent to 4.1840 J of work

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Adenosine 5’-triphosphate (ATP)
Energy Currency of the Cell

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 Sources of energy

electrons released
during oxidation
of chemical
energy sources
must be accepted
by an electron
acceptor

microorganisms
vary in terms of the
acceptors they use

Figure 9.1
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 Role of ATP in Metabolism
• Exergonic breakdown of high energy ATP is coupled
with endergonic reactions to make them more
favorable
• ATP +H2O ADP + Pi + H+
– Go´ = - 7.3 kcal/mol
• Guanosine 5’-triphosphate, cytosine 5’-triphosphate
and uridine 5’-triphosphate also supply some energy

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 Oxidation-Reduction (Redox)
Reactions
• Many metabolic processes involve oxidation-
reduction reactions (electron transfers)
• Electron carriers are often used to transfer
electrons from an electron donor to an electron
acceptor
• Transfer of electrons from a donor to an acceptor
– can result in energy release, which can be
conserved and used to form ATP
– the more electrons a molecule has, the more energy
rich it is
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Electron Carriers

• located in plasma membranes of

chemoorganotrophs in bacteria and archaeal
cells
• located in internal mitochondrial membranes
in eukaryotic cells
• examples of electron carriers include NAD,
NADP, and others

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Electron Carriers
• NAD
– nicotinamide
adenine
dinucleotide
• NADP
– nicotinamide
adenine
dinucleotide
phosphate

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 Biochemical Pathways
• Enzymes can be linked together to form pathways
• Pathways can be varied
– Linear
– Cyclic
– Branching
• Pathways often overlap/feed into each other
– Creates complex networks
– Dynamic pathways can be
used to monitor changes
in metabolite levels (flux) 36
 Enzymes
• carry out reactions at physiological
conditions so they proceed in a timely
manner

• enzymes speed up the rate at which

a reaction proceeds toward its final
equilibrium

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Structure and Classification of Enzymes - 1
• Protein catalysts
– high specificity for the reaction catalyzed and the
molecules acted on
– substance that increases the rate of a reaction
without being permanently altered
• Substrates = reacting molecules
• Products = substances formed by reaction
• Some enzymes are composed solely of one or
more polypeptides
• Some enzymes are composed of one or more
polypeptides and non-protein components
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 Structure and Classification of Enzymes - 2
• Apoenzyme
– protein component of an
enzyme
• Cofactor
– nonprotein component of an
enzyme
• prosthetic group – firmly
attached
• coenzyme – loosely attached,
can act as carriers/shuttles
• Holoenzyme = apoenzyme +
cofactor 41
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 The Mechanism of Enzyme
Reactions
A typical exergonic reaction

E + S  ES‡  P + E

Transition-state complex –
resembles both the substrates and the products

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 How Enzymes Lower Ea
• By increasing concentrations of substrates at active
site of enzyme
• By orienting substrates properly with respect to each
other in order to form the transition-state complex
• Induced fit model for enzyme-substrate interaction

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 Environmental Effects on
Enzyme Activity
• Enzyme activity is significantly impacted by
– substrate concentration
– pH
– temperature

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 Effect of [substrate]
• Rate increases as
[substrate]
increases
• No further
increase occurs
after all enzyme
molecules are
saturated with
substrate

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 Effect of pH and Temperature
• Each enzyme has specific pH and
temperature optima
• Denaturation
– loss of enzyme’s structure and activity when
temperature and pH rise too much above
optima

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 Enzyme Inhibition
• Competitive inhibitor
– directly competes with binding of substrate to active
site
• Noncompetitive inhibitor
– binds enzyme at site other than active site
– changes enzyme’s shape so that it becomes less
active

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Enzyme inhibition
• Noncompetitive inhibitor

- Bind to the enzyme at some location other

than the active site.
- Alter the enzyme’s shape, rendering it
inactive or less active
- Example: Heavy metals as Mercury

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 Allosteric Regulation
• Most regulatory enzymes
• Activity altered by small
molecule
– allosteric effector
• binds non-covalently at
regulatory site
• changes shape of enzyme
and alters activity of
catalytic site
• positive effector increases
enzyme activity
• negative effector inhibits
the enzyme
– Ex – Glutamine synthetase 59