MICROBIAL METABOLISM
Metabolism: Metabolism is the dynamic balance between difference types of reaction( catabolism+ anabolism) that provide the cell with energy or building materials & those to utilize them. It consists of two general activities: i) Energy Production
ii) Energy Utilization
Metabolic pathways are treated as a
sequence of enzymes functioning as a unit, with each enzyme using
as its substrate a product of the preceding enzyme-catalyzed
reaction. This picture of metabolic pathways is incomplete because
we will usually ignore the regulation of pathway operation
for the sake of space and simplicity. However, one should keep in
mind that both regulation of the activity of individual pathways
and coordination of the action of separate sequences are essential
to the existence of life. Cells become disorganized and die without
adequate control of metabolism, and regulation is just as important
to life as is the efficient use of energy. Thus the last part
of this chapter will be devoted to the regulation of metabolism as
a foundation for the subsequent discussion of pathways.
This chapter begins with a brief survey of the nature of energy
and the laws of thermodynamics. The participation of energy
in metabolism and the role of ATP as an energy currency is considered
next. An introduction to the nature and function of enzymes
follows. The chapter ends with an overview of metabolic
regulation, including an introduction to metabolic channeling and
the regulation of the activity of critical enzymes.
The Role of ATP in Metabolism; Many reactions in the cell are endergonic and will not proceed far
toward completion without outside assistance. One of ATP’s major
roles is to drive such endergonic reactions more to completion.
ATP is a high-energy molecule. That is, it breaks down or hydrolyzes
almost completely to the products ADP and Pi with a Go′ of 7.3 kcal/mole.
ATP + H2O ADP + Pi
In reference to ATP the term high-energy molecule does not mean
that there is a great deal of energy stored in a particular bond of
ATP. It simply indicates that the removal of the terminal phosphate
goes to completion with a large negative standard free energy
change, or the reaction is strongly exergonic. In other words,
ATP has a high phosphate group transfer potential; it readily
transfers its phosphate to water. The phosphate group transfer potential
is defined as the negative of Go′ for the hydrolytic removal
of phosphate. A molecule with a higher group transfer potential
will donate phosphate to one with a lower potential.
Thus ATP is ideally suited for its role as an energy currency.
It is formed in energy-trapping and -generating processes such as
photosynthesis, fermentation, and aerobic respiration. In the cell’s
economy, exergonic ATP breakdown is coupled with various endergonic
reactions to promote their completion (figure 8.6). In
other words ATP links energy-generating reactions, which liberate
free energy, with energy-using reactions, which require free energy
input to proceed toward completion. Facilitation of chemical
work is the focus of the preceding example, but the same principles
apply when ATP is coupled with endergonic processes involving transport work and mechanical work.
Structure and Classification of Enzymes:
Enzymes may be defined as protein catalysts that have great
specificity for the reaction catalyzed and the molecules acted on.
A catalyst is a substance that increases the rate of a chemical reaction
without being permanently altered itself. Thus enzymes
speed up cellular reactions. The reacting molecules are called substrates, and the substances formed are the products.
Many enzymes are indeed pure proteins. However, many
enzymes consist of a protein, the apoenzyme, and also a non protein
component, a cofactor, required for catalytic activity.
The complete enzyme consisting of the apoenzyme and its cofactor
is called the holoenzyme. If the cofactor is firmly attached
to the apoenzyme it is a prosthetic group. Often the cofactor
is loosely attached to the apoenzyme. It can even
dissociate from the enzyme protein after products have been
formed and carry one of these products to another enzyme (figure
8.13). Such a loosely bound cofactor is called a coenzyme.
For example, NAD is a coenzyme that carries electrons within
the cell. Many vitamins that humans require serve as coenzymes
or as their precursors. Niacin is incorporated into NAD and riboflavin
into FAD. Metal ions may also be bound to apoenzymes
and act as cofactors .
The Mechanism of Enzyme Reactions:
It is important to keep in mind that enzymes increase the rates of reactions
but do not alter their equilibrium constants. If a reaction is
endergonic, the presence of an enzyme will not shift its equilibrium so that more products can be formed. Enzymes simply speed up the
rate at which a reaction proceeds toward its final equilibrium.
How do enzymes catalyze reactions? Although a complete
answer would be long and complex, some understanding of the
mechanism can be gained by considering the course of a normal
exergonic chemical reaction.
A + B C + D
When molecules A and B approach each other to react, they form a
transition-state complex, which resembles both the substrates and
the products . The activation energy is required to
bring the reacting molecules together in the correct way to reach the
transition state. The transition-state complex can then decompose to
yield the products C and D. The difference in free energy level between
reactants and products is Go′. Thus the equilibrium in our
example will lie toward the products because Go′ is negative (i.e the products are at a lower energy level than the substrates).
Clearly A and B will not be converted to C and D if they are not supplied with an amount of energy equivalent
to the activation energy. Enzymes accelerate reactions by lowering
the activation energy; therefore more substrate molecules will
have sufficient energy to come together and form products. Even
though the equilibrium constant (or Go′) is unchanged, equilibrium
will be reached more rapidly in the presence of an enzyme because of this decrease in the activation energy.
Researchers have expended much effort in discovering how
enzymes lower the activation energy of reactions, and the process
is becoming clearer. Enzymes bring substrates together at a special
place on their surface called the active site or catalytic site to form
an enzyme-substrate complex. The enzyme can interact with a substrate in two general ways. It may be rigid and shaped to precisely fit the substrate so that
the correct substrate binds specifically and is positioned properly
for reaction. This mechanism is referred to as the lock-and-key
model. An enzyme also may change shape when it binds the substrate
so that the active site surrounds and precisely fits the substrate.
This has been called the induced fit model and is used by
hexokinase and many other enzymes (figure 8.16). The formation
of an enzyme-substrate complex can lower the activation energy in
many ways. For example, by bringing the substrates together at the
active site, the enzyme is, in effect, concentrating them and speeding
up the reaction. An enzyme does not simply concentrate its substrates,
however. It also binds them so that they are correctly oriented
with respect to each other in order to form a transition-state
complex. Such an orientation lowers the amount of energy that the
substrates require to reach the transition state. These and other catalytic
site activities speed up a reaction hundreds of thousands of
times, even though microorganisms grow between 20°C and approximately
113°C. These temperatures are not high enough to favor
most organic reactions in the absence of enzyme catalysis, yet
cells cannot survive at the high temperatures used by an organic
chemist in routine organic syntheses. Enzymes make life possible by accelerating specific reactions at low temperatures.
.jpg)
Fig: An example Of Enzyme-Substrate Complex.
Fig: How Do Enzymes Work.
ii) Energy Utilization
Metabolic pathways are treated as a
sequence of enzymes functioning as a unit, with each enzyme using
as its substrate a product of the preceding enzyme-catalyzed
reaction. This picture of metabolic pathways is incomplete because
we will usually ignore the regulation of pathway operation
for the sake of space and simplicity. However, one should keep in
mind that both regulation of the activity of individual pathways
and coordination of the action of separate sequences are essential
to the existence of life. Cells become disorganized and die without
adequate control of metabolism, and regulation is just as important
to life as is the efficient use of energy. Thus the last part
of this chapter will be devoted to the regulation of metabolism as
a foundation for the subsequent discussion of pathways.
This chapter begins with a brief survey of the nature of energy
and the laws of thermodynamics. The participation of energy
in metabolism and the role of ATP as an energy currency is considered
next. An introduction to the nature and function of enzymes
follows. The chapter ends with an overview of metabolic
regulation, including an introduction to metabolic channeling and
the regulation of the activity of critical enzymes.
The Role of ATP in Metabolism; Many reactions in the cell are endergonic and will not proceed far
toward completion without outside assistance. One of ATP’s major
roles is to drive such endergonic reactions more to completion.
ATP is a high-energy molecule. That is, it breaks down or hydrolyzes
almost completely to the products ADP and Pi with a Go′ of 7.3 kcal/mole.
ATP + H2O ADP + Pi
In reference to ATP the term high-energy molecule does not mean
that there is a great deal of energy stored in a particular bond of
ATP. It simply indicates that the removal of the terminal phosphate
goes to completion with a large negative standard free energy
change, or the reaction is strongly exergonic. In other words,
ATP has a high phosphate group transfer potential; it readily
transfers its phosphate to water. The phosphate group transfer potential
is defined as the negative of Go′ for the hydrolytic removal
of phosphate. A molecule with a higher group transfer potential
will donate phosphate to one with a lower potential.
Thus ATP is ideally suited for its role as an energy currency.
It is formed in energy-trapping and -generating processes such as
photosynthesis, fermentation, and aerobic respiration. In the cell’s
economy, exergonic ATP breakdown is coupled with various endergonic
reactions to promote their completion (figure 8.6). In
other words ATP links energy-generating reactions, which liberate
free energy, with energy-using reactions, which require free energy
input to proceed toward completion. Facilitation of chemical
work is the focus of the preceding example, but the same principles
apply when ATP is coupled with endergonic processes involving transport work and mechanical work.
Structure and Classification of Enzymes:
Enzymes may be defined as protein catalysts that have great
specificity for the reaction catalyzed and the molecules acted on.
A catalyst is a substance that increases the rate of a chemical reaction
without being permanently altered itself. Thus enzymes
speed up cellular reactions. The reacting molecules are called substrates, and the substances formed are the products.
Many enzymes are indeed pure proteins. However, many
enzymes consist of a protein, the apoenzyme, and also a non protein
component, a cofactor, required for catalytic activity.
The complete enzyme consisting of the apoenzyme and its cofactor
is called the holoenzyme. If the cofactor is firmly attached
to the apoenzyme it is a prosthetic group. Often the cofactor
is loosely attached to the apoenzyme. It can even
dissociate from the enzyme protein after products have been
formed and carry one of these products to another enzyme (figure
8.13). Such a loosely bound cofactor is called a coenzyme.
For example, NAD is a coenzyme that carries electrons within
the cell. Many vitamins that humans require serve as coenzymes
or as their precursors. Niacin is incorporated into NAD and riboflavin
into FAD. Metal ions may also be bound to apoenzymes
and act as cofactors .
The Mechanism of Enzyme Reactions:
It is important to keep in mind that enzymes increase the rates of reactions
but do not alter their equilibrium constants. If a reaction is
endergonic, the presence of an enzyme will not shift its equilibrium so that more products can be formed. Enzymes simply speed up the
rate at which a reaction proceeds toward its final equilibrium.
How do enzymes catalyze reactions? Although a complete
answer would be long and complex, some understanding of the
mechanism can be gained by considering the course of a normal
exergonic chemical reaction.
A + B C + D
When molecules A and B approach each other to react, they form a
transition-state complex, which resembles both the substrates and
the products . The activation energy is required to
bring the reacting molecules together in the correct way to reach the
transition state. The transition-state complex can then decompose to
yield the products C and D. The difference in free energy level between
reactants and products is Go′. Thus the equilibrium in our
example will lie toward the products because Go′ is negative (i.e the products are at a lower energy level than the substrates).
Clearly A and B will not be converted to C and D if they are not supplied with an amount of energy equivalent
to the activation energy. Enzymes accelerate reactions by lowering
the activation energy; therefore more substrate molecules will
have sufficient energy to come together and form products. Even
though the equilibrium constant (or Go′) is unchanged, equilibrium
will be reached more rapidly in the presence of an enzyme because of this decrease in the activation energy.
Researchers have expended much effort in discovering how
enzymes lower the activation energy of reactions, and the process
is becoming clearer. Enzymes bring substrates together at a special
place on their surface called the active site or catalytic site to form
an enzyme-substrate complex. The enzyme can interact with a substrate in two general ways. It may be rigid and shaped to precisely fit the substrate so that
the correct substrate binds specifically and is positioned properly
for reaction. This mechanism is referred to as the lock-and-key
model. An enzyme also may change shape when it binds the substrate
so that the active site surrounds and precisely fits the substrate.
This has been called the induced fit model and is used by
hexokinase and many other enzymes (figure 8.16). The formation
of an enzyme-substrate complex can lower the activation energy in
many ways. For example, by bringing the substrates together at the
active site, the enzyme is, in effect, concentrating them and speeding
up the reaction. An enzyme does not simply concentrate its substrates,
however. It also binds them so that they are correctly oriented
with respect to each other in order to form a transition-state
complex. Such an orientation lowers the amount of energy that the
substrates require to reach the transition state. These and other catalytic
site activities speed up a reaction hundreds of thousands of
times, even though microorganisms grow between 20°C and approximately
113°C. These temperatures are not high enough to favor
most organic reactions in the absence of enzyme catalysis, yet
cells cannot survive at the high temperatures used by an organic
chemist in routine organic syntheses. Enzymes make life possible by accelerating specific reactions at low temperatures.
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