Download Energy, ATP, and Enzymes Energy - the ability to do work, that is, to

Energy, ATP, and Enzymes
Energy - the ability to do work, that is, to move matter against opposing forces such as
gravity and friction
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kinetic energy - the energy of motion.
potential energy - stored energy, the capacity to do work
Thermodynamics - the study of energy transformation
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The First Law of Thermodynamics - Energy can be transferred and transformed,
but it can neither be created nor destroyed
o The total energy of the universe is constant
o Mass is a form of energy (this is only important when considering atomic
reactions, so we won't dwell on it here...)
The Second Law of Thermodynamics - Every energy transfer or transformation
increases the entropy of the universe
o There is a trend toward randomness
o Energy must be spent to retain order - this spending of energy usually
releases heat, which increases the entropy elsewhere
Free Energy - the portion of a system's energy the can perform work
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It is called "free" energy because this is the energy which can perform work, not
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because there is no energy cost to the system
There still ain't no free lunch
Exergonic Reaction - a process with a net release of free energy
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Sometimes called spontaneous, but that doesn't mean that it will occur rapidly
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Burning paper is exergonic, but paper just doesn't ignite when it is exposed to air it requires an initial input of energy to start the reaction
Endergonic Reaction - a process which absorbs free energy from the surroundings
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Most synthesis reactions are endergonic
Energy Coupling - the use of an exergonic process to drive and endergonic process
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The free energy released from the exergonic process is absorbed by the endergonic
process
Types of Cellular Work
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Mechanical - beating of cilia, muscle contractions, etc.
Transport - pumping of molecules and ions across a plasma membrane against their
concentration gradient, etc.
Chemical - pushing endergonic reactions that would not occur spontaneously
Useful and much more detailed links
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The First Law of Thermodynamics and Entropy
The Second Law of Thermodynamics
Gibbs Free Energy
ATP - Power To Drive Cellular Work
ATP - Adenosine triphosphate - a close relative to Adenine, a nucleotide found in DNA.
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Contains three phosphate groups connected to each other in sequence
The bonds an be broken by hydrolysis
o When the terminal phosphate bond is broken, a molecule of inorganic
phosphate (Pi) is formed
o This forms adenosine diphosphate, ADP + (Pi)
o This generates free energy, which can be used by the cell to do work
Usually, ATP functions by transferring its phosphate group to another molecule,
creating a phosphorylated intermediate.
o This phosphorylated intermediate is usually less stable (more reactive) than
the original molecule, which drives the reaction
Obviously, for the cell to function, ATP must rapidly be regenerated.
o One muscle cell can consume and regenerate over 10,000,000 ATP's a
second
o If ATP couldn't be regenerated, humans would have to consume nearly
their body weight in ATP each day
Enzymes and Chemical Reactions
Catalyst - a chemical agent that changes the state of a reaction without being consumed in
the reaction
Substrate - reactants
Intermediates - compounds formed between initial reactants & products
Products - products
Cofactors- helpers for enzymes (carry e-)
Energy Carriers - sources of quick energy (ATP)
Enzymes are protein catalysts
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Actually, some RNA molecules possess enzymatic functions, but well over 99% of
all enzymes are proteins
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they do not do the impossible - they only speed up reactions
they are not consumed in a reaction
they work for both the forward and the reverse reaction
they are highly selective
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How Energy Relates to Reactions
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Initial state transition state final state must overcome an energy barrier
Any reaction requires some energy to overcome the activation energy barrier
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An enzyme lowers this energy barrier, thus speeding up the reaction
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An enzyme has an active site which holds the reactants in a particular way to
facilitate the bonding/bond breaking
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Note: it lowers the activation energy for the forward and the reverse (but not in a
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proportionate way)
Lock and Key Hypothesis - there is only one active site which precisely fits the
reactants (more or less)
Enzymes are Substrate Specific
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The enzyme binds to the substrate or substrate when there are two or more
reactants
While bound, the catalytic action of the enzyme converts the substrate(s) to
product(s)
An enzyme can distinguish its substrate from similar molecules and even isomers
of the same molecule
Only a restricted region of the enzyme molecule actually binds to the substrate this is called the active site
o This match is not perfect - as the enzyme and substrate come together, a
small conformation change occurs so that the active site fits even more
snugly around the substrate
o This is know as an induced fit. Think of a handshake - as your hands come
together, your fingers move to more tightly grasp the other hand.
When the enzyme and substrate come together, they form an enzyme-stubstate
complex
o Held together by hydrogen and/or ionic bonds
The Catalytic Cycle of an Enzyme
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The enzyme and the substrate form the enzyme-substrate complex
R-groups of the amino acids comprising the active site catalyze the reaction
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They often pull or contort the substrate, temporarily weakening bonds or
some configuration
o In reactions with two or more substrates, they can form a template to guide
the substrates into the most energy-efficient configuration
o The active site may also provide a microenvironment more conducible to
the reaction, such as providing a pocket of low pH in an otherwise neutral
cell
The rate of enzyme action is proportional to the concentration of the substrate
(more substrate, the faster the reaction rate)
o However, saturation can occur
A Cell's Physical and Chemical Environment Affect Enzyme Activity
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An enzyme's function is dependent upon its shape, so environmental conditions
which affect shape will affect the catalytic properties of the enzyme
Temperature - a measure of molecular motion
o For most chemical reactions, as temperature increases, reaction rate will
increase
 More molecules will possess enough energy to cross the activation
energy barrier
o However, as temperature increases, the molecular motion of the enzyme
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also increases
 The enzyme's active site may become unstable and function poorly
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 Once a certain temperature is reached, bonds maintaining the 2 , 3 ,
and 4o structure of the protein collapse and the protein loses
function
 When a protein falls apart like this, it is called a denatured protein
There is usually a temperature at which the enzyme exhibits peak
performance. This is known as the temperature optimum for this enzyme.
The temperature optimum for each enzyme is usually related to the
environment in which it will operate
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A DNA polymerase for a human would have a lower temperature
optimum than that of a hot springs bacteria
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pH - a measure of [H+] - acidic and basic conditions
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Like temperature, most enzymes have a pH at which they perform at peak
efficiency - the pH optimum
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Also like temperature, the pH optimum is related to the conditions in which
it will be found
At extreme pH's, the enzyme may denature
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Cofactors - a non-protein enzyme helper
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aid in enzyme catalytic function
may be bound tightly to the active site or may be loosely bound
may be inorganic, such as a zinc or copper ion, or it may be an organic
molecule
 if organic, it is commonly called a coenzyme
most vitamins are coenzymes or provide raw materials for the construction
of coenzymes, so take your vitamins!
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Enzyme Inhibitors - chemicals which interfere with enzyme function
o Can be reversible (if hydrogen or ionic bonded) or more-or-less permanent
(if covalently bonded to enzyme)
o Some molecules can fit into the active site and may compete for admission
into the active site. These are known as competitive inhibitors.
o Other molecules may bind to the enzyme and cause an conformation
change which affect the ability of the enzyme to bind to the
substrate. These are known as noncompetitive inhibitors
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In cells inhibition usually reversible; that is the inhibitor isn't permanently
bound to the enzyme.
Irreversible inhibition of enzymes also occurs, due to the presence of a
poison.
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Penicillin cause the death of bacteria due to irreversible inhibition
of an enzyme needed to form the bacterial cell wall.
In humans, hydrogen cyanide irreversibly bind to a very important
enzyme (cytochrome oxidase) present in all cells, and this accounts
for its lethal effect on the body.
Enzyme Enhancers - chemicals which increase enzyme function
o Like noncompetitive inhibitors, enzyme enhancers can bind to a non-active
site and cause a conformation change which enhances enzyme function
The Control of Metabolism In many cases, the molecules that naturally regulate enzyme
activity behave like reversible noncompetitive inhibitors
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Alter enzyme's shape and function by binding to an allosteric site
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Allosteric site - receptor site on some part of the enzyme remote from the active
site
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can speed up or slow down enzyme function (enhancers and
noncompetitive inhibitors)
Example - enzymes of catabolic pathways have allosteric sites which can
bind ATP and AMP
 ATP is an inhibitor, AMP is an enhancer
 When ATP prodction is greater than use, ATP will accumulate and
then slow down or shut off the pathway
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When ATP production lags behind use, AMP will accumulate and
enhance the pathway, creating more ATP
Feedback Inhibition - when the product of a pathway acts as an inhibitor of the
pathway
o Prevents too much buildup of product
o The reaction series converting theronine to isoleucine is a classic example
of allosteric regulation.
o Five enzymes acting in sequence catalyze the pathway.
o The final product of the sequence, isoleucine, acts as an inhibitor of the
first enzyme of the pathway, threonine deaminase.
 As the pathway produces isoleucine, any molecules made in excess
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of cell requirements combine reversibly with threonine deaminase
at a location outside the active site.
The combination converts threonine deaminase to the T state and
inhibits its ability to combine with threonine.
The pathway is then turned off.
If the concentration of isoleucine later falls as a result of its use in
cell synthesis, isoleucine releases from the threonine deaminase
enzymes, converting them to the R state in which they have high
affinity of the substrate, conversion of threonine to isoleucine takes
place.