Exam 2 Lecture 4 Flashcards
All living systems
require an ongoing
supply of
energy
energy can be thought of as
the capacity to
cause specific chemical
or physical changes
Cells Need Energy to Drive 6 Different Kinds of
Work which are
- Synthetic work
- Mechanical work
- Concentration work
- Electrical work
- Generation of heat
- Generation of lig
synthetic work
changes in chemical Bonds
formation of Bonds
biosynthesis
The work of biosynthesis
results in the formation of new
chemical bonds and the
synthesis of new molecules
Biosynthesis is required for
growth and maintenance of
cells and cellular structures
Energy that cells require for
biosynthetic work is used to
make energy-rich organic
molecules and incorporate them
into macromolecules
Mechanical Work
Changes in the Location or
Orientation of a Cell or a Subcellular Structure
Mechanical work involves a
physical change in the position
or orientation of a cell or some
part of it
The movement of a cell relative
to its environment often requires
one or more appendages, such
as cilia or flagella
These require energy to move
the cell
Examples of mechanical work
A large number of muscle cells work together in
muscle contraction
Chromosomes move along spindle fibers during
mitosis
Cytoplasmic streaming and movement of
organelles and vesicles along microtubules occur
Ribosomes move along a strand of mRNA
Concentration Work
Concentration work accumulates substances within a cell or
organelle or removes toxic by-products of cellular activity
Examples include the concentration of specific molecules and
enzymes in organelles, digestive enzymes in secretory
vesicles, and the import of sugars and amino acids into cells
Electrical Work
Moving Ions Across a
Membrane Against an Electrochemical Gradient
During electrical work, ions are transported across a
membrane, resulting in differences in both concentration and
electrical potential (or membrane potential)
Every cellular membrane has a characteristic electrical potential
In the case of mitochondria or chloroplasts, the difference is
essential in production of AT
Electrical work in Neurotransmission
Electrical work is important in transmission of nerve
impulses
In this case, a membrane potential is generated by
pumping Na + ions into and K + ions out of the cell
The electric eel (Electrophorus electricus) uses
energy to generate a membrane potential of 150
mV per cell and several hundred volts for the entire
organism
heat
an increase in temperature that is useful to warm-blooded Animals
Living organisms do not use heat as a form of energy as a steam engine does
However, producing heat is a major use of energy in all
homeotherms
Homeotherms: animals that
regulate their body temperature
independent of the environment
Homeotherms:
animals that
regulate their body temperature
independent of the environment
Bioluminescence
the production of Light
Bioluminescence, the
production of light, is important
in a number of organisms, such
as fireflies, certain jellyfish, and
luminous toadstools
Bioluminescence is generated
by the reaction of ATP with
luminescent compounds
Green fluorescent protein (GFP;
from the jellyfish Aequorea
victoria) and its variants are
very useful to cell biologists
Nearly all life on Earth is directly or indirectly
sustained from
sunlight
phototroph
capture light energy from the sun and
transform it into chemical energy, stored as ATP
chemotrophs
obtain energy by oxidizing chemical
bonds in molecules (organic or inorganic)
Autotrophs
an organism that is able to form nutritional organic substances from simple inorganic substances such as carbon dioxide.
Heterotrophs
an organism deriving its nutritional requirements from complex organic substances.
Photoautotrophs
use solar energy to produce all the
carbon compounds they need from CO2
(photosynthesis)
Photoautotrophs include plants, algae,
cyanobacteria, and photosynthetic bacteria
photoheterotrophs
Some bacteria are photoheterotrophs, which harvest
solar energy for some cellular activities but rely on
intake of organic molecules as a source of carbon
chemoautotrophs
A few bacteria are chemoautotrophs, which oxidize
inorganic compounds such as H 2S, H2, or inorganic
ions for energy and use CO 2 as a carbon source
Chemoheterotrophs
ingest and use chemical
compounds (carbohydrates, fats, and proteins) to
provide both energy and carbon for cellular needs
All animals, protozoa, fungi, and many bacteria
are chemoheterotrophs
Energy Flows
Through the Biosphere
Continuously
Oxidation
is the removal of
electrons from a substance,
usually hydrogen atoms (H +
plus one electron)
Oxidation reactions release
energy
reduction
Reduction, the addition of
electrons to a substance
through addition of hydrogen
atoms (and a loss of oxygen
atoms), requires an input of
energy
Phototrophs
the PRODUCERS, use sunlight energy to produce more reduced
cellular compounds through photosynthesis
These compounds are converted to all the materials needed for surviva
Chemotrophs
the CONSUMERS, take in reduced compounds and oxidize
them to release their stored energy
efficiency of Biological Processes
No process in biological systems is
100% efficient; some energy is inevitably released (lost) as heat,
usually dissipated into the
environment
Some of this heat is used
In warm-blooded animals to
maintain body temperature
In plants to attract pollinators or
melt overlying snow
The Flow of Energy Through the Biosphere Is
Accompanied by
a flow of matter
Energy enters the biosphere
as _______________ and leaves as _________ both without _________
Energy enters the biosphere
as photons and leaves as
heat, both without matter
while passing
through the biosphere,
energy exists primarily in the
form of
chemical bond
energies
matter cycles between
phototrophs and
chemotrophs
cyclic flow of matter includes
Carbon, oxygen, nitrogen,
and water all cycle
continuously
They enter the
chemotrophic sphere as
reduced, energy-rich
compounds and leave it as
oxidized, energy-poor
forms
Energy flow is governed by the principles of
Thermodynamics
Thermodynamics
concerns the laws governing
energy transactions that accompany most
physical and chemical processes
Bioenergetics
(applied thermodynamics) applies
principles of thermodynamics to the biological world
Energy can be defined as
the ability to cause
change
The energy under consideration in any particular case is called the
system
the rest of the universe is called
the surrounding
The boundary between the system and
surroundings may be
real or hypothetical
A closed system is
sealed
from its environment and can
neither take in nor release
energy
An open system
can have
energy added to it or
removed from it
Organisms are what type of system
open
systems, capable of uptake
and release of energy
A system is in a specific
state if each of its variable properties is held at a
specified value.
In this situation, the total energy of the system has a unique value.
If the state changes, the total energy change is determined only by the
initial and final states of the system
what are three of the most important variables in biological reactions
Three of the most important variables—temperature, pressure, and
volume—are essentially CONSTANT during biological reactions.
why are temp, pressure, and volume essentially constant during bio rxn
This is because reactions occur in dilute solutions within cells at
approximately the same temperature, pressure, and volume during the
entire reaction.
Oil Rig
Oxidation is losing
reduction is gaining
Exchange of energy between a system and its
surroundings occurs as
Heat or work
is heat a useful energy source for cells?
Heat is not a very useful energy source for cells
because many biological systems are isothermal
(at a fixed temperature)
work is
the use of energy to drive a process other than heat flow
The units for quantifying the energy changes during
chemical reactions are
calories (cal) (1 kilocalorie (kcal)
= 1000 calories).
Physicists prefer the
joule (J); 1 J = 0.239 cal
calorie
the amount of energy required to raise 1 gram of
water by 1 degree centigrade at 1 atmosphere of pressure
first law of thermodynamics
the law of
conservation of energy.
It states that in every physical or chemical change, the
total amount of energy in the universe remains constant.
Energy may be converted from one form to another but
cannot be created or destroyed
In biological systems, the energy that leaves a system
must
equal that which entered it plus the amount
remaining (stored) in the system
Total energy stored within a system is called
internal
energy, or E.
ΔE is the
change in internal energy that occurs during
some process
Calculating ΔE
ΔE is the difference in internal energy of a system before a
process (E1 ) and after it (E2 )
2 1E E E
For a chemical reaction, this can be written as
products reactantsE E E
( see slide)
Enthalpy
change in enthalpy (H),
or heat content, which is related to E, dependent on
pressure (P) and volume (V)
H = E + P V
Enthalpy in biological processes
Enthalpy change of a particular reaction can be
expressed as:
Because pressure and volume change little or not at all in
biological reactions,
ΔH may be either positive or negative
see slide for equation
Exothermic rxn
ΔH is negative
In exothermic reactions, energy is released (e.g., the
burning of gasoline in a car)
If ΔH is positive, a reaction is
endothermic
In endothermic rxn energy is
Absorbed
( melting of an ice cube)
The Second Law of Thermodynamics
States That Reactions Have
directionality
A thermodynamically spontaneous reaction is
one that is a
favorable reaction.
Thermodynamic spontaneity
is a measure of whether or
not a reaction or process can occur
Reactions have directionality, that is
they can proceed
spontaneously only in one direction (e.g., the burning of a
piece of paper).
The second law of thermodynamics is the law of
thermodynamic spontaneity
thermodynamic spontaneity
first law
heat
enthalpy
second law
order
second law explained
in every physical or chemical change, the
universe tends toward greater disorder or randomness
(entropy).
* It allows us to predict what direction a reaction will
proceed under specific conditions, how much energy will
be released, and how changes in conditions will affect it
Entropy and Free Energy Are Two
Alternative Means of Assessing
Thermodynamic Spontaneity
Whether or not a reaction can proceed can be measured
by changes in
entropy or free energy
Entropy (S) is a measure of
randomness or disorder
All processes or reactions that occur spontane (??)
when a system becomes less ordered entropy …
Increases
(e.g., when ice melts or a solvent evaporates)
when a system becomes more ordered
Entropy decreases
ex. when ice forms water
Entropy Change as a Measure of
Thermodynamic Spontaneity
change in S universe is positive for
or every spontaneous process or
reaction (increases the entropy of the universe)
But in the specific system involved, entropy may change
or stay the same.
Expressing the second law in terms of ΔS is not very
useful in predicting the spontaneity of biological
processes.
A measure of spontaneity for a system alone is called
free energy (G)
change in free energy equation
Gproducts - Greactants
ΔG is related to
enthalpy and entropy of a reaction
ΔG = ( in terms of enthalpy and entropy )
ΔG = ΔH − T ΔS (T = temperature of the system in
degrees Kelvin, or C +273)
Free energy is a readily measurable indicator of
spontaneity
Every spontaneous reaction is characterized by a______ in free energy of the system
decrease
So, if ΔG < 0, the reaction is
thermodynamically
spontaneous.
thermodynamically
spontaneous rxn
ΔG < 0
Exergonic rxn are
Exergonic reactions are energy-yielding and occur spontaneously
(ΔG < 0)
endergonic rxn are
Endergonic reactions are energy-requiring and do not occur
spontaneously under the conditions specified (ΔG > 0)
is the oxidation of glucose exergonic or endergonic
the oxidation of glucose (a highly
exergonic process):
6 12 6 2 2 2C H O + 6O 6CO + 6H O + energy
ΔG = −686 kcal/mol
the reverse rxn of glucose oxidation is exergonic or endergonic ?
The reverse reaction is endergonic ( input of energy)
ΔG = +686 kcal/mole
6CO + 6H O + energy C H O + 6O2
The term spontaneous tells us that
a reaction can take
place, not that it will
Whether an exergonic reaction will proceed depends on
on a
favorable (negative) ΔG but also on the availability of a
mechanism.
Usually an input of activation energy is required as well
equilibrium constant
Keq
Keq
is the ratio of product
concentrations to reactant concentration at equilibrium.
At equilibrium, there is no net change in the
concentrations of reactants or products
keq equation
keq = [B]/[A]
what can the equilibrium constant tell you about a mixture
If you know the equilibrium constant for a reaction, you
can tell whether a particular mixture of products and
reactants is in equilibrium.
If the mixture is not at equilibrium, you can tell in what
direction it must proceed to reach equilibrium
what is the concentration ratio
the ratio of products to reactants
what does it mean when the concentration is less than Keq ?
A concentration ratio (products to reactants) less than Keq
means that the reaction will proceed to the right to
generate more product
what does it mean when the concentration is MORE than Keq ?
A concentration ratio greater than Keq means that the
reaction will proceed to the left ( toward reactants)
ΔG is
free energy change
in cal/mol
R is
( when calculating ΔG)
R is the gas constant
(1.987 cal/mol × K
T is
( when calculating ΔG)
is the temperature in
kelvins
Keq is equilibrium constant
at standard temperature of
298 K (25C)
In stands for
natural log
Know how to calculate ΔG
see slides on page 16
what are the limitations on ΔG
it tells us nothing about rate or mechanism of
the reaction
ΔG is a thermodynamic parameter that tells us
whether a
reaction is thermodynamically possible as written
and It also tells us how much free energy would be liberated if
the reaction took place
what are the conditions called for ΔG is made
Biochemists have agreed on conditions to define the
standard state.
25C (298 K), 1 atmosphere
pressure, and all products
reactants at a
concentration of 1.0 M
standard pH = 7.0
the concentration of H + and OH− ions is 10^−7
is water included when calculations of free energy change
The concentration of water is not included in calculations
of free energy change
why are Keq and ΔG written with a′ ?
to indicate standard
conditions: K′eq and ΔG′
in any thermodynamic parameter, the standard change
refers to
The conversion of one mole of a specified reactant to
product or
The formation of one mole of a specified product from
the reactants
The free energy change calculated under these conditions
is called the standard free energy change (ΔGº′
what is the relationship between ΔGº′ and ln K′eq???
Linear relationship
This means that ΔGº′ can be calculated directly from the
equilibrium constant, provided Keq was determined under
the same standard conditions
If K′eq is greater than 1.0, then ΔGº′
will be negative, and the
reaction can proceed to the right (toward the products) under
standard conditions
If K′eq is less than 1.0, then ΔGº′
will be positive, and the
reaction will tend toward the left (toward the reactants) under
standard conditions.
what is important to know about ΔGº′
ΔGº′ is an arbitrary standard, referring to impossible
conditions for most biological systems
what is ΔG′ most useful?
what information does it provide
For real life situations, ΔG′ is the most useful measure of
thermodynamic spontaneity
ΔG′ provides a measure of how far from equilibrium a
reaction is, under the conditions in a cell
what does ΔG′ = 0 mean
the reaction is in
equilibrium; however, reactions in living cells are rarely in
equilibrium
red blood cell, actual concentrations are
jumping beans
Jumping beans are seeds of certain shrubs with moth
larvae inside.
When the larva moves, the seed moves too
see slides with example
ΔG =
( equation)
= ΔH – T(ΔS)
ΔG and the Capacity to Do Work
The change in Gibbs energy is equal to the maximum amount of work that a system can perform on the surroundings while undergoing a spontaneous change (at constant temperature and pressure
in bean example The greater the difference in free energy between the two
chambers, the more work the system can do
work can be performed continuously
work can be performed continuously as long
as equilibrium is never reached
how do cells lower activation energy barrier
using catalysts called enzymes
does ΔG discuss rate
only how much energy is released
Rate depends on
the height of the barrier between the two chambers
Life is possible because cells maintain
in steady state,
with most reactions far from equilibrium
A cell at equilibrium would be
DEAD
At equilibrium, the forward and backward rates are
the same, and there is no net flow of matter
Life Requires Steady-State Reactions
That
Move Toward Equilibrium
Without Ever Getting There
why is steady state possible in cells?
Steady state is possible only because a cell is an open
system.
It receives energy from the environment.
Reactants and products of cellular chemistry are kept far
from equilibrium
Enzyme catalysis
nearly all cellular reactions
involve protein catalysts called enzymes
The presence of the appropriate enzyme
makes the difference between whether a
reaction can take place and whether it will take
place
Activation Energy and the Metastable State
Many thermodynamically feasible reactions in a cell
that could occur do not proceed at any appreciable
rate
For example, the hydrolysis of ATP has
ΔG = –7.3 kcal/mol
ATP + H2O ADP + Pi
However, ATP dissolved in water remains stable
for several days
The presence of the appropriate enzyme
makes the difference between
whether a
reaction can take place and whether it will take
place
what prevents molecules from reacting
lack of sufficient energy
what is activation Energy?
the minimum amount of energy required before
collisions between the reactants will give rise to
products
what is a transition state?
Reactants need to reach
an intermediate
chemical stage called
the transition state
The transition state has
a higher free energy
than that of the initial
reactants
The rate of a reaction is
always proportional to
the
fraction of molecules with
an energy equal to or
greater than EA
The only molecules that
are able to react at a
given time are
those with
enough energy to exceed
the activation energy
barrier, EA
The Metastable State Is a Result of
the Activation Barrier
what does metastable
state
Reactants that are thermodynamically unstable, but
lack sufficient EA
Life depends on high activation energies that
prevent
most reactions in the absence of catalysts
prevents so many reactions from taking place and over working the cell?
most reactions in the absence of catalysts
activation energy barrier
what are the two ways Ea can be overcome
The EA barrier must be overcome in order for
needed reactions to occur
This can be achieved by either increasing the
energy content of molecules or by lowering the EA
requirement
how can you increase the energy content of a system
The input of heat can
increase the kinetic
energy of the average
molecule, ensuring that
more molecules will be
able to take part in a
reaction
also think of mixing sugar and water
is increasing heat helpful in cells? why or why not?
no because cells are Isothermal
Isothermal
constant in temperature
How can Activation Energy be lowered
If reactants can be bound on a surface and brought close
together, their interaction will be favored and the required EA
will be reduced
A catalyst enhances the rate of a reaction by providing such a
surface and effectively lowering EA
Catalysts themselves proceed through the reaction unaltered
what are the three basic properties of catalysts
hey increase reaction rates by lowering the
EA required
2. They form transient, reversible complexes with
substrate molecules
3. They change the rate at which equilibrium is
achieved, not the position of the equilibrium
organic catalysts are
Enzymes
most enzymes are
proteins
However, recently it has been discovered that
some RNA molecules also have catalytic activity
These are called ribozymes
Ribozymes
RNA molecules with catalytic activity
what is an active site
Every enzyme contains a characteristic cluster of amino acids
that forms the active site
- directly involved in the action
This results from the three-dimensional folding of the protein
and is where substrates bind and catalysis takes place
The active site is usually a groove or pocket that
accommodates the intended substrate(s) with high affinity
which amino acids are involved in active sites
These are cysteine, histidine, serine, aspartate,
glutamate, and lysine
These can participate in binding the substrate and
several serve as donors or acceptors of protons
Cofactors
Some enzymes contain nonprotein cofactors
needed for catalytic activity, often because they
function as electron acceptors
These are called prosthetic groups and are
usually metal ions or small organic molecules
called coenzymes
Coenzymes are derivatives of vitamins
what a re prosthetic Groups
Prosthetic groups are located at the active site and
are indispensable for enzyme activity
( normally metal ions?)
Each molecule of the enzyme catalase has a multimeric
structure called a porphyrin ring to which a necessary
iron atom is bound
The requirement for certain prosthetic groups on
some enzymes explains our requirements for trace
amounts of vitamins and minerals
Substrate specificity
Because of the shape and
chemistry of the active
site, enzymes have a very
high
inorganic catalysts are
very nonspecific
Group specificity o
Some enzymes will accept a number of closely
related substrates
Others accept any of an entire group of substrates
sharing a common feature
This group specificity is most often seen in
enzymes involved in degradation of polymers
6 major classes of Enzymes
Oxidoreductases
Transferases
Hydrolases
Lysases
Isomerases
Ligases
see table for more
knwo how they function and the differences between them
how are enzymes characterized
by their sensitivity to
temperature
This is not a concern in homeotherms—birds and
mammals—which maintain a constant body
temperature
However, many organisms function at their
environmental temperature, which can vary widely
At higher temperatures, the rate of enzyme activity
inecreases with temperature as a result of increased
kinetic activity of enzyme and substrate molecules
However, beyond a certain point, further increases
in temperature result in denaturation of the enzyme
molecule and loss of enzyme activity
the reaction rate of human enzymes is maximum at what temp and what is this called?
37 C
(the
optimal temperature), the normal body temperature
Most enzymes of homeotherms are inactivated by temperatures
above 50–55º
Enzymes of cryophilic
(cold-loving) organisms such
as Listeria bacteria can function at low
temperatures, even under refrigeration
General pH range for enzymes
Most enzymes are active within a pH range of about 3–4 units
pH dependence is usually due to
the presence of charged
amino acids at the active site or on the substrate
pH changes affect
the charge of such residues and can disrupt
ionic and hydrogen bonds
what else are enzymes sensitive to
Enzymes are sensitive to factors such as molecules
and ions that act as inhibitors or activators
Most enzymes are also sensitive to ionic strength of
the environment
This affects hydrogen bonding and ionic
interactions needed to maintain tertiary
conformation
why are enzymes highly specific
Because of the precise chemical fit between the
active site of the enzyme and its substrates,
enzymes are highly specific
substrate binding
Once in the active site, substrate molecules are
bound to the enzyme surface in the right orientation
to facilitate the reaction
Substrate binding usually involves hydrogen bonds,
ionic bonds, or both
Substrate binding is readily reversible
The Induced-Fit Model
In the past, the enzyme was seen as rigid, with the
substrate fitting into the active site like a key in a lock
(lock-and-key model)
A more accurate view is the induced-fit model, in
which substrate binding at the active site induces a
conformational change in the shape of the enzyme
conformational change
The induced conformational change brings needed amino acid
side chains into the active site, even those that are not nearby
Once in the active site, the substrate is held in place by specific
noncovalent interactions
These position the substrate optimally for catalysis and
distinguish the real substrate from similar molecules
The role of the active site is
to recognize and bind
the appropriate substrate and also to activate it by
providing the right environment for catalysis
This is called substrate activation, which
proceeds via several possible mechanisms
Three Common Mechanisms of Substrate
Activation
Bond distortion, which makes the bond more
susceptible to catalytic attack
Proton transfer, which increases reactivity of
substrate
Electron transfer, which results in temporary
covalent bonds between enzyme and substrate
The Catalytic Even
the sequence of events
The random collision of a substrate molecule with the
active site results in its binding there
2. Substrate binding induces a conformational change that
tightens the fit, facilitating the conversion of substrate into
products
3. The products are then released from the active site
4. The enzyme molecule returns to the original conformation,
and the active site is now available for another molecule of
substrate
Ribozymes
Are Catalytic RNA Molecules
Catalytic RNA molecules were discovered in the
1980s
These are called ribozymes
Many scientists believe that the earliest enzymes
were catalytic, self-replicating RNA molecules
Tetrahymena RNA
ITetrahymena RNAIn 1981 Thomas Cech and colleagues discovered
an RNA molecule that was self-splicing
This is an example of autocatalysis
Ribonuclease P
is an enzyme that cleaves transfer
RNA precursors to yield functional RNA molecules
Ribonuclease P has an RNA and a protein
component
In the early 1980s, Sidney Altman showed that only
the RNA component was capable of performing the
cleavage
Ribosomes
Ribosomes synthesize proteins. They have protein and RN
A components.
The active site of the large subunit of a ribosome is the
site of peptidyl transferase activity, the catalysis of the
peptide bond.
The ribosomal RN A (rRNA) is the catalyst.
The rRNA is a ribozyme
The rRNA is a
ribozyme
Enzyme kinetics
describes the quantitative
aspects of enzyme catalysis and the rate of
substrate conversion into products
Reaction rates are influenced by factors such as
the concentrations of substrates, products, and
inhibitors
initial Reaction Rates
Initial reaction rates are measured over a brief time,
during which the substrate concentration has not
yet decreased enough to affect the rate of reaction
Monkey Peanut
see slides
[S]
substrate concentration - concentration rep by brackets
how does increase the substrate concentration increase in the cell
faster the time to find the substrate decreases but with diminishing returns
the only way to increase rate is to increase enzyme concentration
Initial reaction velocity (v0)
the
rate of change in product
concentration per unit time depends on the substrate
concentration ([S]).
at low [S], doubling [S] will affect Vo by …
double v0 ; but as [S] increases,
each additional increase in [S]
results in a smaller increase in v0
When [S] becomes very large,
the value of v0 reaches a
Maximum
As [S] tends toward infinity, v approaches an upper limiting
value
maximum velocity (Vmax)
The value of Vmax can be increased by
adding more
enzyme
saturation
The inability of increasingly higher substrate
concentrations to increase the reaction velocity beyond a
finite upper value is called saturation
who postulated a theory of enzyme action and what is it
Michaelis and Menten
Substrate (S) is catalyzed by enzyme (E) to produce
product (P)
The Michaelis–Menten Equation
see slides/ anki
what is a rate constant
A rate constant is the proportionality constant relating the
rate of a reaction to the concentrations of reactants
What Is the Meaning of Vmax and Km?
We can understand the relationship between v0 and [S],
and the meaning of Vmax and Km (the Michaelis constant)
by considering three cases regarding [S]:
1. Very low substrate concentration
2. Very high substrate concentration
3. [S] = Km
reference slides
At very low [S], the initial velocity of the reaction is roughly
proportional to the substrate concentration, [S].
At very high [S], the initial velocity of the reaction is
ndependent of variation in [S], and Vmax is the velocity at
saturating substrate concentrations.
Vmax
Vmax
Vmax is the upper limit of v0
as the substrate
concentration [S]
approaches infinity.
It is the velocity at
saturating
concentrations
The Linear Relationship Between
Vmax and Enzyme Concentration
Vmax is an upper limit
determined by:
The time required for
the actual catalytic
reaction
How many enzyme
molecules are present
The only way to increase
Vmax is to increase enzyme
The lower the Km value for a given enzyme and substrate,
the lower the [S] range in which the enzyme is effective
Vmax is important as a measure of the
potential maximum
rate of the reaction.
By knowing Vmax , Km, and the in vivo substrate
concentration, we can estimate
the likely rate of the
reaction under cellular conditions
turnover number
see slide
The Double-Reciprocal Plot Is a Useful
Means of Visualizing Kinetic Data
see slide
what can influence enzymes
Enzymes are influenced (mostly inhibited) by products,
alternative substrates, substrate analogues, drugs, toxins,
and allosteric effectors
what is a vital control of mechanisms in cells
inhibition
inhibitor important to enzymologists and why are they important
substrate analogues and transition state
analogues
transition state analogue
- analogues - mimic
These are compounds that resemble real
substrates or transition states closely enough to
occupy the active state but not closely enough to
complete the reaction
transition state analogue
transition state analogs have some structural characteristics that are unique to the transition state
substrate analogue
substrate analogs mimic the structural features of the substrates
Substrate analogues are important tools in fighting
infectious diseases
Irreversible inhibitors, + examples
bind the enzyme
covalently, cause permanent loss of catalytic
activity and are generally toxic to cells
Examples: heavy metal ions, nerve gas poisons,
some insecticides
Reversible inhibitors and what are the two forms
bind enzymes noncovalently
and can dissociate from the enzyme
The fraction of enzyme available for use in a cell
depends on the concentration of the inhibitor and
how easily the enzyme and inhibitor can dissociate
E + I EI
The two forms of reversible inhibitors are
competitive inhibitors and noncompetitive
inhibitors
Competitive Inhibition
what is it ? function?
Competitive inhibitors bind the active site of an enzyme and so compete with
substrate for the active site
Enzyme activity is inhibited directly because active sites are bound to
inhibitors, preventing the substrate from binding
( similar structure to the substrate )
Noncompetitive Inhibition
what is the inhibitor and its funtion
Noncompetitive inhibitors bind the enzyme molecule outside the active site
They inhibit activity indirectly by causing a conformation change in the
enzyme that
Inhibits substrate binding at the active site, or
Reduces catalytic activity at the active site
HIV treatment
target specific enzymes within a pathway by knowing the structure of the enzyme such that you can make a substrate analogue to prevent the rxn from taking place
see image for details
difference between reversible and irreversible inhibitor binding to enzyme
irreversible bind to the enzyme COVALENTLY
reversible bind to the enzyme NONcovalently
process of noncompetitive inhibition
get info from slide
why is enzyme regulation important and how does it occur
Enzyme rates must be continuously adjusted to
keep them tuned to the needs of the cell
Regulation that depends on interactions of
substrates and products with an enzyme is called
substrate-level regulation
Increases in substrate levels result in increased
reaction rates, whereas increased product levels
lead to lower rates
how can cells turn enzymes on and off as needed by
two mechanisms?
allosteric regulation and covalent
modification
Usually enzymes regulated this way catalyze the
first step of a multistep sequence
By regulating the first step of a process, cells are
able to regulate the entire process
Allosteric regulation
is the single most important
control mechanism whereby the rates of enzymatic
reactions are adjusted to meet the cell’s needs
- see pathway on slide
need a diff enzyme for each step to produce the next substrate needed for the following step
Feedback Inhibition
It is not in the best interests of a
cell for enzymatic reactions to
proceed at the maximum rate - too much energy and too much waste
In feedback (or end-product)
inhibition, the final product of
an enzyme pathway negatively
regulates an earlier step in the
pathway
see pathway on slide
what are the two conformations of allosteric enzymes needed for regulation
one
in which it has affinity for the substrate(s) and one
in which it does not
Allosteric regulation makes use of this property
by regulating the conformation of the enzyme
An allosteric effector regulates enzyme activity by
binding and stabilizing one of the conformations
allosteric regulation
makes use of this property
by regulating the conformation of the enzyme
allosteric effector
regulates enzyme activity by
binding and stabilizing one of the conformations
binds a site called an
allosteric (or regulatory) site, distinct from the
active site
an allosteric effector may be an
activator or
inhibitor, depending on its effect on the enzyme
Inhibitors shift the equilibrium between the two
enzyme states to the
low-affinity form
low-affinity form
high-affinity form
describe the process of allosteric inhibition
an enzyme subject to allosteric inhibition is active …. pg 51
describe
describe the structure of allosteric enzymes
large, multisubunit
proteins with an active or allosteric site on each
subunit
where are active and allosteric sites located
Active and allosteric sites are on different subunits,
the catalytic and regulatory subunits,
respectively
what does the binding of allosteric effectors affect the subunits
Binding of allosteric effectors alters the shape of
both catalytic and regulatory subunits
Allosteric Enzymes Exhibit_____________ interactions between subunits
cooperative
Many allosteric enzymes exhibit
cooperativity
what is cooperativity of enzymes?
As multiple catalytic sites bind substrate molecules, the
enzyme changes conformation, which alters affinity for the
substrate.
In positive cooperativity, the conformation change
increases affinity for substrate; in negative cooperativity,
affinity for substrate is decreased
In positive cooperativity, the conformation change
increases affinity for substrate
in negative cooperativity,
affinity for substrate is
decreased
what is covalent modification
Many enzymes are subject to covalent modification.
Activity is regulated by addition or removal of groups, such
as phosphate, methyl, and acetyl groups
^ form of regulation
covalent modification example
The reversible addition of phosphate groups is a common
covalent modification
Phosphorylation
the addition of a phosphoryl group
and occurs most commonly by transfer of a phosphate
group from ATP to the hydroxyl group of serine, threonine,
or tyrosine residues in a protein
Protein kinases
catalyze the phosphorylation of other
proteins.
Dephosphorylation
the
removal of phosphate groups
from proteins, is catalyzed by
protein phosphatases
Depending on the enzyme,
phosphorylation may be
associated with activation or
inhibition of the enzyme
Fisher and Krebs won the
Nobel Prize for their work on
glycogen phosphorylase
what is Glycogen
Phosphorylase?
allosteric enzyme
What are the two interconvertible forms of glycogen phosphorylase?
An active, phosphorylated form (glycogen phosphorylase
a)
An inactive, nonphosphorylated form (glycogen
phosphorylase b)
what are the enzymes responsible for regulation of glycogen phosphorylase?
Phosphorylase kinase phosphorylates the enzyme
Phosphorylase phosphatase removes the phosphate
proteolytic cleavage
The activation of a protein by a one-time, irreversible removal of
part of the polypeptide chain is called proteolytic cleavage
Proteolytic enzymes of the pancreas
trypsin, chymotrypsin,
and carboxypeptidase—are examples of enzymes synthesized
in inactive form (as zymogens) and activated by cleavage as
needed.
enzymes can inhibit completely or
reduce rate
allosteric site is also called
regulatory site
is is not a general rule that
phosphorylation activates and dephosphorylation deactivates - it depends ont he enzyme
trypsin
slides on 53
an enzyme that aids with digestion. An enzyme is a protein that speeds up a certain biochemical reaction.
