Different structural forms of a protein that have the same function (iso = similar or same)
What does Km represent
A small Km for an enzyme relfects a high affinity of the enzyme for the substrate
A Large Km has the opposite effect
(Km does not vary with the concentration of the enzyme!!)
What does a high Km mean
A high Km means that a lot of substrate is needed to fill half of the enzyme active sites
The rate of an enzyme reaction is
Directly proportional to the enzyme concentration at any given time
Reaction rate is independent of substrate concentration: A-B; V= k
(All of the enzymes are saturated with substrate)
Reaction rate depends on the concentration of one substrate.
A - B; V = k x [A]
Reaction rate depends on the concentrations of two substrates.
A+ B - C + D; V = k x [A] x [B]
Pseudo-first order reaction:
When there are two substrates but only one is rate limiting.
Example: Hydrolysis reactions in aqueous solution.
A + H2O - C + D; V = k x [A]
Catalyze oxidation-reduction reactions (NADH)
an enzyme that catalyzes the transfer of electrons from one molecule to another
A– + B → A + B–
Catalyze transfer of functional groups from one molecule to another.
Catalyze hydrolytic cleavage
A–B + H2O → A–OH + B–H
Catalyze removal of a group from or addition of a group to a double bond, or other cleavages involving electron rearrangement.
Catalyze intramolecular rearrangement
Catalyze reactions in which two molecules are joined (ATP dependent reactions)
Nonbonding reversible reactions
E + S ⇌ ES → EP ⇌ E + P
An important concept in biochemistry is that exergonic reactions (Delta G < 0) aka. spontaneous reaction
drive endergonic reactions (Delta G > 0) aka. energy is absorbed
When Delta G is negative,
the reaction is spontaneous.
When Delta G is positive,
the reaction is non-spontanous.
When Delta G is zero,
the reaction is at equilibrium
Many important cellular reactions must run against their thermodynamic potential ie. in direction of positive ΔG, how do they do it
By coupling to a favorable reaction
If the overall free energy change is negative
That means that the reaction is spontaneous
Coupled Reactions are
An endergonic and an exergonic that are linked energetically; the endergonic reaction is driven by the exergonic reaction.
Both reactions occur simultaneously and share a common intermediate which cancels out in the final sum.
Delta G°’ is the
Biochemical standard (in vitro) free energy change. This is the free energy change when the reactants and products are initially at 1.0M, at 25°C, at 1atm and the H+ concentration is pH 7.0.
Is the actual free energy change in the cell. It depends on the actual concentrations of reactants and products.
Contain only the polypeptide portion
Contain the polypeptide portion & a non-protein portion; need both for activity
Cofactor (prosthetic group)
The non-protein portion of a conjugated enzyme
The protein portion of a conjugated enzyme
A cofactor can be
An organic cofactor, or a metol ion (Fe2+ , Mg2+ , Zn2+)
The complete, native, enzyme
An inactive precursor of a native enzyme (not the same as apoenzyme) - part of polypeptide has to be removed to give native enzyme
Vitamins are important
An AMP unit is
The most common biological handle
Coenzymes in general are found where in a cell
Water soluble: located in aqueous environment and/or held in enzyme by polar/ionic forces
Lipid soluble: located in nonaqueous environment and/or held in enzyme by van der Waals forces (hydrophobic force)
Coenzymes perform what functions
Accomplish goals amino acid side chain units can not
Chemical changes catalyzed by side chains of amino acids are limited to
acid/base and nucleophilic/electrophilic changes
Most notable use of coenzymes are in
Reductions and oxidations
What two classes of biomolecules use energy acquired from sunlight or food to be used to drive endergonic (energy-requiring) processes in the organism
Reduced coenzymes (NADH, FADH2)
High-energy phosphate compounds - free energy of hydrolysis more negative (-25 kJ/mol).
How do you release the energy from ADP and ATP
You simply hydrolyze them
ADP and ATP are examples of
Phosphoric acid anhydrides
Large negative free energy change on hydrolysis is due to:
Stabilization of products by ionization and resonance
Some biochemical reactions are driven by the hydrolysis of UTP, GTP, or CTP. And are significant because
These are energetically equivalent to ATP.
If [ATP] is low,
degradative pathways are stimulated.
If [ATP] is high,
degradative pathways are inhibited.
Redox (shorthand for oxidation-reduction) reactions describe all chemical reactions in which atoms have their oxidation number (oxidation state) changed.
Oxidation is the loss of electrons
Reduction is the gain of electrons
Redox Coenzymes Two major classes are
Flavins and Nicotinamides
H- is the same as
H+ and two e-
The two different flavins are
Flavin Adenine Mononucleotide
FMN (oxidized form); FMNH2 (reduced form)
Flavin Adenine Dinucleotide
FAD (oxidized form); FADH2 (reduced form)
involved mostly in the redox of C=C bonds
The two types of Nicotinamides
Nicotinamide Adenine Dinucleotide
NAD+ (oxidized form); NADH (reduced form)
Nicotinamide Adenine Dinucleotide Phosphate
NADP+ (oxidized form); NADPH (reduced form)involved mostly in the redox of C=O bonds
The region of the enzyme that binds and acts upon the substrate
Binding = few or many weak attractions that can be reversed like, ion to ion, H-bond, van der Waals
are enzymes that change their conformation upon binding of an effector
The shape of active site
Generally crevice or cavern on surface of enzyme
Active site has a rigid shape that is complementary to that of the substrate
Breaking Reasonance has what effect on a molecule
The molecule is less stable, therfore higher energy
The shape of the enzyme adjusts to fit the proper substrate upon binding of the substrate
A sigmoidal plot on a Rate versus Concentration of Substrate graph what does it indicate
It is an allosteric enzyme
Increasing the concentrarion of an enzyme has what effect
It will increase the rate only to a point, then it flattens out
What effect does temperature have on the rate of an ezymatic reaction
The temp will increase the rate until the heat is so excesssive that it denatures the enzyme
The Km is
The concentration of substrate at which 1/2 of the active sites are filled
The Michaelis-Menten Equation
If the concentration of the substrate is very low, (below Vmax) then
The substrate can be eliminated from the denominator of the equation
Most operations in vivo are operating
When is Vmax acheived
Never, the enzymes are never completely used
What is Kcat
It is the direct measurement of the catylic product under saturated substrate conditions (turnover number). The maximum number of substrate molecules converted to product by the enzyme molecule per unit of time
Inhibitors of enzymes are
Generally molecules which resemble or mimic a particular enzymes substrate(s).
Irreversible inhibitors generally result in
The destruction or modification of an essential amino acid required for enzyme activity. Frequently, this is due to some type of covalent link between enzyme and inhibitor.
Inhibits the enzymes that help make bacterial cell walls