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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
Diisopropyl phosphofluoridate (Irreversible Inhibitor)
Inhibits enzymes with active site Serine, Acetocholinesterace (degrades acetylcholine)
Allopurinol (irreversible inhibitor) is used for what
Used to treat gout, it inhibits the reaction at two places
Large amounts of inhibitor
Swamp out substrate binding, and product formation is suppressed
Likewise large amounts of substrate swamp out inhibitor binding.
In the body Methanol is metabolized by the enzyme alcohol dehydrogenase producing highly toxic formaldehyde. How can you fix consumption of such
Ethanol competes for the same enzyme. Therefore administration of ethanol occupies the enzyme thereby delaying methanol metabolism long enough for clearance through the kidneys.
Ki values are used
To characterize and compare the effectiveness of inhibitors relative to Km.
In general, the lower the Ki value,
The tighter the binding, and hence the more effective an inhibitor is.
As the amount of inhibitor increases, there is more competition at the active site therefore
The enzyme does not bind the substrate as well in the presence of inhibitor and therefore “Km” increases
• Inhibitor and substrate DO NOT have common shape
• Binding is NOT at active site but causes a change in the substrate binding site
• Large amounts of inhibitor prevent access of substrate to binding site
• Large amounts of substrate CANNOT overcome inhibitory effect
NonCompetetive Inhibitors can inhibit the enzyme
Whether there is a substrate or not
What is the difference between competetive inhibitors and allosteric inhibitors
Allosteric inhibitors bind on a different chain then the active site
- Allosteric enzymes are enzymes that change their conformation upon binding of an effector.
- Do not follow Michaelis-Menten Kinetics
Heterotropic Allosteric Effectors
A molecule separate from the substrate, activating and inhibiting effectors that bind at allosteric sites
Substrates acting as effectors are said to be homotropic effectors.
Substrate itself induces distant allosteric effects when it binds to the catalytic site
1. Bond Strain: Strains substrate bonds, which facilitates attaining the transition state.
2. Proximity and Orientation: Binding brings molecules into proximity and helps to properly orient reactive groups.
3. Acid/Base Catalysis: Required catalytic proton donors (acids) or acceptors (bases) are supplied by catalyst.
4. Covalent Catalysis: The reaction is facilitated by formation of a covalent intermediate between the enzyme (or coenzyme) and the substrate.
The Serine Protease Family have catalytic center composed of
A serine, a histidine, and aspartic acid, regardless of specificity of cleavage.
Peptidoglycan hydrolysis, part of ‘innate’ immunity (breaks down cell walls of bacteria). Lysozyme is found in tears, saliva, nasal secretions and lysosomes.
Digestive enzyme, activated by proteolysis
Chymotrypsin has an affinity for
Large bulky amino acids like Phenylalanine
Histidine is the only amino acid that has
Both acid and base qualities, where it can either donate or recieve a proton
A catalytic triad
Three amino acid residues found inside the active site of certain protease enzymes: serine (S), aspartate (D), and histidine (H). They work together to break peptide bonds on polypeptides.
The catylitic triad initiates
The hydrolysis of the serine proteases like Chymotrypsin
One-third of all known enzymes need what to function
Metal ion catalysts like (Fe++, Cu++, Zn++, ect) participate in one of three ways:
a. They bind substrates to orient them for catalysis
b. Through redox reactions gain or loss of electrons.
c. Electrostatic stabilization or negative charge shielding
What is essentially a catalyticaly perfect enzyme, why
Carbonic Anhydrase, because the Kcat/Km is very high
Carbonic Anhydrase and Carbonic Dehydrase occur where in the body
In the lungs and capillaries respectively
The statin drugs (Cholesterol) like mevacor act as potent competitive inhibitors because:
The statins have Ki values several orders of magnitude lower than the Km for the substrate
A cofactor is
a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity.
loosely-bound cofactors termed
Tightly-bound cofactors termed
The term "holoenzyme" can also be applied to enzymes that
Contain multiple protein subunits
Vmax is dependent only on
The amount of available enzyme
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