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enzyme
Mind map of enzymes. Enzymes are a type of biomolecules produced by living cells with catalytic functions, so they are also called biocatalysts. Most enzymes are proteins.
Edited at 2023-10-21 17:06:14
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enzyme
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- Outline
enzyme
Concepts and features
concept
Enzymes are a type of biomolecules produced by living cells with catalytic functions, so they are also called biocatalysts.
Most enzymes are proteins
Biochemical reactions catalyzed by enzymes are called enzymatic reactions
Substances that undergo chemical changes catalyzed by enzymes are called substrates
Commonalities between Enzymes and General Catalysts
Less dosage and high catalytic efficiency
It can change the speed of a chemical reaction, but it cannot change the equilibrium of a chemical reaction
Enzymes can stabilize the transition state formed by the substrate and reduce the activation energy of the reaction, thereby accelerating the reaction.
Features
Efficiency
Enzyme catalysis can increase reaction speed by 10⁶-10¹² times
specificity or selectivity
Enzymes can only act on a specific type of substrate or type of substrate. This specificity is determined by the three-dimensional structure of the enzyme protein.
Enzyme specificity type
structural specificity
The special requirements and selection of the chemical structure of the molecules catalyzed by enzymes
category
relative specificity
absolute specificity
Stereospecificity
In addition to the requirements for the chemical structure of the substrate molecule, enzymes also have certain requirements for their stereoisomerism.
category
Optical isomerism specificity
geometric isomerism specificity
Reaction conditions are mild and easy to deactivate
Enzymatic reactions are generally carried out in pH 5-8 aqueous solutions, and the reaction temperature range is 20-40°C.
High temperature or other harsh physical or chemical conditions will cause enzyme inactivation (instability)
Enzyme activity can be adjusted and controlled
Such as inhibitor regulation, covalent modification regulation, feedback regulation Section, zymogen activation and hormone control, etc.
The catalytic activity of certain enzymes is related to coenzymes, prosthetic groups and metal ions
The chemical nature and composition of enzymes
chemical nature
It is a protein or nucleic acid and has the same physical and chemical properties as protein and nucleic acid.
composition
simple protein
Such as taking enzymes, protease, amylase, lipase and ribonuclease, etc.
conjugated protein
Protein part, also called enzyme protein
The function of enzyme protein: determines the specificity of enzyme reaction
Non-protein parts, also called cofactors
The function of cofactors: directly transfer electrons, atoms or certain chemical groups, determining the type of chemical reaction
holoenzyme=enzyme protein cofactor
category
Classification according to enzyme molecular composition
Simple protease
binding proteases
enzyme protein
Cofactor
Metal ion
metal organics
small organic molecules
Classification based on enzyme protein characteristics
monomeric enzyme
An enzyme composed of a polypeptide chain, such as lysozyme and trypsin
Oligomerase
An enzyme composed of two or more subunits, such as phosphorylase a
multienzyme complex
It is composed of several enzymes chimeric to each other through non-covalent bonds, such as fatty acid synthesis box factor
enzyme cofactor
The cofactor of an enzyme is a heat-stable, non-protein small molecule substance part of the enzyme. Its main function is to participate in the reaction as a carrier of electrons, atoms or certain groups and promote the entire catalytic process.
Cofactors are classified according to how tightly they bind to enzyme proteins.
Coenzyme: A cofactor that is loosely bound to an enzyme protein and can be removed by dialysis
Prosthetic group: It is firmly bound to the enzyme protein by covalent bond and is not easy to remove by dialysis, such as cytochrome oxidase and iron phylloxetine prosthetic group.
effect
Electron transfer bodies: such as Yelin iron, iron-sulfur clusters
Transfer hydrogen (hydrogen transfer body): such as FMN/FAD, NAD/NADP, COQ, lipoic acid
Transfer acyl group: such as COA, TPP, lipoic acid
Transfer phosphate groups: such as ATP, GTP
Pass a one-carbon group: such as tetrahydrofolate
Other functions
Transamination, such as VB₆; transfer CO₂, such as biotin
Classification of enzymes
oxidoreductases
Oxidation-reductase catalyzes oxidation-reduction reactions
Mainly including dehydrogenase (Dehydrogenase) and oxidase (Oxidase). For example, lactate dehydrogenase catalyzes the dehydrogenation reaction of lactate
Transferases
Transferase catalyzes a group transfer reaction, which transfers a group or atom from one substrate molecule to another substrate molecule
For example, the transamination reaction catalyzed by alanine aminotransferase
hydrolytic enzymes
Hydrolases catalyze the hydrolysis reaction of substrates. Mainly include amylase, protease, nuclease and lipase, etc.
For example, the hydrolysis reaction of lipids catalyzed by lipase
lytic enzymes
Lyases catalyze the reaction of removing a group or atom from a substrate molecule to form a double bond and its reverse reaction. Mainly including aldolase, hydrase and deaminase, etc.
For example, dejunase
isomerase
Isomerase catalyzes the mutual conversion of various isomers, that is, the rearrangement process of groups or atoms within the substrate molecule
For example, the reaction catalyzed by glucose-6-phosphate isomerase
Synthetic enzymes
Synthase, also known as ligase, catalyzes the formation of C-C, C-OC-N, and C-S bonds.
This type of reaction must be coupled to the ATP splitting reaction. A B ATP H-O-H ===A—B ADP Pi For example, the reaction catalyzed by pyruvylase
Nucleases (catalyze nucleic acids)
Can catalyze the hydrolysis of phosphate bonds in RNA molecules and its reversible reaction
Allozymes
Enzymes that catalyze the movement of ions or molecules across or within biological membranes
enzyme specificity
reaction specificity
Enzymes generally can only selectively catalyze one or a class of the same type of chemical reaction.
substrate specificity
An enzyme can only act on a certain type or type of substances with similar structural properties.
Enzyme structure and catalytic mechanism
enzyme active site
The area directly related to enzyme activity is called the active site or active center of the enzyme (usually the binding site and catalytic site of the enzyme are collectively referred to as the active site or active center of the enzyme).
enzyme active site structure
binding site
The site or region in the enzyme molecule that binds to the substrate is generally called the binding site
The binding site determines the specificity of the enzyme
catalytic site
The part of the enzyme molecule that promotes chemical changes in the substrate is called the catalytic site.
The catalytic site determines the nature of the reaction catalyzed by the enzyme.
The binding site and catalytic site of an enzyme are usually collectively referred to as the active site or active center of the enzyme.
regulatory site
There are some sites in enzyme molecules that can combine with other molecules to some extent, thereby causing changes in the spatial conformation of the enzyme molecules and activating or inhibiting the enzyme.
The mechanism of enzyme specificity
The catalytic theory of "three-point combination"
It is believed that there are at least three points where the enzyme binds to the substrate, and only one case is the fully bound form. Only in this case can asymmetric catalysis be achieved.
lock and key theory
It is believed that the natural conformation of the entire enzyme molecule has a rigid structure, and the enzyme surface has a specific shape. The combination of enzyme and substrate is like a key to a lock
The mechanism of high efficiency of enzyme action
intermediate product theory
Main factors related to high enzyme efficiency
Enzymatic reaction kinetics
Fundamentals of chemical kinetics
Kinetic equations for enzymatic reactions
1. Rate equation
*Zero-order reaction: The reaction rate has nothing to do with the concentration of the reactants.
* First-order reaction: The reaction rate is proportional to the concentration of the reactants.
* Secondary reaction: The reaction rate is proportional to the square of the concentration of the reactant.
2. Rate constant
*A rate constant is a measure of reaction rate, indicating how fast a reaction can proceed per unit time.
3. Activation energy
* Activation energy is the minimum energy required for a reaction to occur.
4. Catalyst
* Catalysts can reduce activation energy and accelerate reaction speed.
5. Competitive Inhibition
* Competitive inhibition means that the inhibitor competes with the substrate to bind to the active center of the enzyme, thereby reducing the reaction speed.
6. Non-competitive inhibition
* Non-competitive inhibition means that the inhibitor binds to the complex formed by the substrate and enzyme, thereby reducing the reaction rate.
7. Anti-competitive inhibition
* Anti-competitive inhibition occurs when an inhibitor binds to the complex formed by the enzyme and substrate, thereby reducing the reaction rate.
Effect of substrate concentration on enzyme reaction rate
1. Reaction rate constant: The reaction rate constant is a constant that describes the relationship between reaction rate and reactant concentration. When the concentration of the reactant is within the unit concentration range, the reaction rate is proportional to the concentration of the reactant.
2. Michaelis-Menten equation: The Michaelis-Menten equation is an equation that describes the relationship between enzymatic reaction rate and substrate concentration. When the substrate concentration is in the unit concentration range, the reaction rate is proportional to the reciprocal of the substrate concentration.
3. The slope of the Michaelis-Menten equation: The slope of the Michaelis-Menten equation is the ratio of the reaction rate constant to the maximum reaction rate, which can reflect the degree of influence of substrate concentration on the reaction rate.
4. Maximum reaction speed: The maximum reaction speed is the maximum reaction speed in the Michaelis-Menten equation, which can reflect the maximum speed of an enzymatic reaction under given conditions.
5. Competitive inhibition: Competitive inhibition means that the inhibitor competes with the substrate to bind to the active center of the enzyme, thereby reducing the reaction speed. Under competitive inhibition, the slope of the Michaelis-Menten equation remains unchanged, but the maximum reaction speed decreases.
6. Non-competitive inhibition: Non-competitive inhibition means that the inhibitor binds to the active center of the enzyme, thereby reducing the activity of the enzyme. In the case of non-competitive inhibition, both the slope of the Michaelis-Menten equation and the maximum reaction rate decrease.
7. Anti-competitive inhibition: Anti-competitive inhibition means that the inhibitor binds to the enzyme-substrate complex, thereby preventing further binding of the substrate to the enzyme. In the case of anticompetitive inhibition, both the slope of the Michaelis-Menten equation and the maximum reaction rate increase.
Factors affecting the rate of enzymatic reactions
Effect of pH on enzyme reaction rate
At a certain pH, the enzyme has maximum catalytic activity, and this pH is the optimal pH.
Effect of temperature on enzyme reaction rate
Most enzymes have an optimal temperature. Under optimal temperature conditions, the reaction rate is maximum.
As the temperature increases, the higher-order structure of the enzyme will change or denature, resulting in a reduction or even loss of enzyme activity.
As temperature rises, enzymatic reactions speed up
Effect of inhibitors on enzyme activity
The phenomenon of reducing or losing enzyme activity is called enzyme inhibition.
Compounds that can cause enzyme inhibition are called inhibitors.
Features
Similar in chemical structure to the substrate molecule being inhibited or to a transition state of the substrate
It can form a relatively stable complex or conjugate with the active center of the enzyme in a non-covalent or covalent manner.
Classification
irreversible inhibition
The inhibitor binds covalently to the active group in the reaction center of the enzyme, causing permanent deactivation of the enzyme.
Reversible inhibition
Inhibitors bind to enzyme proteins in a non-covalent manner, causing a temporary loss of enzyme activity. Inhibitors can be removed by methods such as dialysis and can partially or fully restore enzyme activity.
How to use inhibitors
competitive inhibitor
(1) Competitors are often structural analogs of enzyme substrates; (2) The binding site between the inhibitor and the enzyme is the same as the binding site between the substrate and the enzyme - the active center of the enzyme (3) The inhibitory effect can be reduced or eliminated by high concentrations of substrates (4) (The apparent Km value increases, but the Vm value remains unchanged
noncompetitive inhibitor
(1) The chemical structure of a non-competitive inhibitor is not necessarily similar to the molecular structure of the substrate; (2) The inhibitor binds to a site outside the active center of the enzyme; (3) Inhibitors have no effect on the combination of enzyme and substrate, so changes in substrate concentration have no effect on the degree of inhibition, which depends on the concentration of the inhibitor. (4) Kinetic parameters: Km value remains unchanged, Vm value decreases.
anticompetitive inhibitor
(1) The chemical structure of the anticompetitive inhibitor is not necessarily similar to the molecular structure of the substrate (2) Inhibitors and substrates can bind to different parts of the enzyme at the same time (3) A substrate must be present for the inhibitor to inhibit the enzyme; the degree of inhibition increases with the increase in substrate concentration; The degree of inhibition depends on the concentration of the inhibitor and the concentration of the substrate (4) Kinetic parameters: Km decreases and Vm decreases.
Regulation of enzyme activity
Allosteric enzymes and enzyme allosteric (allosteric) effects
In addition to the active center on the surface of some enzyme molecules, there are also specific binding sites for regulators called regulatory sites (or allosteric sites). The binding of regulators to the regulatory sites causes the conformation of the enzyme to change. Causes the enzyme activity to increase or decrease. This phenomenon is called allosteric effect. Enzymes with the above characteristics are called allosteric enzymes.
Multiple molecular forms of enzymes (isoenzymes)
A group of enzymes that exist in the same species or different species, in different tissues of the same individual, or in the same tissue or the same cell, with different molecular forms but capable of catalyzing the same chemical reaction, are called isoenzymes
activation of zymogen
The process in which an enzyme precursor (zymogen) in an inactive state in the body is modified and converted into an active enzyme under certain conditions is called zymogen activation. The essence is that the correct molecular conformation and active center are formed when the zymogen is modified. It can be seen that the specific structure of the enzyme molecule and the formation of the active center of the enzyme are the basic guarantee for the catalytic activity of the enzyme molecule.