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Chemistry-Enzymes
An article about chemistry-enzyme mind map, about enzyme research and engineering, including mechanism of action, enzymatic reaction kinetics, factors affecting enzymatic reaction rate, etc.
Edited at 2023-11-19 16:31:03- bacteria
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Chemistry-Enzymes
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- Outline
enzyme
Concepts and features
concept
Bio-catalyst
Produced by biological cells, they are indispensable for metabolism in living organisms and are regulated by many factors.
Most of it is protein and a small amount of RNA
Features
Efficiency
Number of conversions (TN)
The number of molecules of substrate converted per enzyme molecule per unit time (1 s)
High 40 million - Catalase
Low 1-lysozyme
specificity
Enzymes are strictly selective about the type of reaction they catalyze and the reactants
enzymatic reaction
chemical reaction catalyzed by enzyme
substrate
Reactant
Determined by the structure of the enzyme, especially the structural specificity of the active site of the enzyme
sensitivity
Easy to inactivate
High temperature, strong acid, strong alkali, high salt
Requires normal temperature, normal pressure, low salt and near neutral pH
Adjustability
Dynamic balancing
Chemical nature and composition
chemical nature
ribozyme
RNA with catalytic ability
protein
pure protein
Contains only amino acid residues
Urease Amylase Ribonuclease Lysozyme
Conjugated protein (holoenzyme)
There are metal ions
small organic molecules
coenzyme
Prosthetic group: difficult to remove by dialysis
metal organic molecules
transfer electrons
Improve water affinity properties
Static shielding
orient the reaction
The non-protein part is a cofactor
As a carrier of electrons, atoms or certain chemical groups
The protein part is apoenzyme
Binding substrate
Participate in catalysis
type
monomeric enzyme
a polypeptide chain
Oligomerase
two or more subunits
multienzyme complex
Several enzyme chimeric
name
customary nomenclature
Depending on the substrate of the enzyme and the type of enzymatic reaction
Source of enzymes
Lack of systematicity and accuracy
customary nomenclature
Enzymology Committee (EC)
EC.1 (Redox).1 (Large Subcategory).1 (Receptor-NAD).27 (Serial Number)
first number
1 Redox type
2 transferases
3 hydrolysis type
4 Lyases
5 isomerase enzymes
6 Synthetic enzymes
7 Allozymes
Structure and function
Active site and essential groups
active center/active site
A region where chemical groups involved in binding to the substrate are concentrated
catalytic group
Help and promote specific chemical changes in substrates
specific amino acid side chains
enzyme cofactor
binding group
essential group
Groups necessary to maintain the spatial organization of the enzyme
Flexible
isoenzyme
A group of enzymes that catalyze the same chemical reaction, but have different molecular structure composition, physical and chemical properties, immune properties and regulatory characteristics of the enzyme itself
The same reaction step is subject to independent feedback regulation by multiple metabolites, making metabolic regulation very sophisticated.
specificity
structural specificity
absolute specificity
Only works on one
relative specificity
Have family specificity/group specificity
Example: protease
Has key specificity
Example: esterase
Stereospecificity
When there are stereoisomers in the reactants, choose only one enzyme
Optical isomerism specificity
geometric isomerism specificity
significance
Coordinated chemical reactions in living organisms
theory
lock and key theory
transition state complementarity theory
induced fit theory
Mechanism
Enzymes speed up reactions by reducing reaction activation energy
Transition state
For reactants to transform into products, they must enter a higher energy state
Ground state
The state of the reactant molecules with lower energy
activation energy
Transition state molecules have more free energy than ground state molecules
binding energy
The energy generated by enzymes and substrates through these non-covalent interactions
molecular mechanism
The active site of the enzyme molecule binds to the substrate to form an enzyme-substrate complex
proximity effect and facilitation effect
Effects can be cumulative
Non-covalent interactions that promote the formation of substrate transition states
Abzymes/catalytic antibodies
Immunoglobulins with catalytic capabilities
Acid-base catalysis
Catalysts work by donating protons to reactants or accepting protons from reactants
covalent catalysis
The catalyst changes the process and reduces the activation energy by forming a relatively unstable covalent intermediate complex with the substrate.
Metal ion catalysis
Improve water affinity properties
Electrostatic interaction shields negative charges
Use the positive charge to stabilize the negative charge formed during the reaction
Binding substrate orients the reaction
The role of the microenvironment at the enzyme active site
Examples of enzyme mechanisms of action
chymotrypsin
Enzymatic reaction kinetics
The science that studies the rate of enzymatic reactions and the various factors that affect this rate
Kinetic equations for enzymatic reactions
Michaelis-Menten equation
Michaelis constant Km
Km=（k-1 k2）/k1
Factors affecting the rate of enzymatic reactions
inhibitor
Interfering with enzyme catalysis
irreversible inhibitor
competitive inhibitor
Act on the same site
noncompetitive inhibitor
Different sites of action
anticompetitive inhibitor
The enzyme binds to the substrate and then binds to the inhibitor
Reversible inhibitor
temperature
Optimum temperature
The vertex of the curve obtained by plotting reaction rate versus temperature.
pH
Acid denaturation/alkali denaturation
Change the dissociation state of a group
Affects the dissociation state of the substrate and the dissociation state of the intermediate complex ES
Affects the active center conformation of enzymes
Optimum pH
Plant 4.5-6.5
Animal 6.5-8.0
Pepsin 1.5
Papain 4-10 unchanged
activator
Improve enzyme activity
effect
Increase enzyme activity
Mg2 in PCR can increase the activity of DNA polymerase
Control the amount and type of enzyme activators
Excessive Mg2 error rate increases
Separate, purify or preserve by removing activators
DNA preservation-EDTA 4° can be stored for half a year
Regulation of enzyme activity
Adjustment method
Change the amount and distribution of enzymes
Change the activity of existing enzyme molecules in cells
allosteric regulation
A regulatory site in an enzyme that changes the catalytic activity of the enzyme
allosteric enzyme
Enzymes with allosteric regulation
Allosteric regulation of CTP is often called feedback inhibition
effector
Compounds with allosteric modulating effects on enzyme molecules
Positive effectors/allosteric activators
Negative effectors/allosteric inhibitors
synergistic effect
positive synergy
Substrate binds to allosteric enzymes to promote binding
negative synergy
on the contrary
idiosyncratic effect
The active site and regulatory site of the enzyme are different, and the effector is a non-substrate molecule
reversible covalent modification regulation
When an enzyme is catalyzed by other enzymes, certain groups in its peptide chain undergo reversible covalent modification, resulting in the mutual conversion of the enzyme between the active (or highly active) form and the inactive (or low active) form.
covalently regulated enzyme
activation of zymogen
zymogen
inactive precursor of enzyme
activation
Catalysis by specific proteolytic enzymes, irreversible
Enzyme research methods and enzyme engineering
Enzyme activity measurement method
Enzyme activity/enzyme activity
The ability of an enzyme to catalyze a specified chemical reaction
enzyme activity unit
The amount of enzyme required to convert a certain amount of substrate into product per unit time
enzyme specific activity
The number of enzyme activity units per milligram of enzyme protein
Enzyme isolation and purification
Preparation of crude extract
Material selection
broken
extract
purification
Storage of enzyme preparations
Low temperature 0-4°, -20°
Increase storage concentration
Add stabilizer
Freeze drying
Immobilized
Enzyme Engineering
A new application technology formed by organically combining the basic principles of enzymology, chemical engineering technology and genetic recombination technology
immobilization of enzymes
Enzyme molecules are bound to the support through adsorption, covalent binding, encapsulation and cross-linking.
adsorption method
Covalent binding method
Cross-linking method
Gel embedding method
Microencapsulation