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Enzyme (酵素)






Mount Usu / Sarobetsu post-mined peatland
From left: Crater basin in 1986 and 2006. Cottongrass / Daylily

Enzymology (酵素学)

Enzyme (酵素)
0. effective with infinitesimal
1. catalyst

A → [catalyst or enzyme] → P
Ex. Sucrose + H2O → [amylase] → Glucose + Fructose

To promote reaction
low pH + external energy

2. temperature effect
3. pH effect (v-pH relationship)
4. specificity
索引

Enzyme (酵素)


Enzyme nomenclature (酵素命名規約)


Enzyme Committee, EC (酵素委員会)
→ Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes by the Reactions they Catalyse
Every enzyme code consists of the letters "EC" followed by four numbers separated by periods
Those numbers represent a progressively finer classification of the enzyme. Preliminary EC numbers exist and have an 'n' as part of the fourth (serial) digit (e.g. EC 3.5.1.n3).
Three names of enzymes

Trivial name (常用名), called in common use
Recommended name (推奨名), recommended by the newest admonishment from EC
Systematic name (系統名)

Classification proposed by EC
1961 International Union of Biochemistry (in Moscow)

establishing the officially accepted rule of enzyme names
firstly enzymes are classified into six major groups
every enzyme is coded as digits consisting of four parts

  1. oxidoreductases (酸化還元酵素):
    To catalyze oxidation/reduction reactions; transfer of H and O atoms or electrons from one substance to another

    AH + B → A + BH (reduced)
    A + O → AO (oxidized)

    Ex. dehydrogenases, oxydases, oxygenases
  2. transferases (転移酵素):
    Transfer of a functional group from one substance (donor, 供与体) to another (acceptor, 受容体). The group may be methyl-, acyl-, amino- or phosphate group

    AB + C → A + BC

    Ex. kinases, amino transferases (or transaminases)
  3. hydrolases (加水分解酵素):
    Formation of two products from a substrate by hydrolysis

    AB + H2O → AOH + BH

    Ex. esterases, peptidases
  4. lyases (分解):
    Non-hydrolytic addition or removal of groups from substrates. C-C, C-N, C-O or C-S bonds may be cleaved

    RCOCOOH → RCOH + CO2 or [X-A-B-Y] → [A=B + X-Y]

    Ex. decarboxylases, dehydratases
  5. isomerases (異化性酵素):
    Intramolecule rearrangement, i.e., isomerization changes within a single molecule

    ABC → BCA

    Ex. racemases, epinerases, mutases
  6. lygases or synthetases (合成酵素):
    Join together two molecules by synthesis of new C-O, C-S, C-N or C-C bonds by using free energy produced with simultaneous breakdown of ATP

    X + Y+ ATP → XY + ADP + Pi

    Ex. aminoacyl-tRNA-synthetases, peptide synthetases
Ex EC1.1.1.1.

1. = Oxidoreductases
1.1. = CH-OH group
1.1.1. = acceptor is NAD+ or NADP+
1.1.1.1. = Alcohol NAD+ oxidoreductase → the enzyme name
In the same manner, every enzyme is named by this rule
Number of registered enzymes = sharp increase

1961 (yr) = 712, 1964 = 875, 1972 = 1770, 1975 = 1974, 1979 = 2122, present > 3000

[ vitamin ]

Coenzyme (補酵素)


Holoenzyme

= apoenzyme + coenzyme

Ex. heme (containing Fe) + protein = cytochromes

Flavin (フラビン)
Isoalloxazine ring - basic skeleton of flavin

isoalloxazine
Tricyclic ring
isoalloxazine

Flavin group: organic compounds based on pteridine, formed by the tricyclic heterocycle isoalloxazine

FAD (flavin adenine dinucleotide): attached with an adenosine diphosphate
FMN

Oxidoreduction reaction or redox reaction (酸化還元反応)

AH2 + F ↔ A + FH2
flavin
flavin (yellow-colored)______________FMN
Equilibrium between the oxidized (left) and totally reduced (right) forms
flavin = Rivolfavin (vitamin B2, C17H20O6N4)






R



FAD = Flavin adenine dinucleotide (FAD)

FAD
Fig. Fluorescence pattern of
oxidized flavin
FH2 + 1/2O2 → F + H2O2
Response of oxidase containing
flavin

















Riboflavin

NAD·NADP (pyridine nucleotides) (NAD·NADP)
NAD+: nitotineamide adenine dinucleotide
NADP+: nitotineamide adenine dinucleotide phosphate
Thiamin (Thiamine, チアミン)
thiazole ring

thiamin
thiamin diphosphate (TPP)
thiamin

Pyridoxine (ピリドキシン)
Pyridoxial-P-α-AA → Pyridoxiamine-P + α-keto acid
Biotin (ビオチン)
Coenzyme A (CoA, 補酵素A)
the synthesis and oxidation of fatty acids
the oxidation of pyruvate in the citric acid cycle

FMN
CoQ

Ubiquinone, CoQ, UQ (ユビキノン)

Summary of coenzymes

Enzyme: Type of covalent intermediate
  • Serine class: Phosphoenzyme
    • Phosphoglucomulase: Acyl-enzyme
    • Acetylcholinesterase: Acyl-enzyme
    • Trypsin: Acyl-enzyme
    • Chymotrypsin: Acyl-enzyme
    • Elastase: Acyl-enzyme
  • Cystine class
    • Glyceraldehyde-phosphate dehydrogenase: Acyl-enzyme
    • Papain: Acyl-enzyme
    • Acetyl-CoA acetyltransferase: Acyl-enzyme
  • Histidine class
    • Glucose 6-phosphatase: Phosphoenzyme
    • Succinyl-CoA synthetase: Phosphoenzyme
  • Lysine class
    • Fructose-diphosphatase: Schiff's base
    • Transaldolase: Schiff's base
    • D-amino-acid oxidase: Schiff's base
  • Coenzymes in group-transferring reactions
    • Nicotinamide adenine dinucleotide: Hydrogen atoms (electrons)
    • Nicotinamide adenine dinucleotide phosphatase: Hydrogen atoms (electrons)
    • Flavin mononucleotide: Hydrogen atoms (electrons)
    • Flavin adenine dinucleotide: Hydrogen atoms (electrons)
    • Coenzyme Q: Hydrogen atoms (electrons)
    • Thiamin pyrophosphate: Aldehydes
    • Coenzyme A: Acyl groups
    • Lipoamide: Acyl groups
    • Cabamide coenzymes: Alkyl groups
    • Biocytin: Carmon dioxide
    • Pyridoxal phosphate: Amino groups
    • Tetrahydrofolate coenzymes: Methyl, methylen, formyl or forminino groups

Prosthetic group (補欠分子族)


Metals
low molecular and stable to heat
Zn2+: alcohol dehydrogenase, carbonic anhydrase, carbonicpeptidase
Mg2+: phosphohydrolases, phosphotransferases
Mn2+: arginase, phsphotransferases
Fe2+ or Fe3+: cytochromes, peroxidase, catalase, ferredoxin
Cu2+ or Cu+: tryosinase, cytochrome oxydase
Mo: nitrogenase
K+: pyruvate kinase (also required Mg2+)
Na+: plasma membrane ATPase (also required K+ and Mg2+)

FMN
FMN

Flavin mononucleotide、FMN
= riboflavin-5'-phosphate (riboflavin = vitamin B2), a phosphorylated form of riboflavin
assisting NADH dehydrogenase

Kinetics (反応速度論)


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