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Enzyme (酵素)






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

Chemical change (化学変化)

Chemical equation (化学反応式) → chemical property kinetics
The energy variation as a function of reaction coordinate shows the stabilisation of the transition state by an enzyme.

Chemical equilibrium (化学平衡)

condition in the course of a reversible chemical reaction in which no net change in the amounts of reactants and products occurs

chemically stable ⇔ chemically unstable

[ catalyst | enzymology | kinetics ]
索引

Catalyst (触媒, CAT)

____MnO2 (catalyst)
H2O2 → 2H2O + O2
_____MnO2 (catalyst)
2KClO3 → 2KCl + 3O2

enzyme (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

History of enzymology, including catalysis (酵素科学史)

1713 de Réaumur, René-Antoine Ferchault 1683-1757, France: digestion

isolated gastric juice and investigated its role in the digestion of food - meat is digested by the juice

Spallanzani 1783 Spallanzani, Lazzaro 1729-1799, Italy

meat digested in glass tubes by gastric juice at about body temperature - digestion occurred without stomach

1810 Planche, Louis Antoine (1774-1840)

lignum-vitae tincture staining blue by root extract

1833 Payen A (1795–1871) & Persoz JF (1805–1868), French

discovered diastase (ジアスターゼ): isolated a malt-soluble ferment that digests the amide

1830 Robiquet PJ & Boutron-Chalard AF

amygdalin hydrolyzed by bitter almond

1836 Berzelius: proposed the term catalysis
1878 Kühne Wilhelm (1837–1900), Germany

proposed to call enzyme (酵素) as substances promoting fermentation

Debate between Pasteur and Liebig about fermentation

Pasteur: a process of microscopic living entities like yeast
Liebig: a spontaneous decomposition of matter

1897 Buchner Edüard (1860–1917), Germany: in vitro fermentation

sugars in an acellular fraction of yeast

1903 Victor, Henry (1872–1940), French-Russian

all enzymes are proteins

1926 Sumner, James 1887-1955, USA (1943 Nobel Prize)

the first isolation and crystallization of urease (尿素分解酵素) from jack bean

[ 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)
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, NAD+: Hydrogen atoms (electrons)
    • Nicotinamide adenine dinucleotide phosphatase, NADP+: Hydrogen atoms (electrons)
    • Flavin mononucleotide: Hydrogen atoms (electrons)
    • Flavin adenine dinucleotide, FAD: 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

Enzymic activity (酵素活性)

Kinetics (反応速度論)

Zero-order reaction (0次反応)
First-order reaction (1次反応)

Enzyme kinetics (酵素反応速度論)

Enzymatic inhibition (酵素阻害)

Inhibition pattern

reversible inhibition = competitive inhibition + noncompetitive inhibition
irreversible inhibition

Reversible inhibition (可逆阻害)

Competitive inhibition (拮抗阻害)
interruption of a chemical pathway owing to a chemical substance inhibiting the effect of another by competing with it for binding or bonding
1/V0 = (1 + 1/K1)Km/Vmax·1/[S] + 1/Vmax

K1 = [E][I]/[EI]
Km: binding (S ⇄ ES)
Vmax: catalysis (ES → E)

Lineweaver-Burk plot
Noncompetitive inhibition (非拮抗阻害)

Irreversible inhibition (非可逆阻害)

 Table. Summary of reversible enzyme inhibition

Vappmax                  Vappmax/KappM             KappM                               

competitive (拮抗阻害): KM↑ Vmax (unaffected)

Vmax                      (Vmax/KM)/(1 + [I]/KI)    KM(1 + [I]/KI)

mixed (混合阻害)

Vmax/(1 + [I]/KIu)    (Vmax/KM)/(1 + [I]/KI)    KM{(1 + [I]/KI)/(1 + [I]/KIu)}

noncompetitive (非拮抗阻害): KM (unaffected) Vmax↓

Vmax/(1 + [I]/KI)      (Vmax/KM)/(1 + [I]/KI)    KM

uncompetitive (不拮抗阻害): KM↓ Vmax↓

Vmax/(1 + [I]/KIu)     Vmax/KM                      KM(1 + [I]/KIu)

⇓ Lineweaver-Burk plot
inhibition
Competitive             Uncompetitive                        Noncompetitive
inhibition                  inhibition                                inhibition
━━━┅┅┅ inhibitor. ━━━┅┅┅ no inhibitor

Sort of enzymes (酵素種)

[ gastrointestinal system ]

Digestive enzyme (消化酵素)

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)
  1. hydrolases (加水分解酵素):
    Formation of two products from a substrate by hydrolysis

    AB + H2O → AOH + BH

    Ex. esterases, peptidases
  2. 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]

    EC4.1.1 decarboxylase or carboxy-lyases (脱炭酸酵素)
    EC4.2 dehydratase or carbon–oxygen lyases (脱水酵素)
    3. EC4.3.1.24: phenylalanine ammonia-lyase (PAL)
  3. isomerases (異化性酵素):
    Intramolecule rearrangement, i.e., isomerization changes within a single molecule

    ABC → BCA

    Ex. racemases, epinerases, mutases
  4. 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

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