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Metabolism (代謝)

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

Metabolism (代謝)

all of the biochemical reactions by which complex molecules taken into an organism are broken down to produce energy and by which energy is used to build up new molecules
All metabolic reactions fall into one of two general categories:
  1. Anabolic reactions (anabolism): energy is consumed to synthesize amino group substances acids transformation into protein
  2. Catabolic reactions (catabolism): complex molecules are broken down to produce small and usable amount of energy to sustain life
Fig. Primary metabolism and secondary metabolism

[ photosynthesis | animal physiology ]


Biosynthesis (生合成)

≈ assimilation, anabolism
multi-step, enzyme-catalyzed process of which substrates are converted into more complex products in living organisms

Respiration (呼吸)

High energy compounds

High-energy phosphate compound
  1. Pyrophosphate bond
    ATP: P-O-PO-NH~PO(OH)2
  2. Bond to carboxyl group
    Acetyl phosphates: CH3CO~PO(OH)2
  3. Bond to gunidium group
    Phosphocreatine, Phosphoarginine
    energy storage in muscle:

    creatine → vertebrate, arginine → invertebrate

  4. Bond to acidenol group
    PEP (ホスホエノールピルビン酸): COOH-C-O~PO(OH)2-CH2
Table. high-energy phosphate compound (高エネルギーリン酸化合物)
Compound                          ΔG0'      Compound                   ΔG0
Phosphenol-pyruvate         -14.8      ATP                              -7.3
1, 3-di-phospho-glycerate  -11.8      Glucose-1-phosphate   -5.0
Acetyl phosphate               -10.1      Fructose-6-phosphate  -3.8
Phospho-arginine                -7.7                                                     

Respiratory chain (呼吸鎖)

= glycolysis system + TCA cycle + electron transfer system

Researches on respiratory chain

Confirming the various pathwasy by using inhibitors, such as antimycin A, rotenone, amytal and piericidin

Glycolysis system


Fig. Glycolysis

TCA cycle (tricarboxylic acid cycle)

= Krebs cycle

Electron transfer system


Partial reaction (部分反応)

= reversibility of phosphorylation electron transport

  ATP  malate ← OAA ← Fp1 ─┐
                        Fp2 → Q → cyt b → cyt c1 → cyt c → cyt a
                        ⇑                 ⇑
                        succinate         antimycin A
mitochondria            antimycin A
         NADH ← NAD ← Q → cyt c →→
                        ↑     ⇑        Ca2+ ion transport
                  high energy  ascorbate      │

Oligomycin (オリゴマイシン)
one of the antibiotics
macrolides created by Streptomyces that can be poisonous to other organisms

an inhibitor of ATP synthase (ATP合生阻害剤) in oxidative phosphorylation (酸化的リン酸化) by blocking its proton channel (Fo subunit)

Oligomycin A: C45H74O11

791.062 g/mol (mw)

                         R1       R2  R3   R4    R5

    Oligomycin A         CH3      H   OH   H,H   CH3
    Oligomycin B         CH3      H   OH   O     CH3
    Oligomycin C         CH3      H   H    H,H   CH3
    Oligomycin D         H        H   OH   H,H   CH3
    (Rutamycin A)
    Oligomycin E         CH3      OH  OH   O     CH3
    Oligomycin F         CH3      H   OH   H,H   CH2CH3
    Rutamycin B          H        H   H    H,H   CH3
    44-Homooligomycin A  CH2CH3   H   OH   H,H   CH3
    44-Homooligomycin B  CH2CH3   H   OH   O     CH3

Photorespiration (光呼吸)

= oxidative photosynthetic carbon cycle and C2 photosynthesis
1966 Forester: exposed shortly to 14CO2 after growing under 12CO2 photorespiration

Dark: utilize 12CO2 (utilize storage materials)
Light: utilize 14CO2 (use photosynthetic products for short term)

↓ Decrease due to a few substances
Substances are primary products on photosynthesis

⇒ named photorespiration (光呼吸)

Secondary metabolism (二次代謝)

= specialized metabolism
(classical definition) pathways and products of metabolism that are not absolutely required for the survival of the organism

Ex. antibiotics and pigments

Often used for defense

rubber-like polymers/polyisoprenes
phenolic compounds
rare amino acids
plant amines

Chlorogenic acid (クロロゲン酸)
Coumarin (or coumalin クマリン)
Nicotine (ニコチン)
Lignin (リグニン)

Plant pigment (植物色素)

Flower pigment (花色素)

Four major pigments (四大色素)
  1. carotenoid (カロチノイド)
  2. flavonoid (フラボノイド)
  3. betalein (ベタレイン)
  4. chlorophyll (クロロフィル)
1. carotenoid
2. flavonoid (フラボノイド)

Basic structure of flavonoids

flavonol_ flavonol_ flavonol
_______flavonol ↖________↑ anthocyanidin_________↗ catechin
___flavone_____________↓ flavanone___alyl translation chalcone
flavan___ isoflavone
___flavanol (flavan-3-ol)_____isoflavone
Function: tolerance to abiotic stress, signal to pollinators and seed dispersal agents
Flavonoid pathway: specific to land plants
developed during the period of land colonization around 550–470 MYA
3. betalein
4. chlorophyll