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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

Research 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
Glyoxylate cycle (グリオキシル酸回路)
Anabolic pathway occurring in plants, bacteria, protists, and fungi
The conversion of acetyl-CoA to succinate for the synthesis of carbohydrates

Electron transfer system (電子伝達系)


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
1955 Decker: tobacco leaves - post-illumination CO2 burst after (PICB)

respiration is higher under illuminaiton than under darkness

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) ↔ dark respiration (暗呼吸)

Fig. Simplified photorespiration cycle
Fig. The photorespiratory carbon and nitrogen cycle comprises enzymes and transporters distributed between chloroplasts, peroxisomes, mitochondria and cytosol. DiT1 and DiT2: dicarboxylate transporter 1 and 2, are the only transporters identified at the genomic level. CAT: catalase; GDC: glycine decarboxylase; GGAT: glutamate:glyoxylate aminotransferase; GLYK: glycerate kinase; GO: glycolate oxidase; GOGAT: glutamate:oxoglutarate aminotransferase; GS: glutamine synthetase; HPR1: peroxisomal hydroxypyruvate reductase; HPR2: cytosolic hydroxypyruvate reductase; PGP: phosphoglycolate phosphatase; RubisCO: ribulose-1,5-bisphosphate carboxylase/oxygenase; RubP: ribulose-1,5-bisphosphate; SGAT: serine-glutamate aminotransferase; SHMT: serine hydroxymethyl transferase; THF: tetrahydrofolate; 5,10-CH2-THF: 5,10-methylene-THF; 3-PGA: 3-phosphoglycerate. The dashed line represents many enzymatic steps.

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)

Phytoncide (フィトンチッド)

Antimicrobial allelochemic volatile organic compounds derived from plants
1928 Tokin, Boris P (Russian): demonstrated by lab-experiments

certain plants give off active substances that help to prevent them from rotting or being eaten by some insects and animals

Application: forest bathing (shinrin-yoku) - specific in Japan
Allelopathy (アレロパシー)
1937 Molisch, Hans (1856-1937): proposed the term, allelopathy

a plant species produces one or more biochemicals influencing the behaviors, e.g., germination, growth, survival and reproduction, of the other plant species

1925 Massey,: tomato and alfalfa did not grow with Juglans

producing juglone

Solidago canadensis ssp. altissima: C11H12O2, cis-DME

= cis-dehydromatricaria ester = CH3-(C≡C)3-CH=CH-COOCH3

Allelochemicals: chemicals having the function of allelopathy (one of the secondary metabolites)
1. plants ⇔ large mammals
2. plants ⇔ insects
Ecdysone (エクジソン)
Juvenile hormone (幼若ホルモン)
s juvenile

I:__R1 = CH2CH3, R2 = CH2CH3
II:_ R1 = CH2CH3, R2 = CH3
IIII: R1 = CH3, R2 = CH3

3. Plants ⇔ plants
4. plants ⇔ microbes

Plant pigment (植物色素)

Def. any colored material found in plants

absorb and reflect different wavelengths of light

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)

Flower pigment (花色素)

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