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Chemicals (化学物質)

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

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Chemistry: divided into two subjects based on chemical compounds

→ the boundary is a bit unclear

Organic chemistry

researches on the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms (except simple carbon compounds)

Inorganic chemistry

researches on the synthesis and behavior of inorganic and organometallic compounds (i.e., non-organic compounds)

Mole number (物質量)

mole or molar number

Chemical bond (化学結合)

Ionic compounds (イオン化合物)

NO2-: nitrite, NO3-: nitrate
SO32-: sulfite, SO42-: sulfate, HSO4-: hydrogen sulfate ion (/bisulfate) (bi = H)
CO32-: carbonate, HCO3-: hydrogen carbonate (/bicarbonate)
PO43-: phosphate, HPO42- :hydrogen, H2PO4-; dihydrogen (di + 2 atoms)
ClO-: hypochlorite (less oxygen), ClO2-: chlorite, ClO3-: chlorate, ClO4-: perchlorate (more oxygen)

Proton transfer (陽子授受)

Redox (oxidation-reduction or oxidoreduction, 酸化還元)

Redox indicator (酸化還元指示薬)
= oxidation-reduction indicator
indicators that undergo a color change at a specific electrode potential

fast and reversible color change

Ex. KMnO4

• metal complexes of phenanthroline and bipyridine
• organic redox systems. Ex. methylene blue

2, 3, 5-triphenyl tetrazolium chloride (TTC), C19H15ClN4

TTC + 2e- + H+TTC
TTC (colorless)_________________TPF (red)
TTC+ 2H → TTC+ HCl
tetrazolium salt_______formazan

Also used for checking seed viability

TTC + 4H →
ditetrazolium salts

TTC + 2HCl

Table. Tetrazolium salts used for seed viability check
  • Triphenyltetrazolium (TT): 2, 3, 5-triphenyltetrazolium chloride (C19H15N4Cl)
  • Indonitrotetrazolium (INT): 2-p-indophenyl-3'-p-nitrophenyl-5-phenyl-tetrazolium
  • Neotetrazolium (NT): 2, 2'-indophenyl-5, 5'-diphenyl-3, 3'-p-biphenylene-ditetrazolium
  • Tetrazolium blue (TB): 2, 2'-diphenyl-5, 5'-diphenyl-3, 3'(4, 4'-dianisol)-p-biphenylene-ditetrazolium
  • Nitroneotetrazolium (NNT): 2, 2'-diphenyl-5, 5'-(metanitrophenyl)-3, 3'-p-biphenylene-ditetrazolium
  • Nitrotetrazolium blue (NTB): 2, 2'-p-dinitrophenyl-5, 5'-diphenyl-3, 3'-dimethoxy-4, 4'-biphenylene-ditetrazolium
  • Methyl-thazolyltetrazolium (MTT): 2-phenyl-3-(4, 5-dimethylthizaolyl, 2)-5-phenylteterazolium
Table. Major reducing substances and reduction systems reacted to tetrazolium salts

Carbon compound (炭素化合物)

Hydrocarbon (炭化水素, HC)


Alkane (アルカン)
CnH2n + 2IUPAC nomenclature
n  Eq.   nom.       B/Mp  AOTP  Isomers   SSF
1  CH4   Methane -162 /-183  gas     0   CH4
2  C2H6  Ethane   -89 /-184  gas     0   CH3-CH3
3  C3H8  Propane  -42 /-187  gas     0   CH3-CH2-CH3
4  C4H10 n-butane -0.5/-138  gas     2   CH3-CH2-CH2-CH3
        i-butane                         CH3-CH3-CH-CH3
5  C5H12 n-pentane 36 /-130  liquid  3
6  C6H14 n-hexane   69/-95 liquid    5
10 C10H22                   liquid    95
14 C14H30                   liquid  1858

→ many isomers → limitations of nomenclature

Eq.: equation, nom.: nomenclature, B/Mp (oC): boiling and melting points, AOTP: at ordinary temperatures and pressures, SSF: shortened structural formula

Sugar ()

Monosaccharide (単糖類)

Uronic acids (ウロン酸)
Fucose (フコース)
C6H12O5 L-rhamanose (6-deoxy-L-mannose)
L-fucose (6-deoxy-2-galactose)
Pentose (五炭糖)


Hexose (六炭糖)
L-phamnose (6-deoxy-L-mannose)
L-fucose (6-deoxy-L-galactose)
Glucose (グルコース, ブドウ糖)

glyceraldehyde(basic molecule)
glucose + H2O → glucose
α-type, β-type

Starch (デンプン)

Carboxylic acid (カルボン酸)

Succinic acid (コハク酸): HOOC-CH2-CH2-COOH
Malic acid (リンゴ酸): HOOC-CH2-CH(OH)-COOH
Fumaric acid (フマル酸): HOOC-CH=CH-COOH
Oxaloacetate (オキザロ酢酸): HOOC-CH2-CO-COOH
Citric acid (クエン酸): C(OH)(CH2COOH)2COOH

citric acid

Pyruvic acid (ピルビン酸)

= 2-oxopropanoic acid (2-オキソプロパン酸), IUPAC
= α-ketopropionic acid (α-ケトプロピオン酸)
= pyroracemic acid (焦性ブドウ酸)

pyruvate (ピルビン酸塩): the conjugate base, CH3COCOO- → key intermediate in several metabolic pathways

Amino acids and proteisn (アミノ酸とタンパク質)

Amino acid (アミノ酸)

Biologically important organic compounds containing amine (-NH2) and carboxylic acid (-COOH) functional groups

basic → amino radical

__carbon on the center: asymmetric carbon

→ carboxylic radical

Natural amino acids (天然アミノ酸)

1) Non-polar amino acid (非極性アミノ酸)
R =
1) -H: glycine (グリシン, Gly, G)
2) -CH3: alanine (アラニン, Ala, A)
3) -CH2(CH3)-CH·CH3: leusine (ロイシン, Leu, L)
4) -CH(CH3)-CH2·CH3: isoleusine (イソロイシン, Ile, I)
5) -CH2-S-CH3: methionine (メチオニン, Met, M)
6) -CH2-aa: phenylalanine (フェニルアラニン, Phe, F)
7) aa: tryptophane (トリプトファン, Trp, W)
8) aa: proline (プロリン, Pro, P)
9) -CH(CH3)-CH3: valine (バリン, Val, V)
2) Polar and charge-free amino acids (極性だが電荷のないアミノ酸)
10) -CH2OH: serine (セリン, Ser, S)
11) -CHOH·CH3: threonine (スレオニン, Thr, T)
12) -CH2SH: cysteine (システィン, Cys, C)
13) -CH2-aa-OH: tyrosine (チロシン, Tyr, Y)
14) -CH2CONH2: glutamine (グルタミン, Gln, Q)
15) -CH2CH2CONH2: asparagine (アスパラギン, Asn, N)
3) Charged amino acids (電荷を持つアミノ酸)
i) positively-charged amino acids
16) -(CH2)4-NH2: lysine (リジン, Lys, K)
17) aa: histidine (ヒスチジン, His, H)
18) -CH(NH2)-CH-NH-C=NH: arginine (アルギニン, Arg, R)
ii) negatively-charged amino acids
19) -CH2COOH: glutaminic acid (グルタミン酸, Glu, E)
20) -CH2CH2COOH: asparatic acid (アスパラギン酸, Asp, D)
The proteins are formed by these 20 amino acids

D-typed amino acids do not exsist in the nature

4) Non-proteinous amino acids (非タンパク質性アミノ酸)
not present in proteins
-(CH2)3-NH2: L-ornithine (L-オルニチン, Orn)
-(CH2)3-NH(O=C-NH2): L-citrulline (L-シトルリン, Cit)

→ these two amino acids were discovered in ornithine cycle

NH2-CH2-CH2-COOH: β-alanine (β-アラニン)
Coenzyme A: a structural component of pantothenic acid (パントテン酸)
aa: histamine (ヒスタミン)
21) aahydroxyproline (ヒドロキシプロリン)

→ occupying 12% of proteins in collagen

22) -(CH2)2-CH·OH-CH2-NH2: hydroxylisine (ヒドロキシリジン)

→ rich in collagen, as well as hydroxyproline

→ number of essential amino acids (for the structural components of proteins) is 22 when these two amino acids are included

Protein (タンパク質)

Table. Classification of proteins based on biological functions
__Types and examples ___ function
  1. enzymes
    hexokinase ___ phosphorylates glucose
    lactate dehydrogenase ___ dehydrogenates lactate
    cytocrome c ___ transports electrons
    DNA polymerase ___ replicates and repair DNA
  2. storage proteins
    ovalbumin ___ egg-white protein
    casein ___ a milk protein
    ferritin ___ iron storage in spleen
    gliadin ___ seed protein of wheat
    zein ___ seed protein of corn
  3. transport proteins
    hemoglobin ___ transports O2 in blood of vertebrates
    hemocyanin ___ transports O2 in blood of invertebrates
    myoglobin ___ transports O2 in muscle cells
    serum albumin ___ transports fatty acids in blood
    β-lipoprotein ___ transports lipids in blood
    iron-binding globulin ___ transports iron in blood
    ceruloplasmin ___ transports copper in blood
  4. contractile, motor proteins
    myosin ___ thick filaments in myofibril *
    actin ___ thin filaments in myofibril *
    dynein, tublin (鞭毛運動タンパク質) ___ cilia and flagella

    *: most of motor proteins

  5. protective proteins in vertebrate blood
    antibodies, e.g., Ig = immnoglobrin, Ig-type ___

    from complexes with forein proteins
    complexes with some antigen-antibody systems

    fibrinogen → enzyme ___ precursor of fibrin in blood clotting
    thrombin____________component of clotting mechanism
  6. toxins

    Botulinum toxin ___ causes bacterial food poisoning

    Diphtheria toxin ___ bacterial toxin
    snake venoms ___ enzymes that hydrolyze phosphoglycerides
    ricin ___ toxic protein of castor bean
    gossypin ___ toxic protein of cottonseed
  7. hormones
    insulin ___ regulates glucose metabolism
    ACTH* ___ regulates corticosteroid synthesis, insulin

    * ACTH (adrenocorticotrophic hormone) does not contain much amino acid, and therefore, is usually grouped into peptide

    growth hormones ___ stimulates growth of bones
  8. structural proteins
    viral-coat proteins ___ sheath around nucleic acid
    glycoproteins ___ cell coats and walls
    α-keratin ___ skin, feathers, nails, hoofs
    sclerotin ___ exoskeletons of insects
    fibroin ___ silk of cocoons, spider webs
    collagen ___ fibrous connective tissue (tendons, bone, cartilage)
    elastin ___ elastic connective tissure (ligaments)
    mucoproteins ___ mucous secretions, synovial fluid

Polyphenol (ポリフェノール)

polus (G. many or much) + phenol
= polyhydroxyphenols: large multiples of phenol structural units

Phenolic acid (フェノール酸)

Rutin (ルチン)
Anthraquinone physcion Anthraquinone edmodin
Anthraquinone physcion_____________Anthraquinone edmodin
Anthraquinone physcion
Resveratrol: Giant knotweed contains much resveratrol, one of the biologically active molecules.

Lipids (脂質)