Category:BMAA

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==Class Overview==
 
==Class Overview==
 
{{Twocolumn|
 
{{Twocolumn|
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<p>
 
 
An amino acid has a carbon connected by an amino group and a carboxyl group (called an alpha carbon).  Proteins are constituted from 20 amino acids.   
 
An amino acid has a carbon connected by an amino group and a carboxyl group (called an alpha carbon).  Proteins are constituted from 20 amino acids.   
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</p>|<p>
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たんぱく質を構成するアミノ酸は20種類あります。いずれもアミノ基、カルボキシル基、水素が結合した炭素（α炭素）を持ち、残りの結合手が異なる構造になっています。
 
たんぱく質を構成するアミノ酸は20種類あります。いずれもアミノ基、カルボキシル基、水素が結合した炭素（α炭素）を持ち、残りの結合手が異なる構造になっています。
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</p>
 
 
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  ! colspan="6"| Straight Class
 
  ! colspan="6"| Straight Class
 
  |-
 
  |-
−
  |{{SearchLink/Main|BMAAS2|BMAAS2}}
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  |{{MapLink|FunctionalGroupBM|BMAAS2}}
−
  |style="text-align:center"|Straight length 2<br>Gly<br>[[Image:BMAAS2.png|90px]]
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  |style="text-align:center"|Straight length 2<br>[[{{GetMetaboliteID|Glycine||BMAA}}|Gly]]<br>[[Image:BMAAS2.png|90px]]
−
  |{{SearchLink/Main|BMAAS3|BMAAS3}}
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  |{{MapLink|FunctionalGroupBM|BMAAS3}}
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  |style="text-align:center"|Straight length 3<br>Ser, Cys, Ala<br>[[Image:BMAAS3.png|90px]]
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  |style="text-align:center"|Straight length 3<br>[[{{GetMetaboliteID|L-Serine||BMAA}}|Ser]], [[{{GetMetaboliteID|L-Cysteine||BMAA}}|Cys]], [[{{GetMetaboliteID|L-Alanine||BMAA}}|Ala]]<br>[[Image:BMAAS3.png|90px]]
−
  |{{SearchLink/Main|BMAAS4|BMAAS4}}
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  |{{MapLink|FunctionalGroupBM|BMAAS4}}
−
  |style="text-align:center"|{{SearchLink/Main|Straight length 4}}<br>Asp, Asn, Thr<br>[[Image:BMAAS4.png|90px]]
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  |style="text-align:center"|Straight length 4<br>[[{{GetMetaboliteID|L-Aspartate||BMAA}}|Asp]], [[{{GetMetaboliteID|L-Asparagine||BMAA}}|Asn]], [[{{GetMetaboliteID|L-Threonine||BMAA}}|Thr]]<br>[[Image:BMAAS4.png|90px]]
 
  |-
 
  |-
−
  |{{SearchLink/Main|BMAAS5|BMAAS5}}
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  |{{MapLink|FunctionalGroupBM|BMAAS5}}
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  |style="text-align:center"|Straight length 5<br>Gln, Glu<br>[[Image:BMAAS5.png|90px]]
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  |style="text-align:center"|Straight length 5<br>[[{{GetMetaboliteID|L-Glutamine||BMAA}}|Gln]], [[{{GetMetaboliteID|L-Glutamate||BMAA}}|Glu]]<br>[[Image:BMAAS5.png|90px]]
−
  |{{SearchLink/Main|BMAAS6|BMAAS6}}
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  |{{MapLink|FunctionalGroupBM|BMAAS6}}
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  |style="text-align:center"|Straight length 6<br>Lys<br>[[Image:BMAAS6.png|90px]]
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  |style="text-align:center"|Straight length 6<br>[[{{GetMetaboliteID|L-Lysine||BMAA}}|Lys]]<br>[[Image:BMAAS6.png|90px]]
 
  | ||
 
  | ||
 
  |-
 
  |-
 
  ! colspan="6"| Branched Class
 
  ! colspan="6"| Branched Class
 
  |-
 
  |-
−
  |{{SearchLink/Main|BMAAB4|BMAAB4}}
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  |{{MapLink|FunctionalGroupBM|BMAAB4}}
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  |style="text-align:center"|Branched length 4<br>Val, Met<br>[[Image:BMAAB4.png|90px]]
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  |style="text-align:center"|Branched length 4<br>[[{{GetMetaboliteID|L-Valine||BMAA}}|Val]], [[{{GetMetaboliteID|L-Methionine||BMAA}}|Met]]<br>[[Image:BMAAB4.png|90px]]
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  |{{SearchLink/Main|BMAAB5|BMAAB5}}
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  |{{MapLink|FunctionalGroupBM|BMAAB5}}
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  |style="text-align:center"|{{SearchLink/Main|Branched length 5}}<br>Arg, Leu, Ile<br>[[Image:BMAAB5.png|90px]]
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  |style="text-align:center"|Branched length 5<br>[[{{GetMetaboliteID|L-Arginine||BMAA}}|Arg]], [[{{GetMetaboliteID|L-Leucine||BMAA}}|Leu]], [[{{GetMetaboliteID|L-Isoleucine||BMAA}}|Ile]]<br>[[Image:BMAAB5.png|90px]]
−
  |{{SearchLink/Main|BMAAB6|BMAAB6}}
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  |{{MapLink|FunctionalGroupBM|BMAAB6}}
 
  |style="text-align:center"|Branched length 6<br>[[Image:BMAAB6.png|90px]]
 
  |style="text-align:center"|Branched length 6<br>[[Image:BMAAB6.png|90px]]
 
  |-
 
  |-
−
  ! colspan="6"| Cyclic Class
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  ! colspan="6" |[[:Category:BMAC|Cyclic Class (click here to visit another page)]]
−
|-
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|{{SearchLink/Main|BMAACCBZ|BMAACCBZ}}
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|style="text-align:center"| with benzene<br>(Phe, Tyr)<br>ベンゼン環<br>[[Image:BMAACC.png|120px]]
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|{{SearchLink/Main|BMAACCID|BMAACCID}}
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|style="text-align:center"| with indole<br>(Trp)<br>インドール環<br>[[Image:BMAACCID.png|90px]]
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|{{SearchLink/Main|BMAACCPL|BMAACCPL}}
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|style="text-align:center"| with pyrrolidine<br>(Pro)<br>ピロリジン環<br>[[Image:BMAACCPL.png|90px]]
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|-
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|{{SearchLink/Main|BMAACCIZ|BMAACCIZ}}
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|style="text-align:center"| with imidazole<br>(His)<br>イミダゾール環<br>[[Image:BMAACCIZ.png|90px]]
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| ||
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|}
 
|}
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−
<!----
 
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|[[:Category:BMAAB7|BMAAB7]]
 
−
|style="text-align:center"|[[:Category:BMAAB7|Branched length 7]]<br>[[Image:BMAAB7.png|90px]]
 
−
|[[:Category:BMAAB8|BMAAB8]]
 
−
|style="text-align:center"|[[:Category:BMAAB8|Branched length 8]]<br>[[Image:BMAAB8.png|90px]] ---->
 
  
 
== Physicochemical Characters ==
 
== Physicochemical Characters ==
 +
{{Aritalab:Lecture/Biochem/Amino Acid/Table}}
  
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{| class="collapsible" border="1" cellspacing="0"
 
−
! colspan = 7 | Character of amino acids
 
−
|-
 
−
| Name || Code || Symbol || Structure || Character || pI || Required for human?
 
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|-
 
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| alanine || Ala || A || -CH<sub>3</sub> || neutral || 6.0 ||
 
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|-
 
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| serine || Ser || S || -CH<sub>2</sub>OH || neutral || 5.7 || 
 
−
|-
 
−
| threonine || Thr || T || -CH(OH)CH<sub>3</sub> || neutral || 5.6 || yes
 
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|-
 
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| valine || Val || V || -CH(CH<sub>3</sub>)<sub>2</sub> || neutral, branched || 6.0 || yes
 
−
|-
 
−
| leucine || Leu || L || -CH<sub>2</sub>CH(CH<sub>3</sub>)<sub>2</sub> || neutral, branched || 6.0 || yes
 
−
|-
 
−
| isoleucine || Ile || I || -CH(CH<sub>3</sub>)CH<sub>2</sub>CH<sub>3</sub> || neutral, branched || 6.0 || yes
 
−
|-
 
−
| aspartic acid || Asp || D || -CH<sub>2</sub>COOH || acidic || 2.8 ||
 
−
|-
 
−
| glutamic acid || Glu || E || -CH<sub>2</sub>CH<sub>2</sub>COOH || acidic || 3.2 ||
 
−
|-
 
−
| asparagine || Asn || N || -CH<sub>2</sub>CONH<sub>2</sub> || acidic, amido || 5.4 ||
 
−
|-
 
−
| glutamine || Gln || Q || -CH<sub>2</sub>CH<sub>2</sub>CONH<sub>2</sub> || acidic, amido || 5.7 ||
 
−
|-
 
−
| lysine || Lys || K || -(CH<sub>2</sub>)<sub>4</sub>NH<sub>3</sub> || basic || 9.7 || yes
 
−
|-
 
−
| arginine || Arg || R || -(CH<sub>2</sub>)<sub>3</sub>NHC(=NH)NH<sub>2</sub> || basic || 10.8 ||
 
−
|-
 
−
| cysteine || Cys || C || -CH<sub>2</sub>SH || neutral, S || 5.1 ||
 
−
|-
 
−
| methionine || Met || M || -(CH<sub>2</sub>)<sub>2</sub>SCH<sub>3</sub> || neutral, S || 5.7 || yes
 
−
|-
 
−
| phenylalanine || Phe || F || -CH<sub>2</sub>-Benz || neutral, aromatic || 5.5 || yes
 
−
|-
 
−
| tyrosine || Tyr || Y || -CH<sub>2</sub>-Benz-OH || neutral, aromatic || 5.7 ||
 
−
|-
 
−
| tryptophan || Trp || W || -CH<sub>2</sub>-Indole || neutral, aromatic || 5.9 || yes
 
−
|-
 
−
| histidine || His || H || -CH<sub>2</sub>-Imidazole || basic, atomatic || 7.6 || yes
 
−
|-
 
−
| proline || Pro || P || -NH-(CH<sub>2</sub>)<sub>3</sub>- || neutral, cyclic, 2nd amine || 6.2 ||
 
−
|}
 
−
 
−
<br>
 
 
==D and L in Amino Acid==
 
==D and L in Amino Acid==
−
===Definition===
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{{Aritalab:Lecture/Biochem/Amino Acid/DL}}
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{{Twocolumn|
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−
Except for glycine, an amino acid contains a chiral carbon, distinguished by D or L (R or S).  In the Fischer projection, which places the carboxyl group upward and amino acid-specific side-chain downward, the amino group must comes either left or right, protruding from the paper plane.  If the hydrogen is left and amino group is right, the amino acid is called D, after D-glyceraldehide.  If the amino group is left, it is called L.
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|
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−
Glycineを除いて全てのアミノ酸は不斉炭素を持ち、D,L (R,S)の区別があります。カルボキシル基を上に、アミノ酸毎に異なる側鎖を下にしたFischer投影式を描くと、（紙面より上向きに配置される）アミノ基が左と右の場合があります。このうち水素が左アミノ基が右になるほうをD-グリセルアルデヒドに倣ってD-アミノ酸、アミノ基が左にくるものをL-アミノ酸とします。D-グリセルアルデヒドとセリンを並べてみると、ＤとＬの理由がよくわかります。
+
−
}}
+
−
<center>
+
−
{|
+
−
| [[Image:D-glyceraldehyde.gif]]
+
−
| [[Image:D-serine.gif]]
+
−
| [[Image:L-serine.gif]]
+
−
|}
+
−
</center>
+
−
 
+
−
===DL and RS do not coincide===
+
−
{{Twocolumn|
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−
In the Cahn-Ingold-Prelog (or RS) notation, 19 L-amino acids become S-form (when H is placed behind the paper plane, the amino group, carboxyl group and side chain are arranged anticlockwise).  Only L-cysteine becomes R-form because S in its side chain makes the arrangement in the different order: amino group, side chain, and carboxyl group.  For this reason, although its tetrahedal configuration is the same as the rest of amino acids, it is R-form.  Likewise, cystine is R-form too.
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|
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アミノ酸をCahn-Ingold-Prelog則(RS)により表記してみると、１９のＬ-アミノ酸がS体となります（Ｈを紙面の裏側に配置したとき、アミノ基、カルボキシル基、側鎖の順にまわると左回りになる）。ただひとつL-cysteineは、側鎖にSがくるためにアミノ基、側鎖、カルボキシル基の順番に回ります。そのため正四面体構造における配置は一緒なのですが、R体となります。システインのほかにシスチンも同様の理由でR体となります。
+
−
}}
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−
===Glycine has no chiral carbon===
+
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{{Twocolumn|
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−
Glycine has two Hydrogen branches and therefore not chiral.  The amino group of proline is included in the ring sturucture and therefore secondary amine.
+
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|
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Glycineは側鎖にＨを２つもつため、不斉炭素になりません。また、prolineはアミノ基が環構造の中に入っており、２級アミンとなります。}}
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Latest revision as of 12:50, 2 June 2011

Amino Acids


Basic Metabolism Top
(代謝トップ) 		Molecule Index
(化合物索引) 		EC classes
( EC分類) 		Input New Data
(新規入力)

Upper classes : BM Basic Metabolites

Contents

[edit] Class Overview

An amino acid has a carbon connected by an amino group and a carboxyl group (called an alpha carbon). Proteins are constituted from 20 amino acids.

Straight Class
 BMAAS2 (1 pages) Straight length 2
Gly
BMAAS2.png 		 BMAAS3 (19 pages) Straight length 3
Ser, Cys, Ala
BMAAS3.png 		 BMAAS4 (16 pages) Straight length 4
Asp, Asn, Thr
BMAAS4.png
 BMAAS5 (16 pages) Straight length 5
Gln, Glu
BMAAS5.png 		 BMAAS6 (6 pages) Straight length 6
Lys
BMAAS6.png
Branched Class
 BMAAB4 (2 pages) Branched length 4
Val, Met
BMAAB4.png 		 BMAAB5 (3 pages) Branched length 5
Arg, Leu, Ile
BMAAB5.png 		 BMAAB6 (0 pages) Branched length 6
BMAAB6.png
Cyclic Class (click here to visit another page)

[edit] Physicochemical Characters

Character of amino acids
ID Code Symbol 構造 特徴 pI 必須アミノ酸？
L-Alanine Ala A -CH3 neutral 6.0
L-Serine Ser S -CH2OH neutral 5.7
L-Threonine Thr T -CH(OH)CH3 neutral 5.6 yes
L-Valine Val V -CH(CH3)2 neutral, branched 6.0 yes
L-Leucine Leu L -CH2CH(CH3)2 neutral, branched 6.0 yes
L-Isoleucine Ile I -CH(CH3)CH2CH3 neutral, branched 6.0 yes
L-Aspartate Asp D -CH2COOH acidic 2.8
L-Glutamate Glu E -CH2CH2COOH acidic 3.2
L-Asparagine Asn N -CH2CONH2 acidic, amido 5.4
L-Glutamine Gln Q -CH2CH2CONH2 acidic, amido 5.7
L-Lysine Lys K -(CH2)4NH3 basic 9.7 yes
L-Arginine Arg R -(CH2)3NHC(=NH)NH2 basic 10.8
L-Cysteine Cys C -CH2SH neutral, S 5.1
L-Methionine Met M -(CH2)2SCH3 neutral, S 5.7 yes
L-Phenylalanine Phe F -CH2-Benz neutral, aromatic 5.5 yes
L-Tyrosine Tyr Y -CH2-Benz-OH neutral, aromatic 5.7
L-Tryptophan Trp W -CH2-Indole neutral, aromatic 5.9 yes
L-Histidine His H -CH2-Imidazole basic, atomatic 7.6 yes
L-Proline Pro P -NH-(CH2)3- neutral, cyclic, 2nd amine 6.2

[edit] D and L in Amino Acid

[edit] Definition

Except for glycine, an amino acid contains a chiral carbon, distinguished by D or L (R or S). In the Fischer projection, which places the carboxyl group upward and amino acid-specific side-chain downward, the amino group must comes either left or right, protruding from the paper plane. If the hydrogen is left and amino group is right, the amino acid is called D, after D-glyceraldehide. If the amino group is left, it is called L.

D-glyceraldehyde.gif D-serine.gif L-serine.gif

[edit] DL and RS do not coincide

In the Cahn-Ingold-Prelog (or RS) notation, 19 L-amino acids become S-form (when H is placed behind the paper plane, the amino group, carboxyl group and side chain are arranged anticlockwise). Only L-cysteine becomes R-form because S in its side chain makes the arrangement in the different order: amino group, side chain, and carboxyl group. For this reason, although its tetrahedal configuration is the same as the rest of amino acids, it is R-form. Likewise, cystine is R-form too.

[edit] Glycine has no chiral carbon

Glycine has two Hydrogen branches and therefore not chiral. The amino group of proline is included in the ring sturucture and therefore secondary amine.

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