Monday, August 20, 2012

Amino acid



Nonpolar Side Chains
 
There are eight amino acids with nonpolar side chains. Glycine, alanine, and proline have small, nonpolar side chains and are all weakly hydrophobicPhenylalanine, valine, leucine, isoleucine, and methionine have larger side chains and are more strongly hydrophobic.

Polar, Uncharged Side Chains 
There are also eight amino acids with polar, uncharged side chains. Serine and threonine have hydroxyl groupsAsparagine and glutamine have amide groups. Histidine and tryptophan have heterocyclic aromatic amine side chains. Cysteine has a sulfhydryl groupTyrosine has a phenolic side chain. The sulfhydryl group of cysteine, phenolic hydroxyl group of tyrosine, and imidazole group of histidine all show some degree of pH-dependent ionization.
Charged Side Chains
There are 
four amino acids with charged side chains. Aspartic acid and glutamic acid have carboxyl groups on their side chains. Each acid is fully ionized at pH 7.4. Arginine and lysine have side chains with amino groups. Their side chains are fully protonated at pH 7.4.
This table shows amino acid names, three- and one-letter standard abbreviations, and linear structures. Click on the amino acid name for its Fischer projection formula (atoms in red are bonded to each other).

NameAbbreviationLinear Structure
Alanineala ACH3-CH(NH2)-COOH
Argininearg RHN=C(NH2)-NH-(CH2)3-CH(NH2)-COOH
Asparagineasn NH2N-CO-CH2-CH(NH2)-COOH
Aspartic Acidasp DHOOC-CH2-CH(NH2)-COOH
Cysteinecys CHS-CH2-CH(NH2)-COOH
Glutamic Acidglu EHOOC-(CH2)2-CH(NH2)-COOH
Glutaminegln QH2N-CO-(CH2)2-CH(NH2)-COOH
Glycinegly GNH2-CH2-COOH
Histidinehis HNH-CH=N-CH=C-CH2-CH(NH2)-COOH
Isoleucineile ICH3-CH2-CH(CH3)-CH(NH2)-COOH
Leucineleu L(CH3)2-CH-CH2-CH(NH2)-COOH
Lysinelys KH2N-(CH2)4-CH(NH2)-COOH
Methioninemet MCH3-S-(CH2)2-CH(NH2)-COOH
Phenylalaninephe FPh-CH2-CH(NH2)-COOH
Prolinepro PNH-(CH2)3-CH-COOH
Serineser SHO-CH2-CH(NH2)-COOH
Threoninethr TCH3-CH(OH)-CH(NH2)-COOH
Tryptophantrp WPh-NH-CH=C-CH2-CH(NH2)-COOH
Tyrosinetyr YHO-Ph-CH2-CH(NH2)-COOH
Valineval V(CH3)2-CH-CH(NH2)-COOH






Amino Acid pKa and pI Values


Amino AcidpKaCpKaNpKaRpI
Glycine
Alanine
Valine
Leucine
Isoleucine
Proline
Serine
Threonine
Cysteine
Methionine
Asparagine
Glutamine
Phenylalanine
Tyrosine
Tryptophan
Lysine
Arginine
Histidine
Aspartate
Glutamate
2.4
2.4
2.3
2.3
2.3
2.0
2.2
2.1
1.9
2.1
2.1
2.2
2.2
2.2
2.5
2.2
1.8
1.8
2.0
2.1
9.8
9.9
9.7
9.7
9.8
10.6
9.2
9.1
10.7
9.3
8.7
9.1
9.3
9.2
9.4
9.1
9.0
9.3
9.9
9.5








8.4




10.5

10.5
12.5
6.0
3.9
4.1
6.10
6.15
6.00
6.00
6.05
6.30
5.70
5.60
5.15
5.70
5.40
5.65
5.75
5.70
5.95
9.80
10.75
7.65
2.95
3.10

 Structures

Nonpolar (hydrophobic)

amino acidthree letter codesingle letter code
glycineGlyG
alanineAlaA
valineValV
leucineLeuL
isoleucineIleI
methionineMetM
phenylalaninePheF
tryptophanTrpW
prolineProP

Polar (hydrophilic)

serineSerS
threonineThrT
cysteineCysC
tyrosineTyrY
asparagineAsnN
glutamineGlnQ

Electrically Charged (negative and hydrophilic)

aspartic acidAspD
glutamic acidGluE

Electrically Charged (positive and hydrophilic)

lysineLysK
arginineArgR
histidineHisH
Alanine
ALA; A
MW: 89.09
IE: 6.00
Formula: C3H7N1O2
Arginine
ARG; R
MW: 174.20
IE: 11.15
Formula: C6H14N4O2
Asparagine
ASN; N
MW: 132.12
IE: 5.41
Formula: C4H8N2O3
Aspartic Acid
ASP; D
MW: 133.10
IE: 2.77
Formula: C4H7N1O4
Cysteine
CYS; C
MW: 121.16
IE: 5.02
Formula: C3H7N1O2S1
Glutamic Acid
GLU; E
MW: 147.13
IE: 3.22
Formula: C5H9N1O4
Glutamine
GLN; Q
MW: 146.15
IE: 5.65
Formula: C5H10N2O3
Glycine
GLY; G
MW: 75.07
IE: 5.97
Formula: C2H5N1O2
Histidine
HIS; H
MW: 155.16
IE: 7.47
Formula: C6H9N3O2
Isoleucine
ILE; I
MW: 131.17
IE: 5.94
Formula: C6H13N1O2
Leucine
LEU; L
MW: 131.17
IE: 5.98
Formula: C6H13N1O2
Lysine
LYS; K
MW: 146.19
IE: 9.59
Formula: C6H14N2O2
Methionine
MET; M
MW: 149.21
IE: 5.74
Formula: C5H11N1O2S1
Phenylalanine
PHE; F
MW: 165.19
IE: 5.48
Formula: C9H11N1O2
Proline
PRO; P
MW: 115.13
IE: 6.30
Formula: C5H9N1O2
Serine
SER; S
MW: 105.09
IE: 5.68
Formula: C3H7N1O3
Threonine
THR; T
MW: 119.12
IE: 5.64
Formula: C4H9N1O3
Tryptophan
TRP; W
MW: 204.23
IE: 5.89
Formula: C11H12N2O2
Tyrosine
TYR; Y
MW: 181.19
IE: 5.66
Formula: C9H11N1O3
Valine
VAL; V
MW: 117.15
IE: 5.96
Formula: C5H11N1O2




CLICK ON THE NAME OF THE AMINO ACID TO SEE THE 3D IMAGE
Name
Abbreviation
Mol WtpICAS
Registry
Number
Structure formula
Alanine
ala a
89.096.0056-41-7CH3-CH(NH2)-COOH
Arginine 
arg r
174.2011.1574-79-3HN=C(NH2)-NH-(CH2)3-CH(NH2)-COOH
Asparagine 
asn n
132.125.415794-13-8H2N-CO-CH2-CH(NH2)-COOH
Aspartic acid 
asp d
133.102.7756-84-8HOOC-CH2-CH(NH2)-COOH
Cysteine 
cys c
121.155.0252-90-4HS-CH2-CH(NH2)-COOH
Glutamine 
gln q
146.155.6556-85-9H2N-CO-(CH2)2-CH(NH2)-COOH
Glutamic acid 
glu e
147.133.2256-86-0HOOC-(CH2)2-CH(NH2)-COOH
Glycine 
gly g
75.075.9756-40-6NH2-CH2-COOH
Histidine 
his h
155.167.4771-00-1N=C-NH-C=C-CH2-CH(NH2)-COOH
|________|
Isoleucine 
ile i
131.175.9473-32-5CH3-CH2-CH(CH3)-CH(NH2)-COOH
Leucine 
leu l
131.175.9861-90-5(CH3)2-CH-CH2-CH(NH2)-COOH
Lysine 
lys k
146.199.5939665-12-8H2N-(CH2)4-CH(NH2)-COOH
Methionine 
met m
149.215.7463-68-3CH3-S-(CH2)2-CH(NH2)-COOH
Phenylalanine 
phe f
165.195.4863-91-2Ph-CH2-CH(NH2)-COOH
Proline 
pro p
115.136.30147-85-3NH-(CH2)3-CH-COOH
|_________|
Serine
ser s
105.095.6856-45-1HO-CH2-CH(NH2)-COOH
Threonine 
thr t
119.125.6472-19-5CH3-CH(OH)-CH(NH2)-COOH
Tryptophan 
trp w
204.235.8973-22-3Ph-NH-CH-C-CH2-CH(NH2)-COOH
|_______|
Tyrosine 
tyr y
181.195.6660-18-4HO-p-Ph-CH2-CH(NH2)-COOH
Valine 
val v
117.155.9672-18-4CH3-CH(CH2)-CH(NH2)-COOH
 Grouping of amino acids based on their charges, hydorphobicity and polarity
  • Non-polar

  • Hydrophobic
  • Negatively charged (acidic amino acids)
  • Polar

  • Hydrophilic
  • No charge (non-acidic amino acids)
  • Polar

  • Hydrophilic
  • Positively charged (basic amino acids; non-acidic amino acids)
  • Polar

  • Hydrophilic
Amino acidpIAmino acidpIAmino acidpIAmino acidpI
Phenylalanine 
phe f
5.48Aspartic acid 
asp d
2.77Cysteine 
cys c
5.02Histidine 
his h
7.47
Methionine 
met m
5.74Glutamic acid
glu e
3.22Asparagine 
asn n
5.41Lysine 
lys k
9.59
Tryptophan 
trp w
5.89Glutamine 
gln q
5.65Arginine 
arg r
11.15
Isoleucine 
ile i
5.94Threonine 
thr t
5.64
Valine 
val v
5.96Tyrosine 
tyr y
5.66
Leucine 
leu l
5.98Serine
ser s
5.68
Alanine
ala a
6.00Glycine 
gly g
5.97
Proline 
pro p
6.30


Amino Acid Reference Data

The data in this table are for amino acid residues. To calculate the mass of a neutral peptide or protein, sum the residue masses plus the masses of the terminating groups (e.g. H at the N-terminus and OH at the C-terminus).
Residue3-
letter
code
1-
letter
code
Mono-
isotopic
mass
Average
mass
Structure
Alanine
C3H5NO
AlaA71.03711471.0779Ala
Arginine
C6H12N4O
ArgR156.101111156.1857Arg
Asparagine
C4H6N2O2
AsnN114.042927114.1026Asn
Aspartic acid
C4H5NO3
AspD115.026943115.0874Asp
Asn or AspAsxB
Cysteine
C3H5NOS
CysC103.009185103.1429Cys
Glutamic acid
C5H7NO3
GluE129.042593129.114Glu
Glutamine
C5H8N2O2
GlnQ128.058578128.1292Gln
Glu or GlnGlxZ
Glycine
C2H3NO
GlyG57.02146457.0513Gly
Histidine
C6H7N3O
HisH137.058912137.1393His
Isoleucine
C6H11NO
IleI113.084064113.1576Ile
Leucine
C6H11NO
LeuL113.084064113.1576Leu
Lysine
C6H12N2O
LysK128.094963128.1723Lys
Methionine
C5H9NOS
MetM131.040485131.1961Met
Phenylalanine
C9H9NO
PheF147.068414147.1739Phe
Proline
C5H7NO
ProP97.05276497.1152Pro
Serine
C3H5NO2
SerS87.03202887.0773Ser
Threonine
C4H7NO2
ThrT101.047679101.1039Thr
Selenocysteine
C3H5NOSe
SeCU150.95363150.0379SeC
Tryptophan
C11H10N2O
TrpW186.079313186.2099Trp
Tyrosine
C9H9NO2
TyrY163.06332163.1733Tyr
UnknownXaaX
Valine
C5H9NO
ValV99.06841499.1311Val



The RNA Codons
Second nucleotide
U
C
A
G
U
UUU Phenylalanine (Phe)
UCU Serine (Ser)
UAU Tyrosine (Tyr)
UGU Cysteine (Cys)
U
UUC Phe
UCC Ser
UAC Tyr
UGC Cys
C
UUA Leucine (Leu)
UCA Ser
UAA STOP
UGA STOP
A
UUG Leu
UCG Ser
UAG STOP
UGG Tryptophan (Trp)
G
C
CUU Leucine (Leu)
CCU Proline (Pro)
CAU Histidine (His)
CGU Arginine (Arg)
U
CUC Leu
CCC Pro
CAC His
CGC Arg
C
CUA Leu
CCA Pro
CAA Glutamine (Gln)
CGA Arg
A
CUG Leu
CCG Pro
CAG Gln
CGG Arg
G
A
AUU Isoleucine (Ile)
ACU Threonine (Thr)
AAU Asparagine (Asn)
AGU Serine (Ser)
U
AUC Ile
ACC Thr
AAC Asn
AGC Ser
C
AUA Ile
ACA Thr
AAA Lysine (Lys)
AGA Arginine (Arg)
A
AUG Methionine (Met) or START
ACG Thr
AAG Lys
AGG Arg
G
G
GUU Valine Val
GCU Alanine (Ala)
GAU Aspartic acid (Asp)
GGU Glycine (Gly)
U
GUC (Val)
GCC Ala
GAC Asp
GGC Gly
C
GUA Val
GCA Ala
GAA Glutamic acid (Glu)
GGA Gly
A
GUG Val
GCG Ala
GAG Glu
GGG Gly
G




TTTPheTCTSerTATTyrTGTCys
TTCPheTCCSerTACTyrTGCCys
TTALeuTCASerTAASTOPTGASTOP
TTGLeuTCGSerTAGSTOPTGGTrp
CTTLeuCCTProCATHisCGTArg
CTCLeuCCCProCACHisCGCArg
CTALeuCCAProCAAGlnCGAArg
CTGLeuCCGProCAGGlnCGGArg
ATTIleACTThrAATAsnAGTSer
ATCIleACCThrAACAsnAGCSer
ATAIleACAThrAAALysAGAArg
ATGMet*ACGThrAAGLysAGGArg
GTTValGCTAlaGATAspGGTGly
GTCValGCCAlaGACAspGGCGly
GTAValGCAAlaGAAGluGGAGly
GTGValGCGAlaGAGGluGGGGly
*When within gene; at beginning of gene, ATG signals start of translation.

Essential Amino Acids (Body cannot make these amino acids, they must come from food or amino acid supplements.)
 Amino Acid


Sym.


Abbr.


Min.
Daily
mg
.


Acid
Base
Neu
.
 # of pathways - One Pathway


Generates


Works With
(Against)


Augments


1
 Isoleucine*


I


Ile


10


n
 1 - threonine --> isoleucine
-
-
muscles


2
 Leucine*


L


Leu


14


n
 1 - keto-isovalerate --> leucine
-
-
blood, muscle, hormone


3
 Lysine


K


Lys


12
B
 2 - asparate --> lysine
-
calcium
herpes, triglycerides


4
 Methionine


M


Met


13


n
 7 - homoserine --> methionine
cysteine
selenium, zinc
hair, skin, chelator


5
 Phenylalanine


F


Phe


14


n
 3 - chorismate --> phenylalanine
tyrosine
B6
depression


6
 Threonine


T


Thr


7


N
 3 - aspartate --> threonine
glycine, serine
-
collagen, tooth enamel


7
 Tryptophan


W


Trp


3.5


n
 1 - chorismate --> tryptophan
niacin, seratonin
-
depression


8
 Valine*


V


Val


10


n
 1 - pyruvate --> valine
-
-
muscles
          Food Sources: Fish - meat - poultry - cottage cheese - peanuts - lentils
          A= acid, B= base, N= Neutral, n= non-polar
          *= BCAA, Branched-Chain Amino Acids, all important in muscle recovery
-

    Non-Essential Amino Acids 
(The body can make these amino acids from the above essential amino acids.)
 Amino Acid


Sym.


Abbr.


Min.
Daily
mg
.


Acid
Base
Neu
.
 # of pathways - One Pathway


Generates


Works With
(Against)


Augments


1
 Alanine


A


Ala
-


n
 4 - valine pyruvate --> alanine
-
-
-


2
 Arginine*


R


Arg
-
B
 4 - citrulline --> arginine
polyamines, creatine
zinc (lysine)
immune, healing, muscles


3
 Asparagine


N


Asn
-


N
 3 - asparate and ammonia
-
-
CNS


4
 Aspartic Acid


D


Asp
-
A
 3 - glutamate --> aspartate
-
-
CNS, brain


5
 Cysteine


C


Cys
-


N
 4 - serine --> cysteine
homocysteine, taurine
B6, Vit.E
skin, hair


6
 Glutamic Acid


E


Glu
-
A
 3 - ketoglutarate --> glutamate
glutamine, GABA
B6
brain


7
 Glutamine


Q


Gln
-


N
 2 - glutamate --> glutamine
-
-
brain


8
 Glycine


G


Gly
-


N
 2 - serine --> glycine
glutathione
GABA, taurine
body protein


9
 Histidine*


H


His
-
B
 1 - histidinol --> histidine
histamine
-
blood, allergy, sex
10
 Proline


P


Pro
-


n
 4 - l-glutamine --> proline
hydroxyproline
Vitamin C
collagen, elastin
11
 Serine


S


Ser
-


N
 1 - phosphoglycerate --> serine
cysteine, glycine
choline
blood sugar
12
 Tyrosine


Y


Tyr
-


N
 2 - phenylalanine --> tyrosine
thyroxin, melanin
 B6
thyroid
              * = These are Essential for infants, since their bodies cannot produce them yet.
-

    Other Amino Acid Factors
-
 Carnitine


-


Car
-
-
 carnitine --> butyrobetaine -->
Lysine, methionine
Vitamin C
fat metabolism
-
 Citrulline


-


Cit
-
-
 argenine --> citrulline --> ornithine
Ornithine
zinc
urea cycle
-
 Hydroxyproline


-


Hyp
-
-
 proline --> hydroxyproline
-
Vitamin C
collagen
-
 Ornithine


-


Orn
-
-
 argenine --> citrulline --> ornithine
-
-
urea cycle
-
 Taurine


-


Tau
-
-
 methionine --> cysteine --> taurine
GABA, glycine
B6
heart, bile
              The above are precursors for, or important products of, the 20 "true" amino acids listed above.




CodesAA Residue
Composition
Mono.
Avg.StructureI
O
N
S
O
U
R
C
E
.
C
O
M
AA Codes AA Residue
Composition
Mono.Avg.Structure
Gly
G
C2H3NO
57.02146457.05
AspDC4H5NO3115.02694115.1
Ala
A
C3H5NO71.03711471.08GlnQC5H8N2O2128.05858128.1
Ser
S
C3H5NO287.03202987.08LysKC6H12N2O128.09496128.2
Pro
P
C5H7NO97.05276497.12GluEC5H7NO3129.04259129.1
Val
V
C5H9NO99.06841499.07MetMC5H9NOS131.04048131.2
Thr
T
C4H7NO2101.04768101.1HisHC6H7N3O137.05891137.1
CysCC3H5NOS103.00919103.1PheFC9H9NO147.06841147.2
LeuLC6H11NO113.08406113.2ArgRC6H12N4O156.10111156.2
IleIC6H11NO113.08406113.2TyrYC9H9NO2163.06333163.2
AsnNC4H6N2O2114.04293114.1TrpWC11H10N2O186.07931186.2


H1.0078250,1.008   O15.994915, 16.00   OH17.00274,17.01H2018.01057,18.02   NH317.02655,17.03
CH3*14.01565,14.03   CH3CO*42.01057, 42.04 
* The mass of these groups observed after the displacement of a proton, for example the addition of a methyl group CH3 should displace a proton and thus the mass change is equivalent to the addition of CH2.  See our policy for rounding and significant figures.



Best Wishes: Dr.Ehab Aboueladab, Tel:01007834123 Email:ehab10f@gmail.com,ehababoueladab@yahoo.com ehab fathy aboueladab
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