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The Genetic Code Specifies 20 L - -Amino Acids
Of the over 300 naturally occurring amino acids, 20 constitute the monomer units of proteins. While a non redundant three-letter genetic code could accommodate more than 20 amino acids, its redundancy limits the available codons to the 20 L - -amino acids listed in Table 3–1, classified according to the polarity of their R groups. Both one- and three-letter abbreviations for each amino acid can be used to represent the amino acids in peptides and proteins (Table 3–1). Some proteins contain additional amino acids that arise by modification of an amino acid already present in a peptide.
Examples include conversion of peptidyl proline and lysine to 4-hydroxyproline and 5-hydroxylysine; the conversion of peptidyl glutamate to -carboxy glutamate; and the methylation, formylation, acetylation, prenylation, and phosphorylation of certain amino acyl residues. These modifications extend the biologic diversity of proteins by altering their solubility, stability, and interaction with other proteins.
Only L - -Amino Acids Occur in Proteins
=IEP
ion
In acidic medium (
+
) pH<IEP isoelectric point zero „ 0
” pH=IEP and basic medium minus (
) pH>IEP:
-C OO H & N H
3
+ positive charge
.............................
-C OO & N H
3
+
..................................
charge is negative -C OO & N H
2
Acids positive + pH<IEP base pH>IEP negative – charge! │Blood pH=7.36 ion concentration [ H + ]=10 -7,36 M
Kā skābe
Kā skābe
R-C
RN
OO
H
3
+
H
At physiologic pH 7.36
R-C OO
–
+ H + ,
RN H
2
+ H + R
H
H
N
+
H
C
H

O
C O amino acids call as zwitter (amphi) ions and blood plasma protein molecules have negative charge at http://aris.gusc.lv/ChemFiles/Albumin/1E7GpI.doc
!E7G.pdb;IgG1.pdb
pH=7.36 value .
Amino Acid pKa-C OO H pKaN H3+ pKa R group Table5.3 Reginald H. Garrett, Charles M. Grishman,
Isoleucine
Valine
2.36
2.32
9.68
9.62
Biochemistry , University of Virginia 1995
Albumin IEP=5,1=pH, γ globulin IEP=7.91=pH.
Leucine 2.36 9.60
Phenylalanine
Cysteine
Methionine
1.83
1.96
2.28
9.13
10.28
9.21
8.18
Physiologic pH=7.36 value albumin molecule has great negative charge, as pH=7.36> 5,1 =IEP, but
Alanine 2.34 9.69 gamma globulin has positive charge, as
Proline
Glycine
1.99
2.34
10.96
9.60 pH=7.36< 7.91 =IEP.
Iso electric point pI calculates of side residues R
Threonine
Serine
2.11
2.21
9.62
9.15 constants sum ΣpKa
Rside residue plus pKa
Nterminal N H3+
and plus pKa
CterminalC OO–
Tryptophan
Tyrosine sum dividing with number NpKa of acidic groups pI=(ΣpKa
R side residue
+pKa
Nterminus
+pKa
Cterminus
) /NpKa
Histidine
Aspartate
Glutamate
Asparagine
Glutamine
Lysine
2.38
2.20
1.82
1.88
2.19
2.02
2.17
2.18
9.39
9.11
9.17
9.60
9.67
8.80
9.13
8.95
10.07
6.00
3.65
4.25
10.53
Figure Separation of serum proteins by electrophoresis .
(a) A sample is applied as a narrow line at the origin. After electrophoresis at pH 8.8
, the paper is dried and stained.
(b) A plot of color intensity of each spot.
γ
Globulin moves slower as Albumin .
Arginine 2.17 9.04 12.48 Proteins move this direction←spot line position Sample origin at start
Positive (+) electrode
← 
(a)
Negative
Seleno cysteine, the 21st L - -Amino Acid
(-)
Seleno cysteine is an L - -amino acid found in a electrode handful of proteins, including certain peroxidases and reductases where it participates in the (b) catalysis of electron transfer reactions.
As its name implies, a selenium Se atom Albumin gamma Globulin replaces the sulfur S of its structural analog, cysteine. The p K
3 of seleno cysteine 5.2 is 3 units lower than that of cysteine. Since seleno cysteine is inserted into polypeptides during translation, it is commonly referred to as the
"21st amino acid." However, like the other 20 genetically encoded amino acids, seleno cysteine is specified by a simple three-letter codon U G A (see class 16 week Nucleo proteins tRNA 62 anticodons).
12

Student self studies (home work) Name, Surname___________________________________________Group
Study Task correct: Harper’s Biochemistry tab1e-3 on 15-16 pages wrong D-amino acids convert to L-
amino acids http://aris.gusc.lv/06Daugavpils/Research/Amineac20L.doc
; to fill table below as L-
amino acids! Santa
Barbarbara University: http://aris.gusc.lv/ChemFiles/MCDB108A/tw-amn/aasframes.htm
3D amino acid molecules
R
Harper’s Biochemistry Illustrated Table 3-1 shows D-amino acids Fisher projections, which not present in human organism proteins. To show L-
amino acids
H
H
C

H
N
+
H
C
O
O
CW Clock Wise
H
H
N
+
C
H

H
O
Your task is converts D-amino acids Fisher projections to natural present
R C O
Lamino acids Fisher projections CCW (Counter Clock Wise)
In nature proved 20 proteino genic amino acids in protein polymers are
L-amino acids optical isomers
Table I.1 The 20 common L -
amino acids found in protein. Each should be shown as it would be at pH 7.36.
Protein-Derived Amino Acids Name
With aliphatic Side Chains
1
2
Glycine
Alanine
Symbol Show Fisher projection Structural Formula
Gly [G]
Ala [A]
3 Valine Val [V]
5
4
Leucine
Isoleucine
Leu [L]
Ile [I]
With Side Chains Containing Hydroxyl (— O H) Groups
6 Serine Ser [S]
7 Threonine Thr [T]
18 Tyrosine Tyr [Y]
With Side Chains Containing Sulfur Atoms (— S
— ; —
S H)
9
8 Cysteine
Methionine
Cys [C]
Met [M]
Show below ↓ .
13

Student self studies (home work) Name, Surname___________________________________________Group
Table I.1
The 20 common L amino acids found in protein. Each should be shown as it would be at pH 7.36.
Name Symbol Show Fisher projection Structural Formula
With Side Chains Containing Acidic (—C OO ) Groups or Their Amides (—C O — N H
2
)
10 Aspartic acid Asp [D]
11
12
13
Asparagine
Glutamic acid
Glutamine
With Side Chains Containing Basic (— N H n
(+) ) Groups
Asn [N]
Glu [E]
Gln [Q]
14 Arginin Arg [R]
16
15 Lysine
Histidine
Lys [K]
His [H]
Containing Aromatic Rings
Imino Acid
16
17
18
19
20
Histidine
Phenylalanine
Tyrosine
Tryptophan
Proline
His [H]
Phe [F]
Tyr [Y]
Trp [W]
Pro [P]
Show above ↑
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Student self studies (home work) Name, Surname___________________________________________Group
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