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The atom nuclei are indicated by balls which can be turned off using the toggle switch for "CPK sphere". Remember that in this system carbon atoms are GREEN, oxygens are RED,nitrogens are BLUE and hydrogens are WHITE (depending upon the perspective in the figure).
The pKa's for the different ionizable groups are indicated by turning on the "labels"
L-Asparagine Asn N Mass = 132 Residue Mass = 114 Isoelectric Point = 5.41
Asparagine is derived from Aspartic acid, the side chain carboxylic acid being converted into an amide. The electron withdrawing effect of the amido group results in an appreciable reduction in the pK values for the alpha-amino and carboxyl groups relative to those of, say, glycine or alanine.
L-Glutamine Gln Q Mass = 146 Residue Mass = 128 Isoelectric Point = 5.65
Like asparagine, glutamine is derived from the corrrespomding acidic amino acid, glutamic acid. As with asparagine, the electron-withdrawing effect of the amido group reduces the pKa values for the ? substituents relative to those seen with the non-polar amino acids. Because the side chain is longer in glutamine, the effect is less marked than in asparagine.
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L-Serine Ser S Mass = 105 Residue Mass = 87 Isoelectric Point = 5.68
Serine has a primary alcoholic side chain. Its electron withdrawing effect reduces the pKa values on the alpha-substituents to a moderate degree. In the active site of some enzymes the serine hydroxyl may aquire a reactivity that does not normally occur with primary alcohols. This reflects the highly unusual chemical environment in the interior of proteins.
L-Threonine Thr T Mass = 119 Residue Mass = 101 Isoelectric Point = 5.87
Threonine possesses a secondary alcohol group in its side chain. This again has the effects on the ionizing groups of the amino acid associated with electron withdrawal.
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L-Cysteine Cys C Mass = 121 Residue Mass = 103 Isoelectric point = 5.07
The thiol group in the side chain of this amino
acid is a very weak acid, but will be significantly ionized at physiological
pH. The ionization events on the amino group and the thiol affect each other.
The apparent pKa value for the thiol is 8.3, and that for the alpha amino group
is 10.78. This is very different from that seen in glycine and indicates
the extent of this interaction. The carboxyl ionization is also promoted - the
low pKa value of 1.92 may be attributed to a strong electron withdrawing effect
by the sulphur.
The sulfhydryl anion is a reactive nucleophile.
It may be modifed chemically by any number of electrophilic reagents - for instance
iodoacetic acid. It will also react with organo mercury compounds.
Two cysteine residues may be joined (to form a Cystine residue) by their sulphydryl groups being oxidized to a disulphide"bridge". Such bridges are important in many proteins in holding the structure together.
L-Tyrosine Tyr Y Mass = 181 Residue Mass = 163 Isoelectric Point = 5.66
Tyrosine has a phenolic side chain. The phenolic
hydroxyl may participate in hydrogen bonding. The aromatic ring has acharacteristic
ultraviolet absorption, generating a peak at 275 nm. The phenolic group may
ionize under alkaline conditions when its ultraviolet absorption nearly doubles,
and the peak absorption increases to 293 nm. Tyrosine contributes significantly
to the ultraviolet absorption of proteins and is a major contributor to the
intrinsic fluorescence of proteins.
Tyrosine has typical phenolic reactivity and can be substituted ortho to the hydroxyl group by electrophilic substitution. Tyrosines may thus be easily iodinated or nitrated.
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L-Tryptophan Trp W Mass = 204 Residue Mass = 186 Isoelectric Point = 5.89
Tryptophan has a large planar aromatic side chain. It contributes to the ultraviolet absorption of proteins, having an absorption peak at 280 nm. It also contributes to the intrinsic fluorescence of proteins. Its indole ring is moderately reactive and may be oxidized by, for instance, by iodine, N-bromosuccinimide or by ozone. Although one might expect the aromatic side chain to have a hydrophobic character, the heterocyclic nitrogen confers a polar character such that the amino acid side-chain has a modest preference for an aqueous environment. Tryptophan occurs to the extent of only about 1% of total protein amino acids.
Tryptophan, tyrosine and phenylalanine are often classified together as a group - the aromatic amino acids.
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The kinemages shown have been written using the kinemage writing facility of RasMol v2.5 of R.Sayle.
Data were taken from pdb files in the Brookhaven protein database.
Kinemages by A G Clark, Victoria University of Wellington
"Organic Chemistry of Biological Compounds" R Barker. PrenticeHall Inc. (1971)
"Proteins" T E Creighton. W H Freeman and Co, New York (1984)
"Principles of Biochemistry" ( 2nd Ed) A L Lehninger, D L Nelsonand M.M Cox. Worth Publishers. New York (1993)
"Biochemistry" D Voet and J G Voet. J Wiley and Sons , New York. (1990)