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Amino Acids

What Are the Structures and Properties of Amino Acids, the Building Blocks of Proteins?

• Amino acids contain a central tetrahedral carbon atom • There are 20 common amino acids • Amino acids can join via peptide bonds • Several amino acids occur only rarely in proteins • Some amino acids are not found in proteins

Amino Acids Building Blocks of Proteins

Anatomy of an amino acid. Except for proline and its derivatives, all of the amino acids commonly found in proteins possess this type of structure.
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Amino Acids Can Join Via Peptide Bonds

The α-COOH and αNH3+ groups of two amino acids can react with the resulting loss of a water molecule to form a covalent amide bond.

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20 Common Amino Acids
You should know names, structures, pKa values, 3-letter and 1-letter codes • • • • Non-polar amino acids Polar, uncharged amino acids Acidic amino acids Basic amino acids

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Several Amino Acids Occur Rarely in Proteins

• • • •

Hydroxylysine, hydroxyproline - collagen Carboxyglutamate - blood-clotting proteins Pyroglutamate – in bacteriorhodopsin Phosphorylated amino acids – a signaling device

The structures of several amino acids that are less common but nevertheless found in certain proteins. Hydroxylysine and hydroxyproline are found in connectivetissue proteins, pyroglutamic acid is found in bacteriorhodopsin (a protein in Halobacterium halobium), and aminoadipic acid is found in proteins isolated from corn.

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The structures of some amino acids that are not normally found in proteins but that perform other important biological functions. Epinephrine, histamine, and serotonin, although not amino acids, are derived from and closely related to amino acids.

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What Are Acid-Base Properties of Amino Acids?

• Amino Acids are Weak Polyprotic Acids • H2A+ + H2O HA0 + H3O+

• Ka1 = [ HA0] [ H3O+ ] [H2A+ ]

The second dissociation (the amino group in the case of glycine): • HA0 + H2O → A¯ + H3O+ • Ka2 = [ A¯ ] [ H3O+ ] [ HA0 ]

The ionic forms of the amino acids, shown without consideration of any ionizations on the side chain. The cationic form is the low pH form, and the titration of the cationic Chemistry 40 (Summer 2007) species with base yields the zwitterion and finally the anionic form.

pKa Values of the Amino Acids
• Alpha carboxyl group - pKa = 2 • Alpha amino group - pKa = 9

pKa Values of the Amino Acids

• Arginine, Arg, R: pKa(guanidino group) = 12.5 • Aspartic Acid, Asp, D: pKa = 3.9 • Cysteine, Cys, C: pKa = 8.3 • Glutamic Acid, Glu, E: pKa = 4.3 • Histidine, His, H: pKa = 6.0

pKa Values of the Amino Acids
• • • • Lysine, Lys, K: pKa = 10.5 Serine, Ser, S: pKa = 13 Threonine, Thr, T: pKa = 13 Tyrosine, Tyr, Y: pKa = 10.1

Titration of glycine, a simple amino acid. The isoelectric point, pI, the pH where the molecule has a net charge of 0, is defined as (pK1+ pK2)/2.

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Titration of glutamic acid.

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Titration of lysine.

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A Sample Calculation
What is the pH of a glutamic acid solution if the alpha carboxyl is 1/4 dissociated? •pH = 2 + log10 [1] [3] •pH = 2 + (-0.477) •pH = 1.523

Another Sample Calculation
What is the pH of a lysine solution if the side chain amino group is 3/4 dissociated?

• pH = 10.5 + log10

[3] [1]

• pH = 10.5 + (0.477) • pH = 10.977 = 11.0

Reactions of Amino Acids
• Carboxyl groups form amides & esters • Amino groups form Schiff bases and amides • Side chains show unique reactivities – Cys residues can form disulfides and can be easily alkylated – Few reactions are specific to a single kind of side chain

The pathway of the ninhydrin reaction, which produces a colored product called “Ruhemann’s Purple” that absorbs light at 570 nm. Note that the reaction involves and consumes two molecules of ninhydrin.

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Stereochemistry of Amino Acids
• All but glycine are chiral • L-amino acids predominate in nature • D,L-nomenclature is based on D- and Lglyceraldehyde • R,S-nomenclature system is superior, since amino acids like isoleucine and threonine (with two chiral centers) can be named unambiguously

Enantiomeric molecules based on a chiral carbon atom. Enantiomers are nonsuperimposable mirror images of each other.

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The configuration of the common L-amino acids can be related to the configuration of L(-)glyceraldehyde as shown. These drawings are known as Fischer projections. The horizontal lines of the Fischer projections are meant to indicate bonds coming out of the page from the central carbon, and vertical lines represent bonds extending behind the page from the central carbon atom.
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The stereoisomers of isoleucine and threonine. The structures at the far left are the naturally occurring isomers.
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The assignment of (R) and (S) notation for glyceraldehyde and L-alanine .
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Spectroscopic Properties
• All amino acids absorb at infrared wavelengths • Only Phe, Tyr, and Trp absorb UV • Absorbance at 280 nm is a good diagnostic device for amino acids • NMR spectra are characteristic of each residue in a protein, and high resolution NMR measurements can be used to elucidate three-dimensional structures of proteins

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Separation of Amino Acids
• Mikhail Tswett, a Russian botanist, first separated colorful plant pigments by ‘chromatography’ • Many chromatographic methods exist for separation of amino acid mixtures – Ion exchange chromatography – High-performance liquid chromatography

Cation (a) and anion (b) exchange resins commonly used for biochemical separations.

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