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Biochemistry 2/e - Garrett & Grisham

Copyright 1999 by Harcourt Brace & Company

CHAPTER 4

Amino Acidsto accompany

Biochemistry, 2/e

byReginald Garrett and Charles Grisham

All rights reserved. Requests for permission to make copies of any part of the work

should be mailed to: Permissions Department, Harcourt Brace & Company, 6277Sea Harbor Drive, Orlando, Florida 32887-6777

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Outline

4.1: Amino Acids: Building Blocks of Proteins

4.2: Acid-Base Chemistry of Amino Acids

4.3: Reactions of Amino Acids 4.4: Optical Activity and Stereochemistry of

Amino Acids

4.5: Spectroscopic Properties of Amino Acids

4.6: Separation and Analysis of a.a. Mixtures

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Amino Acids

Building Blocks of Proteins

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Amino Acids Can Join Via Peptide Bonds

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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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Uncommon Amino Acids

We'll see some of these in later chapters

Hydroxylysine, hydroxyproline - collagen Carboxyglutamate - blood-clotting proteins

Pyroglutamate - bacteriorhodopsin

Phosphorylated amino acids - signalingdevice

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4.2 Acid-Base Chemistry

Amino Acids are Weak Polyprotic Acids

H2A+ + H2O HA

0 + H3O+

Ka1 = [ HA

0

] [ H3O

+

]__________________________[H2A

+ ]

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4.2 Acid-Base ChemistryThe second dissociation (the amino group

in the case of glycine):

HA0 + H2O A+ H3O+

Ka2 = [ A

] [ H3O+

]_______________________[ HA0 ]

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pKa Values of the Amino Acids

You should know these numbers and

know what they mean!

Alpha carboxyl group - pKa = 2 Alpha amino group - pKa = 9

These numbers are approximate, butentirely suitable for our purposes.

/ G & G

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know what they mean

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

Bi h i t 2/ G tt & G i h

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know what they mean

Lysine, Lys, K: pKa = 10.5

Serine, Ser, S: pKa = 13

Threonine, Thr, T: pKa = 13

Tyrosine, Tyr, Y: pKa = 10.1


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Titration of Glycine


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Titration of Glutamic Acid


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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


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Titration of Lysine


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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

Biochemistr 2/e Garrett & Grisham

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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

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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 L-glyceraldehyde

R,S-nomenclature system is superior,

since amino acids like isoleucine andthreonine (with two chiral centers) canbe named unambiguously


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Spectroscopic Properties

All amino acids absorb in infrared region

Only Phe, Tyr, and Trp absorb UV

Absorbance at 280 nm is a gooddiagnostic device for amino acids

NMR spectra are characteristic of each

residue in a protein, and high resolutionNMR measurements can be used toelucidate three-dimensional structures

of proteins


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Separation of Amino Acids

Mikhail Tswett, a Russian botanist, firstseparated colorful plant pigments by

chromatography Many chromatographic methods exist

for separation of amino acid mixtures

Ion exchange chromatography High-performance liquid chromatography


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