CHAPTER 4§ΗΜ-028... · 2010-10-02 · Stereochemistry of Amino Acids •All but glycine are...

Biochemistry 2/e - Garrett & Grisham

CHAPTER 4

Amino Acidsto accompany

Biochemistry, 2/eby

Reginald Garrett and Charles Grisham

All rights reserved. Requests for permission to make copies of any part of the workshould be mailed to: Permissions Department, Harcourt Brace & Company, 6277Sea Harbor Drive, Orlando, Florida 32887-6777

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

ΑµινοξέαΔοµικές µονάδες των πρωτεϊνών

Amino Acids Can Join Via Peptide Bonds

20 Αµινοξέα

• Μη-πολικά• Πολικά, µη-φορτισµένα• Όξινα• Βασικά

Uncommon Amino AcidsWe'll see some of these in later chapters

• Hydroxylysine, hydroxyproline - collagen• Carboxyglutamate - blood-clotting proteins• Pyroglutamate - bacteriorhodopsin• Phosphorylated amino acids - signaling

device

4.2 Acid-Base Chemistry

Amino Acids are Weak Polyprotic Acids

• H2A+ + H2O → HA0 + H3O+

• Ka1 = [ HA0 ] [ H3O+ ] __________________________

[H2A+ ]

4.2 Acid-Base ChemistryThe second dissociation (the amino group

in the case of glycine):

• HA0 + H2O → A¯ + H3O+

• Ka2 = [ A¯ ] [ H3O+ ] _______________________

[ HA0 ]

pKa Values of the Amino Acids

You should know these numbers andknow what they mean!

• Alpha carboxyl group - pKa = 2• Alpha amino group - pKa = 9• These numbers are approximate, but

entirely suitable for our purposes.

pKa Values of the Amino AcidsYou should know these numbers and

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

pKa Values of the Amino Acids

You should know these numbers andknow 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

Titration of Glycine

Titration of Glutamic Acid

A Sample Calculation

What is the pH of a glutamic acid solutionif the alpha carboxyl is 1/4 dissociated?

• pH = 2 + log10 [1]

¯¯¯¯¯¯¯ [3]

• pH = 2 + (-0.477)• pH = 1.523

Titration of Lysine

Another Sample Calculation

What is the pH of a lysine solution if the sidechain 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 canbe easily alkylated

– Few reactions are specific to a single kindof side chain

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

Spectroscopic Properties

• All amino acids absorb in infraredregion

• 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 resolutionNMR measurements can be used toelucidate three-dimensional structuresof proteins

Separation of Amino Acids

• Mikhail Tswett, a Russian botanist, firstseparated colorful plant pigments by‘chromatography’

• Many chromatographic methods existfor separation of amino acid mixtures– Ion exchange chromatography– High-performance liquid chromatography

CHAPTER 4§ΗΜ-028... · 2010-10-02 · Stereochemistry of Amino Acids •All but glycine are...

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