Amino Acids and ProteinsAmino Acids and Proteins

• Proteins are composed of amino acids.

• There are 20 amino acids commonly found in proteins. All have:

Cαα

H

COOHNH2

R

Amino acids at neutral pH are dipolar ions (zwitterions) because their αα-carboxyl and αα-amino groups are ionized.

C COONH3

H

R

+

[NaOH][NaOH]0. 50. 5

22

44

66

88

pK1pK1

pK2pK2

Titration curve for Glycine:Titration curve for Glycine:

pHpH COOH=COO-COOH=COO-

NH3+

NH2

NH3+ =NH2

[NaOH][NaOH]0. 50. 5

22

44

66

88

pK1pK1

pK2pK2

pHpHCOOHCOOH

NH3+NH3+

[NaOH][NaOH]0. 50. 5

22

44

66

88

pK1pK1

pK2pK2

pHpHCOOHCOOH

NH3+NH3+

Isoelectric point (no net charge)

Isoelectric point (no net charge)

pKa Values of the Amino Acids

You should know these numbers and knowwhat they mean!

• Alpha carboxyl group - pKa = 2

• Alpha amino group - pKa = 9

• These numbers are approximate, butentirely suitable for our purposes.

COO-

- C -H3+N H

CH3CH3

COO-

- C -H3+N H

CH2CH2

CHCHCH3CH3 CH3CH3

COO-

- C -H3+N H

H C H - C -

CH3CH3

CH2CH2

CH3CH3

Aliphatic Non-Polar Amino Acids

Alanine (Ala, A)

COO-

- C -H3+N H

CHCHCH3CH3 CH3CH3

Valine (Val, V)

Leucine (Leu, L) Isoleucine (Ile, I)

CH2

+N

COO-

H2C H2C CH2CH2

CH2CH2H

Proline (Pro, P) COO-

- C -H3+N H

CH2CH2

SS

CH3CH3

CH2CH2

Methionine (Met, M)

Aromatic Non-Polar Amino Acids

COO-

- C -H3+N H

CH2CH2

Phenylalanine (Phe, F)

COO-

- C -H3+N H

CH2CH2

CHCHCC

NN

Tryptophan (Trp, W)HH

Polar Uncharged Amino AcidsPolar Uncharged Amino AcidsCOO-

- C -H3+N H

CH2OHCH2OH

Serine (Ser, S)CH3CH3

COO-

- C -H3+N H

CHOHCHOH

Threonine (Thr, T)

COO-

- C -H3+N H

CH2CH2

SHSH

Cysteine (Cys, C)

COO-

- C -H3+N H

HH

Glycine (Gly, G)

Tyrosine (Tyr, Y)

COO-

- C -H3+N H

CH2CH2

OHOH

pKa=13pKa=13

pKa=10.1 pKa=8.3

Polar Uncharged Amino AcidsPolar Uncharged Amino Acids

COO-

- C -H3+N H

CH2CH2

CCOO NH2NH2

CH2CH2

Glutamine (Gln, Q)

COO-

- C -H3+N H

CH2CH2

CCOO NH2NH2

Asparagine (Asn, N)

Acidic Amino AcidsAcidic Amino Acids

COO-

- C -H3+N H

CH2CH2

CCOO

Aspartate (Asp, D)

O-O-

COO-

- C -H3+N H

CH2CH2

CCOO

CH2CH2

Glutamate (Glu, E)

O-O-

pKa=3.9pKa=4.3

Basic Amino AcidsBasic Amino Acids

CH2CH2

COO-

- C -H3+N H

NH3+NH3+

CH2CH2

CH2CH2

CH2CH2

Lysine (Lys, K)

COO-

- C -H3+N H

H2+NH2+N NH2

NH2

CH2CH2

CH2CH2

CH2CH2

NHNH

CC

Arginine (Arg, R)

COO-

- C -H3+N H

NN

CH2CH2

CC

NHNHCCHH

HCHC=

Histidine (His, H)

pKa=10.5pKa=12.5

pKa=6.0

COO-

- C -H3+N H

CH2OHCH2OH

serine

CH3CH3

COO-

- C -H3+N H

CHOHCHOH

threonine

COO-

- C -H3+N H

CH2OPO32-CH2OPO32-

phosphoserine

CH3CH3

COO-

- C -H3+N H

CHOPO32-CHOPO32-

phosphothreonine

Serine and Threonine can be PHOSPHORYLATED:Serine and Threonine can be PHOSPHORYLATED:

ATP ADP, Pi

ATP ADP, Pi

COO-

- C -H3+N H

CH2CH2

S S

COO-

- C -H3+N H

CH2CH2

SS

Disulfide Bond:Two cysteine residues condense. Disulfide bonds may occur between cyteine residues within the same protein (intrachain) or between two cysteine residues occuring in different proteins (interchain). Disulfide formation is a major factor in the determination of protein structure.

Permanent waving is the result of the reduction of disulfides in the αα-keratin protein (that hair is made of) and spontaneous re-oxidation of those disulfide bonds in air.

Cystine

Uncommon Amino Acids

• Hydroxylysine, hydroxyproline - collagen

• Carboxyglutamate - blood-clotting proteins

• Pyroglutamate - bacteriorhodopsin

• Phosphorylated amino acids - signalingdevice

Titration of Glutamic Acid

Titration of Lysine

A Sample Calculation

What is the pH of a glutamic acid solution ifthe 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 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 andamides

• Side chains show unique reactivities– Cys residues can form disulfides and can be

easily alkylated

– Few reactions are specific to a single kind ofside 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) can benamed unambiguously

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

Separation of Amino Acids

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

• Many chromatographic methods exist forseparation of amino acid mixtures– Ion exchange chromatography

– High-performance liquid chromatography