amino acids & peptides

Chapter Three Amino Acids and Peptides

Amino Acids

•• Amino acid:Amino acid: a compound that contains both an amino group and a carboxyl group•• --Amino acid hasAmino acid has an amino group

attached to the carbon adjacent to the carboxyl group

• -carbon also bound to side chain group, R

• R gives identity to amino acid• Two steroisomers of amino acids

are designated L- or D-. Based on similarity to glyceraldehdye (Figure 3.2)

Amino Acid Structure and Properties

• With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the - carbon) and are chiral (stereoisomers)• the vast majority of -amino acids have the L-

configuration at the -carbon (Proline is usually D)• Side-chain carbons in other amino acids designated

with Greek symbols, starting at a carbon (…etc)• Amino acids can be referred to by three-letter or one-

letter codes. Table 3.1 (KNOW THESE)

Individual Amino Acids

• Group A: Nonpolar side chains- Ala, Val, Leu, Ile, Pro. Phe, Trp, Met.

• Ala, Val, Leu, Ile, Pro- contain aliphatic hydrocarbon group. Pro has cyclic structure.

• Phe- hydrocarbon aromatic ring.

• Trp- Indole ring side chain, aromatic.

• Met- Sulfur atom in side chain.

Amino Acids (cont’d)

• Group B: Neutral Polar side chains- Ser, Thr, Tyr, Cys, Glu, Asn

• Ser, Thr- Side chain is polar hydroxyl group

• Tyr- hydroxyl group bonded to aromatic hydrocarbon group

• Cys- Side chain contains thiol group (-SH)

• Gln, Asn- contain amide bonds in side chain

Amino Acids (cont’d)

• Group C: Acidic Side Chains: Glu, Asp

• Both have a carboxyl group in side chain

• Can lose a proton, forming a carboxylate ion

• These amino acids are negatively charged at neutral pH

Amino Acids (cont’d)

• Group D: Basic side chains: His, Lys, Arg

• Side chains are positively charged at pH 7

• Arg-side chain is a guanidino group

• His-side chain is an imidazole group

• Lys-side chain NH3 group is attached to an aliphatic hydrocarbon chain

Amino acid summary

Important structural features:

1. All 20 are -amino acids

2. For 19 of the 20, the -amino group is primary; for proline, it is secondary

3. With the exception of glycine, the -carbon of each is a stereocenter

4. Isoleucine and threonine contain a second stereocenter

5. 3, and 1-letter codes in Table 3.1.

Uncommon Amino Acids

• Each derived from a common amino acid by a modification• hydroxylysine and

hydroxyproline are found only in a few connective tissues such as collagen

• thyroxine is found only in the thyroid gland

Ionization of Amino Acids

• In amino acid, carboxyl group (-) and amino group (+) are charged at neutral pH.

• In free amino acids -carboxyl, and a-amino groups have titratable protons. Some side chains do as well

Ionization of Amino Acids

• Remember, amino acids without charged groups on side chain exist in neutral solution as zwitterions with no net charge

Titration of Amino Acids

• When an amino acid is titrated, the titration curve represents the reaction of each functional group with the hydroxide ion

Titration of alanine with NaOH

Titration of histidine with NaOH

Acidity: -COOH Groups

• The average pKa of an -carboxyl group is 2.19, which makes them considerably stronger acids than acetic acid (pKa 4.76)• the greater acidity of the amino acid carboxyl group is

due to the electron-withdrawing inductive effect of the - NH3

+ group

Basicity: -NH3+ groups

• The average value of pKa for an -NH3+ group is

9.47, compared with a value of 10.76 for a 2° alkylammonium ion

Basicity (cont’d)

Guanidine Group• The side chain of arginine is a considerably stronger

base than an aliphatic amine• basicity of the guanido group is attributed to the large

resonance stabilization of the protonated form relative to the neutral form

Imidazole Group• The side chain imidazole group of histidine is a

heterocyclic aromatic amine

Ionization vs pH

• Given the value of pKa of each functional group, we can calculate the ratio of each acid to its conjugate base as a function of pH

• Consider the ionization of an -COOH

• writing the acid ionization constant and rearranging terms gives (remember Ch. 2)

[-COO H][-COO -]Ka = [ H3O+ ] = Ka

[-COO H][-COO -]

[ H3O+ ]or

pKa = 2.00COO-COOH + H3 O++ H2 O

Ionization vs pH (cont’d)

• substituting the value of Ka (1 x 10-2) for the hydrogen ion concentration at pH 7.0 (1.0 x 10-7) gives

• at pH 7.0, the -carboxyl group is virtually 100% in the ionized or conjugate base form, and has a net charge of -1

• we can repeat this calculation at any pH and determine the ratio of [-COO-] to [-COOH] and the net charge on the -carboxyl at that pH

= Ka[-COO H][-COO -]

[ H3O+ ]= 1.00 x 105

1.00 x 10-7

1.00 x 10-2

=

Ionization vs pH (cont’d)

• We can also calculate the ratio of acid to conjugate base for an -NH3

+ group; for this calculation, assume a value 10.0 for pKa

• writing the acid ionization constant and rearranging gives [-NH 2 ]

[-NH 3+ ]

Ka=[H 3 O+ ]

+pKa = 10.00

NH2NH3+ H3 O++ H2 O

Ionization vs pH

• substituting values for Ka of an -NH3+ group and

the hydrogen ion concentration at pH 7.0 gives

• at pH 7.0, the ratio of -NH2 to -NH3 + is

approximately 1 to 1000• at this pH, an -amino group is 99.9% in the acid

or protonated form and has a charge of +1

[-NH 2 ][-NH 3

+ ] Ka=

[H 3 O+ ]= 1.00 x 10-10

1.00 x 10-7= 1.00 x 10 -3

• We have calculated the ratio of acid to conjugate base for an -carboxyl group and an -amino group at pH 7.0

• We can do this for any weak acid and its conjugate base at any pH using the Henderson-Hasselbalch equation (Ch. 2)

[weak acid][conjugate base]log=pH pKa +

Henderson-Hasselbalch Equation

Isoelectric pH

•• IsoelectricIsoelectric pH, pI:pH, pI: the pH at which the majority of molecules of a compound in solution have no net charge

• the pI for glycine, for example, falls midway between the pKa values for the carboxyl and amino groups

• Isoelectric pH values for the 20 protein-derived amino acids are given in Table 3.2

pI = 12 ( pKa COOH + pKa NH3

+ )

= 21 (2.35 + 9.78) = 6.06

Electrophoresis

•• Electrophoresis:Electrophoresis: the process of separating compounds on the basis of their electric charge• electrophoresis of amino acids can be carried out

using paper, starch, agar, certain plastics, and cellulose acetate as solid supports

• in paper electrophoresis, a paper strip saturated with an aqueous buffer of predetermined pH serves as a bridge between two electrode vessels

Peptide Bonds

• Individual amino acids can be linked by forming covalent bonds.

•• Peptide bond:Peptide bond: the special name given to the amide bond between the -carboxyl group of one amino acid and the -amino group of another amino acid

Geometry of Peptide Bond

• the four atoms of a peptide bond and the two alpha carbons joined to it lie in a plane with bond angles of 120° about C and N

• to account for this geometry, a peptide bond is most accurately represented as a hybrid of two contributing structures (resonance structures)

• the hybrid has considerable C-N double bond character and rotation about the peptide bond is restricted

• See Figure 3.10

Peptides

•• peptidepeptide: the name given to a short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain

•• dipeptidedipeptide: a molecule containing two amino acids joined by a peptide bond

•• tripeptidetripeptide: a molecule containing three amino acids joined by peptide bonds

•• polypeptidepolypeptide: a macromolecule containing many amino acids joined by peptide bonds

•• proteinprotein: a biological macromolecule of molecular weight 5000 g/mol or greater, consisting of one or more polypeptide chains

Peptides with Physiological Activity

Peptides with Physiological Activity (cont’d)