Amino acids and proteins

Section 13.10 (pages 326-329)

Amino acids

• Amino acids contain at least one amino group and one carboxylic acid group (they are an example of bifunctional compounds)

• α-amino acids are particularly important in living systems.

R

H OH

O

CCNH2

α-carbon

Naming the amino acids

• Amino acids are usually referred to by their trivial names as this is usually shorter than the systematic name. (see sheet)

Thinking about amino acids

• We’ve just said that they have (generally) one amino group and one carboxylic acid.

• What can you tell me about each of these functional groups?

• The amino group is basic.• The carboxylic acid is acidic.

R

H OH

O

CCNH2

A quick recap on acids and bases

• We think of them as proton acceptors and donators.

R

H OH

O

CCNH2

OH

O

CROH3+

O-

O

CROH2

NH2R OH-

NH3+

ROH2

Thinking about amino acids

• So what?• The ends can react with each other and we get :

• This is called a zwitterion (the name for a particle containing both +ve and –ve charged groups)

R

H OH

O

CCNH2

R

H O-

O

CCNH3+

Physical properties of amino acids

• Have you ever seen a sample of amino acids?• They are crystalline solids• They area also highly soluble in water because

they are effectively ionic• And (unless there is another ‘ionisable group’)

they are neutral in aqueous solution

Amino acids in solution

• They form what we call ‘buffer’ solutions. (?)• A buffer solution is a solution that can

withstand the addition of small amounts of acid or alkali with little change to the pH.

HO- + H3N+-CHR-COO- H2O + H2N-CHR-COO-

H3O+ + H3N+-CHR-COO- H2O + H3N+-CHR-COOH

Peptides (or poly peptides)

• An amines can react with a carboxylic acid to form a secondary amide.

• Water is eliminated so this is a condensation reaction

• When this happens between amino acids we call the secondary amide group a peptide link

O

NH2

CH3

OH+

O

NH2OH

O

NH2NH

O

CH3

OH

+ OH2

A la n in e (A la )G ly c in e (G ly )

GlyAla

The structure of proteins

• The Primary structure is the unique sequence of amino acids (residues).

• Most proteins have a precise shape• Secondary structure refers to the initial

folding. Two common arrangements are sheets and helices

The (α) helix

• Each carbonyl (C=O) forms a hydrogen bond with an N-H group 4 peptide links along.

The (β- pleated) sheet

• Chains lying along side each other

Tertiary structure

• After regions of secondary structure have formed many proteins fold further to give their final shape, the tertiary structure.

• As well as Hydrogen bonds the following are also very important• Instantaneous dipole-induced-dipole• Ionic bonds• Covalent bonding

Hydrolysis

• This can be done by heating in in a moderately concentrated acid or alkali solution

• In living organisms this hydrolysis is catalysed by enzymes

• Chromatography can be used to identify individual amino acids present in a polypeptide.

Summary

• Amino acids exist as zwitterions.• Protein structure has three levels.• There are four kinds of bonding involved in

protein structure: what are they?