Amino acids

Essential Amino Acids

• 10 amino acids not synthesized by the body

• arg, his, ile, leu, lys, met, phe, thr, trp, val

• Must obtain from the diet

• All in diary products

• 1 or more missing in grains

and vegetables

• All proteins are composed of the 20 standard amino acids. They are referred to as α-amino acids with the exception of proline

-Amino Acids

NH2 always attached to the -carbon

(the carbon attached to COOH)

C = -carbon

H2N C

H

COOH

R

• In the physiological pH range, both the carboxylic acid group and the amino groups of the α-amino acids ionize. An Amino acid can therefore act as both an acid and a base.

• This property is called amphoteric, and they are referred to as ampholytes.

Physiological Amino Acids

• Molecules that bear charged groups of opposite polarity are called zwitterions or dipolar molecules.

H C

COO-

R

NH3+

Amino Acids as Acids and Bases

• Ionization of the –NH2 and the –COOH group

• Zwitterion has both a + and – charge• Zwitterion is neutral overall

+

NH2–CH2–COOH H3N–CH2–COO–

glycine Zwitterion of glycine

• Because they are dipoles, they have physical properties characteristic of ionic substances.

• This makes amino acids more soluble in polar solvents than in nonpolar ones.

• Most α-amino acids are very soluble in water but largely insoluble in most organic solvents

pH and ionization

H+ OH–

+ +

H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–

COO–

Positive ion zwitterion Negative ion

Low pH neutral pH High pH

• α-amino acids polymerize through the elimination of a water molecule the resulting CO-NH linkage is known as a peptide bond.

• Polymers composed of 2,3,a few(3-10), and many amino acids residues are known respectively as dipeptides, tripeptides, oligopeptides, and polypeptides.

Peptides

• Amino acids linked by amide (peptide) bonds

Gly Lys Phe Arg Ser

H2N- -COOH

end Peptide bonds end

Glycyllysylphenylalanylarginylserine

Learning Check AA4

Write the three-letter abbreviations for the following tetrapeptide:

H3N CH

CH3

C

O

N

H

CH C

O

N

H

CH C

O

N

H

CH C O-

OCH

CH CH3

CH3

CH2

SH

CH2

CH2

S

CH3

Solution AA4

Ala-Leu-Cys-Met

H3N CH

CH3

C

O

N

H

CH C

O

N

H

CH C

O

N

H

CH C O-

OCH

CH CH3

CH3

CH2

SH

CH2

CH2

S

CH3

The Peptide Bond

Amide bond formed by the –COOH of an amino acid and the –NH2 of the next amino acid

O CH3

+ | | + |

NH3–CH2–COH + H3N–CH–COO–

O CH3

+ | | |

NH3–CH2–C – N–CH–COO–

| peptide bond H

• A protein is an organic polymer composed of amino acids bonded together in one or more chains.

Proteins

• An amino acid has a central carbon atom, to which are bonded a carboxyl group, an amino group, a hydrogen atom, and a variable side chain designated as R, as shown in the following structural formula.

Structure of an Amino Acid

• Amino acids bond to each other by forming a peptide bond, an amide group formed by a condensation reaction between the carboxyl group of one amino acid and the amino group of another.

Structure of an Amino Acid

Structure of an Amino Acid

• Two amino acids linked by a peptide bond form a dipeptide.

Bonding in -Amino Acids

A peptide linkage

There are 20 amino acids commonly found in proteins.

CNH

H

H

R

C

O

N

H

C

H

R'

CO

OH

• A chain of two or more amino acids linked by peptide bonds is called a peptide.

Structure of an Amino Acid

• The term polypeptide is applied to a chain of ten or more amino acids.

• Proteins may have one or several polypeptide chains, and each chain must have an exact sequence of amino acids.

Classification of Amino Acids

• Classified according to their side chains polarity. (R groups)

• This is because in their native conformations, largely in response to the tendency to remove their hydrophobic side chains from contact with water and to solvate their hydrophilic side chains.

• According to this classification scheme, there are three major groups.

• 1. those w/nonpolar R groups

• 2. Uncharged polar R groups

• 3. charged polar R groups

Types of Amino Acids

Nonpolar R = H, CH3, alkyl groups, aromatic

OPolar ll

R = –CH2OH, –CH2SH, –CH2C–NH2,

(polar groups with –O-, -SH, -N-)

Polar/Acidic

R = –CH2COOH, or -COOH

Polar/ Basic

R = –CH2CH2NH2

Learning Check AA1

Identify each as (1) polar or (2) nonpolar

A. NH2–CH2–COOH (Glycine)

CH3

| CH–OH

|

B. NH2–CH–COOH (Serine)

Solution AA1

Identify each as (1) polar or (2) nonpolar

A.(2) NH2–CH2–COOH (Glycine)

CH3

| CH–OH |

B. (1) NH2–CH–COOH (Serine)

Non polar amino acids ( hydrophobic )

• (9)

• Glycine, Alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, and tryptophan

Uncharged polar side chains( hydrophilic)

• (6) these have Hydroxyl, Amide, or Thiol groups

• Serine, threonine, asparagine, glutamine, tyrosine, cysteine.

Charged polar side chains( ionic)

• Can be positively or negatively charged.

• The basic amino acids are (+) charged at Physiological pH values.

• Lysine, arginine, and histidine.

• The acidic amino acids are (-) charged above pH 3

• Aspartic acid, glutamic acid

Learning Check AA2

CH3 CH3

+

H3N–CH–COOH H2N–CH2–COO–

(1) (2)

Select from the above structures

A. Alanine in base.

B. Alanine in acid.

Solution AA2

CH3 CH3

+

H3N–CH–COOH H2N–CH2–COO–

(1) (2)

Select from the above structures

A. (2) Alanine in base.

B. (1) Alanine in acid.

• The 20 amino acids vary considerably in their physical and chemical properties such as polarity, acidity, basicity, aromaticity, flexibility, ability to cross link, ability to hydrogen bond, and chemical reactivity. These characteristics, several that are interrelated contribute to proteins great range of properties.

Non standard amino acids

• The 20 common amino acids are by no means the only amino acids that occur in biological systems. Non standard amino acid residues are often important constituents in proteins. The changes comes from a conformation rearrangement in their 3-D structures. These are called D-amino acids and are quite prevalent in many antibiotics.