bch 201

Federal University NdufuAlike Ikwo (FUNAI)

Department of Chemistry / Biochemistry / Molecular

Biology

General Biochemistry 1

BCH 201by

Oje, Obinna A.

Amino acids

Objectives

What are amino acids ?

Structure of Amino acids

Classification of Amino acids

Reactions of amino acids (chemistry e.t.c.)

Proteins functions and amino acid derivatives.

Methods of isolation and identification

IntroductionProteins mediate virtually every process that takes place in a

cell, exhibiting an almost endless diversity of functions.

Proteins are the most abundant biological macromolecules,occurring in all cells and all parts of cells.

Proteins are the molecular instruments through whichgenetic information is expressed.

All proteins, whether from the most ancient lines ofbacteria or from the most complex forms of life, areconstructed from the same ubiquitous set of 20 amino acids,covalently linked in characteristic linear sequences.

Proteins are found in a wide range of sizes, from relativelysmall peptides with just a few amino acid residues to hugepolymers with molecular weights in the millions.

What is most remarkable is that cells can produce proteinswith strikingly different properties and activities by joining thesame 20 amino acids in many different combinations andsequences. From these building blocks different organisms canmake such widely diverse products as enzymes, hormones,antibodies, transporters, muscle fibers, the lens protein of theeye, feathers, spider webs, rhinoceros horn, milk proteins,antibiotics, mushroom poisons, and myriad other substanceshaving distinct biological activities

Amino acidsThey are the building blocks of proteins.

They are organic compounds, which contain two functional groups, amino group (-NH2) and carboxyl group (-COOH).

The amino group is usually attached to the -carbon atom (next to the -COOH group).

Amino acids present in proteins are of the -L-type i.e. the amino (H2N-) group is present on the left side of the vertical formula.

Structure of Amino acids

Twenty (20) amino acids

Names, 3 letter abbreviation and 1 letter code

Glycine(Gly) (G)

Hydrogen for R, most simple, optically inactive

Alanine (Ala) (A)Methyl for R, a simple functional group to start just

like A (in alanine) starts the alphabet

Valine(Val) (V)

Valine (V) simple again, but shaped like the V in its name

Leucine(Leu) (L)

valineextended by one methylene

Isoleucine (Ile) (I)lopsided valine....?

Proline(Pro) (P)Proline (P) 3 carbon chain to prolines own nitrogen,

structurally special and found in turns

Methionine (Met) (M) special - starts every protein, 3 carbons with a thioether; methyl-blocked sulfhydryl...?

Cysteine (Cys) (C)sulfhydryl alanine, reactive, can form disulfides

Phenylalanine (Phe) (F)

alanine with a phenol group which you

KNOW is aromatic, the Y in phenyl can

remind you which 3 amino acids with names

beginning with T (the Ts) are aromatics

Tyrosine (Tyr) (Y) hydroxylatedphenylalanine, one of 3 Ts

that has Y in its name so it is an aromatic

Tryptophan (Try) (W)one of 3 Ts with a Y so it is aromatic, will

tryp you up because it is hard to remember,

has a 3 carbon start to N (or indole ring on

methylene)

Serine (Ser) (S) hydroxyl alanine

Threonine (Thr) (T) one of 3 Ts, without Y so aliphatic (also

its symbol is the first letter of its name like

the other aliphatics), its threo parts are

methyl, hydroxyl, and hydrogen on a single C

Aspartate (Asp) (D)carboxyl alanine with acidic nature noted

by suffix ate, the alphabetical ordering of

the first letter of their names correlates with

an increase in length of side chain

Glutamate (Glu) (E) aspartate plus one methylene, G is after A

Arginine (Arg) (R) 3 carbon chain linked to a C full of only Ns

(no Hs & C has 4 bonds) through an N

Lysine (Lys) (K) 3 carbon chain plus one methylene to amino,

it lies (Lys) about the 3 carbon trend

Histidine (His) (H) 3 carbons to N and loop back through C n N

Asparagine (Asn) (N)amide derivative of aspartate

Glutamine (Gln) (Q)amide derivative of glutamate

Classification of amino acids

Amino acids can be classified in 4 ways:

1.Based on structure

2.Based on the side chain characters

3.Based on nutritional requirements

4.Based on metabolic fate30Biochemistry For Medics

They are classified in three broad categories:

Mono amino mono carboxylic acid

It is further subdivided in 5 groups:

a. Simple amino acids-example: glycine, alanine

b. Branched chain amino acids-eg: valine,leucine,isoleucine

c. Hydroxyl group containing amino acids-eg: serine, threonine

d. Sulphur containing amino acids-eg: cysteine, cystine, methionine

e. Amide group containing amino acids-e.g.- asparagine, glutamine

1)Classification based on structure

Mono amino dicarboxylic acid

Example :aspartic acid, glutamic acid

Di /poly amino mono carboxylic acid

Example : lysine, arginine



I. Aliphatic Amino Acids:a) Mono-amino mono-carboxylic acids:Simple amino acids: Glycine , Alanine


I. Aliphatic Amino Acids:

a) Mono-amino mono-carboxylic acids:

Branched chain amino acids: Valine, Leucine and Isoleucine




-OH group-containing amino acids: Serine and Threonine

1)Classification based on structureI. Aliphatic Amino Acids:


Sulfur-containing amino acids: Cysteine, Cystine(Formed by linking of two cysteine residues) and Methionine.

1) Classification based on structure



Amide group-containing amino acids:

Glutamine and Asparagine



a) Mono-amino di-carboxylic acids: Aspartic acid and Glutamic acid



a) Di- basic mono-carboxylic acids: Arginine and Lysine


ii ) Aromatic amino acids-

Phenyl alanine and tyrosine

1)Classification based on structureiii) Heterocyclic Amino Acids: Tryptophan and Histidine


iv) Imino acid- Proline

Hydroxl proline


V.Derived Amino Acids:

Non--amino acidse.g.: -alanine, -amino butyric acid (GABA), -amino Levulinic acid


V.Derived Amino Acids:

Derived and Incorporated in tissue proteins:

e.g.: Hydroxy-proline, hydroxy-lysine


V. Derived Amino Acids:

Derived but not incorporated in tissue proteins:

e.g.: Ornithine, Citrulline, Homocysteine, Argino succinic acid

2) Classification based on side chain characters

A. Amino acids with a non-polar side-chain:

e.g.: Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Proline

Each of these amino acids has a side chain that does not bind or give off protons or participates in hydrogen or ionic bonds.

Side chains of these amino acids can be thought of as Oily or lipid like, a property that promotes hydrophobic interactions.

Amino acids with a non-polar side-chain:

2) Classification based on side chain charactersB) Amino acids with a polar but uncharged side-chain:

e.g. Serine, Threonine, Tyrosine, Cysteine, Asparagine and Glutamine.

These amino acids are uncharged at neutral pH,

although the side chains of cysteine and Tyrosine

can lose a proton at an alkaline pH.

Serine , Threonine and Tyrosine each contains a polar hydroxyl group that can participate in hydrogen bond formation.

Side chains of Asparagine and Glutamine

contain a carbonyl group and amide group, they can also participate in hydrogen bond formation.

Amino acids with a polar but uncharged side-chain

2) Classification based on side chain characters

C) Amino acids with a charged side-chain

a)Amino acids with a positively charged side-chain:

The basic amino acids- Lysine, Arginine and Histidine

b)Amino acids with a negatively charged side-chain:

The acidic amino acids- Glutamic acid and Aspartic acid

They are hydrophilic in nature.

Amino acids with a charged side-chain

3)- Classification based on nutritional requirementsI. Essential amino acids:

These amino acids cannot be synthesized in the body and have to be present essentially in the diet. Examples-Valine, Isoleucine, Leucine, Lysine, Methionine, Threonine, Tryptophan and Phenylalanine.

II. Semi-essential amino acids:

These amino acids can be synthesized in the body but the rate of synthesis is lesser than the requirement(e.g. during growth, repair or pregnancy) Examples-Arginine and Histidine.

III. Non-essential amino acids:

These amino acids are synthesized in the body, thus their absence in the diet does not adversely affect the growth.

Examples- Glycine, Alanine, and the other remaining amino acids.

4)-Classification based on metabolic fate

The carbon skeleton of amino acids can be used either for glucose production or for the production of ketone bodies, Based on that

I. Both glucogenic and ketogenic amino acids:

Isoleucine, Tyrosine, Phenylalanine and Tryptophan

II. Purely Ketogenic amino acids:

Leucine and Lysine

III. Purely Glucogenic amino acids:

The remaining 14 amino acids are glucogenic. Alanine, valine ,serine, threonine, glycine, methionine, asparagine, glutamine, cysteine, cystine, aspartic acid, glutamic acid, histidine and arginine.

Non standard amino acids

Of the over 300 naturally occurring amino acids, 20 constitute the monomer units of proteins. These 20 amino acids are called the Primary or Standard amino acids.

Seleno cysteine is the 21st Amino Acid

The other are Pyroglutamate and Pyrolysine.

Naming of Amino acids

Each amino acid has three letter (code) and one letter (Symbol) abbreviations-

Examples-1) Unique first letter

Cysteine- Cys- C

Histidine- His- H

2) Priority of commonly occurring amino acids

Alanine- Ala- A (Preference over Aspartate)

Glycine- Gly-G (Preference over Glutamate)

Naming of Amino acids3) Similar sounding names- Some one letter symbols sound like the amino acids they represent- Example

Tryptophan W (Twyptophan)

Phenyl alanine F

4) Letters close to initial letter

Aspartate- Asx- B( near A)

Lysine Lys- K(near L)

Amino acid abbreviations

Special groups in amino acids

Arginine - Guanidinium group

Phenyl Alanine- Benzene group

Tyrosine - Phenol group

Tryptophan - Indole group

Histidine - Imidazole group

Proline - Pyrrolidine

Proline has a secondary amino group, hence it is an imino acid.

Properties of amino acidsPhysical properties-

Colorless

Crystalline

May be sweet(Glycine, Alanine, Valine), tasteless(Leucine) or bitter(Arginine, Isoleucine). Aspartame- An artificial sweetener contains Aspartic acid and Phenyl alanine.

Soluble in water, acids, alkalis but insoluble in organic solvents

High melting point(More than 2000c)

Isoelectric pointAmino acids can exist as ampholytes or zwitterions in solution, depending upon pH of the medium.

The pH at which the amino acids exist as zwitterions, with no net charge on them is called Isoelectric pH or Isoelectric point.

In acidic medium, the amino acids exist as cations

In alkaline medium , they exist as anions.

Isoelectric point

Titration of amino acidsIf HCl is added drop wise to am amino acid solution, at a particular pH, 50 % of the molecules are in the cationic form and 50% are in the zwitterion form. This pH is pK1 (with regard to COOH)

If the titration is done from the Isoelectric point with NaOH, molecules acquire the anionic form. When 50 % of the molecules are in the anionic form and 50% are in the zwitterion form. This pH is pK2(with regard to NH2)

Titration of GlycineFor mono amino mono carboxylic amino acids-pI = pK1+pK2

-------------

2

The buffering action is maximum in and around pK1 or at pK2 but is minimum at pI

pKa of some amino acids

Optical properties of amino acidsThe carbon of each amino acid is attached to four different groups and is thus a chiral or optically active carbon atom.

Glycine is exceptional because there are two hydrogen substituents at the carbon, thus it is optically inactive.

Amino acids with asymmetric centre at the carbon can exist in two forms, D and L forms that are mirror images of each other and are called Enantiomers.

All amino acids found in proteins are of L- configuration

D- amino acids are found in some antibiotics and in bacterial cell walls.

7/5/2012 Biochemistry For Medics 66

L & D isomers of amino acids

Reactions of amino acids

1)Reactions due to amino group

2)Reactions due to carboxyl group

3)Reactions due to side chain

4)Reaction due to both amino and carboxyl

groups

Reactions due to amino groupOxidative deamination- amino group is removed and

corresponding -keto acid is formed. -keto acid produced is either converted to glucose or ketone bodies or is completely oxidized.

Transamination-Transfer of an amino group from an amino acid to an keto acid to form a new amino acid and a corresponding keto acid.

Reactions due to amino groupFormation of carbamino compound

CO2 binds to amino acid on the globin chain of hemoglobin to form carbamino hemoglobin

The reaction takes place at alkaline pH and serves as a mechanism for the transfer of Carbon dioxide from the tissues to the lungs by hemoglobin.

Reactions due to carboxyl group1) Decarboxylation- Amino acids undergo alpha decarboxylation to

form corresponding amines. Examples-

Glutamic acid GABA

Histidine Histamine

Tyrosine Tyramine

2) Formation of amide linkage

Non carboxyl group of an acidic amino acid reacts with ammonia by condensation reaction to form corresponding amides

Aspartic acid Asparagine

Glutamic acid Glutamine

Reactions due to side chains1) Ester formation

OH containing amino acids e.g. serine, threonine can form esters with phosphoric acid in the formation of phosphoproteins.

OH group containing amino acid can also form: Glycosides by forming

O- glycosidic bond with carbohydrate residues.

Reactions due to side chains 2) Reactions due to SH group (Formation of disulphide bonds)

Cysteine has a sulfhydryl group( SH) group and can form a disulphide (S-S) bond with another cysteine residue.

The dimer is called Cystine

Two cysteine residues can connect two polypeptide chains by the formation of interchain disulphide chains.

Formation of disulphide bond

Reactions due to side chains

3)TransmethylationThe methyl group of Methionine can be transferred after activation to an acceptor for the formation of important biological compounds.

4)Reactions due to both amino & carboxyl groupsFormation of peptide bond

Reactions due to side chains

Special functions of Amino acids Incorporated in to tissue proteins

Niacin, Serotonin and melatonin are synthesized from Tryptophan

Melanin, thyroid hormone, catecholamines are synthesized from Tyrosine

GABA (neurotransmitter) is synthesized from Glutamic acid

Nitric oxide, a smooth muscle relaxant is synthesized from Arginine.

Act as precursors for haem, creatine and glutathione, Porphyrins, purines and pyrimidines.

Colour reactions of amino acidsS.No. Test Significance

1) Ninhydrin reaction Given by all Alpha amino acids

2) Xanthoproteic test Given by aromatic amino acids

3) Millons test Confirmatory test for Tyrosine

4) Biuret test Not given by free amino acids

5) Sakaguchi test Given by Arginine

6) Hopkins Cole reaction Confirmatory test for Tryptophan

7) Lead acetate test Given by cysteine and cystine but not given by Methionine

8) Nitroprusside reaction Given by SH group containing 77

bch 201

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