AMINO ACIDS AND PEPTIDE BOND

MONOMERS OF PROTEINS Proteins are polymers of amino acids ( the building blocks of proteins) united through peptide

bonds.

α-amino acids There are about 300 amino acids occur in nature There are 20 commonly occurring amino acids. Most of the amino acids are alpha amino acids

STRUCTURE OF AMINO ACIDS

4 groups are attached to tetrahedral α carbon atom

1.a carboxylic acid (- COOH) functional group 2.an amino (- NH2) functional group 3.Distinct R-groups 4. Hydrogen

The amino group and the carboxyl group is attached to the same carbon atom.

STRUCTURE OF AMINO ACIDS

H2 N

Amino group

COOH Carboxyl group

C

carbon

R Side chain of specific chemical group

H Hydrogen atom

Amino Acids are Optically ActiveExcept for glycine (R = H), all AAs have 4 different groups attached to the -carbon atom.

The carbon is the asymmetric carbon atom and this gives rise to 2 non-superimposable mirror image forms

+

COO-…… ….. …. .. .

CH3N H

…… ….. …. .. .

R

COO-

CH NH3

…… ….. …. .. .

R

+

…… ….. …. .. .

L-Configuration D-Configuration-COO- is directed up and behind plane of slide

R is directed down and behind the plane of slide

-H and -NH3 are directed towards you

-NH3 on left = L-configuration; on right = D-configuration

At physiological pH (around 7), amino group is protonated while the carboxylic acid group is unprotonated

COO-

H3N H

R

C+

Both positive and negative charges are present,Electrically neutral

Zwitterion or dipolar ion

Degree of ionisation of both the carboxylic and amino groups depends on pH of solution

EFFECT OF PH

The pH at which the molecule carries no net charge is known as iso-electric point or iso- electric pH.

At iso-electric pH the amino acid will carry no net charge. The groups are ionized but the charges will cancel each other.

There is no mobility in an electric field.

Solubility and buffering capacity will be minimum at iso-electric pH .

In acidic solution they behave as cations and in alkaline solutions they behave as anions.

CLASSIFICATION OF AMINO ACID A. Based on structure – AA with aliphatic side chains,

AA with hydroxyl group

AA with sulphur group

Acidic amino acid

Basic amino acid

Aromatic amino acid

Imino acid B. Based on polarity – Non polar amino acid

Polar amino acid with no charge on R

Polar amino acid with positive R charge

Polar amino acid with negative R charge

C. Based on nutrition – Essential amino acid

Non essential amino acid D. Based on metabolic fate – Glycogenic Amino acid

Ketogenic amino acid

and both

BASED ON POLARITY

HYDROPHOBIC OR HYDROPHILIC CLASSES

There are 2 broad classes of amino acids based upon whether the R-group is hydrophobic or hydrophilic. The hydrophobic amino acids tend to repel the aqueous environment , reside predominantly in the interior of proteins This class of amino acids do not ionize & do not participate in the formation of H-bonds.

The hydrophilic amino acids tend to; - interact with the aqueous environment, - often involved in the formation of H-bonds and - found on the exterior surfaces proteins or in the reactive centers of enzyme

Amino acids differ in the R- group present.

Based on R-groups, amino acids are placed into 4 groups;

Group 1 – Amino acids with Nonpolar Side Chains

Group 2 – Amino acids with Polar Side Chains (Neutral)

Group 3 – Amino acids with Acidic Side Chains

Group 4 – Amino acids with Basic Side Chains

GROUP 1

Amino acids with Non-polar Side Chains (hydrophobic)Nonpolar side chains does not bind or give off protons or does not participate in H or ionic bonds, Promotes lipid-like interaction

Glycine Alanine Valine Leucine Total =9 Isoleucine Phenylalanine Methionine Tryptophan Proline (imino group)

Group 1 – Amino acids with Nonpolar Side Chains

GROUP 2 – AMINO ACIDS WITH POLAR SIDE CHAINS

(“Electrically Neutral” = Uncharged at neutral pH)The polar OH gp of tyrosine, serine, threonine can

participate in H bonds.The CO & amide gp of Aspn & Glun – can form H bond

Serine Threonine Tyrosine Total =6 Cysteine Glutamine Asparagine

Group 2 – Amino acids with Polar Side Chains- Neutral (Hydrophilic)

Group 3 – Amino acids with Acidic Side Chains

Aspartate

Glutamate

Group 4 – Amino acids with Basic Side Chains

BASED ON STRUCTURE

ALIPHATIC (ALKANE) AMINO ACIDS

•Glycine(gly, G)-only non-chiral amino acid, not hydrophobic

•Alanine (ala, A) – R-group = methyl-group

•Valine (Val, V) –Think V!

•Leucine (Leu, L) –

•Isoleucine (Ile, I) -2 chiral carbons

Hyd

rop

hobic

ity

AMINO ACIDS CONTAINING HYDROXYL GROUP

Serine

Threonine

AROMATIC AMINO ACIDS All very hydrophobic All contain aromatic group Absorb UV at 280 nm Phenylalanine (Phe, F) Tyrosine (Tyr, Y) – -OH ionizable (pKa = 10.5), H-

Bonding Tryptophan (Trp, W) – bicyclic indole ring, H-Bonding

SULFUR CONTAINING AMINO ACIDS

Methionine (Met, M) – “start” amino acid, very hydrophobic

Cysteine (Cys, C) – sulfur in form of sulfhydroyl, important in disulfide linkages, weak acid, can form hydrogen bonds.

• Contain carboxyl groups (weaker acids than a-carboxyl-group)

• Negatively charged at physiological pH, present as conjugate bases (therefore –ate not –ic acids)

• Carboxyl groups function as nucleophiles in some enzymatic reactions

• Aspartate –

• Glutamate –

ACIDIC AMINO ACIDS

BASIC AMINO ACIDS

Hydrophillic nitrogenous basesContain two or more NH2 groups or nitrogen atoms that act

as base i.e. can bind proton. Positively charged at physiological pH Histidine – imidazole ring protonated/ionized, only amino

acid that functions as buffer in physiol range. Lysine - diamino acid, protonated at pH 7.0 Arginine - guianidinium ion always protonated, most

basic amino acid

IMINO ACID Proline (pro, P)- cyclic “imino acid” In proline, amino group enters in the ring formation

being α-imino gp so proline is an α-imino acid rather than α-amino acid

ESSENTIAL/NON-ESSENTIAL AMINO ACIDS

Essential –histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine

Non-essential – alanine, arginine*, aspartate, asparagine, cysteine*, glutamate, glutamine, glycine*, proline*, serine, tyrosine*

Nutritional classification:

1- Essential amino acids: These amino acids can’t be formed in the body and so, it is essential to be taken in diet. Their deficiency affects growth, health and protein synthesis.

2- Semiessential amino acids: These are formed in the body but not in sufficient amount for body requirements especially in children.

Summary of essential and semiessential amino acids:

Villa HM = Ten Thousands Pound

V= valine i= isoleucine l= lysine l= leucine

A = arginine* H= histidine* M= methionine

T= tryptophan Th= threonine P= phenyl alanine

*= arginine and histidine are semiessential

3- Non essential amino acids: These are the rest of amino acids that are formed in the body in amount enough for adults and children. They are the remaining 10 amino acids.

Metabolic classification: according to metabolic or degradation products of amino acids they may be:

1- Ketogenic amino acids: which give ketone bodies . Lysine and Leucine are the only pure ketogenic amino acids.

2- Mixed ketogenic and glucogenic amino acids: which give both ketonbodies and glucose.These are: isoleucine, phenyl alanine, tyrosine and tryptophan.

3- Glucogenic amino acids: Which give glucose. They include the rest of amino acids. These amino acids by catabolism yields products that enter in glycogen and glucose formation.

Amphoteric properties of amino acids: that is they have both basic and acidic groups and so can act as base or acid.Neutral amino acids (monobasic, monocarboxylic) exist in aqueous solution as “ Zwitter ion” i.e. contain both positive and negative charge. Zwitter ion is electrically neutral and can’t migrate into electric field. Isoelectric point (IEP) = is the pH at which the zwitter ion is formed. e.g IEP of alanine is 6

Chemical properties of amino acids:1- Reactions due to COOH group: -Salt formation with alkalis, ester formation with alcohols, amide formation with amines and decarboxylation

-2- Reactions due toNH2 group: deamination and reaction with ninhydrin reagent.-Ninhydrin reagent reacts with amino group of amino acid yielding blue colored product. The intensity of blue color indicates quantity of amino acids present.

Ninhydrine can react with imino acids as proline and hydroxy proline but gives yellow color.

3- Reactions due to side chain (R):

1- Millon reaction: for tyrosine gives red colored mass

2- Rosenheim reaction: for trptophan and gives violet ring.

3- Pauly reaction: for imidazole ring of histidine: gives yellow to reddish product

4- Sakagushi test: for guanido group of arginine andgives red color.

5- Lead sulfide test (sulfur test): for sulfur containing amino acids as cysteine give brown color.

Non-standard (Non-canonical) amino acids: These are produced by post-translational modification, and not genetically coded, except selenocystein (Sec), which is now accepted as the 21st amino acids.

Amino Acid useful as drugD-amino acids are found in a few small peptides, including some peptides of bacterial cell walls and certain antibiotics (such as penicillin).

D-GluD-Ala

Alexander Fleming discovers penicillin:

Penicillin binds at the active site of the transpeptidase enzyme that cleaves D-Ala-D-Ala and thus cross-links the peptidoglycan strands of the bacterial cell wall. Penicillin binds the enzyme by mimicking the D-Ala-D-Ala residues that would normally bind to this site. Therefore, the bacterial cell wall loses integrity and is susceptible to host defences, or simply bursts.

THE PEPTIDE BOND

Proteins are linear polymers composed of amino acids linked together by peptide bonds.

These 20 amino acids are linked together through “peptide bond forming peptides and proteins (what’s the difference?).

- The chains containing less than 50 amino acids are called “peptides”, while those containing greater than 50 amino acids are called “proteins”.

Peptide bond is formed by the condensation of the carboxyl group of one amino acid and the amino group of the second amino acid with the elimination of water.

2 Amino acids – Dipeptide. 3 Amino acids –Tripeptide 4-10 Amino acids –Oligopeptide >50 amino acids --Protein

NUMBERING OF AMINO ACIDS IN PROTEINS

In polypeptide chain at one end [left end] there will be one free alpha amino group [ N-terminal] contributed by the 1st amino acid.

The other end [right end] has a free carboxyl group[ C- terminal] and this is contributed by the last amino acid.

All the other amino and carboxyl groups are involved in peptide formation.

Numbering of amino acids is from the Amino terminal to carboxyl terminal.

CHARACTERISTICS OF A PEPTIDE BOND

The peptide bond is a partial double bond. The C-N bond is trans in nature and there is no

freedom of rotation because of the partial double bond character.

The side chains are free to rotate on either side of the peptide bond.

The angles of rotation determine the spatial

orientation of the peptide chain.

Examples on Peptides: 1- Dipeptide ( two amino acids joined by one peptide bond):Example: Aspartame which acts as sweetening agent being used in replacement of cane sugar. It is composed of aspartic acid and phenyl alanine.

2- Tripeptides ( 3 amino acids linked by two peptide bonds).Example: GSH which is formed from 3 amino acids: glutamic acid, cysteine and glycine. It helps in absorption of amino acids, protects against hemolysis of RBC by breaking H2O2 which causes cell damage.

3- octapeptides: (8 amino acids)Examples: Two hormones; oxytocine and vasopressin (ADH).

4- polypeptides: 10- 50 amino acids: e.g. Insulin hormone

• A variety of methods have been developed• Important in industry due to the commercial

relevance bodybuilding supplements (for big musles) sources of vitamins not only for human also for

animals

Synthesis of -amino acids