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Amino Acids

Amino Acids

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• Amino acid:Amino acid: a compound that contains an amino group, a carboxyl group and a side-chain that is specific to each amino acid.

• -Amino acid-Amino acid:: an amino acid in which the amino group is on the carbon adjacent to the carboxyl group

• The are 20 common α-amino acids used by the ribosomes to make proteins. These 20 have L chirality at the α-carbon.

• The building blocks of proteins• 20 amino acids are naturally incorporated into polypeptides

and are called proteinogenic or standard amino acids. These 20 are encoded by universal genetic code.

• 10 standard amino acids (Lys, Met, His, Leu, Ile, Thr, , Try, Phe, Val & Arg) are called "essential" for humans because they cannot be created from other compounds by the human body, and so must be taken in as food.

• From these building blocks different organisms can make such widely diverse products as enzymes, hormones, antibodies, antibiotics, and a myriad of other substances having distinct biological activities.

• Also used as single molecules in biochemical pathways

Chemistry of Amino Acids R side chain

| H2N— C —COOH

|H

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Chemistry of Amino Acids

• Two functional groups: –carboxylic acid group –amino group on the alpha () carbon

• Have different side groups (R) –Properties dictate behavior of AAs

Stereochemistry of AAs• All amino acids (except glycine) are optically active (chiral)

2 forms of enantiomers/stereoisomers• d = dextrorotatory ,dextro means right• l = levorotatory, levo means left• D, L = relative to glyceraldehyde

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Amino acids join together via peptide bonds

Two amino acids can react with loss of a water molecule to form a covalent bond.

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• Chain of amino acids = peptide or protein

Amide linkage is planar NH and CO are anti

Classification of Amino Acids

Classification based on side-chain structure:– Non-polar amino acids.

– Polar, uncharged amino acids.

– Acidic amino acids.

– Basic amino acids.

Other side chain structural classifications:

– Aromatic, cyclic, hydroxyl, and thiol amino acids.7

Nonpolar side chains (predominant form at pH 7.0)

H-

CH3-

CH3CH2CH(CH3)-

(CH3)2CHCH2-

CH3SCH2CH2-

NH

(CH3)2CH

glycine (gly, G)

alanine (ala, A)

valine (val, V)

leucine (leu, L)

isoleucine (ile, I)

methionine (met, M)

phenylalanine (phe, F)

tryptophan (trp, W)

NH H

+proline (Pro, P)

Classification of Amino Acids

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R =

Polar side chains (predominant form at pH 7.0)asparagine (asn, N)

glutamine (glu, G)

serine (ser, S)

threonine (thr, T)

H2NCCH2-O

H2NCCH2CH2-O

HOCH2-

CH3CH-OH

Nonpolar side chains (predominant form at pH 7.0)

H-

CH3-

CH3CH2CH(CH3)-

(CH3)2CHCH2-

CH3SCH2CH2-

NH

(CH3)2CH

glycine (gly, G)

alanine (ala, A)

valine (val, V)

leucine (leu, L)

isoleucine (ile, I)

methionine (met, M)

phenylalanine (phe, F)

tryptophan (trp, W)

NH H

+proline (Pro, P)

Nonpolar side chains (predominant form at pH 7.0)

H-

CH3-

CH3CH2CH(CH3) -

(CH3)2CHCH2-

CH3SCH2CH2-

NH

(CH3)2CH

glycine (gly, G)

alanine (ala, A)

valine (val, V)

leucine (leu, L)

isoleucine (ile, I)

methionine (met, M)

phenylalanine (phe, F)

tryptophan (trp, W)

NH H

+proline (Pro, P)

Acidic side chains (predominant form at pH 7.0)

aspartic acid (asp, D) glutamic acid (glu, E)

cysteine (cys, C) tyrosine (tyr, Y)

-OCCH2-

HSCH2-

-OCCH2CH2-

HO CH2-

O O

Classification of Amino Acids

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Basic side chains (predominant form at pH 7.0)

arginine (arg, R) histidine (his, H)

lysine (lys, K)

H2NCNHCH2CH2CH2-NH2

+

H3NCH2CH2CH2CH2-

N

NH

CH2-

+

Essential Amino Acids• An essential amino acid is an amino acid that cannot be synthesized

itself by the organism (usually referring to humans), and therefore must be supplied in the diet.

• 10 amino acids are essential amino acid• They are - arg, his, ile, leu, lys, met, phe, thr, trp, val• Must obtain from the diet• An adequate diet must contain these essential amino acids.

Typically, they are supplied by meat and dairy products• Essential amino acids help the body function and regulate

neurotransmitters, chemicals in the brain that control mood and behavior.

• A lack of essential amino acids can cause emotional or physical difficulties and lead to health disorder

List of Essential& Nonessential Amino Acid

Essential NonessentialHistidine Alanine

Isoleucine AspartateLeucine CysteineLysine Glutamate

Methionine GlutaminePhenylalanine Glycine

Threonine ProlineTryptophan Serine

Valine TyrosineArginine Asparagine

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• Although -amino acids are commonly written in the unionized form, they are more properly written in the zwitterion (internal salt) form (Germ. Zwitter means hybrid)

• Both the –NH2 and the –COOH groups in an amino acid undergo ionization in water.

• At physiological pH (7.4), a zwitterion forms – Both + and – charges– Overall neutral– Amphoteric

• Amino group is protonated• Carboxyl group is deprotonated• Soluble in polar solvents due to ionic character

Zwitterions

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Acid-Base Properties of Amino Acids

Figure : The ionic forms of the amino acids.

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Reactions of amino acids

1- Reactions due to COOH group: - Salt formation with alkalis, ester formation with alcohols, amide

formation with amines and decarboxylation2- Reactions due to NH2 group: Deamination & reaction with ninhydrin Ninhydrin reagent reacts with amino group of amino acid yielding

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

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R CO2

H3N H H3C O CH3

O O

base R CO2H

HN HO

H3C

HOCH2CH3

H+R CO2CH2CH3

H2N H

Amino acids will undergo reactions characteristic of the amino (amide formation) and carboxylic acid (ester formation) groups.

Detecting Amino Acids

Ninhydrin is the classical reagent for detecting amino acids. Reaction requires 2-5 min at 100oC and is sensitive at the nanomole level.

Ruhemann’s Purple570 nm

OH

O

O

OHNH2-CH-COOH

CH3

+

O

O

O

O

NCO2CH3

CHO+ +2

Note: The product from Pro isYellow and absorbs at 440 nm.

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Peptides and Proteins

•20 amino acids are commonly found in protein.

•These 20 amino acids are linked together through “peptide bond forming peptides and proteins.

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

Peptide bond formation: Peptide bondPeptide bond is the is the amide bond between the -carboxyl group of one amino acid and the -amino group of another

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Peptide bond

The trans conformation of the peptide bond.

Peptides and ProteinsPeptide: a short polymer of amino acids joined by peptide bonds;

they are classified by the number of amino acids in the chain

– dipeptide: a molecule containing two amino acids joined by a peptide bond

– tripeptide: a molecule containing three amino acids joined by peptide bonds

– 12-20 residues (Each unit/AA) – oligopeptide.– polypeptide: a macromolecule containing many amino acids

Linear polymers (no branches)AA monomers linked head to tail through formation of peptide

bonds– protein: a biological macromolecule of molecular weight 5000

g/mol or greater, consisting of one or more polypeptide chains19

The Amide Bond

H2N R'+R COOH R

O

HN

R-H20

• Basic amide synthesis is the reaction of a carboxylic acid and an amine with the loss of water.

• Some of the main properties of the amide bond is it’s low basicity, which is useful in purification, and it’s stability, due to resonance.

• Since the free electrons of the N atom are tied up in forming partial (≈ 40%) double bond, N atom can not accept a proton (H+).

• This N also has a partial positive charge which will repel protons and prevent them from binding to the nitrogen (thus no ionization).

R CO

NH2

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• The synthesis of a specific dipeptide such as Ala-Gly from alanine and glycine is complicated because both amino acids have two functional groups.

• As a result, four products—namely, Ala-Ala, Ala-Gly, Gly-Gly and Gly-Ala—are possible.

Peptide Synthesis

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The method can be applied to synthesis of tripeptides and even larger peptides.

Peptide Synthesis

Analysis of the amino acid sequence

• Determine number of polypeptide chains (subunits)• Determine number of disulfide bonds (inter- and intra

chain)• Determine the amino acid composition of each polypeptide

chain• If subunits are too large, fragment them into shorter

polypeptide chains• Determine the amino acid sequence of each fragment using

the Edman degradation method

End-group Analysis

• Number of chains can be determine by identifying the number of N- and C-terminal.• N-terminal analysis – Dansyl chloride – Phenylisothiocynate (PITC)/ Edman reagent – Aminopeptidase

• C-terminal analysis – carboxypeptidase