AMINO ACIDS

• Amino Acids are the chemical units or "building blocks" of the body that make up proteins. Protein substances make up the muscles, tendons, organs, glands, nails, and hair. Growth, repair and maintenance of all cells are dependent upon them. Next to water, protein makes up the greatest portion of our body weight. Amino Acids that must be obtained from the diet are called "Essential Amino Acids" other Amino Acids that the body can manufacture from other sources are called "Non-Essential Amino Acids."

• Of the 20 standard proteinogenic amino acids, 10 are called essential amino acids because the human body cannot synthesize them from other compounds at the level needed for normal growth, so they must be obtained from food. However, the situation is a little more complicated since cysteine, tyrosine, histidine and argenine are semi-essential amino acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed. The amounts required also depend on the age and health of the individual, so it is hard to make general statements about the dietary requirement for some amino acids.

Peptides

• Two individual amino acids can be linked to form a larger molecule, with the loss of a water molecule as a by-product of the reaction.

• The newly created C-N bond between the two separate amino acids is called a peptide bond. The term 'peptide bond' implies the existence of the peptide group which is commonly written in text as -CONH-

• Two molecules linked by a peptide bond become what is called a dipeptide. A chain of molecules linked by peptide bonds is called a polypeptide

• A protein is made up of one or more polypeptide chains, each of which consists of amino acids which have been mentioned earlier.

Peptide Bond

Polypeptide Bond

• Instead of writing out complex formulae, sequences of amino acids are commonly written using the previously mentioned three- or one-letter codes eg. ala-gly-val-leu-phe (3 letter) or AGVLF (1 letter).

The format of the list is: amino acid name - 3 letter code - 1 letter code

(reference to gif image, reference to interactive molecule)

• Amino Acid  3-Letter  1-Letter 

• Alanine Ala A• Arginine Arg R• Asparagine Asn N• Aspartic acid Asp D• Cysteine Cys C• Glutamic acid Glu E• Glutamine Gln Q• Glycine Gly G• Histidine His H• Isoleucine Ile I

• Side chain polarity  Side chain acidity or basicity  

• Nonpolar neutral• Polar basic (strongly)• Polar neutral• Polar acidic• Nonpolar neutral• Polar acidic• Polar neutral• Nonpolar neutral• Polar basic (weakly)• Nonpolar neutral

• Amino Acid   3-Letter   1-Letter   Side chain polarity   Side chain acidity or basicity  

• Leucine Leu L nonpolar neutral• Lysine Lys K polar basic• Methionine Met M nonpolar neutral• PhenylalaninePhe F nonpolar neutral• Proline Pro P nonpolar neutral• Serine Ser S polar neutral• Threonine Thr T polar neutral• Tryptophan Trp W nonpolar neutral• Tyrosine Tyr Y polar neutral• Valine Val V nonpolar neutral

• Sometimes it is not possible two differentiate two closely related amino acids, therefore we have the special cases:

• asparagine/aspartic acid - asx - B • glutamine/glutamic acid - glx - Z

Amino Acids in normal and zwitter ion form

Here is list where amino acids are grouped according to the

characteristics of the side chains: • Aliphatic - alanine, glycine , isoleucine, leucine,

proline, valine • Aromatic - phenylalanine, tryptophan , tyrosine • Acidic - aspartic acid , glutamic acid • Basic - arginine , histidine , lysine • Hydroxylic - serine , threonine • Sulphur-containing - cysteine, methionine • Amidic (containing amide group) –

asparagine, glutamine

Amino Acid 3- & 1- letter codes Side Chain • alanine ala A -CH3 • arginine arg R -CH2-CH2-CH2-NH-C=NH2

NH2

• asparagine asn N -CH2-CO-NH2

• aspartic acid asp D -CH2-COO • cysteine cys C -CH2-SH • glutamine gln Q -CH2-CH2-CO-NH2

• glutamic acid glu E -CH2-CH2-COOH • glycine gly G -H • histidine his H -CH2-C = CH

+N=C-NH H

• isoleucine ile I -CH-CH2-CH3

CH3 • leucine leu L -CH2-CH-CH3

CH3

• lysine lys K -CH2-CH2-CH2-NH3 • methionine met M -CH2-CH2-S-CH3 • phenylalanine phe F -CH2-Ph • proline pro P -CH2-CH2-CH2-

(the terminus is bonded to the main chain amine nitrogen to form a ring)

• serine ser S -CH2-OH• threonine thr T -CH-CH3

OH

• tryptophan trp W -CH2-C = CH Ph -NH (the phenyl group is

bonded at carbons 1 and 2 ie 'ortho' positions)

• tyrosine tyr T (the phenyl group is bonded at carbons 1 and 4 ie 'para' positions)

• valine val V -CH2-CH3

CH3