Amino Acids - Lecture notes 1 PDF

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8/1/19

BMD123 - Biomolecules of life

Amino Acids Chemical composition of bacterial cell:! - A cell may contain about 1000 different types of small organic molecules! - But many of these can be classified into 4 families !

- Four main families of small organic molecules form monomeric building blocks for the formation

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of biological macromolecules! - Sugar! - Fatty acids ! - Amino acids! - Nucleotides! Monomers may also have distinct functions:! - Sugars and fatty acids: energy source! - Nucleotide (ATP): energy carrier!

What are amino acids?! - Consist of ! - An chiral α Carbon! - Amino group (NH2/NH3+)!

- Carboxyl group (COOH/COO-)! - Hydrogen atom! - R group !

- Building blocks of proteins ! - 20 amino acids found in proteins, but other non-protein amino acids are found in all -

organisms! At neutral pH, they exist as dipolar ions ! - ‘Zwitterions’! Amino acid is protonated and carboxyl group is de-protonated!

Blood pH:! - Blood is in contact with nearly every body cell! - Regulation of its pH is particularly critical ! - Normally, blood pH varies within a very narrow range (7.35 to 7.45)! - If blood pH varies from these limits, it may be fatal! - Living range: pH 7.0 - 7.8! - Below pH 7.0: Acidosis ! - Above pH 7.8: Alkalosis!

BMD123 - Biomolecules of life

8/1/19

What is pH?! - pH is a measure of Hydrogen ion concentration (acidity or alkalinity of a solution)! - First important concept:! - Acidity depends only on the free hydrogen ions, not those still bound to anions ! - Polar: an uneven distribution of electron density such as water, which the oxygen has a partial negative charge and the hydrogens which have a partial positive charge.!

Ionisation of water:! - Pure water is a 55.6M solution! - Water dissociates to a very small extent! - H2O → H+ + OH- → H2O! - Keq = 1.8 x 10-16 ! - [H+] x [OH-] = 10-14 M2! - Ionic product of water! - At neutrality, [H+] = [OH-] = 10-7 M! - pH = -log[H+]! - At neutrality when [H+] = [OH-]! - [H+] = 10-7 M! - pH = -log[10-7]! - pH = -(-7) = 7! - When [H+] = 10-2 M! - pH is 2! - When [H+] is 10-2 , then [OH-] is 10-12! - When [H+] is 10-4 , then [OH-] is 10-10! pKa:! - What is pKa?! - pKa = -log[pKa]! - Ka is the acid dissociation constant! - It is the pH at which the acid is half dissociated ! - There are equal amounts of undissociated acid and its conjugate base! - The lower the pKa, the stronger the acid! ! Amino acids are zwitterions at physiological pH?:!

BMD123 - Biomolecules of life

8/1/19

What are amino acids?! - The α Carbon in amino acids is chiral ! - Amino acids can exist in two forms that are mirror images of each other (‘optical active pairs’)! - Called L and D isomers! - Only the L-isomer forms of amino acids are found in proteins !

R groups in amino acids:! - 20 different R groups define 20 amino acids found in proteins ! - Chemical nature of R group determines the properties of the amino acid! - Size! - Shape! - Charge! - Hydrogen bonding capacity ! - Hydrophobicity ! - Chemical reactivity! - Amino acids can be grouped according to the characteristics of their side chain:!

Glycine:! - Smallest amino acid ! - R group is a hydrogen atom ! Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine:!

- All have aliphatic R groups of increasing size! - The longer the aliphatic chain, the more hydrophobic the amino acid! - Hydrophobic amino acids are often found on the inside of proteins away from the aqueous cellular environment !

- Methionine contains a thither (-S-) group which contains a Sulphur atom!

BMD123 - Biomolecules of life ! Proline:! - Has a cyclic aliphatic R group ! - Unique in that R group is bonded to amino group α Carbon! - More structurally restricted! - Often found in bends in proteins ! Phenylalanine, Tyrosine, Tryptophan:! - So called Aromatic amino acids ! - All contain a phenyl ring! - All hydrophobic ! - Tyrosine and Tryptophan have some hydrophilic properties due to -OH and -NHgroups respectively ! - -OH group in Tyrosine quite reactive !

Serine and Threonine:! - Similar to Alanine and Valine! - -OH groups makes them hydrophilic (usually found on outside of proteins)! - -OH also very reactive!

Cysteine:! - Similar to Serine! - Contains reactive thiol group (-SH)! - Pairs of thiol groups come together to form disulphide bonds!

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BMD123 - Biomolecules of life Lysine and Arginine:! - Basic amino acids! - Contain side chains that are positively charged at neutral pH!

Histidine:! - Also a basic amino acid! - Contains imidazole ring! - Has pKa of 6 so can be charged or uncharged at pH near to neutral ! - Often found at active site of enzymes where it can bind and release protons!

Histidine is an important pH buffer in blood:! - The pKa of histidine in Hb is different from that of free His! - Neighbouring groups affect the pKa ! - Oxyhaemoglobin pKa = 6.8! - Deoxyhaemoglobin pKa = 7.8! Aspartic Acid and Glutamic Acid:! - Acidic amino acids! - Sometimes called Aspartate and Glutamate ! - Negatively charged at physiological pH! - Have carboxyl groups (-COOH) at end of side chain !

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BMD123 - Biomolecules of life

8/1/19

! Aspargine and Glutamine:! - Uncharged derivatives of Aspartate and Glutamate ! - NH2 group replaces O- in carboxyl group !

! Amino acids with ionisable side chains:!

Amino acid nomenclature:! - 3 forms of nomenclature ! - Full name e.g. Glycine ! - 3 letter code e.g. Gly! - 1 letter e.g. G! - Abbreviations are mostly obvious with some exceptions!

- In polypeptides (proteins), amino acids are linked by peptide bonds ! - Carboxyl group on one amino acid combines with amino group on adjacent amino acid!

- Side chains (R groups) are not involved in peptide bonding! - Interactions of side chains determine protein folding !...