08.01.19 - Amino acids - Lecture notes 1 PDF

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BMD 123 – Biomolecules of life

Amino acids Chemical composition of a bacteria cell 

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A cell may contain approx. 1000 different cell types of small organic molecules o DNA o RNA o Proteins o Polysaccharides o Phospholipids o Ions But many of these can be classified into 4 families Four main families of small organic monomeric building blocks for the formation of biological macromolecules o Sugars – o Fatty acids o Amino acids – proteins o Nucleotides – DNA Monomers may also have distinctive functions: o Sugars and fatty acids: energy source o Nucleotide (ATP): energy carrier

Amino acids 

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Consist of: o A chiral alpha carbon o Amino group (NH2)/NH3+) o Carboxylate group (COOJ/COO-) o Hydrogen atom o R group They are the building blocks of proteins 20 amino acids found in proteins, but other non-protein amino acids are found in all organisms

Representations of amino acid structure What are amino acids   

At neutral pH exists as dipolar ions Known as zwitterions – found at isoelectric points Amino group is protonated, and carboxylate 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 pH is between 7-7.8

BMD 123 – Biomolecules of life 

Acidosis – normal range – alkalosis

What is pH  pH is the measure of hydrogen ions concentration (acidity or alkalinity of a solution)  Higher pH – lose protons  Lower pH – gains protons First important concept:  Acidity depends only on the free hydrogen ions, not those bound to the anions

Ionisation of water  

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Pure water is a 55.6M solution Water dissociates to a very small extent o H2O  H+ + OH-  H2O o Keq = 1.8 x 10-16 o [H+] x [OH-] = 10-14 M2 o Ionic product of water o At neutrality, [H=] = [OH-] = 10-7 M pH = - log [H+] o At neutrality when [H+] = [OH-] o [H+] = 10-7 M o pH = – log [10-7] o pH = - (-7) = 7 o o

when [H+] = 10 -2 M pH is 2

o o

when [H+] is 10-2, then [OH-] is 10-12 when [H+] is 10-4, then [OH-] is 10-10

pKa     

acid dissociation constant 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 pKa = log Ka

Amino acids are zwitterions at physiological pH

BMD 123 – Biomolecules of life

What are amino acids?    

The alpha carbon in amino acid is chiral Amino acids can exist in two forms that are mirror images of each other (“optically 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 the 20 amino acids found in proteins Chemical neater of R group determines the properties of the amino acid R groups vary in: o Size o Shape o Charge o Hydrogen bonding capacity o Hydrophobicity o Chemical reactivity

Amino acids can be grouped according to the characteristics of their side chains

Polar – Interact with water water well

BMD 123 – Biomolecules of life Non-charged – don’t react with water v well – hydrophobic

Glycine  

Smallest amino acid R group is a hydrogen atom

Glycine, alanine, Valine, Leucine, and Methionine    

Isoleucine

All have aliphatic R groups increasing in 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 thio-ether (-S-) group which contains a Sulphur atom.

Proline    

Has a cyclic aliphatic R group Unique in that the R group is bonded to amino acid group and alpha carbon More structurally restricted Often flounder in bends in proteins

Phenylalanine, tyrosine and tryptophan     

Aromatic amino acids Contain a phenyl ring All hydrophobic Tyrosine and tryptophan have some hydrophilic properties due to -OH and -NH groups respectively -OH group in tyrosine is quite reactive

BMD 123 – Biomolecules of life

Serine and threonine    

Like alanine and valine -OH groups makes them hydrophilic (usually round on the outside of proteins) -OH also very reactive

Cysteine   

Like serine Contains reactive thiol group (-SH) Pairs of thiol groups come together to form disulphide bonds

Lysine and arginine  

Basic amino acids Contain side chains that are positively charged at neutral pH

Histidine    

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

BMD 123 – Biomolecules of life

Histidine is an important pH buffer in blood  The pKa of histidine in haemoglobin is different from that of free histidine  Neighbouring groups therefore affect the pKa value  Oxy-haemoglobin pKa = 6.8  Deoxy-haemoglobin pKa = 7.8

Aspartic acid and glutamic acid    

Acidic amino acids Sometimes called aspartate and glutamate Negatively charged at physiological pH Have carboxylate groups (-COOH) at end side of the chain

Asparagine and glutamine  

Uncharged derivatives of aspartate and glutamate NH2 group replaces O- in carboxylate group

Amino acids with ionisable side chains

Amino acid nomenclature 3 forms of nomenclature  Full name – Glycine  3 letter codes – Gly  1 letter – G

BMD 123 – Biomolecules of life

In polypeptides (proteins), amino acids are linked by peptide bonds  

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