BCM 251 NOTES
CHAPTER 3.1 – AMINO ACIDS
PROTEINS AND AMINO ACIDS’ FACTS
PROTEINS
‐ Proteins serve as the basic structural molecules of all tissues in the body
‐ Proteins make up nearly 17% of the total body weight
‐ 90-140 million molecules of proteins per one yeast cell
‐ Up to 1010 proteins per mammalian cell
AMINO ACIDS
‐ Amino acids are the fundamental building blocks of proteins
‐ Long linear chains of amino acids (polypeptides) make up proteins and determine their
structure, all their properties and the functions
‐ Amino acids consist of the following: carbon, hydrogen, oxygen, nitrogen and sometimes
sulfur
RESIDUES
‐ In proteins, each amino acid residue joined to its neighbour by a specific type of covalent
bond termed peptide bond
‐ Residue – loss of the elements of water when one amino acid is joined to another
AMINO ACID STRUCTURE
‐ general structure of amino acids consists of a carbon centre termed an 𝛼-carbon atom and 4
substituents linked to this atom
‐ 4 substituents:
• One amino group (NH2 → NH3+)
• Carboxyl group (COOH → COO-)
• Hydrogen atom (H)
• R-group (side radical)
‐ R group determines the structural identity and chemical properties of
individual amino acids
‐ The first 3 groups are common o all amino acids
‐ Basic amino acid structure is R-CH(NH2)-COOH → NH3+-RCH-COO-
Photos adapted from lecture slides A.THERON
,PROPERTIES OF AMINO ACIDS
PROPERTIES OF AMINO ACIDS DUE TO CARBOXYL GROUP
‐ Salt formation
• Amino acids are organic acids and may create salts with many cations:
‐ Reaction with alcohols (esterification)
‐ Reaction with amines to form amides
‐ Decarboxylation
• Amino acids may undergo alpha decarboxylation to form the corresponding amines
• This way many NB amines are produced from amino acids in living organisms
➢ Histidine → Histamine + CO2 (local immune response)
➢ Tyrosine → Tyramine + CO2 (role in blood-brain barrier)
➢ Tryptophan → Tryptamine + CO2 (neurotransmitter)
➢ Glutamic acid → 𝛾-amino butyric acid (GABA) + CO2 (neurotransmitter)
➢ Lysine → Cadaverine + CO2 (toxin)
PROPERTIES OF AMINO ACIDS DUE TO AMINO GROUP
‐ Reaction with mineral acids
‐ Reaction with benzaldehyde
• Schiff’s base formation is an intermediate step of the reaction of transamination –
important part of the biosynthesis of amino acids
Photos adapted from lecture slides A.THERON
, ‐ Sangers’ reaction
• Reaction with Sanger’s reagent produces a yellow-coloured derivative, DNB-amino
acid
• This reaction is used to detect amino acid concentrations, free N-terminal amino
acids in polypeptides and can be helpful in protein sequencing
• AA-NH2 + Sanger’s reagent = DNB + HF → REMEMBER THIS AND PRACTICAL USE OF
IT
PROPERTIES DUE TO AMINO GROUP AND CARBOXYL GROUP
‐ Peptide bonding
‐ Ninhydrin reaction
• Oxidative decarboxylation of 𝛼-amino acids
• Oxidised ninhydrin creates with the liberated NH3 a blue-coloured Rhumann’s
complex
• Very sensitive reaction used in analytic chemistry for detection of amino acids
• Remember application of this reaction
‐ Zwitterions
• The name “zwitter” is derived from German word “hybrid”
• Zwitterion (or) dipolar ion is a hybrid molecule containing positive and negative ionic
groups with no overall charge equal to zero
Photos adapted from lecture slides A.THERON
, • One proton is transferred from the carboxyl group to the amino group of self-
molecules at normal pH cellular levels
CHIRALITY OF AMINO ACIDS
‐ Optical properties
• All amino acids except Glycine possess optical isomers due to the presence of the
asymmetric 𝛼-carbon atoms
STEREOCHEMISTRY OF AMINO ACIDS
‐ In many cases – mirror images can be superimposed over the original by rotation
‐ Achiral objects – are superimposable on their mirror images
‐ Chiral objects – are not superimposable on their mirror images
‐ A chiral C-atom (chiral centre) in molecules is attached to 4 different groups
‐ Stereoisomers – molecules that differ from each other only by their 3D configuration
(optical isomer)
‐ Enantiomer – pairs of stereoisomers, which can be superimposed by a mirror reflection
‐ One chiral centre renders 2 optical stereoisomers, which are mirror reflections of one
another
‐ Maximum number of stereoisomers for a molecule: 2n (n = number of chiral centres)
‐ Total number of enantiomers: 2n/2 (n = number of chiral centres)
‐ Majority of natural amino acids, except Glycine, Isoleucine and Threonine – are enantiomers
and have L- and D- stereoisomers
‐ 𝛼-Carbon of all amino acids except Glycine is a chiral centre rendering a pair of enantiomers
(L- and D- stereoisomers)
‐ All amino acids found in proteins are L- stereoisomers
‐ D-amino acids may be found in several natural products synthesised by non-ribosomal
polypeptide synthetases (NRPS) and in cell wall of bacteria
‐ Solid wedge = out of paper plane
‐ Dashed wedge = behind
‐ Horizontal bonds = out of paper plane
‐ Vertical = behind
‐ Special nomenclature proposed by Fisher to specify the absolute configuration of the 4
substituents attached to the chiral carbon atom → D,L system for levorotatory (rotating
polarised light to the left) and dextrorotatory (to the right) glyceraldehyde
‐ L-stereoisomers = stereochemical isomers with the same spatial orientation of functional
groups regarding the aldehyde/carboxyl groups at the chiral centre – i.e. glyceraldehyde
Photos adapted from lecture slides A.THERON
CHAPTER 3.1 – AMINO ACIDS
PROTEINS AND AMINO ACIDS’ FACTS
PROTEINS
‐ Proteins serve as the basic structural molecules of all tissues in the body
‐ Proteins make up nearly 17% of the total body weight
‐ 90-140 million molecules of proteins per one yeast cell
‐ Up to 1010 proteins per mammalian cell
AMINO ACIDS
‐ Amino acids are the fundamental building blocks of proteins
‐ Long linear chains of amino acids (polypeptides) make up proteins and determine their
structure, all their properties and the functions
‐ Amino acids consist of the following: carbon, hydrogen, oxygen, nitrogen and sometimes
sulfur
RESIDUES
‐ In proteins, each amino acid residue joined to its neighbour by a specific type of covalent
bond termed peptide bond
‐ Residue – loss of the elements of water when one amino acid is joined to another
AMINO ACID STRUCTURE
‐ general structure of amino acids consists of a carbon centre termed an 𝛼-carbon atom and 4
substituents linked to this atom
‐ 4 substituents:
• One amino group (NH2 → NH3+)
• Carboxyl group (COOH → COO-)
• Hydrogen atom (H)
• R-group (side radical)
‐ R group determines the structural identity and chemical properties of
individual amino acids
‐ The first 3 groups are common o all amino acids
‐ Basic amino acid structure is R-CH(NH2)-COOH → NH3+-RCH-COO-
Photos adapted from lecture slides A.THERON
,PROPERTIES OF AMINO ACIDS
PROPERTIES OF AMINO ACIDS DUE TO CARBOXYL GROUP
‐ Salt formation
• Amino acids are organic acids and may create salts with many cations:
‐ Reaction with alcohols (esterification)
‐ Reaction with amines to form amides
‐ Decarboxylation
• Amino acids may undergo alpha decarboxylation to form the corresponding amines
• This way many NB amines are produced from amino acids in living organisms
➢ Histidine → Histamine + CO2 (local immune response)
➢ Tyrosine → Tyramine + CO2 (role in blood-brain barrier)
➢ Tryptophan → Tryptamine + CO2 (neurotransmitter)
➢ Glutamic acid → 𝛾-amino butyric acid (GABA) + CO2 (neurotransmitter)
➢ Lysine → Cadaverine + CO2 (toxin)
PROPERTIES OF AMINO ACIDS DUE TO AMINO GROUP
‐ Reaction with mineral acids
‐ Reaction with benzaldehyde
• Schiff’s base formation is an intermediate step of the reaction of transamination –
important part of the biosynthesis of amino acids
Photos adapted from lecture slides A.THERON
, ‐ Sangers’ reaction
• Reaction with Sanger’s reagent produces a yellow-coloured derivative, DNB-amino
acid
• This reaction is used to detect amino acid concentrations, free N-terminal amino
acids in polypeptides and can be helpful in protein sequencing
• AA-NH2 + Sanger’s reagent = DNB + HF → REMEMBER THIS AND PRACTICAL USE OF
IT
PROPERTIES DUE TO AMINO GROUP AND CARBOXYL GROUP
‐ Peptide bonding
‐ Ninhydrin reaction
• Oxidative decarboxylation of 𝛼-amino acids
• Oxidised ninhydrin creates with the liberated NH3 a blue-coloured Rhumann’s
complex
• Very sensitive reaction used in analytic chemistry for detection of amino acids
• Remember application of this reaction
‐ Zwitterions
• The name “zwitter” is derived from German word “hybrid”
• Zwitterion (or) dipolar ion is a hybrid molecule containing positive and negative ionic
groups with no overall charge equal to zero
Photos adapted from lecture slides A.THERON
, • One proton is transferred from the carboxyl group to the amino group of self-
molecules at normal pH cellular levels
CHIRALITY OF AMINO ACIDS
‐ Optical properties
• All amino acids except Glycine possess optical isomers due to the presence of the
asymmetric 𝛼-carbon atoms
STEREOCHEMISTRY OF AMINO ACIDS
‐ In many cases – mirror images can be superimposed over the original by rotation
‐ Achiral objects – are superimposable on their mirror images
‐ Chiral objects – are not superimposable on their mirror images
‐ A chiral C-atom (chiral centre) in molecules is attached to 4 different groups
‐ Stereoisomers – molecules that differ from each other only by their 3D configuration
(optical isomer)
‐ Enantiomer – pairs of stereoisomers, which can be superimposed by a mirror reflection
‐ One chiral centre renders 2 optical stereoisomers, which are mirror reflections of one
another
‐ Maximum number of stereoisomers for a molecule: 2n (n = number of chiral centres)
‐ Total number of enantiomers: 2n/2 (n = number of chiral centres)
‐ Majority of natural amino acids, except Glycine, Isoleucine and Threonine – are enantiomers
and have L- and D- stereoisomers
‐ 𝛼-Carbon of all amino acids except Glycine is a chiral centre rendering a pair of enantiomers
(L- and D- stereoisomers)
‐ All amino acids found in proteins are L- stereoisomers
‐ D-amino acids may be found in several natural products synthesised by non-ribosomal
polypeptide synthetases (NRPS) and in cell wall of bacteria
‐ Solid wedge = out of paper plane
‐ Dashed wedge = behind
‐ Horizontal bonds = out of paper plane
‐ Vertical = behind
‐ Special nomenclature proposed by Fisher to specify the absolute configuration of the 4
substituents attached to the chiral carbon atom → D,L system for levorotatory (rotating
polarised light to the left) and dextrorotatory (to the right) glyceraldehyde
‐ L-stereoisomers = stereochemical isomers with the same spatial orientation of functional
groups regarding the aldehyde/carboxyl groups at the chiral centre – i.e. glyceraldehyde
Photos adapted from lecture slides A.THERON
