These extensive notes are based on the BCM 251 lecture notes and Lehninger Principles of Biochemistry textbook. The notes cover all the work in the module and have also been double checked using the learning outcomes in the study guide to ensure all the information was there. They also include all ...
LECTURE 1 elements of water when one amino acid is joined to
another
GENERAL PROPERTIES OF AMINO ACIDS
Amino acid structure
Protein and amino acids facts • The general structure of amino acids consists of a carbon
Proteins centre and its four substituents, which consists of an
amino group (NH2 → NH3+), an organic acid (carboxyl)
• Proteins serve as the basic structural molecules of all the
group (COOH → COO−), a hydrogen atom (H), and a
tissues in the body. Proteins make up nearly 17% of the
fourth group, referred to as the R-group or side radical,
total body weight. There are 90-140 million molecules of
that determines the structural identity and chemical
proteins per one yeast cell, or up to 1010 proteins per
properties of the amino acid
mammalian cell
• The first three groups are common to all amino acids. The
• To understand protein’s role and function, it is important to
basic amino acid structure is R-CH(NH2)-COOH → NH3+-
know its basic structure and composition
RCH-COO−
Amino acids
General properties of amino acids
• Amino acids are the fundamental building blocks of
protein. Long linear chains of amino acids, called Properties of amino acids due to carboxyl group
polypeptides, make up proteins and determine their • Salt formation. Amino acids are organic acids and may
structure, all their properties and functions create salts with many cations
• Amino acids consist of the following elements: 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. The term residue reflects the loss of the
,• Reaction with alcohols (esterification) Reaction with benzaldehyde
Reaction with amines to form amides Schiff’s base formation is an intermediate step of reaction of
transamination, NB part of biosynthesis of amino acids
Sanger’s reaction. This reaction with Sanger’s reagent
produces a yellow colored derivative, DNB-amino acid
Decarboxylation. Amino acids may undergo alpha
decarboxylation to form the corresponding amines. Thus
important 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) • This reaction is used to detect free N-terminal amino acids
• Lysine → cadaverine + CO2 (toxin) in polypeptides and can be helpful in protein sequencing
• Glutamic acid → γ-amino butyric acid (GABA) + CO2 • Equation: AA-NH2 + Sanger’s reagent = DNB + HF
(neurotransmitter) • And the practical application of this reaction
Properties of amino acids due to amino group Properties due to amino and carboxyl groups
Reaction with mineral acids
Ninhydrin reaction. Oxidative decarboxylation of α-amino
R-CH(NH2)-COOH + HCl = [R-CH(NH+3)-COOH]Cl−
acids
, Optical properties. All amino acids except for glycine
possess optical isomers due to the presence of asymmetric α-
carbon atoms
Chirality of amino acids
Amino acids are 3D molecules
• Ninhydrin then reacts with the liberated NH3 forming blue-
colored Rhumann’s complex. Very sensitive reaction used
in analytic chemistry for detection of amino acids
• Remember the application of this reaction
Zwitterions. The name zwitter is derived from the German
word which means ‘hybrid’. Zwitterion (or) dipolar ion is a
hybrid molecule containing positive & negatively ionic groups.
Basically the proton shifts from carboxyl group to amino group
of the self molecule at normal pH cellular levels
, Stereochemistry of amino acids • In other cases, the mirror images cannot be superimposed
We can imagine a mirror reflection of a 3D object on one another but are related as the right hand to the left
hand
• Chiral objects: those ones which are not superimposable
on their mirror images
• A chiral C-atom (chiral centre) in molecules is such one
that is attached to 4 different groups
• In many cases mirror images can be superimposed over • Achiral objects: those ones which are superimposable on
the original image by rotation their mirror images
• Achiral objects: those ones which are superimposable on • Chiral objects: those ones which are not superimposable
their mirror images on their mirror images
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