BIOCHEMISTRY (I)
LIFS2210
Amino Acids
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Biochemistry I (LIFS2210)
• You are expected to
learn the structure &
function of these
organic compounds:
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1. What are amino acids?
• Amino acids are organic acids
containing an amine group.
• Amino acids are the monomeric units
or "building blocks" of proteins.
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General Structure of Amino Acids
• Twenty common -amino acids have carboxyl
and amino groups bonded to the -carbon atom
• A hydrogen atom and a side chain (R) are also
attached to the -carbon atom
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2. Stereochemistry
• Stereoisomers - compounds that have the same
molecular formula but differ in the arrangement of
atoms in space
• Enantiomers - nonsuperimposable mirror images
• Chiral carbons - have four different groups
attached
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Stereoisomers of -amino acids
mirror plane
Mirror-image pairs of amino acids
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Mirror-image pairs of serine
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Stereochemistry of amino acids
• 19 of the 20 common amino acids have a
chiral -carbon atom (Gly does not)
• Threonine and isoleucine have 2 chiral
carbons each (4 possible stereoisomers each)
• Mirror image pairs of amino acids are
designated L (levo) and D (dextro)
• Proteins are assembled from L-amino acids
(a few D-amino acids occur in nature)
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3. Structures of the 20 common
amino acids found in proteins
Abbreviations can be one letter or three letters
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Side Chains of the Amino Acids
• Side groups are what distinguish the
amino acids from each other.
• The 20 L--amino acids are frequently
grouped according to the chemical
nature of their side chains.
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A. Aliphatic R Groups
• Glycine (Gly, G) - the -carbon is not chiral
since there are two H’s attached (R=H)
• Four amino acids have saturated side chains:
Alanine (Ala, A) Valine (Val, V)
Leucine (Leu, L) Isoleucine (Ile, I)
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Aliphatic amino acid structures
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Aliphatic Amino Acids
• A diverse group - more nonpolar ones, such as VAL, LEU,
ILE prefer interior of protein molecule
• The more hydrophobic amino acids, like Valine, Leucine
and isoleucine, are usually found in the interior of a
protein molecule, where they are shielded from water.
• Glycine has the smallest functional group (hydrogen) of
any of the -amino acids.
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B. Cyclic Amino Acid - Proline
• Proline (Pro, P) - has a three carbon
side chain bonded to the -amino
nitrogen
• Proline has a nitrogen in the
aliphatic ring system
• Cyclic Amino Acid - The heterocyclic
pyrrolidine ring restricts the geometry
of polypeptides
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C. Aromatic R Groups
• Side chains have aromatic groups
Phenylalanine (Phe, F) - benzene ring
Tyrosine (Tyr, Y) - phenol ring
Tryptophan (Trp, W) - bicyclic indole group
• Tyrosine and Tryptophan have some hydrophobic
character, but it is tempered by the polar groups in their
side chains.
• Phenylalanine, together with the aliphatic amino acids
Valine, Leucine, and Isoleucine, are the most
hydrophobic amino acids.
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Aromatic amino acid structures
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Aromatic Amino Acids: Strong
absorption of light in near UV
• Tyrosine, Phenylalanine and Tryptophan exhibit strong
absorption of light in the near-ultraviolet region of the spectrum.
• This absorption is frequently used for the analytical detection of
proteins.
Absorption spectra of the
aromatic amino acids in the
near-ultraviolet region
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D. Sulfur-Containing R Groups
• Methionine (Met, M) - (-CH2CH2SCH3)
• Cysteine (Cys, C) - (-CH2SH)
• Two cysteine side chains can be cross-linked by
forming a disulfide bridge (-CH2-S-S-CH2-)
• Disulfide bridges may stabilize the three-
dimensional structures of proteins
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Methionine and cysteine
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Formation of cystine
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E. Side Chains with Alcohol Groups
• Serine (Ser, S), Threonine (Thr, T) and Tyrosine (Tyr,
Y) have uncharged polar side chains
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Phosphorylation of Ser, Thr & Tyr
• The alcohol chain of Serine, Threonine and Tyrosine is a site of
phosphorylation of many proteins.
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F. Basic R Groups
• Histidine (His, H) - imidazole
• Lysine (Lys, K) - alkylamino group
• Arginine (Arg, R) - guanidino group
• Side chains are nitrogenous bases which are
substantially positively charged at pH 7
(except His)
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Structures of histidine, lysine and arginine
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Basic Amino Acids
• The basic amino acids are strongly polar, and as
a consequence, they are usually found on the
exterior surfaces of proteins, where they can be
hydrated by the surrounding aqueous
environment.
• Histidine is the least basic of the three basic
amino acids.
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G. Acidic R Groups and Amide Derivatives
• Aspartate (Asp, D) and Glutamate (Glu, E)
are dicarboxylic acids, and are negatively
charged at pH 7
• Asparagine (Asn, N) and Glutamine (Gln, Q)
are uncharged but highly polar
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Structures of aspartate, glutamate,
asparagine and glutamine
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Acidic Amino Acids and Their Amides
• Asp and Glu strongly acid.
– Aspartic acid (Aspartate)
– Glutamic acid (Glutamate)
• Asn and Gln polar but not charged.
• Asparagine and Glutamine are classified as
amides because they are an amide derivative of
Aspartic acid and Glutamic acid, respectively.
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4. Ionization of Amino Acids
• Ionizable groups in amino acids: (1) -carboxyl,
(2) -amino, (3) some side chains
• Each ionizable group has a specific pKa
AH A- + H+
• For a solution pH below the pKa, the protonated
form predominates (AH)
• For a solution pH above the pKa, the unprotonated
form predominates (A)
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pKa values of
amino acid
ionizable groups
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Titration curve for alanine
• Titration curves
are used to
determine pKa
values
• pK1 = 2.4
• pK2 = 9.9
• pIAla = isoelectric
point
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Zwitterionic form of amino acids
• A zwitterion is a molecule with equal
numbers of positive and negative charges -
thus the net charge is zero.
• Under normal cellular conditions amino acids
are zwitterions (dipolar ions):
Amino group = -NH3+
Carboxyl group = -COO-
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