Amino Acids 1/29/2003

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Amino Acids1/29/2003
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Amino AcidsThe building blocks of proteins
pK1
pK2
a amino acids because of the a carboxylic and a
amino groups pK1 and pK2 respectively pKR is for
R group pKs pK1 ? 2.2 while pK2 ? 9.4
In the physiological pH range, both carboxylic
and amino groups are completely ionized
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Amino acids are Ampholytes
They can act as either an acid or a base
They are Zwitterions or molecules that have both
a positive and a negative charge
Because of their ionic nature they have extremely
high melting temperatures
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Amino acids can form peptide bonds
Amino acid residue peptide units dipeptides tripep
tides oligopeptides polypeptides
Proteins are molecules that consist of one or
more polypeptide chains
Peptides are linear polymers that range from 8 to
4000 amino acid residues
There are twenty (20) different naturally
occurring amino acids
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Linear arrays of amino acids can make a huge
number of molecules
Consider a peptide with two amino acids
AA1
AA2
20 x 20 400 different molecules
AA1
AA2
AA3
20 x 20 x 20 8000 different
molecules
For 100 amino acid protein the of possibilities
are
The total number of atoms in the universe is
estimated at
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Characteristics of Amino Acids
There are three main physical categories to
describe amino acids 1) Non polar
hydrophobic nine in all Glycine, Alanine,
Valine, Leucine, Isoleucine, Methionine, Proline,
Phenylalanine and Tryptophan 2) Uncharged polar,
six in all Serine, Threonine, Asparagine,
Glutamine Tyrosine, Cysteine 3) Charged polar,
five in all Lysine, Arginine, Glutamic acid,
Aspartic acid, and Histidine
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Amino Acids
You must know Their names Their structure Their
three letter code Their one letter code
Tyrosine, Tyr, Y, aromatic, hydroxyl
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Cystine consists of two disulfide-linked cysteine
residues
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Acid - Base properties of amino acids
Isoelectric point the pH where a protein carries
no net electrical charge
For a mono amino-mono carboxylic residue pKi
pK1 and pKj pK2 for D and E, pKi pK1 and
pKj - pKR For R, H and K, pKi KR and pKj pK2
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The tetra peptide Ala-Tyr-Asp-Gly or AYDG
Greek lettering used to identify atoms in lysine
or glutamate
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Optical activity - The ability to rotate plane -
polarized light Asymmetric carbon
atom Chirality - Not superimposable Mirror
image - enantiomers () Dextrorotatory - right -
clockwise (-) Levorotatory - left
counterclockwise Na D Line passed through
polarizing filters.
Operational definition only cannot predict
absolute configurations

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Stereoisomers
One or many chiral centers N chiral centers 2N
possible stereoisomers and 2N-1 are
enantiomeric For N 2 there are 4 possible
sterioisomers of which 2 are enatiomers and 2
are diastereomers Diastereomers are not mirror
images and have different chemical properties.
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The Fischer Convention
Absolute configuration about an asymmetric carbon
related to glyceraldehyde ()
D-Glyceraldehyde (-) L-Glyceraldehyde
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All naturally occurring amino acids that make up
proteins are in the L conformation
In the Fischer projection all bonds in the
horizontal direction is coming out of the plane
if the paper, while the vertical bonds project
behind the plane of the paper
The CORN method for L isomers put the hydrogen
towards you and read off CO R N clockwise
around the Ca This works for all amino acids.
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An example of an amino acid with two asymmetric
carbons
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Cahn - Ingold - Prelog system
Can give absolute configuration nomenclature to
multiple chiral centers. Priority Atoms of
higher atomic number bonded to a chiral center
are ranked above those of lower atomic number
with lowest priority away from you R highest to
lowest clockwise, S highest to lowest
counterclockwise SHgtOHgtNH2gtCOOHgtCHOgtCH2OHgtC6H5gtCH
3gtH
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The major advantage of the CIP or RS system is
that the chiralities of compounds with multiple
asymmetric centers can be unambiguously described
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Prochiral substituents are distinguishable
Two chemically identical substituents to an
otherwise chiral tetrahedral center are
geometrically distinct.
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Planar objects with no rotational symmetry also
have prochariality
Flat trigonal molecules such as aldehydes can be
prochiral With the flat side facing the viewer if
the priority is clockwise it is called the (a) re
face (rectus) else it is the (b) si face
(sinistrus).
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Lecture 6 Monday Feb 3

• Protein Geometry
• Primary sequence
• Sequence alignments