amino acids

1. Amino Acids
1/29/2003

2. Amino Acids:
The building blocks of proteins
a amino acids because of the a carboxylic and a amino groups
pK1 and pK2 respectively pKR is for R group pK’s
pK1  2.2 while pK2  9.4
pK1
pK2
In the physiological pH range, both carboxylic and
amino groups are completely ionized

3. 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

4. Amino acids can form peptide
bonds
Amino acid residue
peptide units
dipeptides
tripeptides
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

5. 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:
130
100
10
27
.
1
20 x

The total number of atoms in the universe is estimated at
78
10
9x

6. 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

7. Amino Acids
You must know:
Their names
Their structure
Their three letter code
Their one letter code
H2N CH C
CH2
OH
O
OH
Tyrosine, Tyr, Y, aromatic, hydroxyl

10. Cystine consists of two disulfide-linked
cysteine residues

11. Acid - Base properties of amino acids










[HA]
]
[A
log
pK
pH
-
 
j
i pK
pK
2
1
pI 

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

12. The tetra peptide Ala-Tyr-Asp-Gly or AYDG
Greek lettering used to identify atoms in lysine or glutamate

13. 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

14. 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.
Stereoisomers

15. The Fischer Convention
Absolute configuration about an asymmetric carbon
related to glyceraldehyde
(+) = D-Glyceraldehyde
(-) = L-Glyceraldehyde

16. 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
All naturally occurring amino acids that make up
proteins are in the L conformation
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.

17. An example of an amino acid with two
asymmetric carbons

18. 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
SH>OH>NH2>COOH>CHO>CH2OH>C6H5>CH3>H

20. The major advantage of the CIP or RS system is
that the chiralities of compounds with multiple
asymmetric centers can be unambiguously
described

21. Prochiral substituents are
distinguishable
Two chemically identical substituents to an
otherwise chiral tetrahedral center are geometrically
distinct.

22. 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).

23. Lecture 6 Monday Feb 3
• Protein Geometry
• Primary sequence
• Sequence alignments