BAHAN KULIAH BIOKIMIA POWER POINT BAGIAN 1 /BIOCHEMISTRY POWER POINT LECTURES PART 1 | Karya Tulis Ilmiah

Amino Acids
1/29/2003

Amino Acids:
The building blocks of proteins
pK2

pK1

 amino acids because of the  carboxylic and  amino groups
pK1 and pK2 respectively pKR is for R group pK’s
pK1  2.2 while pK2  9.4

In the physiological pH range, both carboxylic and
amino groups are completely ionized

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

Amino acids can form peptide
bonds
Amino acid residue
peptide units
dipeptides
tripeptides
oligopeptides

Proteins are
molecules that
consist of one or
more
polypeptide
chains

polypeptides

Peptides are linear polymers that range from 8 to 4000

amino acid residues
There are twenty (20) different naturally occurring
amino acids

Linear arrays of amino acids can
make a huge number of molecules
Consider a peptide with two amino acids
AA1

20

AA2

x

AA1

20 x

20


= 400 different molecules

AA2

AA3

20 x

20 =

8000 different molecules

For 100 amino acid protein the # of possibilities are:

20100 1.27 x10130
The total number of atoms in the universe is estimated at

9x1078


Characteristics of
of Amino
Amino Acids
Acids
Characteristics
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 

Amino Acids
You must know:
Their names

Their structure
Their three letter code
Their one letter code
O
H2N

CH

C

OH

CH2

Tyrosine, Tyr, Y, aromatic, hydroxyl
OH

Cystine consists of two disulfide-linked
cysteine residues


Acid - Base properties of amino acids
 [A - ] 

pH pK  log
 [HA] 
Isoelectric point: the pH where
a protein carries no net
electrical charge

1
pI   pK i  pK j 
2
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 =

The tetra peptide Ala-Tyr-Asp-Gly or AYDG

Greek lettering used to identify atoms in lysine or glutamate


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

Stereoisomers

Stereoisomers
One or many chiral centers
N chiral centers 2N possible stereoisomers and 2N­1 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.

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

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 C This works
for all amino acids.

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

carbons
asymmetric

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

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

Prochiral substituents are
distinguishable

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

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).

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