Amino Acids

Amino Acids 1.45 MB

Amino Acids:

The building blocks of proteins

pK2

 

pK1

a amino acids because of the a carboxylic and a amino groups

pK 1 and pK 2 respectively pKR is for R group pK’s

pK 1 » 2.2 while pK 2 » 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
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

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
AA2        AA3

20 x 20 = 400 different molecules
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

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

Amino Acids

You must know:

Their names
Their structure
Their three letter code
Their one letter code

Tyrosine, Tyr, Y, aromatic, hydroxyl




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 = pK 1 and pKj = pK 2 ; for D and E, pKi = pK 1 and pKj - pK R ; For R, H and K, pKi = K R and pKj = pK 2
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.
Stereoisomers
One or many chiral centers
N chiral centers 2 N possible stereoisomers and 2 N-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.
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 Ca This works for all amino acids.
An example of an amino acid with two asymmetric carbons
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>NH 2>COOH>CHO>CH 2OH>C 6H 5>CH 3>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).