Amino Acids 1/29/2003. Amino Acids: The building blocks of proteins. pK 1. pK 2. a amino acids because of the a carboxylic and a amino groups pK 1 and pK 2 respectively pK R is for R group pK’s pK 1 2.2 while pK 2 9.4.
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
In the physiological pH range, both carboxylic and amino groups are completely ionized
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 acid residue
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
Consider a peptide with two amino acids
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
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
You must know:
Their three letter code
Their one letter code
Tyrosine, Tyr, Y, aromatic, hydroxyl
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
Greek lettering used to identify atoms in lysine or glutamate
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
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.
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.
Can give absolute configuration nomenclature to multiple chiral centers.
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
The major advantage of the CIP or RS system is that the chiralities of compounds with multiple asymmetric centers can be unambiguously described
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).