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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.

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Amino Acids 1/29/2003

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amino acids the building blocks of proteins
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

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

amino acids are ampholytes
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 acids can form peptide bonds

Amino acid residue

peptide units





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
Linear arrays of amino acids can make a huge number of molecules

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

characteristics of amino acids
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
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
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


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




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.


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.

cahn ingold prelog system
Cahn - Ingold - Prelog system

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

prochiral substituents are distinguishable
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
Lecture 6 Monday Feb 3
  • Protein Geometry
  • Primary sequence
  • Sequence alignments