AMINO ACIDS. The building blocks for proteins. What You Need to Know. Four basic classes of amino acids What are general characteristics and importance for each class? acid-base properties? How do they form peptide bonds? What other way can they be classified?
Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.
The building blocks for proteins
Four basic classes of amino acids
What are general characteristics and importance for each class?
How do they form peptide bonds?
What other way can they be classified?
Biological characteristics of some rare amino acids?
i.e. Hydroxylysine, hydroxyproline, gamma-aminobutyric acid (GABA), histamine
What are the acid base properties of amino acids?
What are the spectroscopic properties of amino acids?
Understand the fundamental structural pattern of amino acids in proteins.
Understand protein structure nomenclature.
Anatomy of an amino acid. Except for proline and its derivatives, all of the amino acids commonly found in proteins possess this type of structure.
The -COOH and -NH3+ groups of two amino acids can react with the resulting loss of a water molecule to form a covalent amide bond.
Peptide formation is the creation of an amide bond between the carboxyl group of one amino acid and the amino group of another amino acid.
The trans conformation of the peptide bond.
(a) The peptide bond has partial double bond character. One of the postulated resonance forms is shown here.
(b) The peptide bond has partial double bond character. One of the postulated resonance forms is shown here.
(c) The peptide bond is best described as a resonance hybrid of the forms shown on the two previous slides.
The coplanar relationship of the atoms in the amide group is highlighted here by an imaginary shaded plane lying between adjacent α-carbons.
On the basis of their R groups the
amino acids can be categorized as:
Non-polar amino acids
Polar, uncharged amino acids
Polar, charged amino acids
has a side chain pKa = 6.4
Thus, 10% of His side chains are
positively charged at pH 7.4.
a) establish folding pattern (globular)
b) promote hydrophobic interactions
Polar, uncharged and charged
a) establish folding pattern (fibrous)
b) promote specific interactions
His, Ser, Lys, Asn, Cys
You should know these numbers and know what they mean!
The ionic forms of an amino acid, shown without consideration of any ionizations on the side chain.
Titration of glycine, a simple amino acid. The isoelectric point, pI, the pH where the molecule has a net charge of 0, is defined as (pK1+ pK2)/2.
The ultraviolet absorption spectra of the aromatic amino acids at pH 6. (From Wetlaufer, D.B., 1962. Ultraviolet spectra of proteins and amino acids. Advances in Protein Chemistry 17:303–390.)
Cation (a) and anion (b) exchange resins commonly used for biochemical separations.
Operation of a cation exchange column, separating a mixture of Asp, Ser, and Lys.
a) The cation exchange resin in the beginning, Na+ form.
(b) A mixture of Asp, Ser, and Lys is added to the column containing the resin.
(c) A gradient of the eluting salt (e.g., NaCl) is added to the column. Asp, the least positively charged amino acid, is eluted first.
(d) As the salt concentration increases, Ser is eluted.
(e) As the salt concentration is increased further, Lys, the most positively charged of the three amino acids, is eluted last.
Chromatographic fractionation of a synthetic mixture of amino acids on ion exchange columns
A second column with different buffer conditions is used to resolve the basic amino acids.
Amino acid composition: Frequencies of the various amino acids in proteins for all the proteins in the SWISS-PROT protein knowledgebase. These data are derived from the amino acid composition of more than 100,000 different proteins (representing more than 40,000,000 amino acid residues). The range is from leucine at 9.55% to tryptophan at 1.18% of all residues.
NOTE: each unit=amino acid residue (dipeptide, tripeptide, tetrapeptide)
If >12 residues=oligopeptide
If several dozen residues=polypeptide
2 or more = multimeric proteins (homomultimeric or heteromultimeric)
a2b2=heteromultimer (tetramer) (4 polypeptides of 2 kinds)
From Table 4.2 Size of protein molecules.
Molecular weights: Insulin, 5,733; Cytochrome c, 12,500;
From: Table 4.2 Size of Protein Molecules
Molecular weights: Hemoglobin, 64,500;
Glutamine synthetase, 600,000.