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Dep. of Chemistry & Biochemistry Prof. Indig. Chemistry 501 Handout 3 Amino Acids, Peptides, and Proteins Chapter 3. Lehninger. Principles of Biochemistry. by Nelson and Cox, 5 th Edition; W.H. Freeman and Company. Amino Acids.
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Chemistry 501 Handout 3Amino Acids, Peptides, and ProteinsChapter 3
Lehninger. Principles of Biochemistry.
by Nelson and Cox, 5th Edition; W.H. Freeman and Company
Steric relationship of the stereoisomers of Alanine to the absolute configuration of L- and D-glyceraldehyde
The amino acid residues in proteins are the L isomers
Reversible formation of disulfide bond by the oxidation of two molecules of cysteine
e.g. two polypeptide chains of insuline
by aromatic amino acids
log (Io/I) = e C L
a # of Ca+ binding proteins
plant cell wall,
Uncommon amino acids also have important functions
Residues created by modification of common residues already incorporated into a polypeptide
~ 300 additional amino acids
have been found in cells
rare, introduced during protein
synthesis rather than created
through a postsynthetic modification
Reversible amino acid modifications involved in regulation of protein activity
Nonionic and zwitterionic forms
of amino acids
Titration of glycine
Titration curves predict the
electric charge of amino acids
Isoelectric point (or isoelectric pH)
pI= ½ (pk1 + pk2) = ½ (2.34 + 9.60) = 5.97
(ampholytes - amphoteric electrolytes)
pka of the –COOH group: 1.8 – 2.4
pka of the –NH3+ group: 8.8 – 11.0
Amino acids with
R groups that do not ionize
Amino acids with ionizable R groups
three stages (three ionization steps three pka values)
Two amino acid molecules can be covalently joined through a substituted amide linkage, termed a peptide bond, to yield a dipeptide
Peptides are named beginning with the amino-terminal
residue, which by convention is placed at the left.
just a few residues oligopeptide
many residues polypeptide
Biologically active peptides and polypeptides occur in a vast range of sizes
If at least two chains are identical → the protein
is said to be oligomeric, and the identical units
(consisting of one or more chains) are referred to
Multisubunit proteins: have two or more
polypeptide chains associated noncovalently
The vast majority of naturally occurring proteins contain fewer than 2,000 amino acid residues.
amino acid compositions
Some proteins contain chemical groups other
than amino acids (conjugated proteins).
The non-amino acid part of the conjugated protein is
usually called its prosthetic group.
Crude extract --> --> --> fractionation
of enzyme in a solution.
A measure of enzyme purity: it increases during purification
of an enzyme and becomes maximal and constant when the
enzyme is pure.
Number of enzyme units
per milligram of total protein.
1.0 unit of enzyme activity = amount of enzyme causing the transformation of 1.0 mmol
of substrate per minute at 25oC under optimal conditions of measurement.
gel stained with a protein-specific
dye (e.g. coomasie blue)
Purification of RNA
polymerize from E. coli
acts as a molecular sieve, slowing the migration
of proteins approximately in proportion to their
Arrangement is space of
Particularly stable arrangements of
amino acid residues giving rise to
recurring structural paterns
All aspects of the 3-D folding
of a polypeptide
Includes disulfide bonds
Amino acid sequence of bovine insulin
(10 years of work by Sanger)
The amino acid sequences of millions of proteins have been determined
Identical in human, pig,
rabbit and sperm whale
Identical in cow, dog,
goat and horse
Sanger’s method for identifying the amino-terminal residue
The Edman degradation procedure (carried out on a sequenator)
reveals the entire sequence
of a peptide
Breaking disulfide bonds
Cleaving the polypeptide chain
Some proteases cleave only the peptide bond
adjacent to particular amino acid residues
Correspondence of DNA and amino acid sequences