Biology 107
Macromolecules II
September 5, 2005
Macromolecules II
Student Objectives: As a result of this lecture and the assigned
reading, you should understand the following:
1. Proteins are biological polymers constructed from amino acid
monomers. Each different protein has a unique structure and
function, and protein diversity is based upon these different
arrangements of a universal set of amino acids.
2. There are eight major functional classes of proteins: 1) structural
proteins; 2) contractile proteins; 3) storage proteins; 4) defense
proteins; 5) transport proteins; 6) receptor proteins; 7) hormone
proteins; 8) enzymes.
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.
Amino acids have the same basic structure, with the amino group
and carboxyl group bonded to a central C atom (the alpha C).
This central carbon also has an attached H atom and a chemical
group called the "R" group.
4.
It is the "R" group that is the variable part of the amino acid and
determines the specific properties of each of the 20+ amino acids
in proteins.
5.
Amino acids are linked together by dehydration synthesis, with the
resulting covalent linkages called peptide bonds.
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6. The specific shape that determines a protein's function comprises
four (4) successive levels of structure, each determined by the
previous level.
a.
The primary structure is the sequence of amino acids forming
the polypeptide chain.
b.
The secondary structure consists of polypeptide chain coils or
folds held in place by hydrogen bonding between the - N - H
and the - C = O groups along the backbone of the chain.
Coiling or folding of a polypeptide chain usually results in one
of two repeating structures, either an alpha-helix or a betapleated sheet.
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c.
Tertiary structure is the overall 3-dimensional shape of a
polypeptide; tertiary structure is maintained by bonding (hydrogen,
ionic and covalent [disulfide bridges]) and hydrophobic or
hydrophilic interactions between the "R" groups of various amino
acids in the polypeptide chain.
d.
Quaternary structure is produced by the bonding interactions of
two (2) or more polypeptide subunits. Quaternary structure is
maintained by hydrogen bonding, ionic interactions, and
hydrophobic interactions.
Structure of Amino Acids with Nonpolar “R” Groups
Structure of Amino Acids with Polar or Ionic “R”
Groups
Primary Protein
Structure
Consist of sequence of amino acids
Has a polarity – amino end (#1 amino
acid of the chain) and carboxyl
end
Dictates the other levels of folding
and structure
Change of a Single Amino Acid in the
Primary Structure of a Protein May Have
Dramatic Functional Consequences
Secondary Protein Structure
Bonds That Stabilize Tertiary Structure
In Water, Hydrophobic Regions
Tend to be on the Inside
Quaternary Protein Structure
Proteins Have Charge Based Upon Amino
Acids Present and Solution Conditions
• each unique protein has a specific isoelectric point, the pH at which the protein
has no charge
• negative charge at pH 7 (high % aspartic and glutamic acids), low pI
• positive charge at pH 7 (high % arginines and lysines), high pI
pepsin, pI ~ 1
negative charge at pH 7
histone, pI ~ 10
positive charge at pH 7
Summary of Levels of Protein Structure
Can Denature
Proteins
Means:
Alter temperature
Alter ionic conditions, pH
Detergents
Consequences:
Lose one or more levels of shape
Alter function
Permit various analysis techniques
Protein Folding in Cells
The structure and function of the
hsp60 family of molecular chaperones.
Protein Electrophoresis
Denaturing conditions
• Proteins treated with SDS (anionic detergent) before
electrophoresis (SDS-PAGE)
– SDS molecules bind to the Protein
– Proteins lose normal shape
– Proteins all have same charge/mass ratio
– Proteins are separated on basis of size only
Charge Mass
+3
30kD
4
42kD
Charge Mass
SDS treatment
300 30kD
420 42kD
PAGE
Effects of Altered Protein Structure on Function