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.

Macromolecules II 3. 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.

Macromolecules II 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 beta- pleated sheet.

Macromolecules II 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 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 negative charge at pH 7 (high % aspartic and glutamic acids), low pI positive charge at pH 7 (high % arginines and lysines), high pI positive charge at pH 7 (high % arginines and lysines), high pI histone, pI ~ 10 positive charge at pH 7 pepsin, pI ~ 1 negative charge at pH 7

Summary of Levels of Protein Structure

Can Denature Proteins Means: Alter temperature Alter ionic conditions, pH DetergentsConsequences: Lose one or more levels of shape Alter function Permit various analysis techniques

The structure and function of the hsp60 family of molecular chaperones. Protein Folding in Cells

Protein Electrophoresis Denaturing conditions Proteins treated with SDS (anionic detergent) before electrophoresis (SDS-PAGE)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 SDS treatment Charge Mass +3 30kD  4 42kD Charge Mass  kD  kD

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Effects of Altered Protein Structure on Function