Biology 107 Macromolecules II

1
Biology 107Macromolecules II

• September 5, 2005

2
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.

3
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.
• 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.
• Amino acids are linked together by dehydration
  synthesis, with the resulting covalent linkages
  called peptide bonds.

4
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.

5
Macromolecules II

• 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.
• 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.

6
Structure of Amino Acids with Nonpolar R Groups
7
Structure of Amino Acids with Polar or Ionic R
Groups
8
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
9
Change of a Single Amino Acid in the Primary
Structure of a Protein May Have Dramatic
Functional Consequences
10
Secondary Protein Structure
11
Bonds That Stabilize Tertiary Structure
12
In Water, Hydrophobic Regions Tend to be on the
Inside
13
Quaternary Protein Structure
14
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

histone, pI 10 positive charge at pH 7
pepsin, pI 1 negative charge at pH 7
15
Summary of Levels of Protein Structure
16
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
17
The structure and function of the hsp60 family of
molecular chaperones.
Protein Folding in Cells
18
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 ?300 30kD ?420 42kD
SDS treatment
19
PAGE
20
Effects of Altered Protein Structure on Function