Biology 107Biology 107

Macromolecules IIMacromolecules II

September 5, 2005September 5, 2005

Macromolecules IIMacromolecules II

Student Objectives:Student Objectives: As a result of this lecture and the assigned As a result of this lecture and the assigned reading, you should understand the following:reading, you should understand the following:

1.1. Proteins are biological polymers constructed from amino acid Proteins are biological polymers constructed from amino acid monomers. Each different protein has a unique structure and function, monomers. Each different protein has a unique structure and function, and protein diversity is based upon these different arrangements of a and protein diversity is based upon these different arrangements of a universal set of amino acids.universal set of amino acids.

2.2. There are eight major functional classes of proteins: 1) structural There are eight major functional classes of proteins: 1) structural proteins; 2) contractile proteins; 3) storage proteins; 4) defense proteins; proteins; 2) contractile proteins; 3) storage proteins; 4) defense proteins; 5) transport proteins; 6) receptor proteins; 7) hormone proteins; 8) 5) transport proteins; 6) receptor proteins; 7) hormone proteins; 8) enzymes.enzymes.

Macromolecules IIMacromolecules II

33.. Amino acids have the same basic structure, with the amino Amino acids have the same basic structure, with the amino group and carboxyl group bonded to a central C atom (the alpha group and carboxyl group bonded to a central C atom (the alpha C). This central carbon also has an attached H atom and a C). This central carbon also has an attached H atom and a chemical group called the "R" group. chemical group called the "R" group.

4.4. It is the "R" group that is the variable part of the amino acid and 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 determines the specific properties of each of the 20+ amino acids in proteins. in proteins.

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

Macromolecules IIMacromolecules II6. The specific shape that determines a protein's function comprises 6. The specific shape that determines a protein's function comprises

four (4) successive levels of structure, each determined by the four (4) successive levels of structure, each determined by the previous level. previous level.

a.a. The primary structure is the sequence of amino acids The primary structure is the sequence of amino acids forming forming the polypeptide chain. the polypeptide chain.

b.b. The secondary structure consists of polypeptide chain coils The secondary structure consists of polypeptide chain coils or or folds held in place by hydrogen bonding between the - N - H folds held in place by hydrogen bonding between the - N - H

and the - C = O groups along the backbone of the chain. and the - C = O groups along the backbone of the chain. Coiling or folding of a polypeptide chain usually results in Coiling or folding of a polypeptide chain usually results in

one one of two repeating structures, either an alpha-helix or a beta-of two repeating structures, either an alpha-helix or a beta-pleated sheet. pleated sheet.

Macromolecules IIMacromolecules II

c.c. Tertiary structure is the overall 3-dimensional shape of a Tertiary structure is the overall 3-dimensional shape of a polypeptide; tertiary structure is maintained by bonding polypeptide; tertiary structure is maintained by bonding (hydrogen, ionic and covalent [disulfide bridges]) and hydrophobic (hydrogen, ionic and covalent [disulfide bridges]) and hydrophobic or hydrophilic interactions between the "R" groups of various or hydrophilic interactions between the "R" groups of various amino acids in the polypeptide chain.amino acids in the polypeptide chain.

d.d. Quaternary structure is produced by the bonding interactions of Quaternary structure is produced by the bonding interactions of two (2) or more polypeptide subunits. Quaternary structure is two (2) or more polypeptide subunits. Quaternary structure is maintained by hydrogen bonding, ionic interactions, and maintained by hydrogen bonding, ionic interactions, and hydrophobic interactions.hydrophobic interactions.

Structure of Amino Acids with Nonpolar “R” Structure of Amino Acids with Nonpolar “R” GroupsGroups

Structure of Amino Acids with Polar or Ionic “R” Structure of Amino Acids with Polar or Ionic “R” GroupsGroups

Primary Protein Primary Protein StructureStructure

Consist of sequence of amino acidsConsist of sequence of amino acids

Has a polarity – amino end (#1 amino Has a polarity – amino end (#1 amino acid of the chain) and carboxyl acid of the chain) and carboxyl endend

Dictates the other levels of folding Dictates the other levels of folding and structureand structure

Change of a Single Amino Acid in the Change of a Single Amino Acid in the Primary Structure of a Protein May Have Primary Structure of a Protein May Have Dramatic Functional ConsequencesDramatic Functional Consequences

Secondary Protein Structure

Bonds That Stabilize Tertiary StructureBonds That Stabilize Tertiary Structure

In Water, Hydrophobic Regions In Water, Hydrophobic Regions Tend to be on the InsideTend to be on the Inside

Quaternary Protein Structure

Proteins Have Charge Based Upon Amino Proteins Have Charge Based Upon Amino Acids Present and Solution ConditionsAcids Present and Solution Conditions

• each unique protein has a specific isoelectric point, the pH at which the protein each unique protein has a specific isoelectric point, the pH at which the protein

has no chargehas no charge

• negative charge at pH 7 (high % aspartic and glutamic acids), low pInegative charge at pH 7 (high % aspartic and glutamic acids), low pI

• positive charge at pH 7 (high % arginines and lysines), high pIpositive charge at pH 7 (high % arginines and lysines), high pI

histone, pI ~ 10histone, pI ~ 10positive charge at pH 7positive charge at pH 7

pepsin, pI ~ 1pepsin, pI ~ 1negative charge at pH 7negative charge at pH 7

Summary of Levels of Protein StructureSummary of Levels of Protein Structure

Can Denature Can Denature ProteinsProteins

Means:Means:

Alter temperatureAlter temperature

Alter ionic conditions, pHAlter ionic conditions, pH

DetergentsDetergents

Consequences:Consequences:

Lose one or more levels of shapeLose one or more levels of shape

Alter functionAlter function

Permit various analysis techniquesPermit various analysis techniques

The structure and function of the The structure and function of the hsp60 family of molecular chaperones.hsp60 family of molecular chaperones.

Protein Folding in Cells

Protein Electrophoresis Denaturing conditions

• Proteins treated with SDS (anionic detergent) before Proteins treated with SDS (anionic detergent) before electrophoresis (SDS-PAGE)electrophoresis (SDS-PAGE)– SDS molecules bind to the ProteinSDS molecules bind to the Protein– Proteins lose normal shapeProteins lose normal shape– Proteins all have same charge/mass ratioProteins all have same charge/mass ratio– Proteins are separated on basis of size onlyProteins are separated on basis of size only

SDS treatment

Charge Mass

+3 30kD

4 42kD

Charge Mass

300 30kD

420 42kD

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Effects of Altered Protein Structure on FunctionEffects of Altered Protein Structure on Function