Proteins

I. Introduction

1. What are the 4 classes of organic macromolecular compounds that are important in biological systems?

2. What are the subunit molecules for each class?

3. The biological functions of proteins:

What are they? How does function relate to the shape of a protein?:

II. Features of Protein Structure

A. The Common Plan

1. How many amino acids are commonly found in proteins?

2. What is the basic structure of an amino acid?

3. How do amino acids differ?

4. What are "R" groups? How many kinds of "R" groups are there?

B. Acid-base properties of amino acids

1. How does pH affect the charge of an amino acid?

2. What are the two ionizable groups in an amino acid?

3. What is the principle function of these ionizable groups in protein synthesis?

4. Why should we be concerned with the acid/base properties of R groups?

C. Polypeptides

1. How are amino acids linked together to form polypeptides?

2. What does the cell need to link amino acids together to make a protein?

3. Describe a peptide bond

Homework: Draw a sketch showing how a peptide bond is formed

Peptide bond movie

4. Other features of the peptide linkage:

• rigidity and rotation
  
• impact of restricted rotation of peptide bonds.
  
• beginning and end of polypeptides:
  

5. The Planar Amide Group

• What is it?
• What are phi and psi?
  
• Ramachandran Plots
  
• sterically allowed conformations are limited to three
  
• These allowed configurations are also referred to as?
  

6. Properties of helical polypeptides

• Helical polypeptides are stabilized by hydrogen bonds between one part of the helix and another.
  
• What chemical groups in a polypeptide are candidates for hydrogen bonding?
  

a. Alpha Helix

• alpha helix (chime)
  
• Pauling & Corey (Nobel Prize)
  
• alpha keratin (ex: hair)
• tropomyosin (muscle protein)
  
• some amino acids interfere with the helix. Why?
  
• Other examples of proteins with alpha helical structure: hemoglobin 

       alcohol dehydrogenase

b. Beta Conformations

• This polypeptide has a fully extended chain:
• conformation?
  
• Beta pleated sheet 

c. Loop Regions (Random Coil)

• common configuration of globular proteins
  
• Where are the loops? Where is the secondary structure?
  
• What is the chemical nature of the amino acids in loop regions?
  

d. Additional points

• different species compared
• functions of loop regions (example: antibody)
• Notes on Schematic Diagrams
  
• Motifs
  

D. Structural Hierarchy of Protein Molecules

1. primary

2. secondary

3. tertiary

4. quaternary

5. Additional information about domains:

• What are domains?
• How many domains do proteins have?
• What determines the folding of an amino acid chain to create the final shape of a protein?
• Anfinsen Experiment
  
• Chaperone proteins
  
• heat shock proteins