Support Materials:

•  Goal:
  To understand the four levels of protein structure.
  I've put together a tutorial on the enzyme carboxypeptidase A. Step through the page links at the left to explore the different levels of protein structure and how they relate to function. The "Gallery" looks at four other proteins - carbonic anhydrase, nitrophorin, myoglobin, and hemoglobin. The "Application" examines an enzyme that's been implicated in 30 % of all human tumors - RAS G Protein.
  
  So what is carboxypeptidase A? This enzyme is a member of a large class of enzymes known as zinc proteases. Their function is to clip amino acids from the C-terminus of a protein substrate, one by one, much like a little pac-person. Zinc proteases are found in many parts of the body. For example, a carboxypeptidase produced in the pancreas is involved in digestion of dietary proteins and the processing of insulin. Excess production of other carboxypeptidases, specifically those found in the extracellular matrix (the space between cells), has been implicated in cancer, arthritis, and hypertension. One of the protein components of the bacterial anthrax toxin is also a zinc protease. Drug companies have invested billions of research dollars in the development of drugs that specifically target these enzymes. For example, a class of drugs called ACE inhibitors are used to treat hypertension (high blood pressure). Another drug, called MLN4760, is currently in clinical trials as a weight loss drug. It targets a carboxypeptidase that is known to trigger the storage of fat.
   
•  Objectives:
   Students will be able to...
   
  • describe primary structure.
    Know how to read the backbone atoms in a polypeptide chain and to identify the N- and C-terminal ends of a protein.
  • describe secondary structure.
  • describe tertiary structure.
  • describe quaternary structure.
    Examples of proteins with quaternary structure: Hemoglobin (Hb), Cytochrome oxidase (COX).
     
  • Interpret chemical equations that describe protein function.
    A simplified reaction for Hb: HbH⁺  +  O₂  ⇌  HbO₂  +  H⁺
    Can you apply Le-Chatlier's effect to this equation? For example, the O₂ concentration is higher than it is in the peripheral tissues. Will the higher oxygen concentration in the lungs shift this reaction to the right or to the left? In other words, will Hb bind or release O₂ in the lungs?
    During an acid burn, the pH of the local blood supply to the exerted muscle decreases. In which direction will this shift the reaction? (In other words, will an acid burn increase or decrease the delivery of O₂ to the muscle?)
    
    O₂  +  4e^-  +  4H⁺  →  2H₂O
    What is the physiological importance of this reaction?
     
  • describe drug treatment strategies for various kinds of disease, such as cancer.
    Example: Does a cancer cell express proteins that are not found in a normal cell (see below)?

   

•  Some questions to think about:
  • What are the main atom types that occur in proteins?
  • What is the difference between secondary and tertiary structure?
  • Which organic functions are hydrogen bonded in secondary structures? (You should also be able to draw these functions and show the hydrogen bond between them using a dashed line).
  • Which of the following are examples of secondary structure?
    The peptide bond; an α-helix; the compact 3-D shape of a protein; a parallel β-sheet; a hairpin turn; a disulfide bond.
  • What is meant by the term scaffold? Does it refer to secondary or tertiary structure? Is it stabilized primarily by charge-charge attraction, hydrogen bonding, or hydrophobic interaction.
  • List, by name, three scaffolds that occur in proteins (see the gallery).
  • What is an active site? How is it different from a scaffold?
  • Can the function of a protein be altered without affecting its scaffold? How?
  • What characteristics must a drug have to inhibit an enzyme's function.
  • List three reasons why a drug may have side effects.
    • the drug forms toxic breakdown products (i.e., acetaminophen).
    • the drug is not specific to a single protein.
    • enantiomerism (i.e., thalidomide).
  • What are three ways that an enzyme, or other protein, can cause disease?
    • over-expression (too much enzyme) - these are good candidates for drug design. The excess enzyme can be targeted by an inhibitory drug to bring expression levels back down to normal.
    • site mutation (there may be normal expression levels, but the expressed enzyme has an amino acid substitution; for example, Hb S) - these are usually not good candidates for drug design since the drug is unlikely to correct the mutation.
    • the disease (i.e., cancer) expresses a protein that is not found in normal cells - these are good candidates for drug design if the drug can selectively target that protein.
  • How would you describe the active site structure of hemoglobin, of cytochrome oxidase, of carboxypeptidase? In particular, name the metals that are required for these proteins to function.