Among the four major groups of macromolecules you have been studying (carbohydrates, lipids, proteins, and nucleotides), proteins are among the largest and by far the most diverse. As with the other macromolecules proteins are large polymers composed of many monomers linked together. In the case of proteins, the monomers are amino acids. In this lesson you will study the basic structure of amino acids, the variety of amino acids used to build proteins, and the complex form that proteins can take and how that shape is related to protein function.
Lesson One: Basic Amino Acid Structure
Go to John Kyrk's web site and study the structure of Glycine, the simplest of all amino acids. Move the cursor over the atoms in the diagram of the molecule until you find the central "alpha" carbon.
- What are the two functional groups attached to the alpha carbon? Write out their formulae.
Now go to the next page of this site (click on the yellow triangle on the left). You should see a table listing the 20 common amino acids found in proteins. Click on the three letter abbreviation of each amino acid and read the information about each one. Study the structure of each amino acid; in particular pay attention to the third group attached to the alpha carbon.
- How may "essential" amino acids are there? What is an essential amino acid?
- Are all amino acids composed of only C, H, O, and N? Explain.
- How many amino acids are polar? Non-polar? Basic, Acidic?
- How do you identify one different amino acid from another? Give an example.
Lesson Two: Primary Structure, Peptide Bonds
Click on the middle yellow triangle to reach the "Primary Structure, Peptide Bonds" page. You may need to view this short animation a few times, but notice how amino acids interact as they link together for form peptide bonds and form a polymer generally called a "polypeptide. The linear sequence of amino acids in a polypeptide (or protein) is called the "primary" structure of the molecule.
- What type of bond is a peptide bond? (hydrogen, covalent, ionic)
- What type of chemical reaction takes place when the peptide bonds are formed? How do you know this?
- In a polypeptide composed of 25 amino acids how many of them will have a complete amino group (NH2) and how many will have a complete carboxyl group (COOH)?
Lesson Three: Secondary Structure, The Alpha Helix and Beta Sheet
Click on the third triangle to go to the page describing the alpha helix. Notice the overall 3D shape of the helix. Then click on the bottom yellow triangle for the page describing the beta sheet; again study its overall shape. These larger structures in a protein molecule are called its "secondary" structure. There may be several alpha helices and beta sheets in a single large protein molecule.
- Describe the shape of an alpha helix.
- Describe the shape of a beta sheet.
- What type of bond (hydrogen, covalent, ionic) holds these structures in place?
Return to Mr. Birch's Biology Class Pages.
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