One of the four main groups of macromolecules you really have been analyzing (carbohydrates, lipids, proteins, and nucleotides), proteins are among the biggest and undoubtedly the most diverse. Much like all the macromolecules proteins are polymers composed of monomers. The monomers are amino acids. In this lesson you will study the assortment of amino acids used to build proteins, the arrangement of amino acids, and also the form that proteins may take and that form is linked to protein function.
Basic Amino Acid Structure
Go to John Kyrk’s Website and study the structure of Glycine, the simplest of amino acids.
What are the two functional groups attached to the carbon dioxide? Write out their formulae.
Today go to the next page of this site (click on the yellow triangle on the left). You should see a table listing the 20 amino acids found in proteins. Click the three letter abbreviation of every amino acid and then read the info about each one. Study the structure of every amino acid; specifically listen to the group attached to the carbon. What is an amino acid?
Are all amino acids composed of only H, C, O, and N? Explain.
How many amino acids are polar? Non-polar? Acidic, Fundamental?
How do you identify one different amino acid from another? Give an example.
Move the cursor over the atoms at the diagram of the molecule until you find the central”alpha” carbon.
Primary Structure, Peptide Bonds
Click on the yellow triangle to achieve the”Primary Structure, Peptide Bonds” page. You may have to see this short cartoon a couple of times, but notice the amino acids socialize as they associate together for form peptide bonds and form a polymer generally called a”polypeptide. The linear arrangement of amino acids in a polypeptide (or protein) is known as the”main” structure of the molecule.
(hydrogen, covalent, ionic)What type of chemical reaction happens when the peptide bonds have been formed? How can you know this? In a polypeptide composed of 25 amino acids how many of them are going to have a comprehensive amino group (NH2) and how many will have a comprehensive carboxyl group (COOH)?
Secondary Structure, The Alpha Helix and Beta Sheet
Click the third triangle to visit the page describing the alpha helix. Notice the overall 3D shape of the helix. Then click on the yellow triangle for the webpage describing the beta sheet examine its form. These larger structures in a protein molecule are called its”secondary” construction. There may be alpha helices and beta sheets in a protein molecule that is single.
Describe the shape of an alpha helix.
Describe the Form of a beta sheet.
Which type of bond (hydrogen, covalent, ionic) holds these structures in place?