SBI4U: Building Models of Proteins
Proteins are polymers of amino acids. Silk and hair are made of a protein called keratin while muscle is made of two proteins called myosin and actin. In addition to playing structural roles, proteins also act as hormones and enzymes. Proteins are covered on pages 40-48 in your text.
Approximately 20 different amino acids have been isolated from proteins. They are found in Figure
29 in your text. They are grouped according to their chemical properties. The chemical properties of amino acids are due to the chemical properties of their side chains (R groups). Each amino acid name has a three letter short form (ex. glycine is 'gly').
1.
Using the structural formulas in Figure 29 of your text build models of two amino acids of your choice.
2.
Join the two model amino acids with a peptide linkage as illustrated in your text. Ensure that the peptide linkage is a bond formed between the terminal carboxyl group and amino group.
What other product is formed?
3.
Record this condensation reaction on paper. Indicate all products. Circle and label the peptide linkage as well as the carboxyl-terminus and amino terminus of the dipeptide. Join your dipeptide to a dipeptide made by your classmate to ensure both of you know how a peptide bond is formed and how amino acids link together to form a polypeptide chain.
4.
Using your text to identify the amino acid from its three letter short name (p. 42-43) and then finding its structure, draw the polypeptide chains for the following short peptides.
1.
aspartame terminus of phe) asp-phe-CH
3
(The -CH
3 will replace the H of the OH of the carboxylic
2.
met-enkephalin tyr-gly-gly-phe-met
3.
leu-enkephalin tyr-gly-gly-phe-leu (enkephalin is a natural pain killer secreted in the brain)
5.
Summarize what is meant by primary, secondary, tertiary and quaternary structure of a protein.
6.
Briefly describe the beta-pleated sheet of silk and the alpha-helix of keratin and how each is relevant to the function of the protein.
7.
The folds of a polypeptide chain are initially due to the interaction of the amino acid side chains with water. From your note, identify the two general groupings of amino acids. Describe how each grouping's side chain (R group) might interact with water molecules in the cytoplasm.
8.
The final folded shape of the polypeptide chain, however, is maintained by four different types of chemical interactions between the side chains of amino acids. These include: van der Waals interactions, hydrogen bonds, disulphide bonds and ionic bonds. Briefly describe how each of these four interactions is involved in protein folding and the conformation of the protein.