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7. What are essential amino acids? How are they different from non-essential amino acids? Do all organisms have the same set of essential amino acids? What role do essential amino acids play in human biochemistry?
8. How and why are protein molecules affected by the pH of their environment? How can the Henderson-Hasselbalch equation be used to tell us about the response of protein molecules to changes in pH?
9. Describe the use of affinity chromatography and explain why it is such a powerful technique for purifying proteins. Why is it more powerful than most other methods.
10. Many biological compounds could potentially exist as more than one stereoisomer, but only one steric form is used for a given function. Why is the selection of only one steric form a necessary feature of living organisms? What would happen to the protein product if an organism could randomly add either D- or L-amino acids during protein synthesis.
What roles do proteins play in cells?
What are the monomers of proteins? Describe their basic structure.
What does the nature of the side chains (R groups) of amino acids suggest about their basic position in membrane proteins? What about in the cytoplasm? Or in the bloodstream?
Specifically how are amino acids linked together?
What is the primary structure of a protein? How is it determined?
Describe the interactions between amino acids that contribute to form the secondary structure of a protein. What are some of the basic configurations that result?
Describe the interactions between amino acids that form the tertiary structure of a protein.
What is the quaternary structure of a protein? Is this always a feature of protein structure?
Describe the role of chaperonins (chaperone proteins) in determining the final structure of a protein. Why are these chaperones necessary?
Use text Figure 5.19 to discuss the importance of protein structure in determining function. Be sure to use the vocabulary relevant to this topic in your discussion.
Proteins are naturally occurring polymers formed by condensation reactions of amino acids, which have the general structure
In this structure, –R represents –H, –CH3, or another group of atoms; there are 20 different natural amino acids, and each has one of 20 different R groups. (a) Draw the general structure of a protein formed by condensation polymerization of the generic amino acid shown here. (b) When only a few amino acids react to make a chain, the product is called a “peptide” rather than a protein; only when there are 50 amino acids or more in the chain would the molecule be called a protein. For three amino acids (distinguished by having three different R groups, R1, R2, and R3), draw the peptide that results from their condensation reactions. (c) The order in which the R groups exist in a peptide or protein has a huge influence on its biological activity. To distinguish different peptides and proteins, chemists call the first amino acid the one at the “N terminus” and the last one the one at the “C terminus.” From your drawing in part (b) you should be able to figure out what “N terminus” and “C terminus” mean. How many different peptides can be made from your three different amino acids?