Study Guide 5
Last revised: Tuesday, September 11, 2001
Topic: Proteins and Nucleic Acids

Chapter 5. This is the second of two study guides covering material in Chapter 5. I strongly recommend the Biology Place tutorial on "Properties of Biomolecules" as additional study material (http://www.biology.com/learning/bioprop/intro.html)

  1. Terms. Be able to recognize and correctly apply the following terms:
    Alpha helix
    Pleated sheet
    Disulfide bridge
    Denaturation
    Chaperone protein
    Pyrimidine base
    Purine base
    Polynucleotide

  2. What are some common functions for proteins? (see notes and table 5.1)
  3. What characterizes an amino acid? How is it different from a sugar? How is it different from a fatty acid? Be able to recognize the difference between these molecules
  4. How many types of amino acids are there? Study Table 5.15. Into what categories are different amino acids grouped?
  5. What is the difference between the terms “peptide”, “polypeptide”, and “protein”?
  6. How is a peptide bond produced? Which of the following is characteristic of a peptide bond: (a) —C—O—N— (b) —C—N— (c) —C—O—O—N— (d) —C—O—C—
  7. Many scientific publications today contain polypeptide amino acid sequence information. You should be able to look at such sequences and interpret them. The following 3 exercises will help you develop this skill. Work through each exercise carefully, including drawing out the structures asked for!
    Polypeptides consist of amino acids linked together by peptide bonds, as indicated in the following diagram:



    The sequence of amino acids is indicated by either a 3-letter code or a 1-letter code. For example:

    3-letter code: Met-ser-leu-val-...
    1-letter code: MSLV

    The table at the end of this guide indicates the names and code symbols for the 20 amino acids found in proteins.

    Exercise 1: Refer to the diagram on page 69 of your text (Figure 5.15), which shows the chemical structure of all 20 amino acids.
    Compare the two peptides shown below. Which one has significantly more non-polar amino acids? (Hint: in Fig. 5.15, notice how the amino acids are grouped in 3 different groups).

    Peptide A: MLVICAAVRGGP
    Peptide B: MDVSEGHGSSGP

    Exercise 2: Here is a diagram of a peptide:



    Identify the amino acids present, using Figure 5.15. Write the 3-letter and 1-letter sequence of this peptide. Note: by convention, the Amino-terminus (NH2-) end of the peptide is always written on the left, and the Carboxy-terminus (-COOH) is always written on the right. Your answer should take the form:
    N-asp-ser-glu-gly-C (these are not the correct amino acids)

    Exercise 3: Here is the beginning of the actual amino acid sequence for a polypeptide:
    LNEHSLIEIEGLNKT.................

    Using the amino acid representations in Figure 5.15 of your text, draw the first five amino acids, illustrating the peptide bonds that join them. Use the diagram in Exercise 2 as a guide to what your drawing should look like.
  8. What are the stages by which proteins fold up? What types of strong or weak chemical bonds contribute to 1o, 2o, 3o, and/or 4o structure? Do all proteins have 4o structure? At what point in folding does a protein acquire active function? What happens to a protein when it denatures? Is denaturation reversible?
  9. How do DNA and RNA differ in structure?
  10. Recognize the difference between a pyrimidine and a purine base.
  11. How do ribose and deoxyribose sugars differ? How are they similar?
  12. What components are found in a nucleotide?
  13. In a base pair such as G-C or A-T, what holds the bases together?
  14. What is the difference between ADP and dADP? Between dGMP and dGTP? Between dCTP and CDP?



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