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Senanu's Bio class

Chapter 3 – Proteins

OBJECTIVE: Describe the formation and breakdown of polymers by dehydration and hydrolysis reactions.

  1. A _____________________ is a long molecule made up of subunits called __________________. They are assembled in a chemical reaction called ____________________ and disassembled in a chemical reaction called ________________.

  2. Look at Fig 3.3 (5.5 in 6th ed.). Why do you think this is called a dehydration reaction?

    OBJECTIVE: Describe the structure and function of amino acids and proteins.

  3. Study diagram 3.1. This is the general form for ALL amino acids. How many covalent bonds does the alpha carbon of an amino acid form? __________Why?
  4. Look at the general structure/formula of an amino acid (fig 3.1). Overall, are amino acids hydrophobic or hydrophilic? Explain why.
  5. Draw the general structure of an amino acid in non-ionized AND ionized forms (Fig 3.1) and label the alpha carbon.
  6. In the structure above, circle and label the two functional groups present in every amino acid (which is why they are called amino acids!).
  7. What would the carboxyl group look like if it came into contact with a base? Remember that a base absorbs H+ ions from the solution.

  8. In Figure 3.2, the amino acids are shown in their ionic forms at pH ~7. Using glycine as an example, show how the general structure of an amino acid would be different at an extremely acidic pH? A very basic pH? Explain.

    Glycine @ pH2 Glycine @ pH7 Glycine @ pH13

    OBJECTIVE: Be able to identify amino acids as hydrophilic or hydrophobic and whether they have polar, nonpolar, or electrically charged side chains. You do NOT need to memorize all amino acids, but you should be able to identify properties if given the structure of an amino acid.

  9. How many different types of amino acids are present in the proteins of living organisms?_______________ What is the word ending (suffix) of most amino acids? __________________
  10. Which part of the amino acids is used to sort them into their groups?
  11. Observe the R-groups in the nonpolar side chains; non-polar (hydrophobic) category. Do you expect to find any amino acids in this category with polar covalent bonds in the R-group? Why or why not?
  12. Which of the amino acids in this category contains a polar covalent bond in its R-group? ______________________________. Draw the structure of this amino acid writing out all the C’s and H’s not shown in the structure in the text and label the polar bond. Why do you think this amino acid is considered non-polar even though it has one polar bond?

  13. Draw the structure of an amino acid with a basic side chain. Show how this region could hydrogen bond with a water molecule.

    OBJECTIVE: Be able to recognize and draw a peptide bond between 2 amino acids

  14. What type of reaction occurs when a monomer is added to a polymer (look back at 2.24 (3.4 in 6th ed))?
  15. What type of bond forms?
  16. What types of reactions occur when a polymer is disassembled/”broken” into monomers?
  17. What types of bonds are broken?

  18. Draw 2 glycine amino acids next to each other. Show with arrows how the peptide bond forms and what molecule comes out of this reaction.

    OBJECTIVE: Understand the difference between a polypeptide and a protein

    OBJECTIVE: Understand how side chains affect the physical properties of polypeptides

  19. What is a polypeptide chain?

  20. How is a polypeptide different from a protein?

    OBJECTIVE: Explain what proteins look like and understand how protein function depends on its structure.

  21. Name the four levels of protein structure organization and list the types of bonds involved in each level.

    Level of protein structure Description Type of bonds
    Primary
    Seconday
    Tertiary
    Quarternary
  22. Which levels of protein structure are present in all proteins?
  23. Refer to Figure 3.12 (3.13 in 6th ed). What happens when a protein is denatured?
  24. Why does denaturation of a protein destroy its function?
  25. Do you agree with the statement that secondary, tertiary, and quaternary structure all depend on the primary structure of a protein? Why or why not?
  26. Name a disease that are caused by mis-folded proteins.

Do this section in on after class…

  1. Draw 3 glycine molecules side-by-side. Draw them in the state in which they would exist in water at pH7.
  2. Connect the 3 glycines with peptide bonds. How many peptide bonds do you need to draw to connect these 3 amino acids?
  3. A protein is usually described as having an N-terminus and a Carboxyl terminus. Label both ends in your drawing above.
  4. Chymotrypsin is a large globular protein shown in Fig 3.6 (3.8 in 6th ed). What type of amino acids (non-polar, polar, or charged) would you expect to see folded into the interior of the protein? What would you expect to see on the surface?