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2.6: Amino Acids and Proteins (Exercises)

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    Questions

    1.1: Amino Acids

    Q1.Read the material at:

    https://chem.libretexts.org/Courses/University_of_Arkansas_Little_Rock/CHEM_4320%2F%2F5320%3A_Biochemistry_1/02%3A__Protein_Structure/2.6%3A_Amino_Acids_and_Proteins_(Exercises) and answer the following questions:

    a. What are essential amino acids?
    b. What are nonessential amino acids?
    c. What happens if you are deficient in an amino acid?

    Q2. Draw the functional groups present in all amino acids.

    Q3. Complete the following for threonine, lysine, and tyrosine.

    a. Draw the amino acid.
    b. Circle the side chain.
    c. Identify whether it is polar, nonpolar, acidic, or basic.
    d. At what pH will it exist as a zwitterion?
    e. What is the range of pH values when it will be positively charged?
    f. What is the range of pH values when it will be negatively charged?

    1.5: Peptides

    Q4. Draw the two dipeptides formed from each pair of amino acids.

    a. tyrosine and lysine
    b. threonine and gluatmine
    c. alanine and histidine

    Q5. Draw and give the full names of the amino acids in the following dipeptides.


    Q6. List of all of the possible polypeptides that can be formed from threonine, alanine, and phenylalanine (use three character abbreviations for each amino acid).

    Q7. Draw the following polypeptides.

    a. Ser-Tyr-Gln
    b. Lys-Met-Gly

    Q8. Identify each of the amino acids in the polypeptide and then name it using the three character abbreviations.

    2.1: Protein Structure

    Q9. Describe the four levels of protein structure.

    Q10. What levels of structure involve hydrogen bonding?

    Q11. What types of structure is the result of interactions between amino acids that are far apart in the primary structure?

    Q12. What types of interactions hold the secondary structure together?

    Q13. What types of interactions hold the tertiary structure together?

    Q14. What levels of structure are affected by denaturation?

    Q15. A protein has one subunit. Would it have a quaternary structure?

    Answers

    1.1: Amino Acids

    Q1

    a. Essential amino acids are those you get from your diet.
    b. Nonessential amino acids are produced in the body.
    c. Illness and/or degradation of body's proteins.

    Q2

    amino_acid_functional_groups.png

    amine and carboxylic acid

    Q3

    Complete the following for threonine, lysine, and tyrosine.

    threonine

    1.  
    2. threonine.png
    3. polar
    4. 5.60
    5. < 5.60
    6. > 5.60

    lysine

    1.  
    2. lysine.png
    3. basic
    4. 9.47
    5. < 9.47
    6. > 9.47

    tyrosine

    1.  
    2. tyrosine.png
    3. polar
    4. 5.63
    5. < 5.63
    6. > 5.63

    1.5: Peptides

    Q4

    Draw the two dipeptides formed from each pair of amino acids.

    a. tyr_lys.png


    b. threonine_gluatmine.png


     

    c. alanine_histidine.png

    Q5

    a. alanine alanine.png glycine glycine.png
    b. proline proline.png phenylalanine phenylalanine.png
    c. tryptophan tryptophan.png lysine lysine1.png

    Q6

    Thr-Ala-Phe

    Thr-Phe-Ala

    Ala-Thr-Phe

    Ala-Phe-Thr

    Phe-Ala-Thr

    Phe-Thr-Ala

    Q7

    a. Ser-Tyr-Gln.png


    b. Lys-Met-Gly.png

    Q8

    13_2_5_b.png

    Arg-His-Thr-Glu-Ser

     

    2.2: Protein Structure

    Q9

    Primary - sequence of amino acids

    Secondary - alpha helix and Beta-pleated sheets held together by hydrogen bonds

    Tertiary - third level of structure of protein often forming globular or fibrous structure, held together by variety of attractive forces

    Quaternary - complex of multiple proteins held together to function as one, held together by variety of attractive forces (same as tertiary)

    Q10

    secondary, tertiary, and quaternary structures

    Q11

    tertiary structures

    Q12

    hydrogen bonds

    Q13

    London dispersion forces, hydrogen bonds, dipole-dipole forces, ion-dipole interactions, salt bridges, and disulfide bonds

    Q14

    secondary, tertiary, and quaternary

    Q15

    No, a quaternary structure must have multiple subunits.

    Concept Review Exercises

    1. What is the predominant attractive force that stabilizes the formation of secondary structure in proteins?

    2. Distinguish between the tertiary and quaternary levels of protein structure.

    3. Briefly describe four ways in which a protein could be denatured.

    Answers

    1. hydrogen bonding

    2. Tertiary structure refers to the unique three-dimensional shape of a single polypeptide chain, while quaternary structure describes the interaction between multiple polypeptide chains for proteins that have more than one polypeptide chain.

    3. (1) heat a protein above 50°C or expose it to UV radiation; (2) add organic solvents, such as ethyl alcohol, to a protein solution; (3) add salts of heavy metal ions, such as mercury, silver, or lead; and (4) add alkaloid reagents such as tannic acid

     

     

    1. Classify each protein as fibrous or globular.

      1. albumin
      2. myosin
      3. fibroin

    2. Classify each protein as fibrous or globular.

      1. hemoglobin
      2. keratin
      3. myoglobin

    3. A protein has a tertiary structure formed by interactions between the side chains of the following pairs of amino acids. For each pair, identify the strongest type of interaction between these amino acids.

      1. aspartic acid and lysine
      2. phenylalanine and alanine
      3. serine and lysine
      4. two cysteines

    4. A protein has a tertiary structure formed by interactions between the side chains of the following pairs of amino acids. For each pair, identify the strongest type of interaction between these amino acids.

      1. valine and isoleucine
      2. asparagine and serine
      3. glutamic acid and arginine
      4. tryptophan and methionine

     

    5. What level(s) of protein structure is(are) ordinarily disrupted in denaturation? What level(s) is(are) not?

    6. Which class of proteins is more easily denatured—fibrous or globular?

     

    This page titled 2.6: Amino Acids and Proteins (Exercises) is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Allison Soult.

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