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16: Proteins: Structure and Function: Questions

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    43930
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    Amino Acids

    (01) For the following five amino acids, examine their side chains and determine whether the side chain is nonpolar, acidic, or basic. Assume each amino acid is at physiological pH.

    1. Tryptophan
    2. Histidine
    3. Methionine
    4. Phenylalanine
    5. Glutamic acid

    (02) For each of the following functional groups, name at least one amino acid that has one in its structure.

    1. an aromatic ring
    2. an alcohol
    3. an amide
    4. an additional amines
    5. a phenol

    (03) A thiol is a functional group that is not commonly focused upon during this course but is present amongst some of the amino acids. What element is found in thiols to distinguish them from other functional groups? How many amino acids contain thiols in their side chains? Name each of them.

    (04) An example of an amino acid is shown below. Answer the following questions relating to its structure.

    4.jpg

    1. Circle the amine functional group. Is the amine neutral or ionic?
    2. Put a triangle around the carboxylate functional group. What is the one thing that differs between a carboxylate and a carboxylic acid?
    3. What is the definition of a zwitterion? Does this particular amino acid fit the definition? Name the amino acids that can NOT be considered a zwitterion at physiological pH.
    4. Box the entire side chain of the amino acid. Use this to identify the name of this amino acid.
    5. Describe the character of the side chain. Is it nonpolar, polar, acidic, or basic?
    6. Sketch the amino acid and what it would look like if you raised the pH up to 11. Is it positively charged, negatively charged or neutral overall? Repeat this with the pH changed down to 4.

    (05) Fill in the following table with ‘Y’ to indicate ‘yes’ and ‘N’ to indicate ‘no’ for each box as it pertains to each listed amino acid in each category. Some of the names are given only as their three-letter abbreviations.

    Amino Acid

    Nonpolar

    Polar

    Acidic Side Chain

    Basic Side Chain

    Essential?

    Proline

    Cys

    Asp

    Serine

    Gln

    Chirality and Amino Acids

    (06) Knowing the definition of chirality, determine if these macro-level objects can meet the definition of being chiral or not.

    1. a compact disc
    2. an arrow
    3. an open palm
    4. a crumpled-up piece of paper
    5. a shoe

    (07) Examine the given pair of molecules and answer the following questions.

    ch16q7.png

    1. What functional group(s) are common to both structures?
    2. Write out the chemical formulas for each compound. Are they the same or different? Do they have the same atoms bonded to the central atom?
    3. Construct a model of the two compounds using your kit. Do they both have the same 3D spatial orientation?
    4. Align two of the groups bonded to the central carbons (either on paper or using your model kit). Which parts overlap identically? Which parts do not?
    5. Are these two compounds non-superimposable mirror images of one another? Rotate your page or models as needed to test this.
    6. Define the term ‘enantiomers’. Can these two compounds be considered a pair of enantiomers?
    7. Do these two compounds fit the definition of ‘chiral’?

    (08) What is a racemic mixture? Sketch the Fishcer projections of the compounds present in a racemic mixture of serine. Specify the relative concentration of each component.

    Peptides

    (09) Amino acids can link together to create chains of varying sizes known as polypeptides. Chains of two amino acids are known as dipeptides. Given the following pairs of amino acids, sketch the dipeptides they form when linked together at physiological pH.

    1. Phenylalanine and proline
    2. Threonine and aspartic acid
    3. Lysine and tryptophan
    4. Tyrosine and methionine
    5. Glutamine and cysteine

    (10) Sketch the following two tripeptide chains: Asp-Gly-Ser and Ile-Asn-Met

    (11) Look carefully at the following polypeptide chain and use its structure to answer the following questions.

    ch16q11.png

    1. Provide the sequence for the peptide using the 3-letter abbreviations.
    2. Which amino acid is the N-terminus? Which amino acid is the C-terminus?
    3. Circle the side chains and classify them as non-polar, polar, acidic, or basic.

    Protein Architecture

    (12) Name the four different types of interactions responsible for creating tertiary structures in proteins.

    (13) Disulfide bridges are limited in that only one particular amino acid can form these types of interactions. Name the amino acid, and sketch two of them forming a disulfide bridge.

    (14) Salt bridges are more commonly formed compared to the aforementioned disulfide bridges. Which amino acids have side chains with the potential to form salt bridges? Sketch an example of two compatible amino acids forming a salt bridge.

    (15) In a globular protein, where would you expect the nonpolar regions to be located? Whereabouts would you expect the more polar regions to be found?

    (16) In general, proteins can be classified into 3 different groups. Name and give a short description of each type and how they are distinct from one another. Provide an example of a macromolecule or other complex structure representing each of the three types.

    (17) Look at the following disulfide bridge. Cleavage of the disulfide bridge will occur via a reduction reaction; sketch the products at physiological pH. Circle and identify any functional groups in each product.

    20a.jpg20b.jpg

    (18) Name at least three amino acids whose side chains have the characteristic of being able to repel water.

    (19) Define denaturation of proteins and list five different ways to denature a protein?

    Enzymes

    (20) Enzymes are large protein structures that require specific parameters to operate. Deviations from optimal conditions can cause them to cease to function. What is the ideal body temperature and pH for them to remain operational? If there is an exception to this general rule, please name an example and how it differs from functioning within the normally accepted environmental conditions within the body.

    (21) Enzymes, like other catalysts, facilitate reactions occurring but do not themselves get ‘used up’ within the reaction. Knowing this, complete the following equations by filling in the blanks. (E stands for enzyme, S stands for substrate, P stands for product.)

    \[ E + ? \rightleftharpoons ES \rightleftharpoons ? + P\]

    (22) If an enzyme works as a catalyst, determine its effect (if any) on the reaction it catalyzes.

    1. ∆H
    2. Ea
    3. reaction rate
    4. equilibrium

    (23) Determine which of the following enable enzyme-substrate complex formation.

    1. Salt bridges
    2. Dipole-dipole interactions
    3. Hydrogen bonds
    4. Covalent bonds
    5. London dispersion forces

    (24) Would it be possible, in general, for biochemical reactions to occur without the aid of enzymes? What type of biochemical reaction(s) do not need a catalyst?

    (25) How does a non-competitive inhibitor work? Is a non-competitive inhibitor considered a specific or non-specific inhibitor? If both competitive and non-competitive inhibitors both prevent a substrate binding to an enzyme in different ways, what other major difference separates them?

    (26) Study the following energy diagram for an enzyme catalyzed reaction. Label Ea or ∆H and indicate whether ∆H is positive or negative.

    rxn energy diagram exo.png

    Contributors

    • Anonymous


    16: Proteins: Structure and Function: Questions is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by LibreTexts.

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