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University of Florida Biochemistry Practice Questions

Questions 1 thru 10 are worth 4 points each, and question 11 is worth 10 points to total 50.

  • Give the one and three letter abbreviations and R group classification for:
    Alanine, Cysteine, Proline, Phenylalanine, Lysine, and Aspartate
  • What bond type forms the primary protein or peptide structure? Where in the cell is this bond created?
  • What are the advantages and disadvantages of HPLC as a technique for the separation of proteins and peptides? Name one other technique one might employ for separating and purifying proteins.
  • Define the term PI as it relates to an amino acid.
  • Which degradation procedure provides information about the primary structure of proteins? Explain this process in detail.
  • What property of amino acids permits the measurement of protein concentration by UV light absorption?
  • Can the amino acid methionine perform the same function as cysteine? ? Explain in detail why or why not.
  • Explain why individual amino acids are soluble in water, and why not all peptides are water-soluble?
  • Name a critical reagent used in electrophoresis to separate polypeptides based on their mass.
  • How do number, sequence, and properties of amino acids in a protein affect its structure and function?
  • Using the UF library resources online, locate the following journal article:
    Touch V, Hayakawa S, and Saitoh K. (2004) Food Chemistry 84 (3): 421-428.

Questions 1 thru 10 are worth 3 points each, and 11 and 12 are worth 10 points each.

  • Many weak interactions contribute to protein tertiary and quaternary structure. What causes peptide bonds themselves to be planar?
  • Explain why Psi (ψ) and Phi (Φ) cannot both be zero.
  • Compare and list the kinds of amino acids that may make up a polypeptide in a α-helix structure with those found in ß-sheet structures. What are the limitations of each of these conformations on the types of amino acid residues that may be incorporated?
  • Explain which technique(s) you would use to determine if a protein has quaternary structure.
  • List the conditions under which proteins become denatured and what bonds and interactions are disrupted during denaturation?
  • Explain in detail whether or not a single amino acid could be an effective antigen and how a single amino acid substitution could affect ligand binding?
  • Describe how an induced fit increases the strength of interaction between and antibody and an antigen.
  • Name a protein that can exist in globular or filamentous form. Explain in detail the process by which one form is converted to the other.
  • Describe the important protein – protein interactions between motor proteins. What other proteins are directly involved in the muscle contraction process?
  • Briefly outline the mechanism by which heme is bound to globin? How could the cooperative binding of oxygen to hemoglobin be demonstrated graphically?
  • Using your text and searching online, list what types of circumstances elicit chaperone proteins. Briefly describe the role of chaperonins and posit how they might be used therapeutically.
  • Proteins comprising receptors can often transition across multiple conformational states.

Locate the following journal article.

Maelicke A, and Albuquerque E. (2000). European Journal of Pharmacology 393 (1-3): 165-170.

  • What property does the nicotinic acetylcholine receptor and the proposed treatment exhibit with regards to cooperative behavior?
  • What other specific example demonstrating this type of modulation of receptor activity is mentioned in the article?
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