Amino acids 1. For the four amino acids below: Ile Arg Asn Glu a. What is the net charge of each amino acid at physiological pH? b. What is the classification of each amino acid? 2. Identify an amino acid that has in its side chain a (an) --------------. a. thiol b. phenol c. sulfide d. alcohol e. amide f. aromatic ring 3. Which nonpolar amino acid has a side chain that can participate in hydrogen bonding? Polypeptides 1. Draw the tripeptide Asp-Val-Ser. Label the terminuses in this tripeptide. 2. List all of the possible polypeptides that can be formed from the three amino acids, cysteine (Cys), leucine (Leu), and arginine (Arg). 3. Which of the 20 amino acids can participate in a disulfide bridge? What level of protein structure involves this covalent bonds between two sulfur atoms? Protein structure 1. What is the primary (1 o ) structure of a protein 2. Describe the two types of secondary (2 o ) structure of proteins. 3. Describe the tertiary structure of a protein. What are the chemical bonds or IMF's responsible for maintaining the 3 o structure? 4. Describe the quaternary structure of hemoglobin. What are the chemical bonds or IMF's responsible for maintaining the 4 o structure? 5. Name pairs of amino acids that have side chains that can participate in salt bridge formation at pH=7? 6. a. Draw the polypeptide fragment shown below in its line bond formula or condensed structural formula at the physiological pH = 7. Leu-Ala-Trp-Phe-Gly b. Label C-terminus & N-terminus of the polypeptide fragment. Circle the peptide bonds. c. In an aqueous environment, will the peptide fragment more likely be buried inside or located on the surface? Why? d. What is most likely to change the biological activity: Replacement of the Leu with Ile residue or the replacement of Leu with Glu? Please discuss why. 7. What distinguishes a protein: a. that has a 4 o structure from one that does not? b. a simple protein form a conjugated (complex) protein? Denaturation 1. What is denaturation? List some of the ways to denaturation a protein. 2. Discuss what happens when a native protein is subjected to the following agents? Identify the IMF's or chemical bonds that are disrupted. a. Alcohol b. Soaps and detergents c. Changes in pH d. Heavy metal ions such as Pb 2 + e. Heat or Agitation 3. True or False: A denatured globular protein -------------. a. contains no peptide bond b. has an abnormal 1 o structure c. is biologically inactive Digestion of Proteins 1. What part of the digestive system is involved in the digestion of proteins? 2. Name the functional group hydrolyzed when a protein undergoes digestion. 3. Name an enzyme that catalyzes the digestion of proteins. 4. What products are formed when a protein undergoes digestion?