INTRODUCTION TO PROTEIN STRUCTURE

Transcription

1 Name Class: Partner, if any: INTRODUCTION TO PROTEIN STRUCTURE PRIMARY STRUCTURE: 1. Write the complete structural formula of the tripeptide shown (frame 10). Circle and label the three sidechains which correspond to the three amino acid residues. 2. Indicate the peptide bonds in the above formula using arrows and labels as appropriate.. 3. Are the four atoms in each peptide group coplanar? 4. Identify the amino acid which is the N-terminus. 5. Identify the amino acid which is the C-terminus. 6. a. Does reversing the order of the 2 amino acids in G-A result in the same peptide? That is, is G-A the same as or different from A-G? b. Does reversing the order of the 3 amino acids in G-A-L result in the same peptide? That is, is G-A-L the same as or different from L-A-G? 7. a. Check the statement below which describes the relationship between G-A and A-G? They are identical They are constitutional isomers. They are stereoisomers. b. Which of the above statements describe the relationship between G-A-L and L-A-G? page 1

2 8. a. How many different dipeptides can have the residues glycine and alanine? Write their simplified formulas below. b. How many different tripeptides can have the residues glycine, alanine, and leucine? Write their simplified formulas below. 9. What can you tell about the number of possible peptide structures as the number of different amino acid residues in a polypeptide increases? 10. Considering your answers to previous questions and considering the large number of residues in proteins, explain why it is important to identify the primary structure of a protein. CONCEPT ASSESSMENT I: 1. How many amino acid residues does the polypeptide shown in the left frame have? 2. Identify each residue and determine which are the N-terminus and the C-terminus. 3. Describe the primary structure for this polypeptide. 4. Give the formula of any 2 constitutional isomers of this polypeptide. 5. Examine all the -CONH- group of atoms (amide groups). Are these atoms coplanar, that is, are they in the same plane? page 2

3 SECONDARY STRUCTURE: The alpha helix 1. Describe the primary structure of the polypeptide shown by determining the number of residues, their identities and their order in the structure. Also, identify the N-terminus and the C-terminus. 2. Considering that the space-filling mode gives a good approximation of the "real" shape of the molecule, how much space or "hole" is really there in the center of the helix? 3. Which display mode allows you to see the colied structure best? 4. Identify the groups of atoms that "stick out" and write their name beow.. 5. All the H s which were stripped off were directed away from the center. Describe how the H atoms on the -NH groups are oriented. 6. Compare the orientation of the H s in -NH with that of the carbonyl O s. 7. What special type of bonding is possible in situations such as this, where a H bonded to the highly electronegative N is adjacent to an electron-rich carbonyl O? page 3

4 8. Complete the following statements: a. The carbonyl O of the 2nd Ala residue is hydrogen bonded to the N of the Ala residue. b. The carbonyl O of the 3rd Ala residue is hydrogen bonded to the N of the Ala residue. c. The carbonyl O of the 4th Ala residue is hydrogen bonded to the N of the Ala residue. 9. From your answers to question 8a, 8b, and 8c, how many residues separate the hydrogenbonded atoms? SECONDARY STRUCTURE: The beta pleats 1. Describe the primary structure of the polypeptide shown by determining the number of residues, their identities and their order in the structure. Also, identify the N-terminus and the C-terminus. 2. Briefly describe why you think this secondary structure is referred to as "pleats" or, sometimes as "pleated sheets." 3. In the alpha helix, the sidechains are directed away from the central axis of the helix. Describe how the sidechains of the residues are oriented in the beta pleat structure. 4. In the beta-pleated structure, do the H-bonds involve the side chains? page 4

5 5. a. Complete the following table listing the residues in increasing numerical order:. Residue # Name of Amino Acid Residue Side chain above or below sheet? b. Is there some kind of order in the way the amino acid residues are arranged above and below the plane of the "sheet"? Can you think of a reason why this arrangement is necessary; that is, why can t all of the sidechains be located above (or below) the sheet? page 5

6 Questions for Tertiary & Quaternary Structure Tutorial 1. Using the amino acid table (link is at the bottom frame), make a list of four other possible pairs of residues whose side chains could form hydrogen bonds with one another. (besides ser-lys) 2. Again, using the amino acid table, give the names of residues other than those shown here (leu, gly, phe, val, ala) which would be energetically favored to be at the center of the structure shown. 3. How would you describe the secondary structure of myoglobin? Starting on pg 12 of this tutorial the buttons are not working. Switch to the "myoglobulin structure" tutorial (in window at the bottom of your screen) to answer the following three questions. If you right click the link and select "open in a new tab" it will be easier to get back to where you were in the current tutorial. 4. What types of residues are found on the surface of myoglobin? How would this explain the solubility of myoglobin in water? 5. What type of residue predominates at the center of the myoglobin molecule? 6. Does your answer to question 5 relate to the fact that myoglobin is globular and compact in its native aqueous environment? Explain.

7 After answering questions 4 6, switch back to tertiary structure tutorial and pick up at pg Use the amino acid table, and list as many pairs of residues as you can, the side chains of which are capable of forming salt bridges. 8. Write the formula of cysteine. 9. What is the difference between the bonds stabilizing tertiary and quaternary structures?