PreClass Questions 1. Draw the chemical structure (show all atoms) of MetCysLysGlnCysGluAla (a heptapeptide
— 7 amino acids joined by 6 peptide bonds) with the ionizable groups as they would appear most of the time in an environment of pH = 7.4. 2. Which two of its side chains can form a salt bridge? lysine and glutamate 3. Which two of its side chains can form a disulfide bond? cysteine and cycteine 4. What determines the primary structure of a protein i.e. the sequence of amino acids from its N
terminus to its Cterminus? Why might the primary structures of some of your proteins be different than your neighbor’s? DNA determines the primary structure of a proteins genetic code is going to vary from one person to the next 5. Describe a wide variety of functions performed by your body’s proteins (page 70 doesn’t mention
enough you can do better!). signaling transportation cell adhesion molecules fuel hormones ion channels enzymes structure protection movement
Protein Structures (Learning Objectives) 1. Describe the functions of your body’s proteins. (page 70 helps, but you can do better!) signaling, transportation (O2, albumin, transferrin), cell adhesion molecules, fuel, hormones/ messengers, receptors, channels/ pumps, enzymes, fibrous structure, cytoskeleton of cells, protection, movement (motor proteins), clotting factors, antibodies, storage which require a water soluble protein? which don't require a water soluble protein? 2. Define primary structure of a protein. Describe how the primary structures of your
proteins are determined by the genetic coding in your DNA. Describe how the primary structure of a protein determines its functional abilities. (pages 70 and 73) primary determined by a sequence of amino acids transcribed and translation from DNA instructions built into DNA's structure >> the sequence specified by the DNA's structure is translated into RNA (series of nucleotides) >> instructions built into mRNA's structure to be translated at a ribosome >> a protein is made based on the structure translated from the mRNA into a sequence of amino acids always built from Nterminus to Cterminus by convention 3. In Parts a) Draw a chemical structure to illustrate the backbone of a polypeptide chain. Given the chemical
structure for a segment of a polypeptide chain, be able to point the direction that would be towards the chain’s Nterminus and the direction that would be towards the chain’s Cterminus. (figures 1.5 and 7.3)
peptide bond the amide functional group b) Draw and describe the structure of a peptide bond. Define an amide. Illustrate the hydrolysis of a peptide bond with chemical structures, showing the products as they would appear most of the time in an environment of physiologic pH. (figure 6.3)
c) Draw a resonance structure to explain why there is not much rotation around peptide bonds. Describe the geometry (cis or trans) of a typical peptide bond. (figure 7.2)
delocalization of pi electrons resonance structures, restricted rotaion 4. Explain how a protein’s structure might be described in terms of four different levels.
Define primary structure, secondary structure, tertiary structure, and quaternary structure. Describe the bonds and interactions that stabilize each of these levels of protein structure. Describe the nature of hydrophobic interactions and how they form. (from page 88 through Quaternary Structure on pages 9697; figure 7.1; slide titled A Salt Bridge)
salt bridge ionic bonds between the peptide residues
5. Distinguish between globular proteins and fibrous proteins. Describe how a globular
protein accomplishes being soluble in water. Distinguish between digestion of and denaturation of a globular protein. Illustrate with chemical structures how a change to a more acidic environment can cause a globular protein to denature. (part A on page 90; part C on page 95; part 2 on page 105; figures 7.8 and 10.17; slide titled A Salt Bridge)
6. Describe the type of hydrogen bonding that stabilizes alpha helix and beta pleated sheet
secondary structures. Draw chemical structures to illustrate hydrogen bonding between atoms of different peptide bonds. For an alpha helix, describe the direction of the side chains relative to the long axis of the helix i.e. pointing outside away from the helix to participate in tertiary and quaternary interactions. (figure 7.3; slide titled Hydrogen Bonds that Stabilize AlphaHelices; figures 7.4, 7.5, and 7.7)
7. Describe how an alpha helix can be ideal for a membranespanning portion of a
transmembrane protein. Explain how proline is a helixbuster. (part D on pages 9596; figure 7.9; slide titled A Helix Buster)
8. Draw structures to illustrate the formation and breakage of disulfide bonds. (Apply redox
terminology appropriately.) Distinguish between interchain and intrachain disulfide bonds. (figure 6.6; slide titled Figure 6.6 in the Context of Protein Structure; figures 26.10 and 7.15)
only occur at cysteine via the oxidation of sulfhydryl groups
9. Describe the structure of a typical IgG immunoglobulin (antibody) molecule. (Section VIII
on pages 100101; figure 7.15)Enzyme kinetics: Predict the effect of an increasing substrate concentration on the velocity of an enzyme catalyzed reaction. Explain why a graph of reaction velocity versus substrate concentration flattens out (approaches Vmax) at higher substrate concentrations. Explain how an enzyme’s Km value is determined. Describe how a Km value reflects how well the enzyme binds its substrate. Explain the benefits that derive from the fact that the liver uses glucokinase, whereas more glucosedependent tissues use hexokinase, for the phosphorylation of glucose. (parts 13 on pages 137138; figures 9.2 and 9.3)
Suggested Review Questions (answers are in the back of the text): #1, #2, and #3 on page 111; #2 on page 170.