1. Protein Structure
C483 Spring 2013

2. A) The peptide bond only.
1. Which statement is false about a globular protein that performs its biological function as a single independent polypeptide chain?
A) Its tertiary structure is likely stabilized by the interactions of amino acid side chains in non-neighboring regions of the polypeptide chain.
B) It could contain α-helices that are stabilized by hydrogen bonding.
C) It likely has extensive quaternary structure to maintain its globular shape.
D) Non-covalent forces are the primary source of stability for the secondary and
tertiary structure.
2. The conformation of the backbone of a polypeptide is described completely by the angle(s) of rotation about which bond(s)?
A) The peptide bond only.
B) N-Cα only.
C) N-Cα, Cα-C and C-N bonds.
D) N-Cα and Cα-C bonds only.
3. Which structure indicates the proper
hydrogen-bonding pattern between amino
acids in an α-helix? (Dashed lines represent
the hydrogen bonds.)

3. 4. What would you expect about the formation of an α-helix for a segment of a protein chain that contains lysine approximately every fourth residue with all other residues being mostly hydrophobic?
A) Helix formation would be favored at low pH.
B) Helix formation would be favored at high pH.
C) Helix formation would be favored at neutral pH.
D) Helix formation would never occur regardless of pH.
5. Supersecondary structures that contain recognizable combinations of α-helices, β-strands and loops (e.g. the Greek Key) are called ________.
A) domains
B) folds
C) homologous regions
D) motifs
6. The principle forces holding subunits of an oligomeric protein to each other are ________.
A) peptide bonds
B) hydrophobic interactions
C) covalent bonds
D) disulfide bonds

4. Protein Structure Configuration and conformation Native structure
Fibrous
Globular
Atomic level and cartoon level

5. Structural Determination
Crystallography
NMR

6. Structural Hierarchy

7. C483 goals Secondary structure dictated by
Peptide bond structure
Atomic level intermolecular interactions
Tertiary and quaternary structure
Importance to protein folding and activity
Familiar with vocabulary so that you can read a paper to learn the details

8. Peptide Bond Resonance Highly polar Trans vs cis conformation
6 planar atoms form a unit
Highly polar
Trans vs cis conformation

9. Conformational Flexibility
If each peptide bond is relatively locked, backbone conformation can be defined by phi and psi
NOT cis/trans
Both stuctures to the right are trans

10. Ramachandran Plots

11. Alpha Helix Right handed Polarity Phi = -57o and psi = -47o
n and n + 4
Ala vs. Tyr
Gly and Pro

12. The average a-helix is 12 residues long. What is its length in nm?
How many amino acids/turn of an alpha helix?

13. Amphipathic Helices Structural Implications Coiled-Coil
Placement in Protein

14. Beta-Sheets

15. Real Beta Sheets Technically, often tertiary structure
Generally bent/twisted
Alternating sidechains can lead to amphipathic sheets

16. Loops and Turns Nonrepeating Change of direction
Turns have about 4 residues
Internal H-bonds
Gly, Pro

17. Tertiary Structure Longer range interactions of secondary features
Driven by hydrophobic effect
Disulfide bridges
Diversity

18. Tertiary Structure Too many shapes to memorize
But not an infinite number of possibilities
Take away the ability to read a paper
Discussions of motifs and why important
Discussion of domains and why important

19. Motifs (Super Secondary Structure)
Recognizable combinations of helices, loops, and sheets
Match
Helix-loop-helix
Helix bundle
Hairpin
b-sandwich

20. Studying Motifs Some Motifs are highly studied Know the Lingo
Leucine zipper
Zinc finger
Often have recurring applications

21. Domains
Discrete, independently folded unit (may maintain shape when cleaved on loop)
May have separate activities: “ATP binding domain” or “catalytic domain”
Similar activity = similar structure across many proteins
Binding pockets at interfaces
How many domains?

22. Common Domains

23. Quaternary Structure Multiple subunits: Oligomers
Homodimer, heterotrimer
Advantages
Economy
Stability
regulation a3
a2b2

24. From your discussion paper…

25. Answers C D B