1. S ASC Answer to Practice Problem
Draw the chemical structure of the tripeptide Ala – Ser – Cys at pH 7.
Answer the following with regard to this tripeptide:
1. Indicate the charge present on any ionizable group(s).
2. Indicate, using an arrow, which covalent bond is the peptide bond.
3. What is the net, overall charge of this tripeptide at pH 7? __________
4. What is this peptide called using the one-letter code system for amino acids? ______ S
ASC

2. Structure and Function
Proteins:
Three Dimensional
Structure and Function

3. Ribbon diagram
Space-filling model
Figure 4.3

4. Levels of Protein Structure
Figure 4.1

5. Resonance structure of
the peptide bond
Figure 4.5

6. Planar peptide groups in a polypeptide chain
Figure 4.6

7. Trans and cis conformations of a peptide group
Figure 4.7
Nearly all peptide groups in proteins are in the trans conformation

8. Rotation in a peptide
Figure 4.8
phi
psi
N-Ca Ca-C

9. Ramachandran Plot
Figure 4.9

10. Secondary Structure of Proteins

11. The alpha helix
Figure 4.10

12. The alpha helix
Figure 4.11

13. An amphipathic alpha helix
Figure 4.12

14. Amphipathic alpha helices are often found on the surface of a protein
Figure 4.13

15. The beta sheet
Parallel
Figure 4.16

16. The beta sheet
Parallel
Figure 4.16 N N N

17. The beta sheet
Antiparallel
Figure 4.16

18. The beta sheet
Antiparallel
Figure 4.16 N N N

19. Side chains alternate from one side to another
The beta sheet.
Side chains alternate from one side to another
Figure 4.17

20. Levels of Protein Structure
Figure 4.1

21. Reverse turns
Figure 4.19
Type II b turn
Type I b turn

22. Reverse turns
Figure 4.19
Type II b turn
Type I b turn

23. Tertiary Structure of Proteins

24. Supersecondary structures, often called “motifs”
Figure 4.20

25. Domain folds in proteins
Figure 4.25

26. Figure 4.24

27. Quaternary Structure
Figure 4.26

28. Protein Folding and Stability

29. How do proteins fold and unfold? The information for proteins to
fold is contained in the
amino acid sequence.
Can proteins fold by themselves or do they need help?

30. Protein folding proceeds through intermediates

31. Intermediates in protein folding
Figure 4.37

32. Heating proteins will unfold or “denature” the molecule.
Figure 4.31

33. Anfinsen’s protein folding experiment
Figure 4.35

34. Protein Folding
A cell can make a biologically active protein of 100 amino
acids in 5 seconds.
If each amino acid could adopt 10 different conformations
this makes different conformations for the protein.
If each conformation were randomly sampled in seconds
it would take 1077 years
Therefore protein folding must not be a random process.

35. Energy well of protein folding
Figure 4.36

36. Forces driving protein folding:
Hydrophobic effect
Hydrogen bonding
Charge-charge interactions
Van der Waals interactions

38. Molecular Chaperones (Chaperonins)
Some proteins don’t spontaneously fold to native structures.
They receive help from proteins called chaperonins
Best characterized chaperonin system is from E. coli.
GroEL / GroES chaperonin system (GroE chaperonin)
These chaperonins bind to unfolded or partially folded proteins
and prevent them from aggregating. They assist in
refolding the proteins before releasing them.

39. GroE
Figure 4.38

40. Chaperonin-assisted protein folding
Figure 4.39

41. Three-dimensional structures of specific proteins
1. Collagen, a fibrous protein
2. Myoglobin and Hemoglobin, O2 binding proteins
3. Antibodies

42. Collagen is a fibrous protein found in vertebrate connective tissue.
Collagen has a triple helix structure, giving it strength greater than a steel wire of equal cross section.

43. 21% Proline + Hydroxyproline The repeating unit is
Collagen is
35% Glycine
21% Proline + Hydroxyproline
The repeating unit is
Gly – X – Pro (HyPro)
The interior of a collagen triple helix is packed with Glycines (red)

44. 4-Hydroxyproline and 5-Hydroxylysine residues
Figure 4.41 and 4.43

46. Allysine and lysine residues form cross-links in collagen
Figure 4.44

47. Allysine residues form cross-links in collagen
Figure 4.44

48. Hemoglobin and Myoglobin bind oxygen
Figure 4.46
Heme
Histidines
Protein

50. Red blood cells (erythrocytes)

51. Myoglobin is monomeric and binds oxygen in the muscles
Figure 4.44
Heme
Histidines
Protein

52. Hemoglobin is tetrameric and carries oxygen in the blood
Figure 4.48

54. His 64
Fe2+ O2
Heme
His 93
Whale Myoglobin
Figure 4.51

55. Oxygen binding curves of hemoglobin and myoglobin
Page 124
Y = Fractional oxygen saturation of myoglobin
Mb = Concentration of myoglobin molecules without bound oxygen
MbO2 = Concentration of myoglobin molecules with bound oxygen
Mb + MbO2 = total concentration of myoglobin molecules

56. Oxygen binding curves of hemoglobin and myoglobin
Figure 4.52

57. Oxygen binding induces protein conformational changes
Figure 4.53

58. Hemoglobin binds 2,3-Bisphosphoglycerate at an allosteric site.
2,3-Bisphosphoglycerate lowers the affinity for oxygen.
Figure 4.54

59. CO2 and H+ bind to hemoglobin and decrease oxygen affinity.
Figure 4.55

60. Antibodies are proteins of the vertebrate immune system.
Antibodies specifically bind to foreign compounds (antigens)
Figure 4.57

61. Binding of three different antibodies to an antigen
Figure 4.59