1. Molecular Cell Biology
Professor Dawei Li
Textbook: MOLECULAR CELL BIOLOGY 6th Ed
Lodish • Berk • Kaiser • Krieger • Scott • Bretscher •Ploegh • Matsudaira
Part 1. Chemical and Molecular Foundations
Life Begins with Cells (p1-30) (Questions)
Chemical Foundations (p31-62) (Self-review)
(1Characteristics of amino acids, 2 Interacting forces)
3. Protein Structure and Function (p63-110)
(Selected Contents)

2. Life Begins with Cells (p1-30) Q&A
Review
Life Begins with Cells (p1-30) Q&A
Chemical Foundations (p31-62) (Self-review)
1. Characteristics of amino acids:
2. Interacting forces: 2

3. Chapter 3 Protein Structure and Function (63-110)
• 3.1 Hierarchical Structure of Proteins
• 3.2 Protein Folding
• 3.3 Protein Function
• 3.4 Regulating Protein Function I:
Protein Degradation
• 3.5 Regulating Protein Function II
Noncovalent and Covalent Modifications
• 3.6 Purifying, Detecting, and Characterizing Proteins
• 3.7 Proteomics

4. Figure 3-1
Overview of
protein structure
and function.

5. 3.1 Hierarchical Structure of Proteins
Figure 3-2
Four levels of
protein hierarchy.

6. The primary Structure of a Protein Is Its LinearArrangement of
Amino Acids
Figure 3-3
Structure of a
polypeptide.

7. Secondary Structures Are the Core Elements of Protein Architecture
The Helix
Figure 3-4
The helix,
a common secondary
structure in protein.

8. β
The Sheet
Figure 3-5
The sheet,another
common secondary
structure in proteins. β

9. β Turns
Figure 3-6
Structure of a turn. β

10. Overall Folding of a Polypeptide Chain Yields Its Tertiary Structure
Figure Oil drop model of protein folding.

11. Different Ways of Depicting the Conformation of Proteins Convey
Different Types of Information
Figure 3-8 Four ways to visualize protein structure.

12. Structural Motifs Are Regular Combinations of Secondary and
Tertiary Structures
Figure 3-9 Motifs of protein secondary structure.

13. Structural and Functional Domains Are Modules of Tertiary
Structure
Figure Tertiary and quaternary
levels of structure.

14. Structural and Functional Domains Are Modules of Tertiary
Structure
Figure Modular nature of protein domains.

15. Protein Associate into Multimeric Structures and Macromolecular
Assemblies
Figure A macromolecular
machine:the transcription-initiation
complex.

16. Members of Protein Families Have a Common Evolutionary Ancestor
Figure Evolution of the globin protein family.

17. The 9 Key Concepts of Section 3.1 (p73)

18. 3.2 Protein Folding Planar Peptide Bonds Limit the
Shapes into which Proteins Can Fold
Figure Rotation between
planar peptide groups in proteins.

19. Information Directing a Protein's Folding Is Encoded In Its
Amino Acid Sequence
Figure 3-15
Hypothetical protein-folding
pathway.

20. Molecular Chaperones
Figure Chaperone-mediated protein folding.

21. Chaperonins
Figure Chaperonin-mediated protein folding.

22. Alternatively Folded Proteins Are Implicated in Diseases
Figure 3-18
Alzheimer's disease is
characterizes by the
formation of insoluble
plaques composed of
amyloid protein.

23. The 6 Key Concepts of Section 3.2 (p78)

24. 3.3 Protein Function
Specific Binding of Ligands Underlies the Functions of most Proteins
CDR: Complemetarity-Determining Region
Figure 3-19 (a)
Protein-ligand binding of anti-bodies.

25. Specific Binding of Ligands Underlies the Functions of most Proteins
Figure 3-19 (b)
Protein-ligand binding of anti-bodies.

26. Enzymes Are Highly Efficient and Specific Catalysts
Figure Effect of an enzyme on the activation energy
of a chemical reaction.

27. An Enzyme's Active Site Binds Substrates and Carries Out Catalysis
Figure Active site of the enzyme trypsin.

28. An Enzyme's Active Site Binds Substrates and Carries Out Catalysis
Figure 3-22
and
for an enzyme-
catalyzed reaction.

29. An Enzyme's Active Site Binds Substrates and Carries Out Catalysis
Figure 3-22 (a) and for an enzyme-
catalyzed reaction.

30. An Enzyme's Active Site Binds Substrates and Carries Out Catalysis
Figure 3-22 (b) and for an enzyme-
catalyzed reaction.

31. An Enzyme's Active Site Binds Substrates and Carries Out Catalysis
Figure 3-23
Schematic model of an enzyme's
reaction mechanism.

32. An Enzyme's Active Site Binds Substrates and Carries Out Catalysis
Figure Free-energy reaction profiles of uncatalyzed
and multistep enzyme-catalyzed reaction.

33. An Enzyme's Active Site Binds Substrates and Carries Out Catalysis
Figure 3-24(a) Free-energy reaction profiles of uncatalyzed
and multistep enzyme-catalyzed reaction.

34. An Enzyme's Active Site Binds Substrates and Carries Out Catalysis
Figure 3-24(b) Free-energy reaction profiles of uncatalyzed
and multistep enzyme-catalyzed reaction.

35. Serine Proteases Demonstrate How an Enzyme's Active Site Works
Figure 3-25(a)
Substrate binding
in the active site
of typsinlike serine
proteases.

36. Serine Proteases Demonstrate How an Enzyme's Active Site Works
Figure 3-25(b)
Substrate binding in the active site
of typsinlike serine proteases.

37. Serine Proteases Demonstrate How an Enzyme's Active Site Works
Figure Mechanism of serine protease-
mediated hydrolysis of peptide bonds.

38. This side-chain of His-57 facilitates catalysis by withdrawing and
donationg protons throughout the reaction(inset).

39. Movements of electrons are indicated by arrows.
This attack results in the formation of a transition
state called the tetrahedral intermediate

40. Additional electron movements result in the breaking of the peptide
bond,release of one of the reaction products,and formation of the acyl
enzyme.

41. An xygen from a solvent water
molecule then attacks the carbonyl
carbon of the acyl enzyme.

42. The formation of a second tetrahedral intermediate.

43. Additional electron movements result in the breaking of the
Ser-195-substrate bond and release of the final reaction product.

44. Serine Proteases Demonstrate How an Enzyme's Active Site Works
Figure 3-27
pH dependence of
enzyme activity.

45. Enzymes in a Common Pathway Are Often Physically Associated
with One Another
Figure 3-28
Assembly of
enzymes into
efficient multi
-enzyme complexes.

46. Enzymes in a Common Pathway Are Often Physically Associated
with One Another
Figure 3-28(a)
Assembly of
enzymes into
efficient multi
-enzyme complexes.

47. Enzymes in a Common Pathway Are Often Physically Associated
with One Another
Figure 3-28(b)
Assembly of enzymes into efficient multienzyme complexes.

48. Enzymes in a Common Pathway Are Often Physically Associated
with One Another
Figure 3-28(c)
Assembly of enzymes into efficient multienzyme complexes.

49. The 18 Key Concepts of Section 3.3 (p85-86)

50. 3.4 Regulating Protein Function I:Protein Degradation
The Proteasome Is a Complex
Molecular Machine Used to
Degrade Proteins
Figure 3-29 Ubiquitin-and-
proteasome-mediated prot-
eolysis.

51. 3.5 Regulating Protein Function II:Noncovalent and Covalent
Modifications
Nonconvalent Binding
Permits Allosteric,or
Cooperative,Regulation
of Proteins
Experimental Figure 3-30
Hemoglobin binds oxygen
cooperatively.

52. Nonconvalent Binding of Calcium and GTP Are Widely
Used As Allosteric Switches to Control Protein Activity
Ca2+/Calmodulin-Mediated Switching
Figure 3-31
Conformational changes
induced by Ca2+ binding
to calmodulin.

53. Switching Mediated by Guanine Nucleotide-Binding Proteins
Figure The GTPase switch.

54. Phosphorylation and Dephosphorylation Covalently Regulate
Protein Activity
Figure Regulation of
protein activityby the kinase/
phosphatase switch.

55. Regulation III: Proteolytic Cleavage Activates or Inactivates Proteins
Coagulation Factor VIII Activation

56. Protein regulation IV: Sub-cellular location change
Protein P retains p38N to the nuclear

57. The 4 Key Concepts of Section 3.4 (p88)
Questions and Answers
Preview Section Figures
Student solution book: select to answer 1 question from P3
Next Class Quiz: one question you prepared