1. Lecture 5 Protein Structure
Biochemistry
Lecture 5
Protein Structure

2. Structure of Proteins

3. Definition of Structural States
Primary Structure (1°) – peptide bond linking amino acid residues in a polypeptide chain (sequence of amino acid residues).
Secondary Structure (2°) – local spatial arrangement of the main-chain atoms in a selected segment of a polypeptide chain.
Tertiary Structure (3°) – overall three-dimensional arrangement of all atoms in a protein.
Quaternary Structure (4°) – arrangement of protein subunits (separate polypeptide chains) in three-dimensional complexes.

4. Chapter 6, Figure 6.1, Three-dimensional folding of the protein myoglobin.

5. Structural Groups

6. Chapter 6, Figure 6.2, The four levels of structural organization of proteins

7. Chapter 6, Figure 6.9, A Ramachandran plot of poly-L-alanine

8. Keratin

9. Collagen

10. Silk

11. Globular Proteins

12. 2° Structural Motifs (Supersecondary Structures)

13. Various Interactions Create 3D Shapes

14. Chapter 6, Figure 6.1, Three-dimensional folding of the protein myoglobin.

15. Quaternary Structure

16. X-Ray Crystallography

17. Nuclear Magnetic Resonance

18. Chapter 6, Figure 6A.9, Nuclear magnetic resonance spectroscopy (NMR)

19. How Do We Obtain Proteins for Structural & Functional Analysis?

20. Purification of Proteins
FIGURE 3-16 Column chromatography. The standard elements of a chromatographic column include a solid, porous material (matrix) supported inside a column, generally made of plastic or glass. A solution, the mobile phase, flows through the matrix, the stationary phase. The solution that passes out of the column at the bottom (the effluent) is constantly replaced by solution supplied from a reservoir at the top. The protein solution to be separated is layered on top of the column and allowed to percolate into the solid matrix. Additional solution is added on top. The protein solution forms a band within the mobile phase that is initially the depth of the protein solution applied to the column. As proteins migrate through the column, they are retarded to different degrees by their different interactions with the matrix material. The overall protein band thus widens as it moves through the column. Individual types of proteins (such as A, B, and C, shown in blue, red, and green) gradually separate from each other, forming bands within the broader protein band. Separation improves (i.e., resolution increases) as the length of the column increases. However, each individual protein band also broadens with time due to diffusional spreading, a process that decreases resolution. In this example, protein A is well separated from B and C, but diffusional spreading prevents complete separation of B and C under these conditions. 20

21. Chapter 5, Figure 5A.6, An overview of ion exchange chromatography

22. Chapter 5, Figure 5A.7, An overview of size exclusion chromatography

23. Chapter 5, Figure 5A.3, An overview of affinity chromatography

24. Protein Analysis - Electrophoresis+ + -
Heat - - - - - - -

25. Folding and Denaturation

26. Chapter 6, Figure 6.24, Contribution to the free energy of folding of globular proteins

27. Denaturation… also known as “Cooking”

28. Misfolding Diseases

29. Mutation Impairs Proper Folding
Sickle Cell
Anemia
Cystic Fibrosis

30. Contagious Misfolding: Prions