1. Chapter 1
Protein

2. Contents 1. Chemical components 2. Molecular structures
3. Structure-function relationship
4. Physical and chemical properties
5. Exploration of proteins

3. What are proteins?
Proteins are macromolecules composed of amino acids linked together through peptide bonds.

4. Section 1 Chemical Components of Proteins

5. Element components of proteins major elements C, H, O, N, S.
trace elements
P, Fe, Cu, Zn, I, …

6. The average nitrogen content in proteins is about 16%.
The protein quantity can be estimated.
protein in 100g sample = N per gram x 6.25 x 100

7. Amino Acids The basic building blocks of proteins
only 20 types of amino acids are used for protein synthesis in biological systems.
L-α-Amino acid

8. L-α-Amino acid

9. A Classification of Amino Acids
Amino acids are grouped as
(1) non-polar, hydrophobic;
(2) polar, neutral;
(3) acidic;
(4) basic.

10. Special amino acids Gly Pro Cys optically inactive
Having a ring structure and imino group
active thiol groups to form disulfide bond

11. Peptide
A peptide is a compound of amino acids linked together by peptide bonds.

12. peptide bond
A peptide bond is a covalent bond formed between the carboxyl group of one AA and the amino group of its next AA with the elimination of one H2O molecule.

13. Biologically active peptides
Glutathione (GSH)
As a reductant to protect nucleic acids and proteins
Peptide hormones
Neuropeptides responsible for signal transduction

14. Section 2 Molecular Structures of Proteins
Primary Structure
Secondary Structure
Tertiary Structure
Spatial structure
Quaternary Structure

15. Primary Structure
The primary structure of proteins is defined as a linear sequence of amino acids joined together by peptide bonds.
Peptide bonds and disulfide bonds are responsible for maintaining the primary structure.

16. Secondary Structure
The secondary structure of a protein is defined as a local spatial structure of a certain peptide segment, that is, the relative positions of backbone atoms of this peptide segment.
H-bonds are responsible for stabilizing the secondary structure.

17. Repeating units of Ca-C(=O)-N(-H)-Ca constitute the backbone of peptide chain.
Six atoms, Ca-C(=O)-N(-H)-Ca, constitute a planer peptide unit.

19. Four common types of secondary structure
α-helix
β-pleated sheet
β-turn
random coil

21. Motif
When several local peptides of defined secondary structures are close enough in space, they are able to form a particular structure---Motif.
Zinc finger
HLH (helix-loop-helix)
HTH (helix-turn-helix)

22. Tertiary Structure
The tertiary structure is defined as the three-dimensional arrangement of all atoms of a protein.

23. Five types of interactions stabilize the protein tertiary structure.
• hydrophobic interaction
• ionic interaction
• hydrogen bond
• van der Waals interaction
• disulfide bond

24. Domain
Large polypeptides may be organized into structurally close but functionally independent units---Domain

25. Chaperon
Chaperones are large, multisubunit proteins that promote protein foldings

26. Quaternary Structure
The quaternary structure is defined as the spatial arrangement of multiple subunits of a protein.
These subunits are associated through H-bonds, ionic interactions, and hydrophobic interactions.

27. From primary to quaternary structure

28. Protein classification
Constituents
simple protein
conjugated protein = protein +
prosthetic groups
Overall shape
Globular protein long/short < 10
Fibrous protein long/short > 10

29. Section 3 Structure-Function Relationship of Proteins
Relationship between primary structure and function
Primary structure is the fundamental to the spatial structures and biological functions of proteins.

30. Example
Proteins having similar amino acid sequences demonstrate the functional similarity.
The alternation of key AAs in a protein will cause the lose of its biological functions.

31. Relationship between spatial structure and function
A particular spatial structure of a protein is strongly correlated with its specific biological functions.

32. Example
1.The denatured protein remains its primary structure, but no biological function.
2. Allosteric change of hemoglobin by O2

33. Section 4 Physical and Chemical Properties of Proteins
Amphoteric

34. isoelectric point (pI)
The pH at which the protein has zero net-charge is referred to as isoelectric point (pI)

35. 2. Colloid property
Hydration shell and electric repulsion make proteins stable in solution.

36. 3 Protein denaturation renaturation, precipitation and coagulation
The process in which a protein loses its native conformation under the treatment of denaturants is referred to as protein denaturation.
• Applications
sterilization, lyophilization

37. 4 UV absorption
Trp, Tyr, and Phe have aromatic groups of resonance double bonds.
Proteins have a strong absorption at 280nm

38. 5 Coloring reactions
Biuret reaction
Ninhydrin reaction

39. Section 5 Exploration of Protein
Isolation and purification
• Centrifugation
• Dialysis
• Precipitation
• Chromatography
• Electrophoresis

40. Protein Sequence Determination
Edman degradation
Deduction from DNA sequence

41. Structure Determination
Circular dichroism spectroscopy
X-ray crystallography
Nuclear magnetic resonance spectroscopy
Computer simulation