1. Dr. Jagdish Kaur, P.G.G.C.,Sector 11 Chandigarh
ProteinS
Dr. Jagdish Kaur,
P.G.G.C.,Sector 11
Chandigarh

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

3. 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

4. L-α-Amino acid

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

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

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

8. 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.

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

10. Molecular Structures of Proteins
Primary Structure
Secondary Structure
Tertiary Structure
Spatial structure
Quaternary Structure

11. Primary Structure The primary structure
A linear sequence of amino acids joined together by peptide bonds.
Peptide bonds and disulfide bonds are responsible for maintaining the primary structure.

12. Secondary Structure The secondary structure
A local spatial structure of a certain peptide segment, the relative positions of backbone atoms of this peptide segment.
H-bonds are responsible for stabilizing the secondary structure.

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

15. Key ideas and terms protein can bind a ligand in the binding site
For an enzyme, the ligand is a substrate and they bind in what is called the active site
ligand has to be the correct shape
ligand has to have the complementary charges and hydrophobicity or hydrophilicity

16. Lock and Key Hypothesis
Protein and ligand have complementary shapes.
Interactions must also be complementary
If enzyme charge is negative, substrate must be positive
If pocket is nonpolar, ligand must be nonpolar
Antibodies

17. Induced Fit
Induced Fit: when the protein and ligand bind, the protein may change conformation to allow for tighter binding
Frequently, both the ligand and the protein change conformation

18. Examples: O2 binding proteins: myoglobin and hemoglobin
oxygen is not water soluble yet needs to be transported
diffusion is not effective
myoglobin is found primarily in muscle tissue
Hemoglobin is in the blood
Both proteins contain heme

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

20. Definition - protein classification
Grouping of similar proteins based on their structure, function, or size
Globular vs filamentous vs helical
Cataytic vs structural
Small vs large vs very large

21. Protein Subunits & Domains
A single polypeptide may have regions along its length that fold up separately - domains
More than one polypeptide coming together to form a protein - subunit

22. Protein - shapes
Globular proteins - polypeptide folds tightly together on itself - most enzymes
Fibrous proteins - elongated structure - span great distances - hair - keratin
Many subunits attached together
Actin & collagen
Strong & rigid (Collagen - ligaments)
Strong & flexible (elastin - skin)

23. 04_24_complexstructure.jpg
04_24_complexstructure.jpg

24. 04_26_spherical shell.jpg
04_26_spherical shell.jpg

25. 04_29_Disulfide bonds.jpg
04_29_Disulfide bonds.jpg

26. Proteins Bind
Biological properties of proteins result from interactions with other molecules
Antibodies, enzymes, structure, etc
Binding is always very specific
Ligand - anything that is bound by a protein
Ligand binding is by ionic bonds only
Many ionic bonds required to stabilize link - matching configurations needed - specificity

27. 04_30_selective binding.jpg

28. Proteins - Binding A ligand binds to a protein at a binding site
A protein may have more than one binding site
It may bind the same ligand many times or it may bind different ligands
Ligands can bind to regulate the activity of the protein
Interior amino acids have a say in the conformation of the molecule too.

29. Proteins - pair with other molecules
Some biologically active molecules are a result of a very cozy relationship
Rhodopsin & Opsin
Retinal (a light sensing pigment) + opsin protein
Haem (Fe containing molecule) + globin protein

30. 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.

31. 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.

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

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