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

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, …

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

L-α-Amino acid

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

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

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

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.

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

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

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.

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.

                                                                                            

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

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

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

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

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

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

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

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

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)

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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

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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.

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

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.

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.

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

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