Structure And Function Of Protein Lecture 2 PDF

References: Basic medical biochemistry, Marks and Marks. Biochemistry. Lippincott’s Illustrated Reviews. Champe and Harvey.  Primary structure determines its tertiary structure. The shape of a 3-D conformation of a globular protein involves interactions between amino acid residues t...

References: Basic medical biochemistry, Marks and Marks. Biochemistry. Lippincott’s Illustrated Reviews. Champe and Harvey.  Primary structure determines its tertiary structure. The shape of a 3-D conformation of a globular protein involves interactions between amino acid residues that may be located far from each other. Globular proteins in aqueous solution is compact with high density atoms in the core of the molecules. Also includes α-helices and β-sheets. Covalent (sharing a pair of electrons) Hydrophobic side chains buried i.e. disulfide bonds and non-covalent in the interior, while hydrophilic (hydrogen & ionic) bonds are involved. groups on the surface. Important to stabilize the tertiary structure. Electrostatic interactions- Interaction between & among cations and anions. Hydrogen bonds - A chemical bond in which a hydrogen atom of one molecule is attracted to an electronegative atom, especially a nitrogen, oxygen, or fluorine atom Hydrophobic interaction -hydrophobic amino acids (such as alanine, valine, leucine, isoleucine, phenylalanine, tryptophan and met hionine) clustered together within the protein.  Domain - fundamental functional & 3-D structural units of polypeptide (with specific function i.e binding site of small molecule. Generally polypeptide with ≥ 200 amino acids will have ≥2 domains. Core domain is built from supersecondary structure (motifs) i.e combinations of ⚫ Therefore each domain has supersecondary structures. characteristics of a small, Folding of peptide chain within compact globular proteins that domain usually occurs is structurally independent of independently of folding in other other domains. domains.   In the cell, not all proteins can fold back into their native conformation. As proteins fold & refold while searching for its lowest energy state, it passes thro many high-energy conformations that slow the process (kinetic barriers). These kinetic barriers can be overcome by heat-shock proteins, which use energy provided by ATP hydrolysis to assist in the folding.    3D structure of a protein composed of multiple subunits. Theses subunits are held together by the same non-covalent interactions (hydrophobic interactions, hydrogen bonds, ionic bonds) involved in tertiary structure. In hemoglobin, subunits are similar. All four contains heme and bind oxygen.  4 polypeptides 2 α-chains 2 β-chains 4 heme groups 4 subunits held together by non-covalent interactions tetramer with 2 identical dimers Dimers (αβ)1 and (αβ)2 2 polypeptide within the dimer is held by hydrophobic interactions ⚫ Proteins are diverse ⚫ Differ in size, shape, charge, hydrophobicity and affinity towards other molecules. ⚫ principle of separation. ⚫ To isolate and characterize. ⚫ Chromatography – technique to isolate and purify all types of biomolecules. ⚫ The samples (solutes) are allowed to interact with mobile and stationary phase. ⚫ Mobile phase – gas /liquid moves the sample through the column. ⚫ Column contains stationary phase Molecules with weak affinity – spend – has ability to bind solutes. more time with mobile phase, rapidly removed from column.  When the pH > pI, a protein has a net negative charge and when the pH < pI, a protein has a net positive charge. 4. 5. 6.  Protein synthesis – translation Changes (chemical modification) after synthesis – PTM. Common PTM – Phosphorylation – addition of phosphate group. Frequently used by the cells to alter activity of enzymes. Fatty acids, ADP-ribose, methyl, acetyl &CHO groups may be added to proteins via PTM by specific enzymes. Glycosylation – addition of sugar moiety on serine, threonine or asparagine. For secreted proteins or to the cell surface. Can occur spontaneously. Occurs at the Golgi app. 3. Enzymes may remove amino acids from the amino end of the protein, or cut the peptide chain in the middle. ⚫ For instance, the peptide hormone insulin is cut twice, and a propeptide is removed from the middle of the chain; the resulting protein consists of two polypeptide chains connected by disulfide bonds. + C peptide