Lecture 9 10 11 - final review.docx

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Dalhousie University
Biochem & Molecular Biology
BIOC 2300
Dr.Carmichael Wallace

Lecture 9/10/11 Loss of Protein Structure - There are small differences in the free energy of folded and unfolded proteins SO protein structure is especially sensitive to environmental factors - Many physical and chemical agents can disrupt a protein’s native conformation - Denaturation = the process of structure disruption, which may or may not involve protein unfolding (NOT usually considered the breaking of protein bonds, aka does not disrupt primary protein structure) o Depending on the degree of denaturation the molecule may partially or completely lose its biological activity o Usually results in observable changes in the physical properties of proteins o USUALLY IRREVERSIBLE – but the reverse process is called renaturation Denaturing Conditions: 1. Strong acids or bases 2. Organic solvents 3. Detergents 4. Reducing agents (urea) 5. Salt concentration (high salt concentrations) 6. Heavy metal ions (mercury and lead) 7. Temperature (heating) 8. Mechanical stress (stirring and grinding) The Folding Problem - The direct relationship between a protein’s primary sequence and its final three- dimensional conformation (and by extension its biological activity) is among the most important assumptions in biochemistry - Painstaking work has been done to be able to predict structure by understanding the physical and chemical properties of amino acids o X-ray crystallography, NMR spectroscopy, and site-directed mutagenesis - Important advances have been made by biochemists in protein-folding research o This research led to the understanding that it is not a single pathway  A funnel shape best describes how an unfolded protein negotiates its way to a low-energy folded state • Numerous routes and intermediates  Small polypeptides (<100 amino acids) often form with no intermediates  Larger polypeptides often require several intermediates, aka (molten globules) • = partially organized globular state of a folding polypeptide that resembles the molecule’s native state)  Many proteins use molecular chaperones to help with folding and targeting Molecular Chaperones – assist protein folding in 2 ways: 1. Preventing inappropriate protein-protein interactions 2. Helping folding occur rapidly and precisely into correct formations Two major molecular chaperone classes in protein folding 1. Hsp70s  a family of chaperones that bind and stabilize proteins during the early stages of folding 2. Hsp60s (chaperonins)  mediate protein folding after the protein is released by Hsp70 a. Increases speed and efficiency of the folding process b. Form a large structure composed of two stacked seven-subunit rings - BOTH PROCESSES use ATP hydrolysis - Both are also involved in refolding proteins o If refolding is not possible, molecular chaperones promote protein degradation Fibrous Proteins - Typically contain high proportions of regular secondary structures (alpha-helices and beta-pleated sheets) - Often have structural rather than dynamic roles and are water insoluble o Ex: keratin (alpha-helices) and silk fibroin (beta-sheets) Collagen = part of the connective tissue matrix synthesized by connective tissue cells and secreted into the extracellular space - 20 major families with diverse functions - Impart special properties to structures (ex: bone and skin) - Glycine and proline are common amino acids Globular Proteins - Biological functions often include precise binding of small ligands or large macromolecules like nucleic acids or other proteins - Each protein possesses one or more unique cavities or cleft whose structure is complementary to a specific ligand - After ligand binding a conformational change occurs in the protein that is linked to a biochemical event o Ex: Myoglobin and hemoglobin (hemoproteins) o Both have specialized heme prosthetic group used for reversible oxygen binding Myoglobin - Found in high concentrations in cardiac and skeletal muscle o The protein component of myoglobin (globin) is a single protein with eight alpha- helices o Encloses a heme (Fe ) that has a high affinity for O 2 Hemoglobin - A roughly spherical protein found in red blood cells - Primary function
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