Biochemistry week 3 notes (ch 6 & 7)
Biochemistry week 3 notes (ch 6 & 7) CHEM 4712
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This 10 page Class Notes was uploaded by ShayD on Saturday February 13, 2016. The Class Notes belongs to CHEM 4712 at University of Missouri - St. Louis taught by Xuemin Wang in Spring 2016. Since its upload, it has received 25 views. For similar materials see Biochemistry in Chemistry at University of Missouri - St. Louis.
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Date Created: 02/13/16
Dudaie 1 Biochemistry: Chapter 6 Chapter 6 Protein: ThreeDimensional Structure Overview structure of the protein: 1. The primary structure polypeptide chain (covered in chapter 5) 2. Secondary structure local spatial arrangement of the polypeptide chain 3. Tertiary structure three dimensional structure of polypeptide chain 4. Quaternary structure the spatial arrangement of a protein’s subunits (multiple tertiary structures of different polypeptide chains) 1. Secondary structure a. 2 types of secondary structures i. αhelix: the righthanded coil 1. this conformation makes it that the c=o group is hydrogen bonded to the NH group 4 residues away on the same polypeptide Dudaie 2 2. has 3.6 residues per turn; which gives a pitch (a distance the helix raises) of 5.4Å 3. The R groups always points out; to avoid steric hindrance ii. βsheets: formed from extended chains 1. These structure hydrogen bond to neighboring polypeptide chains 2. This comes in 2 subcategories: a. Antiparallel βsheets the neighboring chains run in opposite directions b. Parallel βsheets the neighboring chains run in the same direction c. Antiparallel conformations are more stable due to the hydrogen bonds they form 3. These βsheets usually contain between 222 polypeptide strands Dudaie 3 4. Some secondary structure are connected by turns a. Theses turns are stabilized by hydrogen bonds ***other motifs are used as well for a complete list look in the lecture, although we don’t need to memorize them*** 2. Tertiary Structure a. The folding of the secondary structure elements i. Spatially distributed amino acid chains are distributed according to their polarities 1. Polar residues lie on the surface of a proteins a. Nonpolar can be either on the outside or on the inside, usually on the outside 2. Non polar residues are found on the interior of the protein (to keep out of contact from aqueous solvent) ii. Type of bonding 1. Covalent among sulfur containing groups disulfide bonds 2. Hydrogen between polar R groups 3. Ionic between oppositely charged groups 4. Hydrophobic interactions between hydrophobic R groups iii. Combinations of secondary structure form motifs 1. Grouping supersecondary structures or motifs occur in many unrelated globular proteins a. The most common form of supersecondary structures is the ẞαẞ motif α helix connects 2 parallel strands of ẞsheets b. Another common structure ẞ hairpin antiparallel stands connected by relatively tight reverse turns c. αα motif 2 successive antiparallel α helices d. Greek key motif ẞ hairpin is folded over to form 4 stranded antiparallel ẞsheets Dudaie 4 3. Quaternary Structure some proteins contain multiple subunits a. Subunits usually associates noncovalently i. Proteins with more than one subunits are called oligomers and their identical units are called promoters ii. They contain closely packed nonpolar side chains, hydrogen bonds involving the polypeptide chain, and in some cases disulfide bonds b. Subunits are symmetrically arranged i. Proteins cannot have inversion or mirror symmetry, because they would have to convert chiral L residues and D residues 1. Proteins can have rotational symmetry or cyclic symmetry 4. Protein stability a. Native proteins are only marginally stable under physiological conditions, so there are forces that increase protein stability i. Hydrophobic effect causes nonpolar substances to minimize their contact with water; this aggregation of nonpolar side chains is favored by the increase in entropy ii. Metal ions stabilize small domains iii. Disulfide bonds stabilize extracellular proteins iv. Electrostatic interactions b. Proteins can undergo denaturation i. Proteins can be denatured by a variety of conditions: 1. Temperature/microwaves cooking eggs 2. Mechanical forces blender 3. UV sun burn 4. pH digestion Dudaie 5 5. detergents & alcohol interactions with hydrogen bonds 6. oxidizing agents aging 7. heavy metalsflint ii. Many denatured proteins can be renatured 1. Noble prize winning experiment Anfinsen’s experiment: a. His work demonstrated that proteins can fold spontaneously into their native conformation under physiological conditions, this implies that a protein’s primary structure dictates its 3D shape 5. Protein Folding a. A folding protein follows a pathway from high energy and high entropy to low energy and low entropy i. Follow protein pathways: many proteins fold into their native conformations in less than a few seconds via directed pathways rather than stumbling through random conformational searches ii. Since native protein contain compact hydrophobic cores hydrophobic collapse is the driving force of protein folding 1. The collapse is known as molten globule iii. Proteins fold in a hierarchical manner with small elements and then coalescing to yield larger elements iv. The energyentropy relationship which the diagram is known as folding funnel v. Molecular assisted protein folding 1. Protein fold via molecular chaperones, these essential proteins that bind to prevent the improper association Dudaie 6 of exposed hydrophobic segments that might lead to nonnative folding a. Also known as heat shock protein, because their rate of synthesis increased at elevated temperatures vi. Some diseases are caused by protein misfolding 1. Amyloidẞ protein accumulates in Alzheimer’s disease a. This neurodegenerative disease condition that is caused by amyloid plaques 2. Prion diseases are infectious a. A neurological disorder i. Kuruhuman ii. Scrapie sheep and goat iii. Mad cow disease bovine b. Prion (for proteinaceous infectious) C i. PrP = normal cellular form of prion protein. ii. PrP = Scrapie form of prion protein 1. The infected protein aggregate to form rodlike particles that closely resemble amyloid fibrils 6. Protein structure imaging a. X Ray crystallography the technique that directly images molecules i. You shine x rays through a crystalized form of a protein 1. We study the diffraction pattern that arise Dudaie 7 2. two dimensional NMR spectroscopy a. Analyzes protein structure in solution Chapter 7 Protein functions 1. Proteins are either classified as either globular or fibrous depends on overall morphology a. Fibrous Proteins Fibrous proteins are long, thin, and insoluble. They often occur as many adjacent intertwined strands. Fibrous proteins always have a structural role i. 2 types of fibrous proteins: 1. Keratin α keratin is a coiled coil a. It is a mechanically durable and relatively unreactive protein that occurs in all higher vertebrates made up of 2 α keratin polypeptides twist around to form a lefthanded coil= coiled coil i. exists in animal horns, finger nails 2. Collagen is a triple helix a. three coiled polypeptides wound around each other to give a ropelike arrangement b. Multiple repeats of GlyXY where X is often proline and Y is often 4hydroxyproline i. When Pro is converted to Hyp in a prolyl hydroxylase reaction. This enzyme is required for vitamin C deficiency (scurvy), which leads to lack of proper hydroxylation Dudaie 8 and defective triple helix (skin lesions, fragile blood vessels, bleeding gums) c. Collagen is the stress bearing component of bones, connective tissue (tendons), teeth, cartilage, blood vessels, etc. b. Globular proteins Globular proteins are much more compact and locally intertwined. So they are closed, globular structures. Most are water soluble. Globular proteins do almost all the “active” molecular functions in cells i. We examine 2 types: hemoglobin/immunoglobin 1. Hemoglobin: a tetramer of myoglobinlike polypeptides is a more complicated protein that delivers oxygen to tissues throughout the body a. The α and ẞ subunits are structurally and evolutionary related to each other b. Note how side chains (R groups) in the interior would not be exposed to water 2. CO 2oisoning this is caused due to the fact that CO 2 2+ binds to the Fe 200x stronger c. Mutations may alter hemoglobin structure and function i. A single amino acid changes causes sicklecell anemia (Val Glu) 1. A single copy of the gene for sicklecell hemoglobin (hemoglobin S), which causes people to suffer sicklecell anemiawhich deforms the hemoglobin to form sickle like cell Dudaie 9 d. Antibodies all organism are continually subject to attack by other organism these pathogens may penetrate the physical barrier presented by skin and mucus membrane only to be identified and destroyed by the immune system i. The immune response is triggered by the presence of a foreign macromolecule often a protein, known as an antigen ii. All immunoglobulins contain at least four subunits: 2 identical light chains and 2 identical heavy chains; these units are associated by disulfide bonds and by noncovalent interactions that form a Y shape 1. These polypeptides have a variable region and a constant region Dudaie 10 2. Immunoglobulin or antibody has fixed (gray) and variable (red) regions in the light and heavy chains. The antigen binding is done by variable regions. The chains are held together by: disulfide bridges e. Immune diseases i. An autoimmune disease (like arthritis) occurs when a person make antibodies against self. 2. Protein functions: a. Catalyze reactions enzymes b. Transport membrane c. Structural anchors d. Protection skin e. Storage of amino acids f. Energy source muscle contractions g. Signal transduction
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