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Biochemistry week 3 notes (ch 6 & 7)

by: ShayD

Biochemistry week 3 notes (ch 6 & 7) CHEM 4712

Marketplace > University of Missouri - St. Louis > Chemistry > CHEM 4712 > Biochemistry week 3 notes ch 6 7
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About this Document

This study guide covers both the lecture and textbook notes for chapter's 6 & 7. It includes topics like: three-dimensional structures of a protein (secondary, tertiary, and quaternary), protein s...
Xuemin Wang
Class Notes
three-dimensional structures of a protein (secondary, tertiary, and quaternary), protein stability, protein folding, protein structure imaging, protein functions, fibrous/globular proteins, collagen, Hemoglobin, Antigens
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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 anemiawhich 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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