Documents about Sodium Dodecyl
07_interact_rep_dam_repair
Georgia Tech, CHEM 3511
Excerpt: ... SURVEY OF BIOCHEMISTRY Protein-NA Interactions DNA Replication, Damage, and Repair 1 What to Know for Exam 1 Structures: Characterization NA, AA, Classifications Base pairs, numbering system Polypeptide backbone Dihedral angles Processes: General Concepts Beer's Law Protein Purification and SDSPAGE pI 2 Study Tips Read text Review Lecture Notes Practice problems Read text again 3 PRS 1. 2. 3. 4. Which of the following reagents would be suitable for reducing a disufide bond? Methionine 2Mercaptoethanol Sodium Dodecyl Sulfate Cysteine 4 PRS Question The dihedral angle psi is defined by which of the following atoms? 1. NCalphaCcarbonylN 2. CalphaCcarbonylNCalpha 3. CcarbonylNCalphaCcarbonyl 4. NCalphaCcarbonyl=O 5 PRS Question 1. 2. 3. 4. How many Hbond acceptors in adenine participate in WatsonCrick H bonds with thymine? None One Two Three 6 PRS Question 1. 1. 1. 2. How many Hbond acceptors in adenine participate in WatsonCrick H bonds wi ...
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06-proteins_stability
Georgia Tech, CHEM 3511
Excerpt: ... SURVEY OF BIOCHEMISTRY Proteins and Biomolecular Stability 1 Protein Structure Primary (1): amino acid sequence Secondary (2) Alpha Helix Beta Sheet Tertiary (3) Quaternary (4) 2 Primary and Secondary Structure Myoglobin - 2V1K Superoxide Dismutase - 1XSO 3 Recap Structures of 20 amino acids pKa and pI 1: Polypeptide Sequence 2: Secondary Structures Alpha Helices Beta Sheets 4 Recap continued Protein Purification Methods Gel Filtration Ion Exchange Affinity How to assess purification? Purity Yield 5 SDSPAGE Electrophoresis: a method for separating molecules based on size and charge when exposed to an electric field. Name "SDS-PAGE": SDS = sodium dodecyl sulfate PAGE = polyacrylamide gel electrophoresis 6 Sodium Dodecyl Sulfate SDS confers negative charge on proteins and denatures proteins Amphiphilic Hydrophilic Hydrophobic Anionic Detergent in a wide variety of products Sodium Dodecyl Sulfate (Lauryl Sulfate) CH3(CH2)11OSO3 Proteins ...
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Spring 2003 Lecture 11 shorter pdf
Purdue, CHM 333
Excerpt: ... rge 63 CHM333 LECTURES 11: 2/10/03 Cation Exchange Separation by charge Beads with a negative charge SPRING 2003 Professor Christine Hrycyna Increased salt concentration to weaken electrostatic interactions. Change of pH to pH > pI (protein becomes negatively charged) Overall positive charge. Proteins have patches of positive charge Monitoring of proteins during chromatography UV absorbance is monitored dependent upon Trp, Tyr, Phe if protein is an enzyme, its activity can be monitored Electrophoresis separates components based upon their charge and/or size Polyacrylamide gel electrophoresis (PAGE) Proteins vary widely in their charge, size and even shape positive, negative or neutral at pH 7 spheres, rods, or embedded in membranes Use sodium dodecyl sulfate (SDS) to eliminate migration effects due to charge or shape SDS (negatively charged detergent) denatures proteins and binds to hydrophobic regions of the polypeptide Result: imparts a uniform charge/mass ratio ...
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Adamp
SUNY Buffalo, CE 457
Excerpt: ... can use polymer gels Toothpaste Binders ? Works with the Humectant ingredients ? Makes the paste retain water, stabilizes the multiple phases in the paste, controls rheology ? Make of natural colloids usually gums and resins Surfactants/Detergents Two Purposes * Build up a foam * Aid in removal and suspension of hydrophobic debris Most commonly Used Surfactants: Sodium Dodecyl Sulfate Sodium N-lauryl Sarcosinate Sodium lauryl Sulfoacetate Sodium Dodecyl Sulfate a.k.a. Sodium Lauryl Sulfate CMC : 8.2 E -3 mol/l Surfactant concentration must be finely tuned Problems with SDS/surfactants ? Many reports of irritation attributed to SDS ? Condition know as Xerostomia chronic dry mouth many causes and pathways ? Surfactant free toothpastes introduced BETAINE ? Betaine is a toothpaste additive to counter the irritation of SDS/surfactants ? Adsorbs to mouth tissue ? Extensively hydrates form protective layer of water Consumer Satisfaction ? Is easy to apply to brush ? Deforms easily when br ...
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HW3-08
U. Houston, BCHS 3304
Excerpt: ... ion experiment. 2. Your thesis advisor suggests that you make stock solutions for your protein gel electrophoresis experiment to look at your purified myoglobin. She tells you the components for 1x Tris-Glycine electrophoresis buffer, but suggests you actually make a 1.0 L 5x stock so that you simply can dilute the concentrate as you need it. Calculate and describe how you would make a 5x stock of TrisGlycine electrophoresis buffer. (Hint: 1% = 1g/100 ml for an aqueous solution.) 1x Tris-Glycine electrophoresis buffer (25 mM Tris, 250 mM Glycine, 0.1% SDS) Tris MW=121.4 g/mole Glycine MW= 75.07 g/mole SDS ( sodium dodecyl sulfate) MW=288.38 g/mole 3. Your SDS-PAGE gel electrophoresis experiment requires 1.0 L of 1x Tris-Glycine buffer. Calculate and describe how you would make this solution using your 5x stock solution. 4. Name two amino acids that would be found in the core of a protein. What are their three-letter codes? What are their one-letter codes? 5. Name one hydrophobic amino acid. What is its three-l ...
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sp09_outline03
Minnesota, CBS 4004
Excerpt: ... te, antibody, ligand for protein of interest SDS-PAGE ( sodium dodecyl sulfate-polyacrylamide gel electrophoresis) Figs. 8-17, 18, 19 Separates proteins based on molecular mass proteins treated with SDS, -mercaptoethanol Proteins moved by electric field toward positively charged electrode Polyacrylamide gel has small pores, acts a molecular sieve Migration of larger proteins is retarded; smaller proteins move faster Stain with protein dyes to visualize proteins A website with a description of SDS-PAGE is: http:/www.bio.davidson.edu/COURSES/GENOMICS/method/SDSPAGE/SDSPAGE.html Two-dimensional gels separate proteins based on 1) charge (isoelectric point) and 2) molecular weight (Fig. 8-22, 23) Antibodies as tools for purifying, localizing proteins Please review antibody structure on the Cell Biology Interactive disc in the Molecular models folder #25.2 antibodies.mov Antibody (immunoglobulin) protein structure (Figs. 25-21,28,31) Producing antibodies for cell biology experiments: Purify protein to homogenei ...
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482lec8
Mich Tech, BL 482
Excerpt: ... between your CMC GOT and Sigma GOT? Compare the Composition of the Sigma GOT to your purified GOT fraction - do both GOT samples have the same subunit composition? SDS-PAGE (Denaturing PAGE) SDS-PAGE is an electrophoretic method for separating protein subunits after they have been denatured by heating under reducing conditions and bound with the detergent SDS. During denaturation by boiling, all disulfide bonds in the protein are reduced with 2-mercaptoethanol (some times called beta-mercaptoethanol) and the protein subunits (ie polypeptide chains) are uniformly bound with the detergent sodium dodecyl sulfate (SDS), which has the structure CH3(CH2)11-SO3- and the sodium is just a counter ion. The detergent gives the polypeptide a uniform negative charge and binds in proportion to size of the subunit. As a consequence, all the protein subunits in a mixture of proteins have the same charge density and will migrate in an electric field with the same mobility. However, in an SDS-PAGE system, the pores ...
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November17
Laurentian, BIOL 1010
Excerpt: ... Question for the Day November 17, 2006 Figure 1: Structure of Sodium dodecyl sulfate Question 1 Sodium dodecyl sulfate (Fig. 1) is a detergent that is used to disrupt membranes and denature proteins. Explain how this detergent works in disrupting membranes and denaturing proteins (Hint: apply you understanding of membrane and protein structure) (8 Marks) Question 2. The rate of an enzymatic reaction may be affected by a number of factors. List four ways in which you could INCREASE the rate of an enzymatic reaction. (2 Marks) 1) 2) 3) 4) Question 3 a) What is a coenzyme? (2 Marks) b) Give two examples of coenzymes that are used in cellular respiration (1 Marks) 1) 2) ...
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lec09-Detecting Folding Intermediates
MIT, BIOL 7.88
Excerpt: ... gents: Globular proteins can be denatured with a wide variety of agents: Heat o Denatured chains usually partially structured and aggregated (treatment with additional denaturing agents causes further changes). o Often not reversible on cooling outside very narrow set of conditions. o Covalent side reactions as temperature increases. Tropomyosin is an exception! pH o o o o Ionization of side chains breaking ion pairs, salt bridges Denatured chains highly charged: Increased charge density leads generalized electrostatic repulsion; Unfolded chain is structured Organic solvents o Benzene o Phenol o Trichloroethylene o Acetone o Ethanol o Chloroform o Acetonitrile Often neither native nor denatured state soluble in these solvents Difficult to compare conformations between immiscible solvents Some induce alpha-helicity, like TFE Detergents o sodium dodecyl sulfate Enormously important for analysis; denatured state binds 1.4gm/gram of detergent - denatured state is highly structured: Often is mi ...
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220__D
Michigan, CHEM 216
Excerpt: ... O ONa N H 4 3 Acetylation of 4-nitrophenol (3) using propionic anhydride (6) and sodium dodecyl sulfate (SDS) (7) in water. 7 OH Step 1 Synthetic transformation 1: NO2 NH HNO3 H2N OH NH2 H2SO4 H2O OH 1 2 5 Nitration of phenol (1) into 4-nitrophenol (2) using guanidinium nitrate (5). Experimental 1 Guanidinium nitrate (5) (1.318 g, 10.80 mmol) was slowly added to a well-stirred mixture of phenol (1) (1.016) g, 10.80 mmol) and sulfuric acid (16.20 mL, 85%), maintaining a temperature of 0-5 C. When the addition was complete, the mixture was stirred for an additional 2 h at the same temperature. The reaction mixture was then poured into ice water (~100mL). The solid obtained was filtered, washed thoroughly with water, and dried. If solid was not obtained the aqueous layer was extracted with CHCl3 (4 ~50mL). The CHCl3 layers were combined and washed with 10% Na2CO3 (2 ~25mL), water (2 ~25mL) and then dried with anhydrous Na2SO4. After evaporation of the solvent, a brownish residue was obtaine ...
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Lab 24 Notes & Prelab
Stony Brook University, BIO 205
Excerpt: ... Barbell Whiskers present Absent Absent Scale Type Scaleless Ctenoid Ctenoid Sarah Song BIO 205.33 April 29, 2008 Lab 24 Proteomics & Bioinformatics Notes Podcast Activities in order: 1, 3, 2 Activity 1: Inferring phylogenies from protein gels Purpose: Use techniques from proteomics to construct a cladogram of a few species of fish Like DNA lab Use an electrical field in a gel matrix to separate samples based on molecular weight Different from DNA lab Polyacrylamide instead of agarose Polyacrylamide: finer matrix higher resolving power Large fragments of DNA vs. proteins Need to make the charge of the sample uniform hot SDS Proteins can have different charges depending on their amino acids, unlike DNA which is all charged SDS: sodium dodecyl sulfate Detergent Unfolds the protein Disrupts all the hydrogen bonds maintaining the tertiary structure Applies a fairly uniform negative charge to the amino acid chain Binds to protein b ...
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lec20
Purdue, LECT 221
Excerpt: ... neutral pH in 1% sodium dodecyl sulfate (SDS an anionic detergent) and 0.1 M mercaptoethanol most multi-chain proteins bind SDS and dissociate, disulfide linkages are disrupted by mercaptoethanol, secondary structure is lost, and the complexes consisting of protein subunits coated with SDS assume random coil conformations. O SDS structure: CH3-(CH2)10-CH2-O-S-O Bind 1.4 g SDS/g protein on average O The result is uniform shape and idenical charge to mass ratio (charge determined by SDS and not aa side chains). Therefore effective elephoretic mobility is related only to MW of proypeptides due to sieving properties of gel. 87 221 Lecture #20 Disc polyacrylamide gel electrophoresis is an important refinement of zone gel electrophoresis. The "disc" refers not to the the bands in the gel but use of a pH discontiuity that leads to electric field strength discontinuity. Gel set up Stacking gel pH 6.8 Lower I Separation gel pH 9 Higher I Stacking gel lower % acrylamide than separation gel made in buffer of lowe ...
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Naveena12052005
Carnegie Mellon, STRUCTURE 9
Excerpt: ... Naveena V.K. Yanamala Research Report # 5 2005-12-07 Structural Analysis Using NMR Research Goals: 1. NMR analysis of Peripherin Peptides 2. Comparision between 1H-15N HSQC Spectra of hegfr transmembrane-juxtamembrane domain (aa 615-686) with and without Sodium Dodecyl Sulfate 3. Comparision between 1H-15N HSQC Spectra of transducer in Natronobacterium pharaonis with and without Ammonium Sulphate, and analysis at different temparatures 1. NMR analysis of Peripherin Peptides Introduction The cGMP-gated channel of photoreceptors plays a central role in phototransduction by controlling the flow of cations into the outer segment in response to light-mediated changes in intracellular cGMP. The rod channel consists of two homologous subunits termed and that assemble into a heterotetrameric complex (1-4). Each subunit has a cyclic nucleotide-binding domain near the C terminus, six putative transmembrane domains designated S1-S6, and a pore segment between the S5 and S6 membrane-spanning segments. In addition, th ...
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SDSPAGE MW Calculation
UT Arlington, ENZYMOLOGY 4351
Excerpt: ... Purification of Proteins Page 3 of 3 media (similar to gel filtration). Therefore, the electrophoretic mobility of proteins in gels will depend on both the size as well as the charge-to-mass ratio. Therefore, to separate proteins according to size it is necessary to give them to same charge-to-mass ratio. This can be accomplished by denaturing the protein in SDS ( sodium dodecyl sulfate, shown below). The SDS binds to most proteins in a uniform manner giving all proteins the same charge-to-mass ratio. The electrophoretic mobility is defined as the distance migrated in a certain time period. Thus the mobility is directly proportional to the velocity. The effect of the gel matrix is to produce the following dependence of the molecular weight on the mobility. log(M ) = c*Mobility + d r d is the distance between the bottom of the well in which the protein is applied, and the top of the resolving gel Where "c" is a proportionality constant that depends on the gel properties. Each gel has a region where the abov ...
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2009-notes15
Minnesota, CBS 4521
Excerpt: ... acrylamide in the polymerization solution (PAGE) Effect of charge and shape: Proteins: # of charges varies by amino acid composition and pH of the buffer In addition proteins fold into different shapes with different frictional coefficients Treatment before running a denaturing gel: 1. Must denature the protein 2. Introduce a charge on each peptide: anionic detergent, sodium dodecyl sulfate (SDS) 3. Break disulfide bonds: 2-mercaptoethanol Overall charge of biomolecules depend on the pH of the solution In acid, protons attach to basic groups & net charge is +; in base net charge is - due to proton loss. At the isoelectric point the pH is such that there is no net charge on the polymer so s = 0. Isoelectric focusing: pH gradient used along the direction of an applied field to separate protein according to their pI 2D electrophoresis: Protein mixture is first separated by isoelectric focusing to produce a pattern of bands in a gel slab. This first slab is then attached to a second slab and SDS-PAGE is performed ...
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lec10supp
Carnegie Mellon, LEC 03231
Excerpt: ... drophobic amino acids relative to Gtr for glycine (blue circles). The Y-axis is then a G of transfer. The X-axis is the H2O-accessible surface area. 1 Two conclusions from this correlation: 1. All apolar R-groups prefer the organic phase (G is positive). 2. The preference for the organic phase is proportional to surface area. The line has a slope of 22 cal/mol/2. This is the same as the slope obtained from measurements of a large series of hydrocarbons. The graph also shows that G of transfer is negative for 6-7 of the hydrophilic amino acids (red squares). However, a correlation with surface area is not apparent. The graph was made using data in a table of Some Amino Acid Properties that also compiles additional characteristics of the amino acids. D. Factors that stabilize/destabilize proteins Temperature: Cold and heat denaturation. pH: Attractive and repulsive electrostatic interactions. Detergents: SDS ( sodium dodecyl sulfate) solubilizes surface and core residues. Salts affect water structure. ...
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lec10supp
Carnegie Mellon, LEC 03231
Excerpt: ... drophobic amino acids relative to Gtr for glycine (blue circles). The Y-axis is then a G of transfer. The X-axis is the H2O-accessible surface area. 1 Two conclusions from this correlation: 1. All apolar R-groups prefer the organic phase (G is positive). 2. The preference for the organic phase is proportional to surface area. The line has a slope of 22 cal/mol/2. This is the same as the slope obtained from measurements of a large series of hydrocarbons. The graph also shows that G of transfer is negative for 6-7 of the hydrophilic amino acids (red squares). However, a correlation with surface area is not apparent. The graph was made using data in a table of Some Amino Acid Properties that also compiles additional characteristics of the amino acids. D. Factors that stabilize/destabilize proteins Temperature: Cold and heat denaturation. pH: Attractive and repulsive electrostatic interactions. Detergents: SDS ( sodium dodecyl sulfate) solubilizes surface and core residues. Salts affect water structure. ...
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4-electrophoresis
Georgia Tech, CHEM 4581
Excerpt: ... logical macromolecule Disrupts aggregates or folding Week #5 CHEM 4581 5 Sodium Dodecyl Sulfate SDS confers negative charge on proteins and denatures proteins Amphiphilic Hydrophilic Hydrophobic Anionic Detergent in a wide variety of products Sodium Dodecyl Sulfate (Lauryl Sulfate) CH3 (CH2) 11OSO3 Week #5 CHEM 4581 6 2 SDS-PAGE Buffers Buffers maintain pH control Allow gel to fully polymerize Stacking Gel 0.5M Tris-HCl pH 6.8 Resolving Gel 1.5M Tris-HCl pH 8.8 Week #5 CHEM 4581 7 Sample Preparation Ensure that sample has fully dentured! In the Gel Stacking Gel 0.5M Tris-HCl pH 6.8 In the Sample Laemmli Sample Buffer 0.5M Tris-HCl,pH 6.8 SDS Glycerol Bromophenol Blue Resolving Gel 1.5M Tris-HCl pH 8.8 Boil Sample for 1-5 min Week #5 CHEM 4581 8 Electrophoresis Buffer Electrophoresis Buffer Tris Base, Glycine, SDS Fully Protonated + H N-CH -COOH 3 2 Acidic Form Week #5 Loss of 1 Proton + H N-CH -COO 3 2 Zwitterionic Form CHEM 4581 Loss of 2 Protons H2 N-CH2 -COO Basic Form 9 3 SDS- ...
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Protein Electrophoresis
FGCU, BSC 3023
Excerpt: ... the column, and thus become isolated primarily within a limited set of eluted fractions. The electrophoresis performed relies exclusively on mass as a separation mechanism by running the proteins after denaturation and charge-mass ratio standardization with the detergent sodium dodecyl sulfate, in addition to further denaturing through boiling and delinking disulfide bonds with reductive -mercaptoethanol to eliminate secondary structure of any proteins present, but particularly the target caseins. Results Sephardex G-100 gel in a 2M 7.0 pH buffer solution was added to a capped column and drained, leaving about 20 ml gel matrix in the column. The gel column in turn was rinsed by passing through about 50 ml 0.02M tris buffer measured at pH 7.03 (6.057g tris/0.250 L adjusted with 0.6067 ml 6M HCl). The rinse was repeated with an additional 50 ml of the same buffer, which was stopped in the column for multiple days before being drained to a level matching the top of the gel column. Six alquilots of milk were cent ...
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Biochem_651_ING-1_Prelab_Lecture_2009
Wisconsin, BIOCHEM 651
Excerpt: ... Induc&on,AssayandElectrophoresis (ING1) February16,2009 PrimaryTA:MaGCopeland SecondaryTA:AbishekMuraliMohan Objec&ves Usingthelacoperonasamodelsystem,students will: studytheeectsofthenaturalinducer,lactoseAND thegratuitousinducer,IPTG,oncellgrowt ...
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Sodium dodecyl sulfate
CofC, RM 205
Excerpt: ... Material Safety Data Sheet Sodium dodecyl sulfate ACC# 08485 Section 1 - Chemical Product and Company Identification MSDS Name: Sodium dodecyl sulfate Catalog Numbers: AC226141000, AC226145000, AC230421000, AC230425000, AC419530010, AC419530250, AC419531000, S799941, S799942, BP166-100, BP166-5, BP166-500, NC9973507, O2674-25, S529-3, S529-500 Synonyms: SDS; Sodium lauryl sulfate; Dodecyl sodium sulfate; Sulfuric acid monododecyl ester, sodium salt; SLS; Dodecyl hydrogen sulfate sodium salt. Company Identification: Fisher Scientific 1 Reagent Lane Fair Lawn, NJ 07410 For information, call: 201-796-7100 Emergency Number: 201-796-7100 For CHEMTREC assistance, call: 800-424-9300 For International CHEMTREC assistance, call: 703-527-3887 Section 2 - Composition, Information on Ingredients CAS# 151-21-3 Chemical Name Sodium lauryl sulfate Percent >85 EINECS/ELINCS 205-788-1 Hazard Symbols: XI Risk Phrases: 36/38 Section 3 - Hazards Identification EMERGENCY OVERVIEW Appearance: white solid. Causes eye and skin i ...
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ps8a[1]
Berkeley, MCB 100
Excerpt: ... ease A, Mr = 13,700 D) RNA Polymerase, Mr=450,000 E) serum albumin, Mr=68,500 In gel filtration chromatography, larger molecules elute first. The answer is (B) immunoglobulin G. Q4. (i) By adding SDS ( sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to do which of the following? A) determine the amino acid composition of the protein. B) preserve the protein's native structure C) determine a protein's isoelectric point D) separate proteins primarily on the basis of molecular weight E) determine an enzyme's specific activity (ii) If gel electrophoresis were to be carried out without SDS, what complications might arise? Answer: (i) SDS coats the protein with a high negative charge density, and so the total charge on the protein reflects the molecular weight of the protein. Electrophoresis in the presence of SDS allows proteins of molecular weight. Answer = D (ii) if SDS were not used, two factors might complicate the analysis. First, the protein may remain folded, and its pass ...
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Sp09_Biochem_651_ING-2_Prelab_Lecture
Wisconsin, BIOCHEM 651
Excerpt: ... Induc&on,AssayandElectrophoresis (ING2) February23,2009 PrimaryTA:MaFCopeland SecondaryTA:AbishekMuraliMohan Objec&ves Usingthelacoperonasamodelsystem,students will: studytheeectsofthenaturalinducer,lactoseAND thegratuitousinducer,IPTG,oncellgrowt ...
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