Quiz 4 Question Pool Fall 2023

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Feb 20, 2024

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Quiz Question Pool 4 NB: You may have to look at lecture notes and/or on the Internet for the answers to some of these questions! 1) a. In gel filtration, the largest proteins elute F IRST or LAST , while in SDS-PAGE the largest proteins run FASTEST or SLOWEST . (2 points) b. In what way do the two procedures differ that can explain the above? (3 points) In SDS Page we examine to molecular mas of the denatured protein while in gel filtration examines the proteins in native state 2) What does PAGE stand for? (1 point) Polyacrylamide gel electrophoresis 3) a. What is the primary ingredient of the gels that we are running? In other words, what are the gels made of? (1 point) The primary ingredient of the gels is polyacrylamide which is generated from free radical polymerization of the acrylamide monomer and crosslinking co-monomer b. From what is it formed? (2 points) which is generated from free radical polymerization of the acrylamide monomer and crosslinking co- monomer c. Describe the resulting structure in one or two words. (1 point) porous network 4) SDS-PAGE separates proteins based on (1 point): A. Charge B. Molecular Weight C. Configuration D. All of the above E. A and B only 5) In SDS-PAGE, what is approximately the same for all proteins? (1 point) All proteins have the same charge density (charge to mass ratio) 6) What is the function of the stacking gel? (2 points) It results in sharper resolution of protein bands in the gel 7) What effect does SDS have on proteins? Be specific! (3 points) The SDS unfolds/denatures the proteins and then binds to it 8) What effect does β-mercaptoethanol have on proteins? Be specific! Which amino acid(s) does it interact with, and how? (3 points)
The disulfide bonds break and are prevented from rebinding because SDS coats the amino acids. It converts disulfides (cystinnes) to sulfhydryl’s (cysteines) . The S-S bonds are cleaved nd it breaks the tertiary structure of the proteins 9) a. What will we stain our gels with? (1 point) Coomassie blue b. What is the function of acetic acid in the stain? (2 points) Precipitates the proteins and immobilizing them in the structure of the gel 10) a. What will we destain our gels with? (2 points) Dilute solution of acetic acid and methanol b. Will the tracking dye stay in the gel during destaining? (1 point) No the tracking dye will not stay in the gel during destaining c. What will retain the stain? (1 point) the proteins 11) In which fraction(s) do you expect to find bovine serum albumin (BSA) and why ? (3 points) Between the fractions containing reddish and yellow coloring because the molecular weight is larger than food coloring so but smaller than myoglobin and blue dextran 12) Give 2 reasons why SDS-PAGE is not usually used as a method to purify proteins. (2 points) Small amounts of protein can be used and they need to be denatured or else the proteins will not be active The following questions are from previous exams: 13. 1 a. What molecular features would make a molecule hydrophilic? (2 points) If the molecule is polar it is hydrophilic 1 b. What molecular features would make a molecule amphipathic? (3 points) A molecule is amphipathic if it is both polar and nonpolar or has hydrophilic and hydrophobic parts (phospholipids) 1 14. a. If you had a protein and wanted to make it more positively charged, what two amino acids could you add to its sequence? (2 points) Lysine histidine b. What would you replace them with if you wanted to make it more negative? (2 points) Glutamic acid, aspartic acid 1 15. How would you define “Domains” in protein? (3 points) Regions of a protein with structural or function properties 16. 1List three different kinds of domains in protein. (3 points) SH2 DED and Ph 17. Why does NaCl dissolve in water? (3 points) NaCl has the positively charged Na which is attracted to the negative charge of oxygen and the the negative chloride ion is attracted to the positive hydrogen. 18. Why does water expand when it freezes? (3 points)
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