In SDS-PAGE, proteins are completely denatured and converted to be uniformly neg

Question

In SDS-PAGE, proteins are completely denatured and converted to be uniformly negatively charged by ________ and making the polypeptide chains unbranched by ________.

A. SDS/DTT

B. EDTA/SDS

C. DTT/high heat

D. high heat/EDTA

21. In SDS-PAGE, the proteins are uniformly negatively charged at the pH of 8.3, mainly because _________.

A. the high pH turns arg and lys restudies fully protonated

B. the high pH turns asp and glu residues fully deprotonated

C. the -SO4 ions of SDS get attached to the polypeptide chains at that pH

D. the phospholipid molecules get attached to the polypeptide chains at that pH

22. Two polypeptide chains, one 200 amino acids (aa) in size, another 500aa in size and both are treated with excess SDS; which of the two has a higher charge to mass ratio?

A. The shorter one

B. The longer one

C. Both has identical charge to mass ratio

23. In native protein gel electrophoresis, a 200 kD protein may______________.

A. may not migrate at all

B. migrate close to the positive electrode

C. migrate close to the negative electrode

D. may display any of these possibilities

24. You prepared a nuclear extract and resolved it in a 12% SDS-PAGE. You stained the gel with silver stain and found 21 bands there. Which of the following explanations describes the result?

A. The extract had 21 proteins

B. The extract had 21 polypeptide chains

C. The extract has an unknown number polypeptide chains of 21 different sizes

D. Either gel electrophoresis or the protein extraction process was done improperly

25. You resolved three proteins of relative molecular masses of 20 kD, 37 kD and 86 kD in a SDS-PAGE. Which of the proteins will migrate close to the positive (red) electrode?

A. 20 kD

B. 86 kD

C. 20 kD if the protein has only one type of polypeptide chains

D. 80 kD if the protein has only one type of polypeptide chains

26. Challenge question: Had you resolved a pure preparation of gamma globulin (IgG) protein in a SDS PAGE, how many bands you will find?

A. One

B. Two

C. Three

D. Four

27. In 2-D protein gels, the first step is a capillary gel containing several ampholites. The gel has a pH gradient. The purpose is to separate proteins by _______________.

A. size

B. shape

C. net charge

D. size and shape

28. Proteins are treated with the Laemmli (i.e. protein cracking) buffer (it contains SDS, BME, TRis-HCl, Sucrose, and bromphenol blue) before loading onto SDS-PAGE. What is the function of bromphenol blue?

A. To make the polypeptide chains negatively charged

B. To track the migration of the polypeptide chains

C. To make the polypeptide chains unbranched

D. To make the polypeptide chains linear

29. The second step of the 2D protein gel fractionates proteins by ____________.

A. size

B. shape

C. net charge

D. size and shape

30. You extracted proteins from liver cells and liver cancer cells of the same animal and resolved the proteins in 2-D gels. The former sample produced 9209 spots and the later sample showed 9096 spots. Of the spots 8182 are in identical locations of the two gels and the rest are in non-identical locations of the gels. If you want to identify a cancer-causing polypeptide, which of the following spots you would examine?

A. One or more of the common spots

B. One or more of the uncommon spots present in the cancer cells but missing in normal cells

C. One or more of the uncommon spots present in the normal cells but missing in the cancer cells

31. Why do you break the proteins eluted from a spot of a 2-D gel before MS analysis?

A. The entity needed to be made charged

B. The entity should have unique charge/mass ratio to fly through the charged grid

C. The entity must be charged and fly through the charged grid of the spectrometer

32. The MALDI-TOF MS technology identifies the proteins by __________________.

A. comparing the m/z values and a database of known peptides and their m/z values

B. chemically sequencing the peptides and annealing the amino acid sequences of the peptides

C. calculating the m/z values of the peptides and modeling the structure and function of the combined peptides

33. An antibody can be used in all the following purposes but not necessarily to ____________.

A. purify a protein

B. identify a protein

C. quantify a protein

D. to assay the biological activity of a protein

E. locate a protein inside a particular compartment of a cell

Explanation / Answer

1) SDS/DTT - The sodium dodecyl sulfate added to the sample is heated which disrupts hydrogen bonds. The disulfide bonds between the polypetide chains are cleaved by dithiothreitol (DTT).

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