49. Electrophoresis mobility shift assay (EMSA) is a sensitive method to detect protein-DNA interactions. The proteins and fluorescent DNA were combined as indicated and electrophoresed under native conditions, as shown below. Which of the following statements would be most likely?
 
(A) Protein B binds to the DNA independent of protein A.
(B) Protein A binds to the DNA only in the presence of protein B.
(C) Protein A and protein B compete for DNA binding.
(D) Protein A and protein B form a protein complex before binding to the DNA.
(E) Protein B binds to the protein A-DNA complex, resulting in a ternary complex.

45. Which of the following statements accurately describes the Warburg effect? (A) It involves the preferential use of oxidative phosphorylation over glycolysis in cancer cells. (B) It describes the upregulation of gluconeogenesis in normal cells under hypoxic conditions. (C) It signifies the increased reliance of cancer cells on glycolysis, even in the presence of oxygen. (D) It indicates the decreased glucose uptake in tumors compared to healthy tissues. (E) The net effect is to increase the level of ATP.

46. The following plot is for an enzyme with multiple ligand binding sites. Which statement is True for this enzyme? (x: ligand concentration; y: fractional saturation)  (A) This enzyme is a non-allosteric oligomer. (B) The Hill coefficient for this enzyme is 2. (C) ligand binding favors another ligand binding. (D) ligand binding disfavors another ligand binding. (E) The Hill coefficient for this enzyme is -0.5.

47. The diagram depicts the mechanism of a protease inhibitor. What is the target of this inhibitor?  (A) Papain (B) Chymotrypsin (C) Pepsin (D) Carboxypeptidase A (E) Chymosin

48. Scientists covered an affinity chromatography column with microtubules for protein purification. Which of the following proteins would most likely be separated in this method? (A) Tubulin (B) Kinesin (C) Myosin (D) Actin (E) Lamin

50. Production of recombinant proteins in Escherichia coli is a common tool for research and industrial production of proteins. However, during affinity column purification, DnaK, unwanted contamination, is often coeluted with proteins of interest (POI). Which of the following statements about DnaK is TRUE? (A) DnaK binds to the charged regions of the POI and ADP can dissociate the interaction of Dnak with POI. (B) DnaK binds to the hydrophobic regions of the POI and ATP can dissociate the interaction of Dnak with POI. (C) DnaK binds to the polar regions of the POI and GTP can dissociate the interaction of Dnak with POI. (D) DnaK binds to the hydrophobic regions of the POI and GTP can dissociate the interaction of Dnak with POI. (E) DnaK binds to the charged regions of the POI and ATP can dissociate the interaction of Dnak with POI.

51. Based on the enzyme reaction plot shown below, which of the following statements is correct? (A) The of hexokinase IV for glucose is ~10 mM. (B) Hexokinase I works more efficiently than hexokinase IV when the blood glucose concentration is higher than 10 mM. (C) The of hexokinase I for glucose is ~5 mM. (D) Hexokinases catalyze a reaction that adds an AMP group to glucose. (E) At normal fasting conditions, hexokinase IV works better than hexokinase I .

52. Which of the following statements about the initial step of the reaction catalyzed by thermolysin is NOT correct? (A) The enzyme reaction involves the general acid-base catalysis. (B) A glutamate residue deprotonates water and promotes hydroxide attack on the carbonyl carbon of the substrate. (C) The ion stabilizes the buildup of negative charge on the peptide carbonyl oxygen. (D) Collapse of the unstable tetrahedral intermediate links the substrate to the glutamate residue covalently. (E) The enzyme is a member of hydrolases.

53. Which of the following is NOT a property of phosphoglucoisomerase? (A) The carbonyl oxygen of glucose-6-phosphate is shifted from position C-1 to C-2. (B) The enzyme catalyzes the conversion of glucose-6-phosphate to glucose-1- phosphate. (C) The reaction involves the opening of the pyranose ring. (D) The reaction involves an aldose and a ketose. (E) The reaction involves the formation of an enediol intermediate.

54. Proteins can be modified with small regulatory proteins like ubiquitins and small ubiquitin-like protein modifiers (SUMO). Which of the following descriptions about SUMO is NOT correct? (A) SUMO are a highly conserved family of proteins found in all eucaryotes. (B) SUMO are covalently ligated to lysine residues in target proteins. (C) Sumoylated proteins are primarily targeted to the proteasome for destruction. (D) Protein sumoylation is primarily a 3-enzyme conjugating system. (E) Protein sumoylation can be reversed by a small number of isopeptidases that cleave the target protein-SUMO linkages.

55. The Hsp70 molecular chaperones are a group of proteins that assist nascent protein folding. Which of the following statements about the E. coli Hsp70 is NOT correct? (A) In Hsp70-assisted folding, the chaperone binds to nascent polypeptide chains while they are still on the ribosomes. (B) The DnaJ protein binds unfolded proteins during protein synthesis and delivers them to the DnaK: ATP complex. (C) The Dnak protein recognizes exposed, extended regions of polypeptides that are rich in hydrophilic residues. (D) Interaction of DnaK with DnaJ triggers the ATPase activity of DnaK. The resulting DnaK: ADP complex forms a stable complex with the unfolded polypeptide. (E) The reaction cycle requires a nucleotide exchange protein GrpE.