Question 1

The liquid that emerges from the bottom of a chromatographic column is called the supernatant.

Accepted Answer

A) True 
 B)False

Question 2

Which technique is most sensitive and accurate for the determination of a proteinʹs molecular weight?

Accepted Answer

A)  SDS-PAGE 
B)  Gel filtration chromatography 
C)  mass spectrometry 
D)  X-ray crystallography 
E)  osmotic pressure

Question 3

How do the pKa values of an ionizable side chain compare when the amino acid is free versus when it is in a polypeptide chain?

Accepted Answer

A)  The pKa of the side chain is independent of whether the amino acid is in a polypeptide chain or is free. 
B)  The pKa of the side chain is always lower for the free amino acid. 
C)  The pKa of the side chain may be lower or higher in a polypeptide chain due to weaker inductive effects and differences in their microenvironments. 
D)  The pKa of the side chain is usually higher in a polypeptide chain due to stabilization from nearby residues in the three-dimensional structure.

Question 4

During the fractionation process which of the following remain in the supernatant?

Accepted Answer

A)  membrane proteins 
B)  the less soluble impurities 
C)  the Target protein and other more soluble proteins 
D)  the remaining unbroken whole) cells

Question 5

Affinity chromatography can be used to save many purification steps compared to other techniques due to its high specificity for the target protein.

Accepted Answer

A) True 
 B)False

Question 6

Ultraviolet UV) light can be used to estimate protein solution concentrations because

Accepted Answer

A)  phenylalanine absorbs at 260 nm. 
B)  all the amino acids absorb UV light. 
C)  aromatic amino acids absorb at 280 nm. 
D)  tryptophan and tyrosine absorb at 280 nm. 
E)  All of the above

Question 7

In a biochemistry laboratory a student added ammonium sulfate to a tube containing a buffered protein solution. The student then centrifuged the solution. What was the student probably trying to do?

Accepted Answer

A)  change the pH of the buffer solution to solubilize all proteins 
B)  hydrolyze the proteins into their constituent amino acids to determine the percent composition 
C)  derivatize the N-terminal amino acid of all proteins 
D)  selectively precipitate and purify a certain protein

Question 8

Cation-exchange resins have negatively charged groups covalently attached to the column matrix.

Accepted Answer

A) True 
 B)False

Question 9

An octapeptide was determined to have the following amino acid composition: Lys 2), Phe 2), Gly 1), His 1), Leu 1), Met 1). The native peptide was run through one cycle of the Edman degradation and the PTH-leucine derivative was identified by HPLC. When the native peptide was exposed to cyanogen bromide CNBr), a heptapeptide and free glycine were recovered. Incubation of the native protein with trypsin gave a tetrapeptide, a tripeptide, and free lysine. The peptides were separated and each run through one cycle of the Edman degradation. The tetrapeptide yielded the PTH-leucine derivative, and the tripeptide yielded the PTH-phenylalanine derivative. Incubation of the native protein with pepsin produced a dipeptide and two tripeptides. The amino acid composition of the tripeptides not the order) were determined to be Phe, Gly, Met) and Phe, Lys, Lys). What is the sequence of the octapeptide?
Specificities of Proteases
BrCN cuts at the C-terminal side of Met Trypsin cuts at the C-terminal side of Lys or Arg
Pepsin cuts at the N-terminal side of Phe, Trp or Tyr

Accepted Answer

A)  Leu-His-Phe-Lys-Lys-Phe-Met-Gly 
B)  Gly-Met-Phe-Lys-Lys-Phe-His-Leu 
C)  Met-Leu-Phe-Lys-Phe-Gly-Lys-His 
D)  Leu-His-Lys-Lys-Phe-Phe-Gly-Met 
E)  His-Phe-Leu-Lys-Lys-Phe-Met-Gly

Question 10

Which amino acid is ideal for the transfer of protons within the catalytic site of enzymes due to the presence of significant amounts of both the protonated and deprotonated forms of its side chain at biological pH?

Accepted Answer

A)  Lysine 
B)  Asparagine 
C)  Tyrosine 
D)  Cysteine 
E)  Histidine

Question 11

Proline is distinct among the 20 commonly found amino acids because

Accepted Answer

A)  it is a ring compound. 
B)  it is hydrophilic and ionic. 
C)  the nitrogen of the amino group is in a ring. 
D)  the carbon of the carboxyl group is in a ring. 
E)  it has little effect on protein structure.

Question 12

Tyrosine and tryptophan are less hydrophobic than phenylalanine because

Accepted Answer

A)  phenylalanine has an indole group. 
B)  phenylalanine has no polar group in the side chain. 
C)  phenylalanine is a phenol. 
D)  tyrosine and tryptophan have smaller R groups. 
E)  All of the above

Question 13

The primary structure of a protein describes the .

Accepted Answer

A)  number of each type of amino acid percent composition 
B)  linear sequence of amino acids 
C)  overall three-dimensional shape 
D)  Φ and Ψ angles for each amino acid

Question 14

The pH inside cells is normally near pH 7. At pH 7 which statement is true about the charges ionization state of the α-Carboxyland α-Amino groups of an amino acid?

Accepted Answer

A)  The α-Carboxyl group is 1- and the α-Amino group is 1+. 
B)  The α-Carboxyl group is 1+ and the α-Amino group is 1-. 
C)  The α-Carboxyl group is 1- and the α-Amino group is uncharged. 
D)  Both groups are uncharged not ionized) at pH 7.

Question 15

If the R group of an amino acid is -CH3, then the name of this compound is

Accepted Answer

A)  methyl amino acid. 
B)  2-aminopropanoic acid. 
C)  alanine. 
D)  All of the above 
E)  B and C

Question 16

Most purification procedures for proteins are carried out at room temperature.

Accepted Answer

A) True 
 B)False

Question 17

In which technique is a protein solution a pumped through a metal needle at high voltage to create tiny droplets that are analyzed for their mass/charge ratio?

Accepted Answer

A)  electrospray mass spectrometry 
B)  MALDI-TOF 
C)  aerosol microscopy 
D)  Millikan analysis 
E)  SDS-PAGE

Question 18

The distribution of amino acids in a protein often cannot be determined precisely by acid hydrolysis. Why?

Accepted Answer

A)  The side chains of asparagine and glutamine are also hydrolyzed. 
B)  The amine groups on lysine and arginine neutralize much of the acid. 
C)  The side chain of phenylalanine is almost totally destroyed by acid hydrolysis. 
D)  All of the above

Question 19

Proteins are treated with substances such as 2-mercaptoethanol to remove disulfide bonds before being sequenced because the disulfide bonds will interfere with the sequencing procedure.

Accepted Answer

A) True 
 B)False

Question 20

The pKaʹs of arginineʹs α-Carboxyl group, α-Amino group and side chain are 1.8, 9.0 and 12.5, respectively. Calculate the isoelectric point.

Accepted Answer

A)  7.8 
B)  7.2 
C)  10.8 
D)  5.4

Exam 3: Amino Acids and the Primary Structures of Proteins

The liquid that emerges from the bottom of a chromatographic column is called the supernatant.

Which technique is most sensitive and accurate for the determination of a proteinʹs molecular weight?

How do the pK_avalues of an ionizable side chain compare when the amino acid is free versus when it is in a polypeptide chain?

During the fractionation process which of the following remain in the supernatant?

Affinity chromatography can be used to save many purification steps compared to other techniques due to its high specificity for the target protein.

Ultraviolet UV) light can be used to estimate protein solution concentrations because

In a biochemistry laboratory a student added ammonium sulfate to a tube containing a buffered protein solution. The student then centrifuged the solution. What was the student probably trying to do?

Cation-exchange resins have negatively charged groups covalently attached to the column matrix.

Which amino acid is ideal for the transfer of protons within the catalytic site of enzymes due to the presence of significant amounts of both the protonated and deprotonated forms of its side chain at biological pH?

Proline is distinct among the 20 commonly found amino acids because

Tyrosine and tryptophan are less hydrophobic than phenylalanine because

The primary structure of a protein describes the .

The pH inside cells is normally near pH 7. At pH 7 which statement is true about the charges ionization state of the α-Carboxyland α-Amino groups of an amino acid?

If the R group of an amino acid is -CH₃, then the name of this compound is

Most purification procedures for proteins are carried out at room temperature.

In which technique is a protein solution a pumped through a metal needle at high voltage to create tiny droplets that are analyzed for their mass/charge ratio?

The distribution of amino acids in a protein often cannot be determined precisely by acid hydrolysis. Why?

Proteins are treated with substances such as 2-mercaptoethanol to remove disulfide bonds before being sequenced because the disulfide bonds will interfere with the sequencing procedure.

The pK_aʹs of arginineʹs α-Carboxyl group, α-Amino group and side chain are 1.8, 9.0 and 12.5, respectively. Calculate the isoelectric point.