Deck 3: Exploring Proteins and Proteomes

Question 1

Proteins can be separated from small molecules and ions through a semipermeable membrane by __________________.

Answer 1

dialysis

Question 2

In the Edman procedure for peptide sequence, phenyl isothiocyanate is used to selectively remove the __________________ residue as a PTH-derivative.

Answer 2

N-terminal

Question 3

Polypeptides can be fragmented into smaller peptides by cleavage with trypsin, which hydrolyzes the peptide bond at the C-terminal side of __________________ residues.

Answer 3

lysine and arginine OR Lys and Arg OR K and R

Question 4

What technique can be used to determine the mass of a protein without knowing the identity of the molecule?

A) affinity chromatography
B) ion exchange chromatography
C) polyacrylamide gel electrophoresis
D) MALDI-TOF mass spectrometry
E) western blot

Question 5

Mass spectrometric techniques are critical in _________________research, which explores the proteins present in a cell, because it is possible to analyze constituents of large macromolecular assemblies.

Question 6

Which of the following are used to sequence entire proteins?

A) affinity peptides
B) circular peptides
C) overlap peptides
D) labeled peptides
E) synthetic peptides

Question 7

Another name for an antigenic determinant is _____.

A) epitope
B) epimer
C) epinephrine
D) epidemic
E) None of the answers is correct.

Question 8

The ratio of enzyme activity relative to total protein is called _____.

A) inherent activity
B) specific activity
C) explicit activity
D) exclusive activity
E) purified activity

Question 9

The mobility of proteins in SDS-PAGE is inversely proportional to the _____________.

Question 10

The unit for sedimentation coefficients is the _____.

A) Newton
B) radian
C) g
D) Svedberg
E) None of the answers is correct.

Question 11

The advantage to ______________________protein synthesis is that the desired product is bound to beads and excess reagents can be easily removed at each step.

Question 12

Which of the following is often the first step in protein purification from a homogenate?

A) ion exchange chromatography
B) gel-filtration chromatography
C) HPLC
D) centrifugation
E) gel electrophoresis

Question 13

Long proteins are often treated with the enzyme ______________, which cleaves the protein into smaller, easily analyzed peptides.

Question 14

What technique would be used to separate proteins with different sedimentation coefficients?

A) MALDI-TOF mass spectrometry
B) zonal centrifugation
C) HPLC
D) gel-filtration chromatography
E) All of the answers are correct.

Question 15

Which type of protein purification relies on the attraction of the protein for a particular chemical group?

A) affinity chromatography
B) gel-filtration chromatography
C) HPLC
D) gel electrophoresis
E) isoelectric focusing

Question 16

Dithiothreitol or β mercaptoethanol are commonly used to reduce _______________ bonds.

Question 17

__________________ gels are often used as the media for electrophoretic techniques such as SDS-PAGE and isoelectric focusing.

Question 18

_____ can be added prior to gel electrophoresis to fully denature proteins.

A) Coomassie blue
B) polyacrylamide
C) SDS
D) $\beta$ -mercaptoethanol
E) All of the answers are correct.

Question 19

_____ is the term to describe an original amino acid sequence for an uncleaved protein.

A) Apoprotein
B) Holoprotein
C) Nascent
D) Protomer
E) None of the answers is correct.

Question 20

Molecular exclusion or gel-filtration chromatography separates molecules on the basis of __________________.

Question 21

How can a protein's isoelectric point be used in protein purification (i.e., isoelectric focusing)?

Question 22

What is the purpose of determining the specific activity, yield, and purification level of a protein purification protocol?

Question 23

When enzymes are purified, the assay is often based on

A) light absorbance.
D) temperature changes.
B) catalytic activity.
E) mRNA levels.
C) pH.

Question 24

Which technique cannot be used for quantitative analysis?

A) x-ray crystallography
D) All of the answers are correct.
B) ELISA
E) None of the answers is correct.
C) absorbance spectroscopy

Question 25

What types of molecules can serve as antigens?

A) proteins
D) All of the answers are correct.
B) polysaccharides
E) proteins and polysaccharides
C) metal ions

Question 26

Techniques that can be used to obtain information about protein shape are

A) x-ray crystallography.
D) x-ray crystallography and NOESY NMR spectroscopy.
B) NOESY NMR spectroscopy.
E) All the answers are correct.
C) SDS-PAGE.

Question 27

Proteins that are not catalysts are often probed or assayed using

A) antibody binding assays.
D) None of the answers is correct.
B) catalytic activity.
E) All of the answers are correct.
C) genomic analysis.

Question 28

How do gel-filtration and ion-exchange chromatography differ?

Question 29

An ELISA can be used for

A) quantitative analysis.
D) All of the answers are correct.
B) size analysis.
E) None of the answers is correct.
C) protein sequencing

Question 30

Protein databases

A) can identify proteins from small stretches of amino acid sequences.
B) are not useful in proteomics studies due to the complexities of the proteome.
C) are determined from sequence data only, never deduced from genomic data.
D) None of the answers is correct.
E) All of the answers are correct.

Question 31

Cyanogen bromide cleaves the peptide bond at

A) the carboxyl side of Arg and Lys residues.
B) the carboxyl side of Met residues.
C) the amino terminus.
D) None of the answers is correct.
E) All of the answers are correct.

Question 32

Which of the following affect the sedimentation rate of a particle?

A) mass
D) All of the answers are correct.
B) shape
E) mass and shape
C) the density of the solution

Question 33

Two-dimensional electrophoresis is a combination of what two techniques?

A) ion-exchange chromatography and affinity chromatography
B) ion-exchange chromatography and SDS-PAGE
C) SDS-PAGE and affinity chromatography
D) isoelectric focusing and SDS-PAGE
E) isoelectric focusing and ion-exchange chromatography

Question 34

How is lactate dehydrogenase assayed?

Question 35

What is the advantage of adding SDS to gel electrophoresis?

A) SDS colors the proteins for visualization.
B) SDS reduces disulfide bonds.
C) SDS allows proteins to be separated on the basis of approximate mass.
D) None of the answers is correct.
E) All of the answers are correct.

Question 36

A technique used to identify proteins after gel electrophoresis, which employs antibodies in the detection process, is known as

A) northern blot
D) Southern blot
B) southwestern blot
E) None of the answers is correct.
C) western blot

Question 37

Why is an assay necessary for protein purification studies?

Question 38

A technique that can be used to study three-dimensional protein structure is

A) one-dimensional NMR spectroscopy
D) Western blotting
B) fluorescent microscopy
E) ion-exchange chromatography
C) x-ray crystallography

Question 39

Which of the following techniques can be used to determine mass to charge ratio of a molecule?

A) Edman degradation
D) MALDI-TOF
B) affinity chromatography
E) SDS-PAGE
C) diagonal electrophoresis

Question 40

The use of synthetic peptides includes

A) use as antigens for making antibodies.
B) drugs.
C) "hooks" for use in affinity purification.
D) All of the answers are correct.
E) use as antigens for making antibodies and "hooks" for use in affinity purification.

Question 41

How can recombinant DNA technology aid in protein purification?

Question 42

Describe the Edman degradation method for protein-sequence analysis.

Question 43

How are monoclonal antibodies made?

Question 44

Why are monoclonal antibodies more useful than polyclonal antibodies?

Question 45

How can the amino acid sequences be used to design a DNA probe?

Question 46

What are some of the advantages and drawbacks of NMR spectroscopy compared to x-ray crystallography?

Question 47

What type of information can be obtained from ultracentrifugation?

Question 48

What is one advantage of using the recombinant DNA methods to determine protein sequences?

Question 49

After a protein is purified, what is the next step in determining the structure of a protein by x-ray crystallography?

Question 50

Briefly describe how an ELISA works.