Chapter 8

Question 1

Hybridoma

Answer 1

Cell line used in the production of monoclonal antibodies; obtained by
fusing antibody-secreting B cells with cells of a lymphocyte tumor.

Question 2

Monoclonal Antibody

Answer 2

Antibody secreted by a hybridoma cell line

Question 3

Column Chromatography

Answer 3

General term for purification technique in which a mixture of proteins is
passed through a cylinder containing a porous solid matrix.

Question 4

Fusion Protein

Answer 4

Artificial product generated by linking the coding sequences for two different
proteins, or protein segments, and expressing the hybrid gene in
cells.

Question 5

High Performance Liquid Chromatography

Answer 5

Type of chromatography that uses columns packed with special chromatography
resins composed of tiny spheres that attain a high degree of
resolution, even at very fast flow rates.

Question 6

Nuclear Magnetic Resonance Spectroscopy (NMR)

Answer 6

Analysis of the release of electromagnetic radiation by atomic nuclei in a
magnetic field, due to flipping of the orientation of their magnetic dipole
moments.

Question 7

SDS polyacrylamide-gel electrophoresis (SDS-PAGE)

Answer 7

Technique in which a protein mixture is separated by running it through
a gel containing a detergent that binds to and unfolds the proteins.

Question 8

Two Dimensional Gel Electrophoresis

Answer 8

Technique for protein separation in which the protein mixture is run first
in one direction and then in a direction at right angles to the first.

Question 9

Western Blotting Immunoblotting

Answer 9

Technique by which proteins are separated by electrophoresis, immobilized
on a paper sheet, and then analyzed, usually by means of a labeled
antibody.

Question 10

X-Ray Crystallography

Answer 10

The main technique that has been used to discover the three-dimensional
structure of molecules, including proteins, at atomic resolution.

Question 11

cDNA Clone

Answer 11

A DNA clone of a DNA copy of an mRNA molecule.

Question 12

Deep RNA sequencing

Answer 12

The sequencing of the entire repertoire of RNA from a cell or tissue.

Question 13

Bacterial Artificial Chromosome (BAC)

Answer 13

Prokaryotic cloning vector that can accommodate large pieces of DNA
up to 1 million base pairs.

Question 14

genomic library

Answer 14

A collection of clones that contain a variety of DNA segments from the
genome of an organism.

Question 15

Plasmid vector

Answer 15

Small, circular DNA molecule that replicates independently of the
genome and can be used for DNA cloning.

Question 16

PCR

Answer 16

Technique for generating multiple copies of specific regions of DNA by
the use of sequence-specific primers and multiple cycles of DNA synthesis.

Question 17

Restriction Nuclease

Answer 17

One of a large number of enzymes that can cleave a DNA molecule at any
site where a specific short sequence of nucleotides occurs.

Question 18

hybridization

Answer 18

The process whereby two complementary nucleic acid strands form a
double helix.

Question 19

Allele

Answer 19

One of a set of alternative forms of a gene.

Question 20

Epistasis Analysis

Answer 20

Comparing the phenotypes of different combinations of mutations to
determine the order in which the genes act.

Question 21

Genetic screen

Answer 21

A search through a large collection of mutants for a mutant with a particular
phenotype.

Question 22

genotype

Answer 22

The genetic constitution of an individual cell or organism.

Question 23

haplotype block

Answer 23

Ancestral chromosome segment that has been inherited with little
genetic rearrangement across generations.

Question 24

phenotype

Answer 24

The observable character of a cell or an organism.

Question 25

polymorphism

Answer 25

One of a number of common sequence variants that coexist in the population.

Question 26

Transgenetic Organism

Answer 26

Animal or plant that has been permanently engineered by gene deletion, gene insertion, or gene replacement.

Question 27

Robustness

Answer 27

The ability of biological regulatory systems to function normally in the face of frequent and sometimes extreme variations in external conditions or the concentrations or activities of key components.

Question 28

Stochastic

Answer 28

Describes random variations in protein content of individual cells resulting in variations in cell phenotypes.

Question 29

Stochastic

Answer 29

Describes random variations in protein content of individual cells resulting in variations in cell phenotypes.

Question 30

T/F: The Lac operon, which is turned on by a transcription activator and turned off by a transcription repressor, is a classic example of an AND NOT logic gate.

Answer 30

True; Individual cells can be cut away from their neighbors with a laser beam, allowing the cells to be isolated and studied.

Question 31

T/F: Laser-capture microdissection permits isolation of individual cells from a sample of tissue.

Answer 31

True; Individual cells can be cut away from their neighbors with a laser beam, allowing the cells to be isolated and studied

Question 32

T/F: Because a monoclonal antibody recognizes a specific antigenic site (epitope), it binds only to the specific protein against which it was made.

Answer 32

False. A monoclonal antibody recognizes a specific antigenic site, but this does not necessarily mean that it will bind only to one specific protein. There are two complicating factors. First, antigenic sites that are similar, but not identical, can bind to the same antibody with different affinities. If too much antibody is used in an assay, the antibody may bind productively to a protein with a high-affinity site and to other proteins with lowaffinity sites. Second, it is not uncommon for different proteins to have the same antigenic site; that is, the same cluster of five or six amino acid side chains on their surfaces. This is especially true of members of protein families, which have similar amino acid sequences, and are often identical in functionally conserved regions

Question 33

T/F: It is possible to pellet hemoglobin by centrifugation at sufficiently high speed.

Answer 33

True. Present-day ultracentrifuges rotate at sufficiently high speed to generate forces up to 500,000 times gravity, which is more than adequate to drive hemoglobin through solution. Spun long enough, hemoglobin could be driven to the bottom of the tube and pelleted.

Question 34

T/F: Given the inexorable march of technology, it seems inevitable that the sensitivity of detection of molecules will ultimately be pushed beyond the yoctomole level (10–24 mole).

Answer 34

True. Gel-filtration columns exclude proteins that are too large to fit into the pores in the beads, but they fractionate the proteins that can enter the pores. Because the pores are not uniform in size, proteins experience the internal volume of the beads to greater or lesser extents. Proteins that can enter only a small fraction of the pores will elute early from a gel-filtration column, while those that can enter all the pores will elute late. If all the pores were the same size, then a protein would either be excluded from the pores and elute in the external volume, or it would be included in the pores and elute with the external plus internal volume. This answer presupposes that the column is run slowly enough that equilibrium is achieved throughout and that the beads are inert so that there is no interaction between them and the proteins.

Question 35

T/F: Bacteria that make a specific restriction nuclease for defense against viruses have evolved in such a way that their own genome does not contain the recognition sequence for that nuclease.

Answer 35

False. The recognition sequences for the restriction nuclease, where they occur in the genome of the bacterium itself, are protected from cleavage by methylation at an A or a C residue.

Question 36

T/F: Pulsed-field gel electrophoresis uses a strong electric field to separate very long DNA molecules, stretching them out so that they travel endfirst through the gel at a rate that depends on their length.

Answer 36

False. When DNA molecules travel end-first through the gel in a snakelike configuration, their rates of movement are independent of length. In pulsed-field gel electrophoresis, the direction of the field is changed periodically, which forces the molecules to re-orient before continuing to move snakelike through the gel. This re-orientation takes more time for larger molecules, so that progressively larger molecules move more and more slowly.

Question 37

T/F: By far the most important advantage of cDNA clones over genomic clones is that they can contain the complete coding sequence of a gene.

Answer 37

True. Since eukaryotic coding sequences are usually in pieces in genomic DNA, cDNA clones allow expression of the protein directly and permit one to deduce the amino acid sequence of the protein.

Question 38

T/F: If each cycle of PCR doubles the amount of DNA synthesized in the previous cycle, then 10 cycles will give a 103-fold amplification, 20 cycles will give a 106-fold amplification, and 30 cycles will give a 109-fold amplification.

Answer 38

True. If each cycle doubles the amount of DNA, then 10 cycles equal a 210-fold amplification (which is 1024), 20 cycles equal a 220-fold amplification (which is 1.05 × 106), and 30 cycles equal a 230-fold amplification (which is 1.07 × 109). (It is useful to remember that 210 is roughly equal to 103 or 1000. This simple relationship allows you to estimate the answer to this problem rapidly without resorting to your calculator. It comes in handy in a variety of contexts.)

Question 39

T/F: In an organism whose genome has been sequenced, identifying the mutant gene responsible for an interesting phenotype is as easy for mutations induced by chemical mutagenesis as it is for those generated by insertional mutagenesis.

Answer 39

False. Even with a sequenced genome, it is still a laborious process to identify a gene that has been mutated by chemical mutagenesis. Such a mutation must be mapped to a chromosomal location (a time-consuming process) and then candidate genes in that region (many of which are known from genome sequencing efforts) can be screened for the presence of the mutation. Insertional mutagenesis, by contrast, places a known sequence—often a transposable element—into the mutated gene. It is a simple process to obtain sequence information adjacent to a segment of known sequence. In a sequenced genome, a bit of sequence is all that is needed to identify the location of the inserted DNA and the mutated gene.

Question 40

T/F: Loss-of-function mutations are usually recessive.

Answer 40

True. Mutations that eliminate the function of a protein are usually recessive. In a diploid organism, one copy of the wild-type allele can usually compensate for the loss-of-function allele. It is important to note, however, that in some cases half the normal amount of gene product is not sufficient to produce the normal phenotype. This situation, which is called haplo-insufficiency, leads to a mutant phenotype for a loss-offunctionmutation.

Question 41

T/F: If two mutations have a synthetic phenotype, it usually means that the mutations are in genes whose products operate in the same pathway.

Answer 41

False. A synthetic phenotype usually means that the affected genes encode products that operate in different pathways. Two blocks in one pathway are usually no worse than either single block. Mutations that block two different pathways, however, can often generate a worse phenotype than either block can on its own.

Question 42

T/F: To judge the biological importance of an interaction between protein A and protein B, we need to know quantitative details about their concentrations, affinities, and kinetic behaviors.

Answer 42

True. Without quantitative details, it would be impossible to know if the interaction is likely to occur in cells at all, and if it does, whether it is a stable interaction with a long half-life or a dynamic interaction with rapid binding and dissociation.

Question 43

T/F: The association constant, Ka, is equal to 1 minus the dissociation constant, Kd; that is, Ka = 1 – Kd.

Answer 43

False. The association constant is the reciprocal of the dissociation constant; thus, Ka = 1/Kd.

Question 44

T/F: The rate of change in the concentration of any molecular species X is given by the balance between its rate of appearance and its rate of disappearance.

Answer 44

True. This is a fundamental premise in the analysis of biochemical reactions. It applies equally to molecular complexes (such as AB, which forms when proteins A and B bind to each other, and disappears when AB dissociates) and metabolic reactions (for example, when metabolite B forms by chemical modification of metabolite A, and disappears when it is converted to metabolite C).

Question 45

T/F: After a sudden increase in transcription, a protein with a slow rate of degradation will reach a new steady-state level more quickly than a protein with a rapid rate of degradation.

Answer 45

False. A protein with a rapid degradation rate will reach its new steadystate concentration more quickly. The rate of approach to the new steady state is inversely related to the protein’s half-life.

Question 46

T/F: The Lac operon, which is turned on by a transcription activator and turned off by a transcription repressor, is a classic example of an AND NOT logic gate.

Answer 46

True. The Lac operon is turned on maximally when the activator concentration, [A], is high and the repressor concentration, [R], is zero. Thus, the Lac operon displays AND NOT logic ([A] and not [R]).