Chapter 8 Flashcards Preview

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Flashcards in Chapter 8 Deck (46):
1

Hybridoma

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

2

Monoclonal Antibody

Antibody secreted by a hybridoma cell line

3

Column Chromatography

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

4

Fusion Protein

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

5

High Performance Liquid Chromatography

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.

6

Nuclear Magnetic Resonance Spectroscopy (NMR)

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.

7

SDS polyacrylamide-gel electrophoresis (SDS-PAGE)

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

8

Two Dimensional Gel Electrophoresis

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.

9

Western Blotting Immunoblotting

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

10

X-Ray Crystallography

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

11

cDNA Clone

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

12

Deep RNA sequencing

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

13

Bacterial Artificial Chromosome (BAC)

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

14

genomic library

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

15

Plasmid vector

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

16

PCR

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

17

Restriction Nuclease

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

18

hybridization

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

19

Allele

One of a set of alternative forms of a gene.

20

Epistasis Analysis

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

21

Genetic screen

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

22

genotype

The genetic constitution of an individual cell or organism.

23

haplotype block

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

24

phenotype

The observable character of a cell or an organism.

25

polymorphism

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

26

Transgenetic Organism

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

27

Robustness

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.

28

Stochastic

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

29

Stochastic

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

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.

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

31

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

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

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.

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

33

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

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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.)

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.

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.

40

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

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.

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.

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.

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.

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.

43

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

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

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.

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).

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.

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.

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.

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]).