Chapter 5. Exploring Genes and Genomes

Question 1

An artificial bacterial chromosome, a highly engineered version of the E. coli fertility (F factor), that can serve as a cloning vector for inserts as larges as 300 kb.

Answer 1

Bacterial artificial chromosome (BAC)

Question 2

A means of introducing a variety of mutations into a gene of interest. A short segment of plasmid harboring the original gene is removed by restriction enzyme treatment. A synthetic double-stranded oligonucleotide (the cassette) carrying the genetic alterations of interest is subsequently inserted.

Answer 2

cassette mutagenesis

Question 3

Endonuclease enzymes that recognize specific base sequences in double-stranded DNA and cleave both strands of the duplex at specific places.

Answer 3

Restriction enzyme

Question 4

a word, sentence, or verse that reads the same from right to left as it does from left to right. An example is radar. By extension to biochemistry, a sequence of double-stranded DNA that is the same in each strand when the strands are read in the same direction; that is, it displays a twofold rotational symmetry, for example: 3inches-CCTAGG-5inches/5inches-GGATCC-3 inches.

Answer 4

Palindrome

Question 5

DNA complementary to an mRNA sequence.

Answer 5

Complementary DNA (cDNA)

Question 6

a collection of DNA fragments, inserted into vector molecules, that represents the entire genome of an organism.

Answer 6

Genomic library

Question 7

A class of mobile genetic elements that can be up to 10 kbp in length that appear more than a million times in the human genome.

Answer 7

long interspersed elements (LINES)

Question 8

a technique analogous to Southern blotting, in which a mixture of RNA fragments is separated by electrophoresis, transferred to a nitrocellulose sheet, hybridized to a radioactively labeled DNA probe complementary to the desired sequence, and visualized by autoradiography. The technique can therefore be used to locate and identify an RNA fragment containing a specific sequence.

Answer 8

Northern blotting

Question 9

A bacteriophage cloning vector that can be incorporated into the hosts genome and thus be replicated indefinitely or can be expressed and destroy the host.

Answer 9

Lambda (λ) phage

Question 10

an enzyme that catalyzes the formation of a phosphodiester bond between the 3 inch-OH at the end of one DNA chain and the 5 inch-phosphate at the end of the other chain; it is involved in the synthesis, repair, and splicing of DNA.

Answer 10

DNA ligase

Question 11

A plasmid-cloning vector that has been optimized for the expression of large amounts of recombinant protein encoded by the vector.

Answer 11

Expression vector

Question 12

A DNA-sequencing technique that employs controlled interruption of enzymatic replication of the molecule to be analyzed. DNA polymerase I is used with a primer, the four deoxynucleoside triphosphates, and a 2’,3’-dideoxy analog of one of them. Fragments of various lengths are produced in which the dideoxy analog is at the 3’ end. Four sets of chain-terminated fragments (one for each analog) are then displayed by electrophoresis and autoradiography, and the base sequence can be read from the four lanes of the gel.

Answer 12

Controlled termination of replication (Sanger dideoxy method)

Question 13

A means of transforming plant cells. DNA is coated onto 1-mm-diameter tungsten pellets, and these microprojectiles are fired at the target cells with a velocity greater than 400 m s�1.

Answer 13

Gene gun (bombardment-mediated transformation)

Question 14

Highly specific modification of genomic DNA.

Answer 14

genome editing

Question 15

Inactivating a gene and looking for resulting abnormalities in order to determine the gene’s function.

Answer 15

gene disruption (gene knockout)

Question 16

A collection of all of the complementary DNA for all mRNA that a cell contains, which have been inserted into vectors, and then inserted into bacteria.

Answer 16

cDNA library

Question 17

A solid support such as a microscope slide to which are affixed oligonucleotides or cDNAs corresponding to specific genes. Fluorescently labeled cDNA is hybridized to the slide to reveal the expression level for each gene, identifiable by its known position within the microarray.

Answer 17

DNA microarray (gene chip)

Question 18

These are plasmids or bacteriophage that allow the insertion and replication of DNA fragments into bacteria for the purpose of cloning. They often feature a polylinker region that includes many unique restriction sites within its sequence, allowing the region to be cleaved with many different restriction enzymes or combinations of enzymes. This provides great versatility in the DNA fragments that can be inserted.

Answer 18

cloning vectors

Question 19

Small, mobile, non-coding DNA sequences, related to transposons, that can replicate and insert at random sites in the genome.

Answer 19

mobile genetic element

Question 20

a technique used to locate and identify a DNA fragment containing a specific sequence; a mixture of fragments is separated by electrophoresis, transferred to a nitrocellulose sheet, hybridized to a radioactively labeled DNA probe complementary to the desired sequence, and visualized by autoradiography.

Answer 20

Southern blotting

Question 21

a DNA molecule that can be used to clone DNA inserts ranging from 100 to 1000 kb in length; these molecules contain a centromere, an autonomously replicating sequence, a pair of telomeres, selectable marker genes, and an insertion site for the sequence to be cloned.

Answer 21

Yeast artificial chromosome (YAC)

Question 22

Circular duplex DNA molecules that replicate autonomously and act as accessory chromosomes in bacteria; they carry useful genes but are disposable under certain conditions.

Answer 22

Plasmid

Question 23

Complementary single-stranded ends, also called cohesive ends, produced by restriction enzymes that cleave their palindromic target sequences in a staggered fashion.

Answer 23

Sticky ends

Question 24

A DNA molecule that can replicate autonomously in an appropriate host organism. Vectors are designed to enable the rapid, covalent insertion of DNA fragments of interest.

Answer 24

Vector

Question 25

a method for amplifying DNA sequences using DNA polymerase; a series of three-step cycles is employed, in which parental DNA strands are separated by heating, primers to flanking regions of the target sequence are annealed to the separated strands, and the primers are then extended by DNA synthesis.

Answer 25

Polymerase chain reaction (PCR)

Question 26

an enzyme that synthesizes DNA using an RNA template.

Answer 26

Reverse transcriptase

Question 27

Instances of genetic variations.

Answer 27

Polymorphism

Question 28

Platforms that enable the rapid determination of a complete genome sequence by combining breakthroughs in the handling of very small amounts of liquid, high-resolution optics, and computing power.

Answer 28

next-generation sequencing

Question 29

An assembly of specific proteins that facilitate the process of RNA interference.

Answer 29

RNA-induced silencing complex (RISC)

Question 30

Sequences of DNA that resemble actual genes but do not encode functional products.

Answer 30

pseudogene

Question 31

The pattern and level of expression of all genes in a particular cell or tissue.

Answer 31

transcriptome

Question 32

The suppression of the transcription of a gene following the introduction into the cell of double stranded RNA molecule that contained sequences present in the suppressed gene.

Answer 32

RNA interference

Question 33

A mouse that harbors a foreign gene. Transgenic mice are a powerful means of exploring the role of a specific gene in the development, growth, and behavior of an entire organism.

Answer 33

Transgenic mouse

Question 34

Genes which encode readily-detectable markers such as antibiotic-resistance enzymes or fluorescent proteins.

Answer 34

reporter gene

Question 35

A method in which a primer containing a mismatched nucleotide is used to produce a desired change in a DNA sequence. It can readily produce mutant proteins with single amino acid substitutions.

Answer 35

site-directed mutagenesis

Question 36

a radioactively labeled, single-stranded specific base sequence used to locate a complementary sequence among DNA fragments displayed on an electrophoretic gel.

Answer 36

DNA probe

Question 37

A polymerase chain reaction-based technique for determining the amount of individual mRNA molecules present in a population of RNA molecules.

Answer 37

quantitative PCR (qPCR)

Question 38

Plasmids carried by A. tumefaciens that encode instructions for induction of tumor state in infected plants cells. The resulting tumor tissue is called a crown gall.

Answer 38

Tumor-inducing plasmid (Ti plasmid)

Question 39

A class of mobile genetic elements that are short (<500bp). The Alu sequence is an example of a SINE. More than a million copies of the approximately 300 bp Alu sequence are present in the human genome.

Answer 39

short interspersed elements (SINES)

Question 40

In these nucleases, each TALE repeat contains 34 amino acids and two alpha-helices. Only two of these residues are responsible for the unique recognition of a single nucleotide within the double helix.

Answer 40

Transcription activator-like effector nucleases (TALENs)

Question 41

The DNA-binding domain in these nucleases contains a series of zinc finger domains, small zinc-binding motifs that each recognize a sequence of three base pairs.

Answer 41

zinc-finger nucleases (ZFNs)