Chapter 3 Flashcards
there are … common varieties of nucleotides, each composed of a nitrogenous base linked to a sugar to which at least one phosphate group is also attached
8
most common purines are … and … and the major pyrimidines are …, …, and …
adenine; guanine; cytosine; uracil; thymine
the purines form bonds to a five carbon sugar via their … atoms, whereas pyrimidines do so through their … atoms
N9; N1
when the phosphate group of a nucleotide is absent, the compound is known as a …
nucleoside
free nucleotides, which are anionic, are almost always associated with the counterion … in cells
Mg2+
the linkage between individual nucleotides is known as a …, so named because the phosphate is esterified to two ribose units
phosphodiester bond
each nucleotide that has been incorporated into the polynucleotide is known as a …
the terminal whose C5’ is not linked to another nucleotide is called the … end and the terminal end whose C3’ is not linked to another nucleotide is called the … end
nucleotide residue; 5’; 3’
a polymer of nonidentical residues has a property that its component monomers lack–namely, it contains information in the form of its
sequence of residues
the two strands of DNA are antiparallel, but each forms a
right handed helix
the bases occupy the … of the helix and sugar-phosphate chains run along the …, thereby minimizing the repulsions between charged phosphate groups. the surface of the double helix contains two grooves of unequal width: the … and …
core; periphery; major and minor grooves
base pairing often occurs …, giving rise to … structures, or, when loops interact with each other, to more complex structures
intramolecularly; stem-loop
… genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from a cell’s surroundings through its membrane
transformation
there is a specific connection between genes and enzymes: the … theory
one gene-one enzyme
… refers to the study of gene expression, which focuses on the set of mRNA molecules, or …, that is transcribed from DNA under any particular set of circumstances
transcriptomics; transcriptome
… is the study of the proteins (the …) produced as a result of transcription and translation
proteomics; proteome
the human genome contains about … genes, corresponding to about …% of its 3 billion nucleotides
21,000; 1.2
a bacteria can modify certain nucleotides in specific sequences of its own DNA by adding a methyl group in a reaction catalyzed by a modification …
methylase
a … which recognizes the same nucleotide as does the methylase, cleaves any DNA that has not been modified on at least one of its two strands
restriction endonuclease
an … cleaves a nucleic acid within the polynucleotide strand; an … cleaves a nucleic acid by removing one of its terminal residues
endonuclease; exonuclease
Most Type II restriction endonucleases recognize and cleave … DNA sequences
palindromic
most restriction enzymes cleave the two strands of DNA at positions that are .., producing DNA fragments with complementary single strand extensions –> … ends
staggered; sticky
some restriction endonucleases cleave the two strands of DNA at the symmetry axis to yield restriction fragments with fully base-paired …
blunt ends
… method used for sequencing DNA, involving obtaining single polynucleotide strands, separating complementary strands, and generating polynucleotide fragments that terminate at positions corresponding to each of the four nucleotides followed by separating and detecting fragments
chain-terminator method
when the .. analog is incorporated into the growing polynucleotide in place of the corresponding normal nucleotide, chain growth is … because addition of the next nucleotide requires a free 3’-OH group
dideoxy; terminated
sequences of DNA are called …
reads
…: DNA fragments generated by subjecting a solution of stiff double-stranded DNA to high-frequency sound waves
sonification
…: using the DNA template strand to direct the synthesis of its complementary copy
sequencing by synthesis
pyrosequencing: segments of the DNA to be sequenced are immobilized on the surfaces of … under dilution conditions such that no more than … is attached to a bead
microscopic plastic beads; one DNA molecule
in pyrosequencing, DNA is replicated and a primer and DNA polymerase are added , with a … that is introduced. the. if DNA polymerase adds that to the growing DNA strand, … (PPi) is released and undergoes a chemical reaction sequence involving the firefly enzyme …, which generate a flash of light.
dNTP (nucleotide); pyrophosphate; luciferase
Ilumina sequencing: numerous DNA segments are attached to a … and amplified in place to form clusters of millions of identical DNA molecules. to determine their sequences, a solution containing the four dNTPs that are each linked to a different fluorescent group and chemically blocked at their … positions is flowed over the plate so that only a single nucleotide is added, by DNA polymerase, to each primer strand
glass plate;3 ‘
in … the DNA sequences of multiple organisms are analyzed as a single dataset
metagenomic sequencing
the human genome appears to contain only about 21,000 protein encoding genes, known as …
open reading frames
any two people are likely to e about …% genetically identical
99.9
…: a phenomenon in which a given gene transcript can be processed in multiple ways to yield different proteins when translated
alternative gene splicing
…: exchange of DNA between chromosomes
recombination
most of the differences among the various human genomes are due to …: where the DNA sequence differs among individuals at one nucleotide position
single-nucleotide polymorphisms
Recombinant DNA technology, also called … or …, makes it possible to isolate, amplify, and modify specific DNA sequences
molecular cloning; genetic engineering
to obtain and amplify a segment of DNA:
a fragment of the appropriate size is generated by a …, by PCR, or by chemical synthesis
the fragment is incorporated into another DNA molecule known as a .., which contains the sequences necessary to direct DNA replication
the vector is introduced into cells, in which it is replicated
cells containing the desired DNA are identified or selected.
restriction enzyme; vector;
… refers to the collection of cells that contain the vector carrying the DNA of interest or to the DNA itself
clone
plasmid vectors can be used to clone DNA segments of no more than … kilobases. the E. coli plasmid designated pUC18 is a representative cloning vector
about 10
To use bacteriophages as a cloning vector, the central third of the phage genome is replaced with foreign DNA. The resulting recombinant, or … is package into phage particles that can then be introduced into the host cells
chimera
…, which infect insect cells, are similarly used for cloning in cultures of insect cells (similar to how bacteriophages work)
baculoviruses
… are linear DNA molecules that contain all the chromosomal structures required for normal replication and segregation during yeast cell division. …, which replicate in E. coli, are derived from circular plasmids that normally replicate long regions of DNA and are maintained at the level of approximately one copy per cell
yeast artificial chromosomes (YACs); bacterial artificial chromosomes (BACs)
a restriction fragment can be inserted into cut made in a cloning vector by … The complementary ends of the two DNAs form base pairs (…) and the sugar phosphate backbones are covalently …, or spliced together, through the action of an enzyme named DNA ligase (a ligase produced by a bacteriophage can also join … restriction fragments)
the same restriction enzyme; anneal; ligated; blunt-ended
it is essential to select only those host organisms that have been … and that contain a properly constructed vector. in the case of plasmid transformation, selection can be accomplished through the use of … and/or … (color-producing) substances
transformed; antibiotics; chromogenic
…: gene introduced into a cell, especially a bacterium or to cells in culture, that confers a trait suitable for artificial selection
selectable marker
…: a region of lysed bacterial cells
plaque
the cloned set of all DNA fragments from a particular organism is known as its
genomic library
genomic libraries are generated by a procedure known as … The chromosomal DNA of the organism is isolated, cleaved to fragments of cloneable size, and inserted into a cloning vector.
shotgun cloning
given the large size of a genome relative to a gene, the shotgun cloning method is subject to the
laws of probability
… is when DNA is further fragmented and cloned again
subcloning
a different type of DNA library contains only the expressed sequences from a particular cell type. this is called a … and is constructed by isolating all the cell’s mRNAs, copying them to DNA using a DNA polymerase known as … the … (cDNA) are then inserted into cloning vectors to form the library
cDNA library; reverse transcriptase
a cDNA library can be used to construct a … (…), in which different cDNA is immobilized at a specific position on a slide. these can be used for detecting the presence of mRNA in a biological sample (the mRNA, if present, will bind to its …)
DNA microarray (DNA chip); complementary DNA
the DNA corresponding to a complete set of a cell’s mRNAs is known as its … (as opposed to its …, which corresponds to all of a cell’s …)
exome; transcriptome; RNAs
once the requisite number of clones is obtained, the genomic library must be … for the presence of the desired gene
screened
screening can be done by a process known as … or …, where the cloned colonies are transferred to a … filter, which is treated with NaOH which separates the DNA into single strands that bind to the nitrocellulose. the filter is dried to fix the DNA in place and incubated with a labeled … (a short segment of DNA/RNA complementary to the DNA of interest).
colony; in situ hybridization; probe
screening process contd:
… probe is washed away, and the presence of the probe on nitrocellulose is detected, thereby detecting the desired gene as well. these are then retrieved.
unbound
…. (PCR) is used to amplify a specific DNA. in PCR, a DNA sample is separated into single strands and incubated with DNA polymerase, dNTPs, and two oligonucleotide primers whose sequences flank the DNA segment of interest. the primers direct the DNA polymerase to synthesize complementary strands of the target DNA
polymerase chain reaction
a cloned gene must be inserted into an …, a plasmid that contains properly positioned transcriptioned and translational control sequences
expression vector
the production of a protein of interest may reach 30% of the host’s total cellular protein. such genetically engineered organisms are called ..
overproducers
… mimics the natural process of evolution and allows predictions about the structural and functional roles of particular amino acids in a protein to be rigorously tested in the laboratory
site-directed mutagenesis
Synthetic … are required to specifi cally alter genes through site-directed mutagenesis. An oligonucleotide whose sequence is identical to a portion of the gene of interest except for the desired base changes is used to direct replication of the gene. The oligonucleotide hybridizes to the corresponding …(naturally occurring) sequence if there are no more than a few mismatched base pairs. Extension of the oligonucleotide, called a …, by DNA polymerase yields the desired altered gene (Fig. 3-30). The altered gene can then be inserted into an appropriate vector
oligonucleotides; wild-type; primer
Multicellular organisms expressing a gene from another organism are said to be …, and the transplanted foreign gene is called a … For the change to be permanent—that is, heritable—a transgene must be stably integrated into the organism’s …
transgenic; transgene; germ cells
… is an orange pigment that is the precursor of vitamin A
beta-carotene
iron storage protein
ferritin
…. is name for when an organism has been engineered to lack a gene entirely
gene knockout
… is the transfer of new genetic material to the cells of an individual to produce a therapeutic effect
gene therapy
the first documented success of gene therapy in humans occurred in children with a form of … kknown as SCID-X1, which is caused by a defect in the gene encoding …, whose action is essential for proper immune function
severe combined immunodeficiency disease (SCID); gama-c cytokine receptor
a side effect of the gene therapy for SCID X1 is
leukemia
(gene therapy illnesses) …: rare form of blindness
leber’s congenital amaurosis
(gene therapy illnesses) …: defect in a membrane transport protein leads to brain damage
X-linked adrenoleukodystrophy
(gene therapy illnesses) …: a type of severe anemia
beta-thalassemia
(gene therapy illnesses) ..: immunodeficiency disease
wiskott-aldrich disease
