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Biochem > Chapter 3 > Flashcards

Chapter 3 Flashcards

1
Q

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

A

8

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2
Q

most common purines are … and … and the major pyrimidines are …, …, and …

A

adenine; guanine; cytosine; uracil; thymine

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3
Q

the purines form bonds to a five carbon sugar via their … atoms, whereas pyrimidines do so through their … atoms

A

N9; N1

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4
Q

when the phosphate group of a nucleotide is absent, the compound is known as a …

A

nucleoside

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5
Q

free nucleotides, which are anionic, are almost always associated with the counterion … in cells

A

Mg2+

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6
Q

the linkage between individual nucleotides is known as a …, so named because the phosphate is esterified to two ribose units

A

phosphodiester bond

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7
Q

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

A

nucleotide residue; 5’; 3’

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8
Q

a polymer of nonidentical residues has a property that its component monomers lack–namely, it contains information in the form of its

A

sequence of residues

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9
Q

the two strands of DNA are antiparallel, but each forms a

A

right handed helix

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10
Q

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 …

A

core; periphery; major and minor grooves

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11
Q

base pairing often occurs …, giving rise to … structures, or, when loops interact with each other, to more complex structures

A

intramolecularly; stem-loop

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12
Q

… genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from a cell’s surroundings through its membrane

A

transformation

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13
Q

there is a specific connection between genes and enzymes: the … theory

A

one gene-one enzyme

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14
Q

… 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

A

transcriptomics; transcriptome

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15
Q

… is the study of the proteins (the …) produced as a result of transcription and translation

A

proteomics; proteome

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16
Q

the human genome contains about … genes, corresponding to about …% of its 3 billion nucleotides

A

21,000; 1.2

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17
Q

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 …

A

methylase

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18
Q

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

A

restriction endonuclease

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19
Q

an … cleaves a nucleic acid within the polynucleotide strand; an … cleaves a nucleic acid by removing one of its terminal residues

A

endonuclease; exonuclease

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20
Q

Most Type II restriction endonucleases recognize and cleave … DNA sequences

A

palindromic

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21
Q

most restriction enzymes cleave the two strands of DNA at positions that are .., producing DNA fragments with complementary single strand extensions –> … ends

A

staggered; sticky

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22
Q

some restriction endonucleases cleave the two strands of DNA at the symmetry axis to yield restriction fragments with fully base-paired …

A

blunt ends

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23
Q

… 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

A

chain-terminator method

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24
Q

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

A

dideoxy; terminated

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25
Q

sequences of DNA are called …

A

reads

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26
Q

…: DNA fragments generated by subjecting a solution of stiff double-stranded DNA to high-frequency sound waves

A

sonification

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27
Q

…: using the DNA template strand to direct the synthesis of its complementary copy

A

sequencing by synthesis

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28
Q

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

A

microscopic plastic beads; one DNA molecule

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29
Q

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.

A

dNTP (nucleotide); pyrophosphate; luciferase

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30
Q

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

A

glass plate;3 ‘

31
Q

in … the DNA sequences of multiple organisms are analyzed as a single dataset

A

metagenomic sequencing

32
Q

the human genome appears to contain only about 21,000 protein encoding genes, known as …

A

open reading frames

33
Q

any two people are likely to e about …% genetically identical

A

99.9

34
Q

…: a phenomenon in which a given gene transcript can be processed in multiple ways to yield different proteins when translated

A

alternative gene splicing

35
Q

…: exchange of DNA between chromosomes

A

recombination

36
Q

most of the differences among the various human genomes are due to …: where the DNA sequence differs among individuals at one nucleotide position

A

single-nucleotide polymorphisms

37
Q

Recombinant DNA technology, also called … or …, makes it possible to isolate, amplify, and modify specific DNA sequences

A

molecular cloning; genetic engineering

38
Q

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.

A

restriction enzyme; vector;

39
Q

… refers to the collection of cells that contain the vector carrying the DNA of interest or to the DNA itself

A

clone

40
Q

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

A

about 10

41
Q

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

A

chimera

42
Q

…, which infect insect cells, are similarly used for cloning in cultures of insect cells (similar to how bacteriophages work)

A

baculoviruses

43
Q

… 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

A

yeast artificial chromosomes (YACs); bacterial artificial chromosomes (BACs)

44
Q

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)

A

the same restriction enzyme; anneal; ligated; blunt-ended

45
Q

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

A

transformed; antibiotics; chromogenic

46
Q

…: gene introduced into a cell, especially a bacterium or to cells in culture, that confers a trait suitable for artificial selection

A

selectable marker

47
Q

…: a region of lysed bacterial cells

A

plaque

48
Q

the cloned set of all DNA fragments from a particular organism is known as its

A

genomic library

49
Q

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.

A

shotgun cloning

50
Q

given the large size of a genome relative to a gene, the shotgun cloning method is subject to the

A

laws of probability

51
Q

… is when DNA is further fragmented and cloned again

A

subcloning

52
Q

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

A

cDNA library; reverse transcriptase

53
Q

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 …)

A

DNA microarray (DNA chip); complementary DNA

54
Q

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 …)

A

exome; transcriptome; RNAs

55
Q

once the requisite number of clones is obtained, the genomic library must be … for the presence of the desired gene

A

screened

56
Q

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).

A

colony; in situ hybridization; probe

57
Q

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.

A

unbound

58
Q

…. (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

A

polymerase chain reaction

59
Q

a cloned gene must be inserted into an …, a plasmid that contains properly positioned transcriptioned and translational control sequences

A

expression vector

60
Q

the production of a protein of interest may reach 30% of the host’s total cellular protein. such genetically engineered organisms are called ..

A

overproducers

61
Q

… 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

A

site-directed mutagenesis

62
Q

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

A

oligonucleotides; wild-type; primer

63
Q

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 …

A

transgenic; transgene; germ cells

64
Q

… is an orange pigment that is the precursor of vitamin A

A

beta-carotene

65
Q

iron storage protein

A

ferritin

66
Q

…. is name for when an organism has been engineered to lack a gene entirely

A

gene knockout

67
Q

… is the transfer of new genetic material to the cells of an individual to produce a therapeutic effect

A

gene therapy

68
Q

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

A

severe combined immunodeficiency disease (SCID); gama-c cytokine receptor

69
Q

a side effect of the gene therapy for SCID X1 is

A

leukemia

70
Q

(gene therapy illnesses) …: rare form of blindness

A

leber’s congenital amaurosis

71
Q

(gene therapy illnesses) …: defect in a membrane transport protein leads to brain damage

A

X-linked adrenoleukodystrophy

72
Q

(gene therapy illnesses) …: a type of severe anemia

A

beta-thalassemia

73
Q

(gene therapy illnesses) ..: immunodeficiency disease

A

wiskott-aldrich disease

Biochem (23 decks)

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