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BMB 401 > Ch. 3 > Flashcards

Ch. 3 Flashcards

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1
Q

3’ poly(A) tail

A

the addition of adenine-containing nucleotides to the 3’ end of mRNA, which contributes to the stability and translational efficiency of mRNA

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2
Q

3’ UTR

A

a region of a eukaryotic gene that is not translated but instead contains sequences necessary for the termination of transcription by RNA polymerase

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3
Q

5’ cap

A

a modification to the 5’ end of mature eukaryotic RNA that facilitates interactions between the mRNA and the ribosome

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4
Q

5’ UTR

A

a region of a eukaryotic gene that is not translated but instead contains sequences that when transcribed into RNA will facilitate interaction with the protein translational machinery

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5
Q

adaptive immunity

A

the subsystem of the overall immune response consisting of cells that recognize molecules that the organism has been exposed to before; also called acquired immunity. the success of vaccines is based on this response

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6
Q

bacteriophage

A

a virus that infects bacteria; useful as a tool in nucleic acid biochemistry and molecular biology

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7
Q

centromere

A

the region of connection between sister chromatids, composed of heterochromatin; the site of attachment for the mitotic or meiotic spindle

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8
Q

Chargaff’s rule

A

in DNA from any cell of any organism, the percentage of adenine equals the percentage of thymine (%A=%T), and the percentage of guanine equals the percentage of cytosine (%G = %C)

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9
Q

clustered regularly interspersed short palindromic repeats (CRISPR)

A

related DNA sequences in prokaryotic genomes derived from DNA fragments of bacterial viruses, which are used to destroy DNA from similar bacterial viruses after infection

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10
Q

complementary DNA (cDNA)

A

a DNA molecule, usually synthesized by the enzyme reverse transcriptase, that is complementary to a given mRNA; used in DNA cloning

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11
Q

conjugation (plasmid)

A

part of the bacterial mating process in which a donor bacterium transfers a copy of the plasmid to a recipient cell

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12
Q

CRISPR RNA (crRNA)

A

RNA that is transcribed from the CRISPR region in the bacterial genome. the CRISPR RNA forms an RNA: DNA duplex with the invading bacterial virus to identify it as an invading pathogen to be destroyed by the CRISPR-associated (Cas) endonuclease

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13
Q

CRISPR-associated (Cas)

A

the bacterial endonuclease that cleaves the double-strand crDNA:DNA duplex that forms between the crRNA produced by the bacterium and the DNA genome of the invading bacterial virus

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14
Q

denaturation

A

partial or complete unfolding of the conformation of a protein or nucleic acid chain

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15
Q

dideoxynucleoside triphosphate (ddNTP)

A

a key reagent in the Sanger DNA sequencing method that terminates DNA synthesis reactions

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16
Q

DNA ligase

A

an enzyme that cells use to repair a nick in the phosphodiester backbone; it catalyzes the formation of a phosphodiester bond

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17
Q

DNA methylase

A

an enzyme that methylates DNA at specific sequences

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18
Q

euchromatin

A

a region of chromatin that is loosely packed with nucleosomes and associated with actively transcribed genes

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19
Q

exon

A

a coding region of a eukaryotic gene; separated from one another by introns

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20
Q

exon shuffling

A

the mixing and matching of protein-coding sequences during evolution to generate genes with novel functions

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21
Q

gene expression microarray

A

a solid surface, often a microchip, that contains covalently linked deoxyoligonucleotide segments that are used to identify complementary mRNA (or cDNA) sequence in a sample

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22
Q

gene knock-in

A

a modified gene that contains sequences introduced exogenously by a gene-editing method through a homologous recombination event

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23
Q

gene knockout

A

a modified gene that contains point mutations or deletions that destroy the function of the gene by altering the sequence of the transcribed RNA product

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24
Q

G-quadruplex

A

a DNA structure consisting of four base-paired guanine residues derived from one, two, or four DNA strands

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25
heterochromatin
a dense form of chromatin composed of mostly noncoding DNA
26
histone protein
a group of small basic eukaryotic proteins around which DNA wraps to form nucleosomes
27
hutchinson-gilford progeria syndrome (HGPS)
the most common in a group of fatal disorders that cause rapid aging in children as a result of DNA damage
28
hyperchromic effect
the increase in light absorbance at 260 nm as double-stranded DNA unwinds and separates
29
intercalated-motif (I-motif)
four-stranded DNA quadruplex structure containing mostly cytosine residues
30
intron
a noncoding region of DNA in a eukaryotic gene that is flanked by DNA sequences present in exons
31
kilobase
one thousand nucleoride bases
32
kinetochore
a protein complex, assembled at the centromere, that is necessary for proper separation of the chromosomes during cell division
33
linking number
the number of times a strand of DNA winds in the right-handed direction around the helix axis when the axis lies in an imaginary plane
34
major groove
in the DNA double helix, a groove running along the outside of the helix where the distance between the phosphate backbones is larger than in the minor groove
35
melting temperature
the temperature (Tm) at which half of the DNA molecules in a sample become denatured
36
minor groove
in the DNA double helix, a groove running along the outside of the helix where the distance between the phosphate backbones is smaller than in the major groove
37
monocistronic
a gene containing a promoter sequence followed by a single protein-coding region
38
multiple cloning site (MCS)
a segment of DNA that can be cleaved by several sequence-specific endonucleases called restriction enzymes to facilitate gene cloning
39
nucleoside
an organic molecule consisting of a purine or pyrimidine base covalently linked to a five-membered sugar (ribose or deoxyribose)
40
nucleosome
a DNA strand wound around a histone protein core that serves for the packaging of chromatin
41
operon
a polycistronic gene (and its regulatory sequences) that contains coding sequences for proteins involved in a single biochemical process or pathway. it is transcribed as a single mRNA
42
palindrome
a string of letters or numbers that reads the same in both directions; many restriction endonuclease cleavage sites are this when both strands of DNA are read in the same 5' to 3' direction, such as the EcoRI restriction site 5'-GAATTC-3'
43
polycistronic
a gene containing a promoter sequence followed by multiple coding regions
44
polymerase chain reaction (PCR)
a method for in vitro DNA replication to generate multiple copies of a specific target DNA segment on the basis of the positioning of opposing single-strand DNA primers
45
precision medicine
the use of biochemical markers obtained from a patient such as DNA sequence information or metabolite concentrations in blood and urine for the purpose of designing a patient-specific treatment regimen
46
primary (1*) structure
the unique arrangement of monomeric subunits in a single polypeptide chain or nucleic acid
47
promoter
a specific DNA sequence that usually occurs on the 5' side of genes that are transcribed by the enzyme RNA polymerase; transcription factor proteins bind to promoter DNA sequences and recruit RNA polymerase to initiate RNA synthesis
48
protospacer adjacent motif (PAM)
a short sequence adjacent to the target DNA sequence in the CRISPR-Cas9 system that marks the boundary of the target sequence and is recognized by the Cas9 nuclease; the PAM sequence is Staphylococcus aureus recognized by Cas9 is 5'-NGRRN-3'
49
recombinant DNA
DNA molecules from different sources that have been linked together using laboratory methods
50
renaturation
refolding of a denatured protein or nucleic acid chain back to its native structure and function
51
restriction endonuclase
an enzyme that cleaves DNA at specific sequences; isolated from bacteria that use restriction endonucleases to protect against invading bacteriophage
52
restriction modification system
a viral protection mechanism in bacteria consisting of DNA cleaving enzymes (sequence-specific endonuclease) and DNA methylating enzymes (sequence-specific DNA methylase) that work together to destroy viral DNA without damaging the bacterial host DNA
53
reverse transcription
an RNA-dependent DNA polymerase required for retrovirus replication; used in the lab to generate complimentary DNA (cDNA)
54
ribozyme
an RNA molecule with catalytic activity; an RNA enzyme
55
RNA-seq
a gene expression assay that uses PCR amplification to generate cDNA fragments, which are then sequenced by high-throughput DNA sequencing
56
sanger DNA sequencing
a method for determining the nucleotide sequence of DNA on the basis of the incorporation of dideoxynucleoside triphosphate molecule in an in vitro DNA synthesis reaction
57
secondary (2*) structure
the local conformation of a polymer backbone; common types of protein secondary structures are a helix, B strand, and B turn
58
short tandem repeat (STR)
a class of repetitive DNA elements consisting of a variable number of tandem repeat sequences of ~2-10 nucleotides in each repeat
59
single nucleotide polymorphism (SNP)
a single nucleotide change in the genome that can occur when an error is made during DNA replication and is not repaired
60
single-guide RNA (sgRNA)
complementary to the target DNA sequence in the CRISPR-Cas9 gene-editing system and is covalently linked to the constant-region tracrRNA, which recruits the Cas9 endonuclease to cleave the target DNA
61
sister chromatids
two identical copies of replicated DNA contained in a mitotic chromosome
62
supercoil
a coiled molecule, such as DNA, folded upon itself; a coiled coil
63
telomere
a specialized region of heterochromatin located at the ends of chromosomes
64
thymidine
a short term for deoxythymidine (a deoxyribonucleoside containing the pyrimidine base thymine)
65
topoisomers
different forms of circular DNA that differ only in linking number
66
topoisomerase
an enzyme that catalyzes the cleavage of one or both DNA strands and relaxes positive-supercoiled regions, allowing DNA to return to its relaxed state
67
trans-activated crRNA (tracrRNA)
bacterial RNA that recruits Cas endonucleases to the CRISPR-Cas9 complex by forming a binding site for the Cas9 protein; in the CRISPR-Cas9 gene-editing system, it serves as the constant region linked to the variable single-guide RNA needed to cleave target DNA by the Cas9 nuclease
68
transcription factor
a protein that binds a specific cis-acting DNA sequence to regulate gene expression
69
transduction (viral)
a process in which a virus mediates the transfer of genetic material between host cells
70
transformation (plasmid)
a process in which DNA is taken up by bacteria and incorporated into the genome or contained on a DNA plasmid
71
variable number tandem repeat (VNTR)
noncoding regions of DNA containing repetitive sequences; often used for identifying individuals or members of a family
72
T7 RNA polymerase
a highly efficient bacteriophage RNA polymerase used in a variety of biochemical methods
73
DNA polymerase
a group of enzymes that catalyze the synthesis of new DNA molecules

BMB 401 (6 decks)

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