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BMB 401 > Ch. 3 > Flashcards

Ch. 3 Flashcards

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
Q

heterochromatin

A

a dense form of chromatin composed of mostly noncoding DNA

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26
Q

histone protein

A

a group of small basic eukaryotic proteins around which DNA wraps to form nucleosomes

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27
Q

hutchinson-gilford progeria syndrome (HGPS)

A

the most common in a group of fatal disorders that cause rapid aging in children as a result of DNA damage

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28
Q

hyperchromic effect

A

the increase in light absorbance at 260 nm as double-stranded DNA unwinds and separates

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29
Q

intercalated-motif (I-motif)

A

four-stranded DNA quadruplex structure containing mostly cytosine residues

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30
Q

intron

A

a noncoding region of DNA in a eukaryotic gene that is flanked by DNA sequences present in exons

31
Q

kilobase

A

one thousand nucleoride bases

32
Q

kinetochore

A

a protein complex, assembled at the centromere, that is necessary for proper separation of the chromosomes during cell division

33
Q

linking number

A

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
Q

major groove

A

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
Q

melting temperature

A

the temperature (Tm) at which half of the DNA molecules in a sample become denatured

36
Q

minor groove

A

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
Q

monocistronic

A

a gene containing a promoter sequence followed by a single protein-coding region

38
Q

multiple cloning site (MCS)

A

a segment of DNA that can be cleaved by several sequence-specific endonucleases called restriction enzymes to facilitate gene cloning

39
Q

nucleoside

A

an organic molecule consisting of a purine or pyrimidine base covalently linked to a five-membered sugar (ribose or deoxyribose)

40
Q

nucleosome

A

a DNA strand wound around a histone protein core that serves for the packaging of chromatin

41
Q

operon

A

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
Q

palindrome

A

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
Q

polycistronic

A

a gene containing a promoter sequence followed by multiple coding regions

44
Q

polymerase chain reaction (PCR)

A

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
Q

precision medicine

A

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
Q

primary (1*) structure

A

the unique arrangement of monomeric subunits in a single polypeptide chain or nucleic acid

47
Q

promoter

A

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
Q

protospacer adjacent motif (PAM)

A

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
Q

recombinant DNA

A

DNA molecules from different sources that have been linked together using laboratory methods

50
Q

renaturation

A

refolding of a denatured protein or nucleic acid chain back to its native structure and function

51
Q

restriction endonuclase

A

an enzyme that cleaves DNA at specific sequences; isolated from bacteria that use restriction endonucleases to protect against invading bacteriophage

52
Q

restriction modification system

A

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
Q

reverse transcription

A

an RNA-dependent DNA polymerase required for retrovirus replication; used in the lab to generate complimentary DNA (cDNA)

54
Q

ribozyme

A

an RNA molecule with catalytic activity; an RNA enzyme

55
Q

RNA-seq

A

a gene expression assay that uses PCR amplification to generate cDNA fragments, which are then sequenced by high-throughput DNA sequencing

56
Q

sanger DNA sequencing

A

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
Q

secondary (2*) structure

A

the local conformation of a polymer backbone; common types of protein secondary structures are a helix, B strand, and B turn

58
Q

short tandem repeat (STR)

A

a class of repetitive DNA elements consisting of a variable number of tandem repeat sequences of ~2-10 nucleotides in each repeat

59
Q

single nucleotide polymorphism (SNP)

A

a single nucleotide change in the genome that can occur when an error is made during DNA replication and is not repaired

60
Q

single-guide RNA (sgRNA)

A

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
Q

sister chromatids

A

two identical copies of replicated DNA contained in a mitotic chromosome

62
Q

supercoil

A

a coiled molecule, such as DNA, folded upon itself; a coiled coil

63
Q

telomere

A

a specialized region of heterochromatin located at the ends of chromosomes

64
Q

thymidine

A

a short term for deoxythymidine (a deoxyribonucleoside containing the pyrimidine base thymine)

65
Q

topoisomers

A

different forms of circular DNA that differ only in linking number

66
Q

topoisomerase

A

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
Q

trans-activated crRNA (tracrRNA)

A

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
Q

transcription factor

A

a protein that binds a specific cis-acting DNA sequence to regulate gene expression

69
Q

transduction (viral)

A

a process in which a virus mediates the transfer of genetic material between host cells

70
Q

transformation (plasmid)

A

a process in which DNA is taken up by bacteria and incorporated into the genome or contained on a DNA plasmid

71
Q

variable number tandem repeat (VNTR)

A

noncoding regions of DNA containing repetitive sequences; often used for identifying individuals or members of a family

72
Q

T7 RNA polymerase

A

a highly efficient bacteriophage RNA polymerase used in a variety of biochemical methods

73
Q

DNA polymerase

A

a group of enzymes that catalyze the synthesis of new DNA molecules

BMB 401 (6 decks)

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