Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

🔵BMSC 210 > Module 6 > Flashcards

Module 6 Flashcards

1
Q

Affinity tag

A

refers to a short peptide added to the end of a recombinant protein to facilitate purification of the expressed protein.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Ames test

A

a genetics based test to detect carcinogens (mutagens) using changes in reversion rate of a his-Salmonella strain to his+.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Amplification (in PCR)

A

The production of multiple copies of a sequence of DNA or RNA.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Antibiotic resistance

A

occurs when bacterial strains evolve mechanisms that protect them from the effects of antibiotic compounds or medications.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Artificial chromosome

A

specialized cloning vectors that can accommodate very large segments of DNA as inserts and propagate as individual chromosomes in that they have replication control and segregation regions that allow them to be maintained within the cell in single copy.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Auxotroph

A

a mutant bacterium that requires a particular additional nutrient which the wild-type does not.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

BAC

A

bacterial artificial chromosome.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Base analogues

A

A type of mutagen. They are very similar to natural bases in DNA, so they can functionally base-pair with a template partner sufficiently ‘normal enough’ to be inserted by the advancing DNA polymerase. Once incorporated they have a much higher frequency of isomer switching and can shift to favour base-pairing with a different base partner in a subsequent round of replication; once that ‘mistake’ is made permanent by the next round of replication, this mistake becomes a mutation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Base excision repair

A

a form of excision repair that employs damaged base specific enzymes (DNA glycosylases) to cut out the damaged base, then a shared enzyme (AP endonuclease) removes the abasic portion, and DNA polymerase resynthesizes to replace the missing nucleotide.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Cas9

A

a commercialized version of CRISPR-Cas microbial defense systems that has been developed for genome editing as it can be targeted to user defined DNA sequences by creation of an artificial guide RNA (gRNA) with complementarity to the specific target DNA sequence.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

cDNA (complementary DNA)

A

DNA synthesized from a single-stranded RNA template in a reaction catalyzed by the enzyme reverse transcriptase. It is often used to clone eukaryotic genes in prokaryotes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

cDNA library

A

a library of individual random clones each carrying an insert that was created by reverse transcription of mRNA into cDNA (complementary DNA to the message) of sufficient number such every transcribed gene present in the original sample is represented in the collection.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Cloning vector

A

a small piece of DNA that can be stably maintained in an organism, and into which a foreign DNA fragment can be inserted, so that the host can increase the number of copies through its own replication. There are different types; it may be DNA taken from a virus, the cell of a higher organism, or it may be the plasmid of a bacterium.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Competence

A

The ability of a cell to take up and recombine foreign DNA through transformation. Naturally competent species are those that carry the potential to turn on this function while other species can artificially be made competent in the lab (human-induced competence).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Conjugation

A

the transfer of DNA by direct cell-to-cell contact. Ability is encoded by self-transmissible (conjugative) plasmids.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Cosmids

A

hybrids between plasmid and phage vectors. They are designed to clone large fragments of DNA and to grow their DNA as a virus or as a plasmid.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

CRISPR

A

clustered regularly interspaced short palindromic repeats; these are sections of bacterial DNA now known to encode systems that protect against invading viruses (bacteriophages).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Direct repair

A

DNA repair pathways that directly restore a damaged or altered base in DNA back to its original form without excision or resynthesis.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

DNA-modifying agents

A

Mutagens that change a base’s structure and therefore alter its base-pairing specificity.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Electroporation

A

A transformation technique involves mixing cells (bacteria, plant, yeast or animal) with the recombinant DNA and pulsing with a brief dose of high-voltage electricity. This treatment causes the plasma membrane to become temporarily permeable and DNA molecules are taken up by some of the cells allowing for their selection.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Excision repair

A

a common repair pathway that recognizes damaged bases in DNA, removes the base(s) in the first step, then resynthesizes using the undamaged complementary strand as the template.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Expression vector

A

a plasmid or virus engineered to provide controlled expression of a cloned inserted gene.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

F factor (or fertility factor)

A

A well studied conjugative plasmid of E. coli that allows genes to be transferred from one bacterium carrying the factor to another bacterium lacking the factor by conjugation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

F’ factor

A

an F factor that has picked up a segment of host cell genome that was picked up via an in-precise excision from DNA flanking the insertion site when re-entering a plasmid form from an Hfr.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Fluorescence labeling

A

the process of covalently binding fluorescent dyes to biomolecules so that they can be visualized by fluorescence imaging; used to identify recombinant proteins.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Frameshift

A

A mutation caused by a deletion or insertion in a DNA sequence that shifts the way the sequence of codons is read. If just one nucleotide is removed from or added to the sequence, then potentially all of the codons including and following the mutation will have a disrupted reading frame.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Gel electrophoresis

A

a method for separation and analysis of macromolecules (DNA, RNA) and their fragments, based on their size and charge. Nucleic acid molecules are separated by applying an electric field to move the negatively charged molecules through a gel matrix of agarose or other substances. Shorter molecules move faster and migrate farther than longer ones because shorter molecules migrate more easily through the pores of the gel.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Generalized transduction

A

a natural process wherein a newly formed virus randomly carries a segment of DNA from its birth host cell instead of viral DNA and delivers that DNA to another cell that it attaches to in an abortive infection.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Genomic library

A

a collection of randomly cloned segments of genome DNA of sufficient number that collectively the collection carries segments of every part of the cloned genome.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Green fluorescent protein (GFP)

A

a protein with the property of emitting green light (fluorescence) when exposed to shorter wave length light (long range UV). It is commonly used as a gene-fusion tag to create hybrid proteins for visualization of the cellular location of the fused protein of interest.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

gRNA (guide RNA)

A

a short RNA (gRNA) used by CRISPR-Cas restriction systems to identify and destroy target DNA. Commercially or researcher prepared gRNAs are used in the commercial Cas9 genome editing system to target user defined target sequences.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Hfr

A

short for high-frequency recombination; a bacterial cell with an F-plasmid integrated into its genome.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Homologous recombination

A

recombination involving two DNA molecules that are very similar in nucleotide sequence. Mechanism depends on a ‘homology search’ by recombination specific enzymes (RecA and its homologs).

34
Q

Horizontal gene transfer

A

the process wherein genes are transferred from one mature organism to another mature organism (i.e., not from parent cell to daughter cell).

35
Q

Induced mutations

A

that arise (above the background level of spontaneous mutations) due to exposure to a condition or chemical that causes an increase in the ‘wrong’ base being inserted into newly synthesized DNA.

36
Q

Intercalating agents

A

Mutagens that insert themselves between the stacked bases of the DNA double helix. This results in distortion of the helical structure which at low levels can cause slippage during replication, and at saturating levels will cause sufficient distortion to effectively prevent either transcription or replication.

37
Q

Insertion sequence

A

a simple transposable element that contains a recombinase gene and unique inverted repeat sequences at each end that are the recognition site for its recombinase.

38
Q

Lysogenic phage

A

viruses that incorporate their nucleic acid into the chromosome of a host bacterial cell and replicate with it as a unit without destroying the cell.

39
Q

Lytic phage

A

viruses that take over the machinery of a bacterial cell to make phage components, then destroy (or lyse) the cell, releasing new phage particles.

40
Q

Mismatch repair

A

a DNA repair system that recognizes mismatch errors made by an advancing DNA polymerase.

41
Q

Nucleotide excision repair

A

a subtype of excision repair that recognizes distortions in the DNA double helix and removes a small section from one strand, using the other as a template to resynthesize.

42
Q

Metagenomic library

A

a collection of randomly cloned segments of DNA initially isolated from the collection of all species within an environmental sample such that collectively the collection carries segments of every part of every species present in that sample.

43
Q

Mutagens

A

substances that cause elevated rates of mutation (above the background level of spontaneous mutations).

44
Q

Mutations

A

heritable changes in the genome.

45
Q

Natural competency

A

a set of genes that encode protein systems that allow some species of bacteria to take up DNA from their environment. Typically this is growth-cycle regulated activity.

46
Q

Phage and viral vectors

A

bacterial viruses used as tools to clone, transfer, and manipulate genes.

47
Q

Physical agents

A

Mutagens such as radiation, can cause damage that is sufficiently drastic that the affected base(s) cannot serve as a template for DNA replication. Retention of the damage base prevents extension by advancing DNA polymerase (and RNA polymerase), effectively preventing the cell from replicating. Such damage is able to induce changes in the DNA leading to a mutation only by necessitating repair of the damage before replication can proceed.

48
Q

Plasmid

A

a small DNA molecule within a bacterial cell that is physically separated from the chromosomal DNA and can replicate independently.

49
Q

Plasmid vector

A

plasmids used as tools to clone, transfer, and manipulate genes.

50
Q

Point mutation

A

A mutation that only affects a single nucleotide; most commonly involves the substitution of one base for another (which changes the complementary base as well in DNA), but also includes insertions or deletions of a single base pair.

51
Q

Polyhistidine tag

A

a series of histidine (His) amino acids to either the N- of C-terminus of a protein. Used for affinity purification based on the tag’s propensity to bind immobilized nickel or cobalt ions.

52
Q

Polymerase chain reaction (PCR)

A

a technology that uses short single-stranded DNA oligonucleotides (DNA primers) that are complementary to two adjacent regions on a targeted template DNA, but on opposite strands of the double helix, such that when DNA replication primed from the 3’ OH of each primer proceeds to replicate past the annealing site of the partner primer. Multiple rounds of replication, denaturation, reannealing are used to specifically amplify (make multiple copies of) the region of the DNA template bound and between the two primers.

53
Q

Primers

A

a short, single-stranded DNA sequence used in PCR techniques to give DNA polymerases a place to attach new DNA nucleotides to an existing strand of nucleotides, and therefore to lay a foundation for DNA synthesis.

54
Q

Proofreading

A

replicative DNA polymerase exonuclease activity that can remove one or a few bases from the newly added 3’ end of the newly synthesized (nascent) DNA when it detects that the incorrect base was added.

55
Q

R plasmid

A

a self-transmissible plasmid that carries one or more antibiotic resistance genes (often within transposons).

56
Q

Real-time PCR

A

a laboratory technique of molecular biology based on the polymerase chain reaction. It monitors the amplification of a targeted DNA molecule during the PCR, not at its end, as in conventional PCR.

57
Q

Recombination

A

in bacteria is characterized by DNA transfer from one organism (donor) to another organism (recipient). The final result is the production of genetic recombinants, individuals that carry not only the genes they inherited from their parent cells but also the genes introduced to their genomes in one of three main ways: conjugation, transduction, and/or transformation.

58
Q

Recombinational repair

A

Repair pathway that utilizes homologous repair. When a cell carries more than one copy of the chromosome (which is the case for regions that have been replicated, even in haploid bacteria), this type of repair can function to allow a replication fork to continue to replicate the chromosome past the damaged bases. The damaged bases are still present, while the repair prevents stalling of the replication fork at the damage. For this reason, some call this ‘bypass repair’.

59
Q

Recombinases

A

Enzymes that are encoded for by transposable elements, which function in the transposition reaction. There are different families of these enzymes, though collectively they generate novel combinations of genes.

60
Q

Replica plating

A

A technique used to screen for mutants that have lost the ability to grow on a specific media plate.

61
Q

Restriction enzymes

A

endonuclease enzymes discovered in bacteria that each recognize specific short sequences of DNA as their target site for cleavage. Cells expressing these enzymes also produce a cognate methylase enzyme that recognizes the exact same short sequence and adds a methyl group to one of the bases of the sequence rendering the cells’ own copies of the sequence immune to endonuclease attack by their own enzyme. Restriction enzymes have been isolated and commercially packaged to provide the ability to selectively cut DNA at a very large number of specific DNA sequences.

62
Q

Reverse transcriptase (RT)

A

a polymerase enzyme that uses RNA polymerase as a template to make a DNA copy. Initially isolated from retroviruses, and now commercially available to generate cDNA from mRNA.

63
Q

Revertant

A

a mutant cell or strain that undergoes further mutation and reverts to regain a capability from its parent line (such as the ability to grow on a certain media).

64
Q

Screening (for mutants)

A

the process of examining/testing all progeny for the occurrence of a desired mutation.

65
Q

Seamless cloning

A

a cloning technique that utilizes specially designed PCR primers with complementarity to both the cloned segment and the insertion site within the cloning vector that allows insertion of the insert by a series of DNA synthesis reactions rather than by cutting by restriction endonucleases and joining by ligase.

66
Q

Selecting (for mutants)

A

subjecting a population of cells to an environmental condition that only allows for the growth/survival of the desired mutant phenotype.

67
Q

Site-specific recombination

A

Recombination between two DNA molecules that does not involve extensive areas of homology between the two molecules. It is catalyzed by enzymes called recombinases distinct from RecA, and it is the mechanism by which transposition occurs.

68
Q

Slippage

A

A mutation where an advancing polymerase makes an error on either the template or the newly synthesized strand, such that the polymerase loses track of where it is in its copying job, leading to either a deletion or an insertion of base(s).

69
Q

SOS response

A

a multi-pathway coordinated DNA damage response in bacteria that is regulated by a common repressor protein (LexA) which is inactivated when RecA protein is bound to excess single-strand DNA arising from stalled replication and/or incomplete DNA repair.

70
Q

Specialized transduction

A

a natural process wherein a virus that inserts its genome within its host cell genome as a part of its lifecycle mistakenly removes a portion of adjacent host DNA with the virus genome when it excises itself from the chromosome thus creating a hybrid virus that replicates, packages and transports that portion of DNA from one host cell to another.

71
Q

Spontaneous mutations

A

result from errors in ‘normal’ DNA replication or during repair of damage arising from normal cellular physiology (i.e., they happen without any added outside influences on the cell).

72
Q

Transcriptional fusion

A

used when a reporter gene (e.g., GFP) is fused to the promotor of a gene of interest (as opposed to being fused to the actual gene). This provides information on where the gene is transcribed (but not where the translated protein ends up).

73
Q

Transduction

A

the transfer of genes between bacterial or archaeal cells by viruses.

74
Q

Transformation (bacterial transformation)

A

the process by which a bacterial cell takes up naked DNA from outside its cell and brings it into the cell. This process can be artificially stimulated in a laboratory by chemical and physical manipulation of the bacterial cell. This allows researchers to transform manipulated DNA into species that do not naturally take up DNA.

75
Q

Translational fusion

A

used when a reporter gene (e.g., GFP) is fused to the entire gene of interest (as opposed to just fused to its promotor). This provides information on where the translated protein ends up (but not where the transcription occurred).

76
Q

Transposable element

A

specific DNA segments that can repeatedly insert into one or more sites or into one or more genomes.

77
Q

Transposase

A

an enzyme that recognizes the inverted repeat ends of a transposon to facilitate their movement.

78
Q

Transposition

A

the movement of a transposable element from one site within DNA to another.

79
Q

Transposon

A

a complex transposable element that encodes more than the transposase gene required for its own transposition.

80
Q

YAC

A

yeast artificial chromosome.

🔵BMSC 210 (7 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions