Question: Transcription

Answer: The process by which RNA Pol enzymes and other transcriptional proteins and enzymes use the template strand of DNA to synthesize a complementary RNA strand. DNA is converted into RNA.

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Question: Translation

Answer: The process by which mRNA is used to direct protein synthesis. RNA is converted into protein.

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Question: mRNA (messenger)

Answer: A form of RNA transcribed from a gene and subsequently translated to produce a polypeptide or a protein; responsible for protein synthesis. Conveys the genetic message of DNA to ribosomes for translation.

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Question: tRNA (transfer)

Answer: Not translated. Encoded in the genome. Each different one binds a specific amino acid to the ribosome, and then deposits its amino acid to the mRNA for inclusion in the protein chain.

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Question: rRNA (ribosomal)

Answer: Not translated. Combines with proteins to form the ribosome, which is responsible for translation. Sometimes interacts with mRNA to initiate translation.

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Question: snRNA (small nuclear)

Answer: Found in the nucleus of eukaryotic cells. Participates in mRNA processing. Some can unite with nuclear proteins to form the complexes responsible for intron removal.

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Question: miRNA (micro)

Answer: Active in plant and animal cells but not bacteria. Regulate mRNA protein production post-transcription through RNA interference.

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Question: siRNA (small interfering)

Answer: specialized RNA that helps protect plant and animal genomes from virus production and spread of transposable elements within the genome.

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Question: ribozymes

Answer: Catalytically active RNA that can activate cellular reactions such as the removal of introns by self-splicing.

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Question: promoter sequence

Answer: Upstream of the coding sequence, immediately 5' to the start of transcription. Regulates transcription by controlling access of RNA polymerase to the gene.

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Question: terminator sequence

Answer: located immediately downstream - to the 3' end of the coding sequence. This region regulates the cessation of transcription.

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Question: holoenzyme

Answer: an intact complex with full enzymic capacity (one example is RNA Pol)

core enzyme + sigma subunit

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Question: core enzyme

Answer: The component in bacterial RNA Pol that actively carries out transcription.

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Question: Sigma subunit

Answer: the protein to which the RNA Pol binds. Directs the RNA polymerase core enzymes to promoters.

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Question: Promoter

Answer: double-stranded DNA sequence that is the binding site for the RNA Pol

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Question: -10 and -35 Consensus Sequences

Answer: What are the two components of prokaryotic promoters?

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Question: Closed promoter complex

Answer: The point in bacterial transcription initiation when the RNA Pol loosely binds the promoter (the -10 to -35 region)

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Question: consensus sequences

Answer: short regions of highly similar DNA located in the same position relative to the start of transcription in different gene promoters.

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Question: Open Promoter Sequence

Answer: the stage in transcription initiation in which the RNA Pol is bound and a small section of the DNA opens up to allow transcription from the template strand.

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Question: intrinsic termination

Answer: In bacterial termination; DNA-sequence dependent termination mechanism. Inverted repeats cause the formation of a 3' stem-loop structure followed by a string of U's. Most common.

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Question: rho-dependant termiation

Answer: Bacterial termination in which you must have a rho protein.

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Question: Template

Answer: Which strand is transcribed?

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Question: Introns

Answer: ...

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Question: Exons

Answer: ...

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Question: Chromatin

Answer: The complex of nucleic acids and proteins that make up chromosomes

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Question: RNA Pol I (euk)

Answer: Transcribes 3 rRNA genes

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Question: RNA Pol II (euk)

Answer: Transcribes mRNAs that encode polypeptides; most snRNA genes

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Question: RNA Pol III (euk)

Answer: Transcribes all tRNA genes as well as one snRNA.

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Question: RNA Pol II & III (euk)

Answer: responsible for miRNA and siena synthesis

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Question: Band Shift Assay

Answer: Used to locate promoters. If consensus sequences are in the DNA fragment, proteins bind to them. A slower migration means that the proteins have bound, and that the promoter consensus sequence is present.

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Question: DNA Footprint Protection Assay

Answer: You run 2 groups - 1 experimental (transcription protein added) and 1 control (no protein added.) In the place where the bands do NOT form with the experimental sample this is where the promoter region is because the proteins have bound.

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Question: TATA box

Answer: Most common eukaryotic promoter consensus sequence; located around position -25. Most strongly conserved promoter element in eukaryotes.

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Question: Transcription factors (TF)

Answer: Proteins that help RNA Pol II recognize and bind to promoter consensus sequences in eukaryotes. These proteins bind to promoter regulatory sequences and influence transcription initiation by interacting with the RNA pol.

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Question: TFIID

Answer: protein that binds to the TATA box

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Question: enhancers

Answer: DNA regulating sequences that increase transcription of specific genes. They bind specific proteins that interact with the proteins at promoter sequences and up the transcription levels. Often upstream but possibly downstream of the gene they regulate. The proteins form a bridge that bends the DNA.

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Question: silencers

Answer: DNA regulating sequences that repress transcription of target genes. They bind TF's called repressor proteins, making the DNA bend but in this case reducing the transcription levels.

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Question: Signal transduction pathway

Answer: communicate the need for specific regulatory molecules such as TF's in transcription. A series of events that release a regulatory molecule in order to get what is needed.

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Question: 5' end capping, 3' polyadenylation, intron splicing

Answer: What are the three main ways to modify mRNA (from pre-mRNA to mature mRNA)?

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Question: 5' end capping

Answer: addition of a modified nucleotide to the 5' end of mRNA in order to modify it

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Question: 3' Polyadenylation

Answer: cleavage at the 3' end of mRNA and addition of a tail of multiple adenines in order to form the poly-A tail in order to modify mRNA

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Question: Intron splicing

Answer: RNA splicing to remove introns and ligate exons

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Question: mature mRNA

Answer: fully processed product of transcription that moves to the cytoplasm for translation.

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Question: pre mRNA

Answer: initial transcription product, must be modified for translation to occur

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Question: 5' splice site

Answer: located on the end of an intron; contains a consensus sequence with a GU located at the 5' end of the intron.

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Question: 3' splice site

Answer: located on the 3' end of an intron; consensus sequence of 11 nucleotides containing a pyrimidine-rich region and an AG at the 3' end.

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Question: branch point adenine

Answer: near the 3' end of an intron - joins with a guanine from the 5' splice site in order to form a lariat intron.

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Question: snRNPs

Answer: snRNA-protein subunits that make up the spliceosome. U1 - U6

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Question: spliceosome

Answer: A snRNA-protein complex that removes introns from pre-mRNA. Made up by 5 snRNPs.

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Question: lariat intron

Answer: the structure formed when the 5' end of an intron binds to the branch site

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Question: SR Proteins

Answer: Proteins that recruit spliceosome components to 3' and 5' splice sites in intron splicing. Bind to exonic splicing enhancers.

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Question: Exonic Splicing Enhancers (ESE's)

Answer: Bind with SR proteins in intron splicing to ensure that the splicing components bind to the 3' and 5' splice sites in intron splicing instead of to other splice sites not near exons.

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Question: C-terminal domain (CTD)

Answer: Plays an important role in the coupling of the steps in pre-mRNA processing by functioning as an assembly platform and regulator of the machinery needed for the process. Binding of processing proteins to this allows mRNA to be modified as it is transcribed.

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Question: N-terminal

Answer: amino terminal end of a polypeptide corresponding to the 5' end of mRNA

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Question: C-terminal

Answer: carboxyl terminal end of a polypeptide corresponding to the 3' end of mRNA

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Question: 5' UTR

Answer: located between 5' end of mRNA and the start codon. Doesn't undergo translation.

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Question: 3' UTR

Answer: located between 3' end of mRNA and the stop codon. Doesn't undergo translation.

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Question: P site (peptidyl)

Answer: site on the ribosome where AAs are joined by a peptide bond

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Question: A site (aminoacyl)

Answer: site on the ribosome at which incoming charged tRNAs match their anticodon sequence with mRNA codons

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Question: E site (exit)

Answer: site on the ribosome where an uncharged tRNA exits

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Question: Shine dalgarno sequence

Answer: In bacterial translation the consensus sequence at the 5' end of mRNA that orients the start codon on the ribosome.

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Question: Scanning

Answer: the process by which the small ribosomal subunit locates the start codon

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Question: fMet

Answer: AA that initiated bacterial translation

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Question: Kozak sequence

Answer: consensus sequence of eukaryotic mRNA that contains the start codon

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Question: release factors (RF)

Answer: molecules that bind mRNA stop codons and contribute to translation termination

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Question: inosine (I)

Answer: another nucleotide that can be substituted in in 3rd base wobble

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Question: tRNA synthetases

Answer: group of enzymes that catalyze the charging of tRNA and the attachment of the appropriate AA

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Question: codon

Answer: set of 3 nucleotides that codes for a specific AA

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Question: sickle cell disease (SCD)

Answer: A disease affecting the beta-globin gene that is part of hemoglobin protein

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Question: hemolobin

Answer: protein that transports oxygen in blood.

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Question: SNP (single nucleotide polymorphism)

Answer: A single base-pair difference in a genome seen by comparing different genome.

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Question: Restriction enzyme

Answer: DNA-digesting enzyme that cuts DNA at specific recognition sites and generates cleavage at it's restriction sequence.

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Question: Molecular probe

Answer: single stranded nucleic acids that bind to target molecules allowing for identification of a specific protein, DNA or RNA sequence.

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Question: Northern blotting

Answer: mRNA transfer from an electrophoresis gel to a permanent membrane or filter.

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Question: Southern blotting

Answer: DNA transfer from an electrophoresis gel to a permanent membrane or filter.

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Question: Western blotting

Answer: protein transfer from an electrophoresis gel to a permanent membrane or filter.

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Question: Transition mutation

Answer: purine replaces purine or pyrimidine replaces pyrimidine

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Question: Transversion mutation

Answer: purine replaces pyrimidine or vice versa

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Question: reverse mutation (reversion)

Answer: converts a mutant allele to a wild-type allele

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Question: spontaneous mutation

Answer: mutation that occurs due to random spontaneous changes in the nucleotide sequence

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Question: Deamination

Answer: loss of an amino group from a nucleotide base spontaneously. Cytosine gets replaced with uracil.

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Question: Depurination

Answer: A mutation that occurs when a purine base (A or G) is removed from the sugar-phosphate back bone; effectively stops replication. Usually fixed, though. Very common.

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Question: mutagen

Answer: An agent capable of damaging DNA and causing a mutation.

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Question: Frameshift

Answer: What types of mutations are caused by intercalating agents?

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Question: thymine dimer

Answer: the type of lesion formed on DNA due to UV exposure.

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Question: Ames Test

Answer: To determine what chemicals are hazardous to our health by increasing genetic mutation frequency. (To identify the rate of reversion mutations)

Run 2 parallel tests - a control and an experimental. The control liver enzyme is plated on a his- plate. A possible mutagen is added to the experimental test, and then it is also plated on a his- plate. Then you can compare the experimental to the control, and if there is more liver growing on the experimental you have a positive result, reversion. This means that the experimental was probably a mutagen.

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Question: Base excision repair

Answer: A segment of the damage strand is taken out and replaced by the activity of the DNA Pol and DNA ligase

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Question: Nucleotide excision repair

Answer: If you can't repair the modified nucleotide then you can exploit the double-stranded DNA structure and use the undamaged side as a template.Remove the damaged nucleotides and replace them using complementary base pairing.

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Question: DNA recombination repair

Answer: reestablish normal DNA by exchanging a damaged segment of DNA with a normal segment from another chromatid.

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Question: Translesion DNA Synthesis

Answer: allows DNA replication by these alternative polymerases across lesions that block DNA Pol III, the main replicating polymerase in E. Coli.

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Question: non homologous end joining

Answer: An error prone repair process that repairs double stranded breaks before DNA replication.

Protein complex binds DNA ends. Ends are trimmed; nucleotides lost. DNA ligase ligates the ends, forming and intact duplex.

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Question: constitutive transcription

Answer: bacterial transcription - continuous with no regulated control - continually form routine tasks

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Question: regulated transcription

Answer: bacterial transcription - regulated control - need agile and calibrated environmental responses

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Question: negative control

Answer: binding of a repressor protein to a regulatory bacterial DNA sequence prevents transcription of a gene or group of genes

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Question: positive control

Answer: binding of an activator protein to a regulatory bacterial DNA sequence stimulates transcription of a gene or group of genes

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Question: DNA-binding & allosteric

Answer: 2 functional domains of a repressor protein

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Question: Operons

Answer: clusters of genes undergoing coordinated transcription regulation by a shared regulatory region. Common in bacterial genomes. Share transcription control.

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Question: Lac z-

Answer: no functional beta-galactose

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Question: Lac Y-

Answer: no functional permease

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Question: Lac I-

Answer: can't bind to operator

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Question: Lac Is

Answer: Cant bind to inducer

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Question: low glucose level

Answer: High cAMP level

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Question: cis-acting regulatory sequences

Answer: regulate transcription of genes on the same chromosome

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Question: trans-acting regulatory proteins

Answer: can identify and bind to target sequences on ANY chromosome

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Question: locus control region (LCR)

Answer: enhancer elements that regulate the transcription of multiple gene packages in closely related genes

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Question: Insulator sequence

Answer: prevents enhancers from inappropriately activating nearby genes, located between enhancers and promoters to shield the promoter

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Question: Open promoter

Answer: promoters that reside in open chromatin, resulting in constitutive transcription. Have a nucleosome depleted region; no TATA box.

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Question: Covered promoters

Answer: Promoter in which nucleosomes are adjacent to the start site preventing transcription initiation. Nucleosomes must be displaced or removed.

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Question: SWI/SNF

Answer: Chromatin remodelers that open chromatin structure by displacing nucleosomes. Allow binding of TF to initiate transcription.

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Question: ISWI complex

Answer: Chromatin remodelers that control placement of nucleosomes into regions that makes the region transcriptionally silent

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Question: SWR1 Complex

Answer: Chromatin remodelers that replace common histone protein 2A with different kind, altering its pairings and interactions.

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Question: Genomic imprinting

Answer: alleles that show different expression depending on whether or not they are maternal or paternal.

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Question: RNAi

Answer: A regulatory gene-silencing mechanism in which dsRNA targets complementary strands for inactivation.

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Question: dicer

Answer: enzyme that cuts the dsRNA into small fragments in RNAi

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Question: recombinant DNA technology

Answer: Lab techniques for amplifying, maintaining and manipulating specific DNA sequences in vitro and in vivo.

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Question: recombinant DNA vector

Answer: vector and DNA from different sources used in DNA cloning

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Question: nonrecombinant DNA vector

Answer: In DNA cloning this is made when the intended vector doesn't pick up a DNA insert.

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Question: transgenic organism

Answer: an organism harbouring a transgene (a gene modified in vitro by recombinant DNA technology and introduced into the genome.)

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Question: Expression vector

Answer: a cloning vector that has the DNA sequences required for DNA fragments to be inserted and be transcribed and translated.

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