Term
| Carbonate equilibrium system |
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Definition
the balance of CO 2, bicarbonate,
and carbonate that keeps the ocean buffered between pH |
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Definition
| a layer of water characterized by a steep temperature gradient. The penetration of light into the surface water determines the depth of the photic zone. The resultant warming of the waters can lead to the development of a thermocline. |
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Definition
| Planktonic microbes between 0.2 and 2.0 m in size, including the cyanobacterial genera Prochlorococcus and Synechococcus |
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Definition
| a region around the plant root where materials released from the root increase the microbial population and its activities. |
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Term
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Definition
| The surface of a plant root |
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Term
| What factors influence oxygen solubility? How is this important in considering two aquatic environments, ocean and summertime-temperate lakes? |
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Definition
| • Oxygen solubility increases with decreasing temperatures and increasing atmospheric pressures. Oxygen concentration increases with depth due to increased oxygen solubility in cold waters and at high pressure. |
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Term
| Slash-and-burn agriculture |
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Definition
• cutting and burning of vegetation, followed by agricultural use
• in tropical regions can cause almost irreversible degradation of soil |
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Term
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Definition
| the study of community dynamics and the interaction of microbes with each other, with plants and animals, and with the environment in which they live |
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Term
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Definition
| decomposition of organic matter to simpler inorganic compounds (e.g., NH4) |
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Definition
| the nutrients that are converted into biomass become temporarily unavailable for nutrient cycling |
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Term
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Definition
| DNA directs the synthesis of RNA which directs the synthesis of proteins. DNA is structurally more stable than RNA and smaller than protein, so it is the best candidate for storage of genetic information. Proteins do not have a way of unwinding or reading the message of DNA so they need RNA to decode and transport that message to a ribosome where the protein can be synthesized. |
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Term
| Difference Between DNA and RNA |
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Definition
| DNA contains deoxyribose as its sugar whereas RNA has ribose as its sugar. DNA has thymine and RNA has Uracil |
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Term
| DNA polymerase, Why 5' to 3'? |
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Definition
| DNA polymerase uses the OH at the 3’ end as an active site to connect a phosphate from the 5’ end of the next nucleotide. The whole process takes place from 5’ to 3’, but the polymerase works to attach the phosphate from a 5’ carbon to the 3’ carbon of the first nucleotide. For this to work in reverse, it would have to recognize the 5’ carbon as the active site which it cannot do. |
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Term
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Definition
| the base triplet on a tRNA that is complementary to the triplet codon on mRNA |
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Term
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Definition
| The strand of DNA that is discontinuously synthesized by the formation of short Okazaki fragments |
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Term
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Definition
| proteins that assist in the folding and stabilization of other proteins or in directing newly synthesized proteins to secretion systems or other locations in the cell. |
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Term
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Definition
| short stretches of polynucleotides produced during discontinuous DNA replication |
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Term
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Definition
| The way in which nucleotides in DNA and mRNA are grouped into codons for reading the message contained by the nucleotide sequence. |
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Term
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Definition
| A segment in the leader of bacterial and some archaeal mRNA that binds to a sequence on the 16S rRNA of the small ribosomal subunit; it helps properly orient the mRNA on the ribosome |
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Term
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Definition
| A protein that helps bacterial RNA polymerase core enzyme recognize the promoter |
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Term
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Definition
| the loose base pairing between an anticodon and a codon at the third position of the codon. |
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Term
| Many scientists say that RNA was the first of the information molecules (i.e. RNA, DNA, protein) to arise during evolution. Given the information in chapter 12, what evidence is there to support this hypothesis? |
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Definition
| - Answer: RNA is less complex than DNA, it is not double stranded or complementary making it less stable, RNA also codes for amino acids and has catalytic properties and ribosomes are composed of RNA. |
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Term
| How do the genes of prokaryotes and eukaryotes usually differ from each other? |
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Definition
| - Generally speaking the prokaryotes have less genetic material and contain circular chromosomes and plasmids that can be exchanged. Prokaryotes have no introns since they have no nucleus. Eukaryotes have linear DNA, there are more non-coding regions, have introns and only contain circular mitochondrial chromosome |
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Term
| How does tRNA and rRNA genes differ from that of structural genes with respect to posttranscripional modification of the gene product? |
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Definition
| When it comes to procaryotes, posttransciptional modification is rare to begin with. In addition, segments coding for tRNA have spacers inbetween in addition to the introns that are removed during tRNA maturation. rRna are all transcribed as a single, large precursor molecule that is cut up by the ribonucleases after transcription to give final rRNA products. |
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Term
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Definition
| an mRNA that carries several open reading frames, each of which can be translated into a polypeptide. |
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Term
| RNA polymerase core enzyme |
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Definition
| The portion of bacterial RNA polymerase that synthesizes RNA, it consists of all subunits except the sigma factor. |
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Term
| RNA polymerase holoenzyme |
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Definition
| Bacterial RNA polymerase core enzyme together with the sigma factor |
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Term
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Definition
| a prokaryotic protein involved in the termination of transcription. When a poly-Uracil area is not present, thought to bind to mRNA and move along the molecule until it reaches the RNA polymerase halted at the terminator. From here it causes RNA polymerase to dissociate from the mRNA. |
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Term
| Describe posttranscriptional modification, pre-mRNA, 3’ poly-A sequence, 5’ cap, split or interrupted genes, exon, intron, RNA splicing, snRNA, snRNP, and splicesome. |
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Definition
| Post-transcript mod: process from which eukaryotic mRNA rises. First a 5’cap is added to 5’ hydroxyl group of pre-mRNA. May promote initial binding of ribosomes to mRNA, it also protects it from enzymatic attack. After synthesis of pre-mRNA is completed a 3’poly tail is added, it seens to aid in mRNA translation. Introns are intervening sequences not translated into proteins which are transcribed. They are removed from pre-mRNA by RNA splicing which is done by a large complex called the splicesome composed of: pre-mRNA, small nuclear ribonucleopoteins (snRNP’s) and several non-snRNA molecules. Some snRNPs function to recognize expn-intron junctions. |
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Term
| How does bacterial RNA polymerase differ from bacterial DNA polymerase? How does RNA polymerase know when to begin and end transcription? |
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Definition
RNA polymerase: ATP is building block, Bacterial promoters have two characteristic features: sequence of six bases 35 base pairs before transcription begins, and TATAAT sequence callen the Prinbnow box 10 pairs before transcriptional site. Able to unwind DNA w/o aid of helicases. Termination begins when certain sequences form hydrogen bonds within single stranded RNA causing RNA polymerase to stop transcribing DNA. Two kinds Rho-independent. The second needs assistance from protein called rho and is called rho-dependent termination. Can initiate RNA synthesis w/o existing 2’-OH group.
DNA polymerase: dATP is building block. Needs a variety of proteins to aid it. These are found in the replisome and include: DNA polymerase III holoenzyme, helicases, single-stranded DNA binding proteins, and topoisomerases,. Helicases: responsible for unwinding dna; SSBs keep strands apart; toposiomerases; relieve tension generated by unwinding. Has a leading and laggings strand (forms okazaki fragments). Performs proofreading. Termination happens when replisome reaches a termination site on the DNA. In many bacteria it stops randomly when two forks meet. |
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Term
| How do bacterial RNA polymerase and promoters differ from those of Archaea and eucaryotes? |
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Definition
Eucaryotes: 3 Major RNA plymerases. Eucaryotic pre-mRNA arises from posttranscriptional modification.
Archaea: Single RNA polymerase (nut it is larger and in some ways similar to eukaryotic RNA pol). mRNA polycistrionic as in bavteria. |
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Term
| What are the translational and exit domains of the ribosome? Contrast prokaryotic and eukaryotic ribosomes in terms of structure. What roles do ribosomal RNA have? |
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Definition
| T: region directly responsible for translation. The growing peptide chain emerges at the exit domain. Eucaryotic ribosomes bigger than prokaryotic. Ribosomal RNA thought to have three roles: contributes to ribosome structure, 16s rRNA needed for initiation of protein synthesis. 23s hass a catalytic role in protein synthesis. |
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Term
| How do bacterial regulatory proteins control transcription initiation? |
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Definition
| Sigma factor helps the core enzyme recognize the promoter. Holoenzyme begins transcription. Core enzyme completes RNA synthesis once it has been initiated. Alpha subunit seem to be involved in assembly of core enzymes, B’ is is binding site of DNA and w subunit involved in stabilization. |
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Term
| Explain two main regulatory mechanisms of the lac operon |
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Definition
The cell only synthesizes enzymes of the lac operon at high levels when lactose is the only carbon and energy source available. The lac repressor is responsible for inhibiting transcription when there is no lactose. When no lactose is present, repressor binds O1 and operatr site bending DNA in promoter region. RNA polymerase cannot access the promoter as a result.
Also regulated by CAP: allows ecoli to use glucose preferentially over all the other carbon and energy sources via catabolite repression. |
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Term
| Explain two main regulatory mechanisms of the trp operon |
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Definition
Only functions when tryptophan is not available. When tryptophan is available it functions as a co-repressor.
Attenuation: transcription may be terminated at leader region in this process. |
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Term
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Definition
| single stranded rna with a base sequence complementary to a segment of another RNA molecule that can specifically bind to the target RNA and alter its activity. |
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Term
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Definition
| When the repressor is not active, RNA polymerase begins transcription of the leader region but often does not progress to the first structural gene in the operon. Instead it is terminated within the leader region. |
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Term
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Definition
| inhibition of synthesis of several enymes in response to the presence of preferred carbon and energy such as glucose. |
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Term
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Definition
| small molecule that binds and activates a repressor protein thereby inhibits the transcription of a repressible gene. |
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Term
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Definition
| small molecule that stimulates the transcription of an inducible gene by either binding and inactivating a repressor protein or by binding and activating an activator protein. |
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Term
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Definition
| segment of bacterial DNA to which a repressor protein binds. |
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Term
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Definition
| sequence of bases in bacterial/archael DNA that contains one or more structural genes, transcribed from a single promoter. |
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Term
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Definition
| site in the leader of an mRNA molecule that interacts with a metabolite or other small molecule, causing the leader to change its folding pattern, this change alters the transcription or trsanlation levels. |
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Term
| two component signal transduction system: |
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Definition
| signal transduction sysyem that uses the transfer of phosphoryl groups to control gene transcription and protein activity. 2 major components: sensor kinase and a response regulator. |
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Term
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Definition
| a biphasic growth patter in which there is preferential use of one carbon source over another when both are available in environment. |
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Term
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Definition
| The form of gene transfer and recombination in procaryotes that requires direct cell-cell contact. |
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Term
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Definition
| transfer of genes between bacterial or archaeal cells by viruses. |
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Term
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Definition
| mode of gene transfer in procaryotes in which a piece of free dna is taken up by a cell and stably maintained. |
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Term
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Definition
| fertility factor. Plasmid that carries genes for bacterial conjugation and makes its ecoli host the gene donor during conjugation. |
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Term
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Definition
| : mutation that overcomes the effect of another mutation and produces the normal phenotype. |
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Term
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Definition
| base-base tautamerization resulting in purine for purine or pyrimidine for pyrimidine change |
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Term
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Definition
| purine for pyrimide and vice versa mutation. |
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Term
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Definition
| transposable elements which contain genes in addition to those required for transposition. |
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Term
| replicative transposition: |
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Definition
| original transposon remains at the parental site on the chromosome and a replicate is inserted at the target DNA site. |
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Term
| List 3 ways in which spontaneous mutations might arise |
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Definition
| When nitrogenous bases of a template nucleotide takes a rare tutomeric form. These are called either transition or transversion mutation. Replication errors can also occur during deletion and insertion errors. They can also occur from lesions in DNA as well as replication errors. |
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Term
| Explain the differences between silent, missense, nonsense, and frameshift mutations |
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Definition
Silent: Change the nucleotide sequence of a codon but not the amino acid encoded.
Missence: involve a single base substitution that changes a codon for one amino acid into a codon for another. Effect varies from complete loss to none.
Nonsense: convert a sense codon to nonsense. Causes early termination leading to shortened polypeptide.
Frameshift: insertion/deletion of one or two base pairs. |
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Term
| Compare and contrast each of the following repair processes: excision reapri, recombinational repair, direct repair and SOS response |
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Definition
E.R: Corrects damage that causes distortions in the double helix. 2 types: nucleotide excision repair and base excision repair. Both use same approach. Remove damaged portion of a dna strand and use the intact complementary strand as the template for synthesis of new DNA.
R.R: corrects damaged dna in which both bases of a pair are missing or damaged or where there is a gap opposite a lesion. RecA protein cuts a piece of template DNA from a sister molecule and puts it into the gap or uses it to replace a damaged strand.
D.R: photoreactivation repairs thymine dimers by splitting them apart with the help of visible light.
SOS: when damaged greatly. Dna synthesis stops. Sos is activated. Depends on activity of rec a protein. Very error prone used in life or death. |
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Term
| What four fates can DNA have after entering a bacterium? |
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Definition
| Conjugation, transformation, transduction, ? |
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Term
| • What do you think are some major biogenic sources of CO2 emission into the atmosphere? What are the major biogenic sinks of atmospheric CO2? |
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Definition
| – Breakdown of organic matter by fungi is a major source of biogenic CO2 emission into the atmosphere, whereas CO2 fixation by photoautotrophs and chemolithoautotrophs is a major carbon sink. |
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Term
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Definition
| the uptake of naked DNA is a common mode of horizontal gene transfer that can mediate the exchange of any part of a chromosome; this process is most common in bacteria that are naturally transformable; typically only short DNA fragments are exchanged. uptake of naked DNA by a competent cell that is then followed by incorporation of the DNA into the recipient cell’s genome (Slide stuff in black). |
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Term
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Definition
| the transfer of DNA mediated by conjugal plasmids or conjugal transposons; requires cell to cell contact but can occur between distantly related bacteria or even bacteria and eukaryotic cells; can transfer long fragments of DNA. donor HFr cell has F factor integrated into its chromosome |
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Term
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Definition
| the transfer of DNA by phage requires that the donor and recipient share cell surface receptors for phage binding and thus is usually limited to closely related bacteria; the length of DNA transferred is limited by the size of the phage head. |
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