Chapter 7 – Microbiology – Flashcards
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| genetics |
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| the study of inheritance and inheritable traits as expressed in a organism's genetic material |
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| genome |
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| entire genetic complement, including genes and nucleotide sequences that connect genes to one another |
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| genes |
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| specific sequences of nucleotides that code for polypeptides or RNA molecules |
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| nucleotides |
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| -basic building blocks of the polymers nucleic acids -each nucleotide made up of a phosphate group attached to a nucleoside (which is a pentose sugar attached to one of five nitrogenous bases) |
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| base pairs |
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| -the complimentary bases of nucleotides hydrogen bond to one another -DNA: thymine and adenine form two hydrogen bonds -RNA: uracil and adenine form two hydrogen bonds -both: guanine and cytosine form three hydrogen bonds |
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| antiparallel strands of DNA |
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| one strand runs in the 3' to 5' direction while the other runs in the 5' to 3' direction |
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| chromosome |
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| -a molecule of DNA associated with protein -prokaryotes: typically circular and localized in a region of the cytosol called the nucleoid -eukaryotes: threadlike and most visible during mitosis or meiosis |
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| haploid cells |
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| prokaryotes only have a single copy of each chromosome |
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| nucleoid |
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| region of the prokaryotic cytosol containing the cell's DNA/chromosomes |
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| histones |
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| globular protein found in eukaryotic and archeal chromosomes |
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| gyrase |
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| enzyme responsible for further folding and super-coiling the entire prokaryotic chromosome |
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| plasmid |
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| -(prokaryotic) a small, circular molecule of DNA that replicates independently of the chromosome -each carries genes for its own replication and often for one or more nonessential functions -types of plasmids (aka factors): fertility (F), resistance (R), bacteriocin, virulence |
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| fertility (F) plasmid |
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| carries instructions for conjugation |
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| resistance (R) plasmid |
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| -carries genes for resistance to one or more antimicrobial drugs or heavy metals -certain cells can transfer resistance to other cells |
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| bacteriocin plasmid |
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| -carries genes for proteinaceous toxins called bacteriocins, which kill bacterial cells of the same or similar species that lack the plasmid -in this way, a bacterium can kill off its competitors |
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| virulence plasmids |
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| carries instructions for structures, enzymes, or toxins that enable a bacterium pathogenic |
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| diploid cells |
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| eukaryotic cells have two copies of each chromosome |
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| eukaryotic chromosomes |
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| differ from prokaryotic chromosomes in that they are always sequestered within a nucleus and are all linear (rather than circular) |
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| nucleus |
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| an organelle containing the DNA within a cell and is surrounded by two membranes called the nuclear envelope |
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| nuclear envelope |
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| consists of the two membranes that surround the nucleus of a cell |
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| nucleosomes |
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| -DNA, which has an overall negative charge, wraps around the positively charges histones to form 10 nm diameter beads -"in other words": beads of DNA bound to a histone in a eukaryotic chromosome |
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| chromatin fibers |
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| -an association of nucleosomes and proteins found within the chromosomes of eukaryotic cells, 30 nm in diameter -dispersed throughout the nucleus (except during mitosis) |
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| euchromatin |
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| -aka "open chromatin" -in regions of the chromosome where genes are active, the chromatin fibers are loosely packed |
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| heterochromatin |
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| -aka "closed chromatin" -inactive DNA is tightly packed |
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| extranuclear DNA of eukaryotes |
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| -DNA molecules of mitochondria and chloroplasts are circular and resemble the circular chromosomes of prokaryotes -note: some fungi and protozoa carry plasmids |
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| DNA replication |
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| -an anabolic polymerization process that allows a cell to pass copies of its genome to its descendants -semi-conservative b/c each daughter DNA molecule is composed of one original "parent" strand and one new strand -bidirectional: synthesis proceeds in both directions from the origin |
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| triphosphate deoxyribonucleotides |
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| -DNA molecules with three phosphate groups linked together by two high-energy bonds -the building blocks of DNA carry within themselves the energy required for DNA synthesis |
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| origin |
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| a specific sequence of nucleotides in which DNA replication begins |
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| helicase |
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| -unwinds/unzips strands |
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| primase |
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| -sets down an RNA primer -provides the starting point for replication -one primer for leading strand -many for lagging strand: one for each Okazaki fragment |
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| DNA polymerase III |
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| -lays down most of the complimentary strand -note: named the "third" due to it being the third DNA polymerase discovered, NOT b/c of the order of function within DNA replication -also plays role in "proofreading exonuclease function" |
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| DNA polymerase I |
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| -aka "RNAse" -removes the RNA nucleotides that were set down by primase (by digesting the primers) -replaces those with DNA nucleotides |
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| ligase |
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| -fixes the missing covalent bonds on the sugar-phosphate backbone on the lagging strand -"in other words": seals the gaps between the adjacent Okazaki fragments to form a continuous DNA strand |
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| leading strand |
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| **DNA only grows 5' to 3' (only adds to the 3') -leading strand has the 3' end facing the helicase which allows for smooth adding -synthesized continuously |
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| lagging strand |
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| *DNA only grows from 5' to 3' (only adds to the 3') -lagging strand has the 5' end facing the helicase and the 3' end facing away from the helicase (antiparallel strands) -nucleotides are added to the 3' ends and replication is fragmented -fragments called "Okazaki fragments" -NOT slower than leading, just synthesized discontinuously |
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| stabilizing proteins |
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| after helicase splits the DNA molecule, stabilizing proteins bind to the strands so that they do not rejoin while replication proceeds |
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| proofreading exonuclease function |
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| DNA polymerase III recognizes most errors and removes the incorrect nucleotides before proceeding with synthesis |
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| gyrase and topoisomerase |
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| -these enzymes prevent super-coiling of DNA during replication -act by cutting the DNA, rotating the cut ends, and then rejoining the cut ends |
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| methylation |
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| -process in which a cell adds a methyl group to one or two bases that are part of specific nucleotide sequences -bacteria typically methylate adenine bases and only rarely cytosine bases -plant and animal cells only methylate cytosine bases |
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| methylation and cellular processes |
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| 1. control of genetic expression 2. initiation of DNA replication 3. protection against viral infection 4. repair of DNA |
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| replication of eukaryotic DNA |
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| -uses four different DNA polymerases -thousands of replication origins per molecule -Okazaki fragments are shorter than those of bacteria -plant and animal cells methylate cytosine bases exclusively |
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| genotype |
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| -actual set of genes in an organism's genome -genotype determines phenotype by specifying what kinds of RNA and which structural, enzymatic, and regulatory protein molecules are produced |
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| phenotype |
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| refers to the physical features and functional traits of an organism, including characteristics such as structures, morphology, and metabolism |
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| transcription |
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| -process in which the genetic code from DNA is copied as RNA nucleotide sequences -occurs in the nucleoid region of the cytoplasm in bacteria -3 steps: initiation, elongation, termination |
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| translation |
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| -RNA molecules in ribosomes synthesize polypeptides -3 steps: initiation, elongation, termination |
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| central dogma |
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| in genetics, fundamental description of protein synthesis which states that genetic information is transcribed from DNA to RNA and then translated from RNA to polypeptides |
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| 4 types of RNA |
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| transcribed from DNA= rRNA: forms ribosomes tRNA: delivers a.a. to ribosomes mRNA: carries info for making specific proteins from DNA to ribosomes RNA primer: molecules for DNA polymerase to use during DNA replication |
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| RNA primer |
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| molecules for DNA polymerase to use during DNA replication |
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| mRNA |
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| -messenger RNA -carries genetic information from chromosomes to ribosomes as triplet sequences of RNA nucleotides (codons) |
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| rRNA |
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| -ribosomal RNA -combine with ribosomal polypeptides to form ribosomes |
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| tRNA |
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| -transfer RNA -delivers the correct amino acids to ribosomes based on the sequence of nucleotides in mRNA -a sequence of about 75 ribonucleotides that curves back on itself to form 3 main hairpin loops held in place by hydrogen bonding between complimentary nucleotides -bottom loop contains an anticodon -acceptor stem for a specific amino acid at its 3' end |
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| initiation of transcription |
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| a. RNA polymerase binds to a promoter. Sigma factor enhances promoter recognition in bacteria. b. upon recognition of the promoter, RNA polymerase unzips the DNA molecule which creates a "bubble" as it moves |
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| RNA polymerase |
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| -enzyme that synthesizes RNA molecules by linking RNA nucleotides that are complimentary to genetic sequences in DNA -links nucleotides only to the 3' end |
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| promoters |
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| specific DNA nucleotide sequences, each of which is located near the beginning of a gene, and serves to initiate transcription |
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| sigma factor |
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| -in bacteria, a polypeptide subunit of RNA polymerase which is necessary for promoter recognition -variations of sigma factors and promoters affect the amount and kinds of polypeptides produced |
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| elongation of transcription |
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| a. at about 10 nucleotides away from the promoter region, triphosphate ribonucleotides align opposite their compliments in the open DNA "bubble" b. RNA polymerase links two adjacent ribonucleotide molecules using the energy phosphate bonds of the first ribonucleotide c. RNA polymerase moves along the molecule repeating the process and synthesizing mRNA |
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| triphosphate ribonucleotides |
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| -rATP, rUTP, rGTP, and rCTP -contains high energy within the phosphate bonds to support the linking of adjacent ribonucleotide molecules and thus anabolism of mRNA |
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| termination of transcription |
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| -RNA polymerase and the transcribed RNA are released from DNA -two processes: self-termination or Rho dependent termination |
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| self-termination of transcription |
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| transcription of DNA terminator sequences causes the RNA to fold, loosening the grip of polymerase on DNA |
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| enzyme-dependent termination of transcription |
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| Rho pushes between polymerase and DNA, releasing polymerase, RNA transcript and Rho |
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| terminator |
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| sequence of DNA composed of two symmetrical series: one that is very rich in guanine and cytosine bases, followed by a region rich in adenine bases which causes termination of transcription |
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| transcription differences in eukaryotes |
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| -RNA transcription occurs in the nucleus -transcription also occurs in mitochondria and chloroplasts -3 types of RNA polymerases -numerous transcription factors -mRNA processed before translation: capping, polyadenylation, splicing |
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| mRNA processing |
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| 1. capping: guanine nucleotide added to the "front" 5' end of the mRNA molecule 2. polyadenylation: at end of gene, termination proteins cleave the RNA molecule and add 100-250 adenine bases 3. splicing: spliceosome removes introns and splices exons from pre-mRNA in order to make functional mRNA from the exons |
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| pre-messenger RNA |
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| -newly guanine capped and polyadenylated mRNA molecules -contain introns and exons -must be spliced in order to make functional mRNA containing only exon regions |
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| introns |
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| -noncoding sequences of pre-mRNA that may be thousands of nucleotides long -introns are removed from pre-mRNA -"in" refers to intervening sequences |
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| exons |
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| -coding regions of pre-mRNA that are about 150 nucleotides long -functional mRNA is made from only these regions of the pre-mRNA -"ex" refers to the fact that these genes are expressed |
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| spliceosome |
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| -five small RNA molecules associate with about 300 polypeptides to form a spliceosome -acts as a ribozyme (ribosome enzyme) to splice pre-mRNA into mRNA -it removes the introns and splices the exons to produce functional mRNA |
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| ribosomes in translation |
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| -"polypeptide factories" -50S subunit + 30S subunit= 70S prokaryotic ribosome -60S subunit + 40S subunit= 80S eukaryotic ribosome -smaller subunit shaped to accommodate 3 mRNA codons at a time and also 3 tRNA binding sites |
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| genetic code |
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| -4 letter alphabet -genes composed of sequences of 3 nucleotides that specify amino acids -64 possible arrangements of the four different nucleotides in triplets -organisms use 20 (or 21) amino acids -triplets of mRNA molecules=codons |
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| codons |
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| -triplet of mRNA nucleotides that code for specific amino acids -1 start= AUG =>met -3 stops= UAA, UAG, or UGA |
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| anticodon |
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| -bottom loop portion of tRNA molecule that is complementary to a codon on an mRNA molecule |
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| acceptor stem |
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| -3' end of tRNA molecule contains an acceptor stem for a specific amino acid -specific enzymes in the cytoplasm "charge" the tRNA molecule by attaching the appropriate amino acid to the acceptor stem |
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| tRNA binding sites on ribosomes |
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| -A site: accommodates a tRNA delivering an Amino Acid -P site: holds a tRNA and the growing Polypeptide -E site: discharged tRNA's Exit from the E site |
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| initiation of translation |
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| a. smaller subunit of ribosome attaches to mRNA near start codon AUG b. anticodon of tRNA^fMet aligns with the start codon on the mRNA and energy from GTP is used to bind tRNA in place at the P site of ribosome c. larger subunit of ribosome attaches to form an initiation complex- complete ribosome attached to mRNA with binded tRNA at P site |
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| initiation complex |
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| -forms during initiation of translation -includes: two ribosomal subunits, mRNA, several protein factors, and tRNA^fMet |
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| elongation of translation |
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| a. tRNA with the anticodon complimentary to the next codon delivers its amino acid to the A site (elongation factors deliver tRNA along with GTP) b. a ribozyme in the larger subunit forms a peptide bond between the terminal amino acid of the growing peptide chain c. using more energy from GTP, ribosome moves forward another codon (translocation) down the mRNA. this transfers each tRNA to the next binding site d. ribosome releases the "empty" tRNA from the E site e. the cycle repeats |
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| elongation factors |
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| -proteins in the translation process escort "charged" tRNA along with GTP to the A site of the ribosome/mRNA complex |
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| translocation |
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| ribosome moving forward codon by codon |
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| polyribose |
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| as elongation proceeds, ribosomal movement exposes the start codon in order to allow another ribosome to attach to begin translating another identical polypeptide |
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| termination of translation |
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| -release factors somehow recognize stop codons and modify the larger subunit of the ribosome to activate ribozymes which sever the polypeptide from the final tRNA -the ribosome then dissociates from the mRNA into subunits -polypeptides released at termination may function alone or together in quarternary protein structures |
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| regulation of genetic expression |
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| -75% of genes are expressed at all times -other genes are regulated so they are only transcribed and translated when cells need them ->allows cells to conserve energy -regulation of protein synthesis typically halts transcription -regulation at level of translation: riboswitch and short interference RNA siRNA |
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| operon |
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| -special arrangements of prokaryotic genes that play roles in gene regulation -consists of a promoter and a series of genes -some operons are controlled by a regulatory element called an operator |
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| operator |
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| regulatory element in an operon where repressor protein binds in order to stop transcription |
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| repressor protein |
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| -binds to the operator of an operon in order to halt transcription -in the absence of a repressor, transcription is induced |
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| regulatory gene |
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| located outside the operon, codes for the repressor |
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| inducible operons |
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| -not usually transcribed (usually "off") and must be activated by inducers (can be turned "on") **usually genes containing instructions for enzymes in a catabolic reaction -only turned on when the polymer to break down is present -ie: lac operon |
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| lac operon |
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| -inducible operon, induced by the presence of lactose -includes a promoter, an operator, and three genes that encode the proteins involved in the transport and catabolism of lactose -when lactose is present, allolactose binds to the repressor and deactivates it, in order to allow transcription to occur *no lactose=no transcription |
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| repressible operons |
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| -operons that are transcribed continually (usually "on") until deactivated by repressors (can be turned "off) **usually instructions for enzymes needed for anabolic reactions -turned off when the polymer to build is in sufficient or plentiful amounts -ie: trp operon |
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| trp operon |
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| -consists of a promoter, an operator, and five genes that code for the enzymes to build tryptophan -when enough tryptophan is present, some will bind to the repressor to "activate" it so that it can bind to the operator and block transcription |
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| corepressor |
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| -activates the repressor so that it can bind to the operator in an operon system -ie: tryptophan acts as a corepressor stopping its own synthesis |
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| miRNA |
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| -micro RNA: short, about 21 nucleotides, RNA molecule -joins with regulatory proteins to form an RNA silencing complex (RISC) which then binds to the mRNA blocking translation |
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| RISC |
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| -RNA silencing complex -either cleaves the mRNA molecule -or binds to the mRNA molecule, blocking it from the ribosome |
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| siRNA |
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| -short interference RNA -similar to primer, becomes incorporated into RISC, which binds to mRNA -RNA molecule complementary to a portion of mRNA, tRNA, or a gene that binds and renders the target inactive |
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| riboswitch |
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| -RNA molecule which changes shape in response to environmental conditions such as changes in temperature, or shifts in the concentration of nutrients -some mRNA molecules act as riboswitches and block ribosomes and translation of the polypeptide they encode |
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| mutation |
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| -change in the nucleotide base sequence of a genome, particularly its genes -rare event -almost always deleterious -rarely leads to a protein having a novel property that improves the ability of organism and its descendents to survive and reproduce |
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| point mutation |
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| -a genetic mutation in which only one base pair is affected -includes: substitutions |
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| frameshift mutations |
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| -includes insertions or deletions of one base pair -nucleotide triplets after the mutation are displaced -typically result in missense or nonsense mutations |
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| silent mutations |
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| -aka silence -no real change or effect -ie: same amino acid from a different codon |
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| missense mutation |
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| -changing the codon results in a different amino acid -makes sense, but not the "right" sense -ie: sickle cell anemia |
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| nonsense mutation |
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| -changing a base to result in a stop codon -nearly all nonsense mutations result in nonfunctional proteins |
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| spontaneous mutation |
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| -occurs during replication and repair as well as recombination |
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| mutagen |
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| -physical or chemical agent that induces radiation -includes radiation and several types of DNA-alterating chemicals -increase rate of mutation 10 to 1000 times |
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| ionizing radiation |
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| -energizes electrons in atoms, forcing some of electrons out of their atoms; these free electrons strike other atoms and thus creates ions -ions can break the covalent bonds within sugar-phosphate backbone and induce breaks in chromosomes -includes X rays and gamma rays |
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| nonionizing radiation |
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| -causes adjacent pyrimidine bases to covalently bond to one another, forming pyrimidine dimers -ie: UV light |
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| nucleotide analog |
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| -compounds that are structurally similar to normal nucleotides -disrupt DNA and RNA replication and **causes point mutations -ie: 5'bromouracil analog of thymine, can pair with guanine instead of adenine |
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| nucleotide-altering chemicals |
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| -alters the base so that it is misread by RNA -results in base-pair substitution mutations and missense mutations -ie: aflatoxins, nitrous acid |
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| frameshift mutations |
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| -some chemical agents cause insertion or deletion of nucleotide base pairs -results in nonsense mutations -ie: benzopyrene, ethidium bromide, acridine |
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| light repair |
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| mechanism by which prokaryotic DNA photolyase breaks the bonds between ajoining pyrimidine dimers, restoring the original sequence |
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| photolyase |
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| -prokaryotic enzyme activated by visible light -breaks pyrimidine dimers in order to restore the original DNA sequence |
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| dark repair |
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| mechanism by which dark repair enzymes cut out the damaged section (pyrimidine dimers) of DNA from a molecule, creating a gap that is repaired by DNA polymerase I and ligase -can operate with or without light |
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| base-excision repair |
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| enzyme removes the incorrect nucleotide base and DNA polymerase I fills the gap |
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| mismatch repair |
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| -enzyme removes mismatched bases and repairs them -this is done by detection of unmethylated portions of DNA versus old strands of DNA which are methylated |
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| mutant |
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| -descendants of a cell that does not successfully repair a mutation |
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| wild types |
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| cells normally found in nature (the wild) |
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| positive selection |
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| -involves mutants which gained an ability (such as abx resistance) -process by which mutants are selected by eliminating wild type phenotypes -ie: pcn resistant mutants grow on pcn medium while wild types are inhibited |
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| negative selection |
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| -involves mutants which have lost an ability -replica plating: wild type and mutants are inoculated and cultured, sterile stamp used to create 2 plates with different mediums, comparison of both cultured plates will show the mutant is capable of growth in only one of the plates |
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| auxotroph |
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| mutant which has different nutritional requirements than its wild-type phenotype |
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| carcinogens |
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| chemicals capable of causing cancer |
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| Ames test |
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| -fast and inexpensive method for screening mutagens -Salmonella histidine auxotroph which requires histidine in order to grow while the wild type can make histidine -Salmonella auxotroph mutants are mixed with liver extract and the suspected mutagen -if suspected agent is a mutagen, it will cause the salmonella auxotroph to "back mutate" the point mutation which allows the salmonella to grow w/out histidine like its wild type *growth shows that the chemical is in fact a mutagen |
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| genetic recombination |
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| -exchange of segments, typically genes, between two DNA molecules -usually homologous sequences |
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| recombinant |
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| cell or DNA molecule that contain new arrangements of nucleotide sequences from genetic recombination |
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| vertical gene transfer |
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| -replication of genomes in order to provide copies to their descendants (or progeny) -passing of genes to the next generation |
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| horizontal (lateral) gene transfer |
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| -many prokaryotes acquire genes from other microbes of the same generation -process by which a donor cell contributes part of its genome to a recipient cell, which may be a different species or genus from the donor -three types: transformation, transduction, or bacterial conjugation |
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| donor cell |
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| in horizontal gene transfer, a cell contributes part of its genome to a recipient |
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| recipient cell |
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| -in horizontal gene transfer, a cell that receives part of the genome of a donor cell -becomes a recombinant organism |
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| transformation |
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| -method of horizontal transfer in which a recipient cell takes up DNA from the environment such as DNA that may be released from dead organisms -discovered by Frederick Griffith when he studied two different strains of S. pneumonia in mice -strain S=fatal, strain R=non fatal, heat-killed S=non fatal.. but live R and heat killed S=fatal and produced live S |
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| competent |
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| cells that have the ability to take up DNA from their environment |
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| transduction |
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| -method of horizontal transfer in which DNA is transferred from one to another via a replicating virus -normal viral infections do not occur -transduction occurs when a "mistake" in the viral life cycle occurs |
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| bacteriophage |
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| a virus that parasitizes a bacterium |
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| lytic cycle of infection |
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| virus injects its DNA, replicates its phage DNA (in transduction- phages mistakenly incorporate some bacterial DNA), assembles new transducing phages, and bursts out of the bacterium |
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| transducing phage |
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| virus that transfers bacterial DNA from one bacteria to another |
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| lysogenic cycle of infection |
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| involves the genome of the virus inserting into the bacterial chromosome. replicates its genome each time the bacteria replicates. eventually a trigger will cause it excise and start a lytic infection |
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| generalized transduction |
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| -a random piece of bacterial chromosome gets packed into virus particle instead of virus genome. uses the lytic cycle. -any gene can move to new host=>becomes recombinant |
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| specialized transduction |
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| -relies on the lysogenic cycle -mistake occurs during excision to initiate lytic cycle -defective: has some specific bacterial genes near where viral insertion site and left some viral genome behind -when defective: virus moves to new host and inserts. host becomes recombinant but viral infection is a dead end. |
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| prophage |
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| viral/phage DNA incorporated into the bacterial chromosome during lysogenic cycle of infection |
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| conjugation |
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| -method of horizontal gene transfer in which a bacterium containing a fertility plasmid forms a conjugation pilus that attaches and transfers plasmid genes to a recipient -F plasmid: instructs for pilus & instructions for sending a single stranded copy of itself -donor cells= F+ and recipient= F- |
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| HFR cells |
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| -modification of conjugation, the f factor integrates into the chromosome (instead a plasmid within the cytosol) -HFR= high frequency of recombination strains -donor= F+ but plasmid is incorporated into the chromosome -recipient= F- but after conjugation, recipient becomes recombinant and NOT F+ -only a portion of F plasmid (not a full or complete copy) is sent over and thus is not capable of forming a pilus |
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| origin of transfer |
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| the beginning section of a single strand of F plasmid DNA that transfers to a recipient of conjugation |
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| transposons |
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| -"jumping genes" discovered by Barbara McClintock -segments of DNA that transpose (move) themselves from one location in a DNA molecule to another location in the same or different molecule -occurs between plasmids and chromosomes and within and among chromosomes |
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| transposition |
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| mutation in which a genetic segment is transferred to a new position through the action of a DNA segment called a transposon |
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| palindrome |
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| -a region of DNA in which the sequence of nucleotides is identical to an inverted sequence in the complimentary strand -ie: GAATTC is the palindrome of CTTAAG -aka: inverted repeat (IR) |
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| inverted repeat (IR) |
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| -a region of DNA in which the sequence of nucleotides is identical to an inverted sequence in the complimentary strand -ie: GAATTC is the palindrome of CTTAAG -aka: palindrome |
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| simple transposon |
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| -called insertion sequences (IS) -consist of no more than 2 palindromes and a gene that encodes the enzyme transposase |
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| transposase |
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| -the enzyme related to transposition -it recognizes its own inverted repeat (palindrome) in a target site, cuts the DNA at that site, and inserts the transposon (or a copy of it) into the DNA molecule at that site |
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| complex transposons |
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| contain one or more genes that are not connected with transposition, such as R factors (genes for abx resistance) |
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| R factors |
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| genes that carry antibiotic resistance |
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| cut and paste transposition |
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| -the entire transposon is cut and removed from one location and placed into its new location -done with the use of transposase |
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| replicative transposition |
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| -transposase allows for copying of the transposon and placing the copy into a new location |
