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104 Cards in this Set
- Front
- Back
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What are the major components of a nucleotide?
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DNA - Deoxyribose (5 carbon sugar)
Phosphate group Nitrogenous base |
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What is the 5' end of a nucleotide?
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Phosphate group is attached to the 5' carbon and is the 5' end
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What is the 3' end of a nucleotide?
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Hydroxy group is attached to the 3' carbon and forms the 3' end
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What type of bond is formed to create the sugar backbone? What molecules bond to each other?
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Phosphodiester (covalent) bond is created by dehydration synthesis. OH on 3' end bonds to phosphate group on 5' end.q
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What end is of the sugar backbone is "open" for new bonding?
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OH on 3' end
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What type of bond is formed between the nitrogenous bases?
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Hydrogen bonds
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What does it mean that DNA is anti-parallel?
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When 2 strands of nucleotides come together they bond in the opposite orientation
5' - 3' 3' - 5' |
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What is a base pair?
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2 bases that bond together
A&T, C&G |
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What is a complementary base?
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correct base partner for a specific base
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What are the difference between DNA and RNA?
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DNA has deoxyribose sugar; RNA has ribose
DNA is double stranded; RNA is single stranded DNA - thymine; RNA - uracil |
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What is the origin of replication?
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Specific sequence of DNA where strands are separated; split by helicase
prokaryotes have 1 eukaryotes have multiple |
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What does the enzyme DNA helicase do?
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separates DNA strands to start replication; binds to origin of replication to separate strands by breaking hydrogen bonds between bases
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What does RNA primase do?
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Makes an RNA primer with a free 3' OH end
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What does DNA polymerase III do?
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makes DNA strand 5' to 3' direction and proofreads
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What does DNA polymerase II do?
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Removes RNA, rep with DNA
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What does DNA ligase do?
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seals fragments with phosphodiester bond
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What does it mean when you say DNA replication is semi-conservative?
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Every new copy of DNA contains one old strand and one new strand of DNA
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What are three terms that describe the breaking of hydrogen bonds between nitrogenous bases?
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denatured, melted, unzipped
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What is the replication fork?
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Y-shaped structure that is the location where new strand can begin to be made
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Is the leading or lagging strand continuous?
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the Leading strand 5' to 3' is continuous
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How is synthesis of the lagging strand done?
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discontinuously; Okasaki fragments (still formed 3' to 5')
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What does polymerase I do?
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Removes RNA and replaces with DNA
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What does DNA ligase do?
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creates phosphodiester bond to seal gaps between fragments
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What is the process of synthesis on the lagging strand?
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1. Primase synthesizes RNA primer
2. DNA polymerase III adds nucleo. to 3' end 3. DNA polymerase I replaces RNA primer with DNA 4. DNA ligase seals gaps with phosphodiester bonds |
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What is the central dogma of molecular biology?
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DNA used in transcription to make RNA;
RNA used to make proteins |
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What is transcription?
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Gene (DNA sequence) is transcribed into RNA
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What is translation?
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mRNA is translated into an amino acid sequence
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What is a gene?
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DNA sequence
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What is the genome?
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All genes in a cell including chromosomal and plasmid DNA
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What are regulatory RNAs?
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regulatory RNAs regulate which genes in DNA are transcribed and which RNA can be used in translation to make proteins (not rRNA, which is ribosomal)
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What are tRNAs?
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transfer RNA
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What are rRNAs?
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ribosomal RNA
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What are the steps in Transcription?
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1. Initiation - promoter is recognized by RNA polymerase and sigma factor
2. Elongation - synthesis in 5' to 3' direction that begins at the +1 site 3. Termination - terminator on DNA and hairpin loop formed on RNA |
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What is the promoter?
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indicates beginning of gene and point at which transcription should begin; negative 35 and negative 10 sequences, which are common in some bacterial species.
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What is the sigma factor?
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subunit of RNA polymerase that helps to recognize the promoter
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What is the specific name given to the negative 10 base pair?
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Pribnow box (only in prokaryotes); promoter sequence that contains a lot of adenine and thymine
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Where does elongation begin?
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+1 site
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What is the template strand?
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The strand in a double-stranded DNA molecule that is used as a model to synthesize the complementary strand of DNA/RNA during transcription
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Is the promoter found on DNA or mRNA?
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DNA
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What binds to the promoter?
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RNA polymerase (with sigma factor)
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What does RNA polymerase do?
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With sigma factor attached, it recognizes the promoter; transcribes a piece of RNA starting at the +1 site in the 5' to 3' direction; does not need RNA primer
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After sigma factor has helped RNA polymerase recognize the promoter, what does it do?
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moves on to find another RNA polymerase to help
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In what direction does synthesis occur in elongation?
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5' to 3'
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Where does elongation begin?
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+1 site
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Is RNA primer needed to begin synthesis in elongation?
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No
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Where is the termination sequence - DNA or RNA?
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DNA
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What is the hairpin loop?
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Loop formed on RNA b/c bases bind to each other instead of DNA that causes RNA to "fall off" DNA and terminate process; cytosine and guanine-rich, followed by 6 A's
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What is the start site for DNA replication?
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origin of replication
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What is the start site for transcription?
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promoter iniates elongation at +1 site
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What direction is synthesis completed for DNA replication? transcription?
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5' to 3' for both
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What are enzymes involved in DNA replication?
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DNA polymerase III
DNA polymerase I Ligase Primase Helicase |
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What are the enzymes involved in transcription?
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RNA polymerase
sigma factor |
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What signals completion of DNA replication?
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all of chromosomal DNA is copied
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What signals completion of transcription?
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termination sequence on DNA, hairpin loop formed on RNA
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what is translation?
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mRNA used to make proteins
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What is a ribosome made of?
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Protein and ribosomal RNA (rRNA)
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What is the genetic code?
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table of codons, which are sets of 3 nucleotides that code for a specific amino acid
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What does it mean that the genetic code is redundant?
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more than one codon codes for the same amino acid
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what is the start codon in translation?
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AUG - methionine with additional formyl group (f-Met)
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What are the stop codons?
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UGA, UAA, UAG
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What is the reading frame?
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Way the ribosome divides mRNA sequence into codons or sets of nucleotides
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What is the importance of the start codon in determining the reading frame?
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start codon is AUG (f-Met), determines where to start reading sets of 3 nucleotides/codons
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What is tRNA?
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transfer RNA; location of anti-codon
that is T-shaped (or clover leaf) Brings correct amino acid to ribosome at correct time specific tRNA carries specific amino |
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What is the anti-codon?
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sequence of nucleotides that are complementary to the codon on mRNA; doesn't code for anything
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What are the major steps in translation?
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1. Initiation
2. Elongation 3. Termination |
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What happens during translation initiation?
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FORMATION of INITIATION COMPLEX
-Binding of 30s ribosome recognizes and binds to RBS (ribosome binding site) on mRNA seq -start codon AUG on mRNA to determine reading frame -f-Met on a tRNA and 50s bind |
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What happens during translation elongation?
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tRNAs enter ribosome at A site (acceptor), except the first, which enters P site (Peptidal); exit at E site; tRNA leaves empty but forms peptide bond at P site with previous amino acid
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What happens during translation termination?
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ribosome comes across one of 3 stop codons
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In prokaryotes, why can transcription and translation occur at the same time?
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because DNA is not surrounded by membrane
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what is vertical gene transfer?
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DNA passed from organism to its offspring
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What is recombination?
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combining of DNA of 2 different cells resulting in new cell with original DNA plus DNA of donor cell
new cell = recombinant |
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what are the mechanisms for lateral gene transfer?
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transformation
transduction conjugation |
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Who discovered transposons?
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Barbara McClintock in maize
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what are transposons?
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Jumping genes
piece of DNA that can move to different locations within the chromosome or to a plasmid (within cell) |
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What is the enzyme made by the transposon?
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transposase - cuts the gene out of the DNA and inserts it
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What is transformation?
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uptake of "naked" DNA/free floating DNA in environment left by cells that broke open; can be DNA fragments or plasmids
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What is competence?
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ability of cell to take up DNA through outer layers
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What are the steps of transformation for a DNA fragment?
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entry of single strand of DNA
integration of DNA via homologous recombination multiplication of cells containing new DNA |
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What is homologous recombination?
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Switching out of similar piece of DNA with donor DNA
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What is electroporation?
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creating competence with electric current
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what are the indirect methods of lateral gene transfer?
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transformation and transduction
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What is heat shock?
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creates competence with 42 degrees C of heat for 30-60 seconds
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what is transduction? generalized vs specific?
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transfer of DNA by a bacteriophage
generalized - xfer of any gene (virus with host DNA of cell A cannot infect cell B with virus, just homologous recomb of cell A DNA) specific - xfer of specific gene (phage induction) |
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What is conjugation?
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Cell A and B come into direct contact with each other; direct method of lateral gene transfer
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What is required for conjugation in gram- cells?
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F (fertility) plasmid (F+ have it, F- do not)
F or sex pilus time |
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Can gram+ and gram- conjugate with each other?
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no
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what are the requirements for conjugation in gram+ cells?
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Have F plasmid
only allows for plasmid transfer, not chromosomal no sex pilus attach by sticky surface |
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How do cells become Hfr cells?
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F plasmid "jumps" into chromosomal DNA
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What is the origin of transfer?
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enzyme snips one strand at the origin of transfer, taking part of F plasmid and part of chromosomal DNA; new cell still F- though because only part of F plasmid transferred.
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In 1890s researchers learned what about the tobacco mosaic virus?
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1. invisible under light microscope
2. pass through a porcelain filter; "filterable virus" - not captured by filter 3. cell free fluid caused disease; viruses not cells |
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what effect does tobacco mosaic virus have on plants?
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puckered, yellowing leaves
stunts growth 25% reduction in yield of infected plants |
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How is tobacco mosaic virus spread?
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mechanically
can survive smoking in cigarette |
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What are the components of a virus?
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nucleic acid - RNA or DNA, not both
capsid - layer of proteins that surround nucleic acids, aka "protein coat"; together - nucleocapsid On some.... Fiber (on naked only) envelope (on enveloped only) with spikes and matrix proteins that connect envelope and capsid |
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Purpose of the envelope and/or capsid?
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protection of nucleic acid
allows virus to inject its viral nucleic acid into host presence of envelope stimulates a human immune response |
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what are the categories of capsids?
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Icosehedron - 20 sided with 12 corners
helical (ie - tobacco mosaic virus) complex - polyhedral head |
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What are the components of a complex virus?
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head, collar, sheath, tail pins, tail fibers
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Do viruses have enzymes for metabolic processes or protein synthesis?
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No, use the host cell's
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What pre-formed enzymes can viruses have?
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- polymerases
- replicase to copy RNA - reverse transcriptase to make DS DNA from SS RNA (reverse of transcription) - lysozyme |
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How are viruses named?
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family - ends in viridae
genus - end in virus species - usually use common name |
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What are the phases of T-even Lytic Phage multiplication?
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1. Adsorption (attachment) - major basis for host specificity; virus receptors
2. Penetration - with lysozyme on NAM-NAG bonds; begins intracellular stage; also eclipse phase where no intact virus can be detected 3/4. synthesis of phage components; nuclease enzyme to to degrade host DNA so virus can take over 5. assembly/maturation - no longer eclipse 6. release - lysozyme to cause cell lysis |
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Describe the lysogenic replication pathway
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viral DNA is integrated into host DNA
host continues regular functions, such as replication Eventually, excision phage, which connects with lytic step for replication of phage DNA |
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What is a lysogen?
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Host cell with viral DNA integrated into its own DNA
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What is a prophage?
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viral DNA when part of bacterial DNA
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What are the advantages to the host of lysogenic cells
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- immunity from infection by same virus
- new properties to lysogen such viral toxin, ie botulism |
