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147 Cards in this Set
- Front
- Back
What are the three components of DNA metabolism?
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Replication, Repair, and Recombination
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What shapes and governs DNA metabolism?
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Enzymes
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Which strand of DNA is copied continuously?
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The Leading strand, with a polarity of 5'-3'
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What are some characteristics of DNA replication?
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Semi-Conservative
Bidirectional @ Replication Forks Semi-Discontinuous |
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What are the three processes of DNA replication?
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Initiation
Elongation Termination |
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Why is DNA replication considered semiconservative?
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Because the replicated strands contain one parent strand, and one daughter strand.
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How was the semi-conservative nature of DNA replication demonstrated?
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Through the use of Nitrogen isotopes to mark the parental strand of DNA.
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How is DNA replication bidirectional?
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The replication forks work in both directions from where the replication initiated.
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How is DNA replication semidiscontinuous?
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The leading strand synthesis is continuous, and the lagging strand synthesis is discontinuous, therefore leading to a semidiscontinuous replication mechanism.
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What are Okazaki fragments?
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They are fragments generated by the discontinuous replication of the lagging strand.
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What links the Okazaki fragments?
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DNA ligase
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What is required to begin the synthesis of DNA?
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Primase
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Is primase made up of DNA or RNA?
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RNA
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How many primers are required for the synthesis of the leading strand?
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One
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What was the first enzyme discovered that could synthesize DNA?
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DNA Polymerase I
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Who found DNA Polymerase I?
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Arthur Kornberg
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What molecule is required to remove two phosphate groups from dNTP?
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Magnesium (2+)
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What is the rate of error in DNA replication?
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Once in every 10^9 to 10^10 BP
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What are the two enzymes that degrade DNA?
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Exonuclease and Endonuclease
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Name the enzyme that can only degrade DNA from one end of the molecule.
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Exonuclease
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Name the enzyme that can begin to degrade DNA at specific internal sites.
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Endonuclease
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Which DNA replicating enzyme has both 3'->5' and 5'->3' exonuclease activity?
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DNA Polymerase I
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What is the most abundant Polymerase?
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Polymerase I
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What is the role of DNA Polymerase II?
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DNA Repair
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How many beta clamps does DNA Polymerase III have?
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Three
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What keeps DNA Polymerase III from dissociating from DNA?
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Beta Clamps
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What does initiation require?
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DnaA, DnaB, SSB and Primase
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What is another term for DnaB?
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Helicase
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What is the component of initiation that binds to oriC to separate it into single strands?
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DnaA
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Which segment of DNA is AT-rich?
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oriC
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What is the purpose of DnaC?
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It forms a complex with DnaB and is required for the loading of DnaB onto DNA
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In what form does DnaB bind to DNA?
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In the form of a DnaB-DnaC complex.
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What enzyme makes the RNA primers?
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DnaG or Primase
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What is the role of SSB?
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To stablize the denatured DNA strands.
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What is elongation?
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The synthesis of both the leading and lagging strand.
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What is DNA gyrase?
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It is a stablizing element of topoisomerase to stablize the unwound DNA.
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What are seven proteins required for elongation?
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SSB,
DnaB, Primase, DNA gyrase, DNA Polymerase III, DNA Polymerase I, DNA Ligase |
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What is a replisome?
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The combination of the proteins at the replication fork.
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How many sites of termination exist in E. coli DNA?
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Seven
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What proteins bind to the Ter site?
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Tus, to form a Tus-Ter complex.
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What does a Tus-Ter complex accomplish?
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It stops DnaB
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What are the Ter proteins for the Clockwise trap?
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TerG
TerF TerB TerC |
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What are the Ter proteins for the counter-clockwise trap?
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TerE
TerD TerA |
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Why does replication have a high fidelity?
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Cells maintain balanced levels of dNTP's
Polymerase occurs in two stages, which serves as a double check PolI and PolII have proofreading Other enzymes repair residual errors. |
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What is the end of a eukaryotic chromosome called?
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Telomere
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What is the defining feature of Telomeric DNA?
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the G-rich sequence. TTAGGG in humans.
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What synthesizes Telomeric DNA?
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Telomerases
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What are the two negative consequences of DNA damage?
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Cell Death, and Mutations.
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What are four mechanisms of DNA repair?
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Direct Repair
Base Excision Repair Nucleotide Excision Repair Mismatch Repair |
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What is the function of methylation?
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To distinguish parent strands from newly synthesized strands.
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Where does methylation occur in E. coli?
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At the N6 of adenines in (5')GATC
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Which enzyme binds to mismatched base pairs?
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MutS-MutL complex.
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What binds to a hemimethylized GATC sequence?
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MutH, which cleaves the unmethylated strand to mark it for repair.
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What molecules are important to the base-excision repair pathway?
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DNA Glycosylase
AP endonuclease DNA Polymerase I DNA Ligase |
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What are the molecules important in the Nuleotide-Excision Repair mechanism?
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UvrA
UvrB UvrC DNA Polymerase I DNA Ligase |
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What are the two ways to generate diversity within organisms?
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DNA Recombination
DNA Mutation |
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Where does crossover occur in meiosis?
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Prophase I
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Where is the recombination hotspot?
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Chi sequence
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What are the proteins required for recombination?
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RecBCD,
RecA, RuvAB, RuvC |
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What is the function of RecBCD?
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To unwind DNA (when a Chi sequence is encountered)
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Which protein resolves the Holiday junction?
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RuvC
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What is the function of RecA?
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To mediate strand exchange
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What does RuvAB accomplish?
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It drives branch migration.
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Which strand is used to synthesize RNA?
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DNA Template Strand (3'->5')
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How is the DNA supercoil changed during transcription?
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RNA polymerase creates a negative supercoil before it, and a positive supercoil after it.
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What are the four stages of transcription?
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Binding of RNA polymerase to promoter sites
Initiation of polymerization Chain elongation Chain termination |
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What is the rate of RNA synthesis?
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50nt/sec
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What is the elongation enzyme?
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Core polymerase
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What is the rate of error in the Core Polymerase?
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1 in 10,000 bps.
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What are the two mechanisms in transcription?
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Rho
Specific Sequences |
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What is rho?
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It is an ATP-dependent helicase, which unwinds the DNA:RNA hybrid and releases the RNA chain.
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In eukaryotes, what is the function of RNA polymerase I?
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It transcribes rRNA
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Which polymerase transcribes mRNA in eukaryotes?
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RNA polymerase II
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What does RNA polymerase III transcribe?
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5S rRNA, tRNA, and small RNA genes.
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Which enzyme utilizes the TATA and CAAT boxes as promoters?
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RNA polymerase II
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How many promoters does RNA Polymerase I recognize?
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One
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Why do eukaryotes lack precise transcription termination sites?
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Because they undergo post-transcriptional processing that will fix any cleavage errors.
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What are the three major classes of RNA?
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mRNA (messenger)
rRNA (ribosomal) tRNA (tranlational) |
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A 5' capping (G)
Splicing The addition of a 3' PolyA tail and specific site editing are all characteristics of what? |
Posttranscriptional Processing.
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What makes mRNA resistant to 5' exonucleolytic degredation?
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The 5' G Cap
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How can the Poly(A) tail protect mRNA?
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It can protect it from degredation through PABP.
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What are exons?
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They are the protein-coding regions that must be joined by removing introns.
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What is the process of intron removal and exon joining called?
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RNA splicing.
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What are the four classes of introns?
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Group I introns
Group II introns Spliceosome introns ATP and endonuclease dependent introns |
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This intron is self-splicing, with no protein enzymes involved. Requires a guanine nucleoside or nucleotide cofactor. What class of intron am I?
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Group I
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This intron is self-splicing without the need for protein enzymes. It formes a branched lariat as an intermediate. What class of intron am I?
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Group II introns.
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I am the largest class of intron. I am found in nuclear mRNA. I require a large protein complex called spliceosome. What class of intron am I?
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Spliceosome intron.
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I am found in certain tRNA's. I require ATP and endonuclease in action. What class of intron am I?
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ATP and endonuclease dependent intron.
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What are degenerate codons?
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Codons that are decoded into the same amino acid.
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How is the nucleotide sequence read?
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Sequentially, triplet by triplet
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What are the trinucleotide sequences of tRNA?
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Anticodons
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What is the codon for initiation?
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AUG (Met)
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What are the three stop codons?
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UAA
UAG UGA |
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What are the two amino acids that are represented by only one sequence of codons?
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Met and Trp
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How do anticodons bind to mRNA?
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Through Hydrogen bonding
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What allows three tRNA molecules to simultaneously bind in close proximity to adjacent codons on mRNA?
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The narrow width (2-2.5nm)
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What must occur for accurate translation? (Two Steps)
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Correct amino acid must be attacted to a tRNA
The correct aminoacyl-tRNA must pair with a correct mRNA codon. |
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What allows the correct attachment of an amino acid to a tRNA?
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Aminoacyl-tRNA synthetase (aaRS)
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The idea that the first two codon - anticodon pairings follow Watson-Crick geometry and the third wobbles, or does not necessarily follow the pattern is called?
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The Wobble Hypothesis
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What are two characteristics of ribosomes?
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Enormous, and complex
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What are the vital functions of ribosomes?
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Binds mRNA
Has Specific binding sites for tRNA Oversees nonribosomal protein factors, and polypeptide chain initation, elongation, and termination. Catalyzes peptide bond formation Undergoes movement to translate sequential codons. |
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What is the size of the large ribosomal subunit(prokaryote)? And What does it contain?
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50S, 5S and 23S rRNA with 31 different proteins.
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What is the size of the small ribosomal subunit(prokaryote)? and what does it contain?
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30S, 16S rRNA and 21 different proteins.
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What are the sizes of the subunits of the eukaryotic ribosome?
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40S and 60S
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Which site in the ribosome houses an aa-tRNA?
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A site
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Which site in the ribosome houses a peptidyl-tRNA?
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P site
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Which site in the ribosome houses a deacylated tRNA?
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E site
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What are polysomes?
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Multiple ribosomes acting on the same mRNA molecule sequentially.
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Which protein factors are associated with initation?
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IF (Initiation Factors)
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Which protein factors are associated with elongation?
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EF (Elongation Factors)
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Which protwin factors are associated with termination?
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RF (Release Factors)
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What are the three translation stages?
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Initiation
Elongation Termination |
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What is the tRNA that initiates translation?
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Met-tRNAf (N-Formylmethionine-tRNA)
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What is the tRNA that carries internal Met residues?
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Met-tRNAm
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What is the Shine-Dalgarno sequence?
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A purine rich (G and A) tract of 3-10nt which is found before the initation codon.
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What does the mRNA's Shine-Dalgarno sequence base-pair with?
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16S rRNA
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In which step of initation does IF-3 bind to the 30S subunit?
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Step 1
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The binding of IF-2, IF-1, 2GTP, and fMet-tRNA is which step of initation?
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Step 2
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In step 2 of initation, what purpose does IF-1 in the A site serve?
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Prevents the inappropriate binding of a tRNA.
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The release of IF-1, IF-2, and IF-3 occurs in which step of initiation?
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The third step
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What are the three stages of chain elongation?
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Decoding
Transpeptidation Translocation |
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What delivers the right aa-tRNA into the empty A site in the ribosome?
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EF-Tu
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What mediates the GDP exchange by GTP?
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EF-Ts
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What is a G protein?
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Any protein that associates and hydrolyzes GTP
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What is the most abundant protein in E.coli?
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EF-Tu
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What is the proofreading for accurate tRNA selection?
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GTP hydrolysis from EF-Tu
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What is transpeptidation?
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It is the transfer of the peptidyl group on the P-site of tRNA to the A site.
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What plays a catalytical role in peptidyl transfer?
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rRNA, found in the large subunit. Called peptidyl transferase center
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What enables the ribosome to move to the next codon?
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EF-G & GTP hydrolysis
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Which codons does the protein release factor, RF-1 recognize? (in E.coli)
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UAA, and UAG
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Which codons do the protein release factor RF-2 recognize? (In E.coli)
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UAA, and UGA
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Where in the ribosome is the stop codon recognized?
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The A Site
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What causes the release of the polypeptide?
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The binding of RF-1 or RF-2 to the A site
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What causes the release of the deacylated tRNA, release factor, and mRNA from the ribosome?
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RRF, IF-3, and energy from GTP hydrolysis.
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What gene products are present in large amounts?
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Elongation factors required for protein synthesis in bacteria.
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What gene products are present in small amounts?
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Enzymes that repair DNA lesions
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What are the seven processes that affect cellular concentration of a protein?
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1) Synthesis of primary RNA transcript
2) Post transcriptional modification of mRNA 3) Messenger RNA degredation 4) Protein Synthesis 5) Posttranslational mod of proteins 6) Protein targeting and transport 7) Protein degredation |
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What are housekeeping genes?
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Genes for products that are required at all times.
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What is the term for varying expression of genes in response to molecular signals?
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Regulated gene expression
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What affects binding affinity of RNA polymerases?
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Different nucleotide sequences
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What are three proteins that regulate transcription initiation?
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Specificity Factors
Repressors Activators |
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What is the σ subunit of E. coli?
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It is a specificity factor that changes when it is subjected to heat stress
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What are operators?
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Binding sites in prokaryotic cells (near a promoter)
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What is an enhancer?
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Binding site in eukarotic cells (distant from a promoter)
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Where does gene expression controlled in prokaryotes?
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At the level of transcription
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What is an example of a negative regulatory element in E.coli?
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lac repressor
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What is an example of a positive regulatory element in E.coli?
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CRP-cAMP
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