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116 Cards in this Set
- Front
- Back
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What proteins are left behind at promoter escape?
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TBP, TFIIA & B
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Which step of transcription is ATP-dependent in Eukaryotes?
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Formation of the open complex, which initiates transcription
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What are the 6 Transcription Factors in order of appearance?
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TFII..(A),B,F,E,H
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Which Eukaryotic subunit may be bacteria related?
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220-kD Pol II subunit
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(YSPTSPS)n"
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"S and T
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What is the main difference between simple and complex eukaryotic transcription?
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Enhancers work in both orientations
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What does UAS stand for?
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Upstream Activator Sequence
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Who discovered the basic protein complex packaging chromosomal DNA?
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Roger Kornberg discovered the nucleosome
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Name four important differences between Euks and Pros in transcription
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"Processing*
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What occurs under very high [Y]?
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"Trp (Y) repression is active, no Trp is manufactured, and attenuation is irrelevant.
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Under what conditions is the Trp Attenuator active?
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"Under high [Y]
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What is the Attenuator?
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2ndary structure involving Regions 3+4, which kicks RNA Pol outta there!
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How does [Y] affect Trp Operon?
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"As [Y] (tryptophan) increases, the RATE of transcription increases.
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Trp repressor is active under what condition?
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"Bound to TWO Trp molecules.
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(Regulation states)"
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"CRP Active (activator)
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(positive / negative)"
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"Positive regulation
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Describe repressor function
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Molecular signal causes dissociation of repressor allowing RNA Pol to bind promoter
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Transcription is initiated by which complex?
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"Open complex
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How does histone acetylation affect nucleosome packing?
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Histone acetylation unpacks nucleosomes
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Where is the eukaryotic TATA?
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-30 bp
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TFIIH
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"contains ATP-dep DNA helicase that hydrolyzes ATP and unwinds DNA
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TAF
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binds the initiator in the core
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What is TFIID?
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"First transcription factor to bind to the core promoter
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Trp Operon
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Need slide (work on it!)
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What five conditions are met if Lac operon is "ON"?
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"Glu -
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How do different σ's work?
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Recognize different -10 or -35 regions.
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What distinguishes the elongation complex from the ternary complex?
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σ is gone
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Why are binary, ternary complexes named that way?
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"Molecule types:
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Tunicamycin inhibits what?
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"Glycosylation
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What is RNA Pol I responsible for?
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rRNA
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What two things are needed for RNA transport to the cytosol?
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Cap and Tail
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Which compound affects both prok and euk RNA pol?
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Actinomycin D
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Which RNA type is associated with lariat formation?
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snRNA
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What might occur at a stem-loop/poly U structure?
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Synthesis may terminate
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What is the function of ubiquitin in the Eukaryote?
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Targets errant RNA for destruction, GDP replaced by ubiquitin.
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Site-specific recombination occurs in which immunological cells
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B lymphocytes
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How does replicative differ from direct transposition
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The donor loses the transposon in direct transposition
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What is one common function of transposons (jumping genes)?
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Antibiotic resistance
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Barbara McClintock discovered what in the 1950's?
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Transposons
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Site-specific recombination occurs where?
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"Specific base sequences
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RecBCD recognizes __ sites
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Chi sites
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Under what conditions are nucleotides added randomly (nonsense DNA)?
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Double-strand break
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When CH3 groups are removed in DNA repair, what species is ultimately released?
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Formaldehyde
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List the steps of BER (enzymes)
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"Glycosylase
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BER begins with what enzyme?
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DNA glycosylase
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Which Pol repairs the nick?
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Pol III
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In DNA repair, changes are never made to bases which are
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"Methylated
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Why is DNA methylated?
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"Self-recognition
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What is a kink?
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Spatial change between bases within a single strand
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Which mutation type can lead to premature termination?
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"Frameshift
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An amino acid change may result from what type of change?
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Missense
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If a mutation does nothing, what is it called?
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Silent mutation
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Nonsense mutations code what?
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Stop!
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What must occur for a mutation to pass on?
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"DNA replication
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What is the usual outcome of mutagenic sequence changes?
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Repair
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How many copies come out of PCR?
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"2^n*y where y is the original number of strands and n is the number of cycles
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How is DNA sequencing suddenly stopped in vitro?
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dideoxynucleotides (dNTPs)
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Cipro works through what mechanism
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Interferes with DNA gyrase
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What stabilizes the lagging strand?
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"SSBs
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DNA gyrase is aka
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DNA topoisomerase II
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Helicase does what?
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Unwinds the DNA
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What does Primase do?
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Synthesizes short RNA primers to initiate DNA replication on the lagging strand
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Why does Bill O'Reilly hate DNA Replication?
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"It's only semi-conservative
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How can hybridization tell us about currently expressed proteins?
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"Proteins need and mRNA, which has a polyA tail. This can hybridize with polyU or polydT.
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What nucleotide kicks off splicing?
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"Adenylate
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What two things do spliceosomes produce?
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"RNA lariat (intron)
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The functions of the polyA particle complex
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Recognizes consensus sequences on unprocessed mRNA
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Function of the Cap synthesizing complex
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Recognizes 5' triphosphate
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Describe the enzyme activity of the snRNA particles of the spliceosome
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Endonuclease
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Name two enzymes that act on the Poly-A Tail
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"Endonuclease
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Name three enzymes of cap synthesizing complex
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"Phosphohydrolase
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Which type of RNA is missing from Prokaryotes and why?
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snRNA because no introns are present
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List the four main RNA types in order of abundance
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rRNA > tRNA > mRNA > snRNA
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Which regions of mRNA are expressed?
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Exons
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A __ is a section of DNA that codes a protein
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Gene
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Affects eukaryotic transcription only
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"α-Amanitin
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binds the active site of bacterial RNA pol only
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Rifampicin
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binds to certain GpC sequences in DNA preventing open transcription complex formation
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"Actinomycin D
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Prok. differs from Euk mRNA in what three ways?
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"No introns
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Euk. transcription is more complex in what three ways?
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"Different RNAs, different Pols
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How does ρ work?
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Binds CA-rich terminator RNA sequences.
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What is the immediate result of promoter function?
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Separation of the DNA strands.
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Why is TATA not transcribed?
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Holoenzyme opens up the bubble downstream.
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What metal ion is necessary for RNA Pol catalysis?
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Mg
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What is the function of σ?
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"Searchin'..
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What are the functions of the four components of the RNA Pol core enzyme?
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"α - assembly
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What does the DNA-dep. RNA Polymerase require?
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"Core enzyme
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RNA is involved with which 2 processes?
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"Transcription
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DNA is involved with which 2 processes?
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"Replication
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The 2' OH group confers what important property on RNA?
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Alkali Labile
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(Hint: Presence/absence of certain sugars and the states of operators...)"
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"Glu -, Lac +
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The Lac Operon represents what type of regulation?
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Catabolite Repression
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Describe the structure of the inactive Lac Operon
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"Loop, which acts as an RNA-Pol block
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What lactose metabolite has a regulatory effect?
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Allolactose is an inducer
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What 3 genes are on Lac Operon?
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"Y, Z & A
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What three mechanisms regulate σ?
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"Rates of synth., degrad.
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(Think about survival on the Serengheti)"
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"Movement!
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What is the purpose of the σ cycle?
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Allows Pol to switch σ's
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What does σ32 regulate?
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"Heat shock" genes
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What does it regulate?"
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"σ70
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How does Ternary complex become Elongation complex?
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"σ is released
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The RNA Pol apoenzyme consists of how many pieces?
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"Five:
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Regulation of protein synthesis can occur at any of which three concerted steps?
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"Transcription
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What three molecules does the Ternary Complex include?
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"DNA
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(aka complexes)"
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"Closed
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(Hint: Not Ca, Hg, Y, Sn, etc.)"
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Core promoter element
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What is a protein-coding region of a gene called?
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Transcribed Region
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What binds the Promoter?
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RNA Polymerase
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What does UTR stand for?
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"Utah's NPR station
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What two things may be encoded by a gene?
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"Protein
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Eukaryotic packaging is accomplished through what protein?
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"Chromatin
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Protein mediated regulation can either __ or __ gene expression
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Activate or Repress
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You wish you could, right?"
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UGA, UGG, UAG
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Lys?
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AAA
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Phe?
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UUU
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Met/Start?
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AUG
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