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149 Cards in this Set
- Front
- Back
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What are disease states that involve altered trasncription
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1. Cancer
2. Inflammation 3. Obesity/Metabolism |
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What does mRNA encodes the information for
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polypeptide synthesis
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What does tRNA DO?
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reads teh mRNA during transLATION
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What is rRNA
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made of ribosomes
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Are there many additional specialized RNAs that have regulatory or catalytic activity
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YES
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RNA polmerases copy DNA
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into RNA
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How many RNA polmerases in euks
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3
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How many RNA polymeases in PROKS
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1
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THe synthesis of RNA involves what 3 stages
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initaiton, elongation, termianation
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What are 3 parts that makes the sturucture of a gene
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1. Regulatory sequence (PROMOTER)
2. Coding Sequence 3. Termination sequence |
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What items are required for RNA synthesis
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Ribonucletide triphosphates, Mg+2, and a single stranded DNA template stands, adn RNA polymerase
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How are NTP connected in RNA syntehsis
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thorough a phosphodister bond in a step wise fashion
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Are you building RNA one base at a time?
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YES
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In RNA synthesis only ONE strand codes for RNA --which is it
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DNA templates the 2nd strand--must
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THe template strand must be read in what direction
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3'-5'----making RNA in 5-3' direction
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What are 4 major subunits of RNA polymerase structure in PROKS
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alpha B,B' adn sigma70
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What consists of the RNA Holoenzyem subunit
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alpha2 BB' adn sigma 70
a2BBo70 |
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What consists of RNA core enzyme subunit
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a2BB'
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What is sigma70 do?
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recognizes promoters
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What does alpha do
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Scaffold for B subunits
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What does Beta do
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forms phosphodiester bonds
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What does Beta Prime do
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binds to DNA template
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What is the 1st step of iniation
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RNA polymerase holoenzyme binds NON-specially to DNA and "SCANs teh duplex DNA for specific sequences
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What is 1st step of iniation called the Scanning model
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b/c RNA polymerase holoenzyme binds NONspecially to DNA and STOP when it finds the PROMOTER sequence
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What happens after RNA polmerase holoenzyme binds to promoter
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STOPs, adn unwinds 17 base pairs of the duplex DNA
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Where does transcription of DNA template being
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at the promoter
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What are 2 major interation site for sigma region of RNA polyermases on the promoter for PROKS
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The 2 promoter regions sigma recognzies is -35 sequence, and -10 sequence
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What is the consensus sequence, and role it plays with promoter
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consensus is Average sequence, the closer the promoter sequence matches the consences sequence the STRONGER the promoter
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Strong pormoters match the consensus CLOSELY and can iniate transcription
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as often as every 2 secs
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Weak promoters differ in ONE or MORE consesus nucleotides, weak promoters can iniiate transcription
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once every 10 minutes
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Do different sigma subunits recognize different promoter sequences
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YES
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Can Core a2BB' enzyme iniate RNA synthesis
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NO
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What is sigma 70 subunit of the holoenzyme responsible for
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main simga factor and respsonsible for specific recognition of promoter
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Does sigma 70 subunit induce transcription of all genes necesary for normal state
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YES
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What is the sigma 32 holoenzyme responsible for
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trascribing genes during heat shock
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When is sigma 32 synthesizes
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high concentration at made at elevated temperatures
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Does sigma 32 rezognized different -35 and -10 sequences
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YES
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Transcription begins what are the 1st "early genes" transcribed
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RNA polymerase holoenzyem a2BB'o70
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So what happens when a virus "Hijacks the gene transcription machinery"
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the first genes transrcribed is a viral simga 70 subunit
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What does the viral sigma 70 subunit do
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HIJACKS the RNA polymerase to recognize VIRAL promoters
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Once the viral sigma 70 subunit binds it codes for
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another sigam subunit (33/34), which iniates a totally different set of genes
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What does Rifampicin block
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bacterial iniations---by inhibiting the 1st phosphodiester bond by RNA polymerase
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Is chain elongation affected by Rifampicin
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NO--no effect on RNA all ready in processs-only inhibit 1st phsophodiester bond formation
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Does elongation require the sigma factor
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NO--ONLY iniation
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So shortly after RNA synthesis begins what happens
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the sigma subunit FALLS of the holoenzyme complex
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RNA synthesis contiue until
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the end of the gene is reached (termination)
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What composes the "transcription bubble"
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RNA polymerase CORE enzyme, DNA, and the newly transcribed RNA
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In iniation the RNA polymerase bind to the promoter but is not UNWOUND--this is called
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the closed promoter complex
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Onces the DNA begin to unwind it forms what complex, and what phase
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Open promoter complex--DNA MUST be unwound for elongation to occur
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Is the open promoter complex the first step in the transcription of a gene
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YES
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How does Antibiotic Actinomycin work
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inserts or INTERCALATES between double stranded DNA
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What doe Actinomycin Block,
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RNA polymerase elongation,
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What does Actinomycin do at low concentrations
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at low concentration specifically inhibits RNA sysnthesis with NO effect on DNA or protein syntheisi
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How does newly RNA exit?
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through a pore in RNA polymeraseq
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The end of a gene contains a "stop signal" this constists of
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a palindromic region
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Palindromic regions forms
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a stable hairpin stem loop structure
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This RNA hairpin cannot fit through the channel so
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RNA polymerase pauses, adn the DNA/RNA hybrid melts, and RNA polymerase is relased, and DNA strands reannel
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Once the RNA is relseased can transcription ever continue again
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NO--CANNOT JUMP BACK ON
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Is Euks trasncription is much more complex it contains 3 polymereases
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YES
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What is major Euk promoter and is analgous to in prok
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TATA box (-25), similar to Pribnow box
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What are 2 other major regions
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-40 to -100 contain GC box, and CAAT box
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Consitutive genes (genes that are always turned on vs regulated genes tend to have
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GC elelemtns
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In Euks can RNA polymerase initate by itself
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NO--several factors help get things started
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RNA polymerase cannot binds by itself--what factors provide a docking site for RNA polymerase II on RNA
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TFIIA, TFIIB, TFIID, TFIIE
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Where does transcription factors TFIIA,B,D,E help RNA polyermase II bind to
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TATA box
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What helps RNA polymerase II bind to GC box
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SPI protein
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What helps RNA polymerase II bind to CAAT box
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CFT binds
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General trasncription factors are involved at
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inination of all genes
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Where does transcription occur in PROKS
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have no NUCLEUS--so transcription and translation OCCUR in same compartment
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Where does transcription occur in EUKS
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have a nuclues--so transcription occur in NUClues, and translation occurs outside nuclues
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What are 4 major unique to prokarytic transcription
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No nuclear compartment, RNA polyerase has access to all promoters, RNA holoenzyme can indenpently iniation transcription and regualtory elements are small and simple
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What are 4 major unique to EUK transcription
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EUKS have a nuclear compartment, RNA polmerase have to small number of promoters, and Holoenzyme cannot iniate transcription at high level, and high regulation
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In EUKS vs PROKS which ground state is more on than off
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PROKS--ON MORE--more acces to promotes
EUKS OFF more--less access to promoters |
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Regulation of iniation involves what 3 types of proteins
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1. Specificiy factors,
2. Activators 3. Repressors |
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What are specificy factors in proks vs euks
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1. Proks--sigma factors
2. EUKS-general trasncription factors ie(TFIID) |
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What are activators, and what in euks
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increase affinity for a site, in euks called inducible transcription factors
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What are Repressors in proks vs euks
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Proks-factors that block access to promoter
Euks-regulate chromatin sturcutre |
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What do operons allow for
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coordinated regulation of genes
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What are 3 genes of the lac operon
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B-galactosidase,Galactose Permeases, adn Transacetylase
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Is polycystronic (contain information for ONE type of protein) mRNA unquie to proks
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YES
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Can E. coli use lactose as a sole energy source
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YES
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The genes required to utilize lactose are regulated at the level at the level of
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transcription
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How is lactose broken down
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Lacotse is allowed in cell by Glalactose permease, then its cleaved by B-galactosidase to form Galatose and Glucose
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What does B-glalctosidase need to function
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acetyl group, from tranacetylase
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Transcriptions requires energy, so to conserve enegy is lac operon REPRESSED in absense of lactose
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YES
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What is LAC I gene code for, and location
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codes for repressor protein, upsteam with its own separate promoter and NOT in operon gene set
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Once the LAC I gene is transcribed what happens
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it produces the lac repressor protein which binds to the operator and PREVENTS RNA POLYMERASE FROM TRANSCRIBING LAC GENES
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What does lactose act as
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an inducer
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A inducer is a metabolic substrate that is recognized by what
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regulatory protein, adn a metabolic enzyme
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How does lactose act as an inducer?
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When lactose is present, some it converted to the isomer allolactose, which bind to the lac repressor changing its shape so it falls off
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The repressor protein is a tetrameric proteins, each subunit binds
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an allolactose
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In the absence of the inducer, alpha helicies are extened which interact with
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the major groove of the DNA, and the DNA loops around tetramer
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There are 3 operators in Lac operon, how many does the tetramer bind to
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2 operators at once
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How many allolactose molecules are necessary to release the repressor from the complex
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2
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Can changes in lactose concentrations cause massive changes in affinty
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YES
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Is the lac operona promotoer deficient for a binding a sigma factor, and which
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EITHER -10 or -35
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How can RNA polyermase bind to promoter is LAC operon
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other proteins bind to DNA, and help sigma factor bind
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What do protein-protein ineractions provide synergy to
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increase the binding affinity of RNA polyermase to promoter of lac operon
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Is Glucose is E.colis favortie energy chocie
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YES
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What is Catabolite repression
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Glucose is the perferred energy source, so even it lactose is present, operon is turn off, b/c of presence of glucose--its used 1st
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What is basal trasncription defined as
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transcription that occurs without activiation or AN INDUCER
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How many permease channels are found under basal trasncripion, vs activated or induced
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2-5-
activated 100s or 1000s |
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Does Basal expressesion seen in both pros and euks underscore the dynamic, and how does it occur in lac operon
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YES
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Basal transcription--means that a LOW level of transcription is alwasy occuring so a few lactose is always being transcribed, why is this?
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the ressport do not JUST BIND and STAY....that are always binding and unbindnig
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How do transcription factor proteins recognize specific DNA sequences
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recognize feautures of the DNA--such as major groove
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What are features of major groove
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hydrogen bonding acceptros, and donor groups
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Does teh protein alpha hlexi fit perfectly into major groove of DNA
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YES
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Can transcription factors synergistically bind with each other
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YES
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What is an example of a minor groove binding protein
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TATAA Binding protein
(TBP) |
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TBP is one of the 1st factors to bind
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to bind to euk promoter during iniation
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What does TATTA Binding protein do to the DNA, and importance
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causes the DNA to bend, makes it a functional transcription machine
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IS DNA an active particpant in transcription
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YES
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Not all transcription factors use an alpha helix to bind to DNA, what is an example
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NF-KB--interactions with DNA through Beta sheet
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EUK DNA is packaged into
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Chromatin
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What is open chromatin
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DNA is wrapped twice around a complex of 8 histones called a nucleosome
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The 1st level is nucleosome, what is the 2nd level
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nucleosomes are wrapped into 3nm FIBER
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The 2nd level in 3nm fiber, what it be further wrapped to to make
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CLOSED chromatin--PREVENTS transcription
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What type of chromatin does transcription occur
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OPEN chromatin
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Constittively expressed "housekeepign genes have what type of chromatin
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open chromatin--always on--so always being transcribed
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When is ALL DNA ACCESSBILE
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during CELL division "DNA is naked"
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What are 3 classes of proteins involved in Transcriptional activation in EUKS
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1. General Basal Trancription Factors
2. Enhancers 3. Coactivator proteins |
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General basal trasncription factors are required at EVERY
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RNA polymerase II promoter
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Can Trancription factos also bind to enchancers to falcilatre transcription, and they are similar to what is proks
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YES, euk version of operators
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The enhancers can be very far away from the promoter, but still help RNA pol II bind more efficently, how
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DNA can loop to bring components together
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What does coactivator proteins do
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act as intermediateries between the DNA binding transactivators and the RNA polyermase complex
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Do coactivtors BIND
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NO--they interact with trasnscription factors through special activation domains
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What does iniation do to chromatin
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causes remodeling
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The core histone are rich in what, and how removed for iniation
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lysine residues--acetlayed
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Does transcription 1st require the remodeling of nucleosome to allow acces to promoter
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YES
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What do TBP and general transcription factors bind to
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CORE promoter
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What can transcription factors be regulated by
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extracellular signals
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What are 3 types of extracellular singals that ACTIVATE transcription factors
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1. ligand activation
2. phosphorlation 3. release from an inhibiotry complex |
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What is an example of ligand activation
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transcription factor can be activated by steriod hormones which pass directly through cell membrane
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Do we have hundreds of genes by just a few biding sites
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YES
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The making of a protein can be divided into 7 processes
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1. Transcription
2. mRNA processing 3. mRNA degrations 4. Translation 5. Post translation modifications 6. Protein degrations 7. protein targeting |
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Immediately after transcription, mRNA is process what happens 1st
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5' cap added to 5' end
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What is importance of 5' cap and poly A tail
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mRNA transport, stability and translational efficieny
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What is 2nd part of mRNA processing
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3' Poly A tail is added
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Are the poly A tails encoede by the GENE
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NO, added by a complex of protiens
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Since mRNA gets translated in cytoplasm, it has to get transported there, how is it transported
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by 5' CAP
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mRNA is a BIG deal, the more stable the mRNA, the more times
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it can be translated into a protein
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Can proteins be both regulated at the level of transcription, and at the level of mRNA stability
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YES
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Must a rbisome bind to the mRNA at the right place to start translation
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YES
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What is role of 5' cap with ribosomes
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the presence of the 5' cap increases the affinity of the ribosome for the binding to the right SPOT on mRNA
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After the 5' cap, and poly A tail is added its transported into cytoplams, and what happens
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INTERVENTING introns are removed by splicing, and EXONS are joined together
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What are spliceosome made of
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6 different snRNPS as U1-U6
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What is ATP required for in splicing
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ONLY the assembly of spliceomse, but NOT for cleavage or ligation
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What does alternative splicing increase
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the number of gene products
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DO proks have introns or 5' caps or tail
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NO!!!!
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