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MMBIO Quiz 8
| Term | Definition |
|---|---|
| transcription | making RNA using the DNA template (antisense) strand |
| RNA synthesis uses | ATP, CTP, GTP, UTP |
| unlike DNA polymerase, RNA polymerase does not require a | primer |
| the newly synthesized RNA strand is the same as | the DNA coding (sense) strand but with U as a substitute for T |
| 3 steps of transcription | initiation elongation termination |
| initiation (prokaryotic) | brings in necessary proteins to the appropriate locations adds first nucleotides in place |
| elongation (prokaryotic) | adding onto the chain in the 5' to the 3' direction |
| termination (prokaryotic) | stops polymerization and detaches proteins from the DNA |
| -35 +10 | 35 bp upstream of promoter 10 bp downstream of promoter |
| promoter | start site tells RNA polymerase where to bind and start transcription |
| prokaryotic promoter | TTGACA at -35 TATA/Pribnow box at -10 start point at 6-9 bp |
| initiation steps | polymerase binds to promoter in duplex DNA "closed complex" polymerase melts duplex DNA near start site, forming a transcription bubble "open complex" RNA polymerase catalyzes phosphodiester linkage of two rNTPs |
| core enzyme | main part of an enzyme sticks to DNA initially, doesn't have an exact place where to start 5 subunits |
| holoenzyme | core enzyme + sigma factor directs enzyme on where to start, binds to specific gene promoters 6 subunits |
| core enzymes can synthesize RNA but holoenzymes | does it correctly |
| contact-binding-melting | RNA polymerase contacts at -35 sequence closed complex forms over promoter region melting at -10 opens complex starts transcribing at +1 |
| why does bacteria store transcription enzymes on DNA? (eukaryotes can't do this) | so they can react to environmental conditions faster by transcribing new sets of genes quickly |
| termination rho-dependent | rho protein binds at rut site and slides until it hits RNA polymerase, resulting in a signal to stop |
| termination rho-independent | RNAs base pair within the same strand, forming a hairpin (inverted repeat) all the G-C pairing rub polymerase the wrong way and transcription ends |
| for rho-dependent and independent termination the DNA sequences does not stop it, | the RNA itself does |
| inducible gene expression | a gene is normally inactive (not transcribed) but the can be activated ex: lac operon |
| repressible | gene is normally active (transcribed) but can be de-activated ex: trp operon |
| constitutive | gene is always transcribed no matter the conditions |
| operon | a group of coding regions in DNA that is under the control of a single promoter/operator only in prokaryotes! |
| promoter | DNA sequence where RNA polymerase binds to start transcription |
| operator | regulatory DNA sequence located near/overlapping promoter where repressor proteins binds - ON/OFF switch |
| lac operon | enables cells to import lactose into cell and use it for as energy |
| default state of lac operon | inactive for transcription (don't want to waste expression if there is not even lactose present) |
| the lac operon is activated for transcription by an ______ which binds to the repressor and removes the roadblock | inducer |
| positive regulator | gene is inactive, unless something activates it ex: lac operon |
| negative regulator | gene is active normally, unless a repressor binds to inactivate it ex: trp operon |
| open reading frame (ORF) | DNA or RNA sequence with a start and a stop codon |
| monocistronic gene | contains one ORF - one protein (typical in eukaryotes) |
| polycistronic gene | multiple ORFs - codes for multiple proteins (typical in prokaryotes) |
| B-galactosidase (lac Z) | converts lactose into galactose and glucose |
| permease (lac Y) | membrane transport protein that allows lactose into a cell |
| transcetylase (lac A) | transfers acetyl coA to lactose (non-essential) |
| repressor (lacl) | keeps lac operon off (default) |
| allotactose - inducer | binds to repressor and changes its shape so it is unable to bind to the promoter/operator |
| B-gal also converts glucose into | allolactose |
| mRNAs have a short lifespan and are often | degraded before transcription has even terminated so the first ORF is translated more efficiently |
| low glucose upregulates | lac operon (because now lactose is needed) |
| high cAMP singals | cell starvation recruits RNA polymerase to bind to many promoters, increases transcription activates transcription of lac operon |
| cAMP binds to | CAP site |
| lac operon activity very low (-) | lactose absent, glucose abundant, no reason to express lac operon |
| lac operon activity low (+) | starvation mode cAMP helps to get a little expression as repressor breathes on and off |
| lac operon activity middle (+) (+) | prefers to use glucose |
| lac operon activity high (+)(+)(+) | high lactose present, cAMP indicates no glucose uses lactose as primary energy source |
| trypotphan (trp) | essential amino acid, needed for all proteins |
| trp operon | encodes proteins needed to produce trp |
| trp is usually required and ususally not in abundance so the trp operon is | turned ON and is considered repressible |
| how to turn trp operon ON/OFF | when there is plenty of trp present, trp binds to the repressor and changes its shape allowing it to bind to the promoter/operator transcription is blocked completely |
| another way to turn the trp operon ON/OFF - fine tuning | intermediate levels - not completely on or off rate of ribosome movement and attenuator sequences |
| secondary sequences/hairpins | complementary RNA sequences can base pair to make a double-stranded RNA hairpin |
| trp attenuator sequence | part of the trpL (leader) has regions 1, 2, 3, and 4 that like to pair up together |
| 2:3 hairpin | less H bonding (less G and Cs) weaker, less stable CONTINUED transcription - RNA polymerase keeps going |
| 3:4 hairpin | more H bonding (rich in G and Cs) stable, stronger STOPS transcription - RNA polymerase stops/falls off |
| when trp levels are low, RNA pol stalls and waits for trp and ____ hairpin forms | 2:3 hairpin transcription is continued, makes more trp low levels of trp = more trp made |
| when trp levels are high, the RNA pol does not need to wait and can get all the way to the ____ hairpin | 3:4 hairpin transcription is stopped trp levels are high = trp operon is turned off |
| order of the trp operon (draw it) | promoter (trp P) operator (trp O) leader (trpL) - contains attenuator sequence (1234) trpE, trpD, trpC, trpB, trpA |
| ribosomes move _____ when trp levels are high | fast get all the way to 3:4 and STOP |
| ribsomes move _____ when trp levels are low | slow wait for trp, 2:3, can continue, senses need for trp |
Created by:
anyasalmon