Term
| What determines a cell's phenotype? What controls this? |
|
Definition
| The abundance of sets of proteins, controlled by RNA synthesis |
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Term
| What stable RNA's represent 95-98% of all RNA in the cell? |
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Definition
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Term
| What percentage of RNA in the cell are mRNA's? |
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Definition
|
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Term
| What are some characteristics of mRNA? |
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Definition
Short half-life
More complex organisms have more types
Not all mRNA's are expressed at a given time |
|
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Term
| What catalyzes RNA synthesis? |
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Definition
| DNA-dependent RNA polymerase |
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Term
| Compare and contrast RNA synthesis and DNA synthesis |
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Definition
Same: new nucleosides added to 3'OH
addition is 5' -> 3'
template-dependent
energy supplied by cleaving high E bond of NTP
Different:
ribonucleosides instead of deoxyribonucleoside
No primer required to initiate synthesis |
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Term
| How many times more types of mRNA's do humans have than bacteria? |
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Definition
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Term
| What must e. coli polymerase be associated with in order to bind with the DNA template? What does this helper do? |
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Definition
sigma factor, which binds with polymerase and DNA promoter sequences. It also helps
to separate two strands and insert coding strand into the active site of polymerase |
|
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Term
| Where are the promoter regions in e. coli indicating binding for sigma? Where does RNA polymerase bind? |
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Definition
Promoter regions at -35 and -10
RNA pol binds somewhere from about -50 to about - 20 through interactions not depending on sequence |
|
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Term
| When is sigma released from RNA pol in e. coli transcription? |
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Definition
| after a few tens of bp are transcribed |
|
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Term
| What is the optimal promoter sequence at -35 on the nontemplate strand for e. coli RNA pol? |
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Definition
|
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Term
| What is the optimal promoter sequence for signma at -10 on the nontemplate strand in e. coli RNA transcription? |
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Definition
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Term
| What controls the transcription of the lac operon under different conditions |
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Definition
CAP/CRP (Different names for same thing - catabolite activator protein/catabolite receptor protein)
Lac repressor |
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Term
| Where does the lac repressor bind? |
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Definition
|
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Term
| How does the lac repressor inhibit transcription? |
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Definition
| It partially blocks the transcription start site, blocking binding and transcription initiation by RNA polymerase |
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Term
| What causes dissociation of lac repressor? |
|
Definition
| Presence of lactose, which binds to and changes conformation of lac repressor, causing it to fall of |
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Term
| Can the lac operon be transcribed in the presence of lactose? |
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Definition
| Yes, but this only occurs in small amounts until glucose is depleted because the rate of transcription initiation is slow |
|
|
Term
| Why is transcription initiation of lac operon low when glucose is around? |
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Definition
| The promoter sequences at -35 and -10 vary from the optimal ones for sigma binding |
|
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Term
| How is transcription initiation enhanced when lactose is present and glucose is depleted? |
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Definition
| Cyclic AMP binds to CAP, forming a CAMP-CAP complex that binds to transcription control region and interacts with the polymerase bound to the promoter |
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Term
| About how many bp are in the transcription control region of the lac operon? |
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Definition
|
|
Term
| What is the function of the lac operator? |
|
Definition
|
|
Term
| What is the function of the lac promoter? |
|
Definition
|
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Term
|
Definition
| The region that binds cap |
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Term
| What is the first of the three genes in the lac operon? |
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Definition
|
|
Term
| What is the quaternary structure of lac repressor? |
|
Definition
| A dimer of dimers; each dimer binds to one operator |
|
|
Term
| How many lac repressor tetramers are there per e. coli cell? |
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Definition
|
|
Term
| What is a transcriptional unit? |
|
Definition
| The region of DNA that is copied onto a single RNA by RNA polymerase |
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|
Term
| What halts transcription in eukaryotes? |
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Definition
| A site downstream of the termination sequence |
|
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Term
| Where does RNA polymerase bind in prok? |
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Definition
|
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Term
| How many RNA polymerases do prok have? |
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Definition
| One that transcribes all genes |
|
|
Term
| What two factors determine the abundance of a given mRNA? |
|
Definition
Rate of transcription initiation
STability of mRNA |
|
|
Term
| What may join the polymerase complex after sigma is released in prok. transcr.? |
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Definition
|
|
Term
| What is the transcription termination single? |
|
Definition
| The cite that causes RNA pol to cease transcr. in prok. |
|
|
Term
| What form rho-independent termination signals? |
|
Definition
| A hairpin loop (from mirror sequences) followed by a string of A nucleotides in mirror strand |
|
|
Term
| What five factors can regulate gene expression in prok. cells? |
|
Definition
Gene copy number
transcr. initiation
mRNA stability
translation initiation
protein stability |
|
|
Term
| What does it mean that transcription of bacterial operons is polycistronic? |
|
Definition
| one continous mRNA strand spans several structural genes |
|
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Term
| What allows polycistronic mRNA's to be translated into several different proteins? |
|
Definition
| Prok. ribosomes can bind to internal SHine-Dalgarno sites |
|
|
Term
| Why is it imp. that transcr. of prok. operons is polycistronic? |
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Definition
| Allows for making equal amounts of related proteins |
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|
Term
| What's another name for the lac repressor? |
|
Definition
|
|
Term
| What's another name for the lac operon? |
|
Definition
|
|
Term
| How does an inducible repressor work? |
|
Definition
| A repressor is bound until an inducer molecule nbinds to it to repress it |
|
|
Term
| How does an inducible repressor work? |
|
Definition
| The repressor is not bound until a corepresor binds with it. A functional repressor is produced which turns off transcription |
|
|
Term
| What type of operons require an activactor protein? |
|
Definition
|
|
Term
| What is an inducible activator protein? |
|
Definition
| No transcription until coactivator binds to apoactivator, making functional complex. EX: CAP activated by binding to cAMP |
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Term
| What operon uses repressible repressor? |
|
Definition
|
|
Term
| What operons uses inducible activators? |
|
Definition
|
|
Term
| What is a repressible activator |
|
Definition
| One that is always on unless there is an inhibitor |
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|
Term
| WHat is lactose composed of? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
B-galactosidase, which cleaves lactose into glucose and galactose
Can also convert lactose to allolactose, the true inducer |
|
|
Term
|
Definition
| permease, which allows lactose to be taken into cell |
|
|
Term
|
Definition
| transacetylase, which detoxifies lactose metabolities |
|
|
Term
|
Definition
| the sequence of use of carbon sources, such as with e. coli using glucose, then lactose. Cells grow and divide until glucose used up. There is a period of no net growth while lac genes transcribed, then a period of growth as lactose is used |
|
|
Term
| WHat happens when a sugar other than lactose is available to e. coli? |
|
Definition
| repressor and CRP both bound! |
|
|
Term
| What determines the level of cAMP in catabolite activation in eukaryotes? |
|
Definition
| adenylate cyclase (ATP -> cAMP) |
|
|
Term
| What determines adenylate cyclase activity indirectly in prok? |
|
Definition
|
|
Term
| What is directly resp. for adenylate cycl. activity in prok? |
|
Definition
a protein called P-IIIglc in the PEP phosphotransferase system activates adenylate cyclase.
low gluc = high P-IIIglc = high cAMP => active adenylate cyclase
high gluc = low P-IIIglc = lowCAMP -> adenylate cyclase inactive |
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|
Term
| Where doe the CAP-cAMP complex bind in lacP |
|
Definition
|
|
Term
| What does CAP-cAMP binding stimulate? |
|
Definition
| Helix unwinding downstream and binding of RNA pol |
|
|
Term
| What are housekeeping genes? |
|
Definition
| Genes required for maintenance of basal cell function |
|
|
Term
| What are tissue-specific genes? |
|
Definition
Tissues important to different cell types;
Can be regulators of transcription or effectors changing physiological properties of cells |
|
|
Term
| What is req for bio synth of ile and val in prok? |
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Definition
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|
Term
| Are euk genes polycistronic or monocistronic? |
|
Definition
|
|
Term
| What are the main post-transcriptional modifications of euk mRNA? |
|
Definition
methyl cap (set of modified G residues) at 5'
poly A tail (about 100-200 A nucleotides) at 3' |
|
|
Term
| What are the six control points of euk gene expression? |
|
Definition
transcriptional control
RNA processsing
nucear trnasport
rate of translation initiation
mRNA turnover
protein stability |
|
|
Term
| How many RNA pol do euk have? |
|
Definition
|
|
Term
| What does RNA pol I trans? |
|
Definition
| only one gene: precursor for large rRNA |
|
|
Term
| Which transcripts are polyadenylated? |
|
Definition
| only RNA pol II transcripts |
|
|
Term
| What does RNA pol II transcribe? |
|
Definition
| all mRNA's, some snRNA's (miRNA and siRNA) and pre-micro RNA;s |
|
|
Term
| What does pol III transcribe? |
|
Definition
| small genes like tRNAs, U6 snRNA, 5SrRNA |
|
|
Term
| Which is a constant in euk: gene transcr initiation or elongation |
|
Definition
|
|
Term
| What are the steps of euk transc? |
|
Definition
1. RNA pol begins transc at promoters
2. Long transcr unit (about 7000 bp) formed
3. Cap structure added to 5' end
4. primary transcript cleaved and 3' formed
5. polyadenylic acid added to 3' end, introns spliced out and parts ligated
6. processed |
|
|
Term
| How is transc. initiation reg in euk? |
|
Definition
| long control regions of promoters and enhancers and a complex of general and specific transcription factors |
|
|
Term
| What are the three important qualities of euk. enhancers? |
|
Definition
1. They work far from promoter
2. They can be upsream or downstream
3. Can work in forward or reverse orientation |
|
|
Term
| What do eukaryotic gene transc control regions consist of? |
|
Definition
1. Core promoter elements (such as TATAA, or INR at -1 or CpG at -100) determine where transcription is initiated
2. Simple regulatory sequences (CAAT and GC) called "promoter proximal elements) that stimulate or repress transc
3. Complex reg elements called enhancers that stim transc init; work independent of dist or orientation |
|
|
Term
| How can control regions be identified? |
|
Definition
| using reporter eners such s lac Z and luciferase |
|
|
Term
| What is an example of a control region? |
|
Definition
Enhancers at -50 to -1000
GC and CAAT at about -50
TATAA at about -25
Inr at +1 (3' -> 5')
Open reading frame |
|
|
Term
| How many TFII proteins are humans thought to have? |
|
Definition
|
|
Term
| What is the first step of euk transc? |
|
Definition
TFIID binds to TATA box
TFIID is a complex of TP (TATA-binding protein) and several associated proteins (TAFs) |
|
|
Term
| What are the second and third steps in euk DNA transc? |
|
Definition
| TFIIB binds and recruits RNA pol II + TFIF after TFIID bind to promoter |
|
|
Term
|
Definition
|
|
Term
| What are the fourth and fifth steps in euk DNA transc? |
|
Definition
TFIIE and TFIIH required for transcr initiation.
Phosph causes RNA pol to be released and begin elong |
|
|
Term
| Which factor is not released when RNA pol leaves initation complex? |
|
Definition
|
|
Term
| What are the two enzymatic activites of TFIIH? |
|
Definition
Helicase activity
Kinase activity (catalyzes phophor of C term of RNA pol) |
|
|
Term
| What are the two enzymatic activites of TFIIH? |
|
Definition
Helicase activity
Kinase activity (catalyzes phophor of C term of RNA pol) |
|
|
Term
What are trans-activators?
How many types are there in humans? |
|
Definition
Regulator proteins that enhance transc rate by binding to enhancers and recruiting components of basal apparatus
about 1400 of them in humans |
|
|
Term
| What are the three types of domains of transactivators? |
|
Definition
DNA binding domains - allow for binding to certain region of DNA
Activation domain - contact components of balasal app
Dimerization domains - mediate interactions with other protein regulators |
|
|
Term
| What is a helix-turn-helix DNA binding domain? |
|
Definition
One helix of protein makes contact iwht major groove - recog helix
Other sits on rec helix |
|
|
Term
| What are zinc finger proteins? |
|
Definition
| Fingerlike projections are formed (because of zn atom coordinates) that have alpha helix and b pleated sheet sides. Basic residues make contact with major groove. Ex: Sp1 and TFIIIA |
|
|
Term
| What are dimerization domains? |
|
Definition
Allow like or different proteins to form complexes that can interact well with DNA target or not at al
EX: leucine zipper: hydrophobic residues on one face of alpha helix interact
basic helix loop helix - put charge interaction along DNA to bind |
|
|
Term
| What are ligand binding domains? |
|
Definition
LATF - bind small molecule that can change func of activ
EX: retinoic acid rec
steroid hormone rec
Vit D rec |
|
|
Term
| What are examples of trans-act domains? |
|
Definition
Acid blobs - allow recruitment of trans factors to promoter
Gln or pro rich domains |
|
|
Term
|
Definition
1. competing with transact for binding
2. masking acid blob (like gal80)
3. blocking interaction with general aparatus
4. formin a nonbinding heterodimer |
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