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97 Cards in this Set
- Front
- Back
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What are two important factors about eukaryotic cells that allow them to tightly control which genes are transcribed?
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increased complexity of transcriptional machinery processing of mRNA precursors in the nucleus prior to translation |
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What are four examples of increased complexity of transcriptional machinery?
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multiple polymerases transcription factors extracellular signaling chromatin remodeling |
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What are two examples of processing mRNA precursors undergo in the nucleus prior to translation?
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end modification splicing |
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Where does transcription occur?
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nucleus
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What is growing protein called? |
nascent protein
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Why must mRNA be processed? |
it moves to cytoplasm with nucleases
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Why does each of the three polymerases transcribe specific DNA?
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each recognizes its own promoter
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What does RNA polymerase I transcribe? |
rRNA in the nucleolus
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What does RNA polymerase II transcribe? |
mRNA precursors
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What does RNA polymerase III transcribe? |
tRNA and 5S rRNA
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What do most promoters recognized by RNA polymerase II have? |
TATA box
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What do some promoters recognized by RNA polymerase II have? |
CAAT or GC box
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What follows the TATA box? |
initiator element (Inr) at the transcriptional start site
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What may promoters without a TATA box have?
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downstream core promoter element (DPE) from +28 to +32
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Where is the TATA box located in E.coli versus mammals? |
E. coli, -20 position mammals, can move around upstream region |
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Where is the transcriptional start site? |
at initiator element (Inr)
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True or false: promoter includes TATA box and initiator element.
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true
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What binds to the TATA box and what complex is it a part of? |
TATA-box-binding protein (TBP) TFIID |
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What is created when other transcription factors bind TFIID+TBP complex? |
basal transcription complex
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binds and phosphorylates the carboxyl-terminal domain (CTD) of polymerase |
TFIIH
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What begins the elongation phase of translation? |
CTD phosphorylation
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What is CTD? |
carboxyl-terminal domain
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What is one of the last transcription factors to bind?
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TFIIH
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Where do activators bind? |
enhancers upstream of the promoter
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complexes of proteins that form a bridge between activators and proteins attached to the promoter |
mediators
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True or false: only eukaryotes have histones. |
true
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What are two types of genes? |
housekeeping regulated |
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What are the promoters of housekeeping genes like? |
usually strong and constitutive
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expressed at different levels under different conditions |
regulated genes
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What are three ways of controlling transcription? |
promoter activator chromatin remodeling |
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What are two examples of extracellular stimuli when it comes to gene regulation? |
hormones leading to histone modifications DNA unwinding leading to transcription |
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What controls the transcription of genes involved in the development of female secondary sex characteristics? |
estradiol
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What does estradiol form a complex with? |
estrogen receptor
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How do hormones control gene transcription? |
form a complex with receptor complex binds to specific DNA sequences and recruits transcription factors genes are then transcribed |
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What does estradiol cause? (2) |
inside-out signaling increased proliferation changes cell behavior |
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The estrogen receptor is part of a large class of regulatory proteins called what? |
nuclear hormone receptors
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How do nuclear hormone receptors work? (3)
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hormone binds to the ligand binding domain, causing receptor to undergo a structural change zinc-finger domains recognize specific DNA sequences receptor recruits other proteins which regulate transcription |
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What does estrogen cause in some tissues and what does this lead to? |
cells to grow and divide cancer growth |
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What are tamoxifen and raloxifene and what do they do? |
selective estrogen receptor modulators (SERMS) inhibit the estradiol-receptor complex, which slows the growth of tumors |
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What are recruited after the receptor changes shape? |
coactivators
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proteins involved in transcriptional activation that can't bind DNA themselves |
coactivators
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When do corepressors bind? |
when the ligand is absent
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What are the N-termini of histones (tails) rich in? |
positively charged amino acids that interact with negatively charged DNA
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What weakens histone interactions with DNA and loosens their higher order structure and why? |
acetylation by decreasing the net positive charge
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What cause histone aceylation? |
coactivators
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What acetylates histones? |
histone acetyltransferases (HATS)
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What are HATS? |
histone acetyltransferases
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What do HATS do? |
add the acetyl group of acetyl CoA to lysine residues on the histone tails
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What remove the acetyl groups from histones?
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histone deacetylases (HDACs)
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True or false: tight structure allows regulatory proteins to bind.
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false, looser
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True or false: acetylated histones have increased transcription. |
true because looser
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True or false: deacetylated histones have no transcription. |
false, decreased
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What is the effect of acetylation on histones' affinity for DNA? |
reduced
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What do transcription factors interact with on acetylated histones? |
acetyllysines
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What residues bind to acetylated histones and recruit chromatin remodeling proteins? |
acetyllysine residues
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What histone residues are most involved in interactions with DNA?
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positively charged
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What is the precursor to rRNA? |
45S
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What is pre-rRNA spliced into? |
18S, 28S and 5.8S
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What modify some of the bases and riboses of rRNA? |
snoRNPs
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What are snoRNPs? |
small nucleolar ribonucleoproteins
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What happens to pre-rRNA? |
modified via methyl groups then cleaved according to those groups (modified parts kept)
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How is tRNA processed? (3)
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endonucleases remove nucleotides from the 5' end CCA added to the 3' intron removed by endonuclease, and the products are joined by a ligase to create the anticodon |
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What adds CCA to the 3' end of tRNA?
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tRNA nucleotidyl transferase
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When is tRNA active? |
after CCA (amino acid attachment site) is added
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How is eukaryotic mRNA processed? (3) |
5' cap splicing 3' poly A tail |
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Why does mRNA processing not interfere with translation in eukaryotes? |
transcription is separated from translation by the nuclear membrane
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When does mRNA processing occur?
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as RNA is being transcribed
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Why do mRNA precursors undergo modifications in eukaryotes? |
to increase their stability and make them better substrates for translation
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Why is the 5' end capped before the mRNA precursors are completely synthesized? |
to protect the end from exonuclease degradation
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What is required for splicing and is the site where ribosomes bind? |
5' cap
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What enzyme adds the 5' cap? |
guanylyl transferase
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What are splice sites? |
sequences where the introns are cut from the precursor mRNA and the exons are joined
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True or false: genes are 5' to 3'. |
false, either upstream or downstream
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True or false: most eukaryotic genes have introns and exons. |
true
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When does splicing occur? |
after transcription, 5' cap, and poly(A) addition
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What adds up to 250 adenylate residues to the end of the mRNA precursor? |
poly A polymerase
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What is the poly A tail progressively shorted by? |
3' exonucleases
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increases the time before nucleases reach the coding region |
poly A tail
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If the poly(A) polymerase in a cell contained a mutation that made it add longer poly A tails to mRNA, what would be the most likely effect on mRNA half-life? |
it would increase
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complex of small nuclear ribonucleoprotein complexes (snRNPs) that are associated with the precursor mRNA
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spliceosome
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What are snRNPs? |
small nuclear ribonucleoprotein complexes
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What do the catalytic snRNAs facilitate?
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transesterification reactions that remove the introns and join the exons
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What is exon cassette mode? |
splicing out an exon too
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What may cause up to 15% of all genetic diseases? |
defects in splicing or alternative splicing
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degenerative eye disease that can lead to blindness
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retinitis pigmentosa
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due to a mutation in the U4-U5-U6 tri-snRNP |
retinitis pigmentosa
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What is cystic fibrosis caused by? |
mutations of pre-mRNA splicing
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What are both transcription and splicing coordinated by?
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carboxyl-terminal domain of RNA polymerase II
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What does the carboxyl-terminal domain of RNA polymerase II recruit? |
enzymes to cap 5' end components of splicing complex endonuclease that cleaves the pre-mRNA and exposes the site for poly A addition |
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How can RNA editing make different proteins?
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by deaminating a cytidine in the codon for glutamine which forms uridine and generates a stop codon instead
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What is an example of a transcript that is altered by RNA editing? |
apolipoprotein B (B-100 and B-48)
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What do group 1 introns use to self-splice? |
guanosine cofactor
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What were guanosine cofactors indentified in? |
rRNA from tetrahymena
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Which of the snRNAs in the spliceosome are responsible for catalyzing the transesterification reaction?
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U2 and U6
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What are the three enzyme-catalyzed reactions of mRNA 5' cap addition? |
dephosphorylation GMP transfer methylation |
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What does the acetylation of lysine residues on histone tails promote? |
transcription factors interacting with the acetyllysine residues
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