Transcription, translation, regulation of gene expression
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| What is transcription? | RNA synthesis
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| What is translation? | protein synthesis
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| What are the types of RNA? | mRNA, rRNA, tRNA
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| What is the function of mRNA? | messenger
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| What is the function of rRNA? | production of ribosomes
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| What is the function of tRNA? | transfer; brings amino acids to ribosomes and starts translation
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| This DNA helps synthesize RNA. | the template strand
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| This DNA is identical to the RNA produced. | the coding strand
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| These are codons that encode for specific amino acids. | RNA triplets
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| What is the degenerate code? | multiple codons encode for specific amino acids
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| What does the start codon do? | AUG sequence that encodes for methionine; starts translation
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| What does the stop codon do? | UAA, UAG, or UGA sequence that does not encode for an amino acid; stops translation
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| This type of base-pair mutation changes the codon so that it encodes for a different amino acid. | missense mutation
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| This type of base-pair mutation changes the codon to encode for stop instead of an amino acid. | nonsense mutation
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| This type of base-pair mutation does not cause any change in the amino acid translation or protein synthesis. | silent mutation
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| This type of mutation shifts the entire sequence to give different triplets, and other types of mutations. | insertion/deletion; frameshift mutation
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| What are NTPs? | nucleotide ribonucleoside triphosphates; ATP, GTP, CTP, UTP
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| What is a promoter sequence? | the binding site for RNA polymerase that determines the transcription start site
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| What does RNA polymerase do? | unwinds DNA and synthesizes RNA 5'->3'
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| This part of RNA polymerase promotes initiation. | σ (sigma) subunit
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| This part of the promoter sequence is called +1. | start point
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| What are the steps of transcription? | RNA polymerase binds to DNA, initiation/pre-initiation, elongation, termination
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| What are the consensus sequences? | Pribnow Box/-10 sequence (TATAAT), -35 sequence (TTGACA)
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| What happens in Rho factor termination? | the Rho factor (a protein that unwinds new RNA from DNA template) binds to termination sequences
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| What happens in non-Rho termination? | RNA transcribes the G-C rich sites -> hairpin loop formation -> dissociation of RNA from DNA
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| Transcription in bacteria step #1 | RNA polymerase binds to promoter and begins unwinding DNA
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| Transcription in bacteria step #2 | initiation: NTPs added 5'->3' until σ subunit falls off
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| Transcription in bacteria step #3 | elongation: RNA polymerase continues to unwind/rewind DNA and add NTPs to RNA, forming temporary RNA-DNA hybrids
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| Transcription in bacteria step #4 | termination: Rho or non-Rho
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| What is RNA polymerase I? | RNA polymerase involved in eukaryotic transcription found in nucleolus and transcribes rRNA
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| What is RNA polymerase II? | RNA polymerase involved in eukaryotic transcription found in nucloplasm and transcribes mRNA
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| What is RNA polymerase III? | RNA polymerase involved in eukaryotic transcription found in nucleoplasm and transcribes tRNA and 5S rRNA
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| What is the core promoter? | the minimum sequence needed to begin transcription with RNA polymerase I, surrounds start point
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| What is the upstream control element? | a sequence upstream of the core promoter where transcription factors can bind to enhance transcription with RNA polymerase I
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| What is Inr? | the iniatior sequence for transcription with RNA polymerase II that includes the start point and surrounding pyrimidines
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| What is the TATA box? | the TATA sequence at -25 that is preserved during transcription with RNA polymerase II
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| What is BRE? | transcription factor 2 (TF2) B recognition elements; where transcription factors bind to initiate transcription with RNA polymerase II
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| What is DPE? | downstream promoter element; sequences where transcription factors can bind to enhance transcription with RNA polymerase II
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| What are Boxes A, B, and C? | sequences found downstream of the promoter that allow transcription factors to bind to enhance transcription with RNA polymerase III
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| Pre-initiation (using RNA polymerase II) step #1 | transcription factor II D (TFIID) recognizes and binds TATA box
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| Pre-initiation (using RNA polymerase II) step #2 | TFIID recruits TFIIA and TFIIB to form ABD complex
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| Pre-initiation (using RNA polymerase II) step #3 | ABD complex recruits RNA polymerase II (RNApolII)/TFIIF
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| Pre-initiation (using RNA polymerase II) step #4 | TFIIE and TFIIH (helicase) also bind to form pre-imitation complex with RNApolII/TFIIF and ABD complex
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| Pre-initiation (using RNA polymerase II) step #5 | TFIIH phosphorylates RNApolII to begin initaion
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| What is the primary transcript? | pre-m, t, rRNA; the unprocessed result of transcript
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| What are the 4 types of rRNA? | 25-28S, 5.8S, 5S, 18S
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| Which of the 4 types of rRNA make up the large ribosome subunit? | 25-28S, 5.8S, 5S
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| Which of the 4 types of rRNA make up the small ribosome subunit? | 18S
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| This contains separate genes for each rRNA. | the transcriptional unit
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| These separate repeated transcriptional units. | nontranscribed spacers
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| These separate genes for each rRNA. | transcribed spacers
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| What is pre-rRNA? | the RNA with all RNAs still connected by spacers
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| What is mature rRNA? | the separate rRNAs which result from RNA cleavage and degradation of spacers
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| What is a spliceosome? | a complex made up of 5 kinds of RNA and 200+ proteins
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| What are the types of snRNPs? | U1, U2, U4/U6, U5
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| What are the splice sites? | GU (5'), AG (3')
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| What is the branch site? | A located within intron
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| tRNA processing step #1 | leader sequence on 5' end of pre-transcript is cut off
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| tRNA processing step #2 | nucleotides at end of 3' end replaced with CCA so it can attach to an amino acid
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| tRNA processing step #3 | bases are chemically modified
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| tRNA processing step #4 | hairpin loops form
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| tRNA processing step #5 | introns are cut out
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| How is mRNA processed? | 5' cap added, 3' poly A tail added, and splicing
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| What does the 5' cap do? | protects the mRNA from degradation, aids in attachment to ribosome
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| What does the 3' poly A tail do? | protects the mRNA from degradation, aids in nuclear export
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| mRNA splicing step #1 | snRNP U1 binds 5' splice site
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| mRNA splicing step #2 | snRNP U2 binds branch site
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| mRNA splicing step #3 | snRNP U4/U6 bind to form loop (spliceosome)
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| mRNA splicing step #4 | 5' splice site is cleaved -> UG binds A branch site (Lariat structure)
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| mRNA splicing step #5 | 3' splice site is cleaved
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| mRNA splicing step #6 | exons joined by exon junction complex (EJC)
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| mRNA splicing step #7 | introns are degraded
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| What do introns do? | act as spacers, increase frequency of DNA cross-overs, allow for alternative splicing
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| What is alternative splicing? | 1 gene can lead to multiple polypeptides
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| This is made up of a tRNA and an amino acid. | aminoacyl tRNA
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| These aid in translation, and there are 3 types: IFs, EFs, and TFs. | protien factors
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| Where is the mRNA binding site? | in the small ribosome subunit
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| Where is the A site? | in the large ribosome subunit
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| Where is the P site? | in the large ribosome subunit
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| Where is the E site? | in the large ribosome subunit
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| How do tRNAs move through the ribosome? | A->P->E
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| What is the anticodon? | the codon on the tRNA that binds to the mRNA codon it matches in order to add its amino acid to the growing polypeptide
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| What does the aminoacyl tRNA synthetase do? | it makes aminoacyl tRNA
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| Aminoacyl tRNA synthesis step #1 | amino acid and ATP attach to binding sites on enzyme
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| Aminoacyl tRNA synthesis step #2 | ATP hydrolyzes 2 phosphates (pyrophosphate), and amino acid attaches to remaining AMP
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| Aminoacyl tRNA synthesis step #3 | tRNA takes place of AMP on enzyme
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| Aminoacyl tRNA synthesis step #4 | new aminoacyl tRNA is released
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| What is the wobble position? | the #3 spot on the anticodon that allows the anticodon to base pair with bases it normally would not pair with
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| What is I? | inosine, a nucleotide found only in tRNA that is able to bind with A, C, or U
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| What are the 3 types of protein translation factors? | initiation factors, elongation factors, release factors
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| Initiation process in bacteria step #1 | GTP binds IF2
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| Initiation process in bacteria step #2 | GTP/IF2 recruits IF1 and IF3
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| Initiation process in bacteria step #3 | GTP/IF2/IF1/IF3 bind to 30S
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| Initiation process in bacteria step #4 | mRNA and initiator tRNA (fmet) are recruited into GTP/IF2/IF1/IF3 complex, and IF3 is released -> 30S initiation complex
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| Initiation process in bacteria step #5 | GTP hydrolysis -> IF1 and IF2 released, 50S binds -> 70S initiation complex
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| Initiation process in eukaryotes step #1 | eIF2/GTp binds initiator tRNA (met)
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| Initiation process in eukaryotes step #2 | eIF1A and 40S bind to eIF2/GTP/initiator tRNA
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| Initiation process in eukaryotes step #3 | mRNA is recruited
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| Initiation process in eukaryotes step #4 | eIF4F binds
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| Initiation process in eukaryotes step #5 | tRNA binds start codon (AUG in Kozak sequence)
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| Initiation process in eukaryotes step #6 | GTP hydrolysis -> initiation factors released leaving 40S initiation complex (mRNA, initiator tRNA, 40S)
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| Initiation process in eukaryotes step #7 | 60S binds -> 80S initiation complex
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| What is the Kozak sequence? | ACCAUGG
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| What are the bacterial initiation factors? | IF1, IF2, IF3
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| What are the eukaryote initiation factors? | eIF2, eIF1A, eIF4F
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| What are the elongation factors? | EF-Tu, EF-Ts, EF-G
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| Elongation process step #1 | aminoacyl tRNA binds
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| Elongation process step #2 | EF-Tu binds to GTP and aminoacyl tRNA -> binds to codon in A site
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| Elongation process step #3 | GTP hydrolysis -> EF-Tu released and recycled by EF-Ts
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| Elongation process step #4 | peptide bond formation
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| Elongation process step #5 | EF-F/GTP binds ribosome
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| Elongation process step #6 | GTP hydrolysis -> moves tRNAs to E and P sites/mRNA (translocation)
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| Elongation process step #7 | EF-G/GDp is released and recycled
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| Elongation process step #8 | elongation continues
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| Termination process step #1 | stop codon in A site (UAG, UAA, UGA) -> release factors/GTP recruited to stop codon
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| Termination process step #2 | GTP hydrolysis -> translation complex dissociation
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| What is induction? | a catabolic pathway where the production of something induces the gene regulation pathway in bacteria
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| what is an example of an induction pathway? | the lac operon
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| What is end-product repression? | an anabolic pathway where the product inhibits more synthesis of the product
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| What is an example of end-product repression? | the trp operon
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| What does a regulatory gene do? | it encodes for the repressor protien that binds to the operator to regulate gene expression
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| What is the lac operon? | lac Z, lac Y, and lac A sequences
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| What is P-lac? | the lac operon promoter
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| What is the operator? | the sequence next to the promoter that regulates transcription
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| Why is the lac operon inducible? | because the default state is off and it's induced to the on state by the presence of lactose
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| Why is the lac repressor a negative/inhibitory regulator? | when there is no lactose present, the active repressor binds to the operator to block transcription
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| What is CAP? | the catabolite activator protein that binds to cAMP to regulate the lac operon
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| When is CAP used to regulate the lac operon? | when there is no glucose present and there is high [cAMP]
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| Regulation with CAP step #1 | cAMP binds to CAP -> CAP is activated
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| Regulation with CAP step #2 | activated CAp binds the CAP recognition sequence in the operon
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| Regulation with CAP step #3 | RNA polymerase is recruited
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| Regulation with CAP step #4 | transcription
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| Regulation with CAP step #5 | the lac genes are turned on
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| What are chromosome puffs? | sites of chromatin decondensation/increase transcription
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| What is the histone code? | specific histone modifications that activate or silence genes
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| What are proximal control elements? | separate DNA sequences near promoter where the regulatory transcription factors bind
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| What are distal control elements? | separate DNA sequences far away from the promoter where regulatory transcription factors bind
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| What are enhancers? | where activators bind to activate/enhance/increase transcription
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| What are silencers? | where repressors bind to silence/decrease transcription
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| Enhancer process step #1 | activator proteins bind enhancer
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| Enhancer process step #2 | DNA bends
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| Enhancer process step #3 | coactivators (SWI/SNF, HAT) stimulate histone acetylation and chromatin remodeling
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| Enhancer process step #4 | activators bind mediator complex -> positions TFs and polymerase
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| What is the mediator complex? | RNA polymerase + TFs
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| What are response elements? | inverted repeats near the promoter that allow distant genes with similar functions to be controlled together
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| Coordinated gene regulation involving hormones step #1 | hormone receptors (HR) in cytoplasm bind hormone and enter the nucleus
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| Coordinated gene regulation involving hormones step #2 | bind the hormone response elements they match on all strands of DNA having the matching sequences
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| What do hox genes do? | determine the body axes in embryonic development in Drosophila
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| How are genes regulated at the post-transcriptional level? | chemical modifications, cleavage, binding to UTRs, alternative splicing, mRNA degredation/lifespan
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| What is RNAi? | RNA mediated-interference at the transcriptional level
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| RNAi gene regulation step #1 | double stranded RNA (dsRNA) is introduced into the cell
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| RNAi gene regulation step #2 | dicer cleaves dsRNA into single-stranded RNA (siRNA)
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| RNAi gene regulation step #3 | RISC complex binds siRNAs to form siRISC complex
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| RNAi gene regulation step #4 | one siRNA is degraded
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| RNAi gene regulation step #5 (if siRNA inhibits transcription) | siRNA looks for matching DNA in the nucleus
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| RNAi gene regulation step #5 (if siRNA binds mRNA in the cytoplasm) | slicer degrades the mRNA if the siRNA is 100% complementary, translation is inhibited if the siRNA is partially complementary
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| How are genes regulated at the post-translational level? | chemical modification, cleavage, protein targeting/sorting, ubiquitin-targeted degredation involving proteosomes
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