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Chapt 21-23

Transcription, translation, regulation of gene expression

QuestionAnswer
What is transcription? RNA synthesis
What is translation? protein synthesis
What are the types of RNA? mRNA, rRNA, tRNA
What is the function of mRNA? messenger
What is the function of rRNA? production of ribosomes
What is the function of tRNA? transfer; brings amino acids to ribosomes and starts translation
This DNA helps synthesize RNA. the template strand
This DNA is identical to the RNA produced. the coding strand
These are codons that encode for specific amino acids. RNA triplets
What is the degenerate code? multiple codons encode for specific amino acids
What does the start codon do? AUG sequence that encodes for methionine; starts translation
What does the stop codon do? UAA, UAG, or UGA sequence that does not encode for an amino acid; stops translation
This type of base-pair mutation changes the codon so that it encodes for a different amino acid. missense mutation
This type of base-pair mutation changes the codon to encode for stop instead of an amino acid. nonsense mutation
This type of base-pair mutation does not cause any change in the amino acid translation or protein synthesis. silent mutation
This type of mutation shifts the entire sequence to give different triplets, and other types of mutations. insertion/deletion; frameshift mutation
What are NTPs? nucleotide ribonucleoside triphosphates; ATP, GTP, CTP, UTP
What is a promoter sequence? the binding site for RNA polymerase that determines the transcription start site
What does RNA polymerase do? unwinds DNA and synthesizes RNA 5'->3'
This part of RNA polymerase promotes initiation. σ (sigma) subunit
This part of the promoter sequence is called +1. start point
What are the steps of transcription? RNA polymerase binds to DNA, initiation/pre-initiation, elongation, termination
What are the consensus sequences? Pribnow Box/-10 sequence (TATAAT), -35 sequence (TTGACA)
What happens in Rho factor termination? the Rho factor (a protein that unwinds new RNA from DNA template) binds to termination sequences
What happens in non-Rho termination? RNA transcribes the G-C rich sites -> hairpin loop formation -> dissociation of RNA from DNA
Transcription in bacteria step #1 RNA polymerase binds to promoter and begins unwinding DNA
Transcription in bacteria step #2 initiation: NTPs added 5'->3' until σ subunit falls off
Transcription in bacteria step #3 elongation: RNA polymerase continues to unwind/rewind DNA and add NTPs to RNA, forming temporary RNA-DNA hybrids
Transcription in bacteria step #4 termination: Rho or non-Rho
What is RNA polymerase I? RNA polymerase involved in eukaryotic transcription found in nucleolus and transcribes rRNA
What is RNA polymerase II? RNA polymerase involved in eukaryotic transcription found in nucloplasm and transcribes mRNA
What is RNA polymerase III? RNA polymerase involved in eukaryotic transcription found in nucleoplasm and transcribes tRNA and 5S rRNA
What is the core promoter? the minimum sequence needed to begin transcription with RNA polymerase I, surrounds start point
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
What is Inr? the iniatior sequence for transcription with RNA polymerase II that includes the start point and surrounding pyrimidines
What is the TATA box? the TATA sequence at -25 that is preserved during transcription with RNA polymerase II
What is BRE? transcription factor 2 (TF2) B recognition elements; where transcription factors bind to initiate transcription with RNA polymerase II
What is DPE? downstream promoter element; sequences where transcription factors can bind to enhance transcription with RNA polymerase II
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
Pre-initiation (using RNA polymerase II) step #1 transcription factor II D (TFIID) recognizes and binds TATA box
Pre-initiation (using RNA polymerase II) step #2 TFIID recruits TFIIA and TFIIB to form ABD complex
Pre-initiation (using RNA polymerase II) step #3 ABD complex recruits RNA polymerase II (RNApolII)/TFIIF
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
Pre-initiation (using RNA polymerase II) step #5 TFIIH phosphorylates RNApolII to begin initaion
What is the primary transcript? pre-m, t, rRNA; the unprocessed result of transcript
What are the 4 types of rRNA? 25-28S, 5.8S, 5S, 18S
Which of the 4 types of rRNA make up the large ribosome subunit? 25-28S, 5.8S, 5S
Which of the 4 types of rRNA make up the small ribosome subunit? 18S
This contains separate genes for each rRNA. the transcriptional unit
These separate repeated transcriptional units. nontranscribed spacers
These separate genes for each rRNA. transcribed spacers
What is pre-rRNA? the RNA with all RNAs still connected by spacers
What is mature rRNA? the separate rRNAs which result from RNA cleavage and degradation of spacers
What is a spliceosome? a complex made up of 5 kinds of RNA and 200+ proteins
What are the types of snRNPs? U1, U2, U4/U6, U5
What are the splice sites? GU (5'), AG (3')
What is the branch site? A located within intron
tRNA processing step #1 leader sequence on 5' end of pre-transcript is cut off
tRNA processing step #2 nucleotides at end of 3' end replaced with CCA so it can attach to an amino acid
tRNA processing step #3 bases are chemically modified
tRNA processing step #4 hairpin loops form
tRNA processing step #5 introns are cut out
How is mRNA processed? 5' cap added, 3' poly A tail added, and splicing
What does the 5' cap do? protects the mRNA from degradation, aids in attachment to ribosome
What does the 3' poly A tail do? protects the mRNA from degradation, aids in nuclear export
mRNA splicing step #1 snRNP U1 binds 5' splice site
mRNA splicing step #2 snRNP U2 binds branch site
mRNA splicing step #3 snRNP U4/U6 bind to form loop (spliceosome)
mRNA splicing step #4 5' splice site is cleaved -> UG binds A branch site (Lariat structure)
mRNA splicing step #5 3' splice site is cleaved
mRNA splicing step #6 exons joined by exon junction complex (EJC)
mRNA splicing step #7 introns are degraded
What do introns do? act as spacers, increase frequency of DNA cross-overs, allow for alternative splicing
What is alternative splicing? 1 gene can lead to multiple polypeptides
This is made up of a tRNA and an amino acid. aminoacyl tRNA
These aid in translation, and there are 3 types: IFs, EFs, and TFs. protien factors
Where is the mRNA binding site? in the small ribosome subunit
Where is the A site? in the large ribosome subunit
Where is the P site? in the large ribosome subunit
Where is the E site? in the large ribosome subunit
How do tRNAs move through the ribosome? A->P->E
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
What does the aminoacyl tRNA synthetase do? it makes aminoacyl tRNA
Aminoacyl tRNA synthesis step #1 amino acid and ATP attach to binding sites on enzyme
Aminoacyl tRNA synthesis step #2 ATP hydrolyzes 2 phosphates (pyrophosphate), and amino acid attaches to remaining AMP
Aminoacyl tRNA synthesis step #3 tRNA takes place of AMP on enzyme
Aminoacyl tRNA synthesis step #4 new aminoacyl tRNA is released
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
What is I? inosine, a nucleotide found only in tRNA that is able to bind with A, C, or U
What are the 3 types of protein translation factors? initiation factors, elongation factors, release factors
Initiation process in bacteria step #1 GTP binds IF2
Initiation process in bacteria step #2 GTP/IF2 recruits IF1 and IF3
Initiation process in bacteria step #3 GTP/IF2/IF1/IF3 bind to 30S
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
Initiation process in bacteria step #5 GTP hydrolysis -> IF1 and IF2 released, 50S binds -> 70S initiation complex
Initiation process in eukaryotes step #1 eIF2/GTp binds initiator tRNA (met)
Initiation process in eukaryotes step #2 eIF1A and 40S bind to eIF2/GTP/initiator tRNA
Initiation process in eukaryotes step #3 mRNA is recruited
Initiation process in eukaryotes step #4 eIF4F binds
Initiation process in eukaryotes step #5 tRNA binds start codon (AUG in Kozak sequence)
Initiation process in eukaryotes step #6 GTP hydrolysis -> initiation factors released leaving 40S initiation complex (mRNA, initiator tRNA, 40S)
Initiation process in eukaryotes step #7 60S binds -> 80S initiation complex
What is the Kozak sequence? ACCAUGG
What are the bacterial initiation factors? IF1, IF2, IF3
What are the eukaryote initiation factors? eIF2, eIF1A, eIF4F
What are the elongation factors? EF-Tu, EF-Ts, EF-G
Elongation process step #1 aminoacyl tRNA binds
Elongation process step #2 EF-Tu binds to GTP and aminoacyl tRNA -> binds to codon in A site
Elongation process step #3 GTP hydrolysis -> EF-Tu released and recycled by EF-Ts
Elongation process step #4 peptide bond formation
Elongation process step #5 EF-F/GTP binds ribosome
Elongation process step #6 GTP hydrolysis -> moves tRNAs to E and P sites/mRNA (translocation)
Elongation process step #7 EF-G/GDp is released and recycled
Elongation process step #8 elongation continues
Termination process step #1 stop codon in A site (UAG, UAA, UGA) -> release factors/GTP recruited to stop codon
Termination process step #2 GTP hydrolysis -> translation complex dissociation
What is induction? a catabolic pathway where the production of something induces the gene regulation pathway in bacteria
what is an example of an induction pathway? the lac operon
What is end-product repression? an anabolic pathway where the product inhibits more synthesis of the product
What is an example of end-product repression? the trp operon
What does a regulatory gene do? it encodes for the repressor protien that binds to the operator to regulate gene expression
What is the lac operon? lac Z, lac Y, and lac A sequences
What is P-lac? the lac operon promoter
What is the operator? the sequence next to the promoter that regulates transcription
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
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
What is CAP? the catabolite activator protein that binds to cAMP to regulate the lac operon
When is CAP used to regulate the lac operon? when there is no glucose present and there is high [cAMP]
Regulation with CAP step #1 cAMP binds to CAP -> CAP is activated
Regulation with CAP step #2 activated CAp binds the CAP recognition sequence in the operon
Regulation with CAP step #3 RNA polymerase is recruited
Regulation with CAP step #4 transcription
Regulation with CAP step #5 the lac genes are turned on
What are chromosome puffs? sites of chromatin decondensation/increase transcription
What is the histone code? specific histone modifications that activate or silence genes
What are proximal control elements? separate DNA sequences near promoter where the regulatory transcription factors bind
What are distal control elements? separate DNA sequences far away from the promoter where regulatory transcription factors bind
What are enhancers? where activators bind to activate/enhance/increase transcription
What are silencers? where repressors bind to silence/decrease transcription
Enhancer process step #1 activator proteins bind enhancer
Enhancer process step #2 DNA bends
Enhancer process step #3 coactivators (SWI/SNF, HAT) stimulate histone acetylation and chromatin remodeling
Enhancer process step #4 activators bind mediator complex -> positions TFs and polymerase
What is the mediator complex? RNA polymerase + TFs
What are response elements? inverted repeats near the promoter that allow distant genes with similar functions to be controlled together
Coordinated gene regulation involving hormones step #1 hormone receptors (HR) in cytoplasm bind hormone and enter the nucleus
Coordinated gene regulation involving hormones step #2 bind the hormone response elements they match on all strands of DNA having the matching sequences
What do hox genes do? determine the body axes in embryonic development in Drosophila
How are genes regulated at the post-transcriptional level? chemical modifications, cleavage, binding to UTRs, alternative splicing, mRNA degredation/lifespan
What is RNAi? RNA mediated-interference at the transcriptional level
RNAi gene regulation step #1 double stranded RNA (dsRNA) is introduced into the cell
RNAi gene regulation step #2 dicer cleaves dsRNA into single-stranded RNA (siRNA)
RNAi gene regulation step #3 RISC complex binds siRNAs to form siRISC complex
RNAi gene regulation step #4 one siRNA is degraded
RNAi gene regulation step #5 (if siRNA inhibits transcription) siRNA looks for matching DNA in the nucleus
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
How are genes regulated at the post-translational level? chemical modification, cleavage, protein targeting/sorting, ubiquitin-targeted degredation involving proteosomes
Created by: 653527423