BIO340 Ch.12 SG
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| DNA Replication | Makes DNA copies that are transmitted between cells and from parents to offspring
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| Transcription | Produces an RNA copy of a gene from DNA
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| mRNA | A temporary copy of a gene that contains information to make a polypeptide
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| Translation | produces a polypeptide using the information in mRNA
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| What's the first step in gene expression? | Transcription
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| What DNA sequences are directly involved in transcription? | 1) the gene itself (the coding region for either the polypeptide or RNA), 2) the promoter & termination sequences for the beginning & end of transcription, & 3) the regulatory sequences
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| Structural gene | a gene that codes for a polypeptide
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| What are some other nonstructural functions of RNA transcripts? | ribosomes, spliceosomes, signal recognition particles, & RNA interference
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| Promoter | The recognition site for transcription factors which allows RNA polymerase to binds, & is the DNA sequence where transcription starts
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| Terminator | Signals the end of transcription
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| Regulatory sequences | Where regulatory proteins bind; they influence the rate of transcription
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| Start codon | Specifies the first amino acid in a polypeptide sequence (usually formylmetionine)
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| Stop codon | No tRNA has an anticodon for this codon
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| Polycistronic | Encodes two or more polypeptides
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| Ribosomal binding site | translation begins nearby
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| Template strand | The strand that's actually transcribed
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| Coding strand | Opposite of the template strand; its base sequence is identical to the RNA transcript
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| What are the 3 stages of transcription? | Initiation, elongation, & termination
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| What do the 3 stages of transcription involve? | protein-DNA interactions, where proteins interact with specific DNA sequences
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| Closed promoter complex | The initial structure formed between RNA polymerase & DNA during transcription
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| Open promoter complex | Structure formed during the assembly of the transcription initiation complex consisting of RNA polymerase & accessory proteins attached to the promoter, after the DNA has been opened up by the breaking of base pairs
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| Transcription initiation complex | Made up of RNA polymerase & various transcription factors bound to the promoter region
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| Describe the general Initiation process of transcription | 1) Promoter is the recognition site for transcription factors, 2) Transcription factors let RNA polymerase bind to promoter & form a closed promoter complex, 3) DNA is denatured into a bubble- an open [promoter] complex
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| Describe the general Elongation process of transcription | RNA polymerase slides along the DNA in an open complex to synthesize an RNA transcript
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| Describe the general Termination process of transcription | A termination signal is recognized; RNA dissociates from DNA; end of RNA synthesis
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| Consensus sequence | The most common sequence for a particular region
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| How do you determine consensus? | Line up the sequence and see which bases are the most common
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| What's one way to know a consensus sequence is important? | If it's conserved in different organisms
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| How do you determine consensus sequences in prokaryotes? | Compare promoters from different genes in one species
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| What are the sequences of the two most commonly occurring bases? | TTGACA & TATAAT
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| RNA Polymerase | The enzyme that catalyzes the synthesis of RNA
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| Holoenzyme? | E.coli's RNA polymerase consisting of a core enzyme & a sigma factor
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| Core enzyme (of holoenzyme) | has four subunits: alpha, alpha, beta, beta'; function is RNA synthesis
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| Sigma factor (of holoenzyme) | Has one subunit: sigma, whose function is promoter recognition
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| Describe the process of bacterial Elongation of transcription | The core enzyme slides down the DNA in the 5' → 3' direction, creating an open complex as it moves; It uses the template strand to synthesize an RNA transcript; an RNA-DNA hybrid molecule is formed
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| About how many bases long is the open complex formed by RNA polymerase? | 17 bases
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| What's the average rate of RNA synthesis? | 43 nucleotides per second
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| Describe the process of bacterial Termination of transcription | The strands of the short DNA-RNA hybrid of the open complex are separated, & the newly synthesized RNA & RNA polymerase are released
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| Describe the supercoils around the open complex during transcription | There is positive supercoiling ahead of the open complex and negative supercoiling behind
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| What is used to take care of supercoiling during transcription? | Topoisomerase II & I
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| Topoisomerase II | Introduces negative supercoils
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| Topoisomerase I | Removes negative supercoils
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| Does negative or positive supercoiling promote transcription and why? | Negative because (?)
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| What makes eukaryotic gene transcription different from prokaryotes? | Complexity: larger organisms, cellular complexity, & multicellularity and development of tissues (tissue-specific gene expression)
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| What are the three different RNA Polymerases used to transcribe nuclear RNA in eukaryotic transcription? | RNA pol I, II, & III
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| RNA Polymerase I in eukaryotic transcription | Transcribes all rRNA genes (except the 5S rRNA)
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| RNA Polymerase II in eukaryotic transcription | Transcribes all structural genes (& produces mRNA's), & transcribes some snRNA genes
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| RNA Polymerase III in eukaryotic transcription | Transcribes all tRNA genes and 5S rRNA genes
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| What three features are found in most promoters in structural genes? | Transcriptional start site, TATA box, & Regulatory elements
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| Core promoter | consists of two components: the TATA box & the Transcriptional start site
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| TATA box | important in determining the precise starting point for transcription
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| Transcriptional start site | often adenine
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| Basal transcription | The core promoter by itself produces a low level of transcription
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| Regulatory elements | affect the binding of RNA polymerase to the promoter; 2 types- enhancers & silencers
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| Enhancer | Stimulates transcription
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| Silencer | Inhibits transcription
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| Where are the regulatory elements usually at? | They vary in region but are usually at the -50 to -100 region
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| What are the two types of factors that control gene expression? | They're based on location: cis-acting elements & trans-acting factors
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| Cis-acting elements- define & give examples | DNA sequences that regulate gene expression on the same chromosome; ex: TATA box, enhancers, & silencers
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| What happens if there's a mutation on a cis-acting element or a trans-acting factor? | Gene expression may be affected
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| Trans-acting factors | Regulatory proteins that bind to cis-acting DNA sequences to control gene expression
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| CCR5 significance in eukaryotic promoters | A gene that codes for the CCR5 protein on the outside of cells; The protein acts as a co-receptor for HIV & allows it to enter & infect cells; variation in the promoter of the gene makes it less active, so some people are more resistant to getting HIV
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| What three categories of proteins are required for basal transcription? | RNA Polymerase II, GTFs- general transcription factors (5 different proteins or protein complexes), & Mediator (a protein complex)
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| What makes up the basal transcription apparatus? | RNA polymerase + the five general transcription factors (GTFs) + regulatory transcription factors
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| When does most transcription occur? | During interphase
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| Describe chromatins organization | DNA is wound around histone octamers to form nucleosomes 11nm in diameter, 30nm fibers are organized into radial loop domains
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| What are 2 different & common mechanisms that alter chromatin structure? | covalent modification of histones & ATP dependent chromatin remodeling
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| Histone acetyltransferase (HAT) | Adds acetyl groups to positively-charged amino groups, loosening the interaction between histones & DNA
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| Histone deacetylase (HDAC) | Removes acetyl groups, making the interaction between histones & DNA tighter
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| What's the significance of histone acetylation? | Transcription factors & RNA polymerases have easier access to DNA, thus that region is able to be transcriptionally active
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