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