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BIO340 Ch.12 SG

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
Created by: 817229501