RNA Trascription
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| A reticulate network of regulatory mechanisms interect to control when and where genes are expressed. Genes control the expression of ther genes, which in turn control still more genes. | Hierarchies of Gene Regulation
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| What are the three classes of RNA. There are really four types but two types shere the same Pol. | Messenger RNA, Ribosomal RNA , Transfer and Small Nuclear RNA
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| The function of this RNA class is to encode poypeptide sequence. It has the lowest relative abundance. It uses RNA polymerase II. | Messenger RNA (mRNA)
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| The function of this RNA class is to be the components of ribosomes. It has the highest relative abundance. It uses RNA polymerase I | Ribosomal RNA (rRNA)
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| The function of this RNA class is to act as amino acid carrieres, splicing, and to be a compontnet of ribosomes. It has moderate relative abundance. It uses RNA polymerase III. | Transfer RNA and Small Nuclear RNA (tRNA, snRNA, 5S rRNA)
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| Used to discribe the region of a gene relative to the base where transcription starts. 5' to the start of transcription | Upstream
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| Used to discribe the region of a gene relative to teh base where trancription starts. 3' to the start of transcription | Downstream
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| The base where transcription starts is numbered... Upstream bases are ... Down stream bases are.. | +1, negative, positive
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| A region of DNA used to activate or repress transcription of a gene. The position of the region cann not be moved relative to the gene. | Promoter
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| A region of RNA that regulates transcription like a promoter, but can be moved relative to the gene it controls. It can be flipped in its 5' to 3' orientation. Also the distance between this region and its gene can be altered. | Enhancer
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| The smallest region of a full promoter that will drive detectable transcription. Can be though of as priming transcription. They are not responsible for regulation. | Minimal Promoter
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| Most minimal promoters for Pol II possess the consensus sequence of .... known as the ... | TATA A/T A , TATA box
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| A cluster of proteins that assemble around the TATA box to initiate transcription | Initiation Complex
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| The protein that actually binds the TATA box | TATA Binding Protein (TBP)
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| The other proteins that bind TATA Binding Protien | TATA Associated Factors (TAF)
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| Promoters and enhances that are bound by proteins known as particular transcription factors. Usually short, 4 to 10 bp long. OFten palindromic. Are consensuses, so they can vary slightly from gene to gene. | Recognition sequences
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| A recognition sequence for TBP. The most common regocnition sequence in our genome. | TATA box
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| Teh second most common recognition sequence in our genome. It raises baseline transcription. It is bound by a transcrition factor called CP1 | CCATT box
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| The third most common recognition sequence. It consists of GC rich regions 20-50 bp long. It is common in TATAless promoters. | SP1 Recognition Sequence
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| Proteins that bind recognition sequencets to control transcription | Transcription Factors
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| A region of a transcription factor that recognizes and binds a specific sequence of DNA. | DNA binding domain
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| What charge do DNA binding domains usually carry | Positive
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| The region of a transcription factor that induces RNA synthesis by attracting an RNA polymerase | Activation domain
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| What are the four major families of transcription factors | Helix-Turn-Helix, Zinc, Fingers, Helix-Loop-Helix, Leucine Zippers
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| A DNA binding domain in which two alpha helices are positioned at right angles to each other, connected by a short linker region. One alph helix has a basic face that binds the DNA by weding into the major groove. | Helix-Turn-Helix
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| A DNA binding domin in which cystein and histidine residues are chelated to a central zinc ion, creating several loops in the polypeptide. These loops act like fingers wedging themselves into the major groove. | Zinc Fingers
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| What are the three subfamilies of Zinc fingers | C2H2, C4, C6
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| The subfamilie of zinc fingers that consistis of a pair of cysteins 2-4 amino acids apart, a linker region ~11 amino acids long, and a pair of kistidines 3-4 amino acids apart | C2H2
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| The Zinc finger subfamily that consists of two pairs of cysteins with no histidines | C4
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| The Zinc finger subfamily that consists of three pairs of cysteines | C6
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| The DNA binding domain that consists of two alpha helices separated by a long linker region. Two differnt polypeptides must bind to each other before they will bind DNA | Helix-loop-Helix
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| What are the three types of Helix-Loop-Helix polypeptides | Negative Homolog, Positive Homolog, Ubiquitous homolog
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| A helix-loop-helix heterodimer consisting of an ubiquitous homolog paired with a negative homolog is an | Inhibitor
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| A helix-loop-helix heterodimer consisting of an ubiquitous homolog paired with a positiv ehomolog is an | Activator
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| The DNA bind domain that functions as dimeric proteins, either homodimers or heterodimers. The extensions of alpha helices grip the recognition sequence on each side of the DNA like a pair of scissors | Leucine Zippers
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| The region of a protein that specifically binds another protein | Interaction domain
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| In the interaction domain every ... residues is a luecine which means there is a leucine every ... turns | 7, 2
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| RNAs that havve not bee processed | Primary transcript
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| A guanosine is added to the first nucleotide of the primary transcript by an unusual 5' to 5' bond | Capping
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| Removal of a section of the primary transcript | Splicing
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| The region that's spliced out of an RNA transcript | Intron
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| The region that is retained in an RNA transcript after splicing | Exon
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| What splices out introns | Spliceosomes
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| Spliceosomes are composed of | snRNPs and snRNAs
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| The final even of mRNA processing that adds 20-300 adenosines to the 3' end of the transcript | Polyadenylation
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| The signal for polyadenylation | AAUAAA
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