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44 Cards in this Set
- Front
- Back
Name the general transcription factors and the order of which they bind to the initiation complex in transcription by RNAPII |
TFIID, TFIIA, TFIIB, TFIIF (+ RNA pol II), TFIIE, TFIIH |
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Which RNA are products of RNAPII activity? |
snRNA (small nuclear RNA) & hnRNA (mRNA precursors) miRNA precursors |
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Which inhibitor was first used to identify the activity of RNA polymerases in eukaryotes? |
α-amanitin
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What elements are apart of the core classII promoter? |
TATA box, BRE, Inr, DCE, DPE, MTE (Upstream elements are several kb away from the initiation start site and ARE NOT apart of the core promoter elements) |
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What was the experiment used to identify the RNAPII subunits? |
Co-Immunoprecipitation via epitope tagging. The subunits have been isolated by epitope tagging one subunit of the complex. The antibody to this epitope is added to cell lysates, allowing it to bind to its epitope and any other associated proteins.
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Which transcription factors are important for promoter clearance? |
TFIIH & TFIIE -TFIIE recruits TFIIH which phosphorylates the CTD of the RNAP, allowing the enzyme to shed the general TFs and clear the promoter |
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What can gene regulation in eukaryotes be influenced by? |
- environmental conditions - developmental stage - tissue or cell type |
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What is a transcription factor? |
A protein that binds to certain gene sequences, and affects the ability of RNA polymerase to transcribe a gene |
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Do all eukaryotic gene promoters contain a TATA box? |
No, some eukaryotic promoters are TATA-less, in which TBP of TFIID is tethered to TAFs bound to the Inr |
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What modification must occur to allow RNAP II to leave the promoter? |
Phosphorylation of RNAPII CTD by TFIIH |
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What is the function of TFIIA? |
To bind upstream of TFIID and stabilize the interaction of TBP at the TATA box |
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What else asides from promoter clearance, can phosphorylation of the RNAPII CTD allow it to do? |
RNA processing |
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Describe enhancers |
Enhancers are cis DNA elements that bind specific transcription factors called activators. They are usually several kb up or downstream from the initiation start site and are orientation and position independent. Activators bound to enhancers increase gene transcription. |
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True or false: The whole TFIID complex can respond to a wide variety of activators |
True |
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What type of DNA is most susceptible to digestion by DNAse-I? |
"naked DNA" unbound by histones |
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What are zinc finger motifs comprised of? |
An antiparallel β sheet (two Cys residues) followed by an α helix (Two His residues), linked by a zinc ion. Zinc fingers usually occur in ~2-9 tandem repeats |
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What are steroid hormone receptors? |
They can act as activators or repressors of transcription that are controlled by ligand binding. \ Eg. Thyroid hormone receptors bind to the thyroid hormone to recruit activators and increase transcription. In the absence of thyroid, the receptor acts as a repressor as it recruits co-repressors and HDAc |
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What is a nucleosome |
A nucleosome is a basic unit of DNA packaging in eukaryotes. It consists of a segment of DNA (165bp) wrapped around a histone core octamer |
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What is histone H1 and what is its role in DNA regulation? |
It is not a part of the core histones, but is important to induce tighter wrapping of DNA around nucleosomes, and therefore down regulation of genes |
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Which regions in active genes are considered to be DNase I hypersensitive? |
Nucleosome free regions |
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How to proteins that participate in transcription interact with the histone core? |
The proteins bind the acetyl groups on the histone tails via their bromodomains. Acetylation of histones is usually correlated to gene activation, thus bromodomain proteins are usually activators of transcription |
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What is the technique used to determine that a physical association exists between transcription factors, co-repressors, and histone deacetylases? |
Immunopreciptation - One component of the tertiary complex is tagged with a epitope tag, and washed with an antibody for the certain tag. |
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How may methylation of histones result in the formation of heterochromatin? |
Methyl groups added to histone tails by histone methyltrasnferases amplify the positive charge which increases the interaction with DNA. The tighter the DNA- histone interaction, the more condensed DNA becomes. Chromodomains of repressor proteins can bind to these methyl group, further repressing gene expressing. |
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What its the methylation state of heterochromatin? |
hypermethylated. Methylation usually corresponds to gene repression |
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How does the FACT complex facilitate chromatin transcription? |
The subunits of the FACT complex Spt16 and SSRP1 disassemble the core histone by removing the H2A and H2B dimers ahead of the transcription machinery. Once RNAPII has moved through, the FACT complex uses its chaperone activity to reassemble the core nucleosome with the help of Spt6 |
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What is genomic importing? Give an example. |
Genomic imprinting is and example of the effects of DNA (NOT histone) methylation whereby only one copy, from either the mother or father, of specific genes are expressed |
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How does formation of the 5' cap to a newly formed mRNA transcript occur? |
Immediately after the transcript emerges, guanalyl transferase adds a modified guanine residue to the 5' end in a reverse 5'-5' orientation |
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What is the sequence recognized by the CPSF during 3' processing? |
CPSF (Cleavage and polyadenylation specificity factor) recognizes the AAUAAA consensus sequence as a part of the 3' processing complex |
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How many polyadenylation benefit/affect an mRNA transcript? |
- contribute to mRNA stability - contribute the translational initiation - be required for splicing nearest the 3' end |
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How are introns removed from pre-mRNA |
They are removed in a specific order, not in a linear fashion. There may be combinations are which introns are removed, but the introns are never removed at random to produce more invariants. |
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What occurs during the first trasesterificatiron reaction of nuclear mRNA splicing? |
The 2'OH of the conserved A in the branch site attacks the phosphate of the conserved G in the 5' splice site. This breaks the intron-exon bond and creates a lariat structure with the 5' splice site G phosphodiester bound to the invariant A. |
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True or false: U1 snRNA binding to the 5' splice site is required for spliceosome assembly and splicing |
true |
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Which two snRNPs participate in the first transesterification reaction during formation of the C1 complex? |
U2 and U2 (U2/U6 catalysis activated by dissociation of U4) |
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What does control of alternative splicing involve? |
- repressors, which cause exon skipping - enhancers, which increase recognition of weak splice sites - splicing factors which modulate spliceosome factors |
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In the presence of purified polyA binding protein, eukaryotic mRNAs form _________ visible with force field electron microscopy |
circular structures |
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The spliceosome cycle includes the assembly, splicing activity and disassembly of the spliceosome. Assembly begins with the binding of ___ to the splicing substrate to form a commitment complex. ___ is the next snRNP to join the complexly pairing with the branch site (requires ATP). When ___ dissociates from ___, it displaces ___ at the 5' splice site. This ATP dependent step activates the spliceosome, in which ___ brings the two exons together. |
U1, U2, U6, U4, U1, U5 |
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In contrast to siRNA, miRNA |
- Can reduce target mRNA translation without transcript degradation - Are normal and naturally occurring (cis) - Can imperfectly pair with target RNA (usually at 3' UTRs) |
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True or false: Riboswitches can regulate the expression of a gene at the level of transcription or translation. |
True |
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Explain the components of a riboswitch and their roles. |
Each riboswitch is made up of two components, the aptamer and the expression platform. The aptamer binds a small molecule ligand, and in response, undergoes a conformational change. The conformation change of the aptamer causing a change in the adjoining expression platform where an RBS is usually contained. |
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During siRNA amplification, the si-RISC complex can recruit RNA-dependent RNA polymerases (RdRP) to the targeted DNA. The siRNA itself acts as a primer for the RdRP to transform the target into dsRNA, which itself can be acted on by ___ |
Dicer |
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Why has RNAi become a powerful tool for manipulating gene expression? |
- it can target specific genes for inactivation - it exploits naturally occurring process for DNA degradation - it can target degradation of specific mRNA |
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What is the net result after the pre-initiation complex of prokaryotic translation initiation disassembles? |
An intact 70s ribosome paired at the start codon, with the initiator tRNA carry fMet in the P-site and an empty A-site |
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How does the eukaryotic pre-initiation complex for translation find the appropriate start codon. |
The eukaryotic 40s ribosomal subunit binds to the 5' cap, and with the help of eIF1 and eIF1A, scans downstream to find the first favourable start codon that satisfies Kodaks rule. Unlike prokaryotic translation, there is nonrecognition of a Shine-Dalgarno sequence |
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Several eukaryotic initiation factors have similar roles to prokaryotic initiation factors. eIF1 and eIF5 together bind to the ___ and act analogous to prokaryotic ___, while eIF1A binds to the ___ and acts analogous to prokaryotic ___, thus preventing the large ribosomal subunit from binding. |
E site, IF3, A site, IF1 |