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181 Cards in this Set
- Front
- Back
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What do microarray studies document?
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When specific genes are expressed
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What is clustering used for?
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Identification of genes that have similar expression profiles
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What are 2D protein gels used for?
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Identification of proteins expressed in specific cell types
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How many RNA polymerases do prokaryotes have?
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Only one
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How many RNA polymerases do eukaryotes have?
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Three
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What does RNA pol I transcribe?
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Pre-ribosomal RNA
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What does RNA pol II transcribe?
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mRNAs, some snRNAs, and miRNAs
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What does RNA pol III transcribe?
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tRNAs, 5S rRNA, some snRNA
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What does the TATA box do?
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A DNA sequence: Positions the RNA pol II complex in relation to the transcription initiation site
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What is a promoter proximal element?
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A DNA sequence: Regulates transcription but only when in proximity to the promoter (UAS in yeast)
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What are enhancers?
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A DNA sequence: Works from a distance, often 50 or more kb away
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What are transcription factors?
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Proteins that regulate transcription in eukaryotes
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What are basal transcription factors?
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Proteins always present in the transcription initiation complex and required to recruite RNA pol II (TFIIA,B,C...)
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How can transcription factors be purified?
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Standard Chromatography, Affinity chromatography using target DNA, DNAse I footprinting
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What is the activation/repression domain of transcription factors?
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Usually it is a binding site for various co-repressors and co-activators.
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Transcription factors usually have two domains consisting of what?
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DNA-binding domain and Activation/Repression domain
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How do chromatin remodeling complexes work?
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They attach to a gene activator protein then use ATP hydrolysis to disrupt chromatin association, and allowing other proteins to bind to DNA or alter the nucleosomal positioning
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How might binding of chromatin remodeling complexes be regulated to ensure that they remodel proper segments?
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Acetylation of histones
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What are the ways in which activators work?
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- Recruit co-activator histone acetyltranferases to loosen chromatin to expose binding sites
- Recruit co-activating chromatin remodeling complex to move nucleosomes - Recruit chaperones to remove or replace nucleosomes (histone variants - Direct stimulation of Pol II pre-initiation complex - Indirect stimulation of Pol II complex by recruitment of the mediator complex |
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How does activator directed histone hyperacetylation work?
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Activator Gcn4 binds to its upstream activator sequence on DNA and recruits Gcn5 (HAT A) via its activation domain. Acetylation by Gcn5 allow additional transcription factor access and formation of the Pol II complex.
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What is the function of a bromodomain?
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Proteins with a bromodomain can directly bind to acetylated core histones
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How does repressor directed histone deacetlyation work?
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Ume6 binds to URS1 and recruits co-repressor complex Rpd3 via its repressor domain. Histone deactylase of Rpd3 deactylases histones and causes increased chromatin compaction.
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What is the HO gene?
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A gene in yeast involved in mating type switching
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How is the HO gene activated?
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Activator SWI5 binds to an enhancer element and recruits SWI/SNF and Gcn5 (HAT A). Gcn5 acetlyates core histone tails. Decondensation allows SBF activator to bind to the proximal promoter where it recruits the mediator complex. The mediator then allows Pol II preinitiation complex to assemble.
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What is SWI/SNF?
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An activating chromatin remodeling complex.
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What is unique about activation of transcription at the TTR gene promoter in hepatocyes?
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All 5 activators must be present
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What are the steps in pre-mRNA processing?
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-Addition of 5' cap
-Association with hnRNPs -Cleavage of pre-mRNA near the 3' end -Addition of polyA tail at the 3' end -Splicing -mRNA transport from nucleus to cytosol |
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What is the purpose of pre-mRNA processing?
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-Removal of introns
-Stabilization (protection from nucleases) -Preparation for transport from nucleus -Preparation for initiation of translation |
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When is the 5' mRNA cap added?
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As soon as the nascent RNA chain emerges from the transcription bubble
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What is the purpose of the 5' mRNA cap?
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Protection from nucleases and targeting of RNA to cytosol and involvement in initiation of translation
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How are 5' mRNA caps created?
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The Gppp caps are created by a capping enzyme that associates with the phosphorylated CTD of RNA pol II soon after transcription initiation
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Describe the activity of hnRNPs
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Nascent RNA associates with proteins to form hnRNPs which prevent formation of secondary structures and degreadation. It also assists in splicing and transport of RNA out of the nucleus.
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What are splicing complexes associated with?
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The CTD of RNA pol II, which is very long and provides a scaffold for binding of protein complexes that process mRNA
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What is splicing catalyzed by?
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snRNPs. 5 snRNA's associate with 6-10 proteins to form snRNPs which all form the spliceosome. The RNAs of snRNPs are the major catalysts of splicing.
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What is special about intron/exon size?
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Intron size varies significantly while exons are usually 150 bp
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How do SR proteins work?
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They assemble at exon boundaries and bind to sequences inside exons names exonic splicing enhancers, interacting with each other and promoting U1 and U2 snRNP binding
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What is the purpose of SR proteins?
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Defines exons so as to enhance efficiency and accuracy of splicing especially with large introns. They also play a role in alternative splicing and mRNA export
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What is the purpose of the poly A tail?
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Protects mRNA from degradation in the cytoplasm and aids in transcription termination, export from the nucleus, and translation
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What happens in mRNA export?
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mRNAs are exported as a complex with hnRNP and is bound by NXF1/Nxt1. NXF1 interacts with SR proteins. The cap is required for transport. As mRNA moves across the pore, RNA helicase of the pore fibers facilitates remodeling. Some hnRNPs dissociate before entry and some (NXF1, CBC, and PABII) in the cytoplasm. CBC is replaced by eIF4E and PABII by PABI in prep for translation
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How do we know the 5' cap is involved in nuclear export of RNAs?
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snRNAs are transcribed by either RNA pol II or III. Those by III (U6) lack a cap and is not transported out.
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What is special about snRNAs transcribed by RNA pol II?
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They are exported to the cytosol where they associate with snRNP proteins and go back to the nucleus as snRNP particles
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What are Cajal bodies?
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Small subnuclear organelles involved in final assembly of snRNPs and telomerase.
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What is SMN?
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Survival of moter neuron protein, enriched in cajal bodies. Mutation in SMN causes spinal muscular atrophy.
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What are fibrillar regions of the nucleolus rich in?
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RNA pol I
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What are granular regions of the nucleolus rich in?
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Ribosomal subunits
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What function can rRNA genes have?
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Can act as a nucleolar organizer. One gene in drosophila can initiate nucleolus assembly
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How can the nucleolus generate rRNA?
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10 chromosomes from the nucleolus expand outward to contribute rRNA producing DNA loops
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How does RNA pol I contribute to rRNA?
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It synthesizes 45S pre-rRNA
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What happens to 45S pre-rRNA?
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It is packaged into a large 80S RNP particle
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What happens to 45S RNA after packaging into a large 80S RNP?
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45S RNA is cleaved into smaller parts by snoRNPs including U3 RNA
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What happens to 45S RNA after cleavage?
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Methylation of pre-rRNA and conversion of uridine into pseudouridine and incorporation of 5S RNA
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What occurs after incorporation of 5S RNA?
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Formation of a small and large ribosomal subunit (40S and 60S) and export via nuclear pores
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Where does assembly of telomerase occur?
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Nucleolus
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What do correctly folded ribosomal subunits bind in order to exit the nucleus?
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Nmd3 and exportin-1
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Why are some mRNAs not transported by microtubules and microfilaments and where to?
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Some mRNAs are transported to synapses of motor neurons and have shorter poly A tails preventing translation until they reach the synapses where their tails are elongated
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How do haploid yeast cells mate?
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a and alpha cells secrete pheramones which is recognized by the other leading to cell fusion, nuclear fusion and meiosis
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What happens to diploid yeast cells when they have nutrients and without?
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With nutrients meotic growth of diploid cells occurs. Without the cells sporulate into haploid a and alpha cells.
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What is the mating type of yeast cells dependent on?
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Whether the MAT locus contains the a or alpha coding sequence
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How does mating type switching occur in yeast?
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Either a or alpha coding DNA sequence is copied from silenced MAT genes HMLalpha and HMRa
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Where is the HO gene only activated?
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The mother cell so switching can only occur there
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How does HO activation occur?
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Swi5 binds to URS1 and Swi4/Swi6 binds to URS2 upstream from the HO gene
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Why is HO only activated in the mother cell?
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A repressor of Swi5, Ash1, is only present in the daughter cell
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How is Ash1 only present in the daughter cell?
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A myosin V motor, Myo4, distributes Ash1 to daughter cells
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How do miRNAs regulate mRNA translation in the cytoplasm?
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They cause translational repression of mRNAs by being complementary short RNAs that hybridize to the 3’ UTR
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How do siRNAs regulate mRNA translation in the cytoplasm?
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They promote degradation of target mRNA
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Other than miRNAs and siRNAs, how is mRNA translation in the cytoplasm regulated?
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mRNA degradation is initiated by de-adenylation and cytoplasmic polyadenylation stimulates translation initiation
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What is RNAi?
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RNA interference by miRNAs or siRNAs which form double stranded structures which are targeted to mRNAs by RISC
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What is the primary role of siRNA?
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Defense against viruses by cleavage
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Where are degraded mRNA accumulated?
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In cytoplasmic organelles called P-bodies
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What plays a key role in silencing of centromeric DNA?
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Double stranded RNA by binding to repeated sequences of heterochromatin DNA
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What does injection of dsRNAs into plants induce?
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Widespread DNA methylation and transcriptional silencing
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What proteins are required for making dsRNA?
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Argonaut and dicer
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What role may dsRNA have with histones?
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May act as sequence-specific guides to target histone and DNA modification enzymes to specific DNA sequences
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What effect does injection of double stranded siRNA have organism-wide?
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Organism-wide downregulation of the target mRNA
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What does organism-wide downregulation by siRNA suggest since it requires an RNA replicase like enzyme?
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That siRNA can be copied and passed between cells
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What can RNAi be useful for?
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Supression of specific target genes which may be useful in gene therapy, silencing genes in a hyperactive disease state
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What does the length of the poly A-tail regulate?
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longevity of mRNA and their competence for translation
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What is the function of mRNAs with short polyA tails?
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storage for a proper stage in development to be activated for translation
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What does the initiation of mRNA require?
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Activation of a cytoplasmic form of PAP
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What does activation of PAP require?
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phosphorylation of the CPEB protein which recruits CPSF and PAP
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What is the function of PABP1 proteins?
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Binds and stimulates formation of the translation initiation complex
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What is the function of PolyA?
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- Assists in transport of mRNAs into the cytosol
- PolyA-binding protein I stimulates translation by interacting with the ribosomal subunits - PolyA/PABI interacts with eF4E forming a circular polysome |
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What occurs in degredation of mRNAs with a short polyA tail?
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PABI protein falls off and prevents interaction with the 5’ cap and translation initiation factors. Then decapping enzymes remove the cap and degradation occurs from both ends
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What special property do mitotic cells have?
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A dominant M-phase promoting activity (MPF)
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What is M-phase Promoting Factor?
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Activity which can induce a premature M-phase when added to interphase and also describes the same activity found in eggs and oocytes
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In oocytes and eggs the first rounds of the cell cycle occur in the absence of what?
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Transcription
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Where are all cell cycle components that are required stored?
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In the cytoplasm either as inactive protein or in mRNA form
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How are stored proteins for the cell cycle activated?
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Post-translational modifications when needed (phosphorylation)
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What are the events that occur in cycling extracts?
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-Sperm nuclei is added to cycling egg extracts
-Nuclear envelop forms around sperm chromatin -DNA replicates one time -Sperm chromosomes condense -Nuclear envelope breaks down -Nuclei go through metaphase/anaphase -Chromatin decondenses |
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What does MPF activity depend on the presence of?
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Cyclin B
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What needs to be translated to activate cycling?
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Cyclin B mRNA
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What is the cdc2- gene?
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recessive allele, where duplication of DNA occurs but no mitosis, resulting in an elongated cell
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What is the cdcD gene?
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dominant allele that gives the wee phenotype of entering mitosis prematurely, resulting in small cells
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How is wildtype cdc2 gene cloned?
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By complementation. cdc2- cells are grown at a permissive temperature, transformed with a genomic library plasmid, and incubated at 35C. The colonies that grow are picked and the rescuing plasmid isolated and sequenced
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What does cdc2 encode?
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A protein kinase
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What does cdc2's protein suggest about the cell cycle?
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That cell cycle regulation is based on phosphorylation
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What is cdc2 a component of?
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MPF, which is a heterodimer of cyclin B and cdc2 kinase
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cdc2 is one example of a what?
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Cdk (cyclin dependent kinase)
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What is a Cdk?
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A cyclin dependent kinase is a kinase with a regulatory cyclin subunit
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What is cyclin B in yeast encoded by?
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cdc13 gene
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What does MPF phosphorylate?
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-Microtubules for dynamics during mitosis
-Nuclear lamins for disassembly of the nuclear envelope -Condensins for chromosome condensation -Eg5 kinesin-5 for targeting kinesin to centrosomes promoting centrosome separation -Histone H1 for increased chromatin condensation -other proteins including motors which act during prometaphase in chromosome congression |
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How does MPF act as an inhibitor?
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It phosphorylates myosin's inhibitory site until it drops in activity in late anaphase and a phosphatse removes the phosphate
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What does a deficit and excess of cdc25 cause?
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Deficit causes an excess of wee1 resulting in elongated cells, while excess causes deficit of wee1 resulting in small cells
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What is the primary function of cdc25?
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stimulates MPF
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What is the primary function of wee1?
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Inhibition of MPF
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How is MPF regulated?
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wee1 kinase phosphorylates tyrosin and CAK phosphorylates threonine then cdc25 activates MPF by dephosphorylating tyrosine
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What is the importance of CAK?
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It makes MPF competent for activation allowing for accumulation of a large pool of MPF to be activated by one event (dephosphorylation)
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What is important about CDK (cdc2) when free?
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The T loop blocks access of substrate proteins to the ATP site (free CDK has no kinase activity)
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What does binding of cyclin to CDK (cdc2) do?
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Shifts the T loop and activates CDK as kinase
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Where is cyclin B translocated at the onset of prophase?
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Nucleus by phosphorylation of its NES signal sequence
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How is a positive feedback loop active in mitosis onset?
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Active MPF phosphorylates wee1 and cdc25 which activate more MPF
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What does MPF do to lamins?
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Phosphorylates them to disassemble the nuclear envelope
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What important cell cycle events are regulated by ubiquitin?
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-Destruction of mitotic cyclins late anaphase/telophase (APC and Cdh1
-Destruction of securin, triggering anaphase A movement of chromatids (APC and Cdh1) -Destruction of CKI - cyclin inhibitor in the S phase (SFC complex) -polo kinases, spindle proteins, etc |
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Attachment of multiple ubiquitins to what marks the protein for proteolytic degradation?
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A specific lysine
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What activates ubiquitin?
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Enzyme E1
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What happens after E1 activates ubiquitin?
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E2 replaces E1 and acts as a conjugating enzyme
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What happens after E2 addition to ubiquitin?
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E3 recognizes specific substrates and transfers ubiquitin from E2 to the target protein
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What is APC specifically?
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An E3 enzyme
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What does E3 usually need?
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Additional proteins for substrate binding such as Cdh1 for mitotic cyclins and Cdc20 for securins
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What happens to DNA replication forks in S phase?
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Either they pass inside cohesin rings or open up temporarily
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What is MPF's interaction with cohesins?
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It phosphorylates them causing separation of chromatid arms in prophase (opening the rings but not degrading them)
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Why doesn't MPF actually degrade the cohesin rings in the centromeric region?
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The centromeric region contains a dephosphorylase PP2A so that the rings remain until onset of anaphase
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How does APC trigger onset of anaphase?
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It polyubiquitinates securin which acts as anaphase onset inhibitor. This activates separin which cleaves klesin on cohesins triggering the anaphase movement of chromosomes
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What happens to mitotic cyclins in late anaphase?
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cdc14, a phosphatase, activates cdh1 (which is kept inactive by G1 cyclins), which then activates APC to polyubiquitinate MPF
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What is the destruction box?
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Protein sequence recognized by cdc20 or cdh1 for protein degradation. Deletion of it blocks ubiquitination in mitosis.
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When are mitotic cyclins donwregulated?
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In late anaphase/telophase
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Why is MPF downregulated in late anaphase/telophase?
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MPF can no longer oppose competing phosphatases (Cdc14) leading to dephosphorylation
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What happens in late anaphase/telophase to condensins?
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Dephosphorylation promoting chromosome decondensation
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What does dephosphorylation of MPF substrates promote?
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Fusion of ER tubules on the surface of chromatin to form the nuclear envelope
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Membrane reassemble on the surface of chromatin is regulated by what?
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Ran-GTP/importin b pathway
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What occurs with excess importin beta?
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Blocking of fusion of vesicles forming the nuclear envelope
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What happens to sequester importin beta?
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Ran-GEF on chromatin produces Ran-GTP that binds to importin beta and causes release of proteins needed for nuclear envelope assembly
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What events at the surface of chromatin does ran-GTP/importin pathway regulate?
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-nuclear import/export
-spindle assembly -nuclear envelope assembly -nuclear pore insertion/assembly |
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Why are cdc28 and cdc2 interchangeable but the phenotypes of their mutations in their own species different?
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cdc2 is arrested in G2 and cdc28 in G1. In cdc2 there may be enough functional protein to complete G1 and S. Also a mutation may effect its abilty to phosphorylate some cyclins.
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What are the 3 G1 cyclins in yeast?
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CLN1, CLN2, CLN3
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What is an explanation for an extended G1 phase in yeast?
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Only one of three cyclins (CLN1, CLN2, CLN3) is sufficient for survival but mutants lacking one or two have a longer G1
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How is the relative frequency of cells in different stages determined?
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flow cytometry based on the amount
of DNA in each cell |
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CLN3 expression is based upon levels of what?
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High levels of glucose prevent expression of CLN3 due to a GAL1 promoter
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How are G1 cyclins regulated?
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They are constant degraded by ubiquitination and only cells exposed to enough nutrients sufficiently long enough will produce enough of G1 cyclins to counteract their degradation and pass the START point
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What is the cyclin inhibitor of the S phase?
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Sic1
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How is Sic1 regulated?
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In G1 high levels of cyclins phosphorylate Sic1 for degradation which is required at all 6 sites on Sic1 moving the cell to S phase irreversibly
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What is the role of cyclin S phase inhibitor Sic1?
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prevent premature DNA replication
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What do cells require for proliferation?
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Stimulation by growth factors (mitogens), proteins secreted by other cells
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What happens to mammalian cells that undergo differentiation?
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They withdraw from the cell cycle into Go phase where they are metabolically active but do not grow
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What are mammalian cyclins known as?
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Cdk cyclins
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What is RbI?
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a negative regulator of E2F, a TF required for progression into
the S phase and tumor suppressor |
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Retinoblastoma occurs when?
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The Rb gene is mutated and Rb inhibits E2Fs function by recruiting of histone deacetylase co-reppressor to the genes which are targets of E2F
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How is Rb regulated?
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CDKs phosphorylate Rb and prevent its binding to E2F.
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In mammalian cells, what allows cells to pass the START point?
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Production of Cyclin E/cdk2
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What are checkpoint mechanisms?
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Switch mechanisms that allow for control of accuracy of events during the cell cycle
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Where do checkpoints exist?
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If the occurrence of event B is dependent on the completion of a prior event A and if a loss-of-function mutation can be found that relieves the dependence
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What are the monitors of the spindle assembly checkpoint?
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- attachment of kinetochores to microtubules
- tension (that results from attachment to microtubules) |
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What does failure of a single kinetochore to form attachment to microtubules inhibit and how do you avoid this?
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Anaphase. Elimination of the unattached kinetochore using a laser
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What do defects in checkpoints lead to?
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Chromosome missegregation and results in aneuploidy which predisposes multicellular organisms for cancer
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How can spindle assembly checkpoint mutants be identified in yeast?
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anti-microtubule drug addition. cells that are mutants continue to divide and die
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What does MAD2 protein do?
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Assembles on unattached kinetochores inhibiting cdc20
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What is the function p53?
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To arrest the cell cycle in G1 due to exposure to UV radiation.
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How does p53 work?
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Rad proteins recognize UV damage and stabilize p53 against degradation and it activates transcription of downstream genes causing cell cycle arrest and DNA repair (can also trigger apoptosis)
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What is ATM?
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A G2 checkpoint kinase which transmits the damage signal to p53 and Chk1. Mutation causes premature aging, hypersensitivity to radiation, increased risk of cancer
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Where do tumors usually originate?
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Proliferative tissues
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What do tumors, to large extent, result from?
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Accumulation oncogenic mutations
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The chance of occurrence of several oncogenic mutations increases with what?
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Number of divisions
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Tumors rarely occur in what kind of tissues?
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Those that have few dividing cells
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90% of cancers are what?
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Carcinomas - those that occur in epithelial cells
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In epithelial tissue what occurs after a benign tumor (localized) forms?
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It invades the basal lamina then blood vessel and spreads to form a malignant tumor
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Normal cells are controlled by surrounding cells (niche dependent) while cancer cells become what?
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niche independent
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What cells have higher cancer-forming abilities?
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Cancer stem cells
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Why do cancer stem cells take up fluorescent dye slowly?
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They have highly active ABC pumps
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Why can cancer cells can grow in lower concentration of serum?
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some types of cancer cells produce auto-stimulatory growth factors like Transforming Growth Factor alpha
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What do normal cells require to grow but cancer cells do not?
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Substrate attachment
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Normal cells are inhibited in movement by what but cancer cells are not?
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Contact with other cells
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What changes in secretion of proteases occur in cancer cells?
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Tumor cells often secrete large amounts of proteases leading to reduced substrate adhesiveness
and helps cancer cells to invaded blood vessels by promoting digestion of the basal lamina proteins |
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Many oncogenes are components of what signal transduction pathway?
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Mitogen stimulation pathway responsible for withdrawal of cells from Go and stimulation of G1 cells that allows them to pass the “restriction” point
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What mutation in growth factors allows for constitutive activity?
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Mutation in PTK causing permanent dimerization of the receptor
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Knockout of p53 shows that it is not needed for what?
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Normal cell growth and differentiation
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What is MDM2?
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Inhibitor of p52, an oncogene
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What is ATM kinase?
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An activator of p52, a tumor supressor
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What is Bcl2?
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An apotosis suppressor which is overexpressed in cancer cells
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What does placlitaxel do?
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Blocks microtubules during mitosis and phosphorylates Bcl2, enhancing apoptosis
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What is the role of telomerase in cancer?
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Normal cells' telomers shorten and they die as they do not produce telomerase, but cancer cells reactivate telomerase.
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Why aren't cancer rates higher?
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Multiple mutations must occur in the same cell (they must occur over time)
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