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39 Cards in this Set
- Front
- Back
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What are the components of transcriptional regulation? |
- transcription factors bind to enhancers and coactivators - recruit RNA polymerase to bind to start site - cofactors (such as cohesin) stabilize start site - RNA polymerase begins transcription - transcription is paused after 50 bases - elongation factors recruited for continued transcription |
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What is chromatin structure regulated by? |
ATP-dependent remodeling complexes that mobilize the nucleosome - allow regulators and transcription apparatus increased access to DNA sequences |
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What are possible functions proteins can do to remodel chromatins? |
- add modifications - writers - removed modifications - erasers - bind via modifications - readers include acetylation, methylation, phosphorylation, sumoylation and ubiquitination |
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What are master transcription factors? |
- dominant roles in control of specific cell states - capable of reprogramming cell states when expressed in various cell types |
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What is an example of master transcription factors? |
ones expressed as a group in fibroblasts (OCT4, SOX2, KLF4, MYC) used to generate pluripotent stem cells therapeutic potential |
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How do master transcription factors work in other cell types? |
- expressed at high levels relative to other TF - dominate control of gene expression by forming enhancers associated with most active genes in specific cell type - positively and negatively regulate expression of genes (cell-type-specific vs. other cell type specific genes) |
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What is polycistronic vs. monocistronic mRNA? |
polycistronic - multiple proteins can be coded for on the same piece of messenger RNA monocistronic - one gene to one transcript rule |
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What are humans? |
monocistronic mRNA |
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What are the features of human RNA? |
1) 5' end has 7-methylguanosine ribonucleoside added (5' cap) - linkage is 5' to 5' triphosphate bridge and has net positive charge 2) Poly-A tail is added after splicing by poly-A-polymerase - poly-A-binding proteins assemble onto the tail 3) 5' and 3' untranslated regions |
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What is the function of a 5' cap? |
regulate export and translation (cell can recognize cap as mRNA) |
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What is the function of the poly-A tail? |
poly-A tail and PAB proteins involved in mRNA export, stability, and translational efficiency |
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What is the function of the 5' and 3' UTR? |
contain information controlling how mRNA is handled 5' - how efficiently mRNA is translated (affects binding to ribosome, can have structural pieces that makes translation initiation harder) 3' - determines half-life of mRNA |
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Are UTR in exons or introns? |
exons - not all of an exon is translated into amino acid sequence |
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What is mRNA called before it is spliced? |
precursor mRNA (pre-mRNA) |
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What is alternative splicing? |
inclusion or exclusion of different exons leads to generation of multiple transcripts from same gene one gene can produce slightly different versions of same protein |
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What carries out RNA splicing? |
small nuclear RNAs (snRNAs) join with proteins - forms small nuclear ribonucleoprotein (snRNP)- these form spliceosome |
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What are the steps in splicing? |
1) branch point binding proteins (BBP) recognize splicing signal 2) U1 and U2 bind to 5' and 3' splice sites - U2 displaces BBP 3) U4/U6+U5 bind and bring two splice sites into close proximity 4) cleavage and lariat formation - cleavage at 5' and joining to 2' hydroxyl of A (U2 and U6) 5) U4 and U6 split - U6 displaces U1 from 5' site - error check point 6) U1 and U4 leave 7) intronic lariat cleaved from 3' splice and two exons joined together (U5) 8) intronic lariat degraded in nucleus |
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What is an example of branch point binding proteins? |
CUG-GP1 |
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What are common splicing errors? |
- exon skipping: slice out needed exon - cryptic splicing: use of cryptic site instead of splice site - can lead to frameshift both result in non-functional proteins (different than alternative splicing) |
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What is the genetic code made of? |
- codons are three base codes specifying which amino acid to add - code is degenerate - three stop codons |
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What are reading frames? |
three different reading frame changes with frameshift mutation |
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What are clinical features of Huntington's disease? |
- chorea: involuntary spasticity - severe progressive dementia - subcortical degeneration (initially in striatum - caudate and putamen) - genetic anticipation: disease gets worse with each generation (earlier onset or more severe symptoms) |
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What is the genetics behind Huntington's disease? |
- autosomal dominant - HTT gene on chromosome 4 - huntingtin protein - found in nucleus but pathogenic mechanism not fully understood |
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What kind of disorder is Huntington's? |
- polyglutamine (poly-Q) expansion - expansion of track of glutamines close to N-terminus - expanded from 17 repeats in normal to 36 or more - longer repeat = earlier onset |
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What is genetic anticipation in Huntington's disease? |
- DNA hairpin causes nucleotide expansion of the repeat during replication - longer nucleotide repeat causes an earlier onset |
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What is DNA replication? |
semiconservative - double stranded with DNA as own template |
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How does DNA replicate? |
- replication fork forms - DNA polymerase synthesizes 5' to 3' - leading and lagging strands made - lagging strand made of Okazaki fragments - eventually joined by DNA ligase |
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How does DNA expansion occur? |
- DNA polymerase slip/stutter on repeating portion of leading strand = expansion - expansion forms stable hairpin - next round: piece is stretched by DNA helicase and leads to permanent expansion - expansion can get larger and larger over time |
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When can repetitive regions of DNA contract? |
- stable hairpin occurs on lagging strand = shrinkage of repetitive region - DNA polymerase fails to copy this region - less common than expansion |
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What RNA does protein coding? |
mRNA |
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What RNA forms ribosomes? |
rRNA |
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What RNA is a translational adaptor molecule? |
tRNA (transfer RNA) |
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What RNA is responsible for processing of pre-mRNA? |
snRNA (small nuclear RNA) |
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What RNA is responsible for processing rRNA, tRNA and snRNA? |
snoRNA (small nuclear RNA) |
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What RNA is responsible for gene regulation? |
aRNA (antisense RNA) lncRNA (long noncoding RNA) |
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What RNA is involved in translational inhibition and mRNA degradation? |
miRNA (microRNA) |
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What RNA is responsible for postranscriptional gene silencing? |
siRNA (small interfering RNA) |
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What RNA is responsible for protecting genome integrity? |
piRNA (piwi-interacting RNA) |
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What is the function of eRNA? |
enhancer RNA unknown |
