USCSOM: Biochemistry: L34-35 Gene Expression 2
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| What do sigma factors do in E. coli? | direct E. coli RNA polymerase to categories of promoters; sigma-70
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| What is highly repetitive DNA? | 100,000 - 1,000,000 copies per genome
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| What is middle repetitive DNA? | few - 100,000 copies per genome
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| Where is highly repetitive DNA found a chromosome? | ends of telomeres and centromeres
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| What is alpha satellite DNA? | repetitive centromeric DNA
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| What does middle repetitive DNA code for? | rRNA, tRNA, histones, retrotransposons
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| What is a retrotransposons? What are the two types? | DNA sequence that has the ability to spread and move about via reverse transcriptase; SINES and LINES
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| What are SINES? | short interspersed nuclear elements
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| What is a common SINES family? What is it related to? | a1u1 family; related to 7S RNA coding; 300nt long
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| What are LINES? | long interspersed nuclear elements; codes for a reverse transcriptase
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| What is a pseudogene? | integrated DNA versions of fully processed mRNA; lack introns
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| Where does gene loss normally occur in humans? | only in the RBC
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| What happens to most cytosine residues that occur in the sequence C-G | methylated to give 5-methyl-C
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| Are expressed genes methylated or unmethylated with respect to 5-methyl-cytosine | unmethylated
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| Methylation of cytosine residues attracts what regulatory enzymes? | HDACS that prevent binding from transcription factors
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| What are HDACs? | histone deacetylases
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| What is a Barr body? | inactive X chromosome in females; densly staining; heterochromatic
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| What are CG islands? | unmethylated CG regions in promoter sequences; house-keeping genes
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| What is does maintenance methylase do? | methylates CG of the newly synthesized DNA strand based on the methylation of the parent strand
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| What is a "cis-acting" DNA element? | the nucleotide sequence to which a transcription factor binds
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| What is a "trans-acting" factor? | a protein/transcription factor that binds to a cis-acting sequence
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| What is HRE? What is its function? | hormone response element; activated by receptor-steroid complex to stimulate RNA synthesis
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| What are the three general classes of proteins that modulate chromatin structure? | chromatin remodeling; add/removal of acetyl groups; add/remove modules from histones
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| What is CREB? | a transcription factor that is modified by phosphorylation via PKA/cAMP
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| What is Pit-1 and function? | responsible for transcription of GH and prolactin; autoregulates itself once turned on
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| Why is PEPCK important for gene regulation? | has a very diverse transactivator region upstream from promoter; many physiological inputs will stimulate it
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| What is variable splicing? | splicing of a gene based on pre-mRNA molecules bound in exons; calcitonin is an example
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| What is polyadenylation? | use of a different stopping sites; adding or losing exons; IgM is an example
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| How is IgM affected by polyadenylation? | stimulation leads to upstream poly(A)and secretion where downstream poly(A) anchors the protein to the lipid membrane
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| Where does RNA editing occur in humans? | apolipoprotein B; long apoB-100 in liver and small apoB-48 in small intestine
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| How does siRNA work? | introduction of complementary RNA into cell resulting in silencing of the targeted mRNA; mRNA is "knocked down"
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| What is miRNA? | transcript silencing provoked by endogenous ds RNA; drosha processes these in nucleus
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| What is RISC? | RNAi Silencing Complex; finds mRNA with homology to the 22nt ssRNA and cleaves it
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| What nucleotides tend to make mRNAs less stable? | A and U
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| What does a "dicer" do? | dices long ds RNAs into 21-23 nucleotide fragments
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| What does Argonaute protein do? | removes and degrades ds RNA fragments to create a ssRNA fragment
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| What enzyme transports Fe in the blood? | transferrin
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| What enzyme stores Fe in the cells? | ferritin
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| How is ferritin mRNA translationally regulated? | iron causes IRE (iron responsive element)-BP to lose affinity for mRNA allowing synthesis of ferritin
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| How is transferring receptor mRNA stability regulated? | Fe decreases IRE-BP affinity for mRNA, mRNA is degraded more rapidly reducing Transferring receptor synthesis
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| What is used as a means to regulate total protein synthesis? | phosphorylation of eIF2
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| How do interferons affect protein synthesis? | IFNs induce protein kinase R which phosphorylates eIF2 in presence of dsRNA
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| How does heme regulate protein synthesis? | Heme inhibits heme-regulated kinase so that globin chains are made in presence of heme only
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| What AAs destabilize proteins? | PEST: proline, glutamic acid, Ser, Thr
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| What protein is known as the "kiss of death" ? | Ubiquitin
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| What is Beta-Thalassemia? | decreased lvl or abscence of one or two of the globin chains in hemoglobin
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