Ch 12: Cell Nucleus and Gene Expression Flashcards

Question

Telomeres

Answer 1

termial region of chromosomes contain repeated sequences (TTAGGG) repeated up to 500 times found in all vertebrate organisms essential for telomere function

Answer 2

DNA needs an RNA primer to be made RNA is degraded Afterwards -> leads to chromosome shortening = senescence

Answer 3

3' overhang invades DNA duplex and creates loop strucutre binds telomere specific proteins (Protects telomere)

Answer 4

RNA binds to telomere repeat serves as template for DNA polymerization Gap filled by polymerase enz alpha`-primase in germline cells

Answer 5

the shortest telomare length needed for replicative senescence, without this they die. cells expressing telomerase are immorrtal and never reach this =- HeLa and cancer cells

Answer 6

contain a tandemly repeated 171 bp DNA sequence called alpha satellite DNA binds to specific proteins => CENPA protein

Answer 7

related to chromosome activity more active chromosomes are centrally located, whereas periperhal chromosomes are less activee

Answer 8

chromosome capture, transcriptionally active regions are coordinated together (like an operon= expression is corrdenated ) , genes are for a singular/ common biological process

Answer 9

chromatin is crosslinked with transcriptionally active regions are expressed together. OR formaldehyde is used to cross-link protein and bind these DNA fragments in place while they are being transcribed. Digest cross linked DNA, and add biotin Tags and ligated together. the proteins binding the fragments together at the trascription regions is removed, biotin pulls down is used to to pull oyut DNA and is then sequenced for bioinformatics

Answer 10

localized areas of mRNA transcription within the nucleus corrdenated by nuclear matrix protein. nuceuls is isolated in detergents and hihg salt conditions. All that is left is the nuclear matrix protiens; how they were discovered. Play an importnat role in transcription corrdenation in the cell

Answer 11

insolube in high salt and high detergent conditions composed of netword of crisscrossing protien fibrils anchor for machinery for transcription,m RNA processing protein structure scaffold

Answer 12

higher eukaryotes have specialized cells, and specific expression of genes within specilized cells cells become differentiated still retain complete geneic information demonstrated by nuclear transplantation experiments (dolly the sheep)

Answer 13

enucleated egg cells fused with cells derived from mammary gland (epithelial cells) Reduced serum levels caused epithelial cells to enter quiescent state (G0) the unmasked unexpressed genes fused cells activated by brief electric pulse egg implanted in surrogate sheep

Answer 14

Trascriptional: control over whether a specific gene is transcribed and how often Processing level: How a primary transcript is spliced Translational level: control over whether a transcript is translated or not and if so, at what levels Post translational levels: mechanisms that regulate the activity and stability of proteins

Answer 15

yeast cells are grown in two different growth media. then you do a bulk RNA extraction, and synthesize cDNAs with an oligo dt primer (Thiamine nuclotides) when with total RNA they only stick to mRNA because they have poly-A tails. cDNAs are polymerized with fluorescent green dye Cy3 or red Cy5. Then take the mixed populations of cDNA and analyzed on a microarray = microscope grid with little cells, each cell has a gene, and the samples is hydridized to the cells and will either fluoresce red, green or yellow or nothing dictating which genes are being expressed can also tell by fluorecense intensity the level of expression

Answer 16

general transcription factors bind at the core promoter sites specific transcripiton factors bind to specific regulatory sites in gene => also interact with other transcription factors in what is known as cominatorial control DNA binding and protein-protein binding domains

Answer 17

ZInc finger motif Helix-loop-helix Leucine zipper motif

Answer 18

zinc ion coordinated between tow cysteine and two histidine residues makes afinger-like structure that fits intothe DNA groove multiple fingers allow specificity FTIIIA is a TF with 9 zinc fingers bound to DNA of 5S rRNA gene

Answer 19

dimeric MyoD complex basic aa region binds to negative DNA backbone dimerization increases diversity of regulatory factors homo or hetero dimers Myogenin promoter fused to beta-galacrosidase gene myoD(HLH TF) is and activator of myogenin

Answer 20

Helix with a leucine every 7th amino acid, hydrophobic interactions of leucine zip the two helixes together basic aa to bind to the backbone AP-1 is and example heterodimer

Answer 21

phosphoenolpyruvate carboxykinase gluconeogenic gene converts pyruvate to glucose (sort of ) = oxaloacetate to phosphoenol pyruvate enzyme synthesized when glucose is low regulation includees: =DNA regulatory sequences =Specific TF =Signal transductionpathway that activates expressison (hormones)

Answer 22

GRE TRE IRE

Answer 23

glucocorticoid response element binds to glucocorticoid receptor

Answer 24

thyryoid receptor element binds to thyroid hormone receptor

Answer 25

insulin recepotr element binds insulin hormone

Answer 26

for analyzing promoters for regulatory elements Use a reporter plasmid (like GFP) to monitor effect promoter construsts = fused promoter to a reporter and disect the promoter by removing parts of the promoter = delection constructs measured by the intensity of GFP fluorescence

Answer 27

reveals sights within a promoter that are protein binding sights Take DNA fragment (thought to be a promoter) and end lable it (P-32) take nuclear extract (including TF), and mix with labled DNA. TFs will bind to the DNA. Then we treat with DNase I, will digest the DNA but not where the protein is bound. => TF will procect from DNA digestion Fragments are separated by gel electrophoresis the only DNA fragments that will show up on the gel are those with the end lables

Answer 28

treat cells with formaldehyde to kill cells and cross-link transcription factors to DNA Isolate chromatic and shear it into fragments incubate TF bound DNA with antibodies that bind the TF of interct Chromnatic immunoprecipitation (ChIP) reverse cross-links and puriify DNA amplify DNA fragments with flurorescent probes and hybridize DNA to a microarray (this time to intergenic// non-coding regions) to find response elements = promoter sequences

Answer 29

glucocorticoids (chrtisol) secreated during stress glucocorticoid receptors (GR) binds hormone Translocated to nuclues hormone/ receptors dimer binds to GRE palindrome

Answer 30

1) interact with casal transcription machinery (RNA pol) 2) act on chromatin to change stas => Remodeling complex, histone modificaiton complex

Answer 31

acetylation localized primarily int he promoter region of active genes H3K36 methylation occurs moslty in the transcribed regions Methylated HK36 recruits Rpd3 enzyme that deactylates lysine residues Deactylated lysine resides prevents initiation of transcription within the coding region

Answer 32

DNA is respressed state = deactylated GR binds and recruits CPB coactivators (histone acetyltransferase) lysine redsides acetylates acetylated histones recrutie SW1/SNF remodeling complex TFIID binds to open region of DNA-=TAF 250 and RBP acetylate additoinal nucleosomes RNA pol II binds to promoter

Answer 33

sliding exposes TATA site Reorginization of histone octamer provides access to promoter histone variants exchanged for H2A/ H2B Histone octamer disassembled

Answer 34

5' end of gene has highly defined chromatin structure Necleosome free region (NFR) at transcription start site -1 nucleosome undergoes most extensive modifications upon transcriptional activation modificaitons at the beginning and the ending of the gene

Answer 35

RNA pol II held downstream of promoter held in paused state by inhibitory factors DSIF and NELF inhibiton relived by phosphorylation and elonation factors ELL to quickly recruit RNA pol II transcription factors may act at level of transcritipns elongations permits rapid activation of genes

Answer 36

HDAC activitiy deacetylates histones Histone methytransferase methylates histones => Lys 9 of histone H3 figure 12-48 deacytelated and methylated Greater activity of acetylase (KAT) turns promoter on Balance between acetylation and deacetylation can cause promoter to be responsive to activation Greater activity of deacetylase (KDAC) turns promoter off promoters ina responsive state= balance between on and off (not black and white)

Answer 37

lncRNAs guide protein complexes to specific sites on chromatin HOTair lncRNA transcribed form HOXC locus two main roles 3' end interactes with the coREST complex to demethyalltes H3K4 LSD1 resides 5' ends of HOT air interactes with PRC2 complex and methylates H3 K27 resides Results in Transcriptional respression of HOXD locus HOXC gene turns off the HOXD gene

Answer 38

epigenetic control of gene exprsssion by methylation of promoters maintains inactive state methylation at CG rich islands (Dnmt1 enzyme) (Symmerical recognition site)

Answer 39

methylation levels change during development Blastocyst has low level of methylation adult somatic cells highly methylated in Dolly they reversed these methylation paterns to get back to the primordial germ cell stage through starvation

Answer 40

selective methylation of alleles depending on maternal or paternal origin genes remain imprinted in developing embryo associated with rare geneic disorders preder-willi syndrome-deletion of portion of chromosome-15 indiciduals only affected when mutated chromosome inherited from father => maternal chromose is methyalted (not active)

Answer 41

In fibroblasts both exons EIIB and EIIA are present but not in lever mRNA where they are both missing alternative splice varients trans acting factors in different cell types vary

Answer 42

a) changes in 5' splice site can affect pairing with U1 snRNA => two potential 5' splice sites b) SR proteins bind to Exon or Intorn splicing enhancer (ESE, ISE) sites => hnRNP proteins bind to wxon or intron suppressor sites (ESS, ISS) => Reguatles whether U2AF, U1snRNP, and U2snRNP bind to pre-mRNA +> influence if cryptic splicing ro exclusion of the exon

Answer 43

15% of point mutations linked to human disease cause splicing defects mutations often occur in exons => not in splice sites =>dont create cryptic splice sites Often cause exon exclusion or inclusion => mutations in purine rish ESE sites (exon splicing enchancer sites) => also occur in ESS sites (exon splicing supressor sites)

Answer 44

three main transcripts 2kbp in nucleus 6kbp in neurons 9kbp in retina nad peripheral necrvous system in adult human brain exons 2, 3, and 10 are alternatively spiced 5 isoforms of tau protein iclusion of exon 10 produces 4R tau isoform exclusion of exon 10 produces 3R tau isoform ratio of 3R tau to 4R tau is crucial for microtubule assembly 1:1 ratio required

Answer 45

translations control => mRNA localization (fly embryos) => mRNA stability ==> mRNA degredation posttranslational control => protein degradation => proteasome structure/ function

Answer 46

3' UTR sequence determines location of mRNA RNA binding proteins bind recognition sequence Bicoid at anterior end oskar at the posterior end swap UTRs and the chromosomes will move in opposite directions

Answer 47

figure 12-56b does not matter that you are inhibitng the production of transcripts with actinomycin becuase they are already present

Answer 48

CPEB protein phosphorylated (after fertilizaton) => maskin displaced => recruites CPSF protein CPSF protein recruits poly A polymerase => dissociation of maskin from eIF4E => recruitment of eIF4G (required for translation)\ calcium activated protein kinase = CPEB masked to unmasked transcripts

Answer 49

changing cellular environment => stress (heat) activates protein kinases ==> Phosphorylates eIF2 (blocks furhter translation) ``` specific kinases for different stressors => heatshock => viral infection => unfolded proteins => amino acid starvation ```

Answer 50

ferritin protien binds and blocks toxic effect of iron (iron buffer) expression increases in response to high iron levels irons binds the response elements IRP in the inactive state such that translation is active (IRP is repressed//in inactive state)

Answer 51

deadenylase degrades poly A tail decapping enzyme degrades G cap after poly A tail and methyl guanosine cap are removed, exonuclease degrades mRNA in a 5' to 3' direction 3' tail fold mRNA to accosiated wtih 5' cap to protect mRNA from degredation exosome degrades from the 3' end

Answer 52

in cytoplasmic granules called P-bodies

Answer 53

miRNA bind to the 3' UTR to inhibit translation early embryonic development requires miRNA translation control Experiments conducted in whihc specific miRNAs are deleted ``` example =deletion of miR-1 class of miRNA results in defects in heart development ``` -> may be due to overexpression of specific mRNAs

Answer 54

deadenylation followed by decaping and degredation proteolysis: degradaation of nascent peptide initiation block: repressed cap recognition or 60s joining elongation block: slowed elongation or ribosome 'drop-off'

Answer 55

proteaseomes digest abnormal proteins => misfolded, incorrectly associated Proteins marked by ubiquitin protein => directs protein to proteasome