6.1-6.4, 13.4, 9.1 Flashcards

Question

new nucelosomes must be fromed durng dna rep

Answer 1

DNA replication is only one step in chromsome duplication the complex prcoess also incldues the synthesis and incorportaon of histone and nonhistone proetins to rgeenrate nucelosomes and chromatin structure while some aspects are contorversal this is hwo it works: - syntehsis of histones and their transport into the nucleus must be tightly coordinated with DNA synetshsi bc the nascent DNA becomes incropted into nucelosomes within minites of its formation - replication fork disaasembles nucelosomes on parnetal dna - new nucleosomes asemble rapidly on newly formed duaghter dna - the ncuelosomes are mixture of old and newly formed histones, distributed randomly on the two duaghter dna molecules - although some histone modifications may be retained when nucelosomes are dissasmbled and then reasembled during replication, most arent - one reason is bc only recylces histones have mods, while abt half the histones are new - a seocnd reaosn is that hsitone mods are liable (lost quick) and so not all reccled histones retian their original marks given tha t most histone marks ar elost during dna rep, sicnetist are suprised to fid. that histone marks and chromatin strcyres associated with tme are often recaptulated after diffirinated cells undergo mitosis one answr is that after rpelcation, chromatin formed from new nucelosomes is open transcription regulatory proteins in the ncuelus bind to the open chromatin and then recruit histone modifying enzymes, recreating the chrmatin strcture of the parnetal chrosmome alt histone modfyig enzymes can bind to marks retained on some recycled hsitones incrpted ino new nucelosmes

Answer 2

linear chromsomes terminate at both ends in portetcive caps called telomeres compsoed of dna associated withs epcific proteins, these caps contains no genes but are crucial in preserving structrual integrity of each chrosmome the rpelication of ends of linear chromsomes poses a prob fro cells DNA polyemrase cant add nucleotides when the 5' cap is removed from each end - this leaves mising nucleotides in eahc strand and would reuslt in chrosmoems becoming shorter each gen telomeres and enzyme called telomerase provde a countermeasure to this limiatton of DNA polyermase telomeres consist of partcular repeptive DNA seqeunces that dont encode proteins epeats 250-1500 times number of repeats varies in each cell(sperm has highest) the same sequence occur s in all mmamals, some brid, fish etc show that simialrties in repated across phyla show its a vital functio needed for the evolution of eukaryotic organisms telomerase is an unsual enzyme that cosnsist of protein and RNA its called ribonucleoportein the RNA portion of enzyme has repast that are compelmatry to the telomere - sevres as template for adding new repeats to end of the telomere - this new addition countebalances the loss of DNA that cocurs when linear DNA molecules are copied some types of cells take advanatge of abilitu of telomerase to mainatin size of chromsome ends during cell divison but most somatic cells have little to no telomerase - after 30-50 gens, chromsomes begin to lose genes form their ends - show signs of sensecene and then die the lack of telomerase thus ensures that diffeirented somatic cells have a finite life span gemr line cells do express telomerae and miantin tehir chromsal ends without loss of genes - they have a feedback emchnism that miantains the optimal number of repeats at the telomeres so that chrosmome ends nietehr hsorten or lengthen during each gen two kidns of somatic cells do have telomerase = stem cells that allow tissue renewal and tumour cells that divide indefintly becoming immotrla (how they are tring to terat cancer now) chromsomes that are brken and detached from telomeres can be dangerous the cells contain nuclease enzyme that can degrade DNA progessivly inward from teh broken ends a second prob is from enzymes system repsonible for nonhomologous end joinging if two diff chrosmomes broekn at their ends, the nhej enzyme joins the two chrosmomes - this produces an entity with two centromeres during anapahse, if the two centroemres are pulled in opp direction, the dna between them ruptures and broekn chrosmomes segrrgate poorly or disappaer tehse examples demosntate that telomorer on normal unbroek chromsomes have important functions in proetcting the chrosmoems and mainting the correct gemenic complement in cells the protetcive function of telomeres is due to proteins that also bind to the repeats at ends of chromsome - tehse prteins forma. complex called sheltrin that folds up the telomeres into strcutrue that sheilds the repeat seqeunces from nucelases and nhej enzymes

Answer 3

transcription is the process by which the plyemrization of ribonucelotides guided by copmelemry base pairing, produces RNA trasncript of gene the template of RNA trasncript is one strand of the helix

Answer 4

trasncription is divided into 3 phaseS: initiaton, elongation and termination the enzyme rna polyermarse catalyzes transcription DNA seqeunces near the beggiing of genes, called promoters, signal RNA polyermase to begin trasncription - most promoters have idneical nucleotide seqeunces in each two hsotr regions - where rna polyemrase makes strong contact rna polyemrase adds ncuelotides to the growing rna polymer is the 5' to 3' direction - the chemcial mehcnaism of this ncuelotide adding reaction is similar to teh formation of phosphidester bonds between nucelotides during dna replication except transcriptuon using ribonucleotide triphosphates - this eenrgy bond provides enegry needed for elongation seqeunces in teh RNA products, known as terminatiors tell RNA polyermase whrr to stop transcription

Answer 5

initiatin: rna polyermase binds to dna - rna polyermase reocgnzies and binds to promoters, specilized dna seqeunce near transcirption start site the complete rna polymeerase (holoenzyme) consists of a core enzyme and a sigma subunit involved in initation the sigma subunit reduces RNA polymerases general affinity for DNa and inc enzymes affinity for promoter - forms closed promoetr complex after binding to the promoter, RNA polymerase uwnidns part of helix exposing unpaired bases in template strand the complex formed bwteen rna polymerase holoenzyme and unwound prmoter is called an open promoter complex the enzyme ideifes the template strand and guided by base pairing aligns the first two ribonucleotides at the end of the 5' end of new rna soon the rna polymerase releases the sigma subunit elongation: when sigma is released, rna polyemrase loses its enhanced affinity for promotr and gains affinity for any dna this leaves core enzyme to lveae promoter but stay bound to the gene the core enzyme moves alog the chromsome, unwinding dna the enzyme adds correct riboncuelotide to the 3' end of the chain (5' to 3' building) 50 ncuelotides per second the region of dna unwound by rna polyemrase is the trancription bubble in bubble, the nascent rna is base paired with template forming rna dna hybrid - in alreday transcribed rgeions, the dna double helix reforms displacing rna which hands out of bubble as single strand with free 5' end once enzyme has left promoter, other rna polyemrase can initaite trasncript geneticist refer to direction traveeld by rna polyermase - if u star at 5' end of gene at point a and move along in same direction as rna polywemr to ponint b u move downstream but if u start at b and move in opp diretcion to A ur going upstream termination: rna seqeunces that signal end of trasncription are terminators two types exist: intrinsic which cause the RNA polyemrase core to terminate trasncirption on its own and extrinsic terminators which require additional proteins-partcialrly polypeptide Rho to bring abt termination all are speicfic seuqences in mRNa that are trasncribed from the gene terminators often form hairpin loops (stem loops) in whcih nucleotides within the mRNA pair with compelentry ncuelotdies in sae molecule dna has the RNA like strand and the template strand

Answer 6

double stranded dna from rna template eahc vrial particle is a sphere inside whihc lies an enzyme studded genome: two idnetcal strand of RNA asociatd with many moelcules of an unrual dna polyermase known as reverse trasncriptase aids virus inject genome into human immunse system reverse trasncriptase copies viral rna genome into double stranded dna moelcule in the host cells cytoplasm double helix than tarvels into ncuelosu where integrase inserts them into a host chromsome viral genome can do two things: eitehr comandeer the hosts protein sysntehsis mahcinery which wouldj weaken tehri immune system for the HIV genome can lie latent in host chrosmome which copies and trasnmits viral geneome eveeyr cell divison reverse trasncirpate, the foudnation of life cycle of retroviruses is an excepton to the dNA to RNa to protein flow (central dogma) reverse trasncirptase also has higher inaccuracy rates HIV can muyate very often bc of this incacuracy causing it to beat the immune system crtain durgs cant work bc letal to humans etc

Answer 7

in eukaryotes, promoters are more complcated than those in bacteria trhee diff kinds of RNA polymerase exist that transcribe diff genes (like pol 2 trandcirbes genes that encoded porteins) in addition to promoter, sequences called enhancers that can be thosuands of base pairs away are also required for efficient trasncription of eukaryotic genes result of trasncirption is a single strand of RNa known as primary trasncript RNA produced by transcipton in prokaryotes is the messenger rna in euakrotic roganism, primary trasncipt has to udnergo rna processing in the ncuelus

Answer 8

the ncuelotide at the 5' end of mrna is a G in revrse orinettaion from rest of molecule; its connected through triphosphate linkage to first ncuelotide in trasncript backward G isnt trasncribed from DNA - a special capping enzyme adds it after polyermizeation of the few nculeotides enzymes known as methyltransferases then add methyl groups to the G - this forms methlated cap the 3' end isnt encoded by the gene majoriy of it is a poly a tail first a ribonucleuase cleaves the primary trasncipt to form a new 3' end; cleavage depends on sequence AAUAAA whci is ofund in poly A containg mRNA a few nucleotides upstream where the tail is added then enyzme polyA polyermase adds the A to 3' end rna polyemrase 2 continues to trasncirbe the gene for a few thosue ncuelotides downstream of poly a addition signal unlike trasncirption in prokaryotes, rna pol 2 trasncirption doesnt end at a specific location which is confusion abt termination in eukaryotes both teh cap and tail are imprtant Eukayotic translation initiation fatcors bind to the 5' cap while polyA binding protein asscoiates with teh tail at the 3' end of the mRNA the ineteraction of these proetisn shapes the mRNa moelcule into a circle circulization is improynat: it prevents mRNA from degradation and lenthens their time as messengers and it is required for initation of translation DNA nucleotide sequences seem to be longer than corespoding mRNA - likely undergo inetrnal processing seen in DMD gene - 2.5 ncuelotides long but the mRNa is only 14k the gene contains dna seqeunces that arent presnet in mature mRNA sequences found in both a genes DNA and mature mRNA are exons while the ones misisng from mRNA are intron - introns inetrupt or seprate the exon seqeunces that end up in teh mature mRNA mature mRNa must contain all codons need to translate into aa including the initiatiin and termination codons mature mRNA have sequnces at their 5' and 3' ends that arent translated but paly role in efficeny of translation - called 5' and 3' untranslated regions - just after the methylated cap and before poly a tail except for cap and tails, all sequnce in mRNA are trascnried from exons inrons can inetrupt a gene at any location - even betwen a ncuelotide making up a singe codon cells first make a primary transcirpt and then they remove intron by rna splicing (exons joined) a gene must have one more exon than it does intron theres three types of short seqeunces within priamry trasncipt - splice donors, acceptors and branch sites which help speificty of splicing these make it psosole to sevr connecton betwene intron and exon and then allow joing of exons mechnsim of splcing involves two sqeunctial cuts - first is at donor site at 5' end of intron - this new end of intron attaches to an A at the branch site located in the intron - forming a lariat teh seocnd cut is at accpetor site at 3' end - this remove intron which is degraded splicing normally reuqires a complciated intranuclear machine called the spliceosome which ensures all splicing rxns take place in concert splicome has 5 subunits called msall ncuelar ribonucleoproteins - snRNPs - each contanns a small ncuelar RNA snRNA associated with proteins in discrete partcile spliceoms assemble anew on every primary trsncipt through order additions and rearrnagements of these snRNPs allowing some snRNA to base pair with splice donor and acceptor sequnces in teh primary trasncitp bring togetehr the two exons that flank an itnron ultimely catalzing intron removal some primary transcipt can splcie without spliceosome- these rare prmary transcipts function as ribozymes - rna moelculaes that cana ct as enzymes and catalyze a specific biochem rxn ppl thought introns exist so genes rom various exon building blocks that encode modules of protein function happens

Answer 9

often RNA splicing joins togetehr the splice donor and splice accpetor at opp ends of an intron reuslting in removal of the intron and fusion of the two sucessive and adjacent exons RNA splicing is regualted that at certin times some sgnal can be ignored alternative splicing produces a diff mRNA moelcule that can encode related proteins with diff and partially oevrallping aa seqeunces and functions a primary trasncirpt can then form more thna one kidn of polypepetide in mamamls alt splicing of gene encoidng the antivody heavy chan ddtemrines whetehr the antibdy proetins become embedded in membrane of B lympocyte that makes them or instead secreted ito blood the gene for antibody heavy chains has 8 exons and 7 introns - numebr 6 has a splice donor within it - to make memeorane boudn antibody, all exons except for right part of numebr 6 are joiend. to create mRNA thats hydrophobic C termnus for secreted antibody, only the first 6 exons are spliced together including right part of 6 to form hyrophilic temrinus RNA editing: certain adonesine ncuelotdies can bea altered to inosine by ADAR enzymes - this change constitues a form of RNA editing that can alter ideiniy of codons bc I in mRNA is recognzied as G during translation allows a single mRNA splice form to endcoe two diff proteins