mod 4 chap 4 Flashcards
DNA
deoxyribonucelic acid is a linear polymer of 4 diff subunits - moelcules by which herediary info is trasmitted from gen to gen
many expeirments had to be done to show DNA is genetic material - GRiffith showed transmission of genetic info and then Avery, MacLeod and Mcarrt showed that the info carrying macromolecule is DNA
- the virulent bacteria even though killed caused the nonvirulent bacteria to become virulent - Grffith asserted thta a moelcule is present in debris of killed virlent bacteria carries the egntic ifnfo for virulence
- in the other three expeirment when the solution was treated with enzyme that kills DNA (DNase) the extract wasnt able to transorm nonvirulent bacteria into virulent cells - solution no longer lethal meaning DNA is geentic material
to serve as geentic material, DNA would have to be able to store gentic info, make copies, direct synthesis of other macrmolecules in cell - whne strcture of DNA was found this rveealed DNA fucntion
Nucleotides
subunits of DNA are nucleotides
consist of 5x sugar, base and one or more phosphate groups
5c sugar and phospahte form backbone and bases tsick out from sugar giving nucelotide its idnetity
sugar in DNA is deoxyribose its missing the hydroxyl goup of 2’ carbon
phosphate group attached to 5’ carbon has neg charges on two o atoms because of cellular pH whcih ionizes the phosphoris atoms losing the protons or H from hydroxyl
bases are attached to 1’ carbon
Bases are A,G,T and C
Purines are double rings which are adenine and guanine
Pyrimidines are single ring which are thymine and cytosine(technically uracil)
Combon of sugar and base in nuceloside (need phosphate to be nucelotide) - nucleoisde monophosphate and so on
nucleoside triphophates are imprtant because they are used to form DNA and RNA and also are carriers of chem energy in form of ATP and GTP
Phosphodiester bonds
3’ carbon of one nucelotide connects to 5’ carbon of next - linkage known as phosphodiester bond - phosphate in one nucleotide joins with sugar of another
stable bond that can withstand stresses
phosphodiester linkages in DNA strand give it polarity - one end differs from the other - the top has free 5’ phosphate and is 5’ end and the bottom has free 3’ hydroyxl and its 3’ end
Double helix
Watson and Crick took xray crtsalography results from Franlin and Wilkins - it showed that DNA had helical structure with simple repeating structure along its length, but they were incomplete
second piece of info was from CHargaff who said number of nucelotide base adenine equals number of molecules of thymine base and same g and c
third piece of info came from Donohue and Griffith = dtermined that most likely A paired with T adn G with C
Watson and Crick made double helical strcyre with backbone on outside, bases inward, and had the compelntary base pairing
knwoing strcure allowedto understnad how gentic info is stored, replicated and directed syntehsis of other macromoelcules
the outside countours of the twisted strands form an uneven pair of grooves called major and minor groove - important because proteins that interact with DNA often recognzie partciualr sequnce of bases by making contact with bases by the major or minor groove or both
DNA strands are antiparallele
specificty of base pairing is brought about by H bonds that form between A and T (2) and C and G (3) - weak bodns but many together give DNA stablity
Stability also brought by interactions between bases in same strand - base stacking occurs because the nonpolar flat surfaces of bases tend to group together away from water and then stack up on eachother as tight as possible
DNA strcuture and function
genetic info stored in DNA in liner sequence of base pairs
Lack of seuqence constraint implies that genetic info in DNA can be encoded in the seqeunces of bases along DNA
Structure of DNA like base pairing hints how DNa is copied
DNA can serve as genetic material becasue its able to specifiy exact copies of itself through replication
faithful replication is imprtant beacsue it enables DNA to pass genetic ifno from cell to cell and parentto offpsring
compelemtary double stranded nature of double helix suggest emchanism by which DNa replication takes place:
- two stands unwind and sperate into single strands
- parental starans serve as template for duaghter strands
- synthesis of new strand through DNA polymerase
- two moleucles of DNA both conating one parental and one duaghter
- reproducing sequence of ncuelotides as precisely as possible is imprtant becasue unrepaired error reuslts in mutation which is change in gentic info
most active molecules in cells are porteins, icluding enzymes that convert energy into usbale forms and the proteins that rpovide strcural supprt
To specfiy aa seuqence of proteins, DNA acts through RNA
flow of genetic info is from DNA to RNA to protein - central dogma
first step in decoding DNA is trasncription in which geentic info in a moelcule of DNA is used as a template to generate a moleucle of RNA - base pairng between ncuelotides in DNA and RNA enables info stored in dNA to be transferd into RNA (same language)
Secodn step is translation - moelcule of RNA used as a code for seuqence of aa in portein - change of langauge
sometimes info flow can go from RNA to DNA
transcription and translation are two steps in process of geen expression which is the productin of a functional gene product - gene expression is regulated (expressed only when needed)
flow of geentci info form DNA to RNA to protein applies to both prokaryotes and eukaryotes - but details differ
- in prokaryotes trasncription and trasnlation happen in cytoplasm
- in eukaryotes trasncription is in nucleus and translation in cytoplasm - speration allows for additional levels of gene regulation
RNA
polymer of ncuelotides linked by phosphodiester bonds - similar to DNA
- sugar in RNA is ribose which has OH on 2’ carbon
- Base uracil instead of thymine (hydrogen on 5’c)
- the 5’ end of RNA molecule is typically triphosphate (ratehr than monophosphate)
RNA usually shorted than DNA and RNA is single stranded but can fold upon itself to form base pairs
Trancription
As region of DNa unwinds, one strand is used as template for synthesis of RNA trasncript that is complementary but contain U
trasncript produce by polymerization of ribonucleoside triphophates
enzyme that carries out polyemrization is RNA polymerase which acts by adding succesive nucelotides to 3’ end of growing trasncript
nontemplate strand isnt trasncribed
Initation is frist stage: RNA polymease and other proteins are attaracted to double stranded DNa, DNa strands are seperated and tarncription of templates strand begins
Elongation: succesive nucleotides are added to 3’ end of growing RNA transcript as RNA polyemrase proceeds along template
Termination: RNA polyermase encounters sequence in template strand that causes transcription to stop and RNA to be released
nucleic acids synthesized by addition of nucleotides to 3’ end (5’ to 3’ end) - so the DNA template is read in the 3’to5’ direction
Promoter and terminator
Promoters: regions of a few hundred base pairs where RNA polyemrase and associated proteins bind to DNA - on both strands of DNA in order to recruit the porteins
Many promoters contain TATAAA sequence knwn as TATA box
Transcription happens 25 ncuelotdes downstream of TATA box and elongation occurs as RNA polymerase moves along template in 3’ to 5’ direction
Trancription happens until RNA polymerisae encounters terminator sequnce - trasncription stops here and transcript is released
diff genes in same double stranded DNA can be transcribed from opp strands - which strand is transcribed depends on oruentaion of promoter - whne promoetrs in opp direction, transcription occurs in opp directions because trasncription only proceeds by addition of ncuelotides to 3’ end of trasncript
Transcription doenst take place indiscirmntly from promoted but is regulated process
For houskeeping genes, trasncription takes place continually
For other genes, regulation of trasncription often dpeends on whetehr RNA polyermase and associated porteins are able to bind with promoter
In bacterai proomoter regointion is mediated by portein called sigma factor which asccoiaed with RNA polymerase and faciliattes its biding to specific promoters - once transicption is initated it dissaciates
one type of sigma fatcor used for trasncription of hosukeeping genes but there are other ones for genes whose expression is needed under stresful codnitions
promoter recognition in eukaryotes is more complicated
Transcription requires combined action of 6 porteins known as general trasncription factors that assmeble at promoter of a gene - assembly of geenral trasncrpition factors is needed for transcription
it also needs presence of one or more types of trasncriptional activator proteins each of which binds to a specific DNA sequnce known as an enhancer - transcriptional activator protein helps control when and in which cell trasncription of gene occurs - able to bind with enhancer DNA sequnces and with porteins that allow transcription to begin
Presence of trasncriptonal activator protein that bind with enhancers controlling expression is required for trancription to begin
Ocne trasncriptinal activator protein has bound to enhancer they attratc or recruit mediator complex of proteins which recruits theh RNA poleyrmase complex to promoter - DNA miht need to loop around because enhancers are far away from promoter
in eukaryotes RNA polermase complex responble of rtrasncription is clled Pol II - when medaitor complex and Pol II are in place, trasncription begins
RNA polymerase
Once trasncriptional initation takes place succesive ribonculoides are added to grow trasncript during elongation
trasncription happen in. bubble in which two tsrands of DNA are seprated and the grwoing end of RNA trasncript is paired with template strand
polyemrisation rxn: incoming ribonucleoide trisphosphate is accepted by RNA polyemrase if it undergoes proper base pairing - RNA polymerase orients 3’ end of growing strand so that oxygen in hydrocyl atatched to 3’ can access innermost phosphate bond of the triphosphate - oxygen attacks bond, seizes an e- and bond breaks - cleaving of bond releases energy to drive rxn that creates new phosphodiester bond atatching the incoming ncuelotide to 3’ end of growing chain
polymerization relwases pyrophohsphate which can also be cleaved
RNA polymerase
trasncription requires template DNA, supply of ribonuceloside triphosphates and RNA polymerase, the large multiprotein complex in which trasncription occurs
its inside RNa polyemrase that trasncription bubble forms and trancription takes place
Complex contains syctural featues that seperate the DNA strands
Elongation happens in polyermase
Restoring of double helix happens here
RNA polyemrase is very accurate but has no proofreading function
RNA processing
RNA transcript that comes off template DNA is primary transcript - contains complement of eveyry base trasccribes form DNA template
Includes the info needed to direct ribsoem to produce prptein correpoing to the gene
RNA moelcule that combines with ribosome to direct portein synthesis is messenger RNA
Primary trasncript in prokaryotes
primary trasncript is the mRNA in prokaryotes
ribsomes immedatly bind with special seqeunce at the 5’ end and begin process of protein synthesis
happens becasue no nucelus so not spatially seperated - instead they are coupled
primary trasncripst here often contain gentci info for syntheis of two or more proteins
molecules of mRNA that code for multiple proetins are known as polycistronic mRNA
Primary trascnript in eukaryots
Nuclear enevlope is barrier for the processes
speration allows for chem modifcation of primary trancript known as RNA processing which converts it into mRNA which can be translated
- 5’ end gets 5’ cap which is modified nucelotide called 7methylguanosine - enzyme attached modifed nucelotide to 5’ end of primary transcript - cap is linked between the 5’ carbons of the ribose sugars - is needed for translation because ribsome recognzies mRNA by the cap
- polyadenylation - addition of 250 A bearing riboncuelotides to 3’ end forming poly A tail - stabalized RNA transcript - portect the end and increases stability
- trancripts in eukaryotes contain regions of protein coding sequnece called exons and non coding regions called introns - this mod is removal of intron and joing of exons known as RNA splicing - catalyzed by spliceosome
presence of mutlipel introns allow for process of alterntive splciing in which primary trasncrupt can be spliced in diff ways to yield diff mRNA and diff protein prducts
other RNA trasnripts
not all primary transcripts are turned into mRNA - some produced by diff RNA polyermases and go under diff types of RNA processing
ex. ribosomal RNA
ex. trasnfer RNA (carried invidual aa for translation)
ex. small nucelar RNA (part of spliceosome)
