DNA foundations Flashcards
nucleoside vs nucleotide
side is the base and the sugar
tide includes the external phosphate group
describe the structure of DNA
a phosphodiester backbone is found on the peripheral of the unit, which runs in a 5’-3’ direction. this protects the information stored in the hydrophobic bases.
complementary bases pair via HB perpendicularly in the center
there are ~10bp per helical turn
each turn is 34A
the diameter of the unit is 20A
what is the general name(s) for the nulcetides
Adentylate, Guanylate, Cystidenylate, thymidylate, uridylate
note that for DNA there will be a deoxy information of the name, except for thymine which is only found in DNA so the precursor is not needed
why are the major and minor grooves exist
the glycosidic bonds that form between the bases and their sugar are not diametrically opposite from one another. this generates at slight ‘tilt’ in the helix so it is not perfectly symmetrical.
the major grove is 12A
the minor is 6A
why are the grooves significant
they are lined with HB donors and acceptors which allows for the attachment of other proteins for editing or replication
how is DNA compacted in bacteria and in eukary?
in bac, the DNA is commonly in the form of a plasmid. this plasmid will become supercoiled (where all bp have a pair, so its very stable.
in eukary, ~3.6m o are compacted into 5mm in chromosomes. They are wound tightly around histones to make nucleosomes. these are further condensed into chromatin.
what are nucleosome
a histone octomer with 200bp of DNA
how are nucleosomes compacted into chromatin?
the histones have positively charged tails (with asp and lys) which are able to interact with the negatively charge phos backbone
role of helicase
to separate the base pairs. it is the DnaB component to the DnaA unit. It is commonly accompanied by SSB to help stabilize the single strands that are formed.
inorder to cleave the HB a mole of ATP is used
role of primase
to lay down small RNA sequences with an available 3’ OH group, to which DNA pol 3 can attach new bp to
for the leading strand it will apply 1, for the lagging strand it will need to apply many
role DNA pol 3
the enzyme that catalyzes the attachment of new base pairs to a daughter strand, complementary to the parent template strand in the 3’-5’ direction.
it is also able to correct relation errors with exonuclease activity. when an incorrect BP is attached by pol 3, it will cause a pause, enough time for the incorrect base pair to flop into the exonuclease active site to which it will be cleaved.
roel of DNA pol 1
the remove rna primer and replace wiht DNA equivalents. responsible for DNA repair too.
what is needed by pol 3
dNTPs + Mg ( to coordinate the critical interactions with ASP)
template
primer
where does dnaA bind to? how does it know where to bind?
at the OriC site. the site to which it binds to is marked by conserved DNA sequences, slightly downstream from the TATA box
how is the lagging strand synthed
by the use of the dna pol 3 holoenzyme (enzyme with its coenzyme). a clamp loader is used, lopping the lagging strand through the B2 subunit. after 1000 bp or so, the B2 detaches, allowing for primase to enter and lay down another primer unit int the 5’-3’ direction.
