DNA synthesis/packing Flashcards
(26 cards)
what is the nucleosome?
DNA looped round a central core of 8 histone proteins
what is a chromatosome?
DNA looped round a central core of 8 histone proteins plus H1 linker
DNA stability affected by 4 factors
hydrogen bonds
stacking- induced dipole interactions between aromatic bases
cations- positive ions prevents repulsion of Pi backbone
hydrophobic effect- hydrophobic bases buried
melting temp of DNA
70-90 degrees C
GC higher- 3 h bonds
what is the origin of replication
sequence that attracts Dna A which recruits DNA helicase which unwinds the DNA (PROKARYOTES)
parental strands separated and held in single stranded conformation (Replication bubble)
where does the energy for DNA synthesis come from?
3’ OH nucleophilic attack on the alpha phosphate group- releases bipyrophosphate- gives energy for DNA synthesis
how does DNA Pol I work
lagging strand- discontinuous replication
DNA pol I binds the okazaki fragments together and fills in gaps between them. removes primer and adds necleotide
Beta clamp- holds it all together
Single stranded binding proteins maintain it in single stranded confirmation
which polymerase is the most common
DNA pol III
also most efficient
DNA Pol III
3’-5’ exonuclease
5’-3’ polymerase
requires a template
coordinates synthesis of leading and lagging strand
component of replisome
trombone model on leading strand discontinuous replication
what does DNA ligase do
catalyse formation of phosphodiester bond between the nick
how do the histones bind DNA
histones enriched with positive aas means that it has electrostatic interactions with negative phosphate
packing ratio
packing ratio= length of B form/length of nucleus
what is the first form of packing
nucleosome- dna looped around core of 8 histone protein
how many times does the DNA wrap around the histones?
nearly 2 times
1.65
what is the packing ratio normally in the cell and what is it in replication
1000 fold normally
10000 fold in replication
how doest gel electrophoresis seperate DNA
based on molecular weight (BP) the more bp the less far it will travel
gel electrophoresis utilises the negativity of DNA. it exposes the gel to a positive current and the DNA gets pulled along. the big the peice of DNA the less far it will travel- resistance from the gel.
supercoiled travels faster than linear which is faster than coiled
how is gel visualised
using ethidium bromide intercollates between the bases and fluoresces
explain southern blotting
no
what is the difference between prokaryotic and eukaryotic origin/ termination of DNA replication
prokaryotes: one origin one termination
eukaryotes multiple origins and multiple terminations
how does DNA synthesis happen
3’ hydroxide initiates a nucleophilic attack of the new alpha phosphate group this releases bipyrophosphate- this provides energy for DNA synthesis
explain the trombone model of DNA replication
DNA can only be synthesised 5’ to 3’ and lagging strand runs 3’ to 5’ therefore to allow it to be made 5’ to 3’ the trombone model is used.
loop of DNA forms so that the two DNA pol III are moving in the sme direction
what is the replisome
only exists when attached attached to replication fork of DNA
what does the clamp loader do
assists with loading and clamping the DNA
subunits and functions of the DNA pol III prokaryotes
dimer- (two strands of DNA each strand takes a part of the dimer)
α- polymerase element
β-clamp
tau- stability of the dimeric protein- ATPase
γ- clamp loader
epsilon-3’ to 5’
