molecular 401 exam 2 lecture 1

dna to dna is

dna replication

rna to dna is

reverse transcription

rna to rna is

rna dependent rna transcription (the virus that causes covid)

complementary bases in dna through H bonding means

information stored within in each strand is redundant (each strand carries the same genetic information in a complementary form)

nucleotides on single strand can be used to

recontruct nucleotides on newly synthesized partner strand

dispersive

2 dna strands are mix matched with patches of parent and daughter regions

semi conservative

1 parent strand and 1 daughter strand on each dna

conservative

dna of fully parent or daughter strands 

what is the band density expected for conservative dna

2 bands with 1 at original density and 1 with lower density

what type of conserved is dna replication

semi-conservative

how does dna polymerase synthesize dna from 5-3

by adding nucleotides to 3’ end

dna synthesis is on ___ leading strand and ___ on lagging strand

continuous on leading strand and discontinuous on lagging strand

for lagging strand, direction of polymerization is __ to the direction of the replication fork

opposite

priming is

how a polymerase starts adding nucleotides

priming: dna polymerase can not start a new strand from scratch, they can only

add nucleotides to an existing 3’-OH group

they need a primer (a short stretch of nucleotides with a free 3’ end to begin)

priming: rna polymerases

can synthesize de novo (they can start making a new rna strand from nothing)

they don’t need a primer, they can place the first nucleotide and build from there

replication fork

Y shaped region where 2 dna strands are being separated so each can be a template for making a new strand

helicase

unwinds double stranded dna by breaking H bonds between base pairs

replisome/performing complex

cluster of enzymes working together at the fork to copy dna

enzymes at the replisome/performing complex

helicase→ unwinds dna

primase→ lays down rna primers

dna polymerase 3→ extends new dna strands

sliding clamp→ holds dna polymerase in place

dna ligase→ joins okazaki fragments

topoisomerase→ relieves torsional tension

after helicase unwinds dna at replication fork, the single stranded dna is unstable (they tend to re-anneal). what stabilizes them

single stranded binding protiens (SSBs)

primase

add the primers which provide 3’-OH group that dna polymerase needs

how many primers needed on leading strand

1

how many primers needed on lagging strand

multiple (one for each okazaki fragment)

RNase

removes the primers that were put down by primase

dna ligase

joins okazaki fragments together

dna in prokaryotic cells

each bacteria cell contains 1 circular chromosome, 1 origin of replication, 2 replication forks and 2 helicases

how does replication fork grow in dna in prokaryotic cells

grows in both directions until the whole chromosome gets replicated

dna polymerase 1, polymerase domain

low efficiency, low processivity, initiates replication and fills in the gap originally occupied by rna primers

dna polymerase 1, 3-5 domain

exonuclease domain: proofreading

dna polymerase 1, 5-3 domain

exonuclease domain: involved in dna repair

dna polymerase 3

multi subunit enzyme, takes over from polymerase 1

dna polymerase 3, polymerase subunit

high efficiency and high processivity

dna polymerase 3, 3-5 subunit

exonuclease subunit: proofreading

job of topoisomerases during termination of replication

when replication is complete, the 2 circular dna molecules (in prokaryotes) or replicated chromosomes (in eukaryotes) can become interlinked

topoisomerase 2 cuts and reseals dna to separate daughter molecules, allowing them to segregate into daughter cells

relieves supercoiling

why does eukaryotic dna get shorter (end-replication problem)

when final rna primer at the end of a linear chromosome is removed, there is no upstream 3’-OH for dna polymerase to fill in the gap

the very end of the chromosome (the 5’ end of the new strand) remains unreplicated which leads to a shortening with reach round of replication

this does not happen in bacteria because they are circular so there is no end

telomerase

adds repetitive dna sequences (telomeres) to chromosome ends

provides a template to extend 3’ end so normal replication can finish

each eukaryotic chromosome has many __. and each __ gives rise to a ___ with ___ moving in opposite directions

each eukaryotic chromosome has many origins of replication

and each origin gives rise to a replication bubble with 2 replication forks moving in opposite directions

what 3 primary dna polymerases participate directly in nuclear dna replication

polymerase alpha, polymerase delta and polymerase epsilon

function of dna polymerase alpha

begins synthesis, works with primase to make short rna-dna primers on both leading and lagging strands

function of dna polymerase delta

extends the lagging strand, synthesizes dna continuously between primers and fills in okazaki fragments

function of dna polymerase epsilon

extends the leading strand, synthesizes dna continuously in the direction of the replication fork

dna polymerase __: forms complex with __

dna polymerase alpha: forms complex with primase

limited processivity

initiates replication

no 3-5 proofreading

no 5-3 exonuclease activity

polymerase switch

dna polymerase alpha replaced by polymerase epsilon on the leading strand and polymerase delta on the lagging strand to carry out most of dna replication efficiently

synthesis of a new strand of dna only happens in the __ direction

5-3