2 DNA Replication Flashcards
what do a-helices have to do with protein interaction with DNA?
they can fit into the major groove and interact with the nitrogenous bases
when an ORC recognizes an origin site, what happens first?
unzipping of DNA via helicase, establishment of rep fork
what class of protein is T-Ag?
helicase
is helicase ATp dependent?
yes
what are the three major proteins needed to initiate replicaiton?
- helicase (T-ag)
- Humans single stranded binding protein (replication protein A)
- topoisomerase 1
what is the function of SSB (RPA)?
required for replication, stabiliizes single stranded DNA
what is the cause of blooms disease and what are these patients at risk for?
- deficient in helicase
- risk for malignancies
what is the cause of werners syndrome? what are the symptoms?
- gene involved is a helicase
- premature aging, dwarfism, cataracts, scleroderma
what polymerase initiates DNA synthesis? how does it do so?
Pol alpha makes RNA/DNA primers
what polymerase synthesizes the lagging strand? what is this dependent on?
pol delta, PCNA (proliferating cell nuclear antigen) (clamp) dependent
what polymerase synthesizes the leading strand?
pol epsilon, PCNA dependent
what type of reaction occurs as nucleotides are added to the DNA chain?
nucleophilic attack, creating a phosphodiester bond
what is RF-C’s job in DNA synthesis?
this is a clamp loader, it is responsible for secruing PCNA which then recruits the pol delta or epsilon
the pieces of DNA that are synthesized piece meal on the lagging strand are called what?
okazaki fragments
what direction exonuclease activity does pol e and d have?
3’ to 5’ because it goes backwards to do this
what is necessary to join okazaki fragments?
DNA ligase
what is the function of dna pol gama?
mitochondrial DNA synthesis
what is the function of DNA pol beta?
repair DNA synthesis
what class of molecule do AZT (zidovudine) and acyclovir fall into?
nulceotide anologues, used to treat viral infections due to their lack of a 3’ OH
why are the effects of AZT limited?
- very toxic, it inhibits other polymerases
- eventually mutant forms of RT arise that have a lower affinity for the drug
at what checkpoint in cell division does p53 function?
G1/S
what class of protein is p53?
tumor supressor
what happens when you have a mutant p53?
cell growth is not arrested if the DNA is damaged and genetic instability occurs leading to potential malignancies
what is the molecular characterization of li fraumeni syndrome?
mutated p53, leading to multiple tumor sites
what types of insults to DNA result in base-excision repair?
x rays, oxygen radicals, alkylating agents, spontaneous reactions
what sorts of insults lead to nucleotide excision repair?
UV light, polycyclic aromatics, and hydrocarbons leading to PP, bulky adducts, and CPD
what sorts of insults lead to recombinational repair?
x rays, anti-tumor agents, leaing to interstrand crosslink and ds breaks
what sorts of insults to DNA lead to mismatch repair?
replication errors, leading to A-G or C-T mismatches, insertions, and deletions
during mismatch repair in e coli, how is the parent strand recognized?
it is methylated
what protein recognizes a mismatch in e coli?
Mut S
what is the molecular cause of fragile X?
expansion of over 200 trinucleotide repeats
what is the molecular function of myotonic dystrophy?
dramatic expansion of a trinucleotide repeat, over 1000
what is the molecular cause of huntingtons
expansion of a trinucleotide repeat
what areas of the genome are prone to insertions and deletions?
microsatellites
name the basic 4 step process of excision repair and a primary reason it needs to be done?
- incision
- excision
- resynthesis
- ligation
- UV light causes thymine dimers to form
what is xeroderma pigmentosum caused by?
abnormal excision repair nuclease that is responsible for cleaving DNA near the pyrimidine dimers
What enzyme is responsible for removing uracil from DNA when cytosine spontaneously deaminates?
uracil-DNA glycosidase
cytosine is deaminated to form what in the presence of HNO2?
uracil
Adenine deaminates to form what in the presence of HNO2?
hypoxanthine
what does alkylation of N7 of gluanine do to DNA?
causes labilization
what is the primary example of a DNA intercolator? why are these a problem?
ethidium bromide
-gives rise to insertions and deletions
