BB451 exam 2 - DNA Replication, Recombination, Repair Flashcards
DNA structure
double helix, phosphodiester linkages of nucleotides, alternating sugar/phosphate links
complementary base pairs held by
H bonds
anti parallel
one strand 5’ to 3’ paired with other 3’ to 5’
phosphodiester bonds
linkage between 5’ phosphate group of incoming nucleotide and 3’ hydroxyl of previous nucleotide in chain
base pairings
AT with 2 H bonds
CG with 3 H bonds (harder to break)
start with ___ only 1 phosphate added
start with triphosphate, only 1 phosphate added to the strand
major and minor groove from…
asymmetric glycosidic linkage between deoxyribose sugar and each base in double helix
3 major forms of DNA
A, B, Z
A form DNA
right handed helix, franklin published, found only when dehydrated, more compressed/tilted, double stranded RNA (or RNA-DNA duplex)
B form DNA
most common, right handed helix, Watson and Crick published, stole from Franklin, 10.5 base pairs per turn
Z form DNA
left handed helix, marking location of genes in eukaryotic chromosomes
semiconservative replication
each daughter has 1 new strand + 1 old strand
DNA polymerase I function
5’ to 3’ DNA polymerase activity to make DNA
3’ to 5’ exonuclease activity (proofreading)
5’ to 3’ exonuclease activity (remove RNA primer)
most abundant DNA polymerase
DNA polymerase I
falls off
structure of DNA polymerase I
hand structure
bacteria have ____ chromosomes
circular
all DNA polymerases require a ___ to start DNA synthesis
primer formed by primase
DNA polymerase II
repair mechanisms
DNA polymerase III
responsible for most replication very processive - stays on (don't need as many as Pol I) fast - 1000 nucleotides/sec does have proofreading dimer
subunits of DNA polymerase III
2 identical sets of subunits (dimer)
2 cores: where catalysis occurs
beta clamp/sliding clamp - hold to DNA
clamp loader - closes clamp around DNA
helicase
pull strands apart using energy from ATP hydrolysis
fast enough to not slow down Pol III (1000 nucleotides/sec=100 turns/sec=6000 rpm)
single strand binding protein
covers up bases and protects strand after pulled apart
topoisomerase II (gyrase)
relieves tension, changes superhelical density
topoisomerases can…
increase or decrease superhelical density
don’t usually bring it to 10.5 base pairs/ turn (relaxed)
okazaki fragments
segments synthesized on lagging strand
must be combined together
ligase
connects okazaki fragments (after Pol I removes primer)
biotechnologists use to join DNA fragments to create recombinant molecules
___ is faster so..
leading strand is faster so lagging strand loops around –> trombone
removal of RNA primers requires
Pol I’s 5’ to 3’ exonuclease activity
-remove RNA at front end of enzyme as polymerase activity (at back of Pol I) fills in space behind it as it moves along
topoisomerases…
change topological structure of DNA molecule
supercoiling can occur when..
it has something other than 10.5 base pairs per turn
tension relived by
supercoiling
-double strands twist over each other –> helix goes back to approximately 10.5 base pairs per turn
2 types of topoisomerase
type 1 - cut one strand
type 2 - cut both strands (ex: gyrase)
drugs that inhibit topoisomerases..
can be effective antibiotics
ex: naladixic acid, ciprofloxacin
topoisomerase 7
only in E. coli/bacteria
good for antibiotics
unwinds strands, kill them, no effects on us
linking number
L=T+W
twits + writhes
twists (T)
number of times 2 helices cross each other
writhes (W)
number of superhelical turns
can be + or -
when not 0, it is a superhelical, has superhelicity
writhing occurs in an attempt of…
DNA to relax
relaxed = number of base pairs per twist = 10.5
initiation of replication in E. coli occurs at
OriC (origin of replication)
contains 3 repeats of an AT rich sequence
DNA A
several copies bind at origin of replication
DNA wraps around it –> superhelical tension –.strands come apart (AT only 2 H bonds, weak)
DNA BC complex
bind when strands come apart from DNA A
dnaB = helicase, dnaC released
DNA A released when
SSB and primase bind the exposed single strands
eukaryotic chromosomes..
linear, multiple origins or replication
telomeres
at linear ends, junk DNA
thousands of copies of repeats of short sequences
telomerase
builds telomeres
found predominantly in fetal and cancer cells and fertilized eggs, differentiated cells do not appear to have active telomerase
reverse transcriptase -
reverse transcriptase
telomerase
use an RNA template (that it carries) to synthesize DNA
other in retroviruses (HIV)
deamination of adenine –>
hypoxanthine (chemical damage to DNA)
oxidation damage to DNA –>
creation of 8-oxo-guanine
aflatoxin
made by mold, from peanut butter
causes damage to DNA
UV light causes..
dimerization of thymines
lack of repair of DNA sliding (amid repeating sequences) –>
Huntington’s disease
proofreading
3’ to 5’ exonuclease activity, as DNA is being replicated
mismatch repair
fix mismatches, after replication
nucleotide excision repair
excision of group of nucleotides followed by replacement w/ correct ones
by exonucleases
ex: removal of thymine dimers (segment removed by nuclease) or remove aflatoxin
base excision repair
uracil repair
excision of damaged base, nicking by endonuclease, repair
ex: remove U from DNA by uracil glycosylase
deamination of cytosine
–> uracil –> GU base pairs
mismatch repair in E. Coli
MutS recognizes mismatch
MutL recruits MutH
MutH nick newly synthesized strand to allow exonuclease removal of nucleotides around mismatch
p53
critical protein for monitoring DNA for damage prior to division
stop cell cycle is senses damage
if repair cant be performed –> induce apoptosis
which strand made error?
strand that is being copies is methylated
new strand with error is not
