Ch 9 DNA Replication and Recombination Flashcards
semiconservative replication
each of the original nucleotide strands remains in tact (conserved), despite no longer being combined in the same molecule, the original DNA molecule is half (semi) conserved during replication
equilibrium density gradient configuration
in this technique, a centrifuge tube is filled with a heavy salt solution and a substance of unknown density–in this case, DNA fragments
tube is spun in a centrifuge at high speeds; after several days of spinning, a gradient of density develops within the tube, with high-density material at the bottom and low-density material at the top
density of the DNA fragments matches that of the salt; light molecules rise and heavy molecules sink
replicon
a segment of DNA that undergoes replication
theta replication
common type of replication that takes place in circular DNA, such as that found in E. coli and other bacteria, because it generates a structure that resembles the Greek letter theta
replication bubble
the unwinding of the double helix generates a loop
replication fork
the point of unwinding, where the two single strands separate from the double-stranded DNA helix
bidirectional replication
the forks proceed outward in both directions, simultaneously unwinding and replicating the DNA until they eventually meet
requirements of replication
1) A template consisting of single-stranded DNA
2) Raw materials (substrates) to be assembled into a new nucleotide strand
3) Enzymes and other proteins that “read” the template and assemble the substrates into a DNA molecule
DNA polymerases
the enzymes that synthesize DNA, can add nucleotides only to the 3’ end of the growing strand (not the 5’ end) and so new DNA strands always elongate in the same 5’ to 3’ direction (5’->3’)
leading strand
the new strand which undergoes continuous replication
lagging strand
the newly made strand that undergoes discontinuous replication
Okazaki fragments
short lengths of DNA produced by the discontinuous replication of the lagging strand
initiator proteins
known as DnaA in E. coli
bind to oriC and cause a short section of DNA to unwind
DNA helicase
breaks the hydrogen bonds that exist between the bases of the two nucleotide strands of a DNA molecule
binds to the lagging strand template at each replication fork and moves in the 5’->3’ direction along this strand, thus also moving the replication fork
single-strand-binding proteins (SSBs)
attach tightly to the exposed single-stranded DNA
protect the single stranded nucleotide chains and prevent the formation of secondary structures that interfere with replication
bind to any single-stranded DNA
form tetramers (groups of four)
DNA gyrase
a type II topoisomerase
control the supercoiling of DNA
reduces the torsional strain (torque) that builds up ahead of the replication fork as a result of unwinding
primase
an enzyme that synthesizes short stretches (about 10-12 nucleotides long) of RNA nucleotides
primers
provide a 3’-OH group to which DNA polymerases can attach DNA nucleotides
DNA polymerase III
a large multiprotein complex that acts as the main workhorse of replication
synthesizes nucleotide strands by adding new nucleotides to the 3’ end of a growing DNA strand
has two enzymatic activities: it’s 5’-3’ polymerase activity allows it to add new nucleotides in the 5’-3’ direction; it’s 3’-5’ exonuclease activity allows it to remove nucleotides in the 3’-5’ direction enabling it correct errors
DNA polymerase I
first E. coli polymerase to be discovered
also has 5’-3’ polymerase and 3’-5’ exonuclease activities which allow the enzyme to synthesize DNA and to correct errors
also possesses 5’-3’ exonuclease activity which is used to remove the primers laid down by primase and replace them with DNA nucleotides by synthesizing in a 5’-3’ direction
tiall of E. coli’s DNA polymerases…
1) synthesize any sequence specified by the template strand
2) synthesize in the 5’-3’ direction by adding nucleotides to a 3’-OH group
3) use dNTP’s to synthesize new DNA
4) require a 3’-OH group to initiate synthesis
5) catalyze the formation of a phosphodiester bond
6) produce newly synthesized strands that are complementary and antiparallel to the template strands
7) are associated with a number of other proteins
DNA ligase
joins Okazaki fragments by sealing breaks in the sugar-phosphate backbone of newly synthesized DNA
proofreading
second process which corrects errors that do arise in nucleotide selection
incorrect positioning stalls the polymerization reaction and the 3’-5’ exonuclease activity of DNA polymerase removes the incorrectly paired nucleotide
mismatch repair
corrects errors after replication is complete
a deformity in the secondary structure of DNA is recognized by enzymes that excise the incorrectly paired nucleotide and use the original nucleotide strand as a template to replace the incorrect nucleotide
