Ch 9 DNA Replication and Recombination

Question 1

semiconservative replication

Answer 1

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

Question 2

equilibrium density gradient configuration

Answer 2

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

Question 3

replicon

Answer 3

a segment of DNA that undergoes replication

Question 4

theta replication

Answer 4

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

Question 5

replication bubble

Answer 5

the unwinding of the double helix generates a loop

Question 6

replication fork

Answer 6

the point of unwinding, where the two single strands separate from the double-stranded DNA helix

Question 7

bidirectional replication

Answer 7

the forks proceed outward in both directions, simultaneously unwinding and replicating the DNA until they eventually meet

Question 8

requirements of replication

Answer 8

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

Question 9

DNA polymerases

Answer 9

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’)

Question 10

leading strand

Answer 10

the new strand which undergoes continuous replication

Question 11

lagging strand

Answer 11

the newly made strand that undergoes discontinuous replication

Question 12

Okazaki fragments

Answer 12

short lengths of DNA produced by the discontinuous replication of the lagging strand

Question 13

initiator proteins

Answer 13

known as DnaA in E. coli

bind to oriC and cause a short section of DNA to unwind

Question 14

DNA helicase

Answer 14

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

Question 15

single-strand-binding proteins (SSBs)

Answer 15

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)

Question 16

DNA gyrase

Answer 16

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

Question 17

primase

Answer 17

an enzyme that synthesizes short stretches (about 10-12 nucleotides long) of RNA nucleotides

Question 18

primers

Answer 18

provide a 3’-OH group to which DNA polymerases can attach DNA nucleotides

Question 19

DNA polymerase III

Answer 19

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

Question 20

DNA polymerase I

Answer 20

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

Question 21

tiall of E. coli’s DNA polymerases…

Answer 21

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

Question 22

DNA ligase

Answer 22

joins Okazaki fragments by sealing breaks in the sugar-phosphate backbone of newly synthesized DNA

Question 23

proofreading

Answer 23

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

Question 24

mismatch repair

Answer 24

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