Ch. 6 Learning Objectives

Question 1

Explain how a DNA double helix provides a template for its own replication

Answer 1

because DNA has complimentary base pairs

Question 2

describe the resulting daughter helices in terms of their sequence and the distribution of parental and
newly synthesized DNA strands.

Answer 2

the daughter DNA has one of the original (old) and one strand that is completely new. (semiconservative)

Question 3

Recall where along a chromosome DNA synthesis begins (ori)

Answer 3

the initiator protein binds to specific DNA sequences called replication origins

Question 4

function of initiator protein

Answer 4

The initiator protein pry the 2 DNA strand apart breaking

the hydrogen bonds between the bases.

Question 5

explain what characterizes these nucleotide sequences (ori) in simple cells such as bacteria and yeast.

Answer 5

• replication origins span approximately 100 nucleotide
  pair
• composed of DNA (A-T basepairs) that attract initiator proteins

Question 6

why do initiator proteins like to bind to DNA rich in A-T basepairs

Answer 6

they are easier to break because they only have 2 H bonds they have to break

Question 7

Compare the direction in which replication forks move with the direction in which the new
DNA strands are synthesized.

Answer 7

• The 2 forks moves away from the origin in opposite directions
• DNA replication in both bacterial
  and eukaryotic is bidirectional.

Question 8

Do prokaryotes or eukaryotes replicate faster

Answer 8

Prokaryotes because eukaryotes have a more complex chromatin structure

Question 9

Compare the bonds that link together nucleotides in a DNA strand with the bonds that hold
together the two strands of DNA in a double helix.

Answer 9

• Covalent bonds occur within each linear strand and strongly bond the bases, sugars, and phosphate groups
• Hydrogen bonds occur between nucleotides

Question 10

Explain how nucleoside triphosphates provide the energy for DNA synthesis

Answer 10

is provided by the incoming deoxyribonucleoside triphosphate itself

Question 11

Explain why an asymmetrical replication fork poses a challenge for DNA polymerization

Answer 11

• one strand is 5’ –3’ and the other 3’-5’ at each replication fork. This causes an issue with DNA replication as it makes it impossible to synthesized straight forward.

Question 12

how DNA polymerase solves the asymmetrical replication fork problem to keep the replication fork moving forward

Answer 12

• all DNA polymerases add new subunits only to the 3’ end of a DNA strand. A new DNA chain can be synthesized only in a 5’-3’ direction.\
• for the (3’-5’) strand, DNA uses the “backstitching” maneuver.

Question 13

the primers required for DNA replication leading strand

Answer 13

• rna primer is needed only to start replication at the replication origin then DNA polymerase takes over.

Question 14

the primers required for DNA replication lagging strand

Answer 14

• new rna primers are continuously needed
  to keep polymerization going.
• DNA polymerase then adds a deoxyribonucleotide to the Okazaki fragments until it runs into the previously synthesized RNAprimer.

Question 15

what 3 additional enzymes are need to join these Okazaki fragments together:

Answer 15

• nuclease
• DNA repair polymerase
• DNA ligase

Question 16

nuclease function

Answer 16

degrade the RNA primer.

Question 17

DNA repair polymerase function

Answer 17

replace the RNA primers with

DNA

Question 18

DNA ligase function

Answer 18

join the 5’-phosphate to the 3’-hydrolxly

Question 19

Name 7 proteins that form part of the replication machine

Answer 19

• DNA polymerase
• DNA helicase
• Single-stranded DNA- binding protein (SSB)
• DNA topoisomerase
• Sliding clamp
• Clamp loader
• DNA ligase

Question 20

DNA polymerase role in DNA replication

Answer 20

catalyzes the addition of nucleotides to the 3’ end of a growing strand of DNA strand as a template.

Question 21

DNA helicase role in DNA replication

Answer 21

uses the energy of ATP hydrolysis to unwind the DNA double helix ahead of the replication fork.

Question 22

SSB role in dna replication

Answer 22

Binds to single-stranded DNA, preventing base pairs from re-forming before the lagging strand can be replicated.

Question 23

DNA topoisomerase role in dna replication

Answer 23

produces transient nicks in the DNA backbone to relieve the tension built up by the unwinding of DNA ahead of the DNA helicase.

Question 24

sliding clamp role in dna replication

Answer 24

Keeps DNA polymerase attached to the template

Question 25

clamp loader role in dna replication

Answer 25

uses the energy of ATP hydrolysis to lock the sliding clamp onto DNA

Question 26

DNA ligase role in dna replication

Answer 26

uses the energy of ATP hydrolysis to join Okazaki fragments made on the lagging-strand template.

Question 27

Describe the problem created by a moving replication fork

Answer 27

when the end of a chromosome approaches, while leading strand can be replicated all the way to the end, lagging strand cannot.

Question 28

explain how DNA topoisomerases solve the moving replication fork problem

Answer 28

• in bacteria they have circular DNA molecules as chromosomes.
• Eukaryotes, DNA topoisomerase adds long repetitive nucleotide sequences to the ends of every chromosomes.

Question 29

Explain how DNA polymerase contributes to the accuracy of DNA replication.

Answer 29

DNA repair polymerases (I and III) removes the RNA, proofreads, and synthesizes DNA

Question 30

Thermal collisions

Answer 30

• chemical changes in DNA.

- purine bases (A&G) will be lost by a spontaneous reaction called Depurination.

Question 31

Deamination

Answer 31

loss of amino group from a cytosine in DNA to produce the base uracil

Question 32

UV radiation dna damage

Answer 32

cause covalent linkage between two adjacent pyrimidine bases, forming thymine dimer.

Question 33

cell metabolism dna damage

Answer 33

incorrect base-pairing during replication or to deletion of one or more nucleotide pairs

Question 34

List the three main steps involved in repairing damage that affects only one strand of the DNA double helix

Answer 34

Step 1: The damaged DNA is recognized and removed.
Step 2: A repair DNA polymerase binds to the 3’-hydroxl end of the cute DNA strand. the enzyme fills in the gap
Step 3: This nick in the helix is sealed by DNA ligase.

Question 35

Explain how the mismatch repair system recognizes and corrects replication errors.

Answer 35

• removed a portion of the DNA strand containing the error, and then resynthesize the missing DNA

Question 36

Non-homologous end joining

Answer 36

specialized group of enzymes that “clean” the broken ends and rejoin them by DNA ligation

Question 37

Homologous recombination

Answer 37

specific nuclease chews back the 5’ ends of the two broken strands at the break. Then, with the help of specialized enzymes one of the broken 3’ ends “invades” the unbroken homologous DNA duplex and searches for a complementary sequence through base pairing.

Question 38

where are the 3 places that require tons of atp

Answer 38

• dna helicase
• ## sliding clamp