Unit 06: DNA Replication and Repair

Question 1

what is a replication machine?

Answer 1

a cluster of proteins that carries out DNA replication

Question 2

how many replication origins do prokaryotes have?

Answer 2

just 1

Question 3

how many replication origins do eukaryotes have in their entire genome?

Answer 3

10 000

Question 4

how many replication origins do eukaryotes have in each chromosomes?

Answer 4

about 220

Question 5

how long are replication origins?

Answer 5

about 100 nucleotide pairs long

Question 6

what are initiator proteins?

Answer 6

proteins that bind to DNA at the replication origin site, breaking the two strands apart by breaking the hydrogen bonds, and attracting proteins that carry out replication

Question 7

describe the movement of the replication machine.

Answer 7

moves long DNA at fork unzipping the double helix and using the parental DNA stand to synthesize a daughter strand.

Question 8

how fast do prokaryotic and eukaryotic replication machines move?

Answer 8

prokaryote - 1000 nucleotides per second

eukaryote - 100 nucleotides per second

Question 9

nucleotides enter the growing DNA strand as ____

Answer 9

deoxyribonucleic triphosphate

Question 10

how exactly does DNA Polymerase III add nucleotides?

Answer 10

catalyzes formation of phosphodiester bonds between 3’ end of the growing DNA strand and the 5’ end of the incoming nucleotide via complimentary base pairing

Question 11

how often does DNA Polymerase III make an error?

Answer 11

every 10^7 nucleotides

Question 12

polymerization and proofreading are done by different _____ in DNA Pol III

Answer 12

domains

Question 13

the synthesis of which strand in DNA replication is slower?

Answer 13

lagging strand

Question 14

how many RNA primers are needed for a lagging strand made up of 4 Okazaki fragments?

Answer 14

4! one for each Okazaki fragment

Question 15

how many RNA primers are needed for a continuously synthesized leading strand?

Answer 15

1

Question 16

how long are RNA primers?

Answer 16

about 10 nucleotides

Question 17

what is the function of nuclease in DNA replication?

Answer 17

degradation of the RNA primer

Question 18

since DNA Pol 1 is removing RNA primers, what is it using as its primer?

Answer 18

adjacent Okazaki fragments

Question 19

what energy does helicase use to unwind the double helix?

Answer 19

energy from ATP hydrolysis

Question 20

what is a sliding clamp?

Answer 20

what keeps DNA polymerase attached to the template

Question 21

what is the function of a clamp loader?

Answer 21

to lock a sliding clamp around a new DNA double helix

Question 22

when are sliding clamps attached and reattached?

Answer 22

every time a new Okazaki fragment is made

Question 23

why do chromosomes get shorter with each replication?

Answer 23

because the lagging strand is unable to be completely synthesized since the primer at the end is removed, so there is nothing for the DNA Polymerase to add nucleotides to

Question 24

what allows for the cell to recognize the difference between the natural ends of chromosomes and random breaks?

Answer 24

telomeres

Question 25

telomeres vary by ____

Answer 25

cell type and age

Question 26

which proteins protect chromosome ends and maintain telomere length?

Answer 26

telomere binding proteins

Question 27

which type cells keep telomerase on? give examples.

Answer 27

rapidly dividing cells. ex. cells lining digestive tract, bone marrow cells

Question 28

what is depurination?

Answer 28

the removal of a purine from a nucleotide

Question 29

what is deamination?

Answer 29

the removal of an amino grp from a cytosine to produce uracil

Question 30

what does UV radiation cause by promoting covalent linkages between two pyrimidines?

Answer 30

thymine dimers

Question 31

what is xeroderma pigmentosum?

Answer 31

inability to repair thymine dimers

Question 32

what can be some results of unrepaired DNA damage?

Answer 32

- substitution of one nucleotide pair for another - deletion of nucleotide pairs - stalling of replication machinery at site of damage

Question 33

can a cell recognize the difference between good DNA strands and damaged DNA strands? give examples of what can constitute a damaged strand?

Answer 33

yes! ex. thymine dimers and uracil do not belong in DNA.

Question 34

what are the steps for removal of damaged DNA?

Answer 34

1. damaged DNA is recognized and removed by the excision of the sugar phosphate backbone by nucleases, leaving a gap on one strand of the double helix. 2. repair DNA polymerase (usually DNA Pol 1) binds the 3' end of the cut strand and fills gap with complimentary nucleotides 3. DNA ligase seals the gap between new nucleotides and full DNA strand

Question 35

what repair system repairs 99% of replication errors?

Answer 35

mismatch repair system

Question 36

only one mistake in every ____ nucleotides persists using the mismatch repair system

Answer 36

10^9

Question 37

mutation in mismatch repair genes is very common in what illness?

Answer 37

colon cancer

Question 38

what can cause double stranded DNA breaks?

Answer 38

mishaps at replication fork, radiation, chemicals

Question 39

what can double stranded DNA breaks cause?

Answer 39

fragmentation of chromosome and loss of genes

Question 40

describe non-homologous end joining.

Answer 40

sticking of broken ends of double stranded DNA together before the DNA floats apart requiring the loss of some nucleotides at the break site.

Question 41

describe homologous recombination.

Answer 41

if damage occurs to DNA after it has been replicated, the original DNA can serve as a template for repair over the broken region.

Question 42

list out the steps of homologous recombination.

Answer 42

1. nuclease digests 5' end of broken strands 2. 3' end invades unbroken DNA and finds a complimentary sequence via a protein 3. invading strand is elongated by repair DNA Pol, using original strand as template 4. newly elongated strand rejoins its partner, forming hydrogen bonds between complimentary bases 5. DNA Ligase finishes the job.

Question 43

which protein do eukaryotes use to seek out a complimentary sequence in homologous recombination?

Answer 43

rad52

Question 44

which protein do bacteria use to seek out a complimentary sequence in homologous recombination?

Answer 44

recA

Question 45

how many cell cycles does it take for a permanent mutation?

Answer 45

2

Question 46

which type of mutations usually result in child cancers?

Answer 46

germ-line

Question 47

how do adults develop cancer?

Answer 47

mutations in somatic cells

Question 48

beneficial mutations are the driving force for _____

Answer 48

evolution