Lecture 4

Question 1

what are initiator proteins?

Answer 1

several proteins that bind to DNA to unwind the double helix

Question 2

where do initiator proteins bind?

Answer 2

to the origin of replication

Question 3

what does helicase require?

Answer 3

ATP

Question 3

what do initiator proteins require?

Answer 3

ATP

Question 4

what is the job of initiator proteins?

Answer 4

help helicase bind

Question 5

what are the two types of helicase?

Answer 5

one helicase the runs in the 5’ to 3’ direction and the other helicase that runs in the 3’ to 5’ direction

Question 6

what is the job of ssbp?

Answer 6

prevent the two DNA strands from reannealing by preventing hydrogen bonds from forming

Question 7

what does DNA polymerase require to begin transcription?

Answer 7

a bound primer

Question 8

what is the job of primase?

Answer 8

make RNA primer

Question 9

In what direction does primase synthesize the primer?

Answer 9

the in 3’ to 5’ direction

Question 10

what are the steps in bacterial DNA replication?

Answer 10

1) Origin of replication
2) Binding of initiator
proteins
3) Unwinding by helicase
4) Binding of single-strand
binding protein
5) RNA primers made by
primase

Question 11

what would happen if there were no sliding clamps?

Answer 11

DNA polymerase would constantly dissociate from the template strand

Question 11

what is the job of DNA polymerase?

Answer 11

add nucleotides to the template stand in the 5’ to 3’ direction

Question 12

what is the job of the sliding clamp?

Answer 12

hold DNA polymerase on the DNA template

Question 13

how are the Okazaki fragments linked on the lagging strand?

Answer 13

DNA ligase enzyme glues the fragments together using phosphodiester bonds

Question 14

how is the leading strand made in terms of continuity?

Answer 14

continuously

Question 15

where does the leading strand start being made from?

Answer 15

a single RNA primer

Question 16

how is the lagging strand made in terms of continuity?

Answer 16

discontinously

Question 17

how many primers does the lagging strand have?

Answer 17

multiple

Question 18

which strand is the predominant helicase on?

Answer 18

lagging strand

Question 19

what is the primosome?

Answer 19

a group of enzymes involves in priming DNA including helicase and primase

Question 20

what are Okazaki fragments made of?

Answer 20

RNA primer and DNA

Question 21

what is the unwinding problem?

Answer 21

a DNA unwinds, it creates torsional strain

Question 22

which type of molecule is the unwinding problem common in?

Answer 22

circular chromosomes and large linear eukaryotic chromosomes

Question 23

how is the unwinding problem solved?

Answer 23

Solved by DNA topoisomerase

Question 24

what happens at the end of linear chromosomes?

Answer 24

during DNA replication on the lagging strand, DNA polymerase can not replicate the very end of the chromosome because there is no primer

Question 25

what is the direction of DNA replication?

Answer 25

bidirectional

Question 25

why is the shortening at the ends of linear chromosomes a problem?

Answer 25

loss of essential genetic information

Question 26

how does telomerase help the shortening of the ends of linear chromosomes?

Answer 26

adds repeated nucleotide sequences to the 3' end of the parent strand

Question 27

what are the steps of telomere replication?

Answer 27

1) RNA template 2) Resembles: Reverse Transcriptase 3) Generates: G-rich ends 4) Adds nucleotides to: 3’ ends of parental strand template

Question 28

how does loss of telomerase affect cell division?

Answer 28

inhibits cell division

Question 29

what type of cells is telomerase abundant in?

Answer 29

stem and germ cells

Question 30

which type of cell produces high levels of telomerase?

Answer 30

cancer cells

Question 31

what is the error rate of RNA polymerase?

Answer 31

1 in 10^4

Question 32

what is the error rate of DNA polymerase?

Answer 32

1 in 10^9

Question 33

how many times does the genome change every time a cell divides?

Answer 33

three times

Question 34

what are the two mechanisms for proofreading DNA?

Answer 34

1) 3' to 5' exonuclease 2) stand directed mismatch repair

Question 35

what is the job of the 3’-5’ exonuclease?

Answer 35

remove incorrect nucleotides during DNA synthesis

Question 36

what is the job of stand-directed mismatch repair?

Answer 36

detects and repairs abnormalities after DNA synthesis has occurred

Question 37

after DNA synthesis, can DNA still get damaged?

Answer 37

yes

Question 37

what happens if there are defects in repair mechanisms?

Answer 37

it can lead to diseases

Question 38

what can DNA damage be caused by?

Answer 38

oxidation, radiation, heat, chemicals

Question 39

what is depurination?

Answer 39

loss of purine bases (adenine or guanine) from DNA, leaving a gap where the base used to be

Question 40

what are the two types of spontaneous DNA damage?

Answer 40

depurination, deamination

Question 41

what is deamination?

Answer 41

the removal of an amino group from a nucleotide base in DNA

Question 42

what are two general mechanisms of DNA repair?

Answer 42

base excision repair, nucleotide excision repair

Question 43

what happens to DNA that is left uncorrected?

Answer 43

the daughter cells inherit the mutation

Question 44

what is base miexcision repair?

Answer 44

correcting one modified base

Question 45

what is nucleotide excision repair?

Answer 45

correcting groups of modified bases

Question 46

what are the two mechanisms to repair double-stranded bond breaks?

Answer 46

non-homologous end joining, homologous recombination

Question 47

what is non-homologous end joining?

Answer 47

ligating broken parts together but there is a lack of insertion of nucleotide at the repair site

Question 48

what is homologous recombination?

Answer 48

uses a template to repair broken DNA strand