29: DNA replication

Question 1

which subunit is responsible for processivity of DNA-polymerase III

Answer 1

B2 subunit

Question 2

what enzyme unwounds DNA in e-coli

Answer 2

DnaB (helicase)

Question 3

what is the function of topoisomerase II in e-coil? and Why?

Answer 3

Introduce right-handed negative supercoils.

To avoid a topological crisis

Question 4

What steps are necessary for the preparation for the replication of DNA in e.coli?

Answer 4

1- DnaA proteins binding to DNA.
2-Single DNA-strands exposed in the prepriming complex
3- Polymerase holoenzyme assembles

Question 5

Which structure marks the origin of replication

Answer 5

hexamer structure of DnaA-molecules bound to each other and to the DNA

Question 6

in which base-pair rich regions is DNA-separation favoured?

Answer 6

AT rich regions

Question 7

How many nucleotides are synthesised in lagging strand before polymerase III let go of the lagging strand template? which subunit is reponsible

Answer 7

1000 nucleotides

sliding clamp B2

Question 8

what proofreading mechanism does polymerase III have?

Answer 8

3’-5’ exonuclease activity

Question 9

Why is it called trombone model?

Answer 9

because loops lengthen and shorten

Question 10

What is the primase called in e,coli

Answer 10

DnaG

Question 11

how are additional rounds of replication are avoided

Answer 11

by the dissociation of DnaA-assembly from origin of replication

Question 12

binding affinity of DnaA for each other and for DNA

Answer 12

weak, strong

Question 13

How many sites are there in OriC that bind DnaA

Answer 13

5 sites

Question 14

Which family is DnaA a part of?

Answer 14

p-loop NTPases

Question 15

how is replication terminated in e.coli

Answer 15

Ter-sites recognised by termination utilisation sequence (Tus)

Question 16

Tus-tur complexes and replication fork

Answer 16

If it is approached from one side, nothing happens.

approached from the opposite side, replication fork bllocked

Question 17

How many Ter-sites are there in E-coli genome

Answer 17

10 termination sites

Question 18

which chromosomes are subject to shortening

Answer 18

linear chromosomes

Question 19

How many origins of replications are there in a chromosome

Answer 19

several hundreds

Question 20

what are replication units called

Answer 20

replicons

Question 21

what is the hexameric helix in eukaryotes called?
single stranded binding protein
Sliding clamp

Answer 21

Mcm2-7
replication protein A
(PCNA) proliferating cell nuclear antigen

Question 22

how many and what polymerases are used in eukaryotic replication

Answer 22

Polymerase a (primer and polymerase) adds a primer + 20 deoxynucleotides and displaced by polymerase delta

Question 23

how many and what polymerases are used in eukaryotic replication

Answer 23

Polymerase a (primer and polymerase) adds a primer + 20 deoxynucleotides and displaced by polymerase delta

Question 24

why is linear chromosome shortened after each round of replication

Answer 24

because of the removal of RNA-primer leaving an incomplete 5’end

Question 25

G-rich at which end is found in telomeric DNA?

Answer 25

3’end

Question 26

what is the repeating G-rich sequence in telomeric DNA in humans?

Answer 26

AGGGTT

Question 27

How are telomeres replicated? and what is special about this enzyme

Answer 27

telomerases

has an RNA -template + a reverse transcriptase activity

Question 28

what is polymerase switching

Answer 28

one polymerase displaces another in a process

Question 29

mutagenic mismatches

Answer 29

mismatches that result in permanent changes in the DNA sequence

Question 30

what can damage bases

Answer 30

reactive oxygen species
deamination
alkylation

Question 31

why is oxoguanin problematic

Answer 31

binds to adenin

Question 32

why is hypoxanthine problematic

Answer 32

binds C

Question 33

how does ultraviolet light affect DNA

Answer 33

covalently links two adjacent pyrimdin residues

doesnot fit in DNA-helix and replication and gene expression are blocked

Question 34

how can x-ray damage DNA

Answer 34

by inducing breaks

and by producing high concentrations of reactive species

Question 35

which subunit in polymerasse III core enzyme is responsible for 3-5’ exonuclease activity

Answer 35

epsilon

Question 36

what distinguishes uracil from thymine

Answer 36

the presence of a methyl-group at C5 in thymine

uracil is recognised by Uracil DNA glycosylase?

Question 37

what distinguishes uracil from thymine

Answer 37

the presence of a methyl-group at C5 in thymine

uracil is recognised by Uracil DNA glycosylase

Question 38

sporadic mutations

Answer 38

Mutations occuring in somatic cells rather than being inheirted

Question 39

what is salmonella test used for?

Answer 39

used to test the mutagenic and carcinogenic risks of a certain chemical

Question 40

when is recombination of DNA used?

Answer 40

1- repairing of DNA when double stranded breaks are introduced
2- antibodies
3-Vira integrating their DNA in the host genome
4-when replication stalls , they help the replication continue
5- in knockout mice

Question 41

when is recombination of DNA most efficient

Answer 41

when the DNA- strands have very similar sequences

Question 42

which protein initiates dna recombination and what is the process called?

Answer 42

RecA in e.coli. strand invasion

rad51 in human cells

Question 43

In recombination pathways for meiosis, certain recombination structures are formed? which enzymes are used? figure 29.46 page 977

Answer 43

Holliday junctions

recombinases

Question 44

how does branch migration affect DNA-recombination

Answer 44

It affects which DNA-segments are used for the DNA-exchange

Question 45

Recombination of DNA can also occur during Cell-division between non-homologous chromosomes and they are called…..

Answer 45

translocations

Question 46

most helicases move in ……direction

Answer 46

3’-5’ direction