02/06/2025

Question 1

what are the general steps to DNA replication

Answer 1

initiation, elongation, termination

Question 2

what are the requirements for initiation of DNA replication in bacteria?

Answer 2

1.) the GATC sites must be fully methylated at both sides of the strands in ORDER for the AT rich regions to be opened WHEN the DnaA boxes are fully occupied by DnaA binding proteis

Question 3

what are DnaA binding proteins

Answer 3

they are proteins that recognize the sequence of the DnaA boxes which are recognition sequences, with assistance, these can open the AT rich regions

Question 4

What is the role of helicase? what does it NOT do?

Answer 4

disrupts DNA helix by breaking H-bonds between the strands, it does NOT create the fork

Question 5

As helicase opens the fork more, what is formed ahead of the fork? What must be used to counteract this effect?

Answer 5

positive supercoils form ahead of the fork

Gyrase/ topoisomerase II acts to relieve this tension by inducing negative supercoils

Question 6

What are single-stranded binding proteins

Answer 6

Proteins that bind to separated DNA strands to keep them apart

Question 7

What does it mean when something is DNA dependent

Answer 7

it means that it requires DNA as a template

Question 8

what does it mean when something is RNA dependent

Answer 8

it uses RNA as a template

Question 9

what is a DNA dependent DNA polymerase

Answer 9

uses DNA to synthesize DNA

Question 10

what is a DNA dependent RNA polymerase

Answer 10

uses DNA to synthesize RNA

Question 11

what is a RNA dependent DNA polymerase

Answer 11

it uses RNA to synthesize DNA

Question 12

what is an RNA dependent RNA polymerase

Answer 12

it uses RNA to synthesize RNA

Question 13

what is the role of primase and what would happen if we didn’t have it?

Answer 13

primase adds an RNA primer to the template strand which provides a 3’ OH that DNA pol III can synthesize onto

Question 14

before DNA pol III can synthesize new DNA, what must happen first?

Answer 14

primase must make an RNA primer to provide a 3’ OH group

Question 15

what is the leading strand?

Answer 15

the leading strand is continuously synthesized by DNA pol III towards the replication fork

Question 16

how many primers does the leading strand require?

Answer 16

it requires 1 primer

Question 17

what is the lagging strand

Answer 17

the lagging strand is synthesized in spurts by DNA pol III as it is synthesized away from the fork

Question 18

how is the lagging strand synthesized as the fork opens?

Answer 18

as the fork opens, another primer is added by primase.

when DNA pol III is done synthesizing one fragment, it loops back on itself and begins to synthesize another fragment on the new primer

Question 19

how many primers does the lagging strand require

Answer 19

multiple

Question 20

what is an okazaki fragment

Answer 20

they are the fragments that make up the lagging stand

Question 21

when two okazaki fragments run into eachother, how are they fused?

Answer 21

DNA pol I acts to replace the RNA with DNA but Ligase forms the final bond between the replaced nucleotides and the DNA strand synthesized by DNA III

Question 22

what is the role of DNA pol I

Answer 22

it replaces the RNA primer with DNA

Question 23

what is the role of ligase

Answer 23

ligase forms the final phosphodiester bond between the 3’OH and 5’ phosphate group on the replaced okazaki fragments

Question 24

without ligase, would DNA pol 1 be able to fuse the okazaki fragments

Answer 24

no, ligase is required to form the final connection

Question 25

what is the ter protein's role

Answer 25

it binds to the termination sequence and prevents advancement of the replication fork

Question 26

what is the DNA pol III holoenzyme

Answer 26

it describes the 10 subunit complex that makes up DNA pol III

Question 27

what is the overall structural composition of DNA pol III

Answer 27

it is a quaternary structure as it interacts with other polypeptides to form its 10 subunits

Question 28

what is the overall structural composition of DNA pol I

Answer 28

it is a tertiary structure as it is composed of a single polypeptide and does not have other subunits

Question 29

describe the levels of polypeptide structure

Answer 29

primary is the strand itself and sequence of amino acids secondary is local folding tertiary is the 3D structure quaternary is when the 3D structure interacts with other polypeptides

Question 30

why does a gene code for a polypeptide and not a protein

Answer 30

a polypeptide is a sequence of amino acids while a protein describes its function and may require various subunits to do so

Question 31

what does the alpha subunit in the DNA pol III do

Answer 31

it synthesizes DNA at the back of the polymerase

Question 32

what does the ε subunit do in DNA pol III

Answer 32

it regulates the proofreading function

Question 33

what is the proofreading function of DNA pol III

Answer 33

an enzyme in DNA pol III can read in the 3'-5' direction and remove mismatched base pairs

Question 34

what is the 3' exonuclease site

Answer 34

it is where the proofreading occurs when a base pair is mismatched, the end of the new strand will move to the 3' exonuclease site where it will be digested in the 3'-5' direction and then resynthesized in the 5' to 3' direction

Question 35

what direction is DNA digested in the 3' exonuclease site

Answer 35

3'-5'

Question 36

what is the difference between exonucleases and endonucleases

Answer 36

exonucleases cleave DNA/RNA at their ends endonucleases cleave DNA/RNA internally

Question 37

what does proofreading DNA pol III or DNA pol I

Answer 37

DNA pol III

Question 38

when DNA pol I is replacing the RNA primer, which way is its exonuclease activity and which way is its polymerase activity? How does it digest and form?

Answer 38

it removes the primer and synthesizes the new DNA in the 5' to 3' direction

Question 39

when does DNA pol III stop?

Answer 39

when it hits the primer from the next fragment, it cannot seal itself

Question 40

During DNA replication, the leading and lagging strands are synthesized simultaneously by a single DNA polymerase III holoenzyme. Since DNA polymerase can only synthesize DNA in the 5' → 3' direction, how does the lagging strand, which is oriented in the opposite direction, get replicated efficiently?

Answer 40

the lagging strand gets looped out so the DNA polymerase can stay near the newly formed primers and easily "jump" over to start synthesizing at a new RNA primer

Question 41

what does the function of looping out allow?

Answer 41

it allows coordination between the leading and lagging strand and allows it to be synthesized discontinuously

Question 42

what is the specific function of DNA ligase, what type of bond does it form

Answer 42

DNA ligases catalyze a phosphodiester bond and connect DNA fragments

Question 43

between which two groups is the phosphodiester bond formed between in DNA pol?

Answer 43

the innermost phosphate group of the incoming nucleoside triphosphate the 3'OH of the sugar of the previous deoxynucleotides

Question 44

when the nucleoside triphosphate and 3'OH form a phosphodiester bond, what is formed as a byproduct of the triphosphate

Answer 44

the last two phosphate groups in a pyrophosphate form (PPi)

Question 45

what is the exonuclease function of DNA pol I

Answer 45

it is the digestion of RNA in the 5'-3' direction

Question 46

what is the polymerase function of DNA pol I

Answer 46

it is the formation of DNA in the 5'-3' direction

Question 47

what is the replisome

Answer 47

it is the coordination complex of all the enzymes working in sequence and it is associated with two DNA polymerase holoenzymes forming the leading and lagging strand

Question 48

in order for the replisome to coordinate properly, what must be done to the lagging strand

Answer 48

it must loop out

Question 49

what is a dimeric DNA polymerase? which way does it move

Answer 49

two DNA pol III proteins act in concert to replicate the leading and lagging strands it moves as a unit towards the replication forks

Question 50

what is opposite to the origin of replication and why is this significant

Answer 50

at the opposite of the oriC, there are termination sequences where termination binding proteins can adhere to and stop further replication or opening of the fork

Question 51

At the end of bacterial replication, what often results

Answer 51

intertwined molecules called catenanes

Question 52

how are catenanes separated?

Answer 52

by action of topoisomerases

Question 53

Why is DNA pol III not 100% efficient

Answer 53

molecules are dynamic

Question 54

why does DNA replication have a high rate of fidelity

Answer 54

1) instability of mismatched base pairs 2) configuration of DNA pol active site 3) proofreading function of DNA pol III

Question 55

why does the instability of mismatched base pairs contribute to the fidelity of DNA rep

Answer 55

due to complementarity, complementary base pairs are more stable than mismatched ones this accounts for errors 1 per 1000 nucleotides

Question 56

why does the configuration of the DNA pol III active site mater in DNA replication

Answer 56

it helps prevent errors (rate: 1 in 1 million) due to the induced fit phenomenon that occurs in enzymes. It is unlikely catalyze bond formation between mismatched base pairs

Question 57

why is the proofreading function of DNA pol III important

Answer 57

it significantly reduces the error in DNA replication as it can identify mismatched pairs, move backwards in a 3'-5' direction and remove the incorrect base pairs in its 3' exonuclease site before returning to regular replication

Question 58

how are bacterial cells able to divide at such a fast rate given the amount of time it takes for DNA to replicate

Answer 58

they have an ability to control the initiation of replication at the OriC and can fire off multiple rounds of replication before the first one is even done

Question 59

why can bacterial cells not immediately fire off the origin of replication

Answer 59

it takes time for methylase to completely methylate the GATC regions and it takes time to synthesize a sufficient amount of DnaA protein for binding

Question 60

when DNA replication begins, what happens to the fully methylated sites?

Answer 60

they are hemi-methylated and cannot start replication again until they are fully methylated

Question 61

when DNA replication begins, what happens to DnaA binding proteins?

Answer 61

there is an insufficient amount of them available to bind to the DnaA binding sites, so it takes time to produce more.