General features of DNA replication - Week 1

Question 1

what does DNA consist of and where is it found

Answer 1

DNA contains all the genetic structures for all the characteristics of living organisms.​
DNA exists within cells, within the nucleus for eukaryotic cells, in the nucleus DNA is packed in specific structures and specialised cellular structures called chromosomes.​

Question 2

why is DNA important

Answer 2

The genetic material/DNA contains genetic information/instruction which is important to construct an entire organism, this genetic material is passed from cell to cell during cell division.

Question 3

why is DNA important?

Answer 3

The genetic material/DNA contains genetic information/instruction which is important to construct an entire organism, this genetic material is passed from cell to cell during cell division.

Question 4

what is the definition of DNA synthesis

Answer 4

molecular events that allow the assembly of new DNA strands

Question 5

what is the definition of DNA replication

Answer 5

it’s a biological process by which DNA is copied and its very accurate.

Question 6

what does DNA replication mainly include

Answer 6

• DNA chain synthesis
• Initiation, elongation and termination
• daughter strand separation
• distribution of chromosomes

Question 7

why is DNA replication important

Answer 7

it is necessary for cell reproduction before cell division

Question 8

what are the 5 stages a cell goes through and what happens at those stages

Answer 8

As a single cell divides, it goes through 5 stages:​
1.G1​
which is a growth phase
2. G0
the growth arrest phase
3. Synthesis phase​
Where DNA synthesis/DNA replication occurs​
4. G2
which is the 2nd growth phase
- M phases​
Mitosis, where a cell duplicates and DNA will be distributed in both daughter cells​

Question 9

who were Watson and Crick

Answer 9

Watson and Crick were the first scientists that discovered the structure of DNA in 1954, they discovered the structure of DNA and also hypothesised how DNA is copied into 2 new molecules, they hypothesised that DNA is duplicated in a semi-conservative manner.

Question 10

what does the semi-conservative model suggest

Answer 10

The semi-conservative DNA replication suggests that the 2 original strands of the DNA molecule split up, separates and each acts as a template for the formation of the new strand of DNA.

Question 11

why wasn’t the semi-conservative approved at first

Answer 11

At that time the separation of the 2 strands of DNA seemed impossible, so the scientific community disagreed about this hypothesis of Watson and Crick and they proposed other models for DNA replication which were the conservative model and the dispersive model were still plausible until the theories could be disproved.
​

Question 12

what does semi-conservative replication propose

Answer 12

According to the semiconservative model, after one round of replication, every new DNA double helix would be a hybrid that consisted of one strand of old DNA bound to one strand of newly synthesized DNA and after two rounds, two of the DNA molecules consist only of new material, while the other two contain one old and one new strand. ​

Question 13

what does the conservative model propose

Answer 13

According to the conservative replication model, the entire original DNA double helix serves as a template for a new double helix, such that each round of cell division produces one daughter cell with a completely new DNA double helix and another daughter cell with a completely intact old (or original) DNA double helix. This is repeated in the second round. ​

Question 14

what does the dispersive model propose

Answer 14

According to the dispersive model, every round of replication would result in hybrids, or DNA double helices that are part original DNA and part new DNA. thus indicating the two parental strands are distributed more or less randomly between two daughter molecules. Each subsequent round of replication would then produce double helices with greater amounts of new DNA.

Question 15

which experiment was carried out to find out whether conservative, semi-conservative or dispersive is correct

Answer 15

In 1958, Meselson and Stahl devised an experiment to determine whether DNA replicated following a conservative, semi-conservative, or dispersive model.​
the experiment is called the Meselson-Sahl experiment.

Question 16

how was the Meselson-Stahl experiment carried out

Answer 16

how the experiment is carried out:
1. E.coli were grown for several generations in a medium with the heavier 15N isotope
2. E.coli cells with only 15N in their DNA were transferred to a 14N medium and were allowed to divide.
3. DNA was extracted periodically for example after 20 minutes, 40 minutes or 60 minutes, and was centrifuged on a salt density gradient.
4. The isolated DNA is isolated from these samples and then the DNA is detected, the outcome of the experiment is analysed

Question 17

what do the results show from the Meselson-Stahl experiment

Answer 17

What the results show

After 1 cell doubling which is 20 minutes (which is the time that usually a population of bacteria cells duplicate) they obtain the DNA that these bacteria cells, which is lighter compared to the control, this means that the DNA after 1 cell doubling the DNA in these samples were half heavy because they display an intermediate density lighter than the control. ​

After the second cell doubling, like after 40 minutes, the DNA is made of 2 types, this is indicated by the fact that they obtained 2 different bands of DNA, 1 is light and the other is half heavy, this result after 40 minutes is consistent with the semi-conservative model only whereas the results of 1 cell doubling is consistent with both the semi-conservative model and the dispersive model.​

thus the results prove that the semi-conservative model is the correct model.

Question 18

what is the definition of the origin of replication

Answer 18

A unique DNA sequence of a replicon at which DNA replication is initiated and proceeds typically in a bidirectional fashion.

Question 19

what is the replication fork

Answer 19

The point at which replication occurs is called the replication fork. The replication fork is the site of the progressive unwinding of the double-stranded DNA and the duplication of the template DNA, and it travels along the length of the DNA molecule, away from the ORI. ​

Question 20

what is OriC and what does it contain

Answer 20

The origin of replication is prokaryotes is called OriC, this is a well-defined structure and consists of 245 base pairs in length and contains the following elements:​
- AT-rich region​ (3 copies of 13 bp repeats)
- DNA boxes (the binding site of the protein​, 5 copies of 9 bp repeats)
- GATC methylation sites ( methylation of the bacterial origin regulates initiation)

Question 21

how many origins of replication do eukaryotes have

Answer 21

The eukaryote’s chromosomes are usually linear and contain multiple origins of replication, spaced throughout the chromosome that merges during the DNA replication.​
Eukaryotes have many origins of replication that are called replicons.​

Question 22

how many origins of replication do bacteria have

Answer 22

Bacteria has a single orgin of replication (ORI) called OriC

Question 23

where does the knowledge of DNA replication in eukaryotes come from

Answer 23

For eukaryotes, as these organisms are more complex than bacteria, there is no single model of the organism, so all our knowledge that we have regarding DNA replication is based on yeast and Saccharomyces cerevisiae.​
DNA sequences at the replication origins in Higher Eukaryotes, including humans vary and have been much harder to isolate. ​Evidence suggests that the origin of replication in mammalian cells is similar to yeast-type origins.

Question 24

why is the ARS1 sequence important in DNA replication

Answer 24

The autonomous replicating sequences (ARS1) are specific DNA sequences in the genome of eukaryotes that serve as the origin of replication. These sequences are recognized and bound by the Origin Recognition Complex (ORC), which is a protein complex that plays a crucial role in initiating DNA replication.

Question 25

why is RNA primer important in DNA replication

Answer 25

DNA replication is semi-conservative and bi-directional, in DNA replication, the synthesis of a strand in DNA always starts with an RNA primer, this is because the enzyme involved in DNA replication, which is called DNA polymerase, is not able to start the polymerisation from scratch on its own so it needs the RNA primer to start. Thus RNA primer starts the synthesis of the DNA strand.

Question 26

which direction does DNA synthesis occur

Answer 26

the synthesis of DNA occurs in the 5’ to 3’​ direction

Question 27

what are the 2 different strands that DNA can be synthesised into

Answer 27

The 2 strands of DNA are synthesised in different manners, one strand is synthesised as a continuous molecule and the other is made in short fragments, these pieces are called Okazaki fragments, thus 1 strand is referred to as the leading strand, and the other one is a lagging strand. ​

Question 28

what is the leading strand

Answer 28

the leading strand is made as a continuous molecule. The leading strand is the strand of nascent DNA which is being synthesized in the same direction as the growing replication fork. A polymerase “reads” the leading strand template and adds complementary nucleotides to the nascent leading strand continuously.​

Question 29

what is the lagging strand

Answer 29

The lagging strand is made of discontinuous fragments. ​
The newly synthesised DNA strands are formed in the opposite direction of the replication fork movement.​
The lagging strand is synthesized in short, separated segments. On the lagging strand template, a primase “reads” the template DNA and initiates the synthesis of a short complementary RNA primer. A DNA polymerase extends the primed segments, forming Okazaki fragments. ​ Thus the newly synthesised strand is made of Okazaki Fragments​.

Question 30

how is replication terminated in prokaryotes

Answer 30

We don’t know much about how the DNA replication terminates in E.coli, but what we know is that there is a specific sequence on the E.coli genome, that is called the termination sequence that is important for the termination of the replication of DNA, these sequences are called “Ter sites” and are the binding site for the terminator protein called “Tus”.​ Tus terminator protein blocks the progression of replication forks in specific directions.

Question 31

when does DNA replication terminate

Answer 31

Replication terminates when the two growing forks meet in the terminus region, which is located 180º around the circular chromosome from the ORI​.

Question 32

where does bacteria termination specifically happen

Answer 32

Replication is terminated in bacterial systems by a “replication fork trap”, studded with termination sites which causes the bidirectional forks to pause, encounter and fuse within a region called the terminus region (Ter sites). ​

Question 33

how many Ter sites does E.coli have and when is replication terminated in the Ter sites

Answer 33

E.Coli has a total of 10 Ter sites that are present in two clusters, each containing five Ter sites. J, G, F, B and C are arranged opposed to ter sites H, I, E, D and A, and can arrest the fork progressing in the clockwise direction.​
The replication fork progressing in a clockwise direction will encounter the terC site first and pause. If the fork progressing from the anticlockwise direction meets the clockwise fork while paused, replication is terminated, however, if it does not meet its anti-fork it will proceed until it reaches the next termination site, terB, where it will pause again, etc.​
​ when the 2 replication forks meet, there is the termination of the DNA replication.​

Question 34

why are multiple Ter sites important

Answer 34

multiple ter sites are important as they are infrequently utilized as backups, they ensure that the fork does not leave the terminus region, and that termination is completed.
Multiple regions to entrap the replication fork means that if an inactivating mutation arises within a ter site, then arrest can still occur at another ter sequence.​

Question 35

how is DNA replication terminated in eukaryotes

Answer 35

Little is known about the termination of the replication in eukaryotes.​
What is known is that perhaps the replication fork meets at a random position and when they match there is the termination of the DNA replication.​