List and describe the steps of genome replication and the ti

List and describe the steps of genome replication and the timing of them.

Solution

Steps of DNA Replication

1)The first major step for the DNA Replication to take place is the breaking of hydrogen bonds between bases of the two antiparallel strands. The unwounding of the two strands is the starting point. The splitting happens in places of the chains which are rich in A-T. That is because there are only two bonds between Adenine and Thymine (there are three hydrogen bonds between Cytosine and Guanine). Helicase is the enzyme that splits the two strands. The initiation point where the splitting starts is called \"origin of replication\".The structure that is created is known as \"Replication Fork\".

2) One of the most important steps of DNA Replication is the binding of RNA Primase in the the initiation point of the 3\'-5\' parent chain. RNA Primase can attract RNA nucleotides which bind to the DNA nucleotides of the 3\'-5\' strand due to the hydrogen bonds between the bases. RNA nucleotides are the primers (starters) for the binding of DNA nucleotides.

3) The elongation process is different for the 5\'-3\' and 3\'-5\' template.

a)5\'-3\' Template: The 3\'-5\' proceeding daughter strand -that uses a 5\'-3\' template- is called leading strand because DNA Polymerase ä can \"read\" the template and continuously adds nucleotides (complementary to the nucleotides of the template, for example Adenine opposite to Thymine etc).

b)3\'-5\'Template: The 3\'-5\' template cannot be \"read\" by DNA Polymerase ä. The replication of this template is complicated and the new strand is called lagging strand. In the lagging strand the RNA Primase adds more RNA Primers. DNA polymerase å reads the template and lengthens the bursts. The gap between two RNA primers is called \"Okazaki Fragments\". The RNA Primers are necessary for DNA Polymerase å to bind Nucleotides to the 3\' end of them. The daughter strand is elongated with the binding of more DNA nucleotides.

4) In the lagging strand the DNA Pol I -exonuclease- reads the fragments and removes the RNA Primers. The gaps are closed with the action of DNA Polymerase (adds complementary nucleotides to the gaps) and DNA Ligase (adds phosphate in the remaining gaps of the phosphate - sugar backbone

Each new double helix is consisted of one old and one new chain. This is what we call semiconservative replication.

5) The last step of DNA Replication is the Termination. This process happens when the DNA Polymerase reaches to an end of the strands. We can easily understand that in the last section of the lagging strand, when the RNA primer is removed, it is not possible for the DNA Polymerase to seal the gap (because there is no primer). So, the end of the parental strand where the last primer binds isn\'t replicated. These ends of linear (chromosomal) DNA consists of noncoding DNA that contains repeat sequences and are called telomeres. As a result, a part of the telomere is removed in every cycle of DNA Replication.

6) The DNA Replication is not completed before a mechanism of repair fixes possible errors caused during the replication. Enzymes like nucleases remove the wrong nucleotides and the DNA Polymerase fills the gaps.

Replication timing refers to the order in which segments of DNA along the length of a chromosome are duplicated. The temporal order of replication of all the segments in the genome, called its replication-timing program, can now be easily measured in two different ways. One way simply measures the amount of the different DNA sequences along the length of the chromosome per cell. Sequences that duplicate first, long before cell division, will be more abundant in each cell than the sequences that replicate last just prior to cell division. The other way is to label newly synthesized DNA with chemically tagged nucleotides that become incorporated into the strands as they are synthesized, and then catch cells at different times during the duplication process and purify the DNA synthesized at each of these times using the chemical tag. In either case, we can measure the amount of the different DNA sequences along the length of the chromosome either directly using a machine that reads how much of each sequence is present or indirectly using a process called microarray hybridization.

Replication timing and chromosome structure

All eukaryotes have a timing program, and this program is similar in related species.This indicates that it is either important itself, or something important influences the program. It is unlikely that replicating DNA in a specific temporal order is necessary simply for the basic purpose of duplicating a DNA molecule. More than likely, it is related to some other chromosomal property or function. Replication timing is correlated with the expression of genes such that the genetic information being utilized in a cell is generally replicated earlier than the information that is not being used. We also know that the replication-timing program changes during development, along with changes in the expression of genes replication timing dictates the time of assembly of chromatin. Less intuitive is the relationship between replication timing and the three-dimensional positioning of chromatin in the nucleus. It is now well-accepted that chromatin is not randomly organized in the cell nucleus, but the positions of each chromosome domain relative to its neighboring domains is characteristic of different cell types, and after this geography is established in each newly formed cell, the chromosome domains do not move appreciably until the next cell division.In all multi-cellular organisms where it has been measured, early replication takes place in the interior of the nucleus and the chromatin around the periphery is replicated later..