S Phase

After the G$_1$ phase of interphase, the cell has everything it needs to replicate its DNA.

The S phase is a period when chromosomes are duplicated in the cell. The S stands for synthesis, as in synthesis of DNA!

The cell starts with two copies of each chromosome, and each of those chromosomes has one chromatid. Once the chromosomes are replicated, there are still only two copies of each chromosome, but each one now contains two chromatids connected by a centromere.

I know.

This is confusing, but try to use the following diagram to familiarize yourself with chromosomes and chromatids, as this will be very important in learning mitosis and meiosis later on.

S Phase

Interphase progresses from the G1 phase to the S phase, where synthesis occurs, only if the cell has grown enough and the DNA is undamaged.

In the S Phase, DNA is replicated and chromosomes are duplicated.

Reference:

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What happens during S phase?

During G1, the cell checks that there is enough nutrients to support the cell through replication. The transition into S phase is regulated by a positive feedback loop. Once the transition into S phase begins, the cell cannot return to G1.

The purpose of S phase is to double the amount of DNA in the cell by replicating it. For example, if a cell has n chromosomes, after S phase it will have 2n chromosomes.

Throughout G1, pre-replication complexes are distributed through DNA. These packages of proteins are used to open up replication forks when signaled to do so by cyclin-dependent kinases. These replication forks are opened at specific origin of replication sites. The enzyme helicase is used to 'unzip' the double stranded DNA and let DNA polymerases in.

During S phase, new histones are also synthesized. Since the volume of DNA is doubling in size, the amount of histones must also increase so that the new DNA can be packaged into nucleosomes and chromosomes. Histones are created extremely quickly because the RNA sequence for histones does not receive a poly-A tail. Instead, it has a stem loop binding protein. This allows the amount of histones to be rapidly increased while also instantly stopping histone synthesis when S phase ends.

Throughout the replication, the cell scans the DNA for mutations or other problems using replication checkpoints. After replication is complete, the intra-S phase checkpoint searches the DNA for double strand breaks.

After the new DNA is condensed into nucleosomes, they are modified epigenetically to be the same as the original DNA. This includes condensing the DNA into tightly wound chromatin domains.

During this process, the S-M checkpoint is used to block mitosis until all of the genome replication is finished.