S phase begins when the restriction checkpoint of G1 phase is passed. Then, two major things happen: replication of DNA and, in animal cells, duplication of centrioles.
DNA is made up of two single strands of deoxyribonucleotides or bases (Figure 1). The two single DNA strands are joined together by hydrogen bonds established by complementary base pairing (adenine-thymine, cytosine-guanine), which results in a helical double DNA strand. The two single DNA strands are oriented in an anti-parallel manner. That is, the 3' end of one of the strands is close to the 5' end of the other strand, so that there are 3' and 5' ends of single strands in every end of the double strand. During DNA replication, the two single strands become separated from one another after breaking the hydrogen bonds, so that both single strands may be replicated at the same time.
Replication of DNA does not start from just one point since this would take too long. Instead, there are many replication origins, which are places in the genome where replication begins at about the same time. The beginning of replication in each replication origin is a two steps mechanism. In the first step, pre-replicative and pre-initiation molecular complexes are assembled at the replication origins and ready for starting the replication. Some of these complexes are assembled onto the DNA during the G1 phase, but are activated during S phase. It means that a molecular organization is needed before the replicative process starts. The second step is a signal that triggers the beginning of the replication process. The effect of this signal is a process known as DNA replication licensing. Cells have molecular mechanisms to avoid that replication starts twice in the same replication origin. Otherwise, the new cells may have more than two copies of the some DNA segments, which might be dangerous for the cell or for the organism.
A mammalian cell contains 30000 to 50000 replication origins, but not all of them are active during S phase. The activation of a replication origin is influenced by the chromatin environment and the molecular state of histones, both depending in turn on the cell type. It means that the activation pattern of the replication origins may differ in different cell types. However, some replication origins are always activated, usually at the beginning of the S phase, whereas others are activated at the end of the S phase and in only some cell types. Genes that are frequently expressed and those DNA regions with many genes are replicated before those DNA regions with few genes or with genes that are seldom expressed.
For DNA replication, the two single strands get separated by an enzyme known as helicase (Figure 2). After that, two primase enzymes join to the exposed single strands and synthesize a short RNA complementary fragment of about ten nucleotides, one in each single strand. These short fragments are known as primers, and without them DNA polymerases are not able to copy the DNA. Primers recruit δ y ε DNA polymerases, which add complementary nucleotides to the 3' end of each primers toward the 5' end of DNA single strand. In this way, a new complementary DNA strand is synthesized in each of the open single DNA strands. That is why the replication is semi-conservative, the two new double strands will have a new and an old DNA single strands. Subsequently, the primers will be removed by RNAases and these short segments of unpaired DNA are copied by DNA polymerases, which are coming along the single DNA strand from other replication origin.
Opening the DNA double strand leads to the formation of two replication forks (Figure 2). The two single strands in each replication forks are copied at the same time, but in different directions. DNA polymerases add nucleotides only in the 5' to 3' direction of the new synthesized strand (3' to 5' of the copied strand). This means that, whereas the replication process in one of the two strands is continuous and rather straightforward, in the other one it is a bit more complicated. Thus, after adding a primer and copying a segment, a new primer must be synthesized while the replication fork moves away. In this strand, there is a continous process of syntethizing primers, short segments replication, removing primers, copying the segments left by primers, and connecting segments by ligases. The segments are known as Okazaky fragments.
It must be kept in mind that not all the DNA is replicated at same time. It has been estimated that only 10 % to 15 % of the total DNA is being copied at same time during S phase. The replication process is stopped when the quality control system detects DNA breakages. There are many other processes running parallel to the DNA replication, such as histone synthesis, whose number must also be duplicated, and the synthesis of a new centrosome in animal cells for the organization of the mitotic spindle.