The cell duplicates its DNA at rates as high as 1000 nucleotides per second, but how? There are several kinds of protein that help DNA replication.

The cell duplicates its DNA at rates as high as 1000 nucleotides per second, but how? There are several kinds of protein that help DNA replication.

The DNA helicase sits at the very front of the replication machine(on the lagging strand template) where it uses the energy of ATP hydrolysis to propel itself forward, prying apart the double helix as it speeds along the DNA. Because each hydrogen bond is individually weak, it can unzip the double helix at normal temperatures. Moreover, DNA has more AT base pairs at replication origins, for they form less hydrogen bonds than CG base pairs, and thus are weaker.

DNA polymerase catalyzes the addition of nucleotides to the 3’ end of a growing DNA strand. The energy needed in this reaction is provided by the hydrolysis of the incoming nucleotide itself. Then, pyrophospate, which arises in the hydrolysis, is further hydrolyzed to inorganic phosphate to make the polymerization reaction effectively irreversible. On top of that, DNA polymerase has another two special qualities to minimize the number of replication errors. The first one is only when the match(AT or CG) is correct, does it catalyze the nucleotide addition reaction(because GT and CA can also be formed). The second one is the proofreading system with a nuclease. When DNA polymerase makes a rare mistake and adds the wrong nucleotide, it clips off the mispaired nucleotide and tries again. Polymerization and proofreading are carried out by different catalytic domains in the same polymerase molecule. Hence, 5’ to 3’ direction is for proofreading. Also, DNA polymerases don’t proofread RNA primers because RNA stands out as suspect copy to be automatically removed and replaced by DNA. 

On the lagging strand template, single strand DNA binding proteins cling to the single stranded DNA exposed by the helicase, transiently preventing the strands from re-forming base pairs and keeping them in an elongated form so that they can serve as efficient templates.

DNA topoisomerases produce transient nicks in the DNA backbone, which temporarily release the tension. They can reseal the nick before falling off the DNA.

A sliding clamp keeps DNA polymerase firmly attached to the template while it is synthesizing new strands of DNA. The clamp loader hydrolyzes ATP each time it locks a sliding clamp around a newly formed DNA double helix.

For your information,

•On the lagging strand template, RNA primer will be erased by nucleases, a repair polymerase replaces it with DNA and then DNA ligase works and links the two Okazaki fragments. 

•The slower rate of fork movement in eukaryotes(including humans) may be due to the difficulties in replicating DNA through the more complex chromatin structure of eukaryotic chromosomes

my next biology essay is probably about the end replication problem