DNA Replication: Key Concepts

• DNA Polymerase adds nucleotides to a growing chain of polynucleotides during replication.
• Euchromatin is less tightly wrapped regions of DNA.
• Helicase opens the DNA helix by breaking hydrogen bonds during replication.
• Heterochromatin is tightly wrapped DNA.
• Histones are proteins DNA is wrapped around.
• Lagging strand is replicated in short fragments and away from the replication fork during replication.
• Leading strand is synthesized continuously in the 5' to 3' direction in the direction of the replication fork.
• Ligase catalyzes the formation of a phosphodiester linkage between the 3' OH and 5' phosphate ends of the DNA.
• Mismatch repair is a repair mechanism in which mismatched bases are removed after replication.
• Mutation is a variation in the nucleotide sequence of a genome.
• Nucleotide excision repair is a repair mechanism used to remove damaged bases and replace them with the correct base.
• Okazaki fragment is a DNA fragment that is synthesized in short stretches on the lagging strand.
• Origin of replication is a nucleotide sequence where replication begins.
• Point mutation affects a single base.
• Primase synthesizes the RNA primer, which is needed for DNA pol to start synthesis of a new DNA strand.
• Primer is a short stretch of nucleotides that is required to initiate replication; in the case of replication, the primer has RNA nucleotides.
• Proofreading is a function of DNA pol in which it reads the newly added base before adding the next one.
• Replication fork is a Y-shaped structure formed during initiation of replication.
• Silent mutation is a mutation that is not expressed.
• Telomerase contains a catalytic part and an inbuilt RNA template, functions to maintain telomeres at chromosome ends.
• Telomere is DNA at the end of linear chromosomes.
• Topoisomerase causes underwinding or overwinding of DNA when DNA replication is taking place.

DNA Structure

• The two strands that make up the double helix have complementary base sequences and anti-parallel orientations.
• Alternating deoxyribose sugars and phosphates form the backbone and the nitrogenous bases are stacked like rungs inside.
• A purine always pairs with a pyrimidine; A pairs with T, and G pairs with C.
• Most prokaryotes contain a single, circular chromosome.
• Eukaryotic chromosomes contain a linear DNA molecule packaged into nucleosomes and have two distinct regions that can be distinguished by staining and reflect different states of packaging and compaction.

DNA Replication in Prokaryotes

• During cell division, each daughter cell receives a copy of each molecule of DNA by DNA replication.
• The chromosome of a prokaryote/eukaryote consists of a single continuous double helix.
• During replication, the two strands of the double helix separate, and each strand serves as a template from which a new complementary strand is copied.
• Each of the two parental DNA strands acts as a template for new DNA to be synthesized in replication.
• Each double-stranded DNA retains the parental/old strand and one new strand.
• Replication in prokaryotes starts from a sequence on the chromosome called the origin of replication (the point at which the DNA opens up).
• Helicase opens the DNA double helix, resulting in the formation of the replication fork.
• Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides only to the 3' end of a previously synthesized primer strand.
• Both new DNA strands grow according to their respective 5' to 3' directions.
• One strand is synthesized continuously in the direction of the replication fork, called the leading strand.
• The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments.
• This strand is the lagging strand.
• Once completed, the RNA primers are replaced by DNA nucleotides, and the DNA is sealed with DNA ligase, which creates phosphodiester bonds between the 3'-OH of one end and the 5' phosphate of the other strand.

DNA Replication in Eukaryotes

• In eukaryotes, replication starts at multiple origins of replication.
• The mechanism is similar to prokaryotes'.
• A primer is required to initiate synthesis, extended by DNA polymerase as it adds nucleotides one by one to the growing chain.
• The leading strand is synthesized continuously; the lagging strand is synthesized in short stretches called Okazaki fragments.
• The RNA primers are replaced with DNA nucleotides, and the DNA Okazaki fragments are linked into one continuous strand by DNA ligase.
• Telomerase extends the ends of the chromosomes to deal with the problem of primer RNA at the 5' ends of the DNA, and the ends of the chromosomes are protected.

DNA Repair

• DNA polymerase can make mistakes while adding nucleotides and edits the DNA by proofreading every newly added base.
• Incorrect bases are removed and replaced by the correct base before proceeding with elongation.
• Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base if proofreading doesn't work.
• In nucleotide excision repair, a damaged base is removed along with a few bases on the 5' and 3' end, and these are replaced by copying the template with the help of DNA polymerase.
• The ends of the newly synthesized fragment are attached to the rest of the DNA using DNA ligase, which creates a phosphodiester bond.
• Mistakes that are not corrected may result in a mutation, defined as a permanent change in the DNA sequence.
• There are many types of gene mutations such as substitution, deletion, insertion, and trinucleotide repeat expansions.
• Mutations in repair genes may lead to consequences such as cancer, and can be induced or occur spontaneously.