Chapter 25.1: DNA Replication

• Along with catalysts, biological information is one of the two prerequisites for life.
• The faithful maintenance and transmission of genetic information from one generation to another ensures continuity within each species.
• Information is expensive
• The chemistry of joining one nucleotide to the next in DNA replication is elegant and simple. But the enzymatic and thermodynamic commitment to linking one nucleotide to another in DNA far exceeds what would normally be required to successfully form a phosphodiester bond.
• It is not enough to synthesize a phosphodiester bond; that bond must accurately link two particular nucleotides.
• The fidelity of genome maintenance and transmission is not perfect.
• DNA damage happens, often by spontaneous processes.
• DNA replication and repair deal with the bast majority of DNA lesions, providing a high degree of genetic fidelity and stability.
• The few DNA damage events that slip through uncorrected provide fuel for evolution.
• Although considered separately, the processes of replication, repair, and recombination of DNA are not distinct. These processes are highly integrated in cells, and they are required for proper genome maintenance.
• Bacteria genes are typically named using three italicized lowercase letters reflecting a function. Ex: dna, uvr, and rec.
• Capital letters are an added abbreviation to bacterial gene naming to reflect order of discovery, not enzymatic order. Ex: dnaA, dnaB, and dnaQ.
• Bacterial protein naming is often named after their genes using nonitalicized, roman type with the first letter capitalized. Ex: DnaA, RecA
• DnaA is encoded by dnaA.
• RecA is encoded by recA.
• No single convention exists for all eukaryotic systems.
• In Saccarmyces cerevisiae, gene names are three italicized uppercase letters followed by an italicized number. Ex: COX1.
• Eukaryotic protein naming is complex and variable.
• In yeast, some proteins have long common names. Ex: cytochrome oxidase.
• In yeast, some proteins have the same name as the gene, with one uppercase and two lowercase letters in roman type, followed by a number and the letter p. Ex: Rad51p is encoded by RAD51
• A template is a structure that would allow molecules to be lined up in a specific order and joined to create a macromolecule with a unique sequence and function.
• The structure of DNA revealed one strand is the complement of the other, where each strand provides the template for a new strand.
• The basic principles that apply to DNA synthesis in every organism is that DNA replication is semiconservative, replication begins at an origin and usually proceeds bidirectionally, and DNA synthesis proceeds in a 5' to 3' direction and is semiconservative.
• Semiconservative replication is when each DNA strand serves as a template for the synthesis of a new stand.
• Semiconservative replication produces two new DNA molecules, each with one new strand and one old strand.
• Semiconservative replication was established by Meselson and Stahl in 1957.
• Replication forks are the dynamic points where parent DNA is being unwound and separated strands replicated.
• Both DNA strands are replicated simultaneously.
• Bacteria undergo bilateral replication, or both ends of the bacterial chromosome have active replication forks.
• Denaturation mapping shows the selective denaturing of sequences unusually rich to adenine thymine base pairs to provide landmarks along the DNA molecule.
• Denaturation mapping generates a reproducible pattern of single strand bubbles.
• The origin is the location where replication loops are initiated.
• New DNA strands are always synthesized in a 5' to 3' direction.
• The free 3'-hydroxyl group serves as a point of elongation for DNA synthesis.
• Okazaki fragments are short DNA fragments that are synthesized in the replication of one of the new DNA strands.
• Okazaki fragments are 150 to 200 nucleotides long in eukaryotes.
• Okazaki fragments are about 1000 to 2000 nucleotides long in bacteria
• Okazaki fragments are spliced together with DNA ligase.
• The leading strand is when 5' to 3' synthesis proceeds in the same direction as the replication fork moves.
• The leading strand is synthesized continuously.