DNA structure and replication

Nucleic Acids

• Cells produce two types of polynucleotides: RNA and DNA
• DNA is a polymer of nucleotides A, C, G, and T with the sugar deoxyribose
• RNA is a polymer of nucleotides A, C, G, and U with the sugar ribose

Nucleotides

• Nucleotides can be either purines (A and G) with a double ring base or pyrimidines (C, T, and U) with a single ring base

Watson-Crick Model of DNA

• Double helix with sugar-phosphate backbone outside
• Antiparallel strands
• Strict base-pairing of nucleotides (A:T; C:G)
• Two strands held together by hydrogen bonding between bases

DNA Replication

• Semi-conservative replication: each parental strand is used as a template to make a daughter strand along its entire length
• Results in two double helices, each with an “old” DNA strand paired with a “new” DNA strand

Proteins Involved in DNA Replication

• Helicase: breaks hydrogen bonds between bases
• Topoisomerase: relieves strain caused by helicase (overwound DNA)
• Single Strand Binding Protein: prevents DNA strands from winding back together
• Primase: makes an RNA primer
• DNA polymerase III: extends the 3' end of the primer to make a new DNA strand
• DNA pol I: removes the RNA primer and replaces it with DNA nucleotides
• Ligase: links two DNA fragments together with a covalent bond

DNA Replication Process

• Starts at an origin of replication, where origin recognition proteins bind and separate the DNA strands
• A replication bubble consists of two replication forks that move away from each other in opposite directions
• Helicase breaks hydrogen bonds between nucleotides at the fork, making the bubble bigger and exposing new single-stranded DNA
• Topoisomerase relieves strain created by helicase by cutting and repairing the double helix
• Primase makes a short RNA primer to provide a pre-existing 3'-end
• DNA polymerase III extends each primer by adding DNA nucleotides to the 3'-end
• DNA polymerase I removes the RNA primer and replaces it with DNA nucleotides
• Ligase adds a phosphodiester bond between the 3'- and 5'-ends of two fragments, making a single daughter strand

Leading and Lagging Strands

• On the leading strand, the 3'-end of the daughter DNA is towards the fork, so DNA polymerase III follows helicase and makes one long daughter strand
• On the lagging strand, the 3'-end of the daughter DNA is away from the fork, so DNA polymerase III goes the "wrong way" and creates DNA fragments