7.1 - DNA Structure & Replication

The role of nucleosomes in DNA packing histones are used by the cell to package DNA into structures called nucleosomes nucleosome: consists of a central core of eight histone proteins with DNA coiled around the proteins the eight proteins (octamer) consist of 2 copies of 4 types of histones H1, an additional histone protein molecule, serves to bind the DNA to the core particle the association of histones with DNA = supercoiling it allows a great length of DNA to be packed into a small space in the nucleus the nucleosome is an adaptation that facilitates the packing of the large genomes that eukaryotes possess the H1 histone binds to form a structure called the 30 nm fibre that facilitates further packing

The leading strand and the lagging strand synthesis on the two strands occur differently because the two strands are arranged in an anti-parallel way on the leading strand: the strand is made continuously following the fork as it opens on the lagging strand: the strand is made in fragments moving away from the fork new fragments are created as the replication fork exposes more of the strand they are called Okazaki fragments

The direction of replication DNA replication begins at sites called origins of replication the phosphate group of new DNA nucleotides is added to the 3' carbon of the deoxyribose of the nucleotide at the end of the chain replication only occurs in the 5' to 3' direction

Non-coding regions of DNA have important functions only some DNA sequences code for the production of polypeptides these are called coding sequences there are a number of non-coding sequences found in genomes, some have functions (like the ones used to produce tRNA and rRNA) some play a role in the regulation of gene expressions such as enhancers and silencers most of the eukaryotic genome is non-coding

Proteins involved Helicase: unwinds the DNA at the replication fork Topoisomerase: releases the strain the develops ahead of the helicase Single-stranded binding proteins: keep the strands apart, keep them from reannealing long enough for copying fo the strand DNA primase: creates RNA primers on the strands; one on leading, many on lagging DNA polymerase:  it covalently links the deoxyribonucleotide monophosphate to the 3' end of the growing strand DNA ligase: connects the gaps between fragments

How Replication Happens

Helicase Helicase unwinds and separates the double-stranded DNA by breaking the hydrogen bonds between base pairs This occurs at specific regions (origins of replication), creating a replication fork of two strands running in antiparallel directions   DNA Gyrase DNA gyrase reduces the torsional strain created by the unwinding of DNA by helicase It does this by relaxing positive supercoils (via negative supercoiling) that would otherwise form during the unwinding of DNA   Single-Stranded Binding (SSB) Proteins SSB proteins bind to the DNA strands after they have been separated and prevent the strands from re-annealing These proteins also help to prevent the single-stranded DNA from being digested by nucleases SSB proteins will be dislodged from the strand when a new complementary strand is synthesized by DNA polymerase III   DNA Primase DNA primase generates a short RNA primer (~10–15 nucleotides) on each of the template strands The RNA primer provides an initiation point for DNA polymerase III, which can extend a nucleotide chain but not start one   DNA Polymerase III Free nucleotides align opposite their complementary base partners (A = T ; G = C) DNA pol III attaches to the 3’-end of the primer and covalently joins the free nucleotides together in a 5’ → 3’ direction As DNA strands are antiparallel, DNA pol III moves in opposite directions on the two strands On the leading strand, DNA pol III is moving towards the replication fork and can synthesize continuously On the lagging strand, DNA pol III is moving away from the replication fork and synthesizes in pieces (Okazaki fragments)   DNA Polymerase I As the lagging strand is synthesized in a series of short fragments, it has multiple RNA primers along its length DNA polymerase I remove the RNA primers from the lagging strand and replaces them with DNA nucleotides   DNA Ligase DNA ligase joins the Okazaki fragments together to form a continuous strand It does this by covalently joining the sugar-phosphate backbones together with a phosphodiester bond