RNA and DNA Replication

Nucleotides and Nucleic Acids:


     DNA is made up of many nucleotides. Each nucleatide consists of sugar, a phosphate group and a nitrogenous base (ring structure with nitrogen). Nucleotides can join together by forming covalent bonds between the phosphate of one nucleotide to the sugar of another nucleotide. This polymer of nucleotides is called a nucleic acid. Both RNA (ribonucleic acid) and DNA (deoxyribonucleic acid) are examples of nucleic acids. The RNA and DNA differ by the types of sugar that are present. DNA's sugar is deoxyribose and the bases of DNA are adenine, cytosine, quanine and thymine. RNA has ribose sugar and it has the same bases as DNA with the exception of uracil instead of thymine.

The covalent bonds between nucleotides in DNA form a backbone with alternating sugar and phosphate molecules. DNA consists of two complementary strands that are connected at the nitrogenous bases via hydrogen bonds. Each strand consists of differing nitrogenous bases that form an anti-parallel pair such that one strand will be able to code for the other strand. This is because the four nitrogenous bases are paired so that cytosine (C) and guanine (G) are always paired together and adenine and thymine (T) paired as well. The bases guanine and adenine are both purines that are always opposite pyrimidines. Pyrimidines are the cytosine and thymine bases.  Each base pair are held together by hydrogen bonds. There are three bonds between guanine and cytosine while adenine and thymine are held by two hydrogen bonds.Together these two polymers of nucleotides were coiled to form a double helix structure with the sugar phosphate backbones on the outside. One strand goes from the 5 prime (5') to the 3 prime (3') while the other strand goes from the 3 prime (3') to the 5 prime (5') direction.

Supercoiling:
     In eukaryotes, DNA is associated with the protein histone. DNA winds around groups of histones in order to protect itself. A group of these histones are called nucleosomes. A nucleosome of eight histone proteins are gathered in an octomer shape and a different protein links the DNA from one nucleosome to another. The nucleosomes serve to supercoil DNA so that the chromosomes are shorter and fatter when mitosis or meiosis occurs. Transcription is also made easier with the help of nucleosomes.

DNA replication:
     DNA replication is often know as being semi-conservative. It uses one of the original strands as a template for a new strand. The two replicated DNA molecules, therefore, consist of one 'old' strand and one 'new' strand. DNA replication can being at many origin sites in eukaryotic cells while prokaryotic cells only have one origin of replication.

1. Double helix structure of DNA is unwound by the enzyme helicase. The two strands are separated in preparation for arriving nucleotides (nucleoside triphosphate) which will bind, via hydrogen bonds, with the exposed complementary bases. Each nucleoside triphosphate then goes through hydrolysis (splitting with water) to provide the energy to join the new nucleotide to the polymer (original strands)
2. Strands are formed 5' to 3' direction or along the 3' to 5' direction of the old template strand. The enzyme primase makes short sequences of RNA called primers begin the process. Complementary deoxynucleoside phosphates are paired with the template strand of DNA.
3. Nucleotides are only added to the 3' end of the original DNA strand so nucleotides are added in opposite directions. The leading strand has nucleotides that are added in the direction following the helicase. The lagging strand equips a different method during DNA replication. 
4. DNA polymerase III binds to the 3' end of the leading strand of the DNA. Nucleotides of deoxynucldoside phosphates are formed in the 3' to 5'direction (of the leading strand) of the polymerase III 
5. In the lagging strand, RNA primase follows the helicase, but only leaves small sections of RNA primers along the strand. This marks the points where DNA polymerase will work. 
6. Each DNA polymerase binds to each primer and replicates DNA in the opposite direction of the helicase but also following the 3' to 5' direction on the lagging strand. (therefore it replicates DNA in a 5' to 3' direction) When it reaches a primer, it detaches and jumps to the next primer following the helicase. 
7. The remaining RNA primer fragments are called okazaki fragments and they are all removed by DNA polyermase I that follows the direction of the helicase. DNA ligase binds to each okazaki fragments and creates a continuous strand of DNA