DNA Replication

DNA REPLICATION

  

DNA Replication is the biological process by which DNA makes a copy of itself during cell division. DNA is made up of a double helix of two complementary strands. Process replication starts by separating the double helix structure of the DNA molecules. This step is known as DNA unzipping. DNA unzipping is the casual term used where the denaturation of double stranded DNA takes place. This is carried out by an enzyme called helicase which breaks the hydrogen bonds holding the complementary bases of DNA together. (A-T, C-G) . This separation forms a Y shape called replication fork and create semiconservative replication. The two separated strands then will act as templates to create new strands. 

One of the strands is known as the leading strands while the other one known as lagging strand. 

• Leading strand is oriented 5' to 3' direction toward the replication fork.
• Lagging strand is oriented 5' to 3' direction away from the replication fork.

Leading Strand

• A short pieces of RNA called primer produced by ezyme primase bind to the end of the leading strand. The primer acts as the starting point for DNA synthesis.
• DNA polymerase binds to the leading strand, adding new complementary nucleotide bases. (A,C,G,T) to the strand of DNA of the 5' 3' direction. This replication is called continuous.

Lagging Strand

• Numerous RNA primers bind at various point of along the strands.
• Chunks of DNA, called Okazaki fragments, are then added to the lagging strand also in 5' to 3' direction. 
• This sort of replication is called discontinuous.

Then, DNA polymerase synthesizes the new strands by adding nucleotides that complement each strand. DNA replication occurs during the S-stage of interphase.

There are about 5 types of DNA polymerase involved in DNA replication:

• DNA-Pol I : repair and patching of DNA.
• DNA-Pol III : responsible for the polymerization of the newly formed DNA strand.
• DNA-Pol II, IV and V : proofreading and repair enzymes.

PRIMASE 

• catalyzes the copying of a short stretch of DNA template strand to produce RNA primer sequence.

When the strands have proven that there are no mistakes in the new DNA sequences, finally, an enzyme called DNA ligase seals up the sequence of DNA into two continuous double strands. DNA replication produced two DNA molecules consisting of one new and one old chain of nucleotides (semi-conservative). Lastly, the new DNA will automatically winds up into a double helix.

Here is the video of how DNA replication occurs :

Ribonucleic acid (RNA) structures and function

RNA

• Ribonucleic acid (RNA) is a biopolymer macromolecule as DNA. It consists of small subunits called nucleotides composed of:

− Purine nucleobases [Adenine−(A), Guanine−(G)]

− Pyrimidine nucleobases [Cytosine−(C), Uracil−(U)]

− Ribose pentose sugars [C₅H₁₀O₅]

− Phosphate groups [PO₄^3-]






• The nucleobase is attached on the ribose by an glycosidic bond.
• The ribose is bonded to the phosphate group through ester bonds.

• Differences between DNA and RNA

• DNA	RNA
  A,G,C or T base	A,G,C or U base
  Double stranded	Single stranded
  2'−deoxy−D−ribose pentose sugar	D−ribose pentose sugar
  Adenine=Thymine and Guanine=Cytosine	Adenine=Uracil and Guanine =Cytosine

  
  
  
  
  
  
• RNA have 3 types which is mRNA,tRNA and rRNA.
• Messenger RNA (mRNA)-type of RNA that encodes proteins and is translated by the ribosome into proteins. Eukaryotic mRNA usually has a few different regions that look something like this:

Typical human protein coding mRNA

 Eukaryotic mRNAs undergo extensive processing directly after they are transcribed by an RNA polymerase. A cap is added on the 5′ end of the molecule which serves various functions including nuclear export, preventing exonuclease degradation, and aiding in translation initiation. A poly-A tail is also added to the 3′ end that also helps prevent mRNA degradation, among other things. Not to mention all the splicing to create the actual final mRNA.

• Transfer RNA (tRNA)-an essential component of translation, where their main function is the transfer of amino acids during protein synthesis. Therefore they are called transfer RNAs.  tRNA is the smallest of the 3 types of RNA having about 75-95 nucleotides.Each of the 20 amino acids has a specific tRNA that binds with it and transfers it to the growing polypeptide chain. tRNAs also act as adapters in the translation of the genetic sequence of mRNA into proteins. Therefore they are also called adapter molecules.Other than that,tRNAs have a clover leaf structure which is stabilized by strong hydrogen bonds between the nucleotides

• Ribosomal RNA (rRNA)-found in the ribosomes and account for 80% of the total RNA present in the cell.Though ribosomes are often described as proteins when we first learn about them, they are actually a combination of RNA and a bunch of proteins all working together.Different rRNAs present in the ribosomes include small rRNAs and large rRNAs, which denote their presence in the small and large subunits of the ribosome.

rRNAs combine with proteins in the cytoplasm to form ribosomes, which act as the site of protein synthesis and has the enzymes needed for the process. These complex structures travel along the mRNA molecule during translation and facilitate the assembly of amino acids to form a polypeptide chain. They bind to tRNAs and other molecules that are crucial for protein synthesis.

Deoxyribonucleic acid (DNA) structure

DNA

• In the mid twentieth century, geneticists were that DNA (deoxyribonucleic acid) is  genetic material.

• Functions of DNA :

1. It was able to store information for development, structure and metabolism of a cell or organism
2. It was stable so that it could be replicated with high accuracy and transmitted from generation to generation.

• DNA was located in nucleus.

• DNA based on Chargaff's Rule :DNA contains four types of nucleotides, differing in the nitrogen-containing base each contains.

1. The purine base adenine (A)
2. The pyrimidine base cytosine (C)
3. The purine base guanine (G)
4. The pyrimidine base thymine (T)

• A nucleotide from DNA contains one base, one phosphate group, and the sugar deoxyribose.

• DNA based on Franklin’s X-Ray Diffraction Studies : DNA had a helical shape

• DNA based on The Watson and Crick Model : The sugar and phosphate groups are bonded in alternating sequences to form the sides of a twisted ladder. Bases are joined by hydrogen bonds to form the rungs of the ladder.
•  Complementary base pairing occurs,meaning A only bonds with T and G with C.

There are a few level structures of Nucleic Acid.

• 1 structure : the sequence of bases along the pentose-phosphodiester backbone of a DNA                               molecule.                                                                                                                                      -base sequence of bases from the 5' end to the 3' end                                                                              - system notation single letter (A,G,C and T)

• 2 structure: the ordered arrangement of nucleid acid strands which is double helix model.

• 3 structure: three-dimensional arrangement of all atoms of nucleic acid (supercoiling)

• 4 structure: - the structure of chromatin                                                                                                      - each bead is nucleosome(DNA wrapped around histone core)