Structure & Replication of DNA

Nucleotides

 

Basic building block of nucleic acids, such as DNA and RNA. It is an organic compound made up of nitrogenous base, a pentose sugar, and a phosphate group.

Structure of ATP

Polynucleotide

many nucleotides are linked together into a long chain forming polynucleotides DNA/RNA. This happens in the nucleus during interphase. The covalent sugar–phosphate ester bonds (phosphodiester bonds) link the 5-carbon of one sugar molecule and the 3-carbon of the next. The polynucleotide strand is said to have 3΄ and 5΄ ends.

 

Nucleotide Polymerization

Nucleotides polymerize by forming phosphodiester bonds between carbon 3′ of the sugar and
an oxygen atom of the phosphate. This is a condensation polymerization reaction. The bases do not take part in the polymerization, so there is a sugar-phosphate backbone with the bases extending off it. This means that the nucleotides can join together in any order along the chain. Two nucleotides form a dinucleotide, three form a trinucleotide, a few forms an oligonucleotide, and many form a polynucleotide.

 

DNA

is made up of two antiparallel polynucleotide strands lying side by side, held together by hydrogen bonds. The strands are in 3’ to 5’ direction and the other is in the 5’ to 3’ direction hence antiparallel.

  • It has 4 nitrogenous bases: Adenine, thymine, guanine and cytosine.
  • Complementary base pairing: between adenine and thymine (or adenine and uracil in RNA) and between guanine and cytosine.
  • The sugar-phosphate bonds make up a phosphodiester backbone which supports the DNA shape.
  • Hydrogen bonds between the complementary bases hold the DNA double helix together, maintains 3D structure and ensures stability.
    • Purines are nitrogenous bases with double ring structures (Guanine and adenine).
    • Pyrimidines are nitrogenous bases with single ring structures (Thymine, uracil and cytosine).
    • Adenine and Thymine form 2 hydrogen bonds, Guanine and Cytosine form 3.

 

 

‎Replication of DNA

Semi-conservative

It occurs during interphase. The DNA separates into two strands and each strand acts as a template. 2 DNA molecules are formed. Each new DNA molecule consists of one old strand and a complementary new strand.

  • The DNA double helix unwinds and ‘unzips’ as the hydrogen bonds between the base pairs break by DNA helicase enzyme.
  • Both strands are used as templates.
  • Each of the bases of the activated nucleotides (found in nucleus, has 2 extra phosphates that can be broken to release energy for reaction) pairs up with its complementary base on each of the old DNA strands.
  • DNA polymerase catalyzes the synthesis of the phosphodiester backbone by linking adjacent nucleotides. It can only add nucleotides in the 5’ to 3’ direction.
  •  It uses the 3’ to 5’ strand as template and forms the polynucleotide in 5’ to 3’ direction. This strand is continuously synthesized. (Leading strand)
  •  The new strand synthesized in 5’ to 3’ is made in small fragments called okazaki fragment (Lagging strand)
  • okazaki fragments are joined together by DNA ligase enzyme.

 

 

RNA

It’s a single stranded polynucleotide chain present in the nucleus, cytoplasm and ribosome. It contains a pentose sugar (ribose) and has 4 nitrogenous bases: Adenine, uracil, guanine and cytosine. There are different types of RNA which include:

  • mRNA (messenger RNA): carries the genetic information in the form of a template from the nucleus to the ribosome for translation.
  • tRNA (transfer RNA): has a specific amino acid at one end and an anticodon at the other end. It fits onto the mRNA at ribosomes at complementary mRNA codon for protein synthesis.

 

The Genetic Code

  •  Gene: a length of DNA which codes for a specific polypeptide or amino acid chain
  • Codon: sequence of three nucleotide bases which code for a specific amino acid.
  • There are 4 nucleotide bases and hence 4 x 4 x 4 = 64 possible amino acids
  • However only 20 amino acids exist hence the genetic code is:
  • redundant or degenerate – multiple codon codes for the same amino acid.
  • universal – all organisms use the same code
  • Has start and stop codons to mark the beginning and end of the gene for protein synthesis.

 

Protein Synthesis

Transcription

it occurs in the nucleus via the following steps:

  • DNA unwinds to form two strands (template and non-template) and the template strand acts as a template.
  • Free activated RNA nucleotides line up with their complementary base and forms H-bonds.
  • RNA polymerase catalyzes the synthesis of Phosphodiester bonds to form sugar-phosphate backbone.
  • Hydrogen bonds between the DNA and mRNA strand are then broken
  • DNA is reformed
  • mRNA strand then leaves the nucleus through the nuclear pores

 

Post Transcriptional RNA Modification

  • Eukaryotic genes are made of introns are exons
  • Exons: coding sequence
  • Introns: non-coding sequence which is not translated
  • Both introns and exons are transcribed but only exons will be translated into amino acids by RNA splicing.
  • RNA splicing: removal of introns from primary transcript
  • Primary Transcript: original molecule of mRNA before splicing.
  • Exons are joined together to form continuous strand called mature mRNA.

 

Translation

  • Small ribosomal subunit attaches to mRNA
  • tRNA enters the ribosome and attaches to the mRNA
  • A codon on the mRNA attaches to a specific anticodon on the tRNA
    • AUG is start codon; complementary anticodon is UAC that brings amino acid methionine
  • Only 2 tRNA molecules can fit in the ribosome at the same time
  • Each tRNA carries a specific amino acid
  • A peptide bond is formed between the amino acids of 2 adjacent tRNA molecules with the help of peptidyl transferase
  • Ribosome moves along the mRNA, reading the next codon. A third tRNA molecule brings a third amino acid, which joins to the second one. The first tRNA leaves and is reused.
  • The polypeptide chain continues to grow until a ‘stop’ codon: UAA, UAC or UGA.

 

‎ ‎
Gene Mutations

  • Mutation is a change in the nucleotide sequence of a gene, which may then result in an altered polypeptide. Most genes have several different variants called alleles.
  • Can be caused by radiation, carcinogens etc.
  • Harmful as it changes the amino acid sequence which changes the mRNA created, tRNA attaching and polypeptide formation.

 

Types of Mutations

  1. Substitution mutation: a nucleotide base is replaced by a different nucleotide
    • Eg: Sickle Cell Anaemia where the base Thymine is replaced with Adenine (CTT → CAT) so Glutamine becomes Valine.
  2.  Frame-shift mutation: insertion or deletion of one or more nucleotides which cause a change in frame and hence affects the codons from the mutation onwards.
  3. Elimination mutation: removal of one or more than nucleotide and is not replaced
  4. Insertion mutation: a nucleotide base is added

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