Nucleotides and Nucleic Acids

• Nucleotides

  Monomers of nucleic acids. They consist of a pentose sugar, nitrogenous base and a negatively charged phosphate group

  
• What elements do nucleotides contain?

  - Carbon

  - Hydrogen

  - Oxygen

  - Nitrogen

  - Phosphorus
• What are the bases?

  - Adenine, Thymine, Guanine and Cytosine (Uracil in RNA)

  Adenine and Guanine have a double ring structure and are called purines

  - Thymine, Cytosine, Uracil have a single ring structure and are called pyrimidines

  - Purine and Pyrimidine always pair together

  
• General Structure of DNA (Polynucleotide)


  - The pentose sugar is called deoxyribose

  - Has 4 bases: Adenine, Thymine, Guanine and Cytosine

  - The base pairs form a different number of hydrogen bonds: A-T form 2 bonds and C-G form 3 bonds

  - DNA consists of 2 polynucleotide strands which has a sugar-phosphate backbone on the outside. The strands form a double helix

  - The polynucleotide strands run anti-parallel (run in opposite directions)

  - Hydrogen bonds between the bases on opposite strands hold the polynucleotide strands

  - Long molecule (consists of millions of nucleotides)
• General Structure of RNA (Polynucleotide)


  - The pentose sugar is called ribose.

  - Has 4 bases: Adenine, Uracil, Guanine, Cytosine

  - Has only 1 polynucleotide strand

  - Shorter molecule than DNA (only a few hundred nucleotides)

  - RNA is found in the cytoplasm
• Phosphodiester Bond


  - A bond that forms between 2 nucleotides.

  - The bond forms between the hydroxyl (OH) group on carbon three of the pentose sugar on one nucleotide and the phosphate group on the other nucleotide

  - Lots of nucleotides joining together forms a polynucleotide

  
• What releases when a phosphodiester bond is formed?


  Water

  It is a condensation reaction

  - Water can be added to break the bond (hydrolysis reaction)

  
• How is DNA replicated?

  One strand is conserved and one strand is created

  
• Semi-conservative replication (DNA replication)


  1) DNA helicase breaks the hydrogen bonds between the complementary bases. This causes the double helix to unwind and separate into 2 strands, leaving free nucleotides

  2) The free nucleotides align next to their exposed complementary bases on the template strand. Hydrogen bonds form between these pairs. The sugar-phosphate backbone forms

  3) DNA polymerase joins together the nucleotides and complementary bases, forming phosphodiester bond and creating a new polymer chain of DNA. This an example of a condensation reaction. One new strand is formed and one strand is conserved

  
• Importance of replication


  It is important that DNA is replicated accurately. Sometimes, an incorrect base is inserted in the polynucleotide strand or copying errors occur - this changes the DNA base sequence. This is a mutation and it can have serious effects on an organism

  - Mutations are random and occur spontaneously

  
• Protein Synthesis

  Protein synthesis occurs on the ribosomes of the RER (rough endoplasmic reticulum). It happens in 2 stages:

  - Transcription: DNA sequence for one gene is copied into mRNA

  - Translation: mRNA joins with a ribosome and a tRNA molecule brings the specific amino acid the codon codes for

  
• Transcription

  1) DNA helicase breaks the hydrogen bonds between the complementary bases in the 2 strands of DNA

  2) This causes the double helix to unwind and separate into 2 strands; one strand acts as a template

  3) Free RNA nucleotides align opposite next to the exposed complementary bases

  4) The enzyme RNA polymerase joins together the RNA nucleotides and bases, forming a phosphodiester bond and creating a new mRNA polymer chain

  5) mRNA is then modified and then leaves the nucleus through nuclear envelope pores

  
• Start Codon


  At the start of every gene which enables the ribosome to attach
• End Codon


  At the end of every gene there are 3 bases which do not code for an amino acid. It causes the ribosome to detach and ends translation
• Translation


  1) Once mRNA moves from the nucleus to the cytoplasm, it attaches to the small subunit of the ribosome at the start codon.

  2) The tRNA molecule with the complementary anticodon to the start codon aligns opposite the mRNA

  3) The 2 amino acid molecules that have been delivered by the tRNA molecule are joined together via a peptide bond which is catalysed by an enzyme using ATP

  4) The ribosome will move along the next mRNA to the next codon and another complementary tRNA will attach to the next codon on mRNA

  5) This continues until the ribosome reaches the stop codon, causing ribosome to detach and end translation

  6) The polypeptide chain is now created and enters the Golgi body for folding and modification

  (Ribosomes contain a different number of proteins and a type of RNA called rRNA - ribosomal RNA)

  
• Genetic Code


  1) Degenerate code: Amino acids are coded by more than one triplet

  2) Non-overlapping: Each base is read once

  3) Universal: The same triplet of bases codes for the same amino acids of all organisms
• Structure of ATP (Adenine triphosphate)


  - ATP consists of 3 phosphate ions, ribose sugar and adenine as its base

  - The 3 phosphate ions are essential in energy transfer

  - Essential for metabolism

  - Used as an immediate source of energy for biological processes

  
• Hydrolysis of ATP


  ATP + H20 --> ADP + Pi + Energy

  - It releases adenine diphosphate and an inorganic phosphate group (not attached to a carbon-containing molecule)

  - This occurs in cells that need energy
• ADP + Pi --> ATP + H20 (condensation reaction)


  ADP and Pi are recycled back to ATP. As we are adding a phosphate group back onto ADP, it is a phosphorylation reaction.

  - Water is released as well (condensation reaction)