nucleic acids and protein synthesis

• 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 has 3 phosphate molecules, ribose and adenine
• 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.
• 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
• dna has 4 nitrogenous bases: adenine, guanine, thymine and cytosine
• Complementary base pairing: between adenine and thymine (or adenine and uracil in RNA) and between guanine and cytosine
• what bonds support the DNA shape?

  the sugar-phosphate bonds make up phosphodiester backbones
• what bonds hold the DNA double helix together?

  hydrogen bonds between the complementary bases
• 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.
• Semi-conservative replication of DNA: 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.
• DNA semi-conservative replication

  1. DNA double helix unwinds and 'unzips' as the hydrogen bonds between the base pairs break by DNA helicase enzyme

  2. Both strands are used as templates

  3. Each of the bases of the activated nucleotides pairs up with its complementary base on each of the old DNA strands

  4. DNA polymerase catalyses the synthesis of the phosphodiester backbone by linking adjacent nucleotides

  5. DNA polymerase can only add nucleotides in the 5' to 3' direction

  6. DNA polymerase uses the 3' to 5' strand as template and forms the polynucleotide in 5' to 3' direction

  7. The new strand synthesized in 5' to 3' is made in small fragments called the Okazaki fragments

  8. Okazaki fragments are joined together by DNA ligase enzyme
• Activated nucleotides

  Found in nucleus, has 2 extra phosphates that can be broken to release energy for reaction
• Leading strand

  The new strand synthesized in 5' to 3' direction
• Lagging strand

  The new strand synthesized in 5' to 3' direction in small fragments called Okazaki fragments
• DNA helicase: unwinds and unzips the double helix as the hydrogen bonds between the base pairs break
• DNA polymerase: catalyses the synthesis of the phosphodiester backbone by linking adjacent nucleotides
• DNA ligase: joins together okazaki fragments which are small fragments found on the lagging strand
• RNA: 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
• 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.
• 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 64 possible amino acids
• 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.
• in transcription, DNA unwinds to form two strands (template and nontemplate) 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.
• in transcription, the DNA unwinds to form two strands (template and non-template), the free activated RNA nucleotides line up their complementary bases and form H-bonds, RNA polymerase catalyses the synthesis of phosphodiester bonds to form sugar-phosphate backbone, hydrogen bonds and formed between the DNA and mRNA strand are then broken, the DNA is reformed and the mRNA strand leaves the nucleus through the nuclear pores
• where are introns and exons found?

  in eukaryotic genes
• exons are a coding sequence
• introns and a non-coding sequence which is not translated
• both introns and exons are transcribed but only exons are translated into amino acids by RNA splicing
• RNA splicing is the removal of introns from the primary script
• exons are joined together to form continuous strand called mature mRNA
• Translation

  1. Small ribosomal subunit attaches to mRNA

  2. tRNA enters the ribosome and attaches to the mRNA

  3. A codon on the mRNA attaches to a specific anticodon on the tRNA

  4. AUG is start codon; complementary anticodon is UAC that brings amino acid methionine

  5. Only 2 tRNA molecules can fit in the ribosome at the same time

  6. Each tRNA carries a specific amino acid

  7. A peptide bond is formed between the amino acids of 2 adjacent tRNA molecules with the help of peptidyl transferase

  8. Ribosome moves along the mRNA, reading the next codon

  9. A third tRNA molecule brings a third amino acid, which joins to the second one

  10. The first tRNA leaves and is reused

  11. The polypeptide chain continues to grow until a 'stop' codon: UAA, UAC or UGA
• Mutation: 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.
• what causes gene mutations?

  radiation and carcinogens
• why is mutation harmful?

  it changes the amino acid sequence which changes the mRNA created, tRNA attaching and polypeptide formation