IB Molecular Biochemistry

• Nucleic Acids


  DNA (deoxyribose nucleic acid) is the genetic material of life and is used as the blueprint for the production of building blocks. Viruses can have RNA (ribose nucleic acid) or DNA genetic material
• Ribosomes are made up of proteins and rRNA
• rRNA is synthesized by transcription from genes on chromosomes within the nucleolus.
• The ribosome consists of two subunits, one large and one small.
• DNA and RNA is made up of nucleotides to form a polymer. A nucleotide consists of 3 parts:

  1. A sugar with 5-carbon atoms (pentose sugar)
  2. An acidic phosphate group, negatively charged
  3. One of 4-5 different bases that contains nitrogen
• In DNA, the bases are paired together through hydrogen bonds between complementary pairs of bases. The pairing rules are: Adenine always pairs with Thymine; Guanine always pairs with Cytosine
• Each pentose sugar has a nitrogenous base attached to it. There are five types of bases found in nucleic acids: adenine, guanine, cytosine, thymine, uracil
• A DNA or RNA strand's individual nucleotides are linked to polymers in long chains through a condensation reaction (releasing water) forming covalent bonds with a characteristic sugar-phosphate backbone.
• Nucleotides can be joined together to make a chain called a polynucleotide. Polynucleotides have a repeating structure consisting of alternating sugars and phosphates.
• Double-stranded polynucleotides are more stable than single-stranded ones because they have many hydrogen bonds holding them together.
• Polynucleotides can be single-stranded or double-stranded depending on whether they contain only one strand or two antiparallel strands held together by hydrogen bonding between complementary base pairs.
• DNA as a double helix strand:

  • Strands are bonded together in an antiparallel way -> they run in opposite directions
  • Nucleotides are linked together by connecting a sugar with the phosphate group of the next nucleotide -> this forms the sugar-phosphate backbone
  • Weak forces of attraction (hydrogen bonds) connect nucleotides A-T (2 H bonds), C-G (3 H bonds) = complementary base pairing
• DNA Replication


  The replication of DNA is semi-conservative and depends on complementary base pairing
• Semi-conservative


  One strand of the 'parent' DNA is kept in the 'daughter' molecule
• Template strand


  The strand that is kept in the 'daughter' molecule
• DNA Replication


  1. The other half is determined by the code on the template strand

  2. Built up from free nucleotides in the nuclear space around the chromosomes

  3. Takes place in the nucleus

  4. Nucleotides are added one by one to the new strand

  5. According to the rules of complementary base-pairing
• Complementary base-pairing


  • If an adenine is the next exposed base on the original strand, a thymine nucleotide is added and vis versa
  • If a cytosine is the next exposed base on the original strand then a guanine is added and vis versa
• Hydrogen bonds can only form between the template strand and the new strand


  If the correct bases are paired up
• The new DNA molecule has kept half of the parent DNA and then this to create a new daughter strand
• Helicase


  Unwinds the double helix and operates the 2 strands by breaking hydrogen bonds
• DNA replication


  1. Occurs in preparation for mitosis

  2. DNA must be doubled before the parent cell can divide to produce 2 genetically identical daughter cells
• Helicase action


  1. Unwinds the DNA, by flattening out its helical structure

  2. Causes the hydrogen bonds to break between pairs of bases exposing bases on either side
• Helicase action


  Analogy: like untwisting a rope/unzipping a zipper
• DNA replication


  Each single polynucleotide DNA strand acts as a template for the formation of a new strand made from free nucleotides that attracted the exposed DNA bases by base pairing
• DNA polymerase


  Links nucleotides together to form a new strand, using the pre-existing strand as a template
• DNA replication


  1. Following the action of helicase, the template strand is exposed

  2. New nucleotides are joined together by DNA polymerase, which catalyzes condensation reactions, to form a new strand

  3. The original strand and the new strand join together through hydrogen bonding between base pairs to form the new DNA molecule
• Semi-conservative replication


  Half of the original DNA molecule is kept (conserved) in each of the 2 new DNA molecules
• DNA polymerase

  • Synthesizes new DNA strands from the 2 template strands
  • Catalyzes condensation reactions between the deoxyribose sugar and the phosphate groups of adjacent nucleotides within the new strands, creating the sugar-phosphate backbone of new DNA strands
• DNA polymerase


  • Always works in the 5' to 3' direction
  • Adds the 5' terminal of the new nucleotide to the 3' terminal of the strand being built
• Hydrogen bonds form between the complementary base pairs of the template and new DNA strands
• The copying accuracy of DNA is very high, with very few copying errors made in DNA replication
• Semi-Conservative Replication


  1. DNA polymerase links nucleotides together to form a new strand

  2. Using the pre-existing strand as a template
• Before a (parent) cell divides, it needs to copy the DNA contained within it
• This is so that the 2 new (daughter) cells produced will both receive the full copies of the parental DNA
• Semi-conservative replication


  The DNA is copied so that half the DNA is kept
• The process is called this because in each new DNA molecule produced, one of the polynucleotide DNA strands (half of the new DNA molecule) is from the original DNA molecule being copied
• The other polynucleotide DNA strand (the other half of the new DNA molecule) has to be newly created by the cell
• Importance of keeping one original DNA strand:

  • It ensures there is genetic continuity between generations of cells
  • Basically, it makes sure that the new cells produced during cell division inherit all their genes from the parent cells
  • This is important because cells in our body are replaced regularly and therefore we need the new cells to be able to do the same role as the old ones
  • Replication of DNA and cell division also occurs during growth
• Complex Carbohydrates


  Carbohydrates made up of many monosaccharide units
• Monosaccharides joining to form disaccharides


  Via condensation reactions