BIOCHEMISTRY EXAM SEASON

• Learning outcomes


  • Explain the role of these molecules in Biochemistry
  • Draw basic molecules
  • Use nucleotide nomenclature
  • Explain using chemical diagrams why DNA and RNA has polarity
  • Explain using chemical terminology how DNA forms a double helix
  • Explain using chemical terminology how RNA can form multiple structural forms
  • Give examples of how the chemistry of DNA/RNA can be used in the laboratory to understand features of the DNA
• Molecules


  • Energy
  • Monomers make DNA and RNA
  • 2nd messengers
  • Co-factors
  • Cell signalling factors
• Ratio of NAD+/NADH


  Indicator of metabolic state (resting state 700:1)
• FAD and NADP+ have similar structures
• Nicotinamide adenine dinucleotide (NAD)


  Cell's hydrogen carrier for redox enzymes, signalling molecule that controls hundreds of key processes from energy metabolism to cell survival
• NAD+ levels


  Decline with age, resulting in altered metabolism and increased disease susceptibility
• Restoration of NAD+ levels

  Can promote health and extend lifespan
• Components of nucleic acids

  • Base
  • Ribose
  • Phosphate
• Differences between DNA and RNA

  • DNA only
  • RNA only
• Nucleosides


  Can cross cell membranes
• Nucleotides


  Cannot cross cell membranes
• Nucleoside analogues are used as antiviral or anti cancer agents
• Disorders of purine metabolism

  Cause gout (urate crystals in joints)
• Structural features of DNA

  • Antiparallel
  • Major/minor grooves
  • Sequence specific structure
  • Linear or circular
  • Methylation
  • A-DNA
  • Z-DNA
• One of the common themes of biology is self-assembly
• 1. DNA is a common form of DNA
• Types of RNA


  • tRNA
  • mRNA
  • rRNA
  • snRNAs-spliceosome
  • Hammerhead ribozymes
  • siRNAs or RNAi
• Increasing temperature


  Converts dsDNA to ssDNA
• Melting temperature (Tm)


  The temperature where half the DNA molecules are single-stranded
• Spectroscopy is used to determine the melting temperature
• Haematoxylin stains nuclei of cells blue because they are acidic
• Exploiting DNA hybridisation
• The first step is the formation of an enzyme-substrate complex, where the substrate binds to the active site on the enzyme.
• The hydrophobic effect is the tendency of nonpolar molecules to cluster together, leading to the formation of micelles.
• In the second step, the enzyme catalyzes the reaction by lowering the activation energy required for the reaction to occur.
• Micelles are spherical aggregates formed by amphipathic molecules with their polar heads on the outside and nonpolar tails on the inside.
• This allows the reaction to proceed more quickly than it would without the presence of the enzyme.
• Lipid bilayers consist of two layers of phospholipids arranged with their hydrophilic head groups facing outward and their hydrophobic tail regions facing inward.
• Micelle formation occurs when nonpolar molecules aggregate due to their repulsion from water.
• Enzymes can be inhibited through competitive or uncompetitive mechanisms.
• Enzymes can be inhibited through competitive or noncompetitive mechanisms.
• Competitive inhibition involves binding of an inhibitor at the same site as the substrate, preventing its interaction with the enzyme.
• Noncompetitive inhibitors bind at sites other than the active site, preventing the enzyme from functioning properly.
• Competitive inhibitors compete with the substrate for binding to the active site of the enzyme.
• Noncompetitive inhibitors bind to another part of the enzyme, altering its shape and preventing it from interacting with the substrate.
• In the peptide shown below, which amino acids residues are hydrophilic and what is their

  
• Cations


  Positively charged ions
• Anions


  Negatively charged ions
• Metals


  Elements that lose electrons to form positive ions
• Non-metals


  Elements that gain electrons to form negative ions