Workshop questions

• Nucleotide bases in DNA

  • adenine
  • thymine
  • cytosine
  • guanine
• Nucleotide bases in RNA

  • adenine
  • uracil
  • cytosine
  • guanine
• Bond forming base pairs

  hydrogen bond
• Possible base pairs in DNA

  • A-T
  • C-G
• Bond connecting nucleotide bases in a single DNA strand

  Phosphodiester bond
• Bond connecting amino acids in a peptide chain

  Peptide bond
• Bonds stabilising alpha-helix and beta-sheet

  Hydrogen bond
• Functional groups hydrogen bonding in alpha-helix and beta-sheet

  NH & C=O
• Chemical bonds stabilising proteins

  • Hydrogen
  • Disulphide
  • Salt bridge
  • Hydrophobic
• Structural classes of proteins

  • Primary
  • Secondary
  • Tertiary (3D)
  • Quaternary
• Reaction conditions affecting enzymatic rate

  • pH
  • Temperature
  • Substrate concentration
• The graph below is a Michaelis-Menten plot of enzyme kinetics

  
• At Vmax in enzyme kinetics

  Enzyme is saturated with substrate

  
• Difference between curve "a" and "c"

  Reaction "c" is in the presence of a competitive inhibitor
• Difference between curves "a" and "b"


  Reaction "b" is in the presence of a noncompetitive inhibitor
• Km


  Measure of binding affinity between the enzyme and substrate
• Transporting ions against a concentration gradient

  Usually needs to expend energy in the form of ATP
• Ion translocating proteins


  • Na+/K+ ATPase
  • Ca2+ ATPase
• Voltage sensor subunit


  Contains the voltage sensor
• Chemical bonds that allow a ligand to bind to a receptor

  • Hydrogen bonds
  • Ionic bonds
  • Van der Waals forces
  • Covalent
• Classes of receptors


  • Ionotropic
  • GPCRs
  • Enzyme linked
  • Intracellular
• Heterotrimeric G proteins


  Stimulate/inhibit adenylate cyclase
• Adenylate cyclase activation


  Synthesizes cAMP
• Insulin receptor


  Enzyme linked receptor where the enzyme is tyrosine kinase
• Tyrosine kinase activation


  Phosphorylates tyrosine amino acids in proteins
• Intracellular receptors


  Often DNA-linked and upregulate gene transcription when activated
• Cell cycle


  Phases of the cell cycle
• Interphase of the cell cycle

  1. G1

  2. G2

  3. S
• Phases of the cell cycle in order starting with M phase

  1. G1-S-G2
• G1 phase


  • Cellular content excluding the chromosome are duplicated
• S phase


  • Each of the 46 chromosomes is duplicated by the cell
• G2 phase


  • The cell double checks the duplicated DNA for errors and makes any needed repairs
• Cyclin protein


  Approximate mass/size: 56kDa
• Cyclins


  During the cell cycle they are degraded and resynthesized
• Cyclins CDK2 associates with


  • A
  • B
  • C
  • E
• Cyclins


  • Activates the CDK
  • Binds the substrate
• Retinoblastoma protein


  Regarded as a tumour suppressor protein as it sequesters E2F and prevents E2F from upregulating DNA synthesis
• Cyclin/CDK pairs that phosphorylate retinoblastoma protein


  • Cyclin A/CDK2
  • Cyclin D/CDK4
  • Cyclin E CDK2
• CDK-cyclin pairs active in the G1 phase

  • CDK4-cyclin D
  • CDK6-Cyclin D
• CDK-cyclin pair controlling G1 to S phase transition

  CDK2-Cyclin E