Lectures 2-7: Amino acids, proteins and enzymes

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    • What stereoisomer are proteinogenic amino acids?
      L-isomers
    • What standard are L/D isomers compared to?
      D-glyceraldehyde
    • What backbone confirmation do alpha helices prefer?
      Right-handed
    • How are peptide links shown
      The N pointing down and the carbonyl pointing up
    • Which direction do alpha helices rotate when viewed from the N-terminus?
      Clockwise
    • Which amino acid will break an alpha helix?
      Proline
    • What preference rotation do beta sheets prefer?
      Clockwise
    • What is an Å?
      One tenth of a nanometer
    • What is a folded region of a protein called?

      A domain
    • Why is haemoglobin said to be allosteric? 

      Its binding modulates the affinity of other haemoglobin molecules
    • What is a heteromer?
      A protein with different subunit sequences
    • What is a homomer?

      A protein with the same subunit sequences
    • What is an example of an intrinsically disordered protein?

      Keratin
    • Which part of a protein is best preserved?
      The core due to surface interactions
    • What can quaternary proteins bind to?
      Other proteins, molecules, metals, cofactors
    • What is sickle cell anaemia caused by?
      Hydrophobic interactions in erythrocytes
    • What does non-functionality of essential proteins lead to?
      Death
    • What does non-functionality of non-essential proteins lead to?
      Disease
    • Why are protein interaction highly monitored, such as in the case of blood clotting?
      To ensure the necessary outcome occurs at the right time in the right quantity
    • What is a protein with 3 subunits called?
      A trimer
    • What is a protein with 4 subunits called?
      A tetramer
    • How variable is disorder in intrinsically disordered proteins?
      Can be limited to domains or be entirely disordered
    • What does misfolding of proteins cause?
      Disease
    • How is Alzheimer’s disease linked to protein misfolding?
      Beta amyloid forms plaque
    • What are amyloids caused by?

      Beta-sheet misfolding
    • What enzyme facilitates the exit of visions from the host cell?
      Neuraminidase
    • How do drugs like tamiflu prevent viral maturation?
      Competitive inhibition with neuraminidase
    • How does penicillin cause bacterial cells to lyse?
      Beta lactam rings act as inhibitors on penicillin binding sites, preventing cross linkage of the cell wall
    • How have some bacterial strains evolved to evade the effect of penicillin?

      Producing beta-lactamase prevent beta lactcams binding to PBS
    • What are nucleoside-analogue drugs?

      Anti-viral drugs
    • How do nucleoside-analogue drugs work?
      By acting as non-hydrolysable nucleoside competitors that prevent DNA chain extension
    • Why are enzymes important considering the environment of the human body?
      They permit higher reaction rates in milder reaction conditions
    • Keq 

      The equilibrium constant that determines direction of reaction
    • What is a feasible reaction in terms of Gibbs free energy? 

      Less than or equal to 0
    • How do enzymes make converting to products easier?

      The formation of an ES complex reduces the activation energy required
    • What is Vmax?
      Maximum activity when all active sites are full
    • What is Km? 

      Half the value of Vmax
    • What does a high Km mean?
      Low affinity
    • What does a low Km mean?
      High affinity
    • How is Kcat calculated?
      Vmax/ total [enzyme]
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