James P. McDonald Week 3

From OpenWetWare
Revision as of 19:25, 30 January 2013 by James P. McDonald (talk | contribs) (Outline: completed methods of part 1)

Biological Terms

  1. Permease: "General term for a membrane protein that increases the permeability of the plasma membrane to a particular molecule, by a process not requiring metabolic energy." [[1]]
  2. Isomerase: "An enzyme that converts molecules into their positional isomers." [[2]]
  3. Oligonucleotides: "Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesised to match a region where a mutation is known to occur, and then used as a probe (oligonucleotide probes)." [[3]]
  4. Dehydrogenase: "Enzyme that oxidizes a substrate by transferring hydrogen to an acceptor that is either NAD/NADP or a flavin enzyme. An enzyme that is used to remove hydrogen from its substrate, which is used in the cytochrome (hydrogen carrier) system in respiration to produce a net gain of ATP." [[4]]
  5. Synthetase: "Enzymes of class 6 in the e classification, catalyse synthesis of molecules, their activity being coupled to the breakdown of a nucleotide triphosphate." [[5]]
  6. Biosynthetic: "Relating to or produced by biosynthesis." [[6]]
  7. Glutamate: "Major fast excitatory neurotransmitter in the mammalian central nervous system." [[7]]
  8. Glutamine: "A crystalline amino acid occurring in proteins; important in protein metabolism. One of the 20 amino acids that are commonly found in proteins." [[8]]
  9. GAP1: "General amino acid permease, a gene found in Saccharomyces cerevisiae." [[9]]
  10. PUT4: "Proline permease, a gene found in Saccharomyces cerevisiae." [[10]]



  • Saccharomyces cerevisiae was grown in various ammonia concentrations and the effects on the growth was observed.
    • A single dilution rate was using with a range of different ammonia concentrations.
    • The ammonia concentrations were varied to observe its effects on gene expression and enzyme activities.
  • The main result of the study was that nitrogen metabolism is dependent on ammonia concentration, not its flux.


  • Ammonia is the prefferred growth source of Saccharomyces cerevisiae as it results in faster growth.
    • Nitrogen metabolism is regulated by gene expression and enzyme activity.
  • Previous research seems to show that ammonia concentration itself is the most important factor in nitrogen metabolism.
    • But, in these previous studies the cultures have differed in ammonium flux, leaving flux as the possible key factor.
    • This experiment uses cultures with the same level flux, only the ammonium concentrations fed in are different.


Physiological Parameters

  • Saccharomyces cerevisiae SU32 was grown in continuous cultures
    • They were fed with different ammonia concentrations: 29, 44, 61, 66, 78, 90, 96, 114, 118 mM.
    • Contained a fixed glucose concentration at 100 mM.
    • Had a dilution rate of 0.15h-1.
  • Biomass and residual ammonia concentration were measured at the different ammonia concentrations.
  • The ammonium flux was calculated using the biomass, ammonia concentration, and the residual ammonia concentration.
  • The respiratory quotient was calculated using the measured values of CO2 production and O2 consumption at the different ammonia concentrations.
  • Alpha-ketoglutarate, glutamate, and glutamine concentrations were measured and the different ammonia concentrations.

Northern Analyses

Enzyme Activities

Class Links

Journal Entries and Assignments