Ashley Rhoades Week 3

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Ashley Rhoades Week 3 Journal


  1. biomass: total mass of all living material in a specific area
  2. 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
  3. biosynthesis: The production of a complex chemical compound from simpler precursors in a living organism, usually involving enzymes (to catalyze the reaction) and energy source
  4. transferase: A suffix to the name of an enzyme indicating that it transfers a specific grouping from onemolecule to another, for example acyl transferases transfer acyl groups.
  5. metabolite: Any substance produced by metabolism or by a metabolic process. Any substance involved in metabolism (either as a product of metabolism or as necessary for metabolism).An end product as a result of metabolism
  6. steady-state:A dynamic equilibrium.
  7. flux: The total amount of a quantity passing through a given surface per unit time. Typical quantities include (magnetic) field lines, particles, heat, energy, mass of fluid, etc.
  8. glutamate:major fast excitatory neurotransmitter in the mammalian central nervous system
  9. glutamine:A crystalline amino acid occurring in proteins; important in protein metabolism.One of the 20 amino acidsthat are commonly found in proteins
  10. gram negative bacteria: bacteria which lose crystal violet stain but are stained pink when treated by grams method.

Definitions were found at dictionary


Introduction and Background

  • Ammonia is often the source of Nitrogen in Saccharomyces cerevisiae.
  • The metabolism of nitrogen is regulated by gene expression and the activity of enzymes.
  • The ammonium flux is the rate of ammonia assimilation
  • In this study the ammonia flux was constant between different cultures but the feeding ammonia concentrations were different
  • This study looks at how the presence of ammonia affects gene expression and enzyme activity
  • S. cerevisiae SU32 was grown in continuous cultures with ammonia feeds of 29, 44, 61, 66, 78, 90, 96, 114, and 118 mM
  • Figure 1A: shows the increase in biomass with an increase in ammonia until 61 mM after which biomass remained constant because glucose was now limiting
  • The ammonia flux remained constant over different feed concentrations
  • Figure 1B: shows that an ammonia feed above 44 mM the respiration quotient of carbon dioxide and oxygen remain constant intracellular ammonia and alpha ketoglutarate produce glutamate which is converted to glutamine by an additional ammonia ion
  • With increasing concentrations in the ammonia feed alpha ketoglutarate decreased. Glutamate and glutamine increased as seen in Figure 1C.

Northern Analyses

  • The Northern blot looks at the RNA levels of genes related to Nitrogen.
  • Genes involved in the utilization of ammonia were looked at and it was found that increasing concentrations of ammonia repressed and induced RNA expressed.
  • The RNA levels of gene GDH1 decreased and the RNA levels of the gene GDH2 increased
  • Figure 2 shows the RNA levels of nitrogen related genes
  • The genes GAP1 and Put4p decreased when ammonia concentrations went above 44 mM. GAP1 did not change with differing ammonia flux so it is regulated by concentration and not flux.
  • RNA of amino acid biosynthetic pathway genes ILV5 and HIS4 increased with extracelluar ammonia and then decreased

Enzyme Activities

  • This part of the study looked at enzymes involved in converted ammonia into glutamate and glutamine.
  • NADPH-GDH was shown to decrease, in accordance with GDH1 repression at the transcriptional level
  • NAD-GDH was shown to increase, in accordance with expression of GDH2 at the transcriptional level
  • GS slightly decreased and then leveled off and is controlled posttranscriptionally
  • Figure 3: shows the different enzyme activities at different levels of ammonia


  • The data presented in this paper shows that there are several levels of regulation for nitrogen metabolism in Saccharomyces cerevisiae.
  • Keeping ammonia flux constant in this experiment means any changes are due to extra or intracellular ammonia
  • This study could imply that S. cerevisiae has an ammonia sensing system.

Survey of Biomathematics



Ashley Rhoades