Kristen M. Horstmann Week 2 Journal

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Contents

Unknown Bio Terms

  1. glutamate- "excitatory neurotransmitter in the mammalian central nervous system"
  2. glutamine- "crystalline amino acid occurring in proteins; important in protein metabolism. One of the 20 amino acids that are commonly found in proteins"
  3. flux- "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. (Knew term based off of physics and Math 234, wasn't sure if applied to bio as well)"
  4. proline- "One of the 20 amino acids directly coded for in proteins. Secondary amine and so proline is described as an imino acid. Has strong influence on secondary structure of proteins and is much more abundant in collagens than in other proteins, occurring especially in the sequence glycine proline hydroxyproline"
  5. urea- "final nitrogenous excretion product of many organisms. The chief solid component of mammalian urine; synthesized from ammonia and carbon dioxide and used as fertilizer and in animal feed and in plastics.A molecules created from ammonia and carbon dioxide as a result of the urea cycle"
  6. acetaldehyde-"colourless, flammable liquid used in the manufacture of acetic acid, perfumes, and flavors. It is also an intermediate in the metabolism of alcohol. It has a general narcotic action and also causes irritation of mucous membranes"
  7. alpha ketoglutarate- definition for "alpha amino acid":"amino acid of the general formula R-CHNH2-COOH (i.e., the NH2 in the a position); the l forms of these are the hydrolysis products of proteins. In rarer usages, this class of molecules also includes alpha-amino phosphoric acids and alpha-aminosulfonic acids." Based off of this, I am assuming that the alpha ketoglutarate is a specialized amino acid version of the glutamate neurotransmitter, perhaps with an extra NH2 branch or an added acid
  8. permease-encoding- permease: "type of protein believed to be involved in active transport and acts as a protein carrier" so, the specific biological coding genes that create permease proteins"
  9. oligonucleotide-"linear sequence of up to 20 nucleotides joined by phosphodiester bonds. Above 20, the term polynucleotide begins to be used. A short sequence of nucleotides"
  10. proline permease- "PRNB isolated from Aspergillus nidulans"

Article Outline

Overview

  • The main results from the article
    • ammonia concentrations may determine nitrogen metabolism more than originally thought
    • may be related to increased glutamate and glutamine concentrations.
  • Significance
    • metabolism may be determined by ammonia concentration, meaning the cell may have a sensor system for nitrogen
  • Limitations in previous experiments
    • have shown cultures reacting to ammonia but the experiments differ in external concentration and rate, or flux.
    • Shows that flux could have been main driving force over concentration.
  • Methods
    • Same culture of yeast grown under same parameterss: fixed glucose concentrations and a dilution rate of .15h-1
    • Increased ammonia from 29 to 61 mM
    • Changes of metabolism are regulated by extra and intracellular ammonia concentrations
    • Also regulated by changes of alpha ketoglutarate, glutamate, or glutamine
  • Overall Conclusion
    • Ammonia concentration may drive nitrogen metabolism in S. cerevisiae yeast cells; if so, this particular type of yeast cells may have an ammonia sensor.
    • Future directions would be to further streamline the experiment in order to discover if the ammonia concentration truly drives nitrogen metabolism or if it falls in a different category, like the concentration of alpha ketogltarate, glutamate, or glutamine, as the article's conclusion stated that the metabolism may be affected by any of those.

Figures

  1. Figure 1
    • A
      • x axis: NH4+ concentration
      • y axes: Residual NH4+ concentration, biomass, and NH4+ flux
      • Measurements made by increasing the NH4+ concentration levels and observing the reaction of the residual ammonia, the biomass of the cells, and the flux, or movement rate, of the ammonia
      • The graph shows that the residual ammonia concentration increased dramatically as the ammonia increased, the flux increased gradually, and the biomass increased rapidly at first but slowly afterwards. From this, we can draw that the increase of biomass and residual ammonia correlates with the increase of the ammonia concentration.
    • B
      • x axis: NH4+concentration
      • y axis: Oxygen consumpption, carbon dioxide production, respiratory quotient
      • Measurements were made by increasing the ammonia concentration and by measuring and observing the change in the yeast cells' consumption of oxygen and production of carbon dioxide
      • This graph shows that eventually the O2 consumption, CO2 production, and respiratory quotient all even out eventually and plateau with increase in NH4+. At about 40 mM, the measurements plateaued, meaning that the consumption, production, and quotient only depend on ammonia concentration less than 40 mM
    • C
      • x axis: NH4+ concentration
      • y axes: alpha-Ketoglutarate, glutamate, and glutamine
      • Measurement through observing change in the dependent chemicals by increasing the molarity of the ammonia
      • Graph for alpha-ketoglutarate shows decrease in the ketoglutarate, first steadily, then a low plateau as the ammonia increases. The glutamate sharply increases, then slowly after the ammonia reaches about 70 mM. The glutamine increases relatively steadily as the ammonia concentration increases.
      • These graphs show how the different chemicals react to the ammonia and how they correlate. It shows the difficulty in making the set conclusion of if the ammonia concentration, glutamine, or glutamate are the main driving force behind the nitrogen metabolism as all the chemicals may correlate with the nitrogen metabolism and it is hard to differentiate which parameter is making the real difference in the metabolism.
  2. Figure 2
    • X axes: NH4+ concentration
    • Y axes: Percent expression of GDH1 & GDH2, GAP1 & PUT4, and GLN1, HIS4 & ILV5
    • Measured by increasing ammonia concentration and observing the percent expression of the genes. Calculated by finding the ratio between the gene banding and the reference genes.
    • Graph shows many spikes of the genes throughout the ammonia concentration, too sporadic to make a legitimate conclusion. Some of the genes spike then drop, others continuously decrease over the concentration increase.
  3. Figure 3
    • x axis: NH4+ concentration
    • y axes: activity levels of NADPH-GDH, NAD-GDH, and GS transferase
    • Measured by averages of independent samples with the standard mean error
    • Graph shows the change of the chemicals with the ammonia concentration. NADPH-GDH decreases rather steadily, as does GS transferase and GS synthetase. NAD-GDH is the only chemical that increases with ammonia concentration.

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