Stephanie+Shore+Log

=November 11, 2009=

Assignment 3 - nitric oxide [you don't have 5 sources for 5 properties JCB]
DONE [|Wikipedia] MP: 110K BP: 122K Solubility in Water: 7.4 ml/100 ml (7.4%)

[|ChemSpider] MP: -263°F (109K) BP: -241°F (121K) Solubility in Water: 5% Vapor Pressure: 34.2 atm

[|NIOSH] MP: -263°F (109K) BP: -241°F (121K) Solubility in Water: 5% Vapor Pressure: 34.2 atm

[|InChem] MP: -163.6°C (109.4K) BP: -151.8°C (121.2K) Solubility in Water: 7.4 ml/100 ml (7.4%)

[|DrugBank] Solubility in Water: 9.49E+004 mg/L (9.49%)

[|MSDS] Vapor Density (air=1): 1.04 [|MSDS] Vapor Density (air=1): 1.04 MP: -262.6°F (109K) BP: -241.2°F (121K) [|MSDS] Vapor Pressure: 26000mmHg (34.21 atm) Vapor Density (air=1): 1.036

[|CDC] Vapor Density (air=1): 1.0 Vapor Pressure: 26,00 mmHg (34.21 atm)

[|University of Akron] Vapor Density (air=1): 1.04 Vapor Pressure: 26000mmHg (34.21 atm)

[|SigmaAldrich] Vapor Density (vs air): 1.05

=November 2, 2009=

Space, Time, and NO
Simply, biological signaling is important enough to have had numerous theories presented on it. However, mathematical principles only describe the steady-state assumptions of computational biology and do not relate to the feedback pathways of biochem.

Signaling enzymes perform chemistry and transmit information. Steady-state assumptions only work when the enzyme is transmitting data over an extended period of time and doing so slowly.

Nitric Oxide synthase or NOS generates NO from L-arginine with the input of 2O_2_ and 1.5NADPH which is equivilant to three electrons. NO synthysis is controlled by CaM which controls the amount of available electrons to be used in the process.

This study concerns mostly neuronal NOS (nNOS).

The time-dependence of NO is still being studied, but measuring the amount of NO directly is difficult. Therefore, heme is measured.

NOS is inhibited by NO.

Ferriheme is reduced to ferroheme (FeIII --> FeII). O_2_ binds to ferroheme. Oxygenase synthesizes NHA and FeIII (NHA is N-hydroxy arginine, an intermediate in NO synthesis).

The heme proteins have unique spectra as intermediates using Soret difference spectra. Ferroheme is must abundant as shown by the Soret spectra.

Fe-NO complexes dominate as the reaction progresses as expected.

The spectra shows three dominant peaks: initial ferric heme components, Fe-NO intermediates, and final ferric heme components. There are also other peaks that correlate to residuals.

Signal noise was compensated for during the experiment.

When graphing the rates of all the intermediate steps of the synthesis of NO, an exponential graph is approximated.

The enzyme is temperature dependent. The experiment was done at 310K as a measure of confidence that experiments done at lower temperatures were accurate.

CaM binding rates do not have much of an effect on the overall rate of NO synthesis.

EDTA and Calcium were added to the experiment done at 295K to offset the steady-state of the synthesis. Together, EDTA and calcuim acted as a pulse and destroyed any steadiness of the synthesis. Alone EDTA and calcium did not produce a pulse.

With the pulses, there is a slightly greater inhibition at 295K.

A newer model describing the synthesis of NO as developed by this particular experiment is more beneficial to use because it considers the whole catalytic cycle. The older model left out the steps of the transfer of electrons from FMN to heme.

Making NO from arginine can be done with the input of three electrons. The first electron "primes" the enzyme, so it will bind to the substrate. The second electron is delivered much quicker than the first, and is donated by BH_4_. The third electron comes from NADPH. BH_4_ is not included in the older model.

There is some confusion as to when exactly BH_4_ is regenerated.

Two-electron models (the older models) are used, but need to be replaced by three-electron models. The newer models take into consideration stoichiometry. However, the three-electron models are not perfect. They need to be improved in order to determine the rates of reactions with higher accuracy. The newer model does not include rates that are fast.

nNOS can synthesize NO at pulsed states, not just steady states.

Further studies need to be completed in order to fully understand the inhibition of NO synthesis.

Since NO is a rapidly diffusing neurotransmitter, pulse studies are important in order to understand the complete synthesis of NO.

Quasi-geminate NO can also act as an inhibitor.

eNOS is similare to nNOS, so pulse studies will also be done to determine how similar.

Heme reduction in eNOS is much slower than the heme reduction that takes place in nNOS.

It seems that instead of pulses being used to study inhibition, low molecular oxygen levels act as an inhibitor for eNOS.

Quasi-geminate NO produces the feedback cycle of the synthesis of NO.

Removing calcium or phosphorylation results in the inhibition of the transfer of electrons. This inhibition method occurs rapidly, in less than one second.

The synthesis (and the inhibition) of NO is also affected by the sodium-potassium pump and the delocalization of the neuron membrane.

The lingering affects of NO last longer than the membrane action potential.

nNOS can be activated via spikes in the concentration of calcium and high concentrations of CaM (relative to the neuron and synaptic cleft).

The nNOS that was used came from rats.

The UV/VIS spectra was used. The pH was kept constant at 7.5.

Kinetics experiments were also conducted to determine the rates of bonding and the rates of reaction.

[|Space, Time, and NO]
 * [Full Marks JCB]**

=October 22, 2009= Found general articles through ProQuest, NCBI, and Scirus. Still unsure of the specific topic.

=October 8, 2009= Started with Wikipedia: shifting through information to separate biological and chemical relevant information

Read two interesting facts that might narrow down my topic: 1. When nitric oxide is released from phagocytes, it is toxic to bacteria because it is a free radical. It damages DNA and degrades iron-sulfur centers to iron-iron and iron-nitrosyl 2. Drugs are administered to people with heart disease that contain isobutyl nitrite. The body converts it to nitric oxide through a process which is not completely understood.

I have not looked at inhibitors or agonists yet, but have found the general synthesis process.

=September 29, 2009= Potential research topics: 1. functions of nitric oxide as a neurotransmitter **[Excellent starting point - I would suggest starting with Wikipedia and perhaps think about a focus on inhibitors and agonists and the biomolecules involved JCB]**