Hobbz

Sorry foodchain, I cannot answer your question because I do not understand operators enough. You mentioned the idea that life began instantaneously. I don't scientists who have wondered about the beginnings of life assume it occurred instantaneously. My understanding of the common hypothesis for the beginning of life was that in the oceans under very different conditions from today a multitude of organic compounds were synthesized over millions of years and then in time the right molecules got together and were capable of replication and then one could imagine through selection that they evolved.

Here are some interesting papers I found and the one I was referring to earlier was the first paper noted below. They used superoxide dismutase and found that it increased the doubling capacity of the cells. I think the other papers offer some possible explanations for the first however I haven't had much time to look over them. "Manganese superoxide dismutase protects the proliferative capacity of confluent normal human fibroblasts" Antioxid Redox Signal. "H2O2 accelerates cellular senescence by accumulation of acetylated p53 via decrease in the function of SIRT1 by NAD+ depletion." Cell Physiol Biochem. "Cytoplasmic localization and ubiquitination of p21Cip1 by reactive oxygen species" Biochemical and Biophysical Research Communications Enjoy. Sorry I made a mistake the first paper can be found in the Journal of Biological Chemistry and not Antioxidants and Redox Signaling.

Hello Foodchain, I'm not at all familiar with unitary operators and just read about them on wikipedia and I still don't understand how to use them. Could you help me understand what a unitary operator will represent in a model to study the genome and the proteome? You say you could use it to represent various actions a protein might take but what in math will be representing the protein and what would be representing the outcome of its actions?

So, you never calculated Vmax, kcat, or Km without Urea in the sample?

Ummm, I think this thread should be moved to physics. I think you would have a much more capable audience to answer this question there.

Gyrase and I had an extensive discussion on Km recently and we should be on our "A" game for this. So that's a very thought provoking system you have there with the equilibrium between the native and denatured protein in the urea solution. First, your equilibrium between the native and denatured protein would have to equilibriate on a time scale similar to the half-life of your substrate in the system in order to consider it is affecting anything. Second, it still should not change the Km if the equilibrium of the denatured and native enzyme shifts fast enough. It may appear that way when plotting your data on a Michaelis-Menten plot but your system is not following Michaelis-Menten assumptions because the total concentration of active enzyme is changing in your sample. You would need to derive new equations in order to properly calculate the Km of your enzyme in this environment and I that's beyond my ability. Third, your Km may actually be changing because urea may be altering the structure of the native enzyme which could allow for the substrate to get to the enzymes active site faster or slower and leave faster or slower. I hope that helps and I may be wrong.

That makes sense. It's easy to get lost conceptually in enzyme kinetics, thanks for the help. Another perspective that helped reassure me Km does not change with enzyme concentration was when I tried to visualize the difference between one enzyme in the system and then two enzymes. If one gets half saturated at a specific substrate concentration than two enzymes will get saturated at the same substrate concentration.

A couple things about oxygen and ROS. The more oxygen living cells are exposed to the more damaging ROS molecules are, which has been shown irradiating cells exposed to varying amounts of oxygen. So perhaps the more oxygen an organism is exposed (faster heartbeat) the faster ROS can hurt the organism. Cancer is one pathway to death and exposure to ROS certainly increases its likelihood. ROS has also been suggested to play a role in artherosclorosis as well. Funny you mentioned vitamin E, because that is the one supplement that has been shown to decrease the likelihood of cancer and I think artherosclorosis as well in epidemiology studies. Other vitamins and supplements don't have near as strong of evidence as vitamin E. Several experiments have been done in cell cultures with non-immortalized cell lines, cells that have a finite number of divisions. Cells that have upregulated antixodant enzymes will divide longer than normal cells before they go into senescence. And that reminds of another point, are we talking about longevity (lifespan) or aging (losing the capacity to function properly). I'm assuming aging since of course since that's what this thread is titled. Anyway, the role ROS may play role in senescence which some people argue is the cause of aging. And ROS may bring about senescence by pushing the genome to accumulate more mutations which could upregulate genes that prevent cell division. So one experiment could be to look at several cell lines and determine if there is a common amount of mutations in the genome they acquire in order for them to senesce. Then upregulate antioxidant enzymes which will allow them to divide longer and see if they acquire more, less or the same number of mutations before they senesce. I would hypothesize that they(upregulated antioxidant enzyme cells) would acquire the same number of mutations at senescence and have a greater dividing potential.

http://en.wikipedia.org/wiki/Post-translational_modifications Wikipedia above as an extensive list of post-translational modifications and a number of them would be considered co-translational modifications as you pointed out. Co-translational modifications will be considered post-translational modifications since it is after the synthesis of the pepteide chain. So glycosylation won't affect signal pathways that much since it is a more permanent modification. And in biology there are usually exceptions and I tried to find some browsing through pubmed but was unable to find any example of glycosylation of a protein in the cytosol. So, is this what you were looking for?

Phosphoylation (That's a big one!), ubiquitinylation, acetylation, glycosylation, biotinylation, oxidation (disulfide bridges).

I'm a little familiar with the Free Radical Theory of aging. It's not so much that the ROS molecules are damaging proteins and membranes because those are turned over thousands of times in a life span of many organisms. It's more about the accumulation of mutations that occur in DNA due to ROS. Over time the mutations build up and can cause apoptosis, necrosis, senescence or carcinogenesis. One interesting observation in biology is the average lifespan of animals plotted against the resting heart. The slower the heart rate the longer the animal lives.

I understand that k1 k2 and k-1 won't change but I don't understand how Km can't change if you change enzyme concentration. For example, if one were to use 1 pM of enzyme and found the Km to be 100 uM but if one were to change the enzyme concentration to 1 fM that the substrate concentration to half saturate the enzyme would still be 100 uM?

I know that is why you can take 1/2 Vmax to find Km on the curve but won't the curve from a Michaelis-Menten plot change if you change the enzyme concentration. Therefore, Km would be dependent on enzyme concentration. Another way to look at is that Km and Vmax are related. Basically if one was to use less enzyme to make the Michaelis-Menten plot, wouldn't it take less substrate to reach Vmax because that is the point at which the enzyme is saturated with substrate?

I'd like to hop on this because I am very confused about what Km is and would appreciate some clarification. So, Km is mathematically defined as "Km=(k-1 + k2)/k1" in a simple enzyme model. But it is graphically defined on a Michaelis-Menten plot as the substrate concentration at which the rate equals 1/2 of Vmax. These two definitions appear very different to me. Why?... Because if Km can be "graphically defined on a Michaelis-Menten plot as the substrate concentration at which the rate equals 1/2 of Vmax" therefore it will change with enzyme concentration because each Michaelis-Menten plot is specific for a known enzyme concentration. Too put it more simply, the Michaelis-Menton plot will change with enzyme concentration and therefore change the graphically calculated Km. Something must be wrong here and I don't know what?