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NAD+ is important in this step, since it is co-factor for the glyceraldehyde-3-phosphate dehydrogenase (G3PDH), which acts as a acceptor for the hydrogen atom from the C1 (see below). If you look at the reaction, the aldehyde from the C1 is oxidized to a carboxylic acid which in a second step is turned into a phosphoester. To do so, a cysteine from the ...


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Let me first clarify the difference between anaerobic respiration and fermentation. Literally respiration refers to breathing, but its definition has been extended to include cellular metabolism that leads to ATP generation. Fermentation, as you said depends on substrate level phosphorylation. Anaerobic respiration on the other hand just means ATP ...


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Some things to consider. If you spinning too fast and too long, that is going to pack the pellet more. You can spin longer at a slower speed and you will notice your pellet is not as tightly packed. I always do 2000 rpm, 20 minutes, 4C if I'm doing a midi or maxi sized prep and harvesting bacteria in a 50ml conical. If I'm doing a miniprep I will take the ...


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This question got me thinking about what are the metabolic enzymes that take oxygen up in E.coli. I searched the metacyc database for reactions that consume molecular oxygen and there are only 3 that take in oxygen and one that produces oxygen. All three consumers of oxygen in E.coli are the oxidation of ubiquinone by at two sites in cytochrome-bcl or by ...


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It is not uncommon for cells to have parallel pathways for same outcome. This ensures foolproof response and makes the system robust. E.coli also has another sensor for aerotaxis (Aer and Tsr proteins). See my answer on your previous post and the linked paper. Also look for coherent feed forward network motifs.


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The plasma membrane is quite permeable to oxygen and thus oxygen enters the cell simply by diffusion. Reactive oxygen species can be reduced enzymatically in aerobic organisms. Obligate anaerobes lack or don't produce sufficient quantities of these enzymes. An organism that doesn't use oxygen for metabolism but is also not relatively harmed by it can be ...


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I found that E. coli exposed to predators such as amoeba changes completely from normal form to filaments (on agar) that look wound up like spaghetti but are not only longer but significantly wider. In this form the predator can't attack E. coli and it lives among the amoeba for extended periods. It does not look like a simple point mutation to me, which ...


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Answer clarified based on comment by @DurgaDatta What would it mean to say the enzyme activity was tested in vitro on the mutant? When we say the response of the a single gene knock out mutant, the cell should be intact except for lacing one gene, which would mean that the response is in vivo. The knockouts were performed inside the E. coli cells and, ...


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The basic problem is one of prior knowledge. The information you have about E. coli metabolism is in the form of a simple network, i.e. a list of nodes and the edges (along with their weights) that connect them. From this information alone it's impossible to know, for example, that the reactions in the TCA cycle should be plotted as a perfect circle (that's ...


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I'm not sure if they will be useful for your application, but you should look into software used to visualize ecological networks (and maybe also software used for drawing electrical charts). The type of data used there is very similar to what you want to plot, with nodes and links along with metadata for links on e.g. rates or connection strenghts. I can ...


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It is possible to conduct an in vitro experiment with cell extracts. Meaning that you break up the cells and put their pieces into a reaction glass and do your experiment. It is assumed that the cell molecules (enzyme, sugar or cofactors) will still carry out their functions even though the cell is no more. In other words, you used the mutant to produce the ...


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Non-coding transcripts can be as small as 10-15 nucleotides. Once the RNA polymerase initiates, the DNA is melted and the transcription bubble forms. This region is about 10 nucleotides long. But if you are asking the limit of mRNA length, then the answer is different. First of all, to get a protein, the ribosomes have to translate the transcript. To do ...



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