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9

The answer given by Sadegh gives a general correct broad view. But one part of the puzzle is missing, which is molecular recognition. Molecules bind to each other via physical/chemical interaction like forming hydrogen bonds, electrostatic interactions and other mechanisms. The sum of all interaction defines the strength of the binding. If molecules have ...


7

It's both simple and complex. The simple answer is Brownian motion. All the particles in the cell do have mobility which is related to their mass. A small particle like a soluble enzyme undergoes random walks through the cytoplasm or nucleoplasm. Thus by having a grand number of a certain molecule you can be sure that at some point it interacts with the ...


6

So if you're reading the flowchart, understanding the notation of the arrows is important: We have rectangles around the gene products There's a circle, denoted by DNA, noting that the proteins are expressing the product that follows through interaction with DNA The solid line with an arrowhead means there's some sort of interaction The solid line with the ...


3

A pathway shows all the reactions required for the synthesis / metabolism of a given product. A module is a functional unit that can be utilized in a pathway, and some modules are common to many pathways. For example, look at the tetracycline biosynthesis pathway 00253. This pathway has a description at the top that includes this excerpt: Tetracyclines ...


3

I suspect that what you are asking for is years in the future yet. Bear in mind that the use of CRISPR-CAS9 is just entering clinical trials for a very few, well studied diseases. Almost all the work with CRISPR-CAS9 is still limited to model organisms and tissue cultures. Are you referring to Adiposis Dolorosa? Apparently the cause is not actually known ...


3

Shortly, understanding a process called molecular recognition (as stated by @alec_djinn) under crude biological environment would answer all your questions. Before explaining answers for your questions, to understand biochemical aspects of Transcription better, I would highly recommend to read a textbook written by Lubert Stryer. Proteins including enzymes ...


3

Yes; It is possible to inhibit cell death. There are several possibilities, of which many - as correctly recognized by you - involve changes in the activity of the cell death pathway (or related ones); For a long (but still incomplete) list of commercially available drugs that inhibit cell death, please see: https://www.sigmaaldrich.com/life-science/cell-...


3

Pathways in biology are very hard to interpret without being an expert in the subject. Here a link to The Standard Graphical Notation for Biological Networks that might help you understanding the notation used. Pathway are generally based on evidences of links between the players. These links do not require to be found using one particular technique. Those ...


3

How can hormones/molecules have different effects if they all work through cAMP? The short answer is that receptor expression on cell types is highly specific, and only if a cell has a particular receptor will it respond to a particular hormone. Thus two different hormones can have different biologic effects because the cells that contain those receptors are ...


3

Information available on this is huge. I will pin point main points. Generally this signalling will involve four components viz. receptors, transduction machinery, perireceptor processes and downstream processing of chemosensory information. Receptors First step is to receive signal (here odorant or chemicals). Following figure shows comparison between ...


2

It was a simple search. You could have easily searched for glucose oxidase in KEGG, and you would have got this reaction. In fact if you had clicked the link for glucunolactone's compound page, you would have got a list of many different reactions that convert glucose to glucunolactone. You can even click the arrow which opens the KEGG-ORTHOLOGY page. You ...


2

This is somewhat outside my field, but basically it seems they're defining the independence of the three hypothetical metabolic pathways in two different ways: Mathematically the pathways are not independent since P₃ is a combination of P₁ and P₂. Biologically the pathways are independent since each requires a different combination of enzymes and therefore ...


2

This answer is based on a 2002 autobiographical account of the work of Bernard L. Horecker entitled The Pentose Phosphate Pathway. Here he refers to “direct oxidative pathway” but does not unambiguously explain this, so I shall summarize my interpretation and then provide evidence in terms of quotations. Summary of my interpretion of Horecker’s account ...


2

In my experience those terms are primarily used intracellularly, but I wouldn't argue that it is wrong to use them more broadly, it's just that essentially everything released extracellularly is going to have some level of divergence, so it makes more sense to use a separate classification scheme (i.e., endocrine/paracrine). Between cells, the terms are also ...


2

See the manual: PPrel, in each of these, means protein-protein interaction, so we want to approach these by thinking about what the protein products of these genes can do with eachother. For the first and second example, the subtype(s) give more information about the interaction. They aren't necessarily mutually exclusive. For example, phosphorylation can ...


2

If by enzyme you mean "protein" aka polypeptide, than there are such things as catalitic RNAs. Those are molecules of RNA that facilitate chemical reactions but don't change themselves (definition of catalyst). I think that, based on the discovery of such RNAs, it is now believed that life might have started from or with the help of catalytic RNAs (please ...


1

The determining factor is the hereditary traits that are passed on to the organism. Metabolic pathways require protein catalysts of which the instructions to make are stored in DNA. In other words humans can't use the Calvin cycle because our parents can't/couldn't, but plants can because their parents can/could. In the long run though, very slowly ...


1

As far as glycolyis is concerned, the answer is straightforward. In certain cells and tissues there is a pathway working in the opposite direction — gluconeogenesis — in which the ‘irreversible’ steps of glycolysis are, in fact (and of necessity), reversed by a different enzymic reaction in which the position of the equilibrium is in the opposite direction. ...


1

The other big metabolic database site besides Kegg is MetaCyc which certainly responds to searches for lignin and cellulose. The problem with lignin is that it is a very complex molecule, so in both Kegg and MetaCyc there are a many reactions involved in its synthesis. Cellulose is less complex and I have no idea what GAX is, despite an internet search. If ...


1

In mammals gluconeogenesis occurs primarily in the liver (together with the kidney to a much smaller extent). When the blood glucose concentration falls, it is the role of the liver to generate glucose for other tissues that are dependent upon it. Hormones play a key role in this. If one considers the decrease in blood glucose concentration during ...


1

Your interpretation of the pathway map is incorrect. The boxes do not represent KOs (Kegg Orthologues) and they do not represent a protein complex. They are Enzyme Commission (EC) numbers and where there is more than one box this means that there is more than one enzyme that can catalyse the reaction. In the case you cite the two enzymes are EC 5.3.1.9, ...


1

Addition of $O_2$ or removal of H means oxidation. In this process H is removed from sugar, added to NADP as well C is oxidised to $CO_2$. Hence , it is oxidation reaction. HMP pathway is used to produce NADPH. The process directly oxidise glucose to $CO_2$ and $H_2O$. It does not require TCA cycle or ETC. Hence is called direct oxidative pathway. ...


1

How do I score differential activity of cellular pathways in microarray data (not enrichment)? You would look at downstream genes, which are selective for individual pathways - or genes which have binding sites for transcription factors that sit at the end of your pathway. Depending on the existing literature, and your experiment, and the specific pathway, ...


1

Pathway analysis can be a little tricky. Because pathway enrichment is estimated from the enrichment of genes (or miRNA or what have you) that participate in overlapping pathways, certain pathways often show up for reasons that may have little to do with your experiment. Cell cycle related pathways, in particular, come up a lot, since so many genes are "cell ...


1

For any dynamic system defined by different components, the steady state is the state of the system in which the components remain constant over time. If you consider the example of growth (by cell division) the point at which the total number of cells remain constant would be the steady state. This is a point at which birth rate = death rate. Similarly for ...


1

Gi and Gs have a structurally different sub unit in their alpha chain. The receptors for PGE1 and adenosine interact with inhibitory Gi, which contains the same β and γ subunits as stimulatory Gs but a different α subunit (Giα). In response to binding of an inhibitory ligand to its receptor, the associated Gi protein releases its bound GDP and ...


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