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11

DNA is a bit more complicated than some molecules due to it's length and composition variability. Specific data is needed to quantify this accurately and other solvents are likely to be needed for a suitable solvent. Here is a server that can point you to a suitable solvent based on your specific sequence. Ultimately, organic solvents are likely to be needed ...


7

You're basically confusing the fuel source with the energy it produces. For example, a car burns gasoline. That doesn't mean that gasoline is energy, only that gasoline can be used to produce energy. Similarly, a cell uses electrons in the production of ATP (source): In the image above, electrons flow (symbolized by the flat arrow going from ...


6

We can look at the list of amino acids on wikipedia for a start. And we can look at this L-alanine: What makes your image confusing is that it's a Fischer Projection, and I hate those because you have to remember what way the stereochemistry goes. In Fischer Projections, vertical lines face away from you, while horizontal lines face towards you. So if we ...


6

Have a look at this paper. They have isolated a chromoprotein similar to GFP, and like the latter it does not have any prosthetic group. This protein — asFP595 (because it was isolated from the anemone Anemonia sulcata.), is purple coloured under white light and also exhibits a little fluorescent emission in the red region (λmax = 595 nm). Also have a ...


5

Short answer Assuming you wish to have a common name for both of these (widely differing!) pathways I basically agree with @Chris, and I would go for general terminology, namely metabolic pathways. Background The pentose-phosphate pathway is neither anabolic nor catabolic so those terms won't do. The pentose-phosphate pathway is, however, closely linked to ...


5

The rate-limiting step of photosynthesis is the CO2 assimilating enzyme Rubisco (short for ribulose-1,5-bisphosphate carboxylase/oxygenase) (Jensen, 2000). It uses ribulose-1,5-bisphosphate and CO2 as substrates to generate glucose. Given that Rubisco is the rate limiting step in photosynthesis, an increase in its substrate CO2 would expectedly lead to an ...


5

if a person is both (1) hyperventilating and (2) has a low blood pH then this is a case of metabolic acidosis... in metabolic acidosis the patient compensates by breathing heavy... why? because hydrogen ions are captured by bicarbonate (the conjugate base of carbonic acid) which is then exhaled as carbon dioxide... metabolic acidosis is not caused by ...


4

All amino acids with side chains that are charged at physiological pH are, by definition, also amino acids with polar side chains (e.g., lysine or glutamic acid). The converse is not true; in other words not all amino acids with polar side chains are necessarily amino acids with side chains that are charged at physiological pH (e.g., threonine or ...


4

Short anwer 'Non-competitive active site–binding inhibitors' are called mixed-type inhibitors. These inhibitors exhibit features of both competitive and non-competitive inhibitors, as they increase Km (like a competitive inhibitor) and decrease Vmax (like a non-competitive inhibitor). Background What an interesting question! In theory, a reversible ...


4

This is a tough question. I was reading this paper Patrono, C., et al. "Clinical pharmacology of platelet cyclooxygenase inhibition." Circulation 72.6 (1985): 1177-1184. and they seemed t mention this paragraph in the introduction. Platelet Cycloxygenase or prostaglandin (PG) H synthase (i.e., the enzyme that converts arachidonate released from ...


4

Short answer: there are no restrictions in principle on which amino acids can follow which. That means that in principle you can have polypeptide in any configuration: AAAA, WQWQWQ etc. Problem is that polypeptides must be functional and, because they are in aqueous solution, it puts restrictions on how polypeptide form secondary and tertiary structure. It ...


4

ALiceD's comment is perfectly true. (Though in real cases, the short circuiting is seldom absolute as there is usually some finite resistance in the short circuiting wire.) You can understand this in two ways. Intuitively, the uncoupling provides a channel for the hydrogen ions to move across the membrane in the direction of their electrochemical gradient ...


4

Bicarbonate is not carbon dioxide. In acidic conditions, bicarbonate will be protonated to form carbonic acid which in turn decomposes into carbon dioxide and water. The overall result is the removal of a proton (ie increase in pH) and formation of carbon dioxide (which accounts for the rapid breathing). The idea behind giving bicarbonate is that it will ...


3

501 denotes 501st residue in the corresponding PDB entry — 1BDG. See here A single protein can have multiple cavities (see here) and the multiple entries denote centres of different cavities.


3

The paper by Graczyk (2007) is probably relevant for you. It says that the Gini index is a measure of reactive selectivity of kinases, with values close to zero indicating no selectivity and values close to one indicating high selectivity, and it is created in direct parallel to the Gini index in economics, which is used to describe economic inequality. In ...


3

You need to account for free phosphates (Pi) that derive from ATP and are released in phosphatase reactions. The regeneration of 3 ribulose-1,5-2P has the overall reaction 5 glyceraldehyde-3P + 3 ATP $\rightarrow$ 3 ribulose-1,5-2P + 3 ADP + 2 Pi So in total eight phosphates (here counting ATP as 1) are redistributed, 6 of which end up in ribulose-1,5-2P, ...


3

I think that the OP was asking about relevance of using urea with respect to the FASP method. In the FASP method, the primary denaturant is SDS . Protein are denatured with a ~4% SDS solution (buffered to pH 7.5 - 8.0). Then 8 M urea solution is used to replace the SDS. Urea serves two purposes here, first it keeps the protein denatured and in solutions as ...


2

At typical physiological pHs glutamate does exist as glutamate. Broadly the acidity in the digestive track is enough to reduce glutamate to glutamic acid. The stomach for example has a healthy pH of between 1.5 to 3.5. Canadianer points out in the comments that the active site during catalysis are protonated. There are obviously a lot of examples of this ...


2

Since porphyria is not one disease but many, I suppose that with "acute porphyria" you mean acute intermittent porphyria. The reason of the disease is an autosomal dominant mutation on the enzyme porphobilinogen deaminase, an enzyme that converts porphobilinogen to hydroxymethylbilane by a deamination reaction. Now the heme is produced in many steps, and ...


2

Often genes or other DNA fragments are inserted into an expression vector and used to transform bacteria or other cells. When a mixture of vectors is used containing various DNA fragments (e.g. a chopped-up genome), then individual (bacterial) colonies need to be isolated to make sure they carry only one insert. This can be done, e.g., by plating the ...


2

Glucose is the only fuel normally used by brain cells. Because neurons cannot store glucose, they depend on the bloodstream to deliver a constant supply of this fuel. Fatty acids do not serve as fuel for the brain, because they are bound to albumin in plasma and so do not traverse the blood-brain barrier. In starvation, ketone bodies generated by the liver ...


2

Not necessarily, they can be enzymes, but they include a lot more (the whole proteome). It takes a FASTA format file containing a set of query protein sequences from a single organism (a partial or complete proteome) and identifies those sequences that are likely to participate in any of its supported metabolic pathways Path-A predicts the ...


2

The Jaccard index is a measure of similarity between two sets. Take a look at the Wikipedia article here. It is very easy to compute: The Jaccard similarity coefficient for sets X and Y is defined as: J(X,Y) = |intersection(X,Y)| / |union(X,Y)| Where | | indicates the size (number of elements) of the set. Imagine you have two sets X and Y defined as ...


1

While I have never done bacterial stock cultures from spores, I don't think it is necessary, as the standard procedure for making bacterial stocks should work without problems. For that you grow your bacteria in liquid culture until you reach the late log phase (so you have a lot of bacteria in your media), take 1 ml of the culture, mix it with 100% ...


1

The synthesis of N-acetylglutamate is mediated by the enzyme N-acetylglutamate synthase. This enzyme has L-glutamate as its substrate and uses acetyl-coenzyme A as a co-enzyme acetyl donor. Acetylcoenzyme A (Acetyl-CoA) is generally abbreviated in structural formulas, because it is a relatively complex molecule. The only thing of relevance is the acetyl ...


1

You are looking for light-emitting proteins. They gather energy from either absorption of photon (fluorescence) or via random thermal fluctuations. Problem is that fluorescence might be considered forced emission, whereas what you looking for is results of spontaneous transitions. That means that number of photons per second you can expect from latter ...


1

Endless Form Most Beautiful: The New Science of Evo Devo introduces the reader to several classic embryology experiments and some key principles too. I'll edit this answer when I find more books or reading material of this nature.


1

Creatine itself is never converted into ATP. Creatine-phosphate on the other hand can donate its phosphate group to ADP, phosphorylating to form ATP and creatine. This is a buffer system for high-energy phosphates, and is very important in organs with rapid ATP turnover, notably muscle. The mechanism of the findings described in the papers is not fully ...


1

ATP prepares myosin for binding with actin by moving it to a higher-energy state and a "cocked" position. Once the myosin forms a cross-bridge with actin, the Pi disassociates and the myosin undergoes the power stroke, reaching a lower energy state when the sarcomere shortens. ATP must bind to myosin to break the cross-bridge and enable ...


1

If you have access to a laboratory (or at the very least a centrifuge and pipettes) and some laboratory experience you can extract the DNA from the cells which would be much easier to store. There are a number of commercial DNA extraction kits available that are easy to find on google and order online. I don't want to promote any particular brand but I've ...



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