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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, ...


1

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 ...


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 ...


0

This is a hard question to answer. Electrons and energy are different concepts. My overly succinct answer is that the movement of electrons results in free energy changes.


10

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 ...


0

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 ...


2

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 ...


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 ...


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 ...


2

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.


0

IMO, this is by far the best introduction to enzyme mechanisms and protein folding, by a leading researcher in the field. Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding by Alan Fersht


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 ...


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

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 ...


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 ...


0

The problem is the glucosepane bond is very strong, hence the molecules which would break this bond need be necessarily toxic and damaging to other molecules in the body. Glucosepane breakers already exist, but they are too toxic, and perhaps all will necessarily be that way. All hope is not lost however. Other very effective medical drugs (like clot ...


0

@MadScientist: Certain functions require every single one of these 20 amino acids. However, in isolated cases a selected subset of amino acids might very well lead to an active protein.


0

To answer your question: No, there are no restrictions to what amino acid is next ("a nearest neighbor") to its N-terminal or C-terminal neighbor.


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.


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 ...


0

You could store DNA diluted in water at -20C for a very long time. The only problem with at home storage would be the type of freezer most households have. These come standard with defrosting feature, which thaws up the freezer to remove the ice accumulation... This would affect the stability of the DNA at long term scale. Having a styrofoam box to protect ...


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 ...


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

I am not so familiar with enzymatic kits for quantifying glutamine, but most enzyme-based analysis kits come with a number of fairly strong assumptions on the enzymology involved, and in my experience they are difficult to use reliably. Commercial kits are hopeless to troubleshoot since their components are not disclosed --- you don't know what you're ...


1

You are correct that cats consume a lot of protein, and it's safe to assume a large share of this is broken down to amino acids, which are then oxidized to produce energy. But amino acids in general are not catabolized via glucose; instead, they are converted into compounds that feed into the TCA cycle via other biochemical routes. Almost every of the 20 ...


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 ...


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 ...


0

Would you consider the New York Times a suitable level of detail (while admittedly not a book)? If so then you may want to peruse this collection: http://topics.nytimes.com/top/news/science/topics/biology_and_biochemistry/index.html You will have to be selective. This was my first hit in Google searching for 'lay articles on biochemistry.' I would ...


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 ...


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 ...


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 ...


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 ...


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 ...


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 ...


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 ...


0

The splitting of water in chloroplasts is catalysed by the Oxygen Evolving Complex. It's all about redox reactions but in general hydrogen is the less electronegative of biological elements so it is easily ionised in many life reactions.


1

As far as I can tell, enterochelin esterase (Fes) utilizes an Alpha/Beta hydrolase fold to catalyze it's reactions, which means there's a triad of catalytic amino acid side chains. Where Fes differs from other proteins in the pathway is an amino terminal lid domain which confers specificity to the substrates of Fes ((1) dictates this forms a deep pocket in ...


3

The NIH RDA for vitamin B12 is 2-3µg/day. Cyanocobalamin has an $M_r$ of 1355, of which 26, or less than 2% ($CN^-$) is cyanide. Since the Minimal Risk Level for cyanide is 50µg/kg/day, your studies are correct in that 1000x the RDA of vitamin B12 in the form of cyanocobalamin is not lethal, and furthermore is expected to not cause any negative effects ...


5

Potassium cyanide is added to the cobalamins produced by bacteria to give rise to cyanocobalamin. CN is strongly bonded to Co and will not easily dissociate, thereby making this form of B12 inactive. Therefore, it has been argued that cyanocobalamin is not a good vitamin supplement and other variants such as hydroxycobalamin or methylcobalamin should be ...


4

Biotechnology is a gigantic field. You should have a look at the wikipedia entry for biotechnology. Because of the size of the field "biotechnology", because the word biotechnology accept different definitions and because the word interesting is extremely arbitrary it is pretty much impossible to give a good answer to this question. I am using below ...


1

Not 6, but 9 molecules of Pi are formed in the Calvin cycle, from the conversion of 9 ATP to 9 ADP: Source: Columbia University



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