44

One of the main reasons that modern(!) biology uses oxygen as an electron acceptor is availability. Around 2.45 billion years ago, oxygen (O$_2$) started being built up in the atmosphere (which actually killed off a lot of the lifeforms/bacteria at that point). Since then, oxygen consuming lifeforms were able to establish themselves. Before that, most ...


31

Availability and applicability. Availability. In the beginning, there was CO2. It was abundant in the atmosphere, and later, the oceans. Fluorine and neon weren't, and so respiration evolved around what was (and is) available. Ref.: Paeloclimatology / History of the Atmosphere. Applicability. The other point about oxygen is that it works rather ...


19

(my comment reiterating the answer seemed useful, so I've reproduced it here) There are "NMDA receptors" in our body. There is not NMDA naturally in our body*. "NMDA receptor" is just a name people gave to one of the receptors that normally binds glutamate. They could have called it something else, like the "slow glu receptor", or "Glutamate Receptor A", ...


15

I volunteered for 3 years at a large mammal laboratory where we diligently tracked the weight and caloric intake of each of our animals. Diets were weighed out each morning and total calories could be calculated based on the known caloric value of the particular food item. We fed our animals during training sessions and would adjust the individual's food ...


14

The atomic radius of fluorine is just slightly larger than that of carbon. When a fluorine atom bonds to a carbon atom that is part of a carbon backbone, the fluorine atom covers up not only the C-F bond but also the adjoining C-C bonds. This makes it impossible for biological enzymes to access these bonds to break them, and is why fluorinated compounds ...


10

Fatty acids are usually not considered polymers. From a biological viewpoint this is simply because there is only a very limited set of chain lengths that exists in nature (~2-20 or so) and also even numbered chains are much more common than uneven numbered ones. In contrast to this 'true' polymers can have an arbitrary length of chain length (of course ...


10

In the IUPAC Gold Book, IUPAC defines a polymer as follows: A molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass Fatty acids are relatively high in molecular mass compared to the monomer (which is ...


9

Neon just does not work as an electron acceptor. It is that inert that there are currently no known Neon compounds at all. Fluorine would work in principle, but it is rare compared to oxygen and its strong reactivity makes it a very dangerous substance in elementary form. So it seems very natural that life chooses Oxygen and not Fluorine.


9

In a very simple way the equation describes the reaction. NAD is reduced using 2 hydrogen atoms. The two hydrogen atoms can come from one reactant (lactic acid fermentation) or from two (in a reaction of glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate; as shown in the figure below). First of all, I will pick a particular example from glycolysis, ...


8

Hydrogen in breath arises from normal intestinal bacteria, mainly in the colon, which break down (ferment) the undigested nutrients that have passed through the small intestine. Hydrogen is absorbed from the intestine into the blood and exhaled via the lungs. Conditions in which intestinal bacteria produce hydrogen: Normal digestion in which soluble ...


8

Chaperone proteins are still proteins and they can certainly misfold just like any other. If that happens, it will either be assisted by another chaperone and given time to fold successfully or it will be destroyed. If this is happening too often and the amount of chaperones drops too low or the number of unfolded or incorrectly folded proteins becomes ...


7

Your question is rooted in a misundertsanding of the hydrophobic effect. Hydrophillic and hydrophobic molecules do not repel but, rather, attract one another through van der Waals interactions. The tendency of hydrophobic molecules to aggregate in aqueous solution (ie the hydrophobic effect) is, instead of some repulsive force, actually driven entropically. ...


7

Short Answer: As the comments mention, this is a hot topic for pseudoscientists to use as a selling point for their supplements. There is limited evidence that dietary acid intake significantly alters bone resorption, especially in the setting of normal renal function. This paper should answer all of your questions (emphasis mine): Frassetto, Banerjee, ...


6

"Half-life time" is a general term. This is a time after which the amount of substance X decreases by 50%. If you take a bulk of something (say, 100 protein molecules), if this protein has half-life time of 1 hr, then 1 hr later you'll have 50 molecules left. In cellular biology it usually means that 50% of protein got recycled/degraded in given half-life ...


6

Your description is more or less correct, but so are both images. The bottom images shows the predominant form the amino acid would take at neutral pH (or any pH between ~2 and ~9.5). This is because the caroboxylic acid (-COOH) and amino (-NH2) groups are a weak acid and base and can lose or gain a proton (hydrogen cation), respectively. pH below the pKa of ...


6

The situation you ask about was originally part of the 27 ribbon and 2.27 helix structures considered as possibilities by protein chemists (Linus Pauling?) in the 50s or 60s. The diagram below, showing the ribbon, is from the classic text (long out of print) The Structure and Action of Proteins by Dickerson and Geis. This turns out to be very rare in ...


5

I think the description of enzymatic reactions as 'reversible' is potentially a bit misleading. It might be better to think of enzymes as agnostic to reaction direction. The big missing piece is the difference in free energy of the reaction itself. Reactions that remove a phosphate group are energetically favorable in biological conditions. A phosphatase ...


5

I found this paper, which goes very deep into the molecular details of the individual steps of this reaction and also discusses how this is coupled to nucleotide selectivity. The 'basic' details about the reaction (quoted from this section, which also has a nice figure): The polymerization reaction proceeds by a simple nucleophilic attack of the 3'OH ...


5

You can find a great and recent review on this topic, which is thankfully also free to access, here: https://www.sciencedirect.com/science/article/pii/S2319417016000159 Arsenic resistance is ubiquitous among bacteria, they virtually all maintain the ars operon. Among Arsenic-resistant bacteria, this is not an advantage, but Arsenic was and remains a ...


5

It sounds a bit like chem exam question to be honest... Or at least the answer does... namely that O2 being paramagnetic creates a "spin barrier" that prevents most organic compounds from reacting fast with atmospheric oxygen: The magnetic properties of O2 are not just a laboratory curiosity; they are absolutely crucial to the existence of life. Because ...


5

A quick search on Wikipedia showed the same reaction you book is presenting. In metabolism, the compound accepts or donates electrons in redox reactions.[2] Such reactions (summarized in the formula below) involve the removal of two hydrogen atoms from the reactant (R), in the form of a hydride ion (H−), and a proton (H+). The proton is released ...


5

Specific parts — moieties — of an agonist molecule bind to the receptor protein, causing the receptor to change shape, which in turn initiates a signaling pathway inside the cell. Some agonists are better at causing the receptor to change to its "optimal shape" for relaying signal. These are called "full agonists". Other agonists cause a partial change in ...


5

Assuming that your protein can handle being in the new buffer, you have multiple options. Dialysis will work although you might want to consider using a centrifuge spin filter with a suitable MW cutoff to gradually switch buffer and concentrate the sample. Be aware that some of your protein will stick to the filter, giving a loss of sample. Alternatively ...


5

There are a number of ways to address this, and the other answers are certainly correct. Another strategy, especially if you already have the sample in PBS, is just to dilute it in the low salt ion exchange buffer. This works because you don’t need to completely remove the phosphate or salt, just get it low enough so that it doesn’t interfere with binding to ...


4

Glass can be functionalized by organosilanization so that biomolecules can be covalently attached via some cross-linker. As an example, one might aminosilanize the glass and then cross-link their enzyme of interest with glutaraldehyde. For what it’s worth, urease activity can be measured in solution.


4

Short Answer The palindromic symmetry of the restriction site allows a dimeric enzyme to bind the DNA in a manner that bends the double helix in a way that facilitates the endonuclease reaction. More Detailed Answer The ‘palindromic’ nature of the recognition/cleavage site of restriction endonucleases, such as EcoRV (illustrated here) results in a ...


4

There Are Two Similar but Distinct Types of Noncompetitive Binding. Starting from a pharmacological perspective, there are 2 definitions of "noncompetitive" binding that have similar macroscopic effects but differ slightly in their molecular mechanisms. Depending on which definition you use, noncompetitive ligands can bind either orthosterically or ...


4

Thiol-Based Reducing Agents The instability of thiol-based reducing agents in solution is due to their propensity to form disulfide bonds by the following half reaction: $$\ce{2RSH -> RSSR + 2H+ + 2e-}$$ It is clear that disulfide formation requires: Deprotonation of the thiols to form thiolates (RS-). An electron acceptor. Therefore, solutions of ...


4

I am not a plant biochemist but would make a couple of points that may or may not be relevant or helpful. The living organisms that preceded plants had evolved a wide repertoire of systems for transporting ions across membranes, involving variations on a few general designs. Given the importance of inorganic phosphate in living organisms, phosphate ...


4

If you look at the Google ngram for the term ‘Molecular Biology’ you will see that it first appears just before 1960, and it is relevant that the Journal of Molecular Biology was founded in 1959. It is not biochemistry — indeed the name was meant to indicate its difference from biochemistry, and I heard second-hand (so I cannot vouch for its truth) that Hans ...


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