Questions tagged [chemical-biology]
Questions about the application of chemistry to interrogate and modify biological systems and processes.
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Can pyruvate get reduced after glycolysis?
During cellular respiration, the first step is glycolysis where the glucose is split into 2 pyruvates, 2 NADH, and 2 ATP. The pyruvate either goes through the citric acid cycle or goes through lactic ...
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When we take baths, how does the water in the bathtub absorb only the dirtiness on our skin?
I'm 16. I study chemistry in college along with biology, physics, and maths, and I have a general interest in all of them.
I always found this interesting: sometimes when I left the bathtub, even when ...
user129756
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Why don't serine and threonine have a 3rd pKa
Serine and threonine both have an extra OH functional group and hence they should be able to dissociate when the pH gets high enough. However multiple amino acid pH charts do not show the 3rd pKa of ...
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Is it possible to have an anhydrous solvent for virology, specifically in vitro phage assembly?
Typical protocols for lambda phage in vitro assembly call for you to dump all your viral components and buffer solutions into water. Water is a great solvent, drives extraction of energy from atp, and ...
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NAD+ and NADH /H+
The $\ce{NAD^+}$ molecule has an electron-poor carbon susceptible to a nucleophilic attack by a hydride ion: It's the C4 of the pyridine ring, who loses its aromaticity in this way.
Usually, it is ...
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Histidine-Boc deprotectection
A question on Fmoc-solid phase peptide synthesis (SPPS). Is Boc-protected Histidine too labile? Merck's website shows Boc is labile to treatment with Piperidine. Anyone with such experience?
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Biochemically speaking, why aren't the cell membranes of eukaryotic, multicellular organisms made of more heat-resistant stuff?
TL;DR: there are lipids out there that are more heat-resistant than those in current cell membranes, yet current cell membranes don't have them. Why?
I've cobbled together various miscellaneous ...
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Difference between Protoporphyrin and Porphyrin? [closed]
I understand that Porphyrin is defined as 4 pyrole rings linked by methenyl bridges. When this porphyrin ring is associated with a Ferrous ion (Fe 2+) we get the Heme molecule. However my book ...
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Will iron(III) sodium EDTA release its nitrogen into a water medium and become bioavailable to aquatic plants?
I am wanting to create an N-free Hoagland's solution and have discovered a recipe that includes sodium ferric ethylenediaminetetraacetate salt $(\ce{C10H12FeN2NaO8}).$ Will the nitrogen in EDTA ...
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How odorless is "odorless"?
Wikipedia has entries for many odorless gasses such as Ar, CO, etc. How rigorous is odor testing? Is it possible someone with a better sense of smell could smell Ar, CO, etc?
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Phosphate transfer in hexokinase
In glycolysis, hexokinase transfers a phosphate group from ATP to glucose. This is an example of the coupling of an exergonic reaction with an endergonic reaction, such that the endergonic reaction is ...
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Do solids in a solution also apply partial pressure? If yes, can this be used as an intuitive explanation for osmosis?
I know that in a mixture of different gases, we can assign every type of gas molecules a partial pressure so that the total pressure is the sum of all partial pressures. This can be extended to gas ...
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What antimicrobial can be readily synthesized in a school laboratory for a project on antimicrobial resistance? [closed]
I am currently a student studying at a high school hoping to do a project on antimicrobial compound synthesis to use in investigating antimicrobial resistance in E. coli strains. I am hoping to ...
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General cleaning solution for clinical chemistry applications
I want to reuse some plastic and glass items that I am using to do colorimetric concentration analysis of serum and urine. There are some enzymatic assays, mineral assays and so on. I have been trying ...
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What is the maximum length of peptide which considered to be hard for synthesis by the current technology?
I am a molecular biologist and work with recombinant proteins. I am wondering what the cut point, in terms of length, is at which I should produce the peptide using heterologous expression rather than ...
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Classification model from biological assays with different compounds
If I want to use an undersampling approach to construct the machine learning model (classification model predicting whether the target compounds are active or inactive, using chemical fingerprint as ...
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Why does CO2 have a greater affinity for hemoglobin than oxygen?
I know about CO but I am wondering if CO2 has similar mechanism? do you guys have any scientific reference
These species help form interactions between amino-acid residues at the interfaces of the ...
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g-tensor and hyperfine tensor for nitroxide spin label with 15N
Does anyone know where I can find numerical data for the $g$ tensor and hyperfine tensor for a nitroxide spin label where the nitrogen-14 atom has been replaced by a nitrogen-15 atom?
I'm really ...
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Textbook on Food Additives? [closed]
My Question. Is there a comprehensive textbook on (synthetic) food additives?
Many textbooks on nutrition omits any discussion of food additives, so I was hoping there is a book devoted to the subject....
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SARS-CoV - relative size of the spike protein
I am taking an online course in image analysis and have been asked to use the attached image to determine the size of the SARS-S protein of the SARS-CoV relative to the total of its proteins. However, ...
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Are there scales that record weight continuously?
I would like to monitor the weight of something continuously (e.g. once a minute) and access the data easily via a phone app. Is there something like that?
There are numerous options for similar ...
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Is Fluorine more toxic than Chlorine?
Fluorine is more reactive than Chlorine. But does it mean that Fluorine can cause more damage to living tissues? If so, why wasn't Fluorine used in WW1 instead of Chlorine?
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Biological activity of the isotopes of the same element
I have a question regarding biological activity of different isotopes of the same elements, notably $\ce{^206Pb}$ and $\ce{^208Pb}$. Lead is known to be toxic, such that it can replace calcium from ...
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Effects of dispersed nitrous oxide on the body
I'm not sure if this question would be more appropriate in Biology SE, but I wanted to know if the euphoric effects of $\ce{N2O}$ are limited to when it is concentrated in the gaseous phase, or ...
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How does Combinatorial Chemistry differ from Rational Drug Design?
I stumbled on Vertex Pharmaceuticals - Wikipedia.
It was one of the first biotech firms to use an explicit strategy of rational drug design rather than combinatorial chemistry.
Then I looked up ...
user7952
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Do side chain carboxylic acids need to be protected in peptide synthesis?
Consider the synthesis of the dipeptide Glu–Ala (image). The amino acid Glu (glutamic acid) has two carboxyl groups, where one of them should reacts with the amine group from the other amino acid. ...
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Sensitivity vs. Limit of Detection of rapid antigen tests
I'm comparing a bunch of SARS-CoV2 rapid antigen tests:
Columns 4 and 6 list the values for sensitivity and limit of detection (LOD). How come that a test with a several times lower limit of ...
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How to model CRISPR/Cas9 binding and cleavage using a generalized Kittel's zipper model?
I am thinking about how to model the binding of a CRISPR/Cas9+guide-RNA complex to a double-stranded DNA that cause its cleavage.
This post describes four steps at which a CRISPR/Cas9 system binds and ...
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What is the composition, function, and classification of “6-Thio-2-Deoxyguanosine” and “13-mer thio-phosphoramidate”? How do I learn more about them?
I am assigned the task of explaining a biomedical research paper, it is about telomere and telomerase , and it talks a lot about the molecule Thio-2-Deoxyguanosine , 13-mer thio-phosphoramidate and &...
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Is the ratio between base pairs by chargaff accurate? [closed]
I am reading Lehninger's biochemistry textbook. It mentions that DNA may rarely contain uracil. Then it mentions that Chargaff found that the ratio of adenosine bases to thymine bases in DNA is 1.
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What could these letters "S" in red circles mean in a biochemical diagram?
What could be the meaning of the red circles with letters S in them in the diagram below? I searched in the text but could not find.
From "Role of TREK-1 in Health and Disease, Focus on the ...
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Does migraine medicine Topiramate work by supplanting Pyridoxal phosphate in enzymes?
I have seen it said that the precise mechanism of action of migraine medicine Topiramate is not known. But I certainly see a resemblance between that molecule and PLP (Pyridoxal phosphate, the ...
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How does pH affect the spontaneity of biochemical processes? [closed]
A decrease in $\mathrm{pH}$ increases the hydrogen ion concentration, thereby decreasing $Q,$ and decreasing Gibbs free energy as mathematically expressed:
$$\mathrm dG =\mathrm dG^\circ + RT\ln Q$$
...
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How many alternative chemical ways to transport oxygen in living creatures are known?
Mammals and many other groups of animals usually transport oxygen using haemoglobin and other complex proteins, the core of which is based on an iron coordinated to a porphyrin. There are plenty of ...
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A question about ligand binding
I have done part a and part b but I keep getting a negative concentration for part c.
For part a I got $\pu{2 \mu M}$
For part b I got $\pu{5.051 \mu M}$
For part c, I get $2=3.2 + \text{[bound ...
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Fermentation of glucose
I have trouble understanding as to what the last part of the increase in liquid level means. I believe this is the foam formed after the fermentation? I am calculating for the pressure but I have ...
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3' terminal phosphate (p at the end of RNA sequence)
I am reading the paper:
Petersheim, M. and Turner, D.H. (1983) Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ...
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Does cellulase catalyze the hydrolysis (or break down) of soluble starch?
I’m attempting to perform an Iodometric redox titration to evaluate the vitamin c concentration in a particular solution. These solution have dissolved within them up to 2% cellulase enzyme.
In an ...
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Does mixing two different foaming soap make it ineffective?
To save soap during this pandemic, I mixed foaming soap of two different brands and then the solution became cloudy (both originally transparent) . It seems foaming okay. But does this make the soap ...
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Questions Regarding Osmosis
From Costanzo's Physiology:
Osmosis of water is not diffusion of water: Osmosis occurs because of a pressure difference, whereas diffusion occurs because of a concentration (or activity) difference ...
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How is equilibrium achieved in osmosis?
According to BRS Physiology book:
excessive NaCl intake will lead to an increase in the osmolarity of the Extracellular Fluid (ECF) compartment, and thus will lead to water shift from the ...
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Turn Alpha Helix into Beta Pleat
Beta sheets have the peptide backbone parallel whilst the alpha helix has a curled backbone.
But the thing I can't get around my head is why would the same protein always fold into one of these shapes?...
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What exactly is peptone (tryptone?) and why does it not get precipitated?
According to Wikipedia Peptone (also called Tryptone) is a form of amino acid that has been treated by stomach acids. According to Google it also stays in solution when treated with acids or heat. Why ...
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Why is PLGA so expensive in comparison to PLA?
A Google search has lead me to believe that PLGA goes for anywhere between 8 USD and 100 USD per gram. Meanwhile, for PLA (3d printer grade), prices float around 50-100 USD per kilogram.
I understand ...
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What specific toxins are formed during deep frying? And how (chemically) do they attack the body cells? [closed]
From what I understand, deep frying causes the oxidation of lipids into advanced lipid oxidation products. When these are consumed and metabolized by the body, they release ROS or free radicals which ...
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How does sodium rosinate enhances lathering property? [closed]
Why don't we use sodium carbonate or sodium stearate? What does sodium rosinate contain that the other two don't?
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Prostaglandin Nomenclature
Prostaglandins are lipid substances derived from fatty acids, which act as powerful biochemical regulators.
In Wade's Organic Chemistry, they indicate that there are several families of ...
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carbon dioxide and its behaviour in acid base balance [closed]
In human body acid base balance, why and how does the dissolved carbon dioxide increases the hydrogen ion concentration with increasing in its partial pressure..? At the same time bicarbonate ion is ...
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Preferred IUPAC name of Protoporphyrin IX
I was looking up protoporphyrin IX and was surprised to find that no two websites gave the same IUPAC name for the compound. Here are some examples:
3,3'-(7,12-Diethenyl-3,8,13,17-...
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Net production of CO2 in plants
I am trying to understand in a qualitative way photosynthesis. I am not a chemist so please have some patience.
I read on the Wikipedia page for photosynthesis that the way plants use $\ce{CO2}$ is ...
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