Questions tagged [chemical-biology]

Questions about the application of chemistry to interrogate and modify biological systems and processes.

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16 views

What are the initial experiments to hypothesize or decide the method of protein degradation?

For a protein of interest, How to determine it’s degrading method— protease or proteasome? Is it possible through bioinformatics? What are the initial experiments to hypothesize or decide the method ...
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1answer
46 views

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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1answer
53 views

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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28 views

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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1answer
60 views

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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36 views

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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55 views

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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1answer
42 views

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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39 views

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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1answer
608 views

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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28 views

Electrolysis in Electrophoresis of proteins and DNA

Can electrolysis happen in an electrophoresis assay (such as SDS-PAGE)? To perform electrophoresis, the substances must be dissolved in an aquatic buffer with a previously determined ionic strength. ...
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48 views

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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4answers
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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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2answers
100 views

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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38 views

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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1answer
159 views

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 ...
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1answer
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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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1answer
50 views

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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144 views

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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22 views

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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1answer
44 views

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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1answer
506 views

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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1answer
53 views

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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1answer
156 views

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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1answer
65 views

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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48 views

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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2answers
178 views

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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26 views

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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2answers
896 views

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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3answers
246 views

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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1answer
123 views

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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1answer
73 views

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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1answer
243 views

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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1answer
308 views

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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37 views

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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1answer
143 views

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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1answer
294 views

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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1answer
35 views

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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1answer
40 views

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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3answers
649 views

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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1answer
60 views

Indirectly Measuring Diffusion of NO2 into Water

I am working on a data science project with the central hypothesis is that air-born pollutants can become water-born through diffusion. The example I am using as a proof of concept is $\ce{NO2}$. The ...
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1answer
21 views

Effect of pH on sulphur isotope variation on a landscape

I recently ran a forest regression model, this model showed me that increasing soil pH increases sulphur isotope variation across the landscape. I am not how this is possible and if it makes sense
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1answer
44 views

Is hydroxychloroquine an anti-psychotic drug? [closed]

Is hydroxychloroquine an anti-psychotic drug or psychotic drug?
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2answers
59 views

What is meant by position 5' or 3' [closed]

I'm a self-learner that likes to keep up with current research. However, I can't find what is meant by expressions such as 5' or 3' positions on chemical structures. But , in particular, what is meant ...
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1answer
56 views

Chemical Formation Of A Virus [closed]

Many articles and books classify virus as a non living thing which only replicate itself inside a living host, yet some describe virus as a living organism. Virus was first discovered on the year 1892 ...
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3answers
344 views

How can an Organic chemist know the chemical formula of a natural product she isolated from an organism? [closed]

As a non scientist I several times wondered how can an Organic chemist successfully isolate a single molecule which a natural product of an organism; Whether a plant-part/mushroom-part/algae-part or a ...
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Oxidative phosphorylation analogue

Does the salt bridge in galvanic cells resemble the ATP pump in the inner mitochondrial membrane? And if yes than did someone use this pH difference in harvesting this energy?
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2answers
249 views

Why is it important to remove the used up electrons in oxidative phosphorylation?

I get that oxygen is the terminal electron acceptor in oxidative phosphorylation. But why is it essential to accept these electrons and remove them as $\ce{H2O}?$ Oxygen is essential for cellular ...
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45 views

Is there a software that can predict the shape of a custom protein, given its amino acid sequence?

I know that the internet is full of enzyme and protein simulators which can show active site and 3D structure (like bioblender), but the problem with these programs is that they use predefined ...

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