Questions tagged [organic-chemistry]

Chemistry relating to carbon-containing compounds. Should relate to biology as opposed to being purely about chemistry.

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Why can $\alpha$- and $\beta$-glucose molecules not link together?

My textbook states that for two glucose molecues to link together, they must be of the same form, i.e. they must both be either $\alpha$-glucose or $\beta$-glucose molecules. Why is that the case?
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Does baking soda interfere with digestion when cooked into food?

Baking soda is useful for tenderizing meats and leavening baked goods. In the case of meats, it allegedly breaks down proteins/amino acids. However, does this usage pose a risk to digestion? Could the ...
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Why is there no wavelength change in the hyperchromic shift in DNA?

From Wikipedia article on hyperchromicity (emphasis my own): "When the bases become unstacked, the wavelength of maximum absorbance does not change, but the amount absorbed increases by 37%.&...
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Why is ammonia converted to urea rather than secreted in the urine?

Since ammonia is highly soluble in water, my senses keep telling me something like, "Just a little bit of water is enough to flush it, given that a lot of it would dissolve per liter of solvent&...
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What is the minimum number of chemical elements required for life on earth? Does it vary between kingdoms?

As a non-biologist, I assume that there are certain elements that occur in all life forms as we know them. Examples might be carbon, hydrogen, oxygen and so forth. There are also elements that are ...
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Biochemistry - Plastic eating microbes at home [closed]

Is it possible for me to locate, without too much difficulty, and culture, at home, a bacteria (like yeast) on plastic? I tried a similar process with yeast and I was able to culture it on extremely ...
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Why are disaccharides less reducing than monosaccharides?

My teacher told me the statement, but if both monosaccharide and disaccharides have a single free active group, how is this possible?
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What is the representation for Sulfur in organic matter?

We often represent organic matter with the following equation: $$ (CH_2O)_x(NH_3)_y(H_3PO_4)_z \tag{0} $$ For example, the organic matter with the Redfield ratio has the form of $(CH_2O)_{106}(NH_3)_{...
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Measuring the protein content using UV Vis

The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ...
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Can I use dATP instead of ATP (vice versa) for in vitro assay? [closed]

For example, polynucleotide synthesis reaction requires dATP which gives H on 3'end and synthesizes polynucleotide. For this reaction can I use ATP because I knew that ddNTPs are used so that ATP ...
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1% water solution of deoxycholic acid. How is it prepared? [closed]

According to Sigma, the solubility of deoxycholic acid is: 0.24 g/L in water at 15C According to the FDA, Kybella (trademark) is a 1% water solution of deoxycholic acid. How did they do this?
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Is there a chemical reaction that blocks two cysteines by reacting with a third molecule?

The idea is to block the two cysteines so they can't react in the future. We need the reaction to remove the -SH groups of the two cysteines, or modify them. Also important, the reaction should not ...
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Quantification of various amino acids from bacteria?

I would like to characterise how much of various (uncommon) cytosolic amino acids are produced in bacteria, and was wondering if there are good suggestions of how to go about doing this. I know that ...
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Is there anyway from which we can measure the viscosity of honey using a refractometer?

Is it possible to use a refractometer to measure the viscosity of honey because as we know, a refractometer is used to measure moisture and therefore water influences the viscosity of honey so is ...
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Tryptophan side-chain structure, how should it be orientated?

I would like some clarification on whether it matters where the NH and double bond are placed in these two structures of tryptophan (W) that I drew. I marked the right side as correct and the left ...
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Why do we need to amplify DNA sequences?

I am learning about biotechnology. I have no education in biology or chemistry and am simply interested in the subject of biotechnology. I am wondering why we need to have multiple copies of a piece ...
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Living potato clock? [duplicate]

Could a potato stay alive and power a clock while growing in the ground? I know how a potato clock works as a electrochemical cell and involves chemistry, but I am only interested in a growing ...
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Is studying chemical and physical properties of chemical substances that make up organisms really a task of molecular biology?

I have read in a high school textbook that (translated into English by myself): "Branch of science that concerns itself with studying chemical and physical properties of substances that make up ...
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Why does decomposing matter emit a bad smell?

Often, when matter decomposes (such as a rotting carcass), a nasty smell is emitted. After speaking to my teacher, it was likely due to the nitrogen compounds that leads to the bad smell. Is this so?...
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Is there a organ or type of cell that makes Nagalase?

Schindler disease / Kanzaki disease is being described as alpha-N-acetylgalactosaminidase deficiency. So then, which organ or cell(s) produce this alpha-N-acetylgalactosaminidase (Nagalase) ?
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Glycosidic bonds

For the glycosidic bond in maltose, why is the glycosidic bond formed between hydroxyl group on C1 in 1 glucose molecule and hydroxyl group on C4 of the other glucose molecule? Why not between, say, ...
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How do alcohols and aldehydes destroy the plasma membranes of bacteria?

I am interested in knowing why a 60-80% solution of alcohol (usually ethanol or 2-propanol) can effectively kill vegetative bacteria and fungi. I know that it can coagulate essential proteins like ...
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Amino acid structural charges [closed]

Hello, I was wondering if i could get an explanation as to why the charge of this peptide is +2 and -2. How do you figure this out? What is it based on exactly? Thank you
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Preparation of dihydroxyacetone phosphate from glycerine by fermentation

I read on Wikipedia that dihydroxyacetone (DHA) can be obtained from fermentation of glycerin. I would like to obtain dihydydroxyacetone phosphate (DHAP) for a science experiment but, since I'm 15, I ...
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What chemicals will kill P1 Phage but not E. coli?

I'm working with E. coli and P1 Phage. I'm wondering if there is some chemical agent that will kill or disable P1 but leave E. coli untouched? It is not enough to just prevent infection. It must ...
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Is DEET (as in the mosquito repellent), a substituted phenethylamine? [closed]

Am I correct to say that N,N-diethyl-meta-toluamide (DEET) is a part of the phenethylamine class? It's structure meets the requirements to be a phenythylamine, however, I was not able to find anywhere ...
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Why does the brain produce cannabinoids?

I've been reading lately about the brain producing cannabinoids. I was introduced to this idea by the Wim Hof Method which has been shown to increase the amount of cannabinoids (that is, compounds ...
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Can emulsion test be used to detect phospholipids?

The emulsion test- causes a white cloudy colour when lipid is dissolved in ethanol and then water added. Can this be used for phospholipids? I am aware that they are polar so may arrange in a ...
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4 votes
2 answers
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Text Book Recommendation: Cell & Molecular Biology + Organic Chemistry

I am studying undergraduate biology course and I have cell biology and molecular biology in my next semester. Our college recommends three books : Cooper, Lodish & Bruce Alberts. It would be ...
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Why did plants evolve to use opioids? [closed]

I'm reading about medicine and specifically opioids. There seems to be a wide variety of forms of these chemicals, I'm curious as to what purpose these serve in these respective plants, and why they ...
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What will CD spectroscopy show when L- and D- forms of proteins are mixed?

What will happen if equimolar concentration of L- and D- forms of proteins are mixed and we take the circular dichroism reading? Will the positive and negative ellipticity cancel each other out or ...
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What are some uses of oxidative/reductive power inside cells? [closed]

I know respiration and photosynthesis are based on oxidation and reduction, and the formation of NADH and NADPH in them is very important for many cell processes. I know that NADPH, for example, is ...
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Glycogen vs cellulose-curvature of glycogen molecule?

I was wondering if anyone knows what the degree of curvature is or bond angle between the $\alpha$ glucose molecules in glycogen is. I know that glycogen/amylose/amylopectin have a general curved ...
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Can the dietary fibres as chemical compounds be regarded as polymers? [closed]

At the level of molecular structure, can the dietary fibres be regarded as polymers?
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Does mechanotransduction of cells play a role in the biocompatibility of titanium?

What exactly is mechanotransduction as the information varies between sources. Some sources indicate that mechanotransduction is the underlying principle where cells pull on the surface they grow on ...
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What is a lethal dose of THC?

With the oil form of THC being stronger then ever. What would happen if one was to take a stomach full of THC oil?
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Wax layer destruction from seed coats

I'm working with some orchid species, and i encounter a specific issue. Some of those species deposits upon their seed coat a wax layer. This layer makes seeds behave in a very hydrophobic way. You ...
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How can I estimate the CO₂ uptake of a plant?

I would like to make an estimation of the CO2 uptake of plants I cultivate, including, lettuce and aromatic herbs, such as thyme, basil, rosemary. What I want is to end up with a rough indicator for ...
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3 votes
2 answers
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Why are human titin and mice titin considered the same protein?

I have a book that says: In humans titin is a chain of 34,350 amino acids, but in mice it is even longer with 35,213 amino acids. If two polypeptides had different amino acid sequence lengths, how ...
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Blebbistatin effect on vesicles

Blebbistatin is a drug that specifically inhibits the assembly of myosin in the cytoskeleton. What effect would you expect blebbistatin to have on intracellular vesicles? ...
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1 answer
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Anomalous base pairing of nucleotide tautomers

What tautomers base pair with what bases? I know that adenine pairs with thymine and guanine pairs with cytosine normally. My question is what does the imino form of adenine base pair with? Regular ...
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Is household ammonia okay for plants?

My father-in-law claims that since plants need nitrogen to produce proteins, and since ammonia is NH3, that Ammonia should be fine for the plants, since it's just nitrogen and water and hydrogen, ...
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How to calculate the Jaccard index [closed]

I want to calculate the Jaccard index between two compounds. What is the algorithm? I have searched for it, it just gives the formula but how to apply it on compounds is not known to me. Can you help?
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What are these pathways called in Biology?

Considering the pentose phosphate pathway and the sulfate reduction pathway in bacteria; What are these types of reactions called in biology? Bio degradation reactions or bio transformation reactions ...
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Factors on which one compound transforming to another compound depend [closed]

Considering the Metabolic Pathway: http://www.genome.jp/kegg-bin/show_module?M00166 Consider the reaction R01523(the very first reaction). How is it possible to know that the compound C00199(D-...
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Question related to L-arginine biosynthesis

With respect to the L-arginine Biosynthesis pathway, the very first reaction converts L-glutamate to N-acetyl L-glutamate. In the linked reaction scheme, why are only L-glutamate and N-acetyl ...
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Question regarding an Escherichia coli reaction

With respect to this link http://www.biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN-14479 Here the enzyme is mentioned and the two reacting compounds. Now , my question is 1. When these ...
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Do acetyl-CoA, acetyl-CoA carboxylase and acetyl-glutamate carry any charge?

Do the following compounds have any charge? If not, then why? If yes, is there any database that would give me this information if the compound is negatively or positively charged? The compounds are ...
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Water soluble molecules

I believe I may have misunderstood water solubility this entire time. I assumed that water soluble meant that it would literally dissolve in water. It would break down into atoms. A sugar molecule ...
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What is the chemical makeup of mealworm frass?

We have been raising mealworms for some time and while mealworm frass has proven very useful as a plant fertilizer, I started wondering about other potential uses of this leftover waste. Can someone ...
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