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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Carbon dioxide concentration in alkaline media
I am running a batch experiment using penicillin bottles where I have bacteria growing for 21 days in a highly alkaline media (pH 10). I am measuring the CO2 and O2 content in the headspace over time, ...
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Question on protonation/deprotonation of amino acid side chains
I understand that actual pKa of amino acid side chains is greatly influenced by the surrounding environment. I am trying to deeply understand the equilibrium between protonated and deprotonated form ...
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What are major obstacles that OOL research still has to overcome in order to come to a full understanding of how life could have arisen from non-life? [closed]
Dr. James Tour recently uploaded a video titled Dr. James Tour vs Dave Farina | Are we clueless about the origin of life? #abiogenesis.
The description in the video says:
Join us for an exciting ...
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Would fewer cows mean less methane emission?
Rotting grass produces the same amount of methane as cows that digest grass (see this source). So if cows did not eat the grass, it would still emit methane. Therefore, if there were fewer cows, would ...
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Xenobiotic metabolism: phase 1 reduction enzyme
Phase biotransformation reactions can be oxidations, reductions or hydrolysis of the xenobiota molecule.
Phase 1 oxidations are catalyzed by the cytocrome P450 enzyme, abbreviated with the CYP acronym:...
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Are DNA molecules negatively charged at low pH values?
We know, that for each monomer of DNA, phosphate groups are having -1 charge because one of the oxygen is negatively charged (2nd oxygen participates in the phosphodiester covalent bond), but isn't it ...
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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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Does ellagic acid dissolved in DMSO react with Brain Heart Infusion media?
I dissolved 2mg of Ellagic acid in 500 microliter of DMSO. I used 100 microliters of this solution to test for antimicrobial susceptibility against E.faecalis by adding it to 100 microliters of BHI ...
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What is mechanism of action of ellagic acid as an antimicrobial compound?
Ellagic acid (a polyphenol) works as an antimicrobial compound. But what is its mechanism of action?
I found these 2 research papers related to this, however the mechanism of action is not clearly ...
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Why does the luminal test need hydrogen peroxide?
In the chemiluminescent reaction of Luminol in an aqueous solution, the luminol needs to react with molecular oxygen to produce a photon of blue light. In the technique, the hemoglobin of blood ...
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Is the formula of cyclic adenosine monophosphate (cAMP) $\ce{C_{10}H_{11}N_{5}O_{6}P}$ or $\ce{C_{10}H_{12}N_{5}O_{6}P}$? Does it matter?
For some reason, half the sites on the internet say that there are 12 hydrogen atoms in one molecule of cAMP, and the other half claim 11.
Who is correct? Does a single, free, unbounded and ...
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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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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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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 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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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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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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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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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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What does the (-) in the molecule name mean?
I'm reading some text (purchase request) that has the following line in it.
(-)-Norepinephrine
What does the minus sign mean in front that is in parenthesis? Is this some kind of standard way of ...
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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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Glutamine analysis
I use to run a method to analyse all the amino-acids in a food sample. For that I have to hydrololyse the sample and in the last stage of the method I read the amino acids with a ion exchange ...
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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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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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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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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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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 ...
CommunityBot
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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 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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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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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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