Questions tagged [biochemistry]

The study of chemistry within the scope of biology: the compounds that occur and the reactions involving them in living organisms.

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Do lipids have a monomer or not?

My biology class and I have been on the topic of macromolecules for quite some time now. Chapter 2.3 of the Foundations to Biology Textbook says that lipids are not polymers, so they do not have ...
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What is the difference between physiology and physiological processes?

Now I do understand that physiology is the study of processes and mechanisms that make a living organism. And physiological process is understanding the ways the components in the organism work ...
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Why does high redox potential mean less oxygen?

I often see statements about adding reducing agents like cysteine to anaerobic medium to decrease the amount of the dissolved oxygen. However, I am not sure why. I am wondering if it is because under ...
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Do cancer cells use as much NADH as normal cells?

Recent literature shows that cancer cells have a different electron transport chain mechanism from normal cells and both of cancer cells and normal cells use NADH as electron donors. So, is there a ...
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Why aren't complex-stabilizing proteins like transcription factors considered catalysts/enzymes?

I'm not asking the question on a superficial level. Obviously, (most) transcription factors are not acting directly on a substrate to produce a chemical change. I pose the above question as more of a ...
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Topical anti-histamines [migrated]

In more than a dozen pharmacies that I have visited in Greece they don't sell any topical antihistamines In a private database (source given above) I found FDA has approved doxepin and diphenhydramine ...
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Does nature have a mechanism to turn charcoal back to usable carbon?

I have in past asked this about ash, but apart from ash most fires - whether natural or fires in stoves - leave a bunch of charcoal as well. When I was sifting old compost last year, I could identify ...
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Comparison of different glassy matrices for protein immobilization at room temperature

I am completely new to protein biology experiments. I care about experiments where proteins are immobilized near a surface with the help of a glassy matrix or similar materials. I am looking for a ...
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If guanosine transfer reaction in the RNA capping is reversible, should intermediate reactions be reversible as well?

Guanosine transfer is the second step of RNA capping. The enzyme (GTase) first displaces a pyrophosphate of a GTP molecule, forming an unstable covalent enzyme-GMP intermediate (E + Gppp ⇌ E-pG + PPi)....
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Why do low pHs increase zinc uptake by plants?

I am doing a study on zinc’s effect on seed germination and how different pHs enhance and weaken that effect. But it is an in vitro study, so I am worried that pHs affect zinc absorption just in soil (...
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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 specific molecules cause the difference in spectral sensitivity in the cones?

What causes the difference in their spectral sensitivity of the S, M and L cones. I'm guessing that the opsin or photopigments are different, but haven't been able figure out conclusively from my web ...
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PEGylation safety and hybridomas

PEGylation is the covalent attachment of PEG (PolyEthylene Glycol) to molecules (e.g. proteins). It states in wikipedia ("PEGylation"): The covalent attachment of PEG to a drug or ...
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A question about the effect of adrenaline on acetylcholine

I was taught that acetylcholine is the key neurotransmitter in the recruitment of skeletal muscle, and the depletion thereof was the cause for synaptic fatigue. But I was doing a literature search ...
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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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What is the conjugation capacity of the liver?

Our liver conjugates 250-300 mg bilirubin per day under normal circumstances but it is capable of conjugating much more. What is the upper end per day after which it won’t be able to conjugate leading ...
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1 answer
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How does one derive a KD from an equilibrium titration experiment?

If I have an antibody A and a target B, and experimentally titrate the antibody against a single concentration of B, and then measure the % of B that is bound after the solutions reach equilibrium, I ...
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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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Source for "The human body recycles its body weight of ATP each day"?

I have read in many biology textbooks and scientific journals that "you create your own bodyweight in ATP each day", but they are all just stated as facts. I have yet to see a study or ...
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Why does photosynthesis specifically produce glucose?

Why not a pentose? Or a tetrose? Or a deoxy sugar? Or just some other hexose, like fructose? Is there some chemical reason life should have settled on glucose as the standard photosynthetic output, or ...
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How does a turtle develop inside its egg?

This is related to Cause of premature death in turtle eggs, for those interested. I have noticed that Kinosternon spp. eggs have three layers: hard outer shell white opaque membrane (like the one you ...
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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 is protein turnover necessary or important for cells to function?

Cells constantly create new proteins in order to maintain their normal function, this is called protein turnover. Why is that? Do the old molecules wear out as time passes, so that they need a ...
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Why do bacteria denitrify?

Denitrification is the microbial respiration in anoxic condition. If the process is complete we have : $$2 \text{NO}_3^{-} + 10 \text{e}^{-} +12\text{H}^+ \rightarrow \text{N}_2 + 6 \text{H}_2\text{O}$...
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How to reduce PPi concentration in blood samples by PPase

I have some samples of whole blood that are a little bit expensive and I want to significantly reduce the concentration of PPi in the samples by causing a reaction. I don't have any experience in ...
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1 answer
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Are there irreversible metabolic reactions that can happen in opposite ways depending on the cellular conditions?

Irreversible reactions are thermodynamically irreversible, not microscopically irreversible. "Irreversible" here means the reaction happens "out-of-equilibrium". It is a ...
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Do photosynthesis and respiration violate the law of conservation of energy?

I don't know, if it's a physics question, biology or chemistry question but anyways here it is: I have been taught that to produce one molecule of glucose in photosynthesis, 18 ATP molecules are used ...
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Where does the silica found on grass and other plants come from?

Grass has tiny silica "teeth" on it called phytoliths: I have trouble understanding how can a plant possibly extract silica from soil and form anything out of it. Silicon oxide is used for ...
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Why isn't the Ramachandran plot symmetric?

Since only relative position of groups along a bond is considered while calculating torsional strain and considering "+" and "-" means clockwise and anti clock wise rotation, ...
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biofilm model scales

I have a question about the meaning of biofilm modelling scales: Are they microscopic, mesoscopic and macroscopic. Microscopic means individual bacteria macroscopic means large number of concentration ...
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Why do some people accumulate more diglycerides in their muscle cells?

The scientist Gerald Shulman has experimentally found that young lean adults in their early twenties that are children to people with type 2 diabetes often show muscle insulin resistance. He found ...
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What's the best way to purify my His tagged protein? Supernatant super viscous after first sonication?

I am trying to purify my his-tagged protein of interest, disulfide isomerase. It is about 40kDa and is cloned in pET28a vector, at XholI and NdelI, and expressed in BL21. I'm having issues with my ...
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What is the function of dihydrofolate reductase in humans?

According to StatPearls, synthetic folic acid — as an artificial dietary supplement — needs to be converted into the active form tetrahydrofolate (THF) by dihydrofolate reductase. In the cells, folic ...
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Is the pyruvate dehydrogenase reaction considered part of the Krebs Tricarboxylic Acid Cycle?

I’ve encountered questions where I’m asked to find out the CO2 released, the number of oxidative carboxylations etc. in the Krebs tricarboxylic acid cycle. I always include the pyruvate dehydrogenase ...
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Does alternative splicing contribute to the diversity of enzymes?

I understand the role of alternative splicing in generating protein diversity, but for enzymes specifically, is alternative splicing responsible for the diversity of it? My professor told me something ...
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Which animal has the smallest percentage of their body mass made up of water?

It's a "well known" and interesting "fact" that the human body is made up of "mostly water". With percentages from 65% to 90% often being repeated as if they were exact ...
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Anticoagulation of black beans extract

How many ml of lithium heparin do I need to use on 2 ml blood to prevent coagulation for over 15 minutes? I am comparing it to the 4 different dosages of black turtle bean extract that has polyphenols ...
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Adh2 promoter in saccharomyces cerevisiae

I'm looking at expressing a protein in saccharomyces cerevisiae using the Adh2 promoter. My understanding is that the gene will be repressed by the presence of glucose, but when glucose runs out it ...
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Which cancer cell lines do not increase glucose uptake in comparison with their wild type analogues?

I heard that some cell lines which already have a high glucose influx do not increase it upon altering to a cancer phenotype. However, I cannot find any supporting references.
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Mechanism of the calcium-activated protein, Aequorin

In Aequorin, coelenterazine acts as the luciferin, producing light in the presence of calcium and oxygen. It is unclear to me what part of the protein structure actually catalyses this reaction after ...
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Does a protein with a mutated binding site count as an isoform of the original protein?

im an intro level student so sorry if this doesn't make sense, but would a mutant protein whose primary binding remains functional, but whose inactivation site for a small effector molecule is mutated ...
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Why do eubacterial DNA Ligases use NAD whereas eukaryotic and archaeal DNA Ligases use ATP?

DNA ligases in eukaryotes are ATP-dependent (as is the enzyme from bacteriophage T4) but in Escherichia coli the DNA ligase is NAD+-dependent. I cannot understand the reason for this. An extensive ...
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Please explain to me the difference of molecular weight in g/mol versus dalton

From my studies i thought so far that: 1 NA * Da = 1 * NA mu = 1 g, However since 2019 SI says that one dalton is only approximately one gram per mol 1 NA Da ≈ 1 g/mol This makes sense if I consider ...
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Does ATP get broken down naturally? [duplicate]

According to my textbook, ATP is not a good energy store becasue of the instability of the bonds. Does this imply that ATP naturally breaks down due to the unstable phosphate bonds? Over a long time, ...
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How does Clostridium perfringens cause target hemolysis?

I am studying microbiology as a part of my course and I was studying Clostridium perfringens. While studying its hemolytic characteristics, I came to know that it causes target hemolysis (i.e. zone of ...
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Why is NAD used mainly for catabolic reactions and NADP used mainly for anabolic reactions?

NADH is used mainly in cellular respiration and the NAD+ to NADH ratio inside the cell is kept high, but NADPH is mainly used in photosynthesis and the NADPH to NADP+ ratio is kept low in animal cells....
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Can distilled / deionized / demineralized water "attack" teeth?

Demineralized water is claimed by some resources to be highly aggressive (due to their lack of minerals) and to attack all sorts of materials. From the World Health Organization website: ...
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Thermodynamics of one directional passive membrane transporters

I have read in my biochemistry textbook, that some membrane transporters transport only in one direction, moreover, they don't require ATP energy. I wonder, why these proteins do not act as ...
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Has anyone who has ever isolated synaptosomes using subcellular fractionation before know what the 'crude/heavy membrane fraction P2' is?

I am reading a journal paper where they analyse the proteome of synaptosomes. In this paper, they isolate synaptosomes from the hippocampi of mice. I know that synaptosomes contain the complete ...
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Thermodynamics of passive transport

My question is, where does energy come from for passive translocase's conformational changes? I argue it can't be concentration gradient, as concentration is only statistical phenomenon at micro scale,...

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