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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Biochemical Mechanism behind red hibiscus flower on a cream hibiscus plant

I have two 3-4 yrs old cream hibiscus shrubs in my garden. The shrubs seemed normal enough, giving cream colored petals with a red center. But soon I noticed that there are specific branches, which ...
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At what age are mice considered too old for their thymus to stop being functional and produce T cells?

I am studying the effects of radiation on the immune system of mice. After exposing them to radiation, we will be harvesting their spleen, lymph nodes and blood to investigate immune cells such as T ...
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Question on thick filaments

In this photo, I know that the arrows pointing towards the M-line of sarcomere on actin filaments are due to the power strokes of myosin heads. However, what I don't understand are the arrows on the ...
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How is silica transported to the leaves of genus Dendrocnide trees to form stinging needles for toxin delivery?

I just read the NYTimes' This Tree’s Leaves Look Soft and Inviting. Please Don’t Touch Them. which mentions the genus Dendrocnide and that Wikipedia section begins with: Contact with the leaves or ...
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Why is aconitase classified as a lyase?

Aconitase in the TCA (tricarboxylic acid) cycle isomerizes citric acid to isocitric acid via cis-aconitic acid intermediate. Since overall it functions as an isomerase, why it does not belong to ...
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What are the carbohydrates that are found in white rice?

From this Wikipedia page on rice, it is mentioned that 100g of rice contains 80 g of carbohydrates, of which 0.12 g is "sugar" and 1.3 g is "fibre". I believe the "fibre" ...
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Natural Toxins and Medicine

How are natural venoms and toxins (e.g. spider and snake venoms) used to make antidotes? In other words, what is in that venom that is part of a harmful substance but, when used correctly, can ...
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Transcription of two different factors from the same transcription factor - seeking a relation between concentrations

Let's assume that: Factor $X$ enters nucleus and results in the transcription of two different factors, $A$, and $B$. $X$ $\to$ $A$ $X$ $\to$ $B$ Can it be expressed as $[A]=\alpha [X]$ or $[A]=\...
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Why is it thought that silicon based lifeforms never flourished on Earth?

Reading the recent ScienceAlert article "For the first time, living cells have formed carbon-silicon bonds", it is stated that despite the relative abundance of silicon in the surface of the Earth, ...
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How is it thought that phosphine is synthesized by living organisms on Earth?

The recent (Sept. 2020) report of “Phosphine gas in the cloud decks of Venus” states that phosphine (PH3) is only known to occur on Earth due to anaerobic life. Quoting from a report in the New York ...
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Enzyme kinetics; what happens at the peak of the Gibbs energy graph?

At the very peak, the energy is in a state of activation energy. Here, is the substrate just attaching to the enzyme, or is is substrate already breaking?
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Who discovered DNase?

I was recently studying genetics in which DNase had a crucial role in proving DNA to be the genetic material and I tried to find who discovered DNase (like the discoverer of DNA) but in vain. Who ...
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Is there an enzyme that functions without being associated with a complex?

I'm looking for an enzyme that does not function as part of a complex in its active state. Preferably it also is not part of a kinase or other kind of activating cascade as well though I would ...
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Where does the 'C' in exhaled CO₂ mostly come from?

When a human being exhales CO₂, what is, by the numbers, the main source of carbon atoms exiting the body in this way? I mean what class of cells, or which tissues are the biggest on a pie chart of ...
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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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Cold adaptation in proteins, at sequence & structural level

When looking for cold adaptation in unicellular eukaryotes there is not much work found. Most of the time general sequence comparative sequence analysis between marine mesophile & psychrophile ...
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Is a virus a poison?

I've understood that a virus is not a living organism (like e.g. a bacterium). From Wikipedia I get that a poison is a substance that reacts physically or chemically with molecules in the human body. ...
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Killing enveloped viruses with soap

Unlike non-enveloped viruses, enveloped viruses can be killed with soap, alcohol, etc. Why? Why does just having an envelope make it susceptible to soap and alcohol?
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How many protons are pumped out per pair of electrons from NADH in oxidative phosphorylation?

I have searched the web and found that 10 protons are suppose to get pumped out during the electron cycle, but i'm a bit confused. I'm trying to count, for every complex(1/3/4), the number of protons ...
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Design rules for DNA linkers

I want to use double stranded DNA linkers to physically bind two "things" together, by grafting ssDNA on each one of them and using DNA hybridization as the locking mechanism. I do not expect the ...
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What specific markers does a Covid-19 PCR test look for?

I've done a search and can't find anything as to what specifically makes a Covid-19 positive that identifies it as unique. I would expect to see something like this: https://madridge.org/journals-...
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Why are fatty acids synthesized in two carbon units?

Why does long-chain fatty acid synthesis involve the two-carbon precursor, malonyl CoA, rather than the one-carbon acetyl CoA (or even a three-carbon precursor). Is this because fatty acids with an ...
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Could DNA replication fail in the far future? [closed]

Assuming that all environmental conditions on Earth remain the same in distant future, the tendency of nature to increase entropy would cause the chemistry and the mechanism of DNA replication to ...
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How does the light-independent stage of photosynthesis get H+ ions?

From what I understand from my grade 11 biology: During the light-dependent stage of photosynthesis, water molecules split, producing hydrogen and oxygen atoms. The oxygen atoms are basically “waste ...
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Does the harvesting time of broccoli sprouts change their glucoraphanin content and sulforaphane formation capacity?

Does anybody know if the harvesting time affects glucoraphanin content and sulforaphane formation of broccoli sprouts? Do they also get affected by light exposure or lack of it?
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Can sperm cells penetrate the cell membrane of non-ovum cells?

Sperm cells have tiny bags of enzymes on their tip (the acrosome) which allow them to penetrate the ovum. My question is whether or not the process that allows sperm cells to penetrate the cell ...
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Why are there exactly four nucleobases in DNA?

Does someone know why DNA is composed of four nucleobases? In particular, is there an explanation for the number? Why four and not two, or eight?
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What determines whether a reaction using ATP produces ADP or AMP?

Most reactions using ATP seem to involve: ATP → ADP + Pi but in some the reaction is ATP → AMP + PPi followed by hydrolysis of the pyrophosphate: PPi → 2Pi Is there any principle that determines which ...
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Apparent paradox in Glucagon action

Glucagon stimulates glycogenolysis and gluconeogenesis, thus increasing the plasma glucose concentration — so that tissues get enough glucose in the fasting state. However glucagon also inhibits ...
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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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Absorption of glucose in small intestine

During the absorption of glucose in the small intestine, glucose enters the epithelium by Na+/glucose co-transporter by the concentration gradient of Na+. The gradient is generated by pumping 3Na+ out ...
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Coronavirus: Why does soap inactivate the virus on skin, but not on surfaces?

In a comment on "Stability of SARS-CoV-2 in different environmental conditions", published today in The Lancet Microbe, it is stated that household soap is highly effective on the skin. Not ...
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Why severely increased Ligand (eg Hormones) concentration downregulates the Receptor?

As an example continuous high blood level of GnRH in humans causes a suppression of LH and FSH. This is due to the fact that increased GnRH downregulates GnRH-Receptors . My question is how this is ...
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What is the difference among these compounds?

I'll preface this question by making clear that I'm not not well versed in biology. Anyway, within the context of biocides/antimicrobial products using them as active substances, what is the ...
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kcat in uncompetitive enzyme inhibition

Why doesn't $k_\text{cat}$ change in uncompetitive inhibition, given the fact that uncompetitive inhibition lowers the enzyme–substrate complex efficiency (which is the reason for lowering of $V_\text{...
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Why does the sandalwood tree produce a fragrant oil?

Why do sandal trees produce fragrant oil? Is there any purpose for it? Is it to make it unpalatable for other herbivorous animals? If so, why do humans find the fragrance pleasing?
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Partial pressures of different gas in human blood and how they are calculated?

In Respiratory Physiology, we use the $P_x{O_2}$ and $P_x{CO_2}$ in blood at different regions of the peripheral circulation. From my Chemistry knowledge I know that $P_x$ of a gas in a solution is ...
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Do cats produce DMT?

Edit: If somebody (anybody) wants to add an answer so the bounty won't go to waste, please do so! The comments have already introduced me to the Kegg metabolism database, some interesting papers, and ...
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176 views

Activated carrier molecules and their relationship to enzymes

I am reading Molecular Biology of the Cell, and one thing I don't quite get is the difference between an enzyme and an activated carrier molecule. I understand that enzymes lower the activation energy ...
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What would cause a single white eyelash?

I couldn't find a paper who could give me the explanation. Unfortunately, according to my search, it seems there are not many reported case, particularly for the younger population (<30). Would ...
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Can bacteria metabolize fatty acids for fuel?

I'm not a microbiologist, but rather a physiologist curious about microbial metabolism. Much like humans bacteria can utilize glucose, but when it comes to long chain, medium chain, or short chain ...
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202 views

Why doesn't enzyme reaction rate rise linearly with substrate concentration?

This is the graph of the Michaelis-Menten equation which describes the relationship between reaction rate and substrate concentration: I don't understand why it is hyperbolic. Intuitively, I would ...
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Enzyme kinetics at the chemical level

I am stumped by two questions: Why do we take only the initial 10%(or may be 9.99999....%) of S conversion as the rate of the enzyme reaction. why not more than 10%? Why doesn't the velocity keep on ...
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Why does the HPV vaccine not work on already infected people?

With my limited knowledge, I understand that the vaccine works by inserting fake HPV-like material in the body, thus inducing the immune system to build up defenses against it, so when the body is ...
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What is the biochemistry of love?

How is love induced between humans? Say, between mother and child, couples, etc. Does the phenomenon of love exist in other mammals, too?
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What is the ultimate source of ADP/ATP in humans?

I am teaching myself Cell Biology from the internet. Despite my usually good Googling skills, I'm stuck in a loop with this question. Q: What is the source of ATP? A: ADP Q: What is the source of ...
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Why is it (allegedly) dangerous to feed ducks with breadcrumbs and pieces of bread?

I used to go down to the local lake all the time with leftover bread and throw little pieces of it to the hungry duckies, who very eagerly fetched it and ate it while happily quacking away. I thought ...
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How do anticholinesterase pesticides kill nematodes?

Compounds that inhibit the enzyme acetylcholinesterase are commonly used as pesticides. In animals with centralized respiratory systems controlled by the nervous system, poisoning with an ...
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State of extracted DNA

A well-known and commonly-done experiment is to extract DNA from strawberries or other fruit by first mashing the fruit of choice, adding the mush to a mixture of water, salt, and detergent, and then ...
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Is there an antidote for caffeine, e.g. as a supplicant for caffeine-intolerant persons?

First, let me state I'm not talking about a medical emergency. No one is in a serious condition. My girlfriend is, we think, caffeine-intolerant. She loves the smell of coffee and the habit of coffee ...

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