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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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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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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What is the source of phosphate in a cell?

Biology literature makes it sound like as long as you have enough ATP to start with, you can keep phosphorylating ADP and effectively recycle phosphates. But, we know that lots of things in cells get ...
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What are the differences between how latewood and earlywood forms and how does this effect it's properties?

In trees the earlywood forms a somewhat abrupt transitions to the darker latewoods that happen during the summer months. What are the chemical differences that arise in this wood at the cellular and ...
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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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educational sources for learning biochemistry

I just finished high school and am going into a biology undergraduate degree, I'm getting into biochemistry too and would like to learn more about it through online platforms or even non-fiction books ...
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What is the effect of sun irradiation and Finnish sauna on blood cells?

Is it possible that sun irradiation or Finnish sauna can reduce the number of mutated lymphocytes in the blood, in particular for people affected by Chronic Lymphatic Leukemia? Here is a paper showing ...
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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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Biochemistry of production of a yogurt counterpart from coconut milk

About yogurt: The biochemistry of changing animal milk to yogurt is well known. Recapitulating: After some preperatory steps the milk is inoculated with bacteria that consume lactose, producing lactic ...
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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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Will ammonia continue to accumulate in an aquarium tank if a strong antibacterial or chlorine is added to the water?

I've always wondered what would happen if dead plants and fecal matter lay in chlorinated waters and/or waters treated with strong antibacterials or antibiotics. I've heard that aquarium tanks ...
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If Melatonin is anti-gonadal, why is it associated with early sexual maturity in congenitally blind girls?

If melatonin is anti-gonadal, that is, it delays sexual maturity, then shouldn’t it delay sexual maturity in congenitally blind girls rather than helping them attain sexual maturity at an early age?
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Cellulose structure

In cellulose structure, some beta glucose are inverted. I’ve read that therefore the hydroxyl groups stick on both sides, but aren’t there hydroxyl groups on both sides anyways whether it was inverted ...
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Reverse oxidative phosphorylation?

I noticed that all of the cellular energy production methods that I covered have a fixed ratio of ATP to NAD(P)H out. For example, in the combined process of glycolysis, pyruvate oxidization, and the ...
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What is depyrimidination?

Depurination is cleaving the purines from the DNA. Why depurination is preferred and not depyrimidination while performing the DNA estimation test?
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Vitamin A Deficiency

I have a quick question regarding Vitamin A deficiency. The photoreceptor molecules in both rods and cones have the same general structure which is retinal which is bound to a protein called opsin ...
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VPg priming of the replication of RNA viruses

I'm doing a presentation on the replication of SARS-CoV-2 for my chemistry class, and I found that to replicate its RNA, the virus uses RNA-dependent RNA polymerase, which is primed by a VPg primer. ...
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Why does the high consumption of saturated fats lead to more risk of cardiovascular diseases and increased cholestrol levels? [duplicate]

People with higher consumption of saturated fats are more at risk of developing cardiovascular diseases as compared to people who mostly consume unsaturated fat. The only structural difference is a ...
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CO2 availability to phytoplankton in oceans and climate change impacts

I learned through research that increasing levels of atmospheric CO2 was increasing the acidity level of ocean waters. I then was looking into how this was affecting the phytoplankton and read that ...
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What exactly happens to hydrogen atoms in step 4 of citric acid cycle?

It seems that there are four hydrogen atoms in alpha-ketoglutarate and one in HS-CoA (not counting the ones in CoA), five in total. Two of them go to NADH and H+, so there should be three atoms in ...
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Histone Deacetylase Inhibition

So I am trying to brush up on my knowledge of HATs and HDACs. I am reading the just the 1st paragraph of the background of this study I remember learning that HATs turn things on on, and HDACs turn ...
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If a cell has two different GPCRs, how does the cell differentiate between the phosphorylation cascade caused by each?

In my biochem course, we learned that GPCR receptors trigger a phosphorylation cascade, with the end result being a large amplification of the signal in the form of cAMP. We never studied any ...
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Why don't our tongue receptors for salt and sugar adapt to them, like the ones for pepper do?

Many (most?) physiological receptors adapt to the substance they bind to, leading to higher dosages required to elicit the same response. In pharmacology, it’s called “drug tolerance”. In physiology, ...
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Do chilli peppers change in composition after they change color?

I grow some chilli peppers and was wondering when the time is right to harvest them. Of course gardening-focused sources say that they are ripe when they change color. This usually happens very ...
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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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How it will taste if one puts two substances on tongue simultaneously?

If we put two substances having different taste on tongue simultaneously how it will taste? Does specific part of tongue is sensitive to specific taste?
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Does the brain absorb heme and non-heme iron differently?

I know that for the brain to absorb iron, the iron must first pass through the blood brain barrier. Is this absorption different for heme and nonheme iron?
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Are there any known consequences of the right-handedness of the DNA double helix?

In this article it is suggested (without evidence) that the right-handedness of DNA may be the cause that "kick[s] off asymmetry in the early embryo [of snails]". On the one hand we know that ...
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Testing the viscosity of honey?

I am carrying an experiment where I will be measuring the viscosity of honey using Zahn cup but I don't know what is the optimal and efficient size and the size of the opening to purchase if you can ...
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Reasons why this protein is not suitable as an immunogen?

In a paper entitled "Progress and Prospects on Vaccine Development against SARS-CoV-2", the authors write the following in section 2.5: "Compared with S, N, and M protein, E protein is not suitable ...
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What's the role of bromelain in pineapple?

Bromelain refers to one of two proteases found in pineapple and its relatives. Like other proteases, many believe it has therapeutic uses and it's the subject of a lot of research. But what role does ...
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How many histidine tags are in the glucose dehydrogenase?

How many histidine tags are in the glucose dehydrogenase (from Bacillus subtilis) and how does this number influence the process of affinity chromatography?
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Basic Molecule Editor for use in journals / theses?

My background is Geosciences and Physics and I am going to study water and biomolecules in the Autumn. I was reading a PhD thesis about peptides and peptoids by someone in my research group and I had ...
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Does it make sense to express membrane transporters as concentration?

Let's assume a situation where a molecule, S, is transported out of the cell by membrane transporter T. For simplicity we do not consider any other synthesis or production processes. Furthermore, we ...
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How does exercising/starved muscle import glucose (released by liver)?

Adrenaline releases glucose from the liver during sport or if starved. This glucose goes to the blood through GLUT2 transporter. But how does it get transported into the muscle cells? GLUT4 is the ...
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Can muscles remake pyruvate from lactic acid, or does it have to go to the liver in the Cori cycle?

When the muscle is exercising, and only anaerobic respiration is done, pyruvate -> lactate to regenerate NAD+. Lactate is then transported out of the muscle and into the liver, to regenerate glucose, ...
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Can receptors exist on nanoparticles?

Given I have x amount of Gold nanoparticles or some type of nanoparticles that I wanted to bond together to create some sort of molecule or even a macro structure. Would it be possible to mimic the ...
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What relation do glycerol-3-P DH and acyl-CoA DH have with Complex II of the ETC?

I am sorry if this may be a purely definitional/nomenclature question. Complex II of the electron transport chain (ETC) would be succinate dehydrogenase, transporting electrons to ubiquinone (and ...
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What makes the cytoplasm a reducing environment?

It is known that the cytoplasm is a "reducing" environment, where disulfide bonds cannot form (will soon be reduced to 2 cysteines) [I'm not putting a link as this is a fact in many biology textbooks]....
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Does an FAD:FADH2 ratio exist in the cytoplasm? (similar to NAD+:NADH ratio?)

I have learned about a lot of enzymes/proteins which are covalently bound to FAD, and use this as an oxidising agent. In vivo, FAD is (almost) always protein bound (very low concentrations of free FMN/...
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Sickle-cell trait : Why is only one type of beta chain found in any one hemoglobin molecule?

I was reading a textbook (iGenetics, 3rd edition page 71), and came across the following passage: Homozygous bS bS people make Hb-S, the defective hemoglobin, with two normal a chains specified ...
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Base-stacking interactions versus hydrogen bonds

Is it correct that the hyperchromic shift in DNA is a result of the disruption of the base-pairing hydrogen bonds, but the actual denaturation of dsDNA has more to do with the base-stacking ...
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Overcoming palmitic acid intolerance

What can stop the body from being able to process or break down palmitic acid? The acid stays in the stomach and burns causing a similar reaction as heart burn when the volume is high. Heart burn ...
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Is there any free software similar to CellDesigner that allows me to represent large networks of biochemical reactions in the human body?

I continually have to review multiple articles, in multiple journals. These articles present how various enzymes, proteins, lipids, carbohydrates, etc. intervene in the processes that lead to certain ...
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Why is it that evolution of organisms had oxygen as their life-supporting gas?

On Earth, gaseous N2 is abundant. However, life began by dealing with O2 and CO2. What can be considered the major reason for life developing in such manner?
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What causes the localization of myoglobin in turkey to regions of muscle tissue?

I've read that myoglobin localization is responsible for the darker colour of leg muscles in turkeys. Why does this localization occur in terms of any of cell biology, molecular biology, or ...
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Growing Mouth Bacteria in a bowl of sugar water

I want to teach my nephew why brushing in necessary and how sugar in mouth reduced by bacteria to acid. I plan to put sugar mixed water in bowl and take swab from his mouth and dip in bowl, and test ...
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How do microtubules “Push” agaisnt the cell membrane if they are polymerizing at the very tip that makes contact with the membrane?

Trying to understand the reasoning behind the various Push VS pull microtubule arrangements, if it is "push" then I dont see how it would be able to push up against the cell membrane while ...
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Are there any organisms that do not perform glycolysis (or anything similar)?

To clarify I know that there are alternative pathways similar to glycolysis, what I mean is are there any organisms that perform a different pathway that is radically different from glycolysis, but ...

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