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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51 views

What happens to the brain during meditation?

I've read several experiments on the internet according to which it is possible to reach a psychedelic state without taking any psychedelic drugs like DMT, LSD and other tryptamine derivatives. It ...
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172 views

Why do plants produce and store both amylose and amylopectin?

Since both forms of starch has its primary purpose of storing glucose and hence releasing energy, why are there 2 variations of this sugar? Is it possible for an organism to contain/depend only on 1 ...
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What happens during fixation of Nucleic acids on nylon membrane

In Southern blotting technique, fixation of DNA to nylon membrane is a step prior to hybridisation with probe. It is done by baking at 80ºC and according to this cross linking between DNA and nylon ...
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What do we mean when we say that a muscle fiber contracts strongly?

Sounds dumb but anyway, i heard that superfast fibers contract more strongly than fast twitch fibers. And i never thought of muscle contraction as something that has a magnitude (i thought of it as "1 ...
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387 views

In what reaction of mitochondrial respiration is hydrogen peroxide an anomalous product?

I understand that hydrogen peroxide is produced in an anomalous manner during mitochondrial respiration, which also produces other by-products or free radicals. Does anyone know the details of the ...
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127 views

Origin of melatonin: oxidative stress defense OR circadian rhythm?

Question Which functional role of melatonin came first? Regulation of the circadian rhythm Defense against oxidative stress Other Background I was well aware of the important role melatonin plays ...
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126 views

Can NADP be converted to NADPH using d glucose?

For one of our reaction, we require NADPH enzyme. We have NADP in our stock. Is it possible to convert NADP to NADPH using D-glucose anhydrous and if so please provide me how to go about it?
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25 views

How does DNA damage increase the activity of p53?

I understand the steps leading up to the halting of the S-cdK checkpoint from there, but I can't find the mechanism by which DNA damage actually increases the activity of p53.
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64 views

What are some good examples of phonotaxis in plants and other inanimate beings?

Reaction to the sound waves by plants is commonly unobserved. A physical movement or chemical release examples due to phonotaxis would be good to know about.
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100 views

When can helices form coiled-coils?

The other day, my teacher suggested we find out whether a chain of the following amino acid sequence would be able to form a coiled-coil: N-KIAEVRAQYEDVANKVRLIVE-C ...
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212 views

Modulating the level of acetyl CoA

Describe what might happen if there were no mechanisms for modulating the level of acetyl CoA. I am not sure what is meant by "modulating the level of acetyl CoA", or what mechanisms contribute to ...
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Where am I going wrong in a Reactive Oxygen Species Assay done in N9 cells?

I have followed the modified protocol that was given to me by my senior (who was using for his RAW 264.7 cells - Reference article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308605/ ) for ...
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147 views

Why do basil leaves turn black?

I notice that when I buy basil it is fresh and green in the store, but when I take it home it wilts and turns black within 24 hours. Why does it do this?
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154 views

How well can proteins discriminate between ATP and GTP? Can ATP act as a GTP mimetic?

GTP and ATP are similar structures with the adenosine and guanosine groups differing. Both are involved in a vast array of biological functions. However it has been shown that in certain cases, GTP ...
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48 views

Looking for dataset of proteotypic and non-proteotypic peptide

I doing experimentation for peptide prediction using machine learning. I need some data for testing. My background is Computer Science. Any advice how to find proteotypic and non-proteotypic peptides....
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42 views

How do organoarsenics improve digestion efficiency in poultry?

It struck me as very surprising that these organoarsenic compound with structure looking not very compatible with living system is widely used as food additive to increase weight gain and improve food ...
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176 views

Can aptamers be used to identify the terminal amino acid residue of a peptide?

Suppose there were DNA or RNA aptamers that bind specifically to a certain terminal amino acid residue. Let's name it aaSA (amino acid specific aptamer). For example, the aptamer binding to terminal ...
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633 views

Convert flux value in nmol/min/mg protein to nmol/min/cell?

This is a question about unit conversion. I found an experimental measurement of the saturation uptake of glucose in yeast: $$V_\textrm{max} \approx 650 \textrm{nmol}/\textrm{min}/\textrm{mg protein}$$...
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286 views

PCR that worked previously is now only showing primer dimers and a smear on gel

PCR amplification of a promoter sequence for gel extraction worked beautifully using Phusion HF enzyme with GC (higher error but less picky) buffer. However, DNA concentration from the gel extraction ...
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129 views

Nail polish toxicity studies?

Are there any well-founded studies that authoritatively demonstrate negative effects from the use of nail polish, particularly in children? I've been brought into the fray of a couple of folks who ...
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499 views

How much energy would it cost to synthesize all cholesterol requirements de novo?

Imagine a scenario in which some person is unable to absorb any dietary cholesterol because of some intestinal mutation (for example). Thus, they have no cholesterol available from their diet for ...
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67 views

What is the difference between cell, membrane and animal based assay?

I am reading a review about MRP1, discussing it's ability to extrude different compounds from cell interior. When describing the different experiments conducted to observe the MRP1's reaction to ...
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560 views

Proteases in the blood

I’m reading on hormones and the book talks about how peptide or amine hormones are easily broken down by proteases present in the blood plasma. This has led me to question the interactions between ...
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104 views

Which Lactobacillales (Lactic acid bacteria — LAB) strains are capable of degrading starch?

I've been researching bacteria strains but am having trouble finding amylolytic LAB strains with amylolytic and lactic acid producing character. The only species I've found, that are capable of ...
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48 views

Is there a good easy protocol for extracting proteins (enzymes) from fungal mycelium?

I quantify the enzyme (polygalacturanase) activity by DNSA method. To determine endo-polygalacturonase activity I'm searching for a good easy enzyme extracting method. Any suggestions for a suitable ...
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81 views

Birth control hormones in the water? Or not?

This prior question talks about natural estrogen (TL;DR: Months to years): How quickly do estrogens break down in the environment? Ref: http://dx.doi.org/10.1038/485441a A lot of media has said, "...
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176 views

Textbook for quantitative biochemistry with thermodynamics, as an alternative to Voet, Voet & Pratt (Fundamentals of Biochemistry)?

I'm looking for a great textbook on biochemistry that covers core topics: relevant aspects of thermodynamics, reaction kinetics, metabolism (e.g. krebs cycle, respiration, etc.). Ideally it would also ...
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49 views

What are all of the currently known variations of the G zipper motif?

The G zipper motif is found in transmembrane proteins at an above random frequency and there are models explaining how it might help with multiple transmembrane intra-membrane helix bundle assembly. ...
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120 views

Why doesn't the body optimize how many fatty acids it burns?

Ketone bodies are produced due to an excess of fatty acids being burned (accumulation of acetyl-CoA) so my question is: Why doesn't the body simply regulate how many fats it burns so it doesn't have ...
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121 views

Which method would more accurately help to identify the unknown concentration of a protein sample between the A280 and the Bradford methods?

I quantified my protein using the standard Bradford method and the A280 methods and obtained values that were far off from the theoretical value of the protein of interest, and therefore was wondering ...
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200 views

Zinc and brewer's yeast

I'm hoping for some information relating to yeast nutrition (specifically Saccharomyces cerevisea) in beer fermentation. Zinc is well-known to be necessary for yeast cultures to perform successful ...
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41 views

Which biosynthetic pathways take place in the plastid and were are they located?

I know that the isoprenoid, jasmonate, glucosinolate, fatty acids, chlorophyll, starch, and aromatic amino acid syntheses are located in the plastid. But I don't know if they are located in the ...
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163 views

Why does the ovum prefers to be arrested at metaphase 2 of meosis before fertilization? What is the possible advantage of this process?

Why does the human ovum prefers to be arrested at metaphase 2 of meosis before fertilization? What is the possible advantage of this process??Please help me with it.
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287 views

What are the ingredients of Pheromone Trap using for controlling Fruit flies of cucumber?

Pheromone Traps are used for fruit fly control. But I have no idea which ingredients or chemicals are used for preparing Pheromone trap
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Why is a nicotinamide-tryptophan combination used to treat affective episodes in a few older clinical trials?

At least one of the journal articles that reported on such clinical trials allured to the nicotinamide-tryptophan pathway that I assume must be related to the metabolism of tryptophan into serotonin ...
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533 views

What tests can be performed to test the purity and quality of the raw peptide HCG (Human Chorionic Gonadotropin)

What tests could be run to test the purity and type of HCG? We are looking to purchase HCG from China but the purity and quality varies between labs, we are able to receive samples of the raw peptide ...
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453 views

Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
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1answer
51 views

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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1answer
16 views

Values of the blood tests pancreatic amylase and lipase

Anyone know what is considered slightly elevated, moderately elevated and strongly elevated values of pancreatic amylase and lipase? Many different laboratories in my country divide between these ...
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1answer
85 views

Is this experiment to check enzyme reaction rate according to substrate concentration correct?

We just had an experiment to check enzyme reaction rate according to it's substrate concentration. In the experiment, we used a varying amount of substrate and the same amount of enzyme: (1.5mm enz, ...
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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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38 views

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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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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1answer
77 views

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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What causes the overactivity of keratin production and expression in the cells of the nail bed/ nail matrix after some traumata?

What is the cellular mechanism of traumatic(sterile) onychodystrophy(hypertrophy)? I.e one hits his toenail and has it removed twice( once after the first trauma and then again 3 years after the first ...
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Toxicity of stannous fluoride in toothpaste?

I recently purchased a new brand of toothpaste, and when I looked at the medicinal ingredients, it listed stannous fluoride 0.454% w/w, instead of the regular sodium fluoride. I was a bit concerned ...
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Examples of alkali metal and halogens covalently bonded in biological molecules?

Divalent and monovalent ions are often non-covalently bonded in biological molecules, they are primary building blocks of the machinery of biology. Iodine, the halogon in period 5, is covalently ...
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Rescuing a virus from naked (c)DNA

Reading the articles it seems that for several human virus strains, synthesizing the full-length genome then electroporating into vero cells and incubating a few days gave birth to living viruses that ...
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92 views

Tryptophan structure

Currently trying to memorize the different amino acid structures for my own learning purposes. I think I am confusing myself, and would like clarification to see if it matters where the NH and double ...
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24 views

About the mechanism of coupled reaction/metabolism with ATP

I am not in the field of biochemistry so this may be a rookie question or misconception. I heard occasionally about the energy "released" from ATP hydrolysis fueling (endergonic) biological reactions....