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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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Can onion consumption cause Heinz bodies in humans?

It was well attested that eating onions can cause the presence of Heinz bodies in the blood of cats, dogs, and other animals, due to the toxic effect of, apparently, thiosulfate, which denatures ...
Martin C.'s user avatar
1 vote
1 answer
40 views

About tomatoes pigments, why red tomatoes rather than yellow ones

How the first tomatoes (yellow) that arrived in Europe turned from yellow to red ? I know the yellow pigment is xantophylle and the red one is lycopene, but my question is, was it an adaptation of the ...
Quidam's user avatar
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4 answers
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Why are heavy metals toxic? Lead and Carbon are in the same group. One is toxic, the other is not

I have read the different answers on the toxicity of heavy metals but I am still confused about the topic. Why does the mass of the nuclei matter when chemical reactions only involve the electrons. ...
Shaktyai's user avatar
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How do I find genes related to monocytes in mice gut?

My PI just gave me a task where I've got to find genes related to monocytes in the mice gut using single-cell RNA seq. I feel all out of my depth. I've looked up cell expression atlas but don't ...
jai yadav's user avatar
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Why can't a third acetyl-CoA condense with acetoacetyl-CoA in the same way, as two acetyl-CoAs condense in the thiolase reaction?

In the biochemical ketogenesis pathway, acetoacetyl-CoA reacts with acetyl-CoA to form HMG-CoA (3-hydroxy-3-methylglutaryl-CoA), in a reaction catalysed by HMG-CoA synthase. But why can't acetoacetyl-...
Muhammad Nasir Hussain's user avatar
9 votes
2 answers
977 views

Understanding association kinetics

I would like to understand the classic kinetic model of association / dissociation that tries to describe the concentration of a compound $[\ce{AB}]$. Let's say we have a model: $\ce{A + B} \...
Salmon's user avatar
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1 answer
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Human metabolic pathways involving particular proteins

I am currently working on a project that involves analyzing the pathways in which certain proteins are involved. I have compiled a list of proteins, and I am keen to explore the pathways they ...
Shadan's user avatar
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7 votes
1 answer
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Are there any completely, or 'true', Mendelian traits that do not display any polygeny at all?

Recently, I learned about polygenic traits and it got me wondering, are there any truly Mendelian traits where the trait displayed exists in a total binary? I have looked at some questions on the ...
gzkts's user avatar
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3 votes
0 answers
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How does the recently discovered nitroplast fix nitrogen?

Nitroplast is a newly discovered eukaryotic organelle that can perform nitrogen fixation. Like chloroplast, nitroplast was derived from a cyanobacteria species (UCYN-A). Cyanobacteria are the only ...
哲煜黄's user avatar
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Atp as energy currency [duplicate]

I have seen that ATP and sometimes GTP is used to deliver energy to reactions in the cell. What is the reason that no other chemical is used for the purpose ? What is the charistiristics of the ...
User51's user avatar
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How to prevent small-protein smearing in SDS-PAGE?

I am doing SDS-PAGE for ubiquitin-6xhis (9.6kDa), and all my hand-cast gels produce a smeared band (see image). I typically use 5% acrylamide for stacking, 15% for resolving gel layers. I don't ...
Tom Murphy's user avatar
2 votes
1 answer
48 views

What goes on in the muscle during static exercise?

Starfish opens mollusc's shell by applying static force for several hours. Mollusc gets tired and cannot hold shell closed. Muscles spend some energy even when static exercise is done. But it is not ...
Vashu's user avatar
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4 votes
1 answer
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Central diabetes insipidus and antidiuretic hormone

Are the levels of antidiuretic hormone in the plasma somehow hard to measure or are the results unreliable, and if so why? Some countries have moved away from testing for ADH (the national health care ...
George Ntoulos's user avatar
2 votes
1 answer
80 views

How do I identify the carbonyl atoms in a PDB file

Can I infer it from the atom name alone? Or do I need to look at the structure of the residue it is in?
Ivan Spirandelli's user avatar
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Rectangle-like structures and their folding in biology

I've heard that mathematics helps to explain some biological problem. For example gömböc, which was a well hidden body from mathematicians, explains the body structure of some tortoises in relation to ...
Mikhail Gaichenkov's user avatar
3 votes
2 answers
132 views

What is H-activation vs. O-activation in the context of cellular respiration?

I was reading this article on Albert Szent-Gyorgyi and on page 7 there's this statement: Now, I thought myself capable of tackling a biochemical problem. I embarked on biological oxidations. At that ...
imrobert's user avatar
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1 answer
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How to reduce the viscosity of an extract from a plant seed

I extracted a sample from a plant seed using PBS buffer. The extracted sample is very viscous, even after centrifugation at 15000 rpm for 30 min. The sample is like a thick mucus so that it becomes ...
DitaA's user avatar
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2 votes
1 answer
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Improving contrast between dot and paper in dot blot

Currently using dot blot to attempt to determine if a serum contains antibodies for some reagents I am testing. I pipetted samples as 10-5ul dots on whatman paper. Incubation steps were for 1 hour ...
Thomas Hunt's user avatar
2 votes
0 answers
26 views

Is Regenerative Brain Tissue Technology In The Near Future?

I got 99% of my information from articles I found in NIH's library; I can't cite anything now because I am on a timed session in a public library. I've been reading material from research papers in ...
Salus's user avatar
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1 vote
0 answers
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Why can't the fructose monomer in sucrose be α-fructose?

In all academic sources, sucrose is identified as α−glucose (1-->2) β−fructose. However, I cannot find any explanation anywhere as to why the fructose monomer has to be in the β configuration. ...
MD P's user avatar
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11 votes
4 answers
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Why is the retention of ability to synthesize non essential amino acids of negative survival value?

In my textbook "Harper's illustrated biochemistry" chapter 27 it is written that The existence of nutritional requirements suggests that dependence on an external source of a specific ...
Lakshya Kumar Singh's user avatar
2 votes
1 answer
32 views

Free diving physiological changes

When training for free diving, there are several physiological and psychological changes that enable this activity, however one of the changes that I do not understand is increased resistance to blood ...
Evamentality's user avatar
0 votes
1 answer
25 views

Why do monoclonal and polyclonal antibodies behave differently as labeled secondary antibodies?

According to the MBL guide to generating antibodies, the differences between monoclonal and polyclonal antibody extend beyond the fact that the latter is heterogeneous, binding to various epitopes for ...
cmcca's user avatar
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How to identify unknown RNA species that copurified with protein

So I have been studying an E. coli protein. As the first step I purified it in a pretty standard way - overexpressed it in BL21 DE3 cells and placed it in an ion exchange column, followed by size ...
margarine's user avatar
1 vote
1 answer
141 views

What is the difference between digesting sugar and carbohydrates?

To understand where I'm coming from, first some commonly distributed (mis?)conceptions: (Obviously to be taken with a big grain of salt because they are somewhat contradictory) Sugar is bad for your ...
KGM's user avatar
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1 vote
0 answers
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Which position do retro aldol reactions occur in (comparing glucose and fructose)?

Regarding glycolysis, my text states: What is the biochemical rationale for the isomerization of glucose 6-phosphate to fructose 6-phosphate and its subsequent phosphorylation to form fructose 1,6-...
TheAnonymous's user avatar
3 votes
1 answer
114 views

Use of ADP hydrolysis for driving energy-requiring processes?

The free energy of the hydrolysis of the β-γ phosphoanhydride bond of ATP is used to drive energy-requiring biological process such as chemical synthesis, movement, ion transport and production of ...
Archonic's user avatar
0 votes
1 answer
31 views

Why does harper states that aldehyde dehydrogenase is a oxidase? Is it a misnomer then?

Oxidases are those which uses O2, but dehrydrogenases doesn’t? Then is my book wrong ? Is it a misnomer that aldehyde dehydrogenase is correctly a oxidase?
Dr Tenma's user avatar
1 vote
1 answer
116 views

How to calculate the osmolality of Hepes solution?

Here is an excerpt from Kollmann et al. (2020, J. Physiol.): This ring was placed in a recording chamber continuously perfused with 37°C aerated Hepes solution containing (in mM) 136 NaCl, 10 glucose,...
Jasmine's user avatar
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What is the optimal pO2 concentration for automated reactor batch mode EColi expression?

I am wondering what is the optimal pO2 level for an reactor based expression? All protocols I have found indicate for E.Coli pO2 levels just bigger 20%. So, I am wondering what is the optimal level? ...
raptorlane's user avatar
1 vote
0 answers
143 views

Can you store 5% BSA, in TBST, in -20C?

I have stock solution of 5% BSA prepared in TBST I use to make primary antibody dilutions for western blot. I'll admit I just assumed -20C, with freezing and thawing as needed, was an acceptable means ...
Tom Murphy's user avatar
1 vote
1 answer
198 views

Why don't membrane potentials violate the principle of electroneutrality?

The principle of electroneutrality states that the number of anions and cations in a solution must be the same, i.e., that there will be no charge excess in any side of the membrane separating two ...
TheAnonymous's user avatar
18 votes
3 answers
2k views

Are stable isotopes ever used in pharmaceuticals?

Carbon has two stable isotopes, C-12 and C-13. Since they both have the same electronic structure they can both make up the same molecules, but presumably they may perform different functions in ...
imrobert's user avatar
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1 vote
0 answers
34 views

Does aerobic exercise increase the incidence of disease via free radicals?

Aerobic respiration produces ROS, atleast one of which (the hydroxyl radical) cannot be neutralized by any known antioxidant and is always damaging surrounding tissue. I know ROS plays a role in ...
Samid's user avatar
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-1 votes
1 answer
97 views

max % of oxygen not harmful for breathing?

Is breathing pure oxygen bad for you? Human blood is designed to capture oxygen and safely bind it to a molecule known as hemoglobin. However, if you breathe in a high concentration of oxygen, it will ...
Root's user avatar
  • 21
1 vote
0 answers
60 views

How to elute the protein that is bound to biotinylated RNA immobilized with streptavidin?

I would like to test the proteins that bind to biotinylated-RNA by mass spectrometry , I was using Dynabeads™ MyOne™ Streptavidin C1 (invitrogen) coupled with biotinylated-RNA,than mix these beads up ...
Fino's user avatar
  • 11
0 votes
1 answer
70 views

How come SSBPs in RPA don't bind primers?

I've started reading about the recombinase polymerase amplification (RPA). I'm learning that in RPA, recombinase enzyme binds to primers, then makes them anneal to the complementary target DNA strand, ...
Andrew Roots's user avatar
0 votes
0 answers
31 views

How many pyrophosphate groups are released during dinucleotide formation?

I can't seem to fathom how a dinucleotide is formed. My textbook says that initially both nucleotides have 3 phosphate groups before the join but the formation releases only one pyrophosphate If ...
Spluesh's user avatar
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0 votes
0 answers
22 views

Validating Generative Models for 3D Conformations of Inactive Dopamine Receptors in Protein Design

Considering a dataset comprising 3D conformations of Dopamine receptors in an inactive state, we aim to train a generative model capable of capturing the distribution of these receptors and generating ...
SilicoMar's user avatar
2 votes
1 answer
505 views

Can humans metabolize D-malate?

Only the L-isomer is produced naturally, while racemic mixtures are produced synthetically and used commercially as food additives and energy supplements. So what happens when we consume D-malate? ...
ManRow's user avatar
  • 395
1 vote
1 answer
68 views

Can a non-pure culture be used for reliable rapid phenotypic diagnostic tests?

Can a non-pure culture be used for reliable rapid phenotypic diagnostic tests (e.g. catalase, oxidase & gram stain)? "Slide Test Method Obtain a pure culture of the organism to be tested. ...
Freezing Soul's user avatar
0 votes
1 answer
83 views

Why can mitochondria make only 34 molecules (rather than 61 molecules) of ATP ?

Why can mitochondria make only 34 molecules (not 61 molecules) of ATP from the energy obtained from the oxidation in the electron transfer system of NADH and FADH2 generated by oxidation of glucose in ...
Blue Various's user avatar
2 votes
0 answers
27 views

How to measure cytochrome P450 activity in owls?

I hope you're all doing well. I'm currently working on a research project focused on owls and their exposure to anticoagulation rodenticides such as brodifacoum. As part of my study, I need to measure ...
mohammed 's user avatar
0 votes
1 answer
39 views

Induction of IFN-beta in HEK293T

I'm trying to increase expression of a protein we're attempting to study, UBL7, supposedly unregulated by Type I Interferon and particularly IFN-beta. I've tried treating HEK293T cells (~60% ...
Tom Murphy's user avatar
0 votes
0 answers
57 views

Where is the source of H+ in the matrix that will be pumped during the electron transfer system? Where does the OH generated at that time go?

In the electron transfer system, it has been mentioned in prior questions that complexes I, III, and IV are proton pumps and that these pumps pump protons from the matrix into the intermembrane space. ...
Blue Various's user avatar
1 vote
1 answer
94 views

Fate of GTP produced in the TCA cycle

As someone already mentioned in one of the following questions, the TCA circuit generates GTP in addition to NADH and FADH2. The fate of NADH and FADH2 is clear: they are used to pump protons in the ...
Blue Various's user avatar
0 votes
0 answers
24 views

Examples of mechanisms of metabolic trapping inside cells that create concentration gradient

I am looking for examples in biology in which a metabolite that can diffuse freely across a cell membrane (through passive diffusion), once inside, gets modified to a form that cannot diffuse back ...
Massimo Bilancioni's user avatar
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0 answers
39 views

Effects of oxygenated water on bacteria

I was curious if any of you would happen to have any experience with this but any hypotheses regarding how this would turn out would be much appreciated. I’m wondering if water fully aerated with ...
Jaston's user avatar
  • 1
5 votes
1 answer
654 views

According to an online course, ribose and adenine can bond to make ATP. Is this true?

I recently came across this question in the MIT Open Learning Library Pre-7.01 Biology Course. It is question 2d in Problem Set 1 (archived link). The question, as well as the correct answers and ...
Ben Zelnick's user avatar
0 votes
0 answers
19 views

Bi-phenyl degradation pathway in lignin

I am studying lignin - and really like the bi-phenyl degradation pathway of DDVA by SYK-6, as shown below But I can't find any literature on whether this pathway transfers from the dimer to the ...
erdos's user avatar
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