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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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-1 votes
0 answers
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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 ...
10 votes
4 answers
5k views

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. ...
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 ...
4 votes
1 answer
97 views

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 ...
0 votes
0 answers
19 views

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 ...
2 votes
1 answer
3k views

Relation of conformational entropy and protein folding

I'm trying to figure out the relation between conformational entropy and protein folding. I read the following in Lehninger, Principles of Biochemistry (6th edition): Most of the net change in ...
0 votes
0 answers
18 views

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-...
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} \...
1 vote
1 answer
32 views

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 ...
3 votes
3 answers
2k views

Does the Miller-Urey experiment explain the origin of life?

According to the Miller-Urey experiment, the early earth atmosphere could have supported the formation of amino acids. This could provide an explanation for the origin of life. However, I do not ...
7 votes
1 answer
778 views

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 ...
4 votes
1 answer
564 views

Why choose strawberries for DNA extraction?

The NileRed video What is DNA and what does it taste like? | Edible Chem shows the extraction of a surprisingly large amount of DNA from some strawberries. At 02:22 ...
2 votes
1 answer
789 views

Raphide toxicity in Pothos plant

Recently I found out that the common houseplant Pothos (Epipremnum aureum) is toxic to cats and dogs due to the presence of "insoluble raphides." I have a lot of these plants around my house and my ...
7 votes
2 answers
571 views

Bacteria trapped in crystal inclusions found 'alive' after 50,000 years - what were they eating all that time?

The phys.org article Biologists find weird cave life that may be 50,000 years old describes the announcement by NASA Astrobiology Institute director Penelope Boston at the 2017 AAAS meeting$^{(1)}$ of ...
1 vote
1 answer
805 views

Effect of pH, temperature and enzyme concentration on Km

I understand that enzyme concentration doesn't affect Km since the Michaelis–Menten equation is based on the steady state approximation which requires high levels of substrate compared to enzyme (that'...
3 votes
0 answers
67 views

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 ...
1 vote
0 answers
43 views

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 ...
0 votes
0 answers
16 views

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 ...
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 ...
15 votes
3 answers
761 views

Are there any plants that fix their own nitrogen?

I know that most nitrogen is fixed through industrial processes and bacterial symbiotic relationships. However, are there any plants that can fix their own atmospheric nitrogen?
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?
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 ...
1 vote
1 answer
56 views

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 ...
1 vote
0 answers
230 views

Can mold grow on copper pipes? [closed]

Couple months ago noticed something was literally, for lack of a better term, eating paint off of lead pipes. And I noticed joints in copper pipe seemed to be "leaking" flux. Now all the water in my ...
4 votes
0 answers
82 views

Why can polar molecules like water pass aquaporin better than unpolar like H2 or CO2

We learned in our lecutre, that aquaporin lets Water pass, but blocks Ions like H+ and unpolar molecules like CO2 and H2. The reasons for the Ion blocking are comprehensible, but I dont get, why less-...
1 vote
0 answers
62 views

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 ...
4 votes
0 answers
66 views

Is blood typing still useful for analysis of ancient tissues?

Modern techniques. In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be extracted ...
11 votes
4 answers
1k views

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 ...
2 votes
1 answer
40 views

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 ...
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 ...
1 vote
0 answers
23 views

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. ...
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 ...
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 ...
0 votes
0 answers
20 views

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 ...
6 votes
1 answer
154 views

Different enzymes catalyzing the same reaction but in opposite directions

Nelson, D. L., & Cox, M. M. (2017). Principles of Biochemistry 7e. W. H. Freeman. 13.3: Phosphoryl Group Transfers and ATP: Inorganic Polyphosphate Is a Potential Phosphoryl Group Donor. (This ...
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 ...
7 votes
1 answer
417 views

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 ...
1 vote
0 answers
25 views

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-...
-2 votes
1 answer
1k views

What is ATP and why is it said to be a source of energy? [closed]

Is ATP a molecule or a kind of energy. When I studied the active transport, it's said the ATP would release energy to change the carrier protein shape. So confused. Thanks for your help.
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 ...
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?
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,...
3 votes
2 answers
300 views

How should I measure the oxygen dispersed during photosynthesis in pondweeds?

I am to conduct a lab investigating how different wavelengths of light affects photosynthesis in Egeria pondweeds. The idea is to put color filters on light bulbs and shine them on the pondweed in a ...
2 votes
1 answer
115 views

Sucrose inhibits onion root mitosis? Why?

I am doing an experiment about the growth of onion roots. I put onion plants in different solutions of sucrose in water — 0.1M, 0.2M, 0.3M, 0.4M, 0.5M — with the root touching the water. Measurements ...
0 votes
1 answer
51 views

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 ...
5 votes
2 answers
2k views

What is the purpose of DMT in plants?

N,N-Dimethyltryptamine (DMT) is found, besides humans and other animals, in many plants(50+). In humans (in the pineal gland) it is suggested that it is used for our immune system. ...
0 votes
0 answers
13 views

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? ...
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 ...
5 votes
2 answers
543 views

About the definition of ketogenic amino acid

I am studying biochemistry and have been looking at metabolic network diagrams showing the different intermediates of glycolysis and the citric acid cycle that amino acids can be converted to. I have ...
-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 ...

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