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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100 views

Is there a short-term, very strong anesthetic, which can be blocked/delayed by other substances?

Question migrated from World Building SE. (For fictional use only, of course :) ) I am looking for an anasthetic which fulfills the following criteria: very strong effect, induces a comatose state ...
1
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0answers
14 views

Can Nanodiscs be used to study membrane energetics?

Nanodiscs have changed they way we can study the structures, insertion, and functions of transmembrane proteins. Below is an image of a nanodisc bilayer. The key difference, as far as I can tell, ...
6
votes
1answer
41 views

Why do humans require vitamin B12 supplementation while herbivores do not?

This question came about from reading the comments of this (very unclear) question, which the author did not properly clarify. Vegans are often recommended to take vitamin B12 supplements, as the ...
0
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0answers
30 views

About the small intestine's Vitamin K absorption and large intestine's Vitamin K absorption [on hold]

Why in the small intestine does Vitamin K absorb to the lymph, while in the large intestine it absorbs to the blood?
4
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2answers
99 views

How does decreasing surface tension of lipids help to emulsify them?

According to my chemistry book, water has higher surface tension than lipids. But in my biology book it is written that "the gall forms an emulsion of water and lipids by lowering the lipid's surface ...
5
votes
2answers
29 views

Need some good resources to learn about Protein function and structure

I'm taking a course on biochemistry at edx. Since I'm a computer science student, I'm having some trouble in understanding many biochemical concepts. While the first module was just fine, I found the ...
6
votes
1answer
54 views

What is the biochemical explanation for tingling and burning sensation in brain due to certain food?

Consumption of mustard (spicy English Mustard), wasabi and horseradish based food dressings usually result in a burning, tingling or freezing sensation in the brain/scalp and nostrils as the vapour ...
1
vote
1answer
52 views

Why does my anti-ubiquitin antibody visualization not work on my PAGE gel?

I am using 2D gel electrophoresis to visualize polyubiquitinated proteins. However, while I can see actin and heat shock protein using when appropriate antibodies, I cannot visualize them using ...
3
votes
2answers
251 views

What does this equation about DNA replication mean?

Could someone help me understand this equation please? I found it in a paper which said that it was DNA replication, but why? $\ce{dNTP + dNMP_{n} -> dNMP_{n +1} + PPi}$ I found that dNTP means ...
2
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0answers
21 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. ...
1
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2answers
72 views

Why do many DNA solutions contain additional compounds?

DNA solubility data in only water is scarce. A previous question asked for a quantification of DNA solubility in water. It seemed like it would be easily answerable, however isn't quite that simple ...
3
votes
1answer
83 views

Michaelis-Menten equation type - how it is derived?

Can somebody explain how is the following differential equation found? It is about the blood alcohol content. See this article (pages 3 and 4). They say the concentration of blood alcohol ...
7
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0answers
57 views

What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?

First definition. Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly ...
2
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0answers
64 views

What biological processes can affect the temperature of the shadow a tree casts?

Assuming two trees have similar shape and leaf coverage, could differences in the biological processes among them lead to differences in the temperature of the shadow they cast? What biological ...
0
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0answers
15 views

Is it possible to measure Secondary Bile Acid Kinetics?

Is it possible to measure secondary bile acid kinetic and flux measurements in vivo? Anyone have any experience with this sort of technique?
2
votes
1answer
39 views

How is the subunit molecular weight different from the native molecular weight?

I noticed that the native molecular weight for an enzyme is different from its subunit molecular weight. Why are they different? Aren't the genes needed to express the enzyme the same in the native ...
5
votes
3answers
135 views

How can a ligand be an integral membrane protein?

My background is in mathematics, and not biology, so please bear with me. I am currently working on a project involving the effects of Epidermal growth factor treatment (EGF) on cell migration. I am ...
3
votes
0answers
31 views

Can I leave BL21(DE3) cells in room temperature?

I am preparing competent cells, and I finished inoculating a single colony in SOB. It has been incubating at 37 degrees Celsius for almost 16 hours since, and it's getting very late where I live. I ...
4
votes
1answer
52 views

Which are mobile and immobile elements in plants?

I am confused with this element or nutrient classification in the plants, since some authors set elements like $\ce{S}$ and $\ce{Ni}$ as mobile and other as immobile elements (Citation 1, 2, 3, 4, 5). ...
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0answers
18 views

Help with STRING database

How can I generate a graph on the STRING web server for physical interacting proteins only? I know we could extract the data and use Cytoscape to create a graph, but I would prefer to have a graph ...
1
vote
1answer
44 views

Background correction when reading ELISA with TMB substrate

I'm doing some ELISA development, and I'd like some justification/best practices for background correction. I'm using a horseradish-peroxidase (HRP) detection system along with a TMB substrate and an ...
1
vote
0answers
18 views

Would it be possible to regulate proper phosphorylation so the UPR wouldn't initiate a reactionary cell death in important cells?

In studying the correlation of folded versus unfolded proteins and their impact on neuro-degeneration, it looks like improper phosphorylation in the chaperones (at least, in part) causes the ...
1
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0answers
17 views

aluminum sulfate vs (NH4)2SO4 in Colloidal Coomassie Staining Sol

I have been interested in Colloidal Coomassie Staining to detect proteins in PAGE gel. I found 2 different recipes: one of them uses aluminium sulfate, the other, (NH4)2SO4. I am wondering about ...
2
votes
1answer
46 views

How to calculate the Jaccard index [closed]

I want to calculate the Jaccard index between two compounds. What is the algorithm? I have searched for it, it just gives the formula but how to apply it on compounds is not known to me. Can you help? ...
5
votes
1answer
32 views

Is there a protocol for freezing and thawing Bacillus subtilis cells?

There is a book that says to store Bacillus spores in 50% glycerol at -70 degrees Celsius (doesn't mention if the 50% is final concentration or not). But from what I know, the cells themselves can be ...
0
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1answer
45 views

What are these pathways called in Biology?

Considering the pentose phosphate pathway and the sulfate reduction pathway in bacteria; What are these types of reactions called in biology? Bio degradation reactions or bio transformation reactions ...
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0answers
7 views

What is isomeric threshold and isomeric count?

Found the terms isomeric point and isomeric threshold in the following paper: http://lib.gen.in/ocean/9064caa3202a71977f338ecb430280a7/10.1007%40s12539-012-0119-8.pdf It siad that the isomeric point ...
0
votes
1answer
24 views

Factors on which one compound transforming to another compound depend [closed]

Considering the Metabolic Pathway: http://www.genome.jp/kegg-bin/show_module?M00166 Consider the reaction R01523(the very first reaction). How is it possible to know that the compound ...
3
votes
1answer
27 views

How exactly is glyceraldehyde 3-Phosphate reverted to ribulose 1,5-bisphosphate for the continuation of the calvin cycle?

Around 6 molecules of G3P is produced at the end of the Calvin Cycle (light independent reactions of photosynthesis), and 5 of which are reverted back to RuBp. The general equation that I read is 5 ...
2
votes
1answer
21 views

What is the protein sequence taken as input in the Path-A prediction system

Considering the Path-A based metabolic pathway prediction (http://nar.oxfordjournals.org/content/34/suppl_2/W714.short). It uses machine learning for pathway prediction. Suppose that the input was a ...
6
votes
1answer
69 views

THYROGLOBULIN (19S) comes to a heavier position than ferritin (51S). Why?

Sedimentation values of thyroglobulin and ferritin containing iron are 19S [1] and 51S [2], respectively. But, by density gradient centrifuge, it seems thyroglobulin (19S) migrates faster than ...
1
vote
0answers
91 views

Why do I smell chlorine when my sinuses are clogged? [closed]

I constantly smell chlorine after blowing my nose. I know it has to do with the sodium-chlorine ion channels but I don't know exactly what role they play. Related: I know in the disease "cystic ...
2
votes
0answers
48 views

What effects would be caused by exposure to common life forms with opposite enantiomer biology? [closed]

Pretend a human had their body "reflected": heart on the wrong side, etc.; but also at the biochemical level: proteins, sugars, cells, DNA, everything. What would the effects be of that human's ...
-3
votes
2answers
77 views

What is the difference between electrons and energy? [closed]

I'm studying microbiology right now and I have come across something confusing to me. I thought electrons provided energy to the cell by being incorporated into reducing powers and eventually driving ...
13
votes
1answer
229 views

Solubility of DNA in water

This would seem to be an easy to answer question, but I was unable to find an answer (in g/L) for generic double-stranded DNA or plasmid neither on Google nor on BioNumbers. I would expect the ...
2
votes
1answer
23 views

Question related to L-arginine biosynthesis

With respect to the L-arginine Biosynthesis pathway, the very first reaction converts L-glutamate to N-acetyl L-glutamate. In the linked reaction scheme, why are only L-glutamate and N-acetyl ...
2
votes
1answer
38 views

What does the Gini index mean in a biochemical context?

What is the meaning of the Gini index, as specificed in this link, which describes the Gini index of beta-glucopyranose bound to hexokinase? Is this true that if Gini index has a very low value that ...
4
votes
1answer
35 views

How does loss of the electrochemical gradient result in heat production?

As far as I understand, uncoupling of the flow of protons and ATP-synthase provides a bypass for protons between the outer and the inner membrane of mitochondria so that the protons don't have to go ...
5
votes
1answer
62 views

How does CO₂ concentration affect photosynthesis?

I have heard the theory that with the increase of CO2 in the air, the speed of the photosynthesis would increase, thereby limiting the increase of CO2 levels. What is currently the rate limiting ...
4
votes
1answer
73 views

Questions regarding a particular paper

With respect to the following paper: Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study I have a few questions: in page ...
2
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0answers
23 views

Does blood typing still provide a use for ancient tissue analysis?

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 ...
0
votes
1answer
50 views

What is the difference between polar and charged amino acids?

Chemically polar amino acids have an uneven (AKA polar) distribution of electrons over their surface. Charged amino acids have a charged ion in their structure. This is probably where my knowledge ...
0
votes
1answer
27 views

What is meant by clonal isolates?

With respect to this website: http://horfdb.dfci.harvard.edu/ what does the term clonal isolates mean?
6
votes
1answer
98 views

Why is the brain dependent on glucose?

The strict dependence of the (human) brain on glucose has always been puzzling to me. While ketones can substitute for a portion of the brain's energy needs, it cannot substitute completely: blood ...
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0answers
44 views

Importance of organic chemistry in biochemistry/molecular biology? [closed]

I'm halfway through my biochemistry and molecular biology degree in Australia and i'm concerned about a lack of organic chemistry. My friends studying biochemistry back home in Canada take units upon ...
5
votes
2answers
106 views

Proteins that give color (without fluorescence)

Is there proteins that have strong color, that could be seen without the need of UV and with naked eyes (with white light) - in mammalian cells? Searching for reporter, something like GFP, but that ...
4
votes
2answers
55 views

A doctor might give bicarbonate (HCO₃¯) to a patient who is breathing very rapidly. What is the doctor assuming about the patient’s blood chemistry?

The answer is: The doctor is assuming that the rapid breathing is the body’s response to low blood pH. (Source: Campbell Biology) But this answer doesn't make sense. Why would the doctor give the ...
2
votes
2answers
61 views

Recommend good conversational books to learn about cell and developmental biology or biochemisty?

I'm an engineer by training and teaching myself the basics of cell and developmental biology. I'm using Scott F. Gilbert's Developmental Biology and Alberts' Essential Cell Biology right now, and they ...
6
votes
2answers
105 views

The effect on the efficacy and potency of a non-competetive antagonist binding to the active site of the receptor (dose-response curve)

According to the book "Principles of Pharmacology: The Pathophysiologic Basis of Drug Therapy" by Golan et al, non-competetive antagonists can bind to both the allosteric site and the active site. I ...
0
votes
1answer
41 views

Why in acute phorpyria? [closed]

I am having confusing about treatment of phorpyria . I read it somewhere that for treating phopyria hemin and glucose is given IV . Please give me an easy explanation of it