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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What is the reaction mechanism of dopamine hydroxylase converting dopamine to norepinephrine?

The reaction is basically shown below. Dopamine hydroxylase is an enzyme, so I'm not sure if we can have a theory based on organic chemistry. On the other hand, maybe there is a theory that involves ...
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77 views

What chemicals/substances exist in green capsicum (peppers) that do not exist in red capsicum?

I have known 3 people in my life that have incredibly adverse reactions (one called it an "allergy" and his symptoms did resemble such) to consuming any form of green pepper (capsicum) but have no ...
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123 views

How to build a trimeric protein structure from monomeric PDB file?

Problem: I have a PDB file, with a monomer, but I would like to show the entire structure - which is trimeric - but I don't understand how to merge/build or combine the monomeric units to its full ...
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257 views

What is a mechanical cue?

I was attending a talk related to neurogenesis. So one professor was asking a question related to biochemical cues and mechanical cues (related to signaling pathways I believe). Cue as far as I ...
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54 views

dAT joining: please define

I came across a reference to dAT joining in my reading of Genentech by Sally Hughes. The technique is described in passing as a technique for joining DNA fragments used around the late sixties to ...
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143 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 ...
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89 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?
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89 views

Does mung bean nuclease cleave a phosphate group when it's chewing off 5' or 3' ssDNA ends?

I'm looking to create blunt ends from sticky ends with mung bean nuclease for subsequent ligation. Does anyone know full mechanism by which mung bean nuclease will do this? In particular after the ...
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114 views

Edman method to identify peptides with Phenylisothiocyanate (PTH)

We all know that in this method the PTH reacts with the first amino acid (aa) from the N-terminal to the peptide and separates from it giving PTH-aa so that we can know the amino acids sequence in the ...
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73 views

Can drinking caffeine, alcohol and other diuretics be part of a good drinking regime?

Tea, Coffee, Beer, Coke etc… I wonder if the benefit from amount of fluid we get from them is bigger or smaller then the handicap of dehydration. In other words it is worth to drink them if we want ...
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Making the sense of enzyme Km comparisons

I have encountered comparisons of the Michaelis-menton constant (Km) a few times. Generally speaking if Km of an enzyme is higher, then it's affinity to its substrate is lower. How does this make ...
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781 views

Why would an Eadie-Hofstee Plot be non-linear? [closed]

Besides cooperativity between multiple active sites on an enzyme, what are the other reasons for the Eadie-Hofstee plot to be non-linear?
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90 views

Help me understand my membrane potential assignment

Epithelial with the ability to transport NaCl is bathed in an isotonic salt solution with these values (in mM): 136 Na, 6 K, 140 Cl. The intracellular concentrations are: 45 Na, 100 K, 13 Cl. The ...
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857 views

What are the ways to test for protein in the canine urine?

I know that one way is to use the reagent sticks and the refractometer, but this is inaccurate. Is protein distinguishable when using a microscope? Is it time sensitive(i.e. have to test it right away)...
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28 views

epitope prediction/ mapping

B-CELL EPITOPE PREDICTION Regarding this article: "Such a molecule can be synthesized or, in case of a protein, its gene can be cloned into an expression vector."----- is a particular line in ...
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156 views

Bohr effect in respiration

Would I be correct in saying that the Bohr effect is ONLY related to the concentration of [H+] in the tissues. Obviously the concentration of carbon-dioxide can contribute to this concentration by ...
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264 views

naturally occuring fatty acids

The double bonds in naturally occurring fatty acids present in our body are in cis configuration while the enzymes for beta oxidation can act on trans double bond. Then what will be the significance ...
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108 views

H O N C alternatives for organic life?

Most organic structures built from hydrogen, oxygen, nitrogen and carbon. They are represent 1-,2-,3-,4- bond relations (chemical valence) which allow to build variety of chain structures. Are there ...
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65 views

Measurement of glucose concentration in the human brain

If I want to measure the exact glucose concentration in a human brain then how can I proceed to do that? Is there any technique or assay to do that?
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77 views

Why doesn't the avocado turn brown when it is kept with its seed?

Why doesn't the avocado turn brown when its kept with its seed? What does the seed release that slows down the oxidation process?
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955 views

What can cause the bloating in high protein diet of Whey proteins?

I am thinking what can cause the swelling of gastrointestinal system i.e. bloating after high protein diet of Whey proteins. Liver does breaks those proteins to branched chain amino acids (BCAA), ...
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83 views

Quorum Sensing in Vibrio cholerae

This is a figure summarising the quorum sensing mechanism in Vibrio cholerae. In this video by Bonnie Bassler, she explains how quorum sensing can be targeted to control infections. At 15:09 she ...
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Isopropanol precipitation of DNA - duration and magnitude of cold storage

DNA prep protocols often include a final precipitation step with alcohol, often isopropanol, where the DNA must be kept in the alcohol, at a low temperature such as -20C or -70C, often overnight. ...
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320 views

DNA ligase mechanism

I am unable to understand what happens to the phosphates from ATP. What are they used for ?Charging 3' end or 5'end ?
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Why is the function of lacA (encoding thiogalactoside transacetylase) not clearly understood?

It's almost half a century since the lac operon was discovered but isn't it weird that the precise role of transacetylase isn't clearly understood ? Here a wikipedia article with a link to a journal ...
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Can the excessive consumption of mineral water lead to kidney stones or other health issues?

I heard that drinking too much mineral (bottled) water could lead to problems such as kidney stones because of the high amount of minerals in it. Is it true? If so, what is considered to be excessive?
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What biochemical molecule viewer allows for changes in amino acids and resulting tertiary structure?

I am familiar with the Jmol, Rasmol and PyMoL softwares, and was recently introduced to BioBlender. However, I am completely unaware if any of these programs (or others) are capable of loading a .pdb ...
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341 views

Does the Urea Cycle exist in invertebrates?

Do invertebrates (like Drosophila and C.elegans) have a urea cycle?
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62 views

Diet of free-range herbivores

Giving minimal credence to estimates in popular media of the average biomass of insects/arachnids, etc. in an acre of land, it seems that a "free-range" cow (I don't mean to pick on cows) might be ...
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1answer
65 views

Electron balance for biomass synthesis: is my professor right?

I'm studying for my exam and I came across these notes written by the professor himself. He's talking about the general reaction of biomass production in a bioreactor: $$\ce{C6H12O6 + NH4+ + O2 -> ...
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1answer
61 views

Optimizing Gel Electrophoresis: Ampere, Volts and Buffer concentrations

I am a master student in biochemistry, and I have used gel electrophoresis many times before. What I want to know is how one should adjust the mA (mAmpere) compared to the voltage and the buffer one ...
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1answer
42 views

Differences among competent cells?

What are the differences among the following competent cells DH5 alpha, Nove blue, and BL21? Why some of them are for cloning and others are for protein expression? Any references where I could find ...
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567 views

How to find the concentration of an enzyme?

I need to know the concentration of pectinase enzyme (sigma aldrich) which has stated 5KU, 5U/mg protein (lowry) and lot result 20U/mg protein in the label of the enzyme bottle. This is all it has ...
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37 views

Finding a reaction from a KEGG map

I have come across a map and a part of it looks like this: Now I have not been able to locate the reaction that converts alpha D-Glucose to Glucono-1,5-lactone but was successfully able to locate ...
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100 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 anti-...
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28 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 ...
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102 views

Does creatine-phosphate (CP) supplementation regenerate NADH?

I have the following facts: It is possible to convert ATP <-> creatine vice-versa. (ref - non scientific) CP supplementation protects against metabolic syndrome. ref1 ref2 Fructose digestion ...
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151 views

How to preserve leaves between sampling (collection) and analysis?

Suppose I spend a day in a forest, collecting different kinds of leaves, which I would like to analyze under a compound microscope. Now, obviously, measures should be taken to preserve the leaves some ...
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89 views

Conversion and storage of glucose to glycogen

Why is excess glucose, synthesized to glycogen, stored only in limited amounts, as compared with lipids/triglycerides that are stored in our body? Why is mature glycogen arranged (polymerized) in 12 ...
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23 views

Relative sweetness

I have noticed that when I eat something sweet, then afterwards, I eat something else that is sweet, the second sweet food is not as sweet as it usually is. I am pretty sure many others have a similar ...
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63 views

Can plants directly use sulfuric acid?

In the explanation of the sulfur cycle, it is often said that sulfur moves from the atmosphere to the ground by acid rain in the form of sulfuric acid. Can plants directly use sulfuric acid to ...
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26 views

Are the cpli and ctli tests time senstive(i.e. is it needed to test right away in order to get accurate results)?

I'm sending the blood samples to a lab and this takes some time until the actual testing. Some information on the tests. TLI : http://www.vcahospitals.com/main/pet-health-information/article/animal-...
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46 views

What is the biding site code recognized by the parts of the spliceosome

Another question about another Youtube video. At 0:50, the splicing process begins to remove the non-coding section of the DNA (intron), so the different parts of the spliceosome attach to the borders ...
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125 views

Mesoporous silica particles as anti cancer drug delivery method

If this question is a little off topic for Biology, I'm sorry. I've recently read a lot about mesoporous silica nanoparticles as a promising drug delivery method. The huge range of customizability of ...
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263 views

Fatty Acid Synthesis

I have a problem in my reasoning on the fatty acid synthesis in the human body. In the synthesis process you have this homodimer. So the synthesis starts with the transfer of a acetyl group from ...
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1answer
35 views

Roles of creatine and bilirubin in foetus circulation

I think they are not inputs from maternal placenta. I think they are the results of foetus metabolism. However, I do not understand it how and where exactly. What are the roles of creatine and ...
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1answer
37 views

Does amylolysis occur in vegetables if stored below 0⁰ Celsius?

Assume that we have a plant, e.g. kale, which is prone to amylolysis if not harvested during a frost period. If it is harvested and put in a household freezer, such that it is frozen solid slowly ...
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406 views

Why is cyanide poisonous?

I know cyanide inhibits complex IV in the electron transport chain, but I don't understand why this makes it so toxic. If cyanide is bound to the complex, can't the electrons just bypass it and ...
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Why is Thermus aquaticus and Taq Pol stable?

What is the molecular basis of the stability of the bacterium Thermus aquaticus and the enzyme Taq Pol it produces ? I have tried googling this but did not get a good answer.
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Excretion of various wastes and water requirement

A common fact is that Ammonia, Urea and Uric acid are the most common excreted metabolites and their removal needs varying amount of water, highest for ammonia (hence suited only for aquatic animals) ...