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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Why does Glutamine have the symbol Q?

Spent a half hour googling this and the best I could find was this: Now for some rhymes: Arginine = R. R we having fun yet? Asparagine = N The kNights of Ne say "Ne". Glutamine is a cute ...
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231 views

Why is funnel web spider venom so lethal to humans and not so much for other mammals?

According to the information from this article, People and other primates are exquisitely sensitive to funnel web venom but, intriguingly, other mammals such as mice, rabbits, guineapigs, dogs ...
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3answers
307 views

Why do neurones use chemical signalling at synaptic junctions?

Problem. When a neurone fires, it sends an electrical signal that jumps down the axon via the nodes of Ranvier very rapidly. At a synaptic junction, chemical brownian diffusion signalling with ...
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2answers
291 views

Can any one reaction in a cell be at equilibrium?

I know that metabolism as a whole can never be at equilibrium (otherwise the cell is dead !) but I wonder whether a few reactions in the cell could be at chemical equilibrium at a given point of ...
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336 views

What is DNA binding domain? It is not clear what the domain means

I am confused about the term DNA binding domain. Does it mean that there are some parts of the DNA that tends to coil up? Does it happen because some proteins tend to stick around that area? Also it ...
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20 views

Function of heparin and dextran sulfate for removing proteins

From this article : The reaction was terminated and the histones, and most nonhistones, were removed by adding the nuclease-treated chromosomes to a solution containing dextran sulfate (2 ...
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1answer
161 views

Can replication occur if DNA is methylated?

Can a methylated strand of DNA be replicated without removing methylation? Does it make any difference if the strand is methylated or not (during replication)?
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1answer
37 views

Significance of lipids in biological membranes…?

Membranes are specifically designed by lipids to maintain internal hydrophilic environment in narrow range.There are hydrophobic amino acids among naturally occurring 20 amino acids and as well as ...
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1answer
141 views

Negative feedback in the fructose metabolism in liver

What happens in liver when large amount of fructose is consumed? I vaguely remember my biochemistry lecturer telling us that the enzymes that process fructose in the liver does not have negative ...
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1answer
980 views

What are the units of Q10 (temperature sensitivity)?

Q10 is the increase in a rate (e.g. activity of an enzyme) observed with a 10 degree temperature increase. According to Wikipedia: It is apparent that the units of R (e.g. mol/g/s) cancel out, ...
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270 views

Does caffeine increase the speed at which sperm travels?

I'm not even sure if this claim is true, but... This source states that Caffeine gives both types of sperm a boost, but the Y-sperm would get a little more of a boost. This article reinforces ...
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266 views

Troubleshooting bioconjugates migration in a SDS-PAGE gel?

We do a lot of bioconjugation chemistry (click chemistry in particular but also NHS and Maleimide chemistries). Our method to valid the conjugation reactions have been to use SDS-PAGE gels followed ...
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1answer
176 views

Is there an optimal composition and length for protein linkers in FRET?

I'm designing a protein that I'd like to use in FRET reporting. General idea on the shape is: FRETprotein1--Linker--CleavageSite--Linker--FRETprotein2. I would like to know what AA are best for the ...
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87 views

Are similar smells usually based on similar chemicals?

Building off of this question: Why does freshly cut grass smell like a watermelon?, is it usually the case that things that we perceive as having similar smells are, in fact, the same or a similar ...
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1answer
125 views

What molecular processes are involved in pseudopodial extension?

I am curious as to the processes and mechanisms involved in the extension of pseudopodia in amoeba. How does the cell know and control the direction and extent of pseudopodia formation at a molecular ...
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2answers
148 views

What software is there available for Quantitative structure–activity relationship (QSAR) pharmacological studies?

QSAR modelling in pharmacology basically hangs on using mathematical modelling to approximate the effects different molecules will have on various pharmacological targets. I would like to know what ...
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1answer
109 views

Can compounds be predicted from Polyketide synthases gene clusters?

I've seen a few talks on the subject. From a gene cluster, there is some decent ability to determine which domains contribute to certain functional groups in the final metabolites. It sounds like this ...
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1answer
235 views

Ammonium sulphate precipitation assay pH dependence

In general does the pH effect the precipitation, e.g. would a pH of 6 cause less precipitation than pH 7.5. Or are they unrelated?
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1answer
470 views

How does blue white screening work in selecting E coli that have taken up a plasmid vector?

The plasmid vector I am referring to is pCR 2.1 - TOPO. I added the vector to the E coli and plated them up onto LB+amp+X-gal plate, then incubated. After incubation the plates had two types of ...
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1k views

Simple diffusion of lipid-soluble molecules through phospholipid bilayer — does anything get “stuck” in transit?

It's a pretty elementary concept, and when I first learned of it I don't think I had the foundations to even think of such a question, but I found myself the other day thinking about the amphipathic ...
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1answer
198 views

How do multiple replication forks function without 'colliding', and what is the benefit of this method?

I'm currently reading a little about DNA replication, and have come accross the following statement; Replication starts from a fixed point and is bi-directional ... In Eukaryotes, there are ...
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1answer
46 views

How can you improve solubility of colloidally dispersed substances?

If you solve collidally dispersed substances then the particles can form large colloids. This may block narrow passages and diffusion into dense structures may become completely impossible. What can ...
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2answers
39 views

Why do humans circulate monosaccharides instead of disaccharides as in plants?

Plants transport food mostly in the form of disaccharides like sucrose but humans transport them in the form of a monosaccharide - glucose. What is the reason behind this ?
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62 views

Classification of glycosidic anomeric bonds (alpha vs. beta)

In the process of studying for my upcoming biochemistry exam, I have stumbled over the classification of glycosidic bonds. I want to be able to distinguish $\alpha$- from $\beta$-glycosidic bonds. ...
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39 views

Common Ancestry of ETCs and ATP Synthase complexes

Rickettsiales are widely regarded as the ancestor of eukaryotic mitochondria through endosymbiosis. Cyanobacteria are widely regarded as the ancestor of eukaryotic chloroplasts through endosymbiosis. ...
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84 views

Which hydroxyl from either the phosphate or the glycerol is taken during synthesis of a phospholipid head?

The oxygen anion in the phosphate group is likely to be bonded with a hydrogen cation and thus forming a hydroxyl. When the phosphate group is condensed with glycerol to make a phospholipid, is the ...
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100 views

Are there any methods to quantify H2O2 (hydrogen peroxide) which don't rely on horseradish peroxidase?

I can't use HRP since my substrates interfere with it and I need a real-time method because I want to measure kinetic parameters of some oxidases.
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55 views

What is the translation termination efficiency in mammalian cells?

When I express proteins in bacteria I put at least two stop codons at the end of the gene to increase the termination efficiency. Is this the case in eukaryotic cells too? If I put a single stop codon ...
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39 views

enzymes that stabilize DNA loops

As a follow-up of a previous question, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops. I have read that cohesin is one of ...
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0answers
34 views

Statistics on energy consumption breakdown per biological functions across organisms?

Are there any statistics available on how much energy organisms use for each biological functions (i.e. something similar to the line of "Bacteria spend X% of energy on information processing, Y% for ...
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32 views

How different are tissue-specific fibroblasts from each other?

I am planning to utilize a new system in our lab, in which I will co-culture cancer cells from different tissues with fibroblasts. I have the option to receive skin-derived primary fibroblasts. I ...
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46 views

Excretion of monovalent and divalent ions in sharks

I have heard that sharks excrete $\ce{Na+}$ and $\ce{Cl-}$ by their gill surfaces but divalent ions like magnesium are excreted through feces. What could be the reason behind this?
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74 views

How do you store membrane proteins?

We're producing some membrane proteins and they aren't amenable to freeze thaws even when we add glycerol. The proteins are solubilized in detergent above the cmc so they should be in micelle form in ...
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19 views

Does Doxylamine have any Influence on the Monoaminergic System?

Does doxylamine have any affects on the monoaminergic system? Specifically I am interested in adrenergic or serotonergic activity but additional information on its dopaminergic activity won't hurt ...
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2answers
134 views

Can a dNTP be built into a RNA strand?

DNA consists of deoxyribonucleotides, RNA consists of ribonucleotides. They differ mainly (apart from the uracil / thymine difference) in the sugar part, the deoxyribose and the ribose. Those two ...
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3answers
417 views

Michaelis-Menten Kinetics: Does measuring apparent Km and Vmax take into account competing reactions?

I am learning about why it is important to measure Km and Vmax for each experimental setup because measuring the "apparent" Km and Vmax includes enzyme inhibitions of which one might not be aware. ...
2
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1answer
33 views

Substitute 25mM dNTPs mix with 10mM dNTPs

I need to make a solution of multiple compounds, one of them is dNTPs. The recipe calls for 20 μl 25 mM dNTPs in a 1250 μL master mix. Unfortunately I do not have it available at that concentration, ...
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3answers
514 views

Histidine aromaticity

I understand that the imidazole ring in histidine is aromatic. I also realize that it retains it's aromaticity when protonated. I am wondering why it is not mentioned at all in basic text books such ...
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1answer
2k views

Melting point of a fatty acid?

What factors determine the melting point of a fatty acid? Chain length The number of methylene group The ionized state of the fatty acid Its degree of saponification Its ability to alter the ...
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3answers
79 views

Is DNA mutation locally energetically stabilizing the DNA molecule

I am no biologist, but as a physicist, a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system, at least locally. So I wonder if any research has been done ...
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1answer
35 views

Structure of biological membranes?

Integral membrane proteins have functional asymmetry i.e. they have two different domains of proteins performing different functions. these proteins have Tyr and Trp amino acid residues at the ...
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1answer
51 views

How is it decided that one drug is better than others by X times?

I read in Tortora and Derrickson that : Enkephelins are 200 times powerful than morphine in their analgesic effects. I wonder how exactly researchers arrive at a number (like 200 here). I also ...
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2answers
251 views

What exothermic reaction distinguishes warm blooded animals?

I would appreciate an answer specifically in the form of an exothermic chemical reaction. Namely, the one primarily responsible for generating heat in warm blooded animals that does not take place in ...
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2answers
121 views

What chemicals can be detected from one's sweat?

This question came to mind after reading this article. The article speaks of inducing sweating to determine by a roundabout fashion the amount of salt therein. I'm no medic but I find myself wondering ...
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1answer
523 views

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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1answer
31 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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1answer
61 views

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. ...
2
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1answer
843 views

Why is FADH2 made instead of NADH in one of the reaction of Krebs cycle?

FADH2 is made in conversion of Succinate to Fumarate. Why is this so ? Why not NADH ?
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Why restriction enzymes cut (usually) at palindromic sequences?

Restriction enzymes usually cut only at palindromic sequences. Is there any specific reason for that ? Is there any advantage for bacteria if it cuts up virus at this type of sequences ?
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2k views

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? ...