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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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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4k 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. ...
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299 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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10k 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? ...
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3answers
126 views

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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316 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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35 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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41 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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399 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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1answer
36 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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87 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 ...
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27 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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90 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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2answers
129 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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2answers
82 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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86 views

Glycerol 3-phosphate nomenclature

Why is Glycerol 3-phosphate named in such way? Shouldn't it be named as Glycerol 1-phosphate by proper IUPAC- nomenclature?
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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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54 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 : ...
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1answer
45 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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1answer
120 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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1answer
232 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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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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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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364 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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76 views

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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2k views

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) ...
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1k views

Is there any advantage of having a mitochondria for aerobic respiration?

If we consider the pathway of breakdown of glucose which includes glycolysis, the citric acid cycle and the electron transport chain, all these processes takes place in some prokaryotes and ...
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1answer
612 views

How to calculate or know by experiment the entropy of enzymes or protein?

How do you calculate or experimentally determine the entropy of enzymes or protein? In particular, I am interested in Boltzmann and conformational entropy, and Gibbs free energy. Any references are ...
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2k views

Why is allolactose the LacI inducer?

For what reason(s) is allolactose, instead of lactose, the "natural" inducer of lac operon repressor?
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143 views

Electron transport in granal stacks

See paper for distribution of PS-I and PS-II within grana As explained in the above paper, the PS-I complex is primarily located within non-appressed thylakoid region and stroma lamella, while PS-II ...
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1answer
50 views

Are CoA and CoAS the same thing in a compound?

Is CoA-S-R the same as CoA-R, and is CH3C(=O)CoA the same as CH3C(=O)SCoA? Eg. Above is the compound on the right just coenzyme A or is it actually another compound and not just notation?
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222 views

Does precipitation influence the UV spec reading?

I have been checking my sample for Hydroxyl radical scavenging activity. I have dissolved Hydrogen peroxide in Phosphate buffer. My sample is clear and reagent is also clear but when I have mixed my ...
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355 views

What is the biochemical reason for mental fatigue?

Is it known exactly why the brain needs sleep? What's dropping low / going high when we experience mental fatigue? I can see why low glucose could result in mental fatigue, are other reasons known?
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329 views

What happens to colloidal particles in a liquid medium? And how to stabilize it?

Definition Colloid is a dispresion of small particles of one material in another. Definition 2 (Wikipedia) A colloidal system consists of two separate phases: a ...
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47 views

Why does protein kinase C activated by different means have different effects?

I could be way off base but I think I remember learning that Protein Kinase C has some effects when activated by one pathway and other effects when activated by another. How does this happen? Is it ...
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29 views

Advantage of GCPRs over RTKs or other receptor protein kinases

My book lists two important differences between GCPRs and receptor protein kinases: GCPRs do not directly activate a signal transduction pathway. It only does so indirectly, via a G protein. On the ...
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1answer
1k views

What is the role of glycine in the running buffer for SDS-polyacrylamide gel electrophoresis

We used pH6.8 in stacking and pH8.8 in resolving gel. In the class, the professor explained that the glycine change is like: ...
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1answer
50 views

Chemosynthesis in Bacteria

The light reactions, if seen as a whole, are basically the oxidation of water to provide energy (ATP) to fuel the Calvin Cycle. The photons provide the activation energy for the same. How then can ...
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1answer
65 views

All-trans-retinal being converted back to 11-cis-retinal or vitamin A

There are two pathways all-trans-retinal can take after detaching from the scotopsin: (1) it can convert back to 11-cis-retinal, or (2) it can convert to all-trans-retinol (form of vitamin A), which ...
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206 views

Anomalous base pairing of nucleotide tautomers

What tautomers base pair with what bases? I know that adenine pairs with thymine and guanine pairs with cytosine normally. My question is what does the imino form of adenine base pair with? Regular ...
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1answer
50 views

Where does the inverse seconds unit come from in the association constant?

I'm working to determine Kd(s) kinetically by generating association and disassociation curves. Kon (association constant, or on-rate) is in inverse seconds multiplied by inverse molar. I get that ...
2
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1answer
68 views

Fibronectin glass surface adsorption

Short summary I'm having a glass surfaces and I want to adsorb proteins onto them. I have no problem, when I first adsorb fibronectin (human) onto some areas and afterwards any other protein. The ...
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1answer
90 views

What happens when we eat excess fat?

The fats in our body are stored in fat cells. When we over eat fats does the size of our fat cells increase, are more fat cells generated, or do we "throw out" excess fat?
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1answer
78 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, ...
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1answer
40 views

Question regarding an Escherichia coli reaction

With respect to this link http://www.biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=RXN-14479 Here the enzyme is mentioned and the two reacting compounds. Now , my question is 1. When these ...
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1answer
70 views

Are more molecules of ADP than inorganic phosphate returned to the light reaction in photosynthesis?

During the dark reaction, 9 molecules of ATP are consumed for every 3 carbon dioxide molecules, yet only 6 molecules of inorganic phosphate ultimately leave the cycle. Does that mean that there is a ...
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53 views

Why are 2 electrons transported from photosystem II at the same time?

I only know that electrons are captured by the primary electron acceptor and then go through the electron transport chain, ultimately ending up at photosystem I. But why do 2 leave photosystem II in ...
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53 views

What does it mean when a protein has a different excitation spectra than wildtype, but the same emission spectra?

We have a GFP mutant that displays a different excitation spectra with emission at 510nm than the WT. However, their emission profiles with excitation at 490nm are the same, and we do not observe the ...