The scientific study of chemical processes in living organisms, including, but not limited to, living matter.

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Looking for dataset of proteotypic and non-proteotypic peptide

I doing experimentation for peptide prediction using machine learning. I need some data for testing. My background is Computer Science. Any advice how to find proteotypic and non-proteotypic peptides....
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10 views

Coconut oil vs Olive oil: Spray dynamics

Ps: If this would better fit Physics then please move it there or let me know. I put it here based on fact that viscosity and colloids were part of chemistry curriculum 10/15 yrs back in school. Let'...
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24 views

Can sunlight and its heat create a caustic or toxic substance from coconut oil on human skin? [on hold]

I heard that story quite often, if it's true, how does it work? Notice that I’m not talking about using coconut oil as a sunscreen (it’s another topic) but about the action of the sun on the oil and ...
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16 views

Why do Bence-Jones proteins behave differently in urine heat test?

The preliminary test for proteinuria (proteins in urine) is precipitation/turbidity on heat due to denaturation. This turbidity should not disappear when 10% acetic acid is added - to differentiate ...
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19 views

What makes DNA/Protein in a gel run in straight lines?

In a gel electrophoresis, let's assume an SDS-PAGE, I understand that the sample is loaded on a cuboidal well and the electric field is straight downward. It is easy to assume that the sample is going ...
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44 views

Gel electrophoresis separates proteins on the basis of what property?

In SDS-PAGE for separation of proteins, SDS is an ionic detergent that coats the unfolded protein to mask its native charge and give at a uniform charge to length ratio. Since the length of the ...
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1answer
27 views

Can fungi metabolize pluronic polyol f127?

I am looking for a gelling agent that can be used in place of agar, where its carbon must not be bioavailable for fungi. I have read about pluronic polyol f127 as substitute for agar. Can fungi ...
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19 views

name the elements A,B,C,D,E,F,G,H,I [closed]

A,B,C,D,E,F,G,H,I are 9 consecative elements in a periodtable ionization energy 1 of elements E,F,G is E
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1answer
37 views

Why does a larger DNA gel box require a higher voltage to move DNA at the same speed?

If I run a small agarose DNA gel and use a voltage of 90V, the DNA migrates the length of the gel in about an hour. If I use a medium size gel I have to use a voltage of 140V to move the same DNA the ...
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64 views

How does entanglement explain myoglobin's preference for O₂?

I was reading an article about the myoglobin's unusual preference for O2 than CO, in which I found: It turns out that some electrons in the myoglobin involved in binding CO and O2 exhibit a ...
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2answers
29 views

Why is partial pressure used as a metric for oxygen in blood?

I know haemoglobin basically acts as an oxygen buffer. But when we talk about non-bound oxygen in blood (or water), we're referring to the amount of O2 in solution (aqueous state). From a biochemistry ...
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11 views

Electron balance for biomass synthesis

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 (not balanced): $$ \ce{C6H12O6 + ...
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1answer
39 views

Alternative to Hanging Drop Crystallization

Forgive my ignorance if I am way off, but I was having a look at the crystallization of a number of different substances (e.g. proteins) through the hanging drop vapour diffusion method. The examples ...
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1answer
67 views

What is the molecular mechanism behind oncotic pressure?

I can't wrap my head around the idea of oncotic pressure and osmolarity, logically. I imagine a blood vessel. It is filled with proteins, like a ton of proteins and solutes. So this means, according ...
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5 views

Parameter effects on kinetics of esterification for bio-diesel production

I want to discuss the effect of parameters on the kinetics of esterification for bio-diesel production. In esterification process, temperature effect and molar ration are two important parameters. ...
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1answer
37 views

Superoxide dismutase of Mn (SOD) [closed]

I have a little problem with my paper about Mn superoxide dismutase. On this picture we have "B" behind the 3 OH ions, I really don't understand what is this. Where is this "B" from? Please, help me, ...
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13 views

Mechanism of thyroid hormone synthesis: iodation and free radical formation

In the synthesis of thyroid hormone, what part of the thyroid peroxidase hormone is specifically responsible for abstracting the free radicals from the aromatic side chains in the iodated tyrosine ...
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1answer
25 views

Are β-sheets formed from one or more polypeptides?

I know that a β-strand forms bonds with another β-strands and so on and thus a β-sheet is formed, but are those strands from the same polypeptide? And does their distance matter? Do they have to be ...
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1answer
22 views

Chondroitin Sulfate (greater volume in solution than in crystal form)

I've read in a textbook on biophysics that chondroitin sulfate occupies a greater volume in a solution than in crystalline form. Why is that? Is it because of hydrogen bonds in solution that the ...
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19 views

Loooking for dataset of proteotypic and non-proteotypic peptide

I doing experimentation for peptide prediction using machine learning. I need some data for testing. I already have one dataset, but I need another one or two for verification. I'm looking for one a ...
1
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1answer
31 views

How was cholestyramine discovered?

How were the properties of bile acid sequestrants like cholestyramine discovered? The earliest reference to the chemical I could find was the following article which does not discuss the history of ...
2
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1answer
43 views

Dipole and size of a thioether relative to hydrocarbon

I am an enzymologist and I would like to check whether the consensus of how enzymes tell thioethers from hydrocarbons on substrates is a fact or fiction. So are any of these wrong? S–π ...
3
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2answers
102 views

Separating Lipids from Milk

I am trying to develop a procedure to test the percent mass of lipids in (update: homogenized) milk. It doesn't need to be very accurate, just an interesting application of chemical principles. As I ...
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16 views

How to tell when DNA will be positively or negatively supercoiled?

Is there any indication of when DNA will be + or - supercoiled based on the number of base pairs or number of pairs per turn or any other metric?
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0answers
16 views

Glycogen Hydrolase

Can glycogen hydrolase cleave both glycogen and starch bonds? My intuition says yes because they are both a 1-4(6) glycosidic linkages but I bet I am missing something.
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15 views

Effect of a double mutation on the stability of a folded protein?

the question is shown as follows: My reasoning is that the mutation leads to stabilisation of the protein as Tyr121 is a better H-donor than Ser53 therefore stronger H-bonds formed. Also there seems ...
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1answer
39 views

Deriving kinetic equations for a complex reaction system

I have a system of protein reactions that I've derived differential equations for the kinetics of. I'm using them to run simulations to fit the rate parameters, but the simulations at present are ...
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36 views

What is the structural difference between ketogenic amino acids and glucogenic amino acids?

We know some amino acids could go in ketogenosis path way ,some in glucogenic and some in both ..i 'm wondering to know what the differences are between the amino acids the make this situation.
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1answer
37 views

Enzyme Specificity vs Selectivity

Background: I can see a difference in stereoselective and stereospecific reactions in organic chemistry. However, both terms are used interchangeably as synonyms in a biochemistry class. Question: ...
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1answer
942 views

Why/how is blood red? (colours of hemoglobin)

Oxyhaemoglobin is red, deoxyhaemoglobin is bluish-purple, and carboxyhaemoglobin is a cherry red colour. Evidently in the porphyrin around the iron molecule in heme there is a conjugated pi system ...
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1answer
13 views

Does mechanotransduction of cells play a role in the biocompatibility of titanium?

What exactly is mechanotransduction? The definition seems to vary from source to source. Some indicate that mechanotransduction is the underlying principle where cells pull on the surface they grow on ...
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26 views

Microarray SPR imaging vs “regular” SPR?

Background: I am taking a biochemistry course, and we have had some basic introduction to surface plasmon resonance (SPR). I don't have a very strong background in biophysical chemistry. Task: I am ...
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9 views

Thiosulfate from N-acetylcysteine

Can you derive thiisulfate (S2O3 (-2)) from n-acetylcysteine (C5H9NO3S) in a biological system such as the airways? If so, how?
3
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1answer
52 views

l- versus d-glucose

I recently purchased Dextrose from a local bulkfood store. I want to use it instead of table sugar. My concern is that it may be l-glucose instead of d-glucose. According to Wikipedia l-glucose is too ...
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3answers
109 views

Why is the Mg2+ ion preferred over other ions in chlorophyll?

Chlorophyll has a $\ce{Mg^2+}$ ion. Why is it preferred over other ions? I mean, what happens if there is $\ce{Zn^2+}$ or $\ce{Ca^2+}$ or any other cation instead of $\ce{Mg^2+}$?
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24 views

Differences between anionic and cationic surfactant in DNA extraction?

What's the main difference in DNA extraction between using an anionic surfactant (like SDS) or a cationic surfactant (like CTAB)?
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0answers
12 views

Can (2,4-dinitrophenyl)hydrazine be used in osazone test?

For osazone test we use phenylhydrazine but what difference it would make if we replace it by its derivative (2,4-dinitrophenyl)hydrazine and will there be any change in crystal structure of the ...
13
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2answers
199 views

Why does fluorine act as a leaving group in organophosphates?

C-F bond is the strongest single bond in organic chemistry with a bond energy of $\ce{453 kJ\,mol^{-1}}$. And it is very difficult to break this bond and F does not act as a leaving group. However, ...
3
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18 views

Measuring reaction rates when reactants and products both have (different) molar extinctions at the chosen wavelenghth

In my Biochem labs we would always measure the consumption of NADH, and they always noted that it was useful that NAD+ had essentially no absorbance at 340 nm, which allowed us to directly relate ...
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1answer
24 views

Why is the effect of competitive antagonist less than the effect of non-competetive antagonists?

Drugs can be provided as a competive or non-competitive form of agonists. But the effect of non-competitive antagonists is much more than the other, so what is the cause of that? And are there some ...
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24 views

Molecular mechanism describing the action of serotonin [closed]

I am doing an assignment of serotonin and i was wondering if you could explain how serotonin's molecular structure gives it its favorable properties. I have done so much research on the molecular but ...
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0answers
21 views

Molecular mechanism behind the action of neurotransmitter Citalopram [closed]

What parts of the neurotransmitter Citalopram (which blocks the reuptake channels of Serotonin) on a molecular level enable it to do its job. the chemistry behind it for a grade 12 chemistry ...
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0answers
18 views

Proteolytic enzyme assay using casein as the substrate

To determine the proteolitic activity of an enzyme, the enzyme assay can be used using the casein as the substrate. In the laboratory can I use a fresh milk sample instead of casein?
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1answer
27 views

What is the chemistry behind heat produced when blood is bleached?

When I discard blood (20-40 mL) in a beaker containing bleach (400mL), I can feel that heat is produced in the beaker. What is the chemistry behind it? Will heat be produced due to Lysis of haem ...
2
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1answer
65 views

Why can't electrons be transferred using hydrogen ions?

I have a homework question that asks: Recognizing how oxidation and reduction occurs is essential for analyzing and understanding biochemical reactions. Which of the following methods would NOT ...
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0answers
24 views

How to calculate molar concentration of phenol red when mixed with water and a buffer?

The concentration of phenol red is 1E-4 M. The initial volume used was .1 mL and is then mixed with .9 mL of water and 4.0 mL of a .1M borate buffer of pH 9.8. I used a simple M1V1 = M2V2. Where M1 = ...
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0answers
19 views

Lookup for transporter locations in human organisms [closed]

I am scared that this question is a bit naive and probably even wrongly placed here... However, I'll give it a try and hope for the best :) I am interested in several transporters and cotransporters (...
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1answer
29 views

Difference between biosynthesis in organism versus lab

Are there different terms for biosynthesis of a compound naturally in an organism versus the biosynthesis using chemicals in the laboratory or is it just "biosynthesis"?
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1answer
132 views

Relation between Gibbs energy and net reaction rate

I have come across some papers in biochemistry that seem to claim that a reaction can be "near equilibrium" even though the flux through the reaction (net reaction rate) is large. For example, this ...
3
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1answer
163 views

Find the number of water molecules “embedded” in sucrose

Recently I got a question as follows: How many molecules of water are joined with 12 atoms of carbon in a molecule of sucrose ? (A) 12 (B) 11 (C) 6 (D) 10 I am unable to ...