Questions tagged [biochemistry]

This tag is for questions concerning biochemical methods (e.g. electrophoresis) or those concerning biochemical mechanisms or research. Do not use this tag if your question is merely about compounds often used in areas related to biochemistry or associated with these. These may fall under organic chemistry or the appropriate compound’s functional groups’ tags.

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56 views

Identify “decoupling sites” in glucose oxydase reaction

Given the following coupled reactions: $$\ce{glucose + O2 + H2O + glucose~oxydase -> gluconic~acid + H2O2}$$ $$\ce{H2O2 + TMB(star) -> TMB}$$ Identify: A potential reagent or ...
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171 views

What is the Chemistry behind “good” and “bad” cholesterol & their relation to Cis/Trans fatty acids?

I have searched Google for this but cannot seem to find an explanation. My question is as follows - what is the Chemistry/Biochemistry behind cis and trans fatty acids resulting in "Bad" LDL and "Good"...
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358 views

Delta G values for Pyruvate--> Alanine vs. Oxaloacetate -> Aspartate ->Asparagine

What are the delta G values for the mammalian (human) biosynthesis of alanine from pyruvate, and for the conversion of oxaloacetate to asparagine? (assuming no particular cellular restriction or other ...
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90 views

Enzyme Assay - pectinase

I am working on Enzyme Assay.I assayed the enzyme in different buffers from $pH\ 1-12.5$ However,the enzyme has good activities starting from $pH\ 1-10.5$ Is that possible to have enzyme activity in ...
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78 views

Mercury binding agents which cross the blood brain barrier

The two substances I have come across are cilantro and lipoic acid. How effective would either of them be? Are there any other agents known which produce the desired results?
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220 views

Can TBE electrophoresis buffer be stored in a PETE container?

I'm doing a science project on agarose gel electrophoresis and would like to know if it is safe to store Tris/Borate/EDTA buffer solution inside a PETE container since I will be making about 10L of ...
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70 views

Determine max of 2 parameter functions

I have 12 experimental tables with OD(substrate concentration, time), where OD is optical density and one table with $\mu$ (substrate), where $\mu$ is growth speed. OD and $\mu$ are functions. The ...
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15 views

Hydrolysis of phosphoryl-oximes

When acetylcholinesterase that has been inhibited by an organophosphorus compound is reactivated by an oxime, a phosphoryl-oxime is formed, which is then somehow hydrolyzed in the blood. One study ...
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54 views

Finding the sensitivity of zero-order ultra sensitivity and its parameter dependence

I am provided a one-dimensional reaction system showing zero-order ultra sensitivity. $$\ce{X_1 ->[f_1] X_2}, \quad \quad \quad \ce{X_2 ->[f_2] X_1}$$ The reaction rate function is the reduced ...
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26 views

How is presupposition of the order of reaction justified in Michaelis-Menten model?

from what I have understood, to derive Michaelis-Menten equation, we first suppose that $\ce{E + S <=>[k_1][k_{-1}] ES->[k_2]E + P }$ and make the 'steady-state assumption', that $k_1[E][S]=...
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12 views

Collagen digestion

As far as I know, pepsin is used very often in collagen solutions extraction. Since it only cleaves the telopeptides and leaves the triple helix chains of the collagen intact. I was wondering if there ...
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24 views

When and how do mineral chelates separate in the body?

If one consumes an amino acid chelate such as iron bisglycinate, it is generally absorbed intact as far as I am aware. At some point, presumably the iron could be used for say hemoglobin synthesis and ...
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43 views

Why is Cadmium so carcinogenic compared to other heavy metals?

This free article as well as this article do a good job highlighting the carcinogenic effects of Cadmium and the mechanisms by which they occur. However, my question is why is Cadmium so carcinogenic ...
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10 views

In vivo, does it take energy to move double bonds from cis to trans long chain unsaturated fatty acids

In vitro, long chain fatty acids may yield more energy when bonds break, but in vivo, I understood that energy is burned before unsaturated fatty acids can be oxidized because the side groups with ...
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22 views

Pyridinium ion in inositol nicotinate

I have read about inositol nicotinate which is used as a medication for deficiency in vitamin B-3. I think that if acetic acid was applied to this medication it would form pyridinium ion and acetate ...
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28 views

How to convert pepsin into powder form?

I have pepsin powder which is now hydrated due to humidity. I want to convert it back to the powder form. How to do it? I don't have access to a freeze-dryer . I prefer any cheap procedure other than ...
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28 views

Selective Esterification of Amino Acid

I am going to prepare tert-butyl protected threonine. I was going for the classic esterification methodology which is acid catalyzed (sulfuric acid) esterification under reflux of tert butyl alcohol + ...
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33 views

Protein purification pressure limits confusion, about the X-MPa limit for FPLC?

I have always been a bit confused about column pressure limits. I have to elaborate a bit on the problem to get to my question: In protein purification we use the äkta purification machines (e.g. ...
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35 views

Which Flocculant/Coagulant is ideal for harvesting Algae?

While dealing with Algae fit for human consumption (as protein supplements), which is the most suitable coagulant/Flocculant available? Factors to consider: 1) Cost Effectiveness (for instance poly ...
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58 views

How to recreate bioluminescence in fireflies in a lab?

I have several mg/mL of D-luciferin, luciferase (firefly), ATP solution (25 mmol) and MgSO4 (for the mg2+ ions). The experiment has to be done in cuvettes of 2,5 mL (if I get any results, it will be ...
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15 views

Lipophilicity computational prediction

Is there a web based (or otherwise) computational chemistry tool which is able to calculate lipophilicity of a given compound?
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42 views

Mobility of Cations in the Environment

I have recently performed an experiment in which I tested the affects of phytotoxic cations on the rate of germination of the common navy bean. I did this out of curiosity, as I have recently been ...
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178 views

What is the purpose of tetrazole in oligonucleotide synthesis?

The ATDBio book on nucleic acids describes tetrazole as an activator required to couple nucleotides. The diisopropylamino group of the nucleoside phosphoramidite is protonated by the activator, ...
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201 views

redox signaling molecules and electrolysis

There is a product whose presentation screams of snake oil, allegedly consisting of nothing but electrically treated salt water. The product is claimed to be chock full of "redox signaling molecules" ...
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131 views

Why does blood turn reddish brown?

Why does blood take on such a colour after a couple of hours? Is this the iron in my blood being oxidised to iron (III) oxide or is this something else? I have checked this article, and no I do not ...
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27 views

Why Fe(III) can't coordinate with O2 in methemoglobin

I know methemoglobin's heme group has a change on its shape, what makes oxygen unable to coordinate, but... What causes that change? Does the electronic structure of $\ce{Fe(III)}$ matter or it's only ...
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57 views

Approaches to cap/modify the terminal 3' OH of DNA polymer

I am looking for a procedure that would cap/protect the 3' hydroxyl of DNA molecules with high efficiency. I have tried to perform a similar step enzymatically using dideoxynucelotide triphosphates ...
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1k views

What is the difference between transaldolase and transketolase in the pentose phosphate pathway?

What is the difference between transaldolase and transketolase in the pentose phosphate pathway? From what I understand, they both catalyze the transfer of carbon chains from 1 aldose into 1 ketose to ...
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162 views

Simulated Body fluid recipe

I'm working on preparing SBF in my school's lab however a couple of components are missing which are $\ce{NaHCO3}$ (0.350 g) and $\ce{K2HPO4}$ (0.228 g) . Is it possible to replace these components ...
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164 views

How pure is this chloroform?

hopefully this question is in the right place. I'm a biologist not a chemist (so sorry if this is a stupid question!)- I'm doing some RNA extractions from brain tissue which requires the use of ...
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110 views

What is the mechanism that dihydrolipoic acid undergoes to be oxidized by FAD?

The mechanism for dihydrolipoic acid oxidation in the pyruvate hydrogenase complex is not clearly demonstrated in any Lehninger textbook, other than the fact that FAD becomes FADH2. I am wondering ...
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236 views

Calculating with Method of Equal-area differentiation

I have been trying to understand this method although I admit, don’t have a very good calculus background just yet. For a given reaction where $x$ is time, $f(x)$ is cell concentration and assuming it ...
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1k views

Why do heavy metals like mercury and lead have an affinity for sulfur or sulfur compounds?

Many of the heavy metals such as mercury, lead, thallium, cadmium, and arsenic exert toxic effects largely by binding to or otherwise interfering with organic sulfur compounds or groups in the body. ...
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102 views

Stability of Fe(II)

How stable is Fe(II) in a solution? I am doing simple photometry with fresh samples and I feel like it doesn't oxidize that quickly, but have to use a stabilizing agent (dihydroxyfumaric acid) ...
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39 views

Comparing magnesium ion sensitivity in ribosomes to sensitivity in double-stranded DNA

I was doing some reading on this, and $\ce{Mg^2+}$ has a much greater sensitivity to ribosomes than to dsDNA (double-stranded DNA). It seems the best answer I can think of it that $\ce{Mg^2+}$ ...
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129 views

How to determine the speed of GLUT1 transporter using Michaelis-Menten kinetics?

I am reviewing a passage in my Lehninger Biochemistry Textbook (6th Edition), and the following passage has me very confused. How can one sentence from this passage claim that when [S]out = Kt, the ...
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706 views

NaOH CO2 trap troubleshooting

I was wondering if anyone could help troubleshoot an experiment I'm working on. I'm running an experiment to measure the microbial respiration of compost samples using a $\ce{NaOH}$ trap. Each ...
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38 views

How to model Chemical Kinetics when both ligand and receptors are moving?

I am not a chemistry student but trying to understand something that requires Chemistry. My problem is that when we have Ligand and receptor reaction to form complex we normally assume as from ...
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270 views

Differentiating random and ordered sequential mechanisms in enzyme kinetics

Can random and ordered sequential mechanisms be descern by Lineweaver-Burk plot? Why or why not? Because for orederd sequential mechanism I got different LB plot depending on which substrate is held ...
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133 views

If Substance A is more soluble in water than Substance B, will Substance A be more easily absorbed by the body?

I am comparing the solubilities of artificial vs natural sweeteners for my Chemistry IB Internal Assessment. I must demonstrate personal engagement, so I am relating my topic to weight management in ...
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124 views

Why aren't there iron bones and eggs in nature?

As far as I know, most of the "hard things" in living creatures composed of calcium (for example, bones plated with calcium over the keratin structure, and eggshells and seashells with $\ce{CaCO3}$). ...
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44 views

Can we create human muscles artificially?

Can chemical processes create sarcomeres? Not the entire cell with mitochondria, just what basically makes the muscle contract, myosin and actin, in the goal of reproducing our muscles. The source of ...
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47 views

Shallenberger Acree example

At the moment I'm writing a paper about sweeteners and want to compare saccharides, polyoles and synthetic sweeteners like cyclamate. I'm having some problems trying to apply the Shallenberger–...
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81 views

What chemicals could be added to human urine to cause harmful chemicals to precipite out?

What chemicals could be added to human urine to render it drinkable with no harmful side effects? Urine is salty and contains other dissolved solids. Thus, drinking untreated urine would result in ...
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23 views

bio-compatible thermoset resin

I am looking for something rather odd and specific. I need a chemical resin that is liquid up to 250 deg. F, Is a thermoset (it cures at temperatures above 250 F), and is biocompatible in that if ...
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726 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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21 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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276 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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137 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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302 views

Comparing pKa of Alpha and Beta Amino Acids

The $\mathrm{p}K_{\mathrm{a}}$ of the functional groups in L-glutamic acid (shown below on the right) from left to right are $4.1$, $9.5$, and $2.1$. Predict the $\mathrm{p}K_{\mathrm{a}}$ values of B-...