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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44 views

removing mercury from the brain

I have conducted many searches on this subject with regards to agents which cross the blood brain barrier. I have read about lipoic acid. Is anybody on here aware of any studies or findings which show ...
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Bohr Effect - related to H+ only?

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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415 views

What makes sulfur-containing compounds such good antioxidants?

Many sulfur-containing compounds (like glutathione and cysteine groups) have high antioxidant activity. Why?
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173 views

Psychoactive ingredients in this soap?

Could any ingredients from this product be psychoactive in some people, if the are sensitive to them? https://www.lush.co.uk/products/honey-i-washed-kids I have found the product to be relaxing as ...
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3k views

Units for dissociation constant and relationship to Gibbs Free Energy

How does one "convert" between an equilibrium constant calculated from the Gibbs free energy for a dissociation reaction and experimentally determined dissociation constants? $$ \Delta G^\circ=-RT\...
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411 views

Atomic coordinates for DNA bases as they appear in a B-form or A-form duplex

Where can I find atomic coordinates for guanosine / cytosine / thymine / adenine (either the ribonucleotide or deoxyribonucleotide bases) where the atoms are configured in the manner we would expect ...
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1answer
50 views

Which mutated enzymes act as better drugs than their non-mutated form?

Is there an enzyme which is used as a drug (let it be called version $A$) and a mutated version of it ($M$), where the activity of $M$ was found to be higher than $A$? Any references on such a case ...
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1answer
202 views

Do proteins bind to carbon? If so how?

Can someone explain me whether a protein (like an antibody) would bind to carbon? The carbon arises due to electron beam induced deposition of Polyethylglycol (PEG). The carbon molecules that arise ...
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How do I remove free biotin after biotin-protein conjugation?

I want to quantify a biotin-protein conjugate after chemical biotinylation. After biotinylation, the solution contains both biotinylated protein and free biotin. I intend to use a HABA-avidin biotin ...
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1answer
275 views

What does the adenosine do in ATP?

This is an extremely basic question about biochemistry from someone who doesn't know much about organic chemistry. I'm aware of how organisms store energy ATP and release it by dephosphorylating it ...
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1k views

Greater entropy: an atom or macromolecule?

A question that appeared on my last chemistry exam was : Which of the following has greater entropy A) An atom B) A macromolecule The question doesn't specify anything else(i.e. type/size of ...
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What is the mechanism of monofunctional glycosylase catalysis? [closed]

I am learning about base excision repair mechanisms. I understand the main idea how glycosylases are working, but I am trying to understand this in much more detail. I found a paper where they have ...
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69 views

Quaternary ammonium anti-microbials

Also good against fungi, amoeba, and enveloped viruses,[7] quats are believed to act by disrupting the cell membrane. Quaternary ammonium cleaners have long-alkyl substituent chains. Why is this so? ...
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11k views

Is Chemical Engineering a good pathway to Biomedical Engineering for graduate school? [closed]

I have been thinking about my future goals and I have recently decided to go for Biomedical Engineering. sites recommend to start in Chemical Engineering because its a good pathway for biomedical ...
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797 views

What is the active ingredient in this "stimulant?"

It is an easily defensible argument that this is a medical question rather than a chemistry one, however, I feel that it leans ever so slightly towards chemistry, and so I posted it here. There is a "...
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1answer
236 views

Human Body and RNA/DNA

After research I found that enzymes are responsible for metabolism, specifically catabolism and anabolism. This in turn creates the necessary chemicals in your body. The only question left is: what ...
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23k views

Basic chemistry of the Shinoda test for flavonoids?

In this test, four pieces of magnesium fillings (ribbon) are added to the ethanolic extract followed by a few drops of concentrated hydrochloric acid. A reddish colour indicates the presence of ...
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735 views

What is the oxidation state of Calcium in teeth?

What is the oxidation state of Calcium found in human teeth?
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How do I go about calculating protein concentration to make a set of protein standards for protein quantification via dot blot?

I have been given a protein of unknown concentration and have been asked to make a set of standards using a protein with a known concentration so we can quantify roughly via dot blot. I need to know ...
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1answer
162 views

(+)-Bicuculline, what does (+) mean?

I was looking up some ion channel blockers. What does (+) or (-) below mean? (+)-Bicuculline (-)-Bicuculline methiodide
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1answer
2k views

Biochemistry for a mathematics student? [closed]

I am a second year mathematics student. I am mostly interested in statistics. Right now my curriculum doesn't offer me much choice (all second year courses are mandatory) but next semester I will be ...
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1answer
2k views

What software is used to generate the PDB molecule of the month images?

What software does the PDB use to generate these "cel-shaded" protein models with outlines around foreground atoms? (Leptin: May 2012 Molecule of the Month by David Goodsell)
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1answer
72 views

How is Humic substance destroyed in nature?

Humic substance consists of many, to my knowledge poorly understood, species of organic matter, mostly carbohydrates chained in intersting (and also poorly understood) ways. Humic substance is an ...
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1answer
329 views

Test for glyphosate in water, boolean style

Testing for contamination of the ever so popular glyphosate based herbicide "Roundup" in water is a service that many labs provide, one of them is the Microbe Inotec Laboratory . They use an enzyme to ...
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1k views

Deriving goldman equation

So I've been trying to follow the derivation of the Goldman-Hodgkin-Katz equation on Wikipedia (https://en.wikipedia.org/w/index.php?title=Goldman_equation ) - I can follow it through after it sets up ...
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1answer
6k views

Assay over 100% (L-Cysteine Hydrochloride Monohydrate)

In reading a COA (Certificate of Analysis), I came across an Assay line: The Assay is 100.5% where "Lower Limit" is 98.5 and "Upper Limit" is 101.0 This product ...
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4k views

What is "stuffy"/"stale" air composed of?

When a room is not ventilated for a long time (days if people are present, weeks if not), humans perceive a change in air quality commonly described as "stale" or "stuffy" air. What is going on here ...
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1answer
1k views

Products of the o-Toluidine oxidation with glucose oxidase and peroxidase

Could anybody describe which product is formed in the following reaction (o-Toluidine oxidation)? $$\ce{H2O2 + o-Toluidine_{uncolored} - Peroxidase -> H2O + 1/2 O2 + o-Toluidine\; Oxidate_{...
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710 views

Can luciferin + ATP → luciferyl adenylate + PPi be reversed?

Reading about the light emitting reaction of luciferin + ATP, catalysed by luciferase I am confused about the following. On this webpage the partial formula is written as: luciferin + ATP → ...
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257 views

Would it be possible to produce a non-toxic atmosphere using a coal fire and frozen oxygen?

A Pail of Air is a classic science fiction short story by Fritz Leiber from 1951 describing how a family survives on an Earth that has left its orbit around the sun, using desparate low-tech methods: ...
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260 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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1answer
1k views

What molecular features create the sensation of sweetness?

There are many compounds that taste sweet. Many of the artificial ones taste much sweeter than natural sugars (which is why they contribute little to energy intake when use as sweeteners). A range ...
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2answers
418 views

How can enzyme/substrate reactions that adhere (largely) to quantum theory also require 'Newtonian' consideration of gravity?

I'd just like to ask for a little clarification here due to confusion from interdisciplinary studies. I'm currently reading the 1976 paper related to the recent 2013 Nobel Prize for Chemistry, by 2 ...
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1answer
146 views

Isoelectric pH of colloids?

How did we derive the relation between the isoelectric pH and the dissociation constants for the amino and carboxyl groups on zwitterionic amino acids. $$pI=\frac {pK_{a1}+pK_{a2}}{2}$$ where $$\ce{...
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83 views

An alternative to dimethylsulfoxide (DMSO) for cryoprotection?

Is there an appropriate alternative to DMSO? I mean for embryo or oocyte freezing? I am a PhD student at present. I am going to study this substance and I'm very interested in this field.
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321 views

Thermodynamic vs. Kinetic products

With regards to complexes, I read that thermodynamic products are favored over kinetic products, which are labile. Why wouldn't the first product formed be the most prominent?
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41 views

Are phosphomonoesterases solid?

What state of matter are phosphomonoesterases? I am not a biochemist; while I've found various lists of such enzymes, and plenty of (to me) barely comprehensible articles describing their production, ...
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1answer
407 views

Impact of detergent on internal living tissue?

There was some spirited debate between the members of my chemistry lab today about the theoretical consequences of ingesting a large amount of the detergent Triton X-100 at a 100% concentration. The ...
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1answer
2k views

Dead-body Ashes: biodegradable or not?

In many cultures, human dead bodies are burnt to ashes, which is then thrown in rivers and some time buried in earth. Are human ashes after burning dead bodies biodegradable? Note: Earlier I posted ...
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1answer
104 views

Plastic: Reputable Publications

I would just like some reputable textbooks and or publication companies that have extensive research on plastics, as, for example, dealing with life cycles of plastics, degradation factors, effect on ...
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1answer
198 views

What metabolite intermediate will accumulate in a mammalian cell-free extracts capable of glycolysis if lactate dehydrogenase is inhibited?

I know the reaction proceeds as follows: Pyruvate accepts the electrons from NADH to form lactate. What would be the intermediate in this reaction? Would it be NADH or NAD+?
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3k views

How is the time for a test tube in a centrifuge determined?

I came across some hairy math that's used for analytical centrifugation, mostly for things like determining the sedimentation rate for liquids. However, what I don't understand is how someone ...
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1answer
181 views

What are the factors controlling the fate of post-adhesed volatile molecules of the olfactory epithelium?

What happens to volatile molecules that reach the main olfactory epithelium in the nasal cavity after they bind and the neural stimulus fades? To what extent do such factors as receptor kinetics and ...
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1answer
581 views

Why do we need to incubate this system for 18 hours at 60 degrees Celsius?

I am conducting a bio-chemistry related experiment and I have been unable to understand a step which is commonly performed. The procedure that is confusing me is outlined in the supporting information,...
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1answer
201 views

Does tolerance to alcohol affect blood/breath alcohol levels?

When blood / breath alcohol levels are taken to determine how intoxicated a person is, does it depend on their tolerance ? i.e. If you had two people of identical age, weight, fitness, etc. person A,...
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3k views

How can I control the oxygen in an erlenmeyer flask in a bioprocess?

I need to control oxygen in a erlenmeyer flask in a bioprocess. I need to remove overall oxygen in a erlenmeyer flask, and after I need to add oxygen in controlled amounts to a culture in a shaken ...
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72 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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767 views

Molecular explanation of the Hofmeister Series

The Hofmeister Series is a useful metric in understanding how to precipate proteins. However, wikipedia and many other source indicate that the order of the series is rather empirical. I'm curious ...
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199 views

What are the border definitions in the Ramachandran plot?

I've heard some people mention that this or that program isn't "up to date" with respect to the borders used in the Ramachandran plots to classify φ/ψ as being in the most favorable/acceptable/...
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483 views

What is the timescale of disulfide bond formation?

What is the timescale of disulfide bond formation in a given protein? What influences it? Finally, how does one actually measure it? From what I understand, the reduction and oxidation of bonds ...

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