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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2
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2answers
689 views

What does 2 vol (w/v) mean?

I came across a protocol saying: Homogenize 50 g powdered plant material (accurately weighed and recorded) in 2 vol (w/v) acidified methanol. What does 2 vol (w/v) mean?
4
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1answer
422 views

What is the mechanism behind the decomposition of enediol phosphate intermediate to methyl glyoxal?

I can't seem to figure out the mechanism for the decomposition of enediol intermediate (in glycolysis) to methyl glyoxal? How does the phosphate group get replaced by a hydrogen?
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153 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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1answer
135 views

Asking about definitions of word “sugar” in biochemistry

In a lecture about anabolic pathways of sugar, the lecturer was not clear when stating the name of a multiple sugar carrier & it sounded like "dolichol"so is it correct?
7
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2answers
4k views

Formation of zwitterion from amino acids

Why it is easier for the carbonyl group to lose a proton to become negatively charged and the amino group to accept a proton to become positively charged? I know it has to do with the very polar bond ...
2
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2answers
167 views

Why is the E2 protein important for protein degradation?

In the ubiquitination process, the E2 protein transfers ubiquitin from E1 to E3. Why can't E1 work with E3 directly to tag some protein with ubiquitin? Going further, why can't one of the E(1-3) ...
5
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1answer
119 views

Are there proteins with permanently bound magnesium?

Do you know something about the existence of a magnesium containing protein/enzyme in which magnesium is coordinated in the structure and the structure is stable? (like iron in haemoglobin or zinc in ...
7
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2answers
744 views

Wouldn't radiolabelled phosphorus in DNA break it apart as it disintegrates?

The Hershey-Chase experiment was designed to prove that DNA is the genetic material in organisms. In this experiment, two batches of viruses were grown in two separate media A and B, with A having an ...
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2answers
370 views

Is consumption of chlorine, like fluorine, harmful to bones? [closed]

Is consumption of chlorine harmful to bones ? I know fluorine consumed with water can cause fluorosis to bones and joints. Can chlorine, a similar halogen like fluorine, also cause damage to bones ...
5
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1answer
60 views

What method is used to discover oxidation state of drug binding cysteine residue?

I was reading this article and found this sentence: KC group found that some cancer cells became resistant to Boehringer Ingelheim’s covalent TKI afatinib (Giotrif) due to the oxidation of its ...
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0answers
47 views

What component of the human DNA reacts with 4,5-benzo[a]pyrene oxide and 7,8-benzo[a]pyrene oxide to produce cancerous tumors

I read in an article that we have this enzyme called P450 that converts aromatic compounds into water soluble compounds that can be eliminated. This enzyme converts aromatic compounds into arene ...
0
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1answer
31 views

What is (approximately) the minimum exchange current for a potentiometric measurement?

Is there a rule of thumb for what should be the minimum exchange current to detect a certain redox couple in an aqueous solution? I would like to make a rough calculations to see whether any of my ...
2
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1answer
4k views

What is the importance of iron in complexes and in the process of electron transport?

What is the importance of the iron in complexes and in electron transport? This question is related to synthesis of ATP. I have read about iron-sulfur proteins, but I don't understand how this works.
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0answers
385 views

How can I calculate the percentage of urea in animal feed?

I'am having some doubts in the calculation that concerns the urea percentage in animal feed using the method AOAC $967.07$ How can I calculate the urea percentage using the following data: The ...
4
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0answers
53 views

Thyroid peroxidase - can atomic iodine serve as iodinating agent?

McMurry's Organic Chemistry (7th Ed.) states, that Tyrosine is iodinated by mechanism of electrophilic aromatic substitution and the iodinating agent is $\ce{I+}$ or $\ce{HIO}$ formed by thyroid ...
2
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1answer
56 views

translation of a sentence involving antigen/buffer/solution

I'm trying to translate a sentence about biochemical testing into English. So far, I can figure out the following: Make a 10,000 pg/ml stock solution from[?] antigen into[?] 7.5 % BSA-TSA buffer. ...
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2answers
67 views

In this specific case is the proton considered product or catalyst?

Assuming we have a reaction of $$\ce{CO2 + H2O -> HCO3- + \color{red}{H+}}$$ then is the proton (in red) is considered a product or a catalyst? I read the Wikipedia article titled Product (...
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3answers
13k views

How do you recognize a carbohydrate molecule?

I am studying carbohydrates in organic chemistry and I am confused a bit on what they are and how you recognize whether a molecule is a carbohydrate or not. For example, will a carbohydrate always ...
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0answers
156 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 ...
0
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1answer
43 views

Variation of current with time in gel electrophoresis

During gel electrophoresis, if the voltage of the power supply is kept constant, how would the current in the circuit change over time? I was wondering whether the electrical resistance of the gel ...
1
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1answer
828 views

LeChatelier's Principle - Phosphofructokinase in Glycolysis [closed]

In glycolysis, PFK is allosterically regulated by ATP, F6P, etc. When the concentration of F6P increases, the concentration of ATP increases too. I understand that high levels of ATP shift the eq ...
3
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0answers
408 views

How do thiol groups act as reducing agents?

In my biochemistry practicals, we used reducing agents such as beta mercaptoethanol: and dithiothreitol (DTT) Both of these have S-H groups, and I am sure that these are involved in the reduction ...
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1answer
2k views

If concentration of K+ ions inside the cell is almost equal to concentration of Na+ ions outside of the cell why these ions cross the membrane?

I'm a bit confused about electrochemical gradients of sodium and potassium ions. They have similar concentrations and are kind of similar ions but their distribution is different across the membrane. ...
12
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1answer
191 views

What are the chemical process responsible for the warping of wood?

Background: According to this Wikipedia article: Wood warping costs the wood industry in the U.S. millions of dollars per year. Straight wood boards that leave a cutting facility sometimes ...
5
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2answers
226 views

Isn't 11-trans-retinal more stable than 11-cis-retinal?

11-cis-retinal can be found as a part of rhodopsin and it is the non-excited form of retinal. By absorbing light, retinal goes to a higher energy state and converts to 11-trans-retinal. At least I ...
4
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2answers
5k views

Which steps are most critical in driving glycolysis foward?

I'm assuming that the non-reversible steps (1,3,10 on the chart below) in glycolysis are the most critical in driving it forward, but I have a feeling it might be something else. If so, why are they ...
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1answer
1k views

Making artificial sweat

I'm currently working on a chemistry investigation wherein I need to dilute a compound with artificial sweat. I have looked at various forums, including this, which gave answers, but is very outdated. ...
12
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2answers
587 views

What does “gamma” in gamma-oryzanol mean?

The structure of gamma-oryzanol is: What does the "gamma" in its name mean?
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1answer
2k views

Why does ATP inhibit glycogen synthase?

Why is ATP an inhibitor? I mean, if there are high levels of ATP, it means that the cell has adequate amounts of energy. Therefore, if it doesn't need the energy, then glucose needs not go through ...
2
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2answers
609 views

Why energy of some intermediates of glycolysis increases?

It is possible that I do not understand the concept of energy, but according to the diagram in my book, the energy between steps 4 and 5 and between 6 and 8 increases. How is this possible? Also, as ...
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0answers
101 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 ...
2
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1answer
447 views

Gromacs: What can be reason of getting final potential energy greater than the starting one?

I wanted to optimize potential energy of a molecule using Gromacs software (v. 5.0.4, single precision). I was really surprised when I discovered that after running Conjugate Gradients integrator, the ...
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0answers
173 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 ...
1
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1answer
177 views

What is the significance of Sphingolipids in human?

I want to know the significance of sphingolipids in human. I have learnt that sphingomyelin is the most significant type of sphingolipid in human. Also that the sphingomyelin serves as a structural ...
3
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2answers
4k views

If α-glucose is less stable than β-glucose, why is glucose almost always α in its compounds?

Maltose, saccharose, turanose, trehalose, trehalulose, amylopectin, amylose - they are all α. Why? Also, why is cellulose β?
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0answers
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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0answers
101 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) ...
1
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1answer
103 views

Can Isopropyl β-D-1-thiogalactopyranoside be degraded into either 1-deoxy-galactose or just galactose?

This may be a silly question, but is it feasible that Isopropyl β-D-1-thiogalactopyranoside (IPTG) when acted upon by a beta-galactosidase could produce 1-deoxy-galactose or just galactose? The ...
5
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1answer
983 views

Why does mutarotation occur only in specific media?

I was reading a book on biomolecules, and read that muta-rotation in hexoses, can happen only in media like water, which can act as an acid and as a base. Why is this so? Essentially, it is just the ...
2
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0answers
398 views

proteolysis - how to determine the partial or completeness of the cleavage reaction?

Though the question is about biomolecules, we agree the underlying functions, formation, degradation etc come down to chemistry, (then physics and maths). I am posting it here to receive an ...
3
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2answers
1k views

Betaine HCl stomach pH

It seems betaine HCL is often recommended for those suffering from "low stomach acid" -- which, as I understand, is having too high stomach pH for proper digestion (especially for proteolysis via ...
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2answers
37 views

How to determine a poisonous or healthful plant? [closed]

I'm not a chemist or scientist, however i am interested in figuring out if the plants around me: can provide any nutritional value Can be eaten in salads or poisonous I don't have any idea of the ...
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2answers
9k views

In Glucose, how will you prove the presence of the following? [closed]

One carbonyl group 5 hydroxyl groups One primary alcholic group
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0answers
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 $\ce{Mg^2+}$ ...
1
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1answer
30 views

If the same atoms (cells) that now compose my body get arranged in N years away, am I that person? [closed]

Probably a very stupid question, even may deserve to be downvoted, but I have always wondered: Hypothetically, let's say somehow tomorrow I die in an accident. Now lets say that after a long time (e.g....
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1answer
559 views

Why isn't sucrose a reducing sugar but maltose is? [duplicate]

I read one of the answers for a similar question, According to that it is due to the hemiacetale group converting into a carbonyl group. I don't get why the same thing can't be applied to sucrose ...
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0answers
67 views

Where does the water in an egg go on boiling? [duplicate]

Our textbook says that boiling an egg causes coagulation and denaturation of the proteins present in it. Where does the water in it disappear?
2
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1answer
334 views

Cis/trans Proline vs. Double bond character

I am learning about proteins and we have learned that the C-N bond is rigid because of it's partial double-bond character. We have also learned that proline is commonly found in beta turns (type 1) ...
3
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0answers
154 views

How far has “self-organizing chemistry” gone? [closed]

This is my first question here so, please, bear with me if I go out of the style or the scope of the SE section. I think I am quite new here, so I am prone to make mistakes. I am a molecular ...
2
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1answer
127 views

Why aren't the R-side-chains of acidic and basic amino acids the site of polypeptide synthesis?

If polypeptides are synthesized by acid-base reactions between the carboxyl group of one amino acid and the amine group of another amino acid, what stops the formation of a peptide bond between the ...