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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How to remove putrescine odour [duplicate]

Does anyone know how to remove the odour remaining from a decomposed corpse which has fallen onto a wooden floor? Aparently the two main chemicals are putrescine (tetramethylenediamine) and cadaverine ...
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Synthesis of tripeptide using Merrifield peptide synthesis procedure - Inclusion of asparagine

I am supposed to synthesize tripeptide, $\mathrm{Ala-Asn-Phe}$, using Merrifield peptide synthesis procedure. Accordingly, I have done followings: Attached protected $\mathrm{Phe}$ as the first ...
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1answer
30 views

How does a vitamin differ from a mineral [closed]

At the molecular level, I would like to know fundamentally how does a vitamin differs from a mineral. I understand both have, to say, Fe (Iron), then what exactly makes it a mineral Iron or a vitamin ...
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19 views

Simulated body fluid [closed]

How to avoid sharply increase in the pH value of simulated body fluid after immersion. I prepare 1.5 SBF solution and adjust the pH value to be 7.4 after immersion of sample within the solution the pH ...
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1answer
45 views

What do X-ray diffraction and NMR tell about the Proteins? [closed]

I have gone through a simple idea that proteins have different conformations; it is a dynamic system. Moreover, whenever we do ensemble experiments, so we get an average picture. There are some ...
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1answer
73 views

why Ammonia is proton acceptor

I understand that this is an elementary question, but I tried to find answers which I could not get. I am trying to understand why Nitrogen in Ammonia is a proton acceptor. Now as I can see from the ...
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1answer
177 views

What does “parallel in-register” mean for a protein structure in a fibril?

I read a paper by Ross and Poirier [1, p. S12] which has the following lines (see section Commonalities of amyloid structure) that describe the structure of protein in a fibril: The most ...
2
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1answer
27 views

Is it possible to calculate the 'overall' redox potential of a system?

For a solution where many redox reactions occur (e.g. cytosol, soil solution), can we consider anything as 'overall' redox potential of a system? Is there a formula to quantify it in relation to the ...
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1answer
26 views

Can there be a compound which stops the pesticide from entering into the fruit or vegetable? [closed]

Can there be a compound which stops the pesticide from entering into the fruit or vegetable? For example, a solution which is sprayed before pesticides and somehow blocks pesticides from entering into ...
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3answers
2k views

Why does radiocarbon dating only work in nonliving creatures? [duplicate]

I understand how carbon dating works, though I do not understand why it doesn't happen while a creature is living. Because while we are alive we still have carbon 14 in us, so shouldn't it work?
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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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1answer
40 views

Calculating the Ionic strength of sodium acetylsalicylate

With the addition of aqueous NaOH to an aspirin solutions in water the reaction will yield products of sodium acetylsalicylate and water. I would like to measure the amount of sodium apsirin formed ...
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1answer
42 views

Photosynthesis-Equation [closed]

Everyone knows the simplified photosynthesis-equation from school: $\ce{6CO2 + 6H2O -> C6H12O6 + 6O2}$ Most people assume that the carbondioxide is being split into carbon and oxygen during ...
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0answers
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Copper sulphate use as mould deterrent in evaporative humidifier [closed]

Is it okay to use copper sulphate in an evaporative humidifier to prevent mould growth?
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1answer
40 views

Why can DAP be used to elute a protein in affinity chromatography?

A little background: as part of my bioinformatics degree I have to take Protein Chemistry course, but I miss chemistry basics (have CS background), so that's why I'm asking the following question. We ...
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30 views

Osazone crystal

How does maltose form its osazone crystal? If osazone is to be formed, then there must be aldehyde form for phenylhydrazine to react, but maltose is formed after hemiacetal formation. How do we ...
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2answers
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Do magnetic fields generated from ion flow through a membrane channel have any physiological relevance?

Membrane pores and transporters see millions of ions flow through them per second. This creates a current and therefore a magnetic field. Do cells have any use for these fields (like maybe drawing ...
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1answer
56 views

Chemichal difference between liquid sucralose and powder sucralose [closed]

In my country (Brazil), sucralose comes in this two forms, liquid and powder. Looking on the nutritional table, liquid sucralose have no significant amount of carbohydrates or kcal; On the powder ...
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0answers
8 views

Other metabolic reactions aside, what causes beta oxidation to stop?

To my understanding beta oxidation is when a fatty acid has its carbons plucked off in groups of 2 (acetyl groups) into acetly-coa which we can dump into the TCA. At what point would this process ...
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1answer
42 views

qualitatively: Why are thioesters more reactive than regular esters? [duplicate]

In ochem students are taught that shorter bonds (like alkynes) have more energy than longer bonds such as alkanes. However in biochem we are taught that thioesters are very energetic bonds and release ...
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2answers
398 views

What dictates cathode vs anode nomenclature use?

what was the justification for the use the cathode and anode terminology in IEF? There is no redox taking place in IEF, just proteins interacting with an electric field
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0answers
32 views

Isoelectric point defintion [closed]

My professor said that in order to have PI, both + and - charge have to exist, and therefore phosphoric acid cannot have a Pi. I am confused because I can't find any definition that states both + and -...
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0answers
15 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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1answer
68 views

Ratio of uncharged to charged side chains [closed]

The $\mathrm{p}K_\mathrm{a}$ of the side chain imidazole group of histidine is $6.0.$ What is the ratio of uncharged to charged side chains at $\mathrm{pH}~7?$ Here's my attempt to the solution: $$7 ...
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What is the definition of a “Simple enzyme” exactly? Is it an enzyme that does not require a co-factor?

I'm having a hard time making a distinction between simple and complex enzymes. the definitions I've found so far all say this: Simple enzymes are enzymes that are only made out of protein, and ...
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3answers
354 views

Choice of solvent during thin layer chromatography

I understand most of the theory behind TLC and that different volatile solvents have different polarities and cause the 'spotted' substances to move at different rates, but what is the point of ...
2
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1answer
78 views

Comparing Polarity of Amino Acids

I know that there are polar uncharged amino acids (serine, threonine, asparagine, glutamine, cysteine) and polar charged amino acids (the basic and acidic amino acids). Does the charge on the acidic ...
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How to compute for the ATP molecule that can be produced from an unsaturated Free Fatty Acid?

From studying Beta-oxidation of Free Fatty Acids, I've learned how to compute for the ATP equivalence of Even-Chain and Odd-Chain Free fatty acids. What really bothers me now is how to compute for ...
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1answer
269 views

How do I calculate the ensemble-average net charge of an amino acid at given pH?

I am given an amino acid with an ionizable side chain at a certain pH. How do I determine the net charge of that amino acid when there are mixed protonation states of one or more of the groups at that ...
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1answer
50 views

Is sugar in mead different from “regular sugar”?

My understanding of the process of making mead is that you combine honey, yeast and water in an anaerobic environment. The yeast-bacteria ferments the sugar in the honey and produces ethanol (among ...
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1answer
128 views

Theory behind Experiment: Extraction and Identification of DNA

A few days ago, in my chemistry lab class, I performed an experiment aimed at extracting and identifying DNA. The class is mostly practical oriented, so I thought of asking my theoretical doubts on ...
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1answer
83 views

What Is the Difference Between Radiation and Radioactivity? [closed]

Does all radiation glow green and mutates people on contact?
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1answer
507 views

What are the factors affecting osmosis (bio)? [closed]

Asking from the blood barrier angle. The wikipedia states that glucose, urea, and $\ce{Na/K}$ count. Can there be any other factors, like $\mathrm{pH}$, temperature, hydraulic pressure on the cell ...
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2answers
45 views

Enzyme Kinetics

How come enzymes with a lower $K_\mathrm{m}$ are more easily saturated with substrate than an enzyme with higher $K_\mathrm{m}?$ Is it because enzymes with higher $K_\mathrm{m}$ are able to bind ...
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0answers
20 views

How is serine ionized in serine proteases? [closed]

I read that serine isn't strongly acidic so how is it that in serine proteases it is able to have its pKa lowered by the catalytic triad?
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2answers
168 views

What is the fate of sulfur in cysteine when it participates in gluconeogenesis?

Amino acids can be broken down to yield pyruvate, which in turn can be used to construct glucose molecule in the process of gluconeogenesis. What happens to the sulfur atom in the amino acid cysteine ...
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1answer
47 views

Does aminosugars give positive response in alkaloid tests?

Does aminosugars give positive response to test for alkaloids such as tests with Dragendorff's reagent, mayer's reagent, Hager's reagent, Wagner's reagent etc?
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2answers
109 views

Chemical Reaction Alternative to O2 Respiration in H2/N2 Atmosphere [closed]

Note: If this question does not belong on this Stack Exchange, please direct me to a more appropriate Stack Exchange. This is a "creative chemistry" question as much or more-so than a "give me the ...
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0answers
56 views

pKa values for amino acid

To calculate the pI value, we take the average of the pKa values from the 2 groups that result in a net charge of 0. For that to happen, the pKa values should be at the midpoint of titration where ...
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1answer
33 views

What ratio of bicarb to sugarcane juice with a pH level of 4.5-5.5 to neutralize pH level? [closed]

I am thinking of adding baking soda to sugarcane juice to eliminate the fruity acid that is present. The pH of sugarcane juice ranges from 4.5-5.5. I wonder how much baking soda should I incorporate ...
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1answer
31 views

The time-dependent pH value in a fermentation

I want to know if someone has supporting tips or solutions to my problem: In biotechnology, fermentations are used to grow microorganisms. These need a specific media/broth in which temperature, pH, ...
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2answers
99 views

Why do chiral biological molecules only exist as one enantiomer? Does it have any advantage?

Why is it that chiral biological molecules are enantiomerically pure? The other enantiomer would have the same reactivity, and the only difference is their angle of rotation of plane polarized light. ...
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2answers
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Why isn't aluminium involved in biological processes?

There are so many biological processes which are dependent upon ions of lighter metals (upper part of periodic table) such as $\ce{K+}$, $\ce{Na+}$, $\ce{Mg^{2+}}$ and even early transition elements ($...
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2answers
67 views

Bleaching of chlorophyll stains using hydrogen peroxide

I have been doing some experiments concerning bleaching of chlorophyll stains from cotton clothing. Currently I have found that $\ce{H2O2}$ is fairly effective, but still leaves visible stains. Would ...
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0answers
18 views

Why no specifications for the concentration of Phosphate buffered saline buffer?

I am following a protocol where they use PBS buffer. But they don't specify the concentration of PBS, why is that? How am I supposed to know how to make this buffer if I don't know the concentration ...
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0answers
31 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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1answer
377 views

Does cooling a potato change the nature of its carbohydrates?

A talk-show guest of Joe Rogan claimed that cooling a potato after cooking creates "resistant starch" that's better for human consumption https://www.youtube.com/watch?v=niwqfwA2Lb8 The claim is ...
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26 views

What is the cause for the difference in pH between NaCl and Ringer Lactate

Reading this article, I came across a passage which got me to think of this question: "Normal saline contains approximately $\pu{154mM}$ of each $\ce{Na+}$ and $\ce{Cl-}$ with average pH of 5.0 and ...
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3answers
112 views

what is the difference between how taste and smell are detected?

Taste and smell are both chemical processes ... parts of the food dissolved in saliva come into contact with the taste receptors.[1] These are located on top of the taste receptor cells that ...
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2answers
113 views

DNA-Sequencing (detection of the change of pH-value) after emulsion PCR

I have troubles with understanding the exact order of the steps for DNA-sequencing after the Emulsion PCR (EmPCR). The EmPCR fills each bead with the same DNA strand (copies it $n$ times, till the ...