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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9 views

The Limitation of Solid Phase Peptide Synthesis In Case of Polyglycine

I was wondering if I could use your experience and all the precautions you would like to recommend for a long peptide synthesis via SPPS. I've already got a low loading resin so this way I'll minimize ...
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9 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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Are there any natural products that can be used as a sealant that is machine washable? [closed]

I’m in search of a natural, environmentally friendly product that can be used as a waterproofing, sealant for fabrics that can also be washed in a washing machine.
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90 views

Why are drugs mixed with their sodium salts?

I have come across quite a few drugs that are of the form $\ce{HA + NaA}$, where $\ce{A}$ is your target organic compound. A few examples of this are: Carmicide which is a mixture of Sodium Citrate ...
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How can I turn algae derived oil into a bioplastic in terms of additives, plasticisers etc? [closed]

I want to convert algae derived oil into a bioplastic but am unsure on what I need to add into the oil for it to become bioplastic.
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Link between spatial structure and function in RNA [closed]

Why are the spatial structure of the following RNA molecules particularly suited for performing their respective tasks? -the tRNA of Phenylalanine in yeast -hammerhead-shaped ribozyme -bits of tRNA ...
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19 views

Charge of nitrogenous bases in nucleic acids and dipole interactions

I have read in one of my textbooks that the nitrogenous bases of nucleic acids are positively charged at pH 7. I have tried to confirm this online, but I haven't found much evidence. In case it is ...
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18 views

Link between nitrogenous bases of nucleic acids and spatial structure of nucleic acids [closed]

What are the characteristics of the nitrogenous bases of nucleic acids (both DNA and RNA) that affect the spatial structure of said nucleic acids?
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How can I extract starch from green Algae? [closed]

What are the possible methods of obtaining starch from green algae more desirably using equipment from home?
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1answer
22 views

Using the electrical potential created by the electron transport chain to power electrical systems

My friend and I were discussing the extremely low energy density of modern batteries and read that food has a much higher energy density. Thus, we were considering the possibility of using biological ...
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1answer
46 views

Human gastric lipase

Does anyone know if the human gastic lipase has a quaternary structure? If not, why not? I can not seem to find this information anywhere.
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1answer
31 views

Is the solution isotonic, hypertonic, or hypotonic?

The problem is shown below. I don't understand how can the tonicity of a solution be determined if the solution has multiple solutes dissolved in it. Do I take the total sum of the mass of solutes ...
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1answer
31 views

Estimating protein binding and disassociation

I don't have a background in the area of drugs or pharmacokinetics/Pharmacodynamics but I am trying to understand about protein binding. I was going through this paper. If $C_b$ is the ...
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1answer
77 views

Carcinogenicity of polynuclear hydrocarbons and benzene rings

(1933) established that polynuclear aromatic hydrocarbons (PAHs) were carcinogenic components of pitch. ... Although less is known about their health effects than about those of PAHs, it is clear ...
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Oxidative phosphorylation analogue

Does the salt bridge in galvanic cells resemble the ATP pump in the inner mitochondrial membrane? And if yes than did someone use this pH difference in harvesting this energy?
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2answers
29 views

Why is it important to remove the used up electrons in oxidative phosphorylation?

I get that oxygen is the terminal electron acceptor in oxidative phosphorylation. But why is it essential to accept these electrons and remove them as $\ce{H2O}?$ Oxygen is essential for cellular ...
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36 views

Is there a software that can predict the shape of a custom protein, given its amino acid sequence?

I know that the internet is full of enzyme and protein simulators which can show active site and 3D structure (like bioblender), but the problem with these programs is that they use predefined ...
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1answer
17 views

R and T conformations in relation to Activators and Inhibitors; Km of reaction in relation to uncompetitive and non-competitive inhibitor

Do -Activators -Competitive Inhibitors -Non-Competitive Inhibitors -Uncompetitive Inhibitors all change the conformation of the targeted enzyme from T to R (activator), and from R to T (the rest) ...
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1answer
46 views

A question about thiamine [closed]

How does the the nitrogen of thiazole in thiamine acquire a positive charge without being stabilized by another negative charge or by being a salt of an anion?
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133 views

Why dried, closed coconuts go through carbonation?

Some dried, closed coconuts go through carbonation: The white meat of the coconut becomes disintegrated and smeary The liquid becomes carbonated with a bit sour-salty tasted coconut water (which ...
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21 views

∆G° and ∆G°' for acid dissociation

For the dissociation of an acid AH, where $\ce{AH <=> A- + H+}$, if $∆G°$ is $\pu{+25 kJmol-1}$ at $\pu{300 K}$, what is $∆G°'$? I know that for $∆G°$, $\ce{[H+]}$ is $\pu{1M}$, whereas for $∆G°'...
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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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2answers
368 views

How does one tell (or conclude) if a substance is carcinogenic?

It's common to read statements like: Tetrachloroethene ($\ce{CCl2=CCl2}$) was earlier used as a solvent for dry cleaning, but since it contaminated ground water and is a suspected carcinogen, ...
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2answers
187 views

Peptide bond formation involving side chains of charged amino acids

Peptide bonds are formed as such: Aspartic acid, glutamic acid and lysine all contain either one extra $\ce{-COOH}$ or $\ce{-NH2}$ group in them. Why does that extra group not participate in peptide ...
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4answers
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What is a word for “atom or molecule”?

What is a word for "atom or molecule"? As in: "The entry of an atom or molecule across a cell membrane into a cell is dependent on its size and solubility." This keeps coming up, and it's really ...
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3answers
117 views

Fitting multiple pKa's

I have three histidine residues that are next to each other in a protein. When I compute the fraction of unprotonated states for each individual histidine as a function of $\mathrm{pH}$ my titration ...
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1answer
41 views

Production of Succinic Acid from Crude Glycerol using Fermentation

So I am writing a short paper on how one can produce Succinic acid from glycerol. I have to find a microorganism which can do that. I have found the following microorganism, which are traditionally ...
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0answers
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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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36 views

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
34 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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1answer
50 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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2answers
116 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
187 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 ...
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2answers
34 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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27 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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1answer
45 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
49 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
13 views

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
41 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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1answer
41 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
38 views

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
70 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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1answer
18 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
425 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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35 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
26 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 + ...
2
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1answer
90 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 ...