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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45 views

What are some technologies/biosensors for real time kinetic analysis of reactions? [closed]

I am in a lab that has used surface plasmon resonance (SPR) and ELISA very heavily over the past few years, and we are thinking of getting a new machine. I'm wondering what other technologies exist ...
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1answer
1k views

What is a prosthetic group of protein? What are prosthetic groups?

I have found this term while I studying the topic of ETS in respiration in plants.
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1answer
908 views

Is it practical to extract zymase from yeast for ethanol production?

Suppose I wanted to make some ethanol fuel. Normally, I would get yeast, mix with water, add sugar and wait. However, there is an enzyme (zymase) in yeast that does this. Looking at the Wikipedia ...
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336 views

Mechanism: explanation of final step in synthesis of the thyroid hormones (T4, T3)

In the following mechanism for the synthesis of T3 (triiodothyronine) on thyroglobulin, what are the factors causing the last step to occur? Does it have something to do with the electron density of ...
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1answer
3k views

What is the empirical formula of Haemoglobin?

Everywhere I look on the internet tells me a different formula. Are there genuinely different formulas for Haemoglobin, or are some of my internet sources incorrect? (I know there are different ...
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1answer
658 views

Which coloring agents are responsible for the color in red tea and yellow tea?

Have this question in a biochemistry course, can't seem to find it anywhere. Anyone happen to know an alkaloid or something else involved? Thanks a lot!
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1answer
880 views

How to rationalise the protonation state of amino acids

I am learning about amino acids in various $\ce{pH}$ environments and how their groups are protonated or deprotonated in these environments. I don't need to mention a specific acid for my question, I ...
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1answer
356 views

Is 98%+ purity Reagent Grade Ca-EDTA powder as safe to use as USP Grade in the body? [closed]

Is $98\%+$ purity reagent grade $\ce{Ca}$-EDTA powder as safe to use as USP grade in the body? Or, does the reagent grade have unsafe impurities that USP grade would not have even though they are the ...
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1answer
239 views

How was the composition of DNA studied before the knowledge of its structure?

In a large polymer molecule (such as a DNA chain) which is made from multiple component monomers containing many atoms, how was it determined that the chain was made up from the four groups of ...
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1answer
150 views

Is exposure to amyloid beta proteins dangerous?

Recently, I began working in a lab in which our main area of study is Aβ peptides. My concern is whether or not exposure to high levels of Aβ proteins is hazardous. I suspect that the peptides cannot ...
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1answer
123 views

What happens to the third hydroxyl group in a phosphodiester linkage?

A phosphodiester bond occurs when exactly two of the hydroxyl groups in phosphoric acid react with hydroxyl groups on other molecules to form two ester bonds. But what happens to the third hydroxyl ...
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1answer
1k views

Charge of an amino acid sequence

I have the following problem: A polypeptide has the following sequence (amino end on the left) $$\mathbf{lysine - aspartic~acid-histidine-arginine-serine}$$ Using the $pK_a$ information that ...
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1answer
124 views

Kinetic Barrier of ATP

I do a fair bit of biochemistry, and one of the things I've taken on faith up until now is that ATP is stable because it has a high kinetic barrier for falling apart despite the spontaneity of its ...
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1answer
88 views

Influence of sodium cyanoborohydride on C=N bonds in DNA bases

I would like to crosslink an amino-modified DNA strand with an APTES monolayer (which also has a $\ce{NH2}$ end group) using a glutaraldehyde linker. After the formation of Schiff base linkages ...
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1answer
115 views

Should I include solvation in quantum chemical calculations of a simplified protein-ligand interactions?

I am running a B3LYP-D3/6-31+G geometry optimization of a protein-ligand interaction. Well, not quite, I have simplified the protein to four amino acids surrounding the active site, but I keep the ...
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3answers
4k views

Are biological macromolecules organic or inorganic compounds?

We know that organic compounds are compounds which contain carbon atoms. I want to know whether all biological macromolecules (such as proteins, lipids, carbohydrates, and nucleic acids) are organic ...
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270 views

What are the chemical similarities between gallium and barium?

I am analyzing nutrient concentrations in wood, and I have found that in all my samples the distribution of gallium and barium are closely related. As a related phenomenon, the presence of these ...
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0answers
379 views

What would happen if Carbon-14 was in a molecule, and decayed into Nitrogen? [closed]

This interested me because of Melvin Calvin's experiment with photosynthesis where he used radioactive Carbon-14. If a plant used it as a reactant to make glucose, and that Carbon-14 decayed into ...
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1answer
702 views

Turns in beta-alpha-beta loops (protein motifs)

In the context of protein secondary structure, do the loops between strand and helix in a beta-alpha-beta motif form into the conformation known as a beta turn?
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1answer
2k views

Relationship between inhibition constant Ki and interaction energy?

Inhibition of an enzyme $E$ by an inhibitor $I$: $$ E + I \rightleftharpoons EI $$ The inhibition constant $K_i$ is defined as follows: $$ K_i = \frac{[E][I]}{EI} $$ where $[E]$ is the enzyme ...
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0answers
583 views

Calculating volume ethanol in an fermented aqueous solution of sucrose, water, and ethanol

I've been working on a biology experiment where I calculate the fermentation yield of yeast under various light induced stress responses inhibiting the translation of various fermentation enzymes. My ...
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1answer
2k views

Mechanism of protein precipitation with TCA

In practice, TCA (trichloroacetic acid) is widely used for quantitative protein precipitation, but so far I have failed to discover the exact mechanism of TCA action. I highly doubt it's just the ...
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1answer
92 views

How do transmembrane protein alpha helixes bind to the membrane?

I would post this in biology but as the question is biochemical in nature I decided this would be a more appropriate platform. What I'm asking is how exactly does a transmembrane protein bind to the ...
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1answer
343 views

Visualizing PDB file in VMD, how to upload molecules?

Problem: When I load PDB-file of my protein of interest in VMD, nothing happens. The molecules is uploaded, but when I push "D" the screens with with big "VMD" letter freezes instead of presenting the ...
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1answer
1k views

How to merge PDB-files to build trimer from monomers [closed]

Problem Using WinCoot or SWISS PDB viewer, how would one merge monomeric structures that should be in dimer formation? What I have done: I have downloaded the PDB-file which shows the monomer with ...
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2answers
79 views

Polyethylene biodegradation, how?

Worm guts have bacteria that apparently can degrade polyethylene: The only agents that I have heard of that can degrade a fully-saturated hydrocarbon at room temperature are fluorine (and related ...
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0answers
54 views

Does Beta-ionone posses the same anti-ageing properties as Retinoids if applied topically to the skin?

I read a scholarly article on oxidisation and collagen structure in the dermis and they mentioned the use of Retinoids topically. so I looked into retinoids (admittedly on Wikipedia) for an overview (...
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1answer
186 views

Nuclear Fallout [closed]

If there was a nuclear explosion and years later I come out of a fallout shelter like in the popular game series Fallout, what elements would react to the radiation in a way that could harm humans and ...
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0answers
1k views

Solubility of cholesterol and phospholipids in acetone

I'm having difficulty with this specific part of an assignment. I know that it is to do with polarities of the different parts of cholesterol and that it is because cholesterol is amphiphilic, but I ...
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4answers
12k views

Why is the units of kcat 1/s?

I understand that $k_\text{cat}$ measures the turnover number of an enzyme. This measure is therefore a quantity of molecule conversions per unit of time. I suspect that my problem is more that of a ...
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2answers
227 views

How do biochemists seperate nucleotides from DNA to add to the PCR

How do chemists separate single nucleotides from DNA strands? How do they add those nucleotides to e.g. a PCR reaction in order to replicate DNA? I ask this because in my microbiology class, my ...
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1answer
133 views

How to find out the energy gained from hydrolysis of Dimethylsulfoniopropionate?

I am trying to find out what the energy gain from hydrolysis of DMSP (Dimethylsulfoniopropionate) is, versus the energy gain from oxidation of a sugar or carb (e.g. glucose) in a terrestrial ...
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1answer
10k views

Why does menthol (e.g. peppermint) feel cool to the tongue?

Especially when drinking water after the fact, mint can give a sharp cold sensation inside one's mouth. What process causes the sensation to occur?
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2answers
988 views

Why do chalcogens (Group VI) stink so badly?

For more fun with Dr. Derek Lowe, see this for a primer: Things I Won't Work With - Carbon Diselenide. The short of it is that we carbon-based life forms generally like oxygen. However, move just one ...
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1answer
1k views

Why is the deprotonated form of dopamine more reactive than the protonated/neutral form of dopamine?

See this (from the Wikipedia article on dopamine): Dopamine, like most amines, is an organic base. At neutral or acidic pH levels it is generally protonated. The protonated form is highly water-...
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0answers
97 views

Phlorizin content in grapes

I work in a winery and we have some problems about a new process involving phlorizin. We know that phlorizin is the major dihydrochalcone found in apples. I have been reading that this compound is ...
2
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1answer
964 views

Why does the $V_{\mathrm{max}}$ of an enzyme not change with competitive inhibition? Shouldn't it decrease since there are fewer active sites?

My textbook states that $V_{\mathrm{max}}$ doesn't change for competitive inhibition. This makes no sense to me, since decreasing the amount of active sites available should lower the rate of an ...
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1answer
402 views

Gibbs Free Energy and ATP

Gibbs free energy describes the maximum of useful work that can be done by a chemical reaction. My question is(Sorry I am not into chemistry and biochemistry) : during a chemical reaction that creates ...
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2answers
125 views

What program could I use to create a protein model from scratch?

I would like to create protein models such as the ones in the Protein Data Bank. I have got GROMACS but I don't know if it can be used to model macromolecules.
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1answer
7k views

I have 100 mg of a proteinase K lyophilized powder and I need to make it to a working concentration of 25 mg/mL

So I know that I need to add $4~\mathrm{mL}$ of solution to this powder, which will give me a concentration of the enzyme at $25\ \mathrm{mg/mL}$. What I do not understand is how to decide how much of ...
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1answer
2k views

How does dimethyltryptamine cross the blood-brain barrier?

Is there a specific chemical reaction that enables dimethyltryptamine to cross the capillary edothelial cells?
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0answers
922 views

Why does acid react with skin [closed]

Why does acid reacts with skin?? I can understand the acid would react with blood as it is alkaline in nature. But when i googled pH of skin, its around 4-5, "it is estimated that the 'natural' skin ...
3
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1answer
139 views

Is it possible to make a fuel cell that runs on triglyceride?

I apologize if this is a silly question. The reason I ask is I'm wondering if it would be possible to build a fuel cell that runs on body fat. I know ones for butane exist, could they work for this? ...
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2answers
2k views

pH calculation - adding distilled water after titration [closed]

Will someone help me figure out how can I solve the following question? We are given 110 ml of acetic acid (pKa=4.76), with concentration of 1M, to which we add 10 ml of NaOH with concentration of ...
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1answer
395 views

Tandem mass spectrometry: a1 and immonium ions

In tandem mass spectrometry of proteins one will usually end up with a mix of $b$ and $y$ fragments but also $a$ fragments and immonium fragments. My problem is that wouldn't an $a_1$ ion be the exact ...
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1answer
217 views

Is it possible to use Vmax as Kcat in a Michaelis-Menten reaction?

I am studying a biological system using ODEs. As part of my work I need to use the '$k_\text{cat}$' version of the Michaelis-Menten reaction, which is: $$\frac{V_\text{max}\cdot [\ce{S}]}{(K_\mathrm ...
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3answers
3k views

Can all compounds that plants and animals produce be synthesized in a lab?

I guess a better way to ask the question would be, Are there compounds that exist in biology that humans don't have the capacity to produce in a lab?
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1answer
466 views

Steps in mechanism of pyruvate dehydrogenase

I am having some trouble with certain steps in the mechanism below (from Mike Lu on Proteopedia) detailing the mechanism of action of pyruvate dehydrogenase converting pyruvate to acetyl-CoA. This ...
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1answer
4k views

How does repeatedly freezing and thawing antibiotics decrease their antimicrobial effectiveness?

This is something I have read on forums repeatedly, but I don't understand the mechanism behind how antibiotics lose their effectiveness. I understand how repeatedly thawing and freezing cells would ...
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1answer
80 views

Create combinatorial library of biologically plausible chemical compounds based on library of known compounds

I recently downloaded all the molecular structures (about 13,000) stored in Pherobase, an open library of insect pheromones. I would now like to create a derived, more extensive combinatorial library ...

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