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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12
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4answers
944 views

How can a protein folding transition state have zero lifetime?

I'm doing a module on my Biochemistry course looking at protein folding, and in a discussion of [folding] transition states I was a little confused at the thought of a zero-lifetime transition state - ...
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2answers
48 views

Can you discriminate a monooxygenase from other enzymatic mechanisms by the requirement of NADPH?

I am working on a project about CYPs 450. It seems that most of them function as monooxygenases but there are other categories as well. Assuming that the question makes sense, is it correct to say ...
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1answer
3k views

Why is copper(II) sulfate added drop by drop during the Biuret test?

The Biuret test is a test for proteins. The procedure is to add a strong base, such as NaOH, to dissolve the protein. After that, copper(II) sulfate is added drop by drop into this until a (violet) ...
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2answers
319 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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2answers
74 views

To which extent is protein folding conserving subprotein structures?

I am actually a pure mathematician, who stumbled over this paper «Protein-Folding Analysis Using Features Obtained by Persistent Homology» by Ichinomiya et al. (Biophys. J. 118, 2020, 2926-2937; link),...
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1answer
31 views

Trying to understand phrase in paper: preventing nonspecific binding of AuNP antibody conjugates using a blocking solution

I am working through a paper, Lateral flow immunochromatographic assay on a single piece of paper. I'm having trouble understanding one of the points! Under the Device fabrication question, it says: ...
9
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1answer
688 views

Can sugars dissolve in liquid ammonia?

Can monosaccharides and disaccharides dissolve in liquid ammonia due to hydrogen bond formation? My rationale is that these sugars may be able to form hydrogen bond with ammonia ($\ce{NH3}$).
3
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1answer
384 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 that ...
3
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2answers
415 views

Why is LDL more easily oxidized/damaged than HDL?

Why are low-density lipoproteins (LDL) more easily oxidized than high-density lipoproteins (HDL)? By LDL and HDL, I mean the lipoproteins that carry cholesterol. Oxidation of LDL ultimately ...
2
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0answers
29 views

Gluconeogenesis

So I've been doing research on the production of lactic acid, however, I found that lactate will first reform into pyruvate and then go through gluconeogenesis reforming D-glucose. From what I ...
6
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4answers
821 views

Ramachandran plot Phi(ϕ) Psi(ψ) dihedral angle Convention for Zero, Positive and Negative value- old and new

Update: possible duplicate: What is the precise definition of Ramachandran angles?. Question modified. G.N. Ramachandran et al, in their own work (PMC) (DOI), did not used phi(ϕ) and psi(ψ) as we use ...
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2answers
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Side reactions of N-hydroxysuccinimide esters with nucleophiles

N-Hydroxysuccinimide (NHS) chemistry is commonly used in chemical biology to react with primary amines like lysine and the N-terminus of proteins. I was curious how labile NHS esters are to other ...
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1answer
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Is it possible to chemically treat grass to make it digestible?

Is it possible to chemically treat grass after "harvesting" it to make it digestible by humans? I know we can "eat" grass, but we can't break it down in our stomachs. If there is some chemical ...
7
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1answer
46 views

In solid-phase peptide synthesis, why are the formation of aspartimides a problem but not "glutamides"?

I'm studying solid-phase peptide synthesis (SPPS) at the moment, and a common problem is the formation of aspartimides, which disrupt the synthetic process. I understand how they form and why are they ...
5
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1answer
38 views

Carbon 11 radiolabeled inhaled Beta-2 agonist or corticosteroids, is it possible?

Background Positron emission tomography (PET) is a highly sensitive imaging modality that can provide in vivo quantitative information of biological processes at a biochemical level. PET relies upon ...
3
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0answers
36 views

Why neglecting Bradford Solution Volume in the assay?

I would like to know why do we not need to take account of Bradford agent solution in dilution calculation? For example, $\pu{2.5 \mu g mL-1}$ BSA will calculate from $\pu{0.4 \mu L}$ of $\pu{1 mg mL-...
5
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1answer
171 views

Calculate Michaelis-Menten constant of enzyme catalyzed reaction

I have: $$\begin{array}{c|c} \dfrac{v }{ [S]}/\pu{s^{-1}} & v \cdot 10^2/\pu{mol dm^-3 s^-1} \\ \hline 0.257\ & 5.15\\ 0.895 & 4.48\\ 2.00\ & 3.35\\ 3.59\ & 1.8\\ 4.82\ & 0....
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1answer
3k views

Amino acids: why is charge found by comparing pH and pKa and not pH to pKa + log [A-]/log[H+]?

I am working on problems such as : The charges on the side groups at each pH are found by the following rule: at $\ce{pH < pK_a}$, $\ce{H+}$ on, protonated at $\ce{pH > pK_a}$, $\ce{H+}$ off, ...
4
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1answer
2k views

Why is arginine's positive side chain classified as basic and not acidic?

Arginine has a positive side chain. Doesn't this mean it wants to lose a proton H+? Isn't something that wants to lose or donate a proton an acid? Yet my book states, "arginine has a positively ...
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0answers
36 views

How does the membrane potential change so drastically during an action potential?

I understand that the Nernst potentials $$V = \frac{k_\mathrm{B}T}{e} \ln\left(\frac{c_\mathrm{out}}{c_\mathrm{in}}\right)$$ for all ions inside and outside a cell barely change when an action ...
1
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1answer
2k views

Finding 1/V from absorbance in Lineweaver-burk plot

I’ve got six test-tubes with $0.5\ \mathrm{ml}+0.5\ \mathrm{ml}$ of 0.005 %, 0.0025 %, 0.00125 %, 0.000625 %, 0.0003125 % and 0.0003125 % starch and 4.2 pH phosphate buffer solution (2, 4, 8, 16, and ...
1
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1answer
143 views

What is a triglyceride?

I'm confused on what a triglyceride is, from what my text book it says its a type of gylercide, then from a website it said Glycerides can be subdivided into two categories. The first group, the ...
1
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1answer
54 views

What is an alternate way of preparing a sodium hydrogen phosphate/sodium dihydrogen phosphate buffer through titrating an acid with a strong base?

So my friend and I are stumped. This is in the context of achieving the sodium hydrogen phosphate/sodium dihydrogen phosphate buffer by titrating the acid with a strong base. My friend says the answer ...
3
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2answers
96 views

Explaining a biochemical reaction (protein labelling, e.g. with fluorescent probes)

I am an immunology master student without prior knowledge of biochemistry. Could someone explain to me the following 6 reactions? What I want to understand is why exactly the reactions happen at this ...
3
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1answer
110 views

Reason for protonation of amino group in amino acids at near neutral pH

What happens to the amino group when amino acid is added to a near neutral solution? How does it come about gaining an extra proton? I understand what happen to the carboxyl group, since it is a ...
4
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0answers
40 views

Why is the reverse aldol cleavage of fructose 1,6-bisphosphate highly endergonic under standard conditions?

I have another question similar to this one. I just don't have intuition for why reactions are thermodynamically favorable or unfavorable and I'd like to build it. This time I'd like to ask about ...
3
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2answers
348 views

Coupled and Coupling Reactions

Is Coupling Reactions, Heck Reaction for example, different from Coupled Reactions like the production of Glucose 6-phosphate in living organism?
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1answer
30 views

Do phosphoryl thiocholines, their uncharged analogs, and other organophosphates, interact differently with Acetylcholinesterase?

As asked in the title, would the various salts -such as hydrochloride or methyl iodide- of V-Agents interact any differently with acetylcholinesterase compared to the neutral compound? For instance, ...
2
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0answers
59 views

How to find the reaction rate in an enzyme reaction?

First time posting questions here, so let me know if I need to edit anything. I need to decide $dC/dt$ and $dP/dt$ when the reaction is like this, where I only know we must have 2 substrates $S$ to ...
4
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2answers
109 views

Determine vmax and enzyme concentration (Michaelis–Menten)

I am given that the enzyme concentration is $\pu{15 nM}$ and the following data: $$ \begin{array}{rl} \hline S/\pu{mM} & V/\pu{mM s^{-1}} \\ \hline 1 & 0.202 \\ 2 & 0.368 \\ 5 & 0....
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2answers
56 views

How to run electrochemical tests on Microorganism (bacteria in a medium)?

I am trying to run some electrochemical tests(e.g.CV (Cyclic Voltammetry) & EIS (electrical impedance spectroscopy)) using half cell configuration on micro-organisms (e.g.bacteria). The bacteria ...
4
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1answer
2k views

Photosynthetic rate calculation

What are the steps in calculating the photosynthetic rate ($\pu{\mu mole}~ \ce{O2} \pu{m2/ min}$) for a leaf that has an area of $\pu{0.0025 m2}$ and a $\ce{O2}$ evolution rate of $0.096~\ce{O2}/\pu{...
3
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1answer
1k views

Find the number of water molecules "embedded" in sucrose

Recently I got a question as follows: How many molecules of water are joined with 12 atoms of carbon in a molecule of sucrose ? (A) 12 (B) 11 (C) 6 (D) 10 I am unable to ...
3
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1answer
860 views

Denaturing of Proteins and Nucleic Acids - Effect of Temperature (Heating vs Cooling)

Heating a protein/nucleic acid will disrupt inter-molecular and intra-molecular forces in the tertiary structure. It will also interfere with the shape of the active site if the protein. Does this ...
5
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1answer
602 views

SARS-CoV - relative size of the spike protein

I am taking an online course in image analysis and have been asked to use the attached image to determine the size of the SARS-S protein of the SARS-CoV relative to the total of its proteins. However, ...
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3answers
49 views

When an aqueous extract of a substance is said to be administered at a certain quantity, is the quoted mass analogous to one as original substance?

I'm trying to read studies about the possible toxicity of the leaves of some plant often said to possess positive medicinal properties. In the studies, performed on rats, it is usually said that an ...
28
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1answer
3k views

Why is heroin a more potent drug than morphine, despite having a similar structure?

The structures of heroin and morphine are quite similar, with heroin being formed by acetylation of morphine: Why is heroin so much more potent than morphine, when their structures are so similar? ...
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0answers
27 views

Electrolysis in Electrophoresis of proteins and DNA

Can electrolysis happen in an electrophoresis assay (such as SDS-PAGE)? To perform electrophoresis, the substances must be dissolved in an aquatic buffer with a previously determined ionic strength. ...
0
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1answer
78 views

Carbon atoms types in amino-acids [closed]

I'm looking for a table or another kind of schema where I can find which type of carbon atoms (sp3, sp2 etc.) are present in each amino-acid. In my biochemistry books these informations are not ...
9
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1answer
1k views

How to I neutralize the smell of (VERY) spoiled milk [closed]

Let's say I have a cup full of milk that had been at room temperature for months (apparently my son was running an experiment...). The smell started seeping out of the makeshift lid, and it's horrible....
3
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0answers
69 views

What is the structural formula of a monomer of hydroxypropyl methylcellulose?

I'm studying the properties of the polymer hydroxypropyl methylcellulose (HPMC) with the static scattering technique. I'm trying to interpret the molar mass obtained with a Zimm plot, that is $\pu{(3....
2
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2answers
2k views

What is the charge of the amino acid lysine at pH 2?

What is the charge of the amino acid lysine at $\mathrm{pH}=2$? $\mathrm{p}K_\mathrm{a}$'s are carboxylic: 2.18; amino: 8.95; side chain: 10.79. The side chain of lysine is an amine group, so I ...
3
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0answers
52 views

What do we know about the structure of the amylopectin iodine complex?

I am studying a method of finding the ratio between amylose and amylopectin using the difference in color of the amylose-iodine complex(blue) and the amylopectin-iodine complex (red/brown). Through ...
6
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1answer
65 views

Does the mechanism of AChE inhibition by Isoparathion depend on chirality?

It is known that the inhibition of acetylcholinesterase by isomalathion can proceed either with diethyl succinate as the leaving group or thiomethyl, depending on the specific stereoisomer of ...
3
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1answer
244 views

Why is the formation of a peptide bond not spontaneous?

Why is the formation of a peptide bond from a carboxylic acid and amine not spontaneous? I'm not looking for the free energy calculation; I have it from several sources. I'm just asking for an ...
0
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0answers
27 views

What is meant by the term 'biosynthetic origin'?

I keep seeing the term biosynthetic origin used in medicinal related papers. Does it just refer to the biological precursors to the molecule? So, for example, the biosynthetic origin of Paclitaxel is ...
14
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1answer
2k views

Why do green bell peppers become bitter when cooked?

Why do green bell peppers taste sweet raw, but become bitter when cooked (steamed)? What chemical process is responsible for this? (I don't believe the temperatures are high enough for the Maillard ...
4
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0answers
38 views

Why can't NAD+ undergo single-electron reduction?

$\ce{FAD}$ can undergo single-electron reduction to form a stable radical, which can then be reduced again to $\ce{FADH2}$. This is supposedly possible due to resonance stability, where the unpaired ...
4
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1answer
64 views

Why is the hydrolysis of ATP to AMP more energetic than the hydrolysis of ATP to ADP?

I am confused as to why the hydrolysis of ATP to AMP and pyrophosphate is more energetic than hydrolysis to ADP and inorganic phosphate, especially since pyrophosphates are more unstable than ...
9
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5answers
57k views

What's the difference between ΔG° and ΔG°'?

In biochemistry contexts, one often sees $\Delta G^{\circ\prime}$ ("delta G naught prime"), rather than the normal standard free energy change $\Delta G^{\circ}$ ("delta G naught"). What's the ...

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