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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5
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2answers
174 views

Derivation of time probability distributions for single molecule kinetics

If we have a protein $\ce{A}$ that can bind to protein $\ce{B}$: $$\ce{A + B <=>[$k_\mathrm{fwd,1}$][$k_\mathrm{rev,1}$] AB}$$ and the bound complex $\ce{AB}$ can be converted into $\ce{C}$: $...
5
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1answer
124 views

Hill equation with inhibition and activation

The Hill equation for an activating enzymatic interaction with cooperative multiplicity $n$ is $$\frac{\mathrm d[\ce{P}]}{\mathrm dt} = V_\mathrm{max}\frac{[\ce{S}]^n}{K_\ce{S} + [\ce{S}]^n}\tag{1}$$ ...
3
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1answer
469 views

How are glycosidic linkages formed?

Consider glycosidic linkages in disaccharides. I know a condensation reaction occurs, with the loss of water. But which OH is lost? The O in the linkage belongs to which monosaccharide? Example: ...
5
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0answers
83 views

Why is there no effective alternative to metal salts in antiperspirants?

Metal salts, especially aluminum compounds are used in antiperspirants to prevent sweating. I found out aluminum chloride hexahydrate, which is found in most antiperspirants, undergoes an acid-base ...
0
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1answer
49 views

How do cells form a solid structure? [closed]

How do cells unite to form a solid structure. For example a plant body is made up of a number of cells. The cells are not solid structures. Their consistency is in between solid and plasma. So how ...
3
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1answer
30 views

Purification of Solid Phase Synthesized Peptide

I began working in a newly setup lab, and I'm having a dilysine (K2) peptide synthesized by solid phase method. I plan to cleave the peptides from the resin with a cleavage cocktail of TFA. ...
2
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1answer
96 views

Is hydrolysis of polypeptides and polysaccharides “anabolic” or “catabolic”

When a polysaccharide or polypeptide is hydrolyzed into mono-saccharides or amino acids, the building blocks can be oxidized to release energy. The oxidation is considered to be catabolic since it ...
1
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1answer
104 views

What is the chemical equation for the digestion/decomposition of cellulose?

I'm trying to find the chemical equation/pathway from cellulose $\ce{(C6H10O5)_n}$ to methane $\ce{CH4}$. What are the other reactants or products in the reaction? $$\ce{C6H10O5 + ? -> CH4 + ?}$$ ...
1
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0answers
19 views

Flow of electrons DNMT [closed]

In a paper about the modes of action of DNMT, it said there an increased flow of electrons to carbon 5 following the formation of a covalent bond between DNMT and carbon 6 on cystine. Why is this? ...
4
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3answers
158 views

What is the precise definition of Ramachandran angles?

The Wikipedia article Ramachandran plot is very schematic and doesn't even say when these angles are considered to be zero. It seems to assume that the peptide chain has no end, and always shows the ...
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0answers
30 views

Which Flocculant/Coagulant is ideal for harvesting Algae?

While dealing with Algae fit for human consumption (as protein supplements), which is the most suitable coagulant/Flocculant available? Factors to consider: 1) Cost Effectiveness (for instance poly ...
4
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1answer
147 views

Why is molybdenum that important in inorganic synthesis as well as biosynthesis of ammonia?

We know that Mo (Molybdenum ) is used as a catalyst for Haber's process, during synthesis of Ammonia from Nitrogen. Again, in biological systems, Nitrogen fixation (ALSO forming Ammonia from Nitrogen)...
3
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1answer
75 views

Can glucose and insulin exist in the same container without reacting?

Someone asked if glucose and insulin could be mixed in the same container and used as an injection to provide a quick energy boost. I'm not interested about the medical part of this question, but just ...
0
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2answers
117 views

When amino acids react with each other, how do you know which one reacts using it's carboxylic group and which one with it's amine group?

For example the dipeptide val-ser, between the amino acids valine and serine, does valine's amino group react or does it's carboxylic group with serine's respective group?
3
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1answer
204 views

Histidine vs Lysine

Among the amino acids, histidine and lysine, which is more basic? And why? I tried protonating and checking electronic effects but couldn't reach a satisfactory conclusion.
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0answers
18 views

Why a Differential Scanning Calorimeter (DSC), to measure thermodynamic parameters, has problems?

I want to use a Differential Scanning Calorimeter (DSC) to determine when my protein unfolds as you increase the temperature in a DSC machine. The machine is pressurised (to 3A) during the run, so ...
0
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0answers
45 views

Predicting Glycine-HCl's multiple equivalence points

I have currently completed a titration curve for glycine-HCl (2omL @ 0.1M, therefore 2.0mmol) where I have the known pH at each interval of added NaOH (adding 4mL each interval of 1.0M then measure pH)...
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0answers
25 views

What is the difference between oxalacetate and oxaloacetate?

What is the difference, if any, between oxalacetate and oxaloacetate? Is the former archaic nomenclature? Thanks
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0answers
50 views

How to recreate bioluminescence in fireflies in a lab?

I have several mg/mL of D-luciferin, luciferase (firefly), ATP solution (25 mmol) and MgSO4 (for the mg2+ ions). The experiment has to be done in cuvettes of 2,5 mL (if I get any results, it will be ...
-2
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2answers
41 views

Help required for the calculation of moles [closed]

If 4.5ml of yeast prep + 0.5ml of 0.25 M glucose is separated into 2ml in 2 similar flasks. How many micromoles of glucose are there in one flask? Using M1V1=M2V2 (0.5ml/1000)*0.25M = M2 * 2ml = 0....
2
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0answers
24 views

why do cone cells have broad responsivity spectra peaks?

My understanding of vision is that, although the cone cells in our eyes can detect three colors, there is enough overlap in the responsivity spectra (as shown here: https://en.wikipedia.org/wiki/...
1
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2answers
139 views

How to determine steady state of multi-step reaction with both reversible and irreversible steps?

I am trying to determine the relative concentrations of $\ce{U1}$, $\ce{U2}$, and $\ce{E}$ when the following reaction is at steady state. Note that $k_t$ is the zero order rate constant of new $\ce{...
0
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0answers
68 views

How can the ocean act as a buffer?

I was reading up on the buffering effect of the ocean and I was quite confused about how the buffer is able to do anything. The buffer I will refer to is below: $$\ce{CO3^{-2} +H2O <=> HCO3 + OH^...
3
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2answers
331 views

How does existence of alpha and beta form of glucose prove that it exists as a cyclic structure

My book says that Glucose is found to exist in two different crystalline forms which are named as $\alpha$ and $\beta$. Next it says that This behaviour could not be explained by the open ...
2
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1answer
208 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) ...
2
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2answers
63 views

Measuring a high Michaelis constant using fluorescence

We have the task of measuring kinetic parameters of an oxidase reaction that has a $K_M$ of about $2 \,\text{mM}$. For that, we want to use a fluorescence assay based on Amplex Red. The latter is a ...
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1answer
40 views

Can someone suggest me method to extract carotenoids? [closed]

I want to extract carotenoids, but want to use some inexpensive method. can you suggest me some method?
3
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1answer
59 views

Why would decreasing ionic strength of buffer disrupt hydrogen bonds

I'm reading about cDNA synthesis in my textbook and it mentions that: The captured mRNAs are subsequently released and collected, for example, by decreasing the ionic strength of the buffer so that ...
1
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2answers
104 views

What happens during Glycolysis? [closed]

Can I get brief explanation of the reactions that occur under Glycolysis? What do the curved lines represent?
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1answer
71 views

Complementary base pairing

In the molecular structure of a DNA it is seen that purines (adenine and guanine) bind with pyrimidines (cytosine, uracil and thymine) through hydrogen bonds, and this is always between a purine and a ...
2
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0answers
49 views

What's causing this dip in the FCS curve?

This is a fluorescence correlation spectroscopy measurement of light harvesting complexes. What could be causing the dip at 100 microseconds? Edit: The same thing was observed using fluorescence ...
2
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1answer
77 views

Make paper from hair? [closed]

Hair is fibrous... Is there a good reason, why we don't recycle our own hair (and clothing, what have you) into paper-products? (rather than cutting down trees)?
2
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1answer
55 views

What would happen if we had a different kind of metal in our bloodstream? [closed]

It is a common fact that we have iron in our blood. But what if we had something different in its place? Like instead of iron what if it was copper, or silver, or what if we had gold in our blood ...
-1
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1answer
49 views

Opening the imidazoline ring in tolazoline

Hello. I was studying about the alkaline ring opening or purines. While doing research, i came across this compound. This got me thinking if we can use the same procedure to open the imidazoline ring ...
-1
votes
2answers
569 views

Why does bond breaking in ATP release energy? [duplicate]

We always come across that formation of bonds releases energy, and bond breaking requires energy, but in the case where ATP converts into ADP or AMP (bond breaking), energy is released. Why? Further, ...
1
vote
1answer
59 views

Acid value of linseed oil

For this we weigh $\pu{1.015 g}$ of linseed oil which is dissolved in alcohol. 3 drops of phenolphthalein (pH indicator) are added and a solution of potassium hydroxide of concentration $C = \pu{9.5e-...
1
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0answers
44 views

How many natural products are there in existence? [closed]

Hi I'm doing a project on natural products and I'm wondering if somewhere there is at least an estimated number of how many exist? If this exists somewhere can you please provide a reference. ...
0
votes
1answer
262 views

What do the dots mean in HN.CO.CH3 connected to the second carbon of N- Acetylglucosamine? And what do the N and acetyl indicate?

What do the dots mean in HN.CO.CH3 connected to the second carbon of N- Acetylglucosamine? And what do the N and acetyl indicate?
1
vote
1answer
25 views

EtG formation outside the liver

Ethyl glucuronide (EtG) is formed by conjugation with glucuronic acid catalyzed by the enzyme UDP-glucuronosyltransferase. My question: Is it possible for EtG to form spontaneously in a urine sample ...
1
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1answer
100 views

Why does a lowered dielectric constant cause RNA/DNA precipitation in ethanol precipitation?

For ethanol precipitations, as mentioned in https://en.wikipedia.org/wiki/Ethanol_precipitation, given that the attraction of water molecules to charged ions like phosphates is based on Coulombic ...
0
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1answer
44 views

Are enzymes with superior catalytic properties more sensitive to temperature changes?

I am wondering whether enzymes with superior catalytic properties are more or less temperature sensitive than average enzymes. I know that enzymes lower the activation energy, Ea. So the more ...
3
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0answers
80 views

When the present state of knowledge concerning central noradrenergic transmission was established?

Some time ago I began to search for descriptions of the mechanisms responsible for the regulation of noradrenergic transmission in the central nervous system of man and to my great surprise the most ...
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0answers
15 views

Lipophilicity computational prediction

Is there a web based (or otherwise) computational chemistry tool which is able to calculate lipophilicity of a given compound?
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2answers
38 views

What's the use of adding 73 mM H2O2 to a supertanant? [closed]

Enzyme assays Determination of catalase specific activity The CAT (EC 1.11.1.6) enzyme activity was measured according to Gallego et al.38 Plant samples were grinded in $\pu{0.1M}\ \ce{...
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0answers
40 views

Mobility of Cations in the Environment

I have recently performed an experiment in which I tested the affects of phytotoxic cations on the rate of germination of the common navy bean. I did this out of curiosity, as I have recently been ...
8
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2answers
2k views

Why is arsenic toxic to humans?

I don't understand why arsenic is toxic and why it does damage to humans. Could it be that it is so similar to phosphorous? If so, would that make antimony toxic as well?
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0answers
130 views

What is the purpose of tetrazole in oligonucleotide synthesis?

The ATDBio book on nucleic acids describes tetrazole as an activator required to couple nucleotides. The diisopropylamino group of the nucleoside phosphoramidite is protonated by the activator, ...
1
vote
1answer
400 views

What does it mean to equilibrate a column in size exclusion chromatography and why is a buffer used?

I'm reading a procedure on size exclusion chromatography and it says that the first step is to equilibrate the column with buffer. What does this mean?
1
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1answer
57 views

What citrate is a common anticoagulant?

When I underwent plateletpheresis, something that the staff called "citrate" was added to my blood as an anticoagulant. Everything I can find about this product online refers to it as just "citrate". ...
2
votes
2answers
85 views

Are the stereoisomers of nucleosides actually anomers?

An anomer is an epimer at an (hemi)-acetal carbon like $\ce{R2C(OR')2}$. Why is the 1'-position of a nucleoside referred to as the anomeric center despite the lack of acetal functional groups?