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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1answer
54 views

Why is Nylon-2,6 biodegradable but Nylon-6,6 isn't?

Both have similar functional groups so what causes Nylon 2,6 to be biodegradable while Nylon 6,6 is not?
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General cleaning solution for clinical chemistry applications

I want to reuse some plastic and glass items that I am using to do colorimetric concentration analysis of serum and urine. There are some enzymatic assays, mineral assays and so on. I have been trying ...
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2answers
88 views

Acidity of thiamine - how comes hydroxide anion with pK about 15 ionizes thiamine with pK about 18?

Textbooks say removing proton from thiamine's C atom will produce a resonance stabilized carbanion which is hence bioactive. That's OK, but how comes that 1) we abstract the acidic proton with the OH ...
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1answer
34 views

How to troubleshoot absorbance analysis when readings fluctuate

I am trying to measure creatinine in fluids by using an enzymatic (creatinine) test. I try to determine the concentration by the difference in absorbance before and after 5 minutes after a reagent is ...
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0answers
28 views

What do natural hybrids of peptides and nucleic acids look like?

Until recently I thought that there was a clean distinction between polypeptides and oligonucleotides, but apparently there are recent studies of therapeutic compounds that could be described as "...
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Protein crashing [closed]

I'm an undergrad trying to write a research proposal. I just found out that the protein I want to study is extremely prone to crashing and that the grad students + postdocs in my lab are all afraid of ...
2
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0answers
20 views

What are "molar equivalent amounts" in a description of an immune cross-reaction assay?

From "Folate Receptor Alpha Autoantibodies in Autism Spectrum Disorders: Diagnosis, Treatment and Prevention" (2021): Figure 2. (A) Folate receptor concentrations in milk. (B) Immune cross-...
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1answer
29 views

In electrophoresis of amino acids and dipeptides, how can I rationalize the observed mobilities?

For part b(i) why is the spot tyrosine? I know tyrosine has an overall -2 charge while phenylalanine has an overall -1 charge. However, phenylalanine has a smaller Mr so shouldn't it travel faster? ...
0
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1answer
28 views

What happens when you dilute a surfactant solution at the critical micelle concentration?

Say if instance I have a 100 ml solution with micelles formed using some surfactant. Now if I pour that 100 ml solution into 500 ml of water, will those micelles break up into free surfactant again? ...
2
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1answer
52 views

What is the maximum length of peptide which considered to be hard for synthesis by the current technology?

I am a molecular biologist and work with recombinant proteins. I am wondering what the cut point, in terms of length, is at which I should produce the peptide using heterologous expression rather than ...
2
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1answer
42 views

How to identify 'water' mistakes in protein crystal structures: Are B-factors and occupancy good indicators?

When solving the structure of a protein from diffraction data (x-ray crystallography), it can sometimes be difficult know what should be modelled into small spheres of electron density that are not ...
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What is the point of lipoproteins if albumine exists? [migrated]

Why do Lipoproteins (Apo B 48/100 , Chylomicrones, etc.) exist if Albumine is capable of transporting fatty acids? Why doesn't the body just transport everything via albumine?
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Why can't evaporation be carried out in an Erlenmeyer flask? [duplicate]

Our class was doing an experiment about the precipitation, filtration, and evaporation of potassium iodide and lead(II) nitrate. Our teacher said that we can't use the Erlenmeyer flask for evaporation....
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3answers
274 views

What is the difference between structure assignment and structure prediction?

I am absolutely new to structural bioinformatics (only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using machine learning. ...
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2answers
61 views

Is it false that the absorbance of two concentrations is the sum of the absorbances of the concentrations?

I am in the lab and trying to perform the molybdenum blue test for phosphorus using a photometer. It appears common speak in colorimetric lab sheets that Absorbance of a mix of two concentrations is ...
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0answers
47 views

Why are glyosidic linkage of glucose and fructose rings often occurring at the 1' and 4' prime positions?

Here are some example combinations from my textbook: In all of these combined products, the reactive centres seem to be the carbon at first position/ fourth position from the oxygen in priority. Is ...
0
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1answer
449 views

Why is the 1,6 linkage in Amylopectin an alpha link and not a beta link? [closed]

The alpha link as I have understood it means that the $\ce{OH}$ molecules which make up the glycosidic bond lie on the same side of(above/ below) the plane and for beta, one lies above the plane and ...
3
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0answers
76 views

How to control pH in a fermenter based on the acid produced by mircoorganism

I have got a bioreactor with an aqueous medium which produces biomass (yeast; S.cerevisiae) after inoculation. I am observing and collecting data over the whole process via probes/etc. on different ...
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0answers
75 views

Why don't ant bites kill us?

So, methanol is supposed to be toxic even in minute quantities because it is oxidised in our body to methanal and then methanoic acid. This can cause blindness and even death. Interestingly, ants ...
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0answers
39 views

Why does CO2 have a greater affinity for hemoglobin than oxygen?

I know about CO but I am wondering if CO2 has similar mechanism? do you guys have any scientific reference These species help form interactions between amino-acid residues at the interfaces of the ...
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1answer
570 views

Why are hydrogen bonds in an antiparallel beta sheet stronger than those in parallel beta sheets?

Beta sheets are illustrated as such in most diagrams, where: In an antiparallel β-sheet, the polypeptide strands are arranged such that a $\ce{C=O}$ and an $\ce{NH}$ from adjacent strands face each ...
3
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1answer
69 views

Deactivate lectins in beans by baking

Having dried uncooked beans, I read that the lectins can be deactivated by boiling and soaking for a while. What I could not find any information on is if dry baking beans would eventually deactivate ...
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0answers
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Nanocomposite hydrogel for wet adehsion in biomedical applications

My name‘s Tristan and I‘m a bachelor‘s student in Germany. I‘m trying to synthesize an injectable nanocomposite hydrogel for wound closure and wound healing applications. The problem is that, next to ...
3
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1answer
117 views

Which solvent is good for using SU-8 particle in Optical tweezers?

I'm studying Optical tweezers. I've used Polystyrene for samples. Nowadays, I've got SU-8 pillar. I wanna use that for sample, but its density is heavier than water. I can't use that. So I wanna know ...
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1answer
33 views

How do I expand a selection in Jmol to include entire residues?

I know how to select by distance in Jmol: select within(5, ATP) This selects atoms that are within 5 Angstroms of ATP residues. How do I expand the selection to include the entire residues of the ...
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1answer
48 views

How Bread is made with yeast, sugar and luke warm milk? [closed]

Materials and Apparatus: wheat flour sugar dry yeast glass bowl covering plate milk Procedure: Lukewarm milk is taken in the glass bowl and sugar is added to it. Then, yeast is added to the same. ...
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1answer
3k views

Benzaldehyde and Cyanide - if you can smell one can you smell the other?

Cyanide and benzaldehyde both have an almond-like smell. Some people cannot smell cyanide (specifically, HCN). Can they also not smell benzaldehyde? In other words, do they both trigger the same ...
4
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2answers
1k 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
66 views

What is a non-organic analog of a metabolic pathway?

The wikipedia page on the Belousov-Zhabotinsky reaction states the following: The discovery of the phenomenon is credited to Boris Belousov. In 1951, while trying to find the non-organic analog to ...
2
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1answer
71 views

Finding the sensitivity of zero-order ultra sensitivity and its parameter dependence

I am provided a one-dimensional reaction system showing zero-order ultra sensitivity. $$\ce{X_1 ->[f_1] X_2}, \quad \quad \quad \ce{X_2 ->[f_2] X_1}$$ The reaction rate function is the reduced ...
13
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1answer
52k views

How do you identify reducing / non-reducing sugar by looking at structure?

Identifying reducing / non-reducing sugar been confusing me for a while now , I know that reducing sugar contain aldehyde or ketone group . It's easy to identify them in monosaccharides but this ...
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1answer
132 views

What is the pI of lysine tripeptide?

What the the $\mathrm{pI}$ of a tripeptide of lysine? $$ \begin{array}{l|ccc} \hline \text{Group} & \ce{Lys{-}α{-}NH3+} & \ce{Lys{-}ε{-}NH3+} & \ce{Lys{-}α{-}COOH} \\ \hline \mathrm{p}K_\...
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1answer
152 views

How can I model cellular membranes in terms of topology?

I'm reading from Principles of Physical Biochemistry by Kensal E van Holde (1998-01-06) in order to review some biochemistry and work my way toward a more mathematical approach to understanding ...
2
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0answers
65 views

How is it decided that a particular chemical or compound is useful for a very specific purpose? [closed]

In textbooks, I often find extremely specific uses of chemicals. Is chemistry research mostly focused towards finding specific use cases? For example, I know that boric acid kills snails. How do ...
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1answer
44 views

Using samples in titrations

I've never done an experiment before. So, the methodology provided in this pdf is quite confusing. Link to the pdf: https://www.canterbury.ac.nz/media/documents/science-outreach/vitaminc_iodine.pdf So,...
5
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1answer
304 views

Why does hydrolysis of ADP to AMP yields the same amount of energy as ATP to ADP, if ADP is more stable?

I learned about the resonance stability of ADP and the fact, that ATP is less stable due to intramolecular instability. I was surprised to see that the energy net of conversion of ADP to AMP is the ...
2
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1answer
123 views

Do enzymes that digest D-glucose react with L-glucose?

D-glucose most common in nature and L-glucose is synthesized in the lab. I know that humans can't use L-glucose in their aerobic pathways because it doesn't match the active site of the enzyme ...but ...
4
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3answers
4k views

What's the effect of temperature on buffering capacity?

I did some research online but I still couldn't get any conclusion. Some said that the buffering capacity decreases when temperature increases because of the increase in ionisation of the weak acid ...
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1answer
1k views

Bends in cis Isomers

It’s been said over and over in my biochemistry books that the cis-double bonds between the Cs in the hydrocarbon tails in triglycerides causes a kink. This kink disappears when the bond is isomerized ...
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0answers
38 views

Textbook on Food Additives? [closed]

My Question. Is there a comprehensive textbook on (synthetic) food additives? Many textbooks on nutrition omits any discussion of food additives, so I was hoping there is a book devoted to the subject....
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0answers
30 views

Why there is not a consistent pattern between the carbon chain length and the melting point of fatty acids? [duplicate]

I looked at the melting temperature of different saturated fatty acids and I expected to see that with a longer chain of carbon the melting point would be higher as after all the var der Waals ...
7
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1answer
154 views

Are all protein tetramers considered to be "dimers of dimers"?

Is every tetramer thought to be a dimer of dimers? Because even if every subunit is unique in structure, it could be a heterodimer of heterodimers? Or is the term "dimer of dimers" reserved ...
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4answers
939 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 ...
4
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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
310 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
73 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),...
2
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1answer
30 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
677 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
381 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 ...

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