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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19 views

How carbon nanotube sensors works?

How carbon nanotube sensors works? Is the protein (or chemical compound used as part of the sensor) placed inside the tube or where is it placed? and how is the technology used to place the protein ...
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149 views

How do enzymes affect a reaction's equilibrium?

I am not sure to understand something I read in a educational journal (1) Introduction Lets consider the following reversible enzyme-catalysed reversible reaction; $$E + S \leftrightharpoons ES \...
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2answers
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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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Michaelis–Menten kinetics applied to a solution with two enzymes

Two enzymes are added to a solution containing a tow concentration of a substrate that they can both use. Which statement is correct? A. Both enzymes will use equal amounts of the substrate. B. ...
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4answers
2k views

In sourdough bread baking what do the wild yeast and bacteria not eat during dough fermentation and why?

I bake bread using a sourdough starter. The starter is a culture of lactobacillus and some kind of yeast. They apparently eat the sugars or carbohydrates in the dough during fermentation but when I ...
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1answer
119 views

Does anyone know what program was used to make this molecular structure picture? [closed]

I am a quantum chemistry beginer, and this picture color scheme is classic. I wonder how to make such pictures by myself.
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1answer
59 views

How ph affects aesculune fluorescence?

I am facing a ween problem. I am trying to find out, how would look like the graph for fluroscence of aesculine (intensity of fluoroscence on Y axis and pH on X axis). I know, that increasing the pH ...
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2answers
99 views

Biological activity of the isotopes of the same element

I have a question regarding biological activity of different isotopes of the same elements, notably $\ce{^206Pb}$ and $\ce{^208Pb}$. Lead is known to be toxic, such that it can replace calcium from ...
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34 views

Differences in AChE inhibition kinetics between paraoxon and methyl paraoxon

According to literature, dimethyl paraoxon has a reaction rate constant for the aging (spontaneous dealkylation) of acetylcholinesterase of $\pu{0.186 h-1}$, a spontaneous reactivation rate constant ...
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1answer
63 views

How many alternative chemical ways to transport oxygen in living creatures are known?

Mammals and many other groups of animals usually transport oxygen using haemoglobin and other complex proteins, the core of which is based on an iron coordinated to a porphyrin. There are plenty of ...
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1answer
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Sensitivity vs. Limit of Detection of rapid antigen tests

I'm comparing a bunch of SARS-CoV2 rapid antigen tests: Columns 4 and 6 list the values for sensitivity and limit of detection (LOD). How come that a test with a several times lower limit of ...
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2answers
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What is the mechanism of AChE inhibition by Onchidal?

A naturally-occuring neurotoxin, called Onchidal, produced by a species of sea slug acts as an irreversible inhibitor of acetylcholinesterase. The structure of Onchidal is presented below: How and ...
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Haworth structures of sucrose and lactose

The haworth structures of lactose and sucrose is My question is regarding the glyosidic linkage, in lactose it is represented as a zig zag and in sucrose it is a "V". What does that mean. ...
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Reaction of glucose with 2,4-dinitrophenylhydrazine (DNPH)

In its open-chain form, glucose possesses an aldehyde group; however, glucose does not test positive with 2,4-dinitrophenylhydrazine (which typically forms a yellow/orange/red precipitate with ...
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Differences in AChE inhibition kinetics between VX and VR

According to the referenced paper, VR has an AChE inhibition reaction rate constant almost 4 times that of VX. Interestingly, its reaction rate constant for aging of the enzyme is less than that of VX,...
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2answers
413 views

Why does denaturation of albumen protein cause pH of solution to increase?

I'm interested in the denaturation of proteins by alcohols, specifically by ethanol. I have devised a simple experiment in which I inject solutions of ethanol (of variable concentrations) into ...
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28 views

Structure-Activity Relationship of Chlormephos and Parathion

According to the book "The Chemistry of Organophosphorus Pesticides", the insecticide Chlormephos (S-(chloromethyl) O,O-diethyl phosphorodithioate) has an oral LD50 in rats of 7 mg/k. ...
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1answer
75 views

Why does glycogen phosphorylase only act on the non-reducing end of the glycogen chain?

I read that glycogen phosphorylase only acts on the non-reducing end of the glycogen chain. This enzyme requires an inorganic phosphate molecule and PLP as a cofactor. The mechanism of the enzyme is ...
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32 views

Why is there a mirror image effect in the absorbance and fluorescence spectra?

I've read some answers online but I still can't seem to understand the mirror image effect. Why is the highest energy absorption (v" = 0 to v' = 4) the lowest energy fluorescence (v' = 4 to v&...
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0answers
32 views

How can DI water inhibit peroxidase activity?

I'm troubleshooting an IHC staining issue, and according to Thermo-Fischer's website, "Deionized water can sometimes contain peroxidase inhibitors that can significantly impair enzyme activity.&...
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1answer
43 views

Is the ratio between base pairs by chargaff accurate? [closed]

I am reading Lehninger's biochemistry textbook. It mentions that DNA may rarely contain uracil. Then it mentions that Chargaff found that the ratio of adenosine bases to thymine bases in DNA is 1. ...
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1answer
101 views

How do point mutations affect complementary base-pairing and widths of the nucleotide pairs?

Point mutations are divided into two categories: transitions and transversions. Since point mutations only occur during DNA replication (an integral process of both mitosis and meiosis), the mutated ...
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31 views

Which electrons are in HOMO in a peptide bond?

We've recently studied the absorption of UV light by polypeptides, and found that the peptide bonds itself absorhs UV light at around 210nm. I'm confused about what feature causes this to happen.
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1answer
2k views

Correct way of drawing D-configuration with this stereochemistry?

Hello! I have completely memorized how to draw all 20 amino acids in the way seen in the picture (middle, between the "ball-and-stick" and fisher projection) By my understanding this is in the L ...
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1answer
58 views

Entropy of Dissolution of Hydrocarbons

Here is what I think I know: The entropy of dissolution reactions increases as methylene groups are added (i.e. butanol has higher entropy of dissolution than propanol). Also, acyclic saturated ...
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1answer
35 views

Depicting a mechanism of peptide bond formation with protonated and deprotonated amino group

I've noticed that some textbooks and video lectures use an amino acid wherein the amino group has two hydrogens, and others use an amino acid with three hydrogens in the amino group (in the formation ...
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1answer
65 views

Is selenite (hydrous calcium sulfate) dangerous when you grind it up?

I was wondering about the safety of a specific mineral, Selenite. From my research, I have read that selenite is the crystalline form of gypsum, which is hydrous calcium sulfate. I was wondering if I ...
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30 views

Why is Chlormephos highly toxic despite requiring metabolic activation?

According to the book "The Chemistry of Organophosphorus Pesticides", the insecticide Chlormephos (S-(chloromethyl) O,O-diethyl phosphorodithioate) has an oral LD50 in rats of 7 mg/kg. For ...
2
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0answers
34 views

Right conductivity of protein sample for Protein A purification of human IgG?

A sample from a cell culture has some IgG and this is to be purified using protein A chromatography. Based on the chromatography handbook from GE-Healthcare/Cytiva, the protein sample should have &...
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1answer
49 views

Can soap make an liposome around virsuses?

I have read that soap does not kill bacteria and viruses, but it rather removes them, that is, it strips them off the skin sort of speak by forming micelles around them, which are then rinsed off. But ...
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1answer
43 views

Why polysaccharides are not considered as lipids? [closed]

It is mentioned in my textbook that all lipids have one common trait which defines them :they are insoluble in water;they are hydropohic. I want to ask ,since polysaccharides are also insoluble in ...
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2answers
136 views

How to experimentally determine the elemental composition in fingernails?

I am doing a project in my highschool about analysing C/N and C/S ratio of finger nails of various ages and sexes. Please suggest me a way to do this. I don't know where to start, I know the various ...
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1answer
121 views

Why are isomers of parathion less active acetylcholinesterase inhibitors than paraoxon?

Parathion itself has been found to be a very weak inhibitor of acetylcholinesterase. It normally requires metabolic activation and the conversion into paraoxon in the body to actually start exhibiting ...
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4answers
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What happens if you autoclave HEPES?

Many molecular biology protocols advice against sterilizing HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) solutions by autoclave. Supposedly, HEPES is heat labile, and the high ...
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1answer
34 views

Is incineration of a solid fuel complete or incomplete?

If I have some solid material like biomass and incinerate it at 1000 Celsius degrees for 15 minutes in an oxidized atmosphere within an incineration oven. As an output it gives me ash. Is the ...
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1answer
35 views

Ascorbic acid and aldehydes: Reaction and Influencing Metals

I've researched online and I've read that ascorbic acid can both promote oxidation and reduction depending on the conditions (I've read about trace metals but I've never found which metals affect its ...
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2k views

What methods could be used to preserve scorpion venom?

As extracting scorpion venom goes, how would one most effectively store and preserve the venom for future research? My thoughts are lyophilization, however I am not sure that would be the best of all ...
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2answers
6k views

Lugol's iodine 5 % aqueous solution

There is Lugol's 5 % solution with 5 g of pure iodine and 7.5 g of potassium iodide. In one ml there should be 12.5 mg of iodine in sum. But there are suggestions telling that two drops of this ...
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0answers
20 views

What is the composition, function, and classification of “6-Thio-2-Deoxyguanosine” and “13-mer thio-phosphoramidate”? How do I learn more about them?

I am assigned the task of explaining a biomedical research paper, it is about telomere and telomerase , and it talks a lot about the molecule Thio-2-Deoxyguanosine , 13-mer thio-phosphoramidate and &...
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1answer
37 views

Do antimicrobial abilities of copper boilers decrease over time?

As copper boilers age and develop oxide buildup, does this lessen the copper's antimicrobial abilities in killing bacteria? I was thinking since that coating would be on the copper, there would be ...
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2answers
40k views

ATP break down and energy release?

I have a very basic question. Energy is absorbed to break bonds. Bond-breaking is an endothermic process. Energy is released when new bonds form. Bond-making is an exothermic process. But ATP breaks ...
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0answers
24 views

How do structural differences between neostigmine and TL-599 contribute to differences in toxicity?

Stevens and Beutel studied the activity of several carbamate anticholinesterases. Among other things, they found that the (4-trimethylammonio)phenyl dimethylcarbamate iodide (The para-analog of ...
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0answers
47 views

Why are S-thiocarbamates less toxic than carbamates?

According to Haley and Rhodes, neostigmine bromide (alternatively known as Prostigmine) has an LD50 in mice of around 0.165 mg/kg by IV injection. Pubchem claims that this is also the LD50 for ...
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0answers
142 views

What favors the active transport in a membrane?

I was reading about active transport in membranes where ATP is used. ATP "reacts" with the protein pump and converts into ADP and also make a conformational change to the pump. Now this ...
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1answer
70 views

Cleavage of type 1 collagen by pepsin.

Where does pepsin cleave a human type 1 collagen molecule? Does it occur at multiple locations or only one?
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18 views

pH Dependency of IR Stretching Frequency in CO-binded Heme Protein

If one consumes CO, then CO binds with Heme Protein forming a Fe-CO bond. My question is if there will be any pH dependency on IR Stretching Frequency, i.e. ν(CO) and ν(Fe-CO). And if there is, then ...
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2answers
5k views

Why there is hydrogen bonding involved in salt bridge formation between glutamic acid and lysine?

I saw this figure on Wikipedia: After seeing this image I got really confused about the difference between these two, or maybe the similarities. Of course, I understand that a hydrogen bond can be ...
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0answers
42 views

Molecular dynamics simulation of a protein in acidic medium

I want to perform an MD simulation of a protein under acidic solvent conditions. A quick literature search seems to indicate that people are more interested in the protonation of protein side chains (...
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0answers
57 views

Can bis-quaternary aromatic compounds act directly on acetylcholine receptors?

The book Cholinesterases and Anticholinesterase Agents gives examples of bis-quaternary aromatic compounds that are capable of inhibiting acetylcholinesterase. Page 400 gives examples of some such ...
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24 views

Reaction rate constants for the inhibition of cholinesterases by various carbamates

Darvesh et al. [1] have conducted a study on the anticholinesterase activity of various carbamates derived from phenothiazine. The authors measured the inhibition rate constants of rivastigmine for ...

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