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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22 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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Plastic-eating microbes at home

I wanted to know if I can nurture a bacteria which is not difficult to find and with time I can train them on harsh chemicals and soon introduce plastic into it with the hope that it will eat it up ...
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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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Bioorganic PKS Exam Revision

Hi all, going through exam revision for third-year Chemistry Exams. I'm coming up blank on some bioorganic questions on Poly Ketide Synthases. In the question it asks follows: 1)What post-...
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Biochem homework about fatty acids and DNA [closed]

Fatty acids are a segment of fats yet have a particular compound distinction separated from fats that would permit them to travel reasonably uninhibitedly in the fluid climate of the bloodstream. They ...
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27 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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33 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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30 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
42 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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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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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 ...
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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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What exactly is meant by the structures 2-alpha beta and alpha 2-beta 2?

In the context of protein quaternary structure. What exactly is indicated by 2αβ and α2β2 structures? What distinguishes the two forms and is this nomenclature only used for a dimer of dimers?
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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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Clarification on partial charge on atoms in amino acids in protein [closed]

Assignments of partial charges are different in different references for the same amino acid in a protein. For instance, AMBER force fields assign values to all the atoms. However, in the following ...
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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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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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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 ...
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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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27 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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1answer
102 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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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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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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35 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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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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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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54 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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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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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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1answer
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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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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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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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48 views

Does CH3COOH + H2O (vinegar) lose its antibacterial and antiviral properties when exposed to air?

I have been reading about using CH3COOH + H2O (vinegar) as a mild antibacterial and antiviral agent. For example: https://pubmed.ncbi.nlm.nih.gov/15698693/ Note, before anyone gets confused (or ...
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Do changing opt=modredundant to opt in Gaussian makes geometry optimization not to take into account frozen angles?

I am a newbie to Gaussian and just generated an input for the geometry optimization for some molecules with multi ring system. However, in the article that was a reference for those calculations, some ...
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Is writing D-(+)-glucose more correct than D-glucose? [duplicate]

In one of my books glucose is written as D-(+)-glucose everywhere. D represents the position of -OH group with respect to glyceraldehyde.. So D = (+)-Glyceraldehyde.. So won't writing D-(+)-Glucose ...
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496 views

What could these letters “S” in red circles mean in a biochemical diagram?

What could be the meaning of the red circles with letters S in them in the diagram below? I searched in the text but could not find. From "Role of TREK-1 in Health and Disease, Focus on the ...
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791 views

What are high-energy electrons?

I read that (in cellular respiration) the transported electrons in NADH have a higher energy than those in FADH2. I can't find a (simple or otherwise) explanation of what a "high-energy" ...
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1answer
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What's special about the purine scaffold?

Purine is a remarkable substance, given Nature has chosen it as the scaffold for two nucleobases from DNA/RNA: adenine (A) and guanine (G). Its structure also appears in several other substances of ...
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Understanding Scatchard Plots

Im having trouble understanding Scatchard plots. Y Axis = Bound/Free Ligand X Axis = Bound Ligand The graph has a negative slope. Why when there is almost no Bound (Y axis = 0) do we get a high ...
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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 ...
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201 views

Why is the amino acid cysteine classified as polar?

Cysteine amino acid has an embedded sulfur group in its side chain. Looking at the electronegativity difference of hydrogen and sulfur, it can be considered a non-polar side chain because the ...
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Why does the emission of dansyl group diminish with time in this experiment?

I don't know how to make sense of this. I what is happening when an enzyme (carboxypeptidase, which contains tryptophan as its only chromophore and uses a Zn(II) ion in its active center) hydrolises a ...
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Are all 'dextrorotatory' sugars in biology actually 'd' or '+' in chirality?

When papers or articles say that all proteinogenic amino acids are 'levorotatory' or 'L', they often make a point of saying that only half of them are truly, optically levorotatory. All of them (...
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How does pH affect the spontaneity of biochemical processes? [closed]

A decrease in $\mathrm{pH}$ increases the hydrogen ion concentration, thereby decreasing $Q,$ and decreasing Gibbs free energy as mathematically expressed: $$\mathrm dG =\mathrm dG^\circ + RT\ln Q$$ ...
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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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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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128 views

Why don't proteins form branched polymers?

My reference book (Princeton Review for SAT Chemistry Subject Test) mentions that: Proteins and carbohydrates are both polymers; however, only carbohydrates commonly form branched polymers. Glycogen ...
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1answer
94 views

Whats the driving force behind simple diffusion? Is it just the count of molecules?

If I were to have two separate containers with solutions of different concentrations with a small opening, most of the molecules would flow down the concentration gradient. Does this occur just ...
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Halogen vs H-Bond Donor/Acceptor: How do they differ?

I know that in rational design sometimes the researcher might use Cl or F instead of a H-Bond donor/acceptor. What kind of interaction does a halogen provide compared to the H-bond donor/acceptor? ...
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Ramachandran Plot for Phi and Psi angles of peptides

Why do we consider the normal and extreme limits for Ramachandran plots to be less than the Van Der Waal distances between two atoms?

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