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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46 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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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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1answer
143 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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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
48 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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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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1answer
63 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 ...
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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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30 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
118 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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1answer
41 views

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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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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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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89 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
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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51 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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1answer
61 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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1answer
152 views

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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25 views

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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1answer
503 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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1k 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
107 views

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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1answer
68 views

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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1answer
373 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 ...
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1answer
992 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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25 views

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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1answer
105 views

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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1answer
113 views

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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1answer
59 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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1answer
58 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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2answers
189 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
184 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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0answers
20 views

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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1answer
68 views

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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1answer
176 views

Which textbook is this image on protein tertiary structure from?

I am trying to find the original textbook image that is the inspiration for many schematic figures showing tertiary interactions (hydrogen bonding, ionic interactions, hydrophobic interactions, ...
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43 views

A question about ligand binding

I have done part a and part b but I keep getting a negative concentration for part c. For part a I got $\pu{2 \mu M}$ For part b I got $\pu{5.051 \mu M}$ For part c, I get $2=3.2 + \text{[bound ...
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1answer
50 views

Why is the glycosidic bond between sugars always between the anomeric carbon?

Why can't the hydroxyl group of another carbon condense with another OH of the second sugar (like 2,4 glycosidic bond) Thanks
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2answers
515 views

Does mixing two different foaming soap make it ineffective?

To save soap during this pandemic, I mixed foaming soap of two different brands and then the solution became cloudy (both originally transparent) . It seems foaming okay. But does this make the soap ...
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1answer
29 views

Weak acids compared to strong ones in pH > 7 solution

In the book of Molecular Cell Biology (Big Alberts) by Alberts, at page 46, it is stated that Acids—especially weak acids—will give up their protons more readily if the concentration of > H3O+ in ...
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1answer
107 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 ...
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1answer
226 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 ...
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48 views

Transformed chemical potential of formation: something weird in Alberty 2003

I am trying to wrap my head around transformed chemical potentials, as described in Thermodynamics of biochemical reactions (R. Alberty, 2003), however, two equations seem to be contradictory in this ...
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36 views

In electrophoresis, are positive and negative molecules obviously separated?

I have just studied electrophoresis in biochemistry. The charged particles move to the oppsite charged electrodes whose speed is depended on their particle size. If that so, are negative and positive ...
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77 views

Which amino acids can be totally synthesized? [closed]

I can't find information regarding which amino acids (say the proteinogenic ones or in general) can be totally synthesized. Is there a reference?
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43 views

Solving for Concentration Using pseudo-First Order Kinetics

The following graphs represent a pseudo-first order bi-molecular reversible reaction with the formula $\ce{A + B <=> C}$: The reaction product has an extinction coefficient of $\pu{50000 M-1 cm-...

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