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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2answers
43 views

What exactly makes a carbon atom “α” in a protein residue?

I'm a computer scientist and have no biochemical background, but was working on a project recently that had me going through a lot of protein residues for one reason or other. Feel free to correct me ...
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30 views

How does the cell decide whether to burn off a fatty chain (eg omega-6 fatty acid or a saturated fatty acid) or incorporate it into its cell membrane? [closed]

We hear (e.g. doi: 10.3390/nu8030128) that the percent of omega-6 fatty acids in human fat tissue has increased over the past 5 decades due to the excess use of corn oil/soybean oil/etc. How does the ...
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Lipid Composition in Cell Membrane and Physical Properties [closed]

Describe the physical properties of a membrane comprised of 45 mol % sphingomyelin, 45 mol % PG and 10 mol % cholesterol. Explain.
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Is there a trivial method to create pure glucose? [closed]

Is there a trivial method to create pure glucose? If so, how is it done? If not, what are least expensive, and least time consuming ways to accomplish the task?
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Prostaglandin Nomenclature

Prostaglandins are lipid substances derived from fatty acids, which act as powerful biochemical regulators. In Wade's Organic Chemistry, they indicate that there are several families of ...
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1answer
40 views

Meaning of hydrogen bonds for life [closed]

Why are hydrogen bonds so important for life? Or more generally asked: Why is water so important for life / biological systems? Or maybe again in other words: Why does especially water provide this ...
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1answer
26 views

Preferred IUPAC name of Protoporphyrin IX

I was looking up protoporphyrin IX and was surprised to find that no two websites gave the same IUPAC name for the compound. Here are some examples: 3,3'-(7,12-Diethenyl-3,8,13,17-...
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23 views

How does the pKa of a neutral molecule inform the protonation state of its positively charged molecule?

Let's say we have some neutral molecule A and its protonated form, A+. The pKa of molecule A is known, but we do not know the pKa of molecule A+. Can the pKa of molecule A+ be determined only knowing ...
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Calculate amount of enzyme needed for in vitro phosphorylation?

I have 100 micrograms of STAT1 and its molecular weight is 90 kDa. I calculated the number of moles to be 1 nmoles. The specific activity of JAK1 (the kinase) is 110 nmoles of phosphate per minute per ...
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1answer
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What question could be answered by “because the metabolites in the cell are in ionized form” in the topic of anaerobic metabolism?

I know it might sound a bit absurd, but my teacher gave us some "answers to question", that is, given one answer, write at least one question the answer to which is the given one. I've solved most of ...
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1answer
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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 ...
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tryptophan residues that may vary with regards to solvent accessibility

Please propose an experimental design based on tryptophan fluorescence that would allow for the identification of general populations of tryptophan residues that may vary with regards to solvent ...
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1answer
43 views

What is the rate expression for decomposition of $\ce{H2O2}$ in the presence of a catalyst?

What is the rate expression for decomposition of $\ce{H2O2}$ in the presence of a catalyst? As far as I know for catalase, it is like this: $$\ce{Rate = k[H2O2][Catalase]}$$ I don't know what it is ...
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4answers
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Why do so many biochemical reactions require enzymes?

Studying biochemistry as part of the Great Courses, I am struck that all 10 steps in glycolysis require an enzyme. I’d have thought that evolution would have selected for a “simpler” pathway with ...
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Where does the beta notation come from in the alpha 1,2 beta glycosidic bond (in sucrose)? [duplicate]

I am confused as to where the beta is coming from (in the alpha-1,2-beta glycosidic bond in sucrose). I understand that the alpha is from the anomeric carbon of the glucose, but I don't see how the ...
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1answer
42 views

How do “basic” amino acids (lysine, arginine) act as base under physiological conditions? [closed]

Why do we consider amino acids with high side chain pKa's basic, yet with a higher pKa, less of the amino acid will exist in basic form at equilibrium compared to acid form at physiological pH? What ...
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0answers
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Why/how is 2-hexanone also called butyl methyl ketone?

I was given: butyl methyl ketone. How do I figure out how to draw this to determine that it's also 2-hexanone? Thank you!
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0answers
32 views

Measuring Testosterone Levels Using ELISA [closed]

I am new to this topic so please be patient. I am looking to understand ELISA better and how one may attempt to not only detect but measure the total calculated level present in a sample. I would ...
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2answers
80 views

How the 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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A question about potential difference across a membrane

Membrane potential of living cells arising from the difference of concentration of ions on both sides of the membrane, but why didn't someone use selective polymers as AEM (Anion Exchange Membrane) ...
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1answer
72 views

Periodate oxidation of sugars

When Methyl D-glucopyranoside is treated with $\ce{HIO4}$, what is the amount of $\ce{HIO4}$ (in moles) consumed per mole of the sugar? I have studied that $\ce{HIO4}$ oxidises only those vicinal ...
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26 views

How is presupposition of the order of reaction justified in Michaelis-Menten model?

from what I have understood, to derive Michaelis-Menten equation, we first suppose that $\ce{E + S <=>[k_1][k_{-1}] ES->[k_2]E + P }$ and make the 'steady-state assumption', that $k_1[E][S]=...
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Does ADP + P => ATP produce water?

ADP + P has one oxygen and two hydrogen more atoms than ATP. Are these atoms released as water in the reaction ADP + P => ATP? To balance the equation, would ADP + P => ATP + H2O be more correct?
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Collagen digestion

As far as I know, pepsin is used very often in collagen solutions extraction. Since it only cleaves the telopeptides and leaves the triple helix chains of the collagen intact. I was wondering if there ...
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1answer
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What is a secondary shell in an enzyme?

I've searched the internet for a definition of what the different shells in enzymes/proteins are and haven't found a good answer. This Nature article, which is about an enzyme that catalyzes Kemp ...
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1answer
99 views

What is “dithreitol”?

The article by Hu et al. [1] mentions a compound "dithreitol" in the Saliva Proteome Analysis section (emphasis mine): For the "shotgun" approach, saliva samples (1 mL) were pre-fractionated with ...
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1answer
57 views

Disinfectant production [closed]

One of my friends says that he made a disinfectant. These are the materials: 83% methanol isopropyl alcohol propylene glycol and the others are: citral, geraniol, linalool, dlimonene, l alpha ...
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1answer
151 views

CO2 kills humans. Does it also kill organisms? [closed]

CO2 kills humans. Does it also kill organisms? Does it also kill viruses?
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1answer
38 views

Cadmium Selenide, Cadmium Sulfide, Cinnabar and Lead Oxide toxicity

I have a question about the toxicity of the pigments Cadmium Selenide (Cadmium Red), Cadmium Sulfide (Cadmium Yellow), Mercury Sulfide (Cinnabar or Vermillion) and Lead Oxide (Lead White). Not long ...
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1answer
24 views

How does one refer to the amino acids in a peptide?

Once a part of a peptide an amino acid is no longer an amino acid, so how do we refer to the part of the peptide that was once amino acid x?
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1answer
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Esterification of Glycine

I came upon the following statement in a true/false question: Glycine can be esterified by an alcohol in the presence of inorganic acid Is this statement correct? Glycine contains the basic $\ce{-...
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0answers
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Differences in efficacy of oxime reactivators in organophosphate poisoning

Compounds containing an oxime functional group, such as 2-PAM and obidoxime, are used in the treatment of poisoning with organophosphorus compounds. These oximes reactivate the enzyme ...
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1answer
72 views

How does gefitinib affect the EGFR(ecptor) and why is there relapse

Gefitinib has been shown to be an effective tyrosine kinase inhibitor in a fraction (~$10$%) of non-small cell lung cancer patients. These patients are characterized as having a mutation (usually a ...
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1answer
57 views

Can someone explain the article below? [closed]

This is the article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5611670/ I'm not a Chemist, so I can't understand the article very well. The conclusion states that the molecules tested should not ...
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1answer
135 views

AChE Aging time of organophosphorus compounds containing hydroxyl groups

Organophosphorus compounds are known to inhibit the enzyme acetylcholinesterase (AChE). This occurs when the OPC phosphorylates the serine-203 residue of the enzyme. If the enzyme is not reactivated ...
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0answers
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When and how do mineral chelates separate in the body?

If one consumes an amino acid chelate such as iron bisglycinate, it is generally absorbed intact as far as I am aware. At some point, presumably the iron could be used for say hemoglobin synthesis and ...
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0answers
28 views

To get clear plasma out of a minute particle (such as fibrin), is it necessary to vortex sample before centrifugation? [closed]

I'm going to analyse plasma samples that contain a lot of fibrin. It is necessary to centrifuge the samples to be able to pipette the plasma. After the samples are centrifuged I can't vortex them ...
6
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1answer
60 views

How can subtilisin still function without its catalytic triad?

I read chapter 9 in the book Biochemistry (5th edition), by Berg, Tymoczko, and Stryer (provided in the NCBI site here). It describes the mechanism of action of the chymotrypsin enzyme. The catalysis ...
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12 views

Fed-Batch Titer Calculation

If the titer concentration is provided in g/L. Let us consider the following problem. Problem Lets say that titer concentration is X g/L, and using the titer concentration, the amount of water is ...
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1answer
38 views

Chemical Reaction for making Acetic Acid from Glycerol inside Fermenter

I have been trying to find a chemical reaction for the formation of acetic acid from glycerol. I have been searching different literature, but apparently the reaction can not be found. I was hoping ...
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1answer
50 views

Options to keep someone awake against their will? [closed]

I already asked this on Worldbuilding Stack, but they told me to ask here. It is for a RPG campaign. Are there any options that an evil person could use to keep someone awake against their will? Like ...
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1answer
59 views

How to derive the steady-state solution for simple two-step reaction with differential equations? [closed]

Consider this simple two step reaction, a variant of a Michaelis-Menten type of problem, where $\ce{A}$ and $\ce{B}$ reversibly bind to make $\ce{AB}$, and $\ce{AB}$ and $\ce{C}$ reversibly bind to ...
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0answers
51 views

Data-processing pipeline for protein x-ray crystallography: uncertain of terminology and order of procedures [closed]

Background: I am trying to get an overview of the data-processing pipeline for solving protein structures by x-ray crystallography, and in a very simple way understand what mathematical procedures are ...
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1answer
33 views

Nucleophilicity Of Amino Acid Side Chains [closed]

Out of the side chains of aspartic acid, methionine, threonine, and tyrosine, which is the least nucleophilic?
2
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1answer
172 views

Why can't C-C double bonds rotate? [duplicate]

The alkyl chains of saturated fat molecules can readily rotate about their carbon-carbon single bonds, giving them flexibility and viscosity. What is different about the carbon-carbon double bonds of ...
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0answers
42 views

Why is Cadmium so carcinogenic compared to other heavy metals?

This free article as well as this article do a good job highlighting the carcinogenic effects of Cadmium and the mechanisms by which they occur. However, my question is why is Cadmium so carcinogenic ...
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The Limitation of Solid Phase Peptide Synthesis In Case of Polyglycine

I was wondering if I could use your experience and all the precautions you would like to recommend for a long peptide synthesis via SPPS. I've already got a low loading resin so this way I'll minimize ...
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0answers
10 views

In vivo, does it take energy to move double bonds from cis to trans long chain unsaturated fatty acids

In vitro, long chain fatty acids may yield more energy when bonds break, but in vivo, I understood that energy is burned before unsaturated fatty acids can be oxidized because the side groups with ...
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2answers
154 views

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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1answer
25 views

Using the electrical potential created by the electron transport chain to power electrical systems

My friend and I were discussing the extremely low energy density of modern batteries and read that food has a much higher energy density. Thus, we were considering the possibility of using biological ...

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