Questions tagged [biochemistry]

The study of chemistry within the scope of biology: the compounds that occur and the reactions involving them in living organisms.

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How do transmembrane proteins bind to specific locations on the membrane?

Taking a specific case, how do some GPCRs only bind to dendrites and others only to the axon terminals (reuptake receptors)?
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Why does activated charcoal prevent tetracycline activity in E. coli culture?

My lab just found that using activated charcoal in an E. coli culture prevents tetracycline function. What kind of reaction could be causing this effect? Thanks!
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How does body deside whether to build glucose, fat or proteins from amino acids?

I'm not a biologist so please don't judge my question too harshly. Let's assume, I ate something and I'am having some amino acids in blood. Now, if I'm not mistaking, the liver can make either glucose ...
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Numbering of C atoms of pyrimidine rings in nucleosides

For a presentation of my work I wanted to show a structural representation for dihydrouridine with numbering of the C atoms of the pyrimidine ring, according to this numbering convention. Then I found ...
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Are all organelle lumens a reducing environment like the cytosol, or nonreducing like the extracellular space and the ER lumen?

I am interested to know if cysteine can form disulphide bridges in proteins within organelles. Typically cysteine will not form disulphide bonds in the reducing environment of the cytosol, but will in ...
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Detecting multiple compounds on a lateral flow immunoassay – is this a case of monoclonal vs polyclonal antibodies?

I am working on developing lateral flow immunoassays for drugs of abuse and needed some advice on detecting multiple drug compounds in one immunoassay. As an example, an existing LFIA on the market ...
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What is the point of calculating extinction coefficients of a protein without Cys residues?

ProtParam computes various physico-chemical properties that can be deduced from a protein sequence. One of these parameters are "Extinction coefficients". They provide two values. One value ...
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Why does warfarin decrease biological activity of protein C?

Warfarin inhibits VKOR. Hence it disrupts vitamin K dependent $\gamma$-carboxylation of Fc- II, VII, IX, X. But what exactly it does to Protein C and Protein S? How does it also affect anticoagulant ...
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What is the minimum number of chemical elements required for life on earth? Does it vary between kingdoms?

As a non-biologist, I assume that there are certain elements that occur in all life forms as we know them. Examples might be carbon, hydrogen, oxygen and so forth. There are also elements that are ...
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137 views

Different flowers have same colour

I notice that certain (wild) flowers have the same colour, although they are not closely related. For example, the yellows of the dandelion (Taraxacum) and the buttercup (Ranunculus) are, at least to ...
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Is there an 'opposite' neurotransmitter to dopamine?

Dopamine is a neurotransmitter (i.e. chemical) in the brain that gives us great feeling. From here: Dopamine plays a role in how we feel pleasure. It's a big part of our unique human ability to ...
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Can a constitutively active kinase be highly regulated?

I am studying the protein kinase GSK3 and I am learning about the regulation of its activity. Many journal papers that I have read have stated that GSK3 is unique because it is a constitutively active ...
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Conservation Law in Gene Regulatory Network modelling

I was going through the GRN modelling from Chemical and enzyme kinetics by D. Gonze & M. Kaufman (PDF). The gene has 2 sites for activator/repressor. It say the DNA $D_0$ combines with activator/...
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Can any gas other than nitrogen cause decompression sickness (the bends)?

I know that our bodies use most of the oxygen we breathe in during a dive but, wouldn't our tissues, under pressure, absorb more oxygen than we need? For instance, in normal circumstances, we don't ...
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Is chloride necessary for animals?

Of the twelve well-known atomic constituents of our body eleven elements have specific properties obviously relevant to their rôle, making them indispensable. Oxygen (electronegativity and valence), ...
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Do people need nitrogen from air for health?

Can people breath totally nitrogen-free atmosphere for a long time? I know, nitrogen is essential for life, and in big quantities, but maybe people can take it entirely from food, from proteins, etc?
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Types of structures formed by various types of lipid molecules

Since Phosphatidylcholine (PC) and phosphatidylserine (PS) are roughly cylindrical in shape , they tend to form bilayers. Phosphatidylethanolamine (PE) on the other hand is conical in shape which ...
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How can I clone a gene into a plasmid vector with an N-terminal his tag and TEV cleavage site between the tag and the start of the sequence?

I'm a scientist who has significant experience in chemistry but am relatively new to molecular biology and biochemical techniques. I'm trying to make an isolated domain of a protein (166 residues, 19....
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Pyruvate dehydrogenase: Apparently anomalous NAD/FAD redox reaction

Below is the mechanism for the reactions of the pyruvate dehydrogen complex, which oxidatively decarboxylates pyruvate and transfers the acetyl group to coenyzme A for further metabolism in the Krebs ...
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Do different acids have different effects on the enamel of our teeth?

Do different acids or acidic solutions corrode the enamel of our teeth at different rates or in different ways? Are these effects present even when controlling for pH?
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Is averaged molar CO2 and O2 output/input necessarily identical?

Do we take up identical amounts of oxygen to the amounts of CO2 that we output? Equivalently, do plants take up identical amounts of CO2 as they release O2? (moles, averaged over >24 hours) I was ...
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Quantitative comparison of rate of energy output when burning carbs compared to fat

I'm studying scientific models of endurance exercise such as the one in a paper by Rapoport (see references below, popularization here). If I'm understanding properly, fat burning is in some sense ...
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How to incerase the efficiency of co-immunoprecipitation?

immunoprecipitation recently. My main problem is i am getting very clean and my target protein only (as you see in the lane 3,4,5,6) but when i reduced the NP40 concentration to 0.05 percentage i ...
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Low Density Lipoprotein (LDL) in the endosome

I am learning vesicular transport of LDL endocytosis. I understand as pH of the endosome is lower (around 6.0) than cytosol (around 7.2) due to the H+ pump, so LDL disassembles from the LDL receptor ...
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Nomenclature of substrates for DNA synthesis

I have read in my school textbooks that both deoxyribonucleoside triphosphate and deoxynucleotide triphosphate are used in DNA Replication as substrates. However, it is unclear to me whether the terms ...
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Does anyone have a tutorial or some guide to get started with Rosetta protein modeling and design tool? (I am a Mac user) [closed]

I have been trying to get started with Rosetta protein modeling and design software bundle. I searched online but the tutorials in the Rosetta website are difficult follow. I have the binaries already ...
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How does PCR mutagenesis add restriction site near the gene of interest?

I have been learning about PCR mutagenesis to add restriction site right next to the gene of interest using a primer that's attached with single stranded restriction site (first image). I have drawn ...
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Do carboxylesterases, arylesterases and acylesterases count to the enzyme class of lipases? [duplicate]

I am currently examining the acyl transfer catalysis activity of several enzymes that I was told are all lipases. Through reading a couple of papers including these enzymes I found out that all of ...
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Confusion regarding the Kir2.1 inward-rectifying potassium channel

I was trying to find out more about gustation and the transduction of sourness when I came across the supposed inward-rectifying potassium channel $\ce{K+_{ir} 2.1}$. Here's the thing, despite being ...
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Is protein intake required for the formation of new myosatellite cells?

Hypertrophy of muscle fibers requires an adequate (significant, really) intake of protein, but what about just forming new myosatellite cells as a response to a stress applied to the muscle? Does that ...
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What is the thickness of the membrane if only alpha helixes are embedded of a transmembrane protien?

Given is the representation of a transmembrane protein. Calculate the thickness of the membrane if only alpha helixes are embedded in it. One turn = 5.4Å Please read: The reason I didn't submit my ...
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What is meant by 4 –12% or 8% SDS-PAGE?

I am reading a journal paper and I am looking at the materials and methods section. Regarding the Western blot method in the paper, I have come across the following statement: Proteins were separated ...
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Were nicotinic acid/amide or flavin nucleotides ever part of primary RNA sequence?

NADH and FADH2 redox reactions are built deep into our biochemistry. For example, pyridine nucleotides are involved in >500 enzymatic reactions. When we look at the structure of deamido-NAD+, it ...
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Basis of enzyme nomenclature — pyruvate dehydrogenase

In the formation of AcetylCoA from pyruvate, why is the enzyme called “pyruvate dehydrogenase (complex)” when it involves the decarboxylation of pyruvate or the replacement of a carbonyl group by ...
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Electrochemical and concentration gradient confusion [closed]

I am learning membrane transport and learnt that there are 2 gradients that determine passive and active transport. If the concentration of a cation is higher in the cytoplasm side (hence ions should ...
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Flip-flopping in plasma membrane

Flip-flopping of lipids (and in proteins it is impossible) in plasma membrane is rare due to high energy barrier (video ref). However, it is an important mechanism since it allows asymmetric ...
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Why can't certain nucleoside analogs be used to label bacterial RNA?

A 2020 publication in Nucleic Acids Research 1 includes the following passage: A variety of nucleoside analogs have been developed for metabolic RNA labeling in various eukaryotic cells (9–16). Among ...
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Western blotting: what common tweaks do you make to the protocol and why would you make membrane cuts?

I'm building an app which helps researchers plan out Western blots, record protocol tweaks and receive warnings in the app if: you're trying to multiplex antibodies of similar molecular weight on the ...
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Biochemistry - Plastic eating microbes at home [closed]

Is it possible for me to locate, without too much difficulty, and culture, at home, a bacteria (like yeast) on plastic? I tried a similar process with yeast and I was able to culture it on extremely ...
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The Relationship between Copper and Alzheimer's Disease

I've been reading up about the research concerning the etiological factors behind Alzheimer's and I came across two papers - "Studies on Copper induced stability changes in DNA fragment (GCA ATC ...
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Concentration/molarity of lichen acids (particularly oxalic acid) in soil/rock substrates?

I am trying to design an experiment testing the efficacy of lichen acids to solubilize and mobilize nutrients from minerals in a lunar regolith simulant. My research so far indicates that oxalic acid ...
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Why are disaccharides less reducing than monosaccharides?

My teacher told me the statement, but if both monosaccharide and disaccharides have a single free active group, how is this possible?
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Biochemistry of ageing new discoveries

A scientist from Harvard, David Sinclair, has a few videos, a book and some papers on the topic of ageing. Particularly, I've seen this video a couple of times where he explains their discoveries on ...
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Why do animal cells “mistake” rubidium ions for potassium ions?

So, I was browsing the Wikipedia article for rubidium, and came across this interesting tidbit: Rubidium is not a known nutrient for any living organisms. However, rubidium ions have the same charge ...
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Need help designing an enzyme immunoassay (EIA)

I have a FITC-labelled DNA sequence and an anti-FITC antibody, however this antibody is not conjugated with HRP or any other enzyme. I work in a lab with limited finances, so is there a way I could ...
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How to convert cell units (c.u.) to mole?

If one has values in terms of cell units (c.u.) how may it be converted to $\mu$M? Should I think a "cell unit" as $1\;c.u.= \frac{1}{\text{cell volume}}$ and $1\;c.u.=\frac{1}{\text{cell ...
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VDJ sequencing in mice, DNA or RNA?

I am wondering if anyone who is well versed with VDJ sequencing for TCR repertoire analysis (specifically CDR3) would know if DNA or RNA is a better starting material? We are looking at the effects of ...
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Numbering amino acid residues

While reading about primary structures of protein, I came across the following image. What do the numberings $n-1, n, n+1$ in the below image refer to? I thought about it : The amino acid residues are ...
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Exact average molecular weight of a dsDNA basepair

I am trying to calculate the exact weight of a given dsDNA. On the Internet and the literature, different values for the av. molecular weight of one basepair are given : 660 g/mol (probably wrong), ...
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Is the dehydration process used twice in the preparation of permanent slides?

I am taught "preparation of permanent slides" by one of my teachers in the course of Biological Techniques. He gave me the following steps to prepare a permanent slide: Totally, there are ...

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