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 does medicine work? [closed]

Take aromatase inhibitors for example. In order for a molecule to stop the enzyme aromatase from converting androgens into estrogens, it must meet 6 criteria: Not get broken down by the acidity or ...
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Why do we still bother with grain farming when it's possible to break down cellulose into sugar with simple (bio-)chemical methods? [closed]

All I could find about this was somehow related to biofuels. Why would this be the first application? For reference, here's a paper that talks about acid hydrolysis in the context of biofuel ...
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What does it mean to quantitatively describe a cell?

To begin this question, I will quote Molecular Biology of the Cell (page 38): ... Biological systems are, ..., full of feedback loops, and the behavior of even the simplest of systems with feedback ...
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difference between biotic and living? [closed]

how can we differentiate between biotic and living things,is there any difference? and same for abiotic and non-living? I think it is that biotic is like biomass and living should carry out life ...
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Should fat calories' numerical values be increased to better reflect the new scientific findings?

According to a study discussed on this website, people lose more weight on a calorie restricted fat reduced diet than on a similar calorie restricted carb reduced diet. Is this study a fair dinkum, ...
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What's happening in the “C” and “T” stripes of a covid test kit?

I have a COVID home test kit which produces C and T (control and test) stripes when the solution is applied to the strip. Something similar happens in pregnancy test kits. I understand the purpose of ...
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How easy is it for quantum dots to enter the intracellular portions of cells?

As quantum dots have better quantum yield than organic dyes, many are being developed as a substitute for them. Nonetheless, could these substitutes be small enough to enter inside cells as current ...
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Do some flowers excrete urea or uric acid?

Sometimes when I sniff a flower up close, I can't but help smelling a faint urine like odor. From my layperson's understanding, uric acid and urea both are responsible for giving urine its ...
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62 views

Is there a term that distinguishes extracellular “transport” proteins from membrane-bound “transport” proteins?

I've been researching genetics and biochemistry in my free time and I've noticed that proteins such as albumin and apolipoproteins that facilitate extracellular transport and proteins such as GLUT1 ...
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Thermodynamically, how did the first cell arise?

Living cells are biochemical systems that constantly perform chemical reactions. One of the important consequences of these chemical reactions is the capacity of a living cell to replicate itself. The ...
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58 views

What's the difference between Kd and IC50?

What's the difference between the equilibrium binding constant ($K_d$) and Inhibitory Concentration 50 $IC_{50}$? They both seem to mark halfway points. Is the only difference that $K_d$ refers to any ...
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Why/How can Hydrophobic things pass the lipid bilayer? [duplicate]

I’m just looking for a simple answer for this question. I’m in Bio 10, and don’t know the in depth stuff. So the lipid bilayer is hydrophilic and the ends, but hydrophobic in the middle; so how can ...
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Do Hydrolysis Reactions and Dehydration Reactions both Require ATP energy?

I’m just looking for a simple answer for this question. I’m in Bio 10, and don’t know the in depth stuff. I think both the reactions do require ATP Energy, because for a dehydration reaction, in order ...
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1answer
139 views

Besides fats, proteins, and carbs, what compounds can the body use for energy?

What kinds of chemical species that do not belong to the category of fats, carbohydrates or proteins can the body metabolise? Clarifications: By metabolise, I mean extract energy from (e.g. as ATP). ...
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What is the effect of an acidic solution on hydrolytic enzymes?

I'm working on a school research project and my research question is "What is the effect of increasing concentrations of Acid X on hydrolytic enzymes, measured through the loss of mass of leaf ...
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28 views

Why are symptoms like headache and coma common in patients of metabolic acidosis?

Metabolic acidosis is a systemic electrolyte disorder in humans. Headache is a common symptom of metabolic acidosis. Is the headache due to excess amount of acid and coma when the brain becomes too ...
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Can Ni-NTA-Atto Conjugates bind to single His-tag

Can I label a protein with a single His-tag with Ni-NTA-Atto conjugates? Papers generally use this technique to label 6His-tag.
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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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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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51 views

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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145 views

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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1answer
144 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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1answer
64 views

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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39 views

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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1answer
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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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145 views

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 flat 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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1answer
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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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1answer
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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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