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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difference between biotic and living?

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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How are logarithmic trendline equations used to determine antibody concentrations in ELISA?

For example, say you have plotted a standard curve and managed to obtain a logarithimic trendline equation like: y = mln(x) - b And you are working with data that includes: a) standards,their ...
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Why are fat calories not inflated in their numerical values to better reflect the new scientific findings?

According to this study people lost weight by lowering total calorie intake which was expected, but the study also showed that people lost more weight by reducing fat calories than by reducing carb ...
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What are the differences between ATP and GTP across several factors? [closed]

How do adenosine triphosphate and guanosine triphosphate differ in the following areas? efficiency of conversion of food energy to the molecule in question energy density role in the body (I ...
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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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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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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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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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136 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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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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55 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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Antibody staining

I am staining tissue sections and I did a mistake, I was supposed to have mixed 3 primary antibodies but I stained only with one of them. After the 1h incubation I washed 10 min with PBS and then I ...
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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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What is the reason of symptoms like headache and coma in patients of metabolic acidosis?

Is the headache due to excess amount of acid and coma when the brain becomes too much fatigued coz of chronic low pH or the reason is something else?
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Why is chloride ion classed as a cofactor for amylase rather than as a coenzyme?

I am provided with the two following statements and have to prove which is true and which is false. $\ce{Cl-}$ acts as a coenzyme for amylase $\ce{Zn^2+}$ acts as a prosthetic group for carbonic ...
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1answer
26 views

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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107 views

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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141 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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430 views

Do chaperone proteins misfold?

If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones ...
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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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1answer
51 views

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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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 do organophosphates affect kidney function?

Many organophosphates, besides inhibiting acetylcholinesterase, can also permanently inhibit the enzyme neuropathy target esterase, leading to nerve damage. NTE also happens to be found in the kidneys,...
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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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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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605 views

What tests can be performed to test the purity and quality of the raw peptide HCG (Human Chorionic Gonadotropin)

What tests could be run to test the purity and type of HCG? We are looking to purchase HCG from China but the purity and quality varies between labs, we are able to receive samples of the raw peptide ...
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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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473 views

What is the half-life of dNTPs at 95 °C?

I'm looking for the half-life of dNTPs, either as a whole or broken into individual bases, at 95 °C (or similar). A titration would be great if that exists. I can provide more specifics if need be, ...
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How would one track a mineral nutrient in a plant in order to prove that nutrient has been re mobilized?

Before abscission - senescence of a plant structural components that contain mineral nutrients (E.g. Magnesium, Potassium...) are re-mobilized from the senescent tissue and used in other plant tissue ...
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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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How many cyclic and non-cyclic photo-phosphorylation is required to produce one molecule of glucose?

In non-cyclic photophosphorylation 1 ATP and 2 $NADPH_2$ molecules are produced. In cyclic photophosphorylation 2 ATP molecules are produced. For production of one molecule of Glucose 18 ATP and 12 $...
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Why are nitrogenous bases of DNA hydrophobic if they can hydrogen bond?

Why are nitrogenous bases of DNA hydrophobic if they can hydrogen bond? Is it that they are only relatively hydrophobic? This forum explains it but does not give an example of the structure.
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60 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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1answer
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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2answers
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CAM Photosynthesis Oxygen Generation?

I've been looking into CAM plants - notably the snake plant which is native to West Africa. Upon researching the CAM photosynthesis cycle, I've found it fascinating that the plant stores CO2 at night ...
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Average masses of atoms / amino acids

I recognized that there is some controversy about the average mass of amino acid masses in different online sources. Expasy and Wikipedia report the same masses, but UWPR and Mascot report different ...
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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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143 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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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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130 views

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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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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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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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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Why does cutting onions cause tears?​

Why does cutting onions cause tears?​ From a couple of sites, I found that it is because of sulfuric acid produced by onions. But I could not find more details. What is the biochemical pathway by ...

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