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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Does nacre/mother-of-pearl have a greater compressive strength than human bone?

Exactly what it says on the tin: as measured in mPa, does nacre/mother-of-pearl have a greater compressive strength (i.e. it can take getting squeezed more before breaking) than human bone? I ...
KEY_ABRADE's user avatar
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What is the density of nacre?

What is the physical density of nacre/mother-of-pearl? I can't find an authoritative figure for it.
KEY_ABRADE's user avatar
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Do any animals mix porphyrins and carotenoids in their pigmentation?

Many animals (particularly birds) use carotenoids or porphyrins in their diet to contribute to the brilliance of their skin/fur/feather coloration. A few even mix melanin in with carotenoids to get ...
Carduus's user avatar
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Do quantum mechanical effects such as uncertainty, tunnelling and entanglement play role in the electron transport system of respiration?

The electron transport system of aerobic respiration involves an extensive pathway of electron and proton transfer from one centre to another. Now, since they are quantum mechanical particles, shouldn'...
Arkajyoti Banerjee's user avatar
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How does the hydrophobic amino acid fuse the corona virus with the host cell membrane?

I am reading the article How the coronavirus infects cells — and why Delta is so dangerous. It describes the fusion process of the virus into the host cell as follows right above an animation ...
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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 ...
projective_line's user avatar
6 votes
3 answers
359 views

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 ...
seamos's user avatar
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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 ...
Mohd Saad's user avatar
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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, ...
Constantthin's user avatar
12 votes
1 answer
301 views

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 ...
spraff's user avatar
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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 ...
C-Consciousness's user avatar
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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 ...
ATL_DEV's user avatar
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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 ...
Semper Ambroscus's user avatar
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356 views

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 ...
seamos's user avatar
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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 ...
Seanny123's user avatar
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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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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). ...
Ingolifs's user avatar
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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 ...
Sankalp Kapur's user avatar
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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.
Antoine Roland's user avatar
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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 ...
Roland's user avatar
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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 ...
James's user avatar
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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 ...
Harsh Dua's user avatar
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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 ...
ANA negative's user avatar
1 vote
1 answer
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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 ...
Araucaria's user avatar
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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 ...
NL_Derek's user avatar
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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 ...
stevec's user avatar
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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 ...
Kurt Hikes's user avatar
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1 answer
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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), ...
Incnis Mrsi's user avatar
3 votes
1 answer
290 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?
Anixx's user avatar
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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 ...
Nikhil Verma's user avatar
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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....
magnetic's user avatar
6 votes
2 answers
503 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 ...
chematwork's user avatar
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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 ...
Rengaraj's user avatar
1 vote
1 answer
347 views

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 ...
Kushagra Gupta's user avatar
-2 votes
1 answer
166 views

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 ...
7V7's user avatar
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4 votes
2 answers
766 views

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 ...
Impeccable's user avatar
1 vote
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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 ...
Alina's user avatar
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2 votes
1 answer
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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 ...
chematwork's user avatar
-2 votes
1 answer
124 views

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 ...
Anirudh Kanaparthy's user avatar
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1 answer
475 views

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 ...
ceno980's user avatar
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5 votes
1 answer
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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 ...
Mike Serfas's user avatar
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2 votes
1 answer
69 views

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 ...
Yusuff AbdulMujeeb's user avatar
-1 votes
1 answer
935 views

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 ...
Questions's user avatar
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7 votes
1 answer
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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 ...
acvill's user avatar
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-4 votes
1 answer
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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 ...
Mikul Rai's user avatar
0 votes
1 answer
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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 ...
AOD's user avatar
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2 votes
0 answers
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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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