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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33 views

What happens if the Krebs cycle doesn’t occur [closed]

Suppose that there is a mutation in a single-celled organism where the Krebs cycle (TCA/Citric Acid Cycle) doesn't happen. What would be the consequences for that organism? How would their metabolism ...
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Ritalin/Concerta/Methylphenidate is an amphetamine? [closed]

FIDE says here: The most relevant banned substances for chess are: • Amphetamines – e.g. Adderall, Ritalin (...) Image: I think either Ritalin should be in a separate category called ...
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Is coenzyme A a vitamin? [closed]

My textbook states that: “Sulfur is a constituent of several coenzymes, vitamins (thiamine, biotin, coenzyme A) and ferredoxin.” Is coenzyme A a vitamin? I thought the vitamins were Vitamin A, B etc?...
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440 views

Arrangement of Amino Acids in the Protein alphabet

I am a software engineer with little knowledge of molecular biology. However I am trying to understand some bioinformatics computer code where the protein alphabet appears to be represented as the ...
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82 views

Why cant humans digest dietary fiber when we can digest starch?

So, I can see that there's a couple of questions touching on this subject already, but none of them answer the aspect that I'm curious about: Dietary fiber is a polymer composed of multiple starch ...
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67 views

Why such strange enzyme kinetics?

I measured some enzyme kinetics in a practical course using a substrate-based FRET assay. Unfortunately some of my plots show weird effects. There was always a decrease in signal after 35 minutes. But ...
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49 views

How are some exotoxins heat-stable, despite being proteins?

While studying microbiology, I came across bacterial exotoxins and endotoxins. It's understandable that endotoxins are lipopolysaccharides and hence heat stable. Exotoxins are proteins and hence heat ...
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How can the Na+-dependent Cl/HC03-pump pump several molecules against their gradient?

The molecular biology of the cell (6 ed) claims that: "Another [antiporter] [...] is a $Na^+$-driven$Cl^--HCO_3$-exchanger hat couples an influx of $Na^+$ to an efflux of $Cl^-$ and $H^+$. (so ...
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Why are IMAC and gel filtration combined?

In a practical course I used an Biorad Profina system to purify a protein with a histidine tag. The device uses a column for IMAC and one for gel filtration. Why are these two devices combined in one? ...
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55 views

Contradiction between random molecular collisions and regulated cellular processes [closed]

A cell is a chemical system, consisting of billions of molecules, ions, and atoms. These chemical species are constantly engaged in chemical reactions. Physics gives the impression that chemical ...
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What's so special about nitrogen? [closed]

I understand why carbon is essential for life. It's able to form long chains and has four binding sites. But what about nitrogen? Proteins are the most important class of molecules for life (except ...
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How many different DNA molecule classes does a person have?

Books always refer to human DNA as a unique molecule, and two different humans generally have different DNA molecules. But how many different types of DNA molecule does a person have? In order to make ...
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How can we explain that glucose at its concentration less than a Km for the transporter enters the peripheral circulation?

I'm studying biochemistry from Kaplan's book. In it, I found the following paragraph in the topic on glucose metabolism: "GLUT 2, a low-affinity transporter, is in hepatocytes. After a meal, ...
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1answer
57 views

Identifying substance in body fluid (serum, urine)

I have a large number of serum and 24 hour urine samples from a collection of individuals on many consecutive days. Some of the samples contain a 'large' amount of a substance that has a brown color. ...
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1answer
66 views

Why does the time to reach equilibrium across a membrane decrease with concentration?

We're learning about flux and Fick's law and there's one point I'm having trouble understanding. Assuming we have a higher concentration of a species on one side of a membrane, I understand that ...
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1answer
96 views

How to measure the pH of a bacterial species?

I would like to calculate the pH of a certain bacteria species before after an experiment. I was reading about the pH cell of bacteria and I found out about Bacterial Intracellular pH which I ...
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1answer
93 views

Why is there no wavelength change in the hyperchromic shift in DNA?

From Wikipedia article on hyperchromicity (emphasis my own): "When the bases become unstacked, the wavelength of maximum absorbance does not change, but the amount absorbed increases by 37%.&...
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Is lignification within plants a reversible process? If so which factors can reverse lignification?

Lignification is an important process in plants such as trees to allow for structural rigidity. Is this process reversible by the plant and if so which factors influence this reversibility?
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98 views

Why does Diphenylamine only react with the deoxyribose of purines?

The deoxyribose in DNA in the presence of acid forms β-hydroxylevulinaldehyde which reacts with diphenylamine to give a blue color with a sharp absorption maximum at 595nm. In DNA, only the ...
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1answer
36 views

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 ...
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49 views

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.
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1answer
22 views

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 ...
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85 views

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'...
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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 ...
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3answers
298 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 ...
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1answer
52 views

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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120 views

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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1answer
47 views

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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62 views

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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65 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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95 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 ...
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276 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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1answer
148 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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1answer
31 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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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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66 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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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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62 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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159 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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157 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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209 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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40 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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