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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Why is DNA not single stranded? [duplicate]
From what I have researched DNA is not single stranded, because if it was single stranded, nitrogenous bases (the 'information' of the DNA) would be exposed to the cellular environment (although, I ...
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Antibody structural determinants of epitope size
I am curious whether there are structural correlates in antibodies that relate not to epitope sequence but to epitope size. Specifically, I imagine that the antibody-epitope interface size is ...
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What keeps pyridoxamine phosphate inside the aminotransferase enzyme active site?
In the function of an aminotransferase enzyme after the first substrate (amino acid) has been deaminated there seem to be nothing binding the resulting pyridoxamine phosfate to the rest of the enzyme (...
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Can Iron(III) accept electrons from NADH without the other enzymes?
During the electron transfer chain in cellular respiration, the NADH turns into NAD+ while donating an electron. Those electrons pass through many enzymes and chemical reactions. One such chemical ...
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Why can't other electron acceptors produce as much ATP as oxygen?
I have been wondering about life using a different "Final" electron acceptor(replacing oxygen), but every thing I can find in my research say that oxygen produces more ATP because of its ...
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Why is iodine added to salt? As opposed to fluor or fats/oils like iron and vitamin A?
Is there a particular reason why certain foods are enriched or fortified with certain nutrients? Such as salt with iodine? Or did we just get used to doing things a certain way since we started ...
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Primary charge separation in Photosystem II
I was reading through an article about primary charge separation in Photosystem II when I came across the following graphic:
I assumed that the axis is measured with respect to the unexcited system, ...
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Is it possible to change an amino acid within a protein but not affecting that protein's functions?
In the answer(source - Campbell Essential Biology with Physiology, self-quiz question), it's given that "if the change doesn't affect the protein's shape in any way then it's possible to do so&...
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Xenobiotic metabolism: phase 1 reduction enzyme
Phase biotransformation reactions can be oxidations, reductions or hydrolysis of the xenobiota molecule.
Phase 1 oxidations are catalyzed by the cytocrome P450 enzyme, abbreviated with the CYP acronym:...
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Are all factors (hormonal) necessarily peptides? [duplicate]
While studying the endocrine system I came across the following terms:
Atrial natriuretic factor
Sperm Maturation factor
Growth factor
Are all factors necessarily peptides or can they have other ...
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[IAL Biology]: Struggling to understand how pH and temperature affect haemoglobins affinity for oxygen
As seen in the graph above, why do we say that increasing pH increases haemoglobins affinity for O2, but decreasing pH reduces its affinity? If the pH increases above or decreases below haemoglobins ...
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In drug discovery, what is an undruggable target? [closed]
The term "undruggable" is often use in drug discovery. As far as I understand it, it means "for which no inhibitor has been found so far".
It's a fuzzy, non-satisfying, definition.
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Calvin cycle question [duplicate]
Why does the 6-carbon molecule produced when Rubisco attaches a Co2 onto RUBP split into 2, 3 carbon molecules? Is it because its unstable or is there another reason?
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Advantages of NADP+ dependent Isocitrate Dehydrogenase
I came across a question (Q-5b) that asks:
Isocitrate Dehydrogenase in the [human] TCA cycle is associated with NAD+.
Why does it make good metabolic sense that it should use NADP+? Explain and show ...
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How does labelled N from tyrosine appear in phenylalanine if the latter is an essential amino acid?
A certain question (not my course or instructor or even university) goes:
Exposed to regular metabolic activity in a rat liver, a 13C label in tyrosine will not appear as a 13C label in phenylalanine....
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The nitrogen cycle
As I understand it, bacteria absorb nitrogen from the air, and deposit nitrates in the soil. These are absorbed by plants which use them to build complex molecules such as proteins. This enters the ...
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Why is hydrogen to oxygen ratio used to compare energy storage efficiency?
I came across an article that says that lipids are more efficient energy storage molecules compared to starch because lipids have higher “hydrogen to oxygen ratio”.
I do not understand how “hydrogen ...
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Is atmospheric nitrogen chemically necessary for life?
It is my (very basic) understanding that neither plants nor animals utilize the nitrogen in the atmosphere. Humans do not make use of atmospheric nitrogen through respiration and plants do not ...
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Does the body make alterations to fatty acids before their storage?
I was wondering if you would be at all able to help me with some questions I can’t find the answers to. I’m a first-year uni student doing some research for the fun of it but I’m really struggling to ...
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Could abiogenesis still be ocurring? [duplicate]
From my understanding, most biologists believe that under certain conditions life can form from inert chemicals. If the conditions for this to happen still apply, is it possible that in bodies of ...
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What are the main challenges for developing imaging techniques for cellular-scale structures?
Small disclaimer: I'm not a biologist, so I'll try my best to write a high-quality, objective question, but please forgive me if it doesn't turn out as expected.
Imaging technologies such as MRI and ...
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Why do catabolic reactions release heat despite that breaking bonds absorbs heat?
According to Campbell, the definition of a catabolic reaction is:
Some metabolic pathways release energy by breaking down complex
molecules to simpler compounds. these degradative processes are ...
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What were fed to the rodents in Calhoun's experiments?
From, (https://en.wikipedia.org/wiki/Behavioral_sink) (https://en.wikipedia.org/wiki/John_B._Calhoun) (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1644264/)(https://www.gwern.net/docs/sociology/1962-...
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Biological investigations or Biochemical investigations
I am working on phytochemicals and their antimicrobial and antioxidant activities.
Are these activities investigations called Biological investigations or Biochemical investigations?
What is the ...
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How does red light change the cellular mechanism in cells?
As winter approaches and the amount of sunlight decreases in the northern hemisphere, I have been reading about red light therapy and its supposed beneficial clinical effects.
Yet there is no much ...
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Are DNA molecules negatively charged at low pH values?
We know, that for each monomer of DNA, phosphate groups are having -1 charge because one of the oxygen is negatively charged (2nd oxygen participates in the phosphodiester covalent bond), but isn't it ...
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Do lipids have a monomer or not?
My biology class and I have been on the topic of macromolecules for quite some time now. Chapter 2.3 of the Foundations to Biology Textbook says that lipids are not polymers, so they do not have ...
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Why does low redox potential mean less oxygen?
I often see statements about adding reducing agents like cysteine to anaerobic medium to decrease the amount of the dissolved oxygen.
However, I am not sure why.
I am wondering if it is because under ...
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Do cancer cells use as much NADH as normal cells?
Recent literature shows that cancer cells have a different electron transport chain mechanism from normal cells and both of cancer cells and normal cells use NADH as electron donors. So, is there a ...
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Why aren't complex-stabilizing proteins like transcription factors considered catalysts/enzymes?
I'm not asking the question on a superficial level. Obviously, (most) transcription factors are not acting directly on a substrate to produce a chemical change. I pose the above question as more of a ...
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Does nature have a mechanism to turn charcoal back to usable carbon?
I have in past asked this about ash, but apart from ash most fires - whether natural or fires in stoves - leave a bunch of charcoal as well. When I was sifting old compost last year, I could identify ...
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Comparison of different glassy matrices for protein immobilization at room temperature
I am completely new to protein biology experiments. I care about experiments where proteins are immobilized near a surface with the help of a glassy matrix or similar materials.
I am looking for a ...
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If guanosine transfer reaction in the RNA capping is reversible, should intermediate reactions be reversible as well?
Guanosine transfer is the second step of RNA capping. The enzyme (GTase) first displaces a pyrophosphate of a GTP molecule, forming an unstable covalent enzyme-GMP intermediate (E + Gppp ⇌ E-pG + PPi)....
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Does ellagic acid dissolved in DMSO react with Brain Heart Infusion media?
I dissolved 2mg of Ellagic acid in 500 microliter of DMSO. I used 100 microliters of this solution to test for antimicrobial susceptibility against E.faecalis by adding it to 100 microliters of BHI ...
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What specific molecules cause the difference in spectral sensitivity in the cones?
What causes the difference in their spectral sensitivity of the S, M and L cones. I'm guessing that the opsin or photopigments are different, but haven't been able figure out conclusively from my web ...
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PEGylation safety and hybridomas
PEGylation is the covalent attachment of PEG (PolyEthylene Glycol) to molecules (e.g. proteins). It states in wikipedia ("PEGylation"):
The covalent attachment of PEG to a drug or ...
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What is mechanism of action of ellagic acid as an antimicrobial compound?
Ellagic acid (a polyphenol) works as an antimicrobial compound. But what is its mechanism of action?
I found these 2 research papers related to this, however the mechanism of action is not clearly ...
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What is the conjugation capacity of the liver?
Our liver conjugates 250-300 mg bilirubin per day under normal circumstances but it is capable of conjugating much more. What is the upper end per day after which it won’t be able to conjugate leading ...
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How does one derive a KD from an equilibrium titration experiment?
If I have an antibody A and a target B, and experimentally titrate the antibody against a single concentration of B, and then measure the % of B that is bound after the solutions reach equilibrium, I ...
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Why does the luminal test need hydrogen peroxide?
In the chemiluminescent reaction of Luminol in an aqueous solution, the luminol needs to react with molecular oxygen to produce a photon of blue light. In the technique, the hemoglobin of blood ...
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Source for "The human body recycles its body weight of ATP each day"?
I have read in many biology textbooks and scientific journals that "you create your own bodyweight in ATP each day", but they are all just stated as facts. I have yet to see a study or ...
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Why does photosynthesis specifically produce glucose?
Why not a pentose? Or a tetrose? Or a deoxy sugar? Or just some other hexose, like fructose?
Is there some chemical reason life should have settled on glucose as the standard photosynthetic output, or ...
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How does a turtle develop inside its egg?
This is related to Cause of premature death in turtle eggs, for those interested.
I have noticed that Kinosternon spp. eggs have three layers:
hard outer shell
white opaque membrane (like the one you ...
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Is the formula of cyclic adenosine monophosphate (cAMP) $\ce{C_{10}H_{11}N_{5}O_{6}P}$ or $\ce{C_{10}H_{12}N_{5}O_{6}P}$? Does it matter?
For some reason, half the sites on the internet say that there are 12 hydrogen atoms in one molecule of cAMP, and the other half claim 11.
Who is correct? Does a single, free, unbounded and ...
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Why is protein turnover necessary or important for cells to function?
Cells constantly create new proteins in order to maintain their normal function, this is called protein turnover.
Why is that? Do the old molecules wear out as time passes, so that they need a ...
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Why do bacteria denitrify?
Denitrification is the microbial respiration in anoxic condition. If the process is complete we have :
$$2 \text{NO}_3^{-} + 10 \text{e}^{-} +12\text{H}^+ \rightarrow \text{N}_2 + 6 \text{H}_2\text{O}$...
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How to reduce PPi concentration in blood samples by PPase
I have some samples of whole blood that are a little bit expensive and I want to significantly reduce the concentration of PPi in the samples by causing a reaction. I don't have any experience in ...
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Are there irreversible metabolic reactions that can happen in opposite ways depending on the cellular conditions?
Irreversible reactions are thermodynamically irreversible, not microscopically irreversible. "Irreversible" here means the reaction happens "out-of-equilibrium". It is a ...
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Do photosynthesis and respiration violate the law of conservation of energy?
I don't know, if it's a physics question, biology or chemistry question but anyways here it is:
I have been taught that to produce one molecule of glucose in photosynthesis, 18 ATP molecules are used ...
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Where does the silica found on grass and other plants come from?
Grass has tiny silica "teeth" on it called phytoliths:
I have trouble understanding how can a plant possibly extract silica from soil and form anything out of it. Silicon dioxide is used ...
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