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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What is the fastest way to crystallise lysozyme (for student course)?
High school sudents are going to visit my university and I plan to demonstrate crystallisation of lysozyme. I ordered pure lysozyme from VWR. I can easily crystallise this within 15 min in batch (4% w/...
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What phosphorylates tau protein & and what causes tau to be phosphorylated?
I want to know what phosphorylates tau protein and its 6 isoforms.
I know kinases cause phosphorylation events, and in tau it can be phosphorylated in a healthy neuron in the trans conformation, but ...
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Different enzymes catalyzing the same reaction but in opposite directions
Nelson, D. L., & Cox, M. M. (2017). Principles of Biochemistry 7e. W. H. Freeman. 13.3: Phosphoryl Group Transfers and ATP: Inorganic Polyphosphate Is a Potential Phosphoryl Group Donor.
(This ...
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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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Adh2 promoter in saccharomyces cerevisiae
I'm looking at expressing a protein in saccharomyces cerevisiae using the Adh2 promoter. My understanding is that the gene will be repressed by the presence of glucose, but when glucose runs out it ...
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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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What happens when you cook tree spinach with aluminum?
The Internet is filled with warnings that you shouldn't cook tree spinach(Cnidoscolus aconitifolius) in aluminum, because it will react and create toxins that cause explosive diarrhea when consumed. ...
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The truth behind human urine and marking territory?
So some years ago, I remember watching a survival show in which the host said that human males produce a type of chemical in the urine that animals such as wolves can acknowledge as a territory marker....
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Where do the protons in the mitochondrial intermembrane space originally come from?
I'm currently reviewing this concept in cellular respiration. The book which I'm using is Reece, Minorsky, Campbell's Biology and while it does a good job at explaining the process involved in the ...
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Can an epileptic seizure start in the spinal cord?
My understanding of an epileptic seizure is caused by "invalid electrical signaling" in the brain. Can these start from the spinal cord (outside the brain) and move into the brain and cause an ...
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Does Doxylamine have any Influence on the Monoaminergic System?
Does doxylamine have any affects on the monoaminergic system? Specifically I am interested in adrenergic or serotonergic activity but additional information on its dopaminergic activity won't hurt ...
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Virucides - Herbal and otherwise, for HHV6 type virus or any inner-cell virus
Does anyone know where I can find a reliable list of virucides (not anti-virus) that can be used by humans? This virucide must be able to affect viruses that are already inside the cells. St John's ...
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How does Clostridium perfringens cause target hemolysis?
I am studying microbiology as a part of my course and I was studying Clostridium perfringens.
While studying its hemolytic characteristics, I came to know that it causes target hemolysis (i.e. zone of ...
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How should I measure the oxygen dispersed during photosynthesis in pondweeds?
I am to conduct a lab investigating how different wavelengths of light affects photosynthesis in Egeria pondweeds.
The idea is to put color filters on light bulbs and shine them on the pondweed in a ...
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How does NaF protect G proteins from denaturation?
Below is presented Figure 4 from the 1977 paper of Ross and Gilman, which provided evidence for the existence of G proteins:
The protocol (and rationale) is as follows:
Wild-type cell membranes was ...
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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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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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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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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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Cracking sounds made by glowing plankton
Recently I had opportunity to swim in place with glowing plankton, it was amazing experience and it as well gave birth to few questions in my head.
I manged to google that they can glow thanks to ...
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Light/Heavy Isotopes in Living Organisms
I was wondering, why are lighter isotopes (e.g. carbon-12 as opposed to carbon-13) preferentially used by life on Earth? Is their increased stability the only factor?
Thanks in advance!
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How do molecular biologists determine biochemical pathways?
I'm new to this community, so hopefully this is the right place to ask this question.
I know my question is really general, but in all of my biology courses we are merely taught the chemical pathways ...
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Can low melatonin levels and/or LED lights cause or exacerbate macular degeneration?
I have two questions that may or may not be interconnected. My first question is:
Does melatonin prevent macular degeneration? Could low melatonin levels (caused by blue-rich light exposure in the ...
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Effect of the Marcus Theory on Photosynthesis
As far as I know, the Marcus Theory explains the rates of electron transfers in reactions as a function of differences in free energy between the product/reactant's potential well.
Furthermore, there ...
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Why can polar molecules like water pass aquaporin better than unpolar like H2 or CO2
We learned in our lecutre, that aquaporin lets Water pass, but blocks Ions like H+ and unpolar molecules like CO2 and H2. The reasons for the Ion blocking are comprehensible, but I dont get, why less-...
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Preparation of dihydroxyacetone phosphate from glycerine by fermentation
I read on Wikipedia that
dihydroxyacetone (DHA) can be obtained from fermentation of glycerin. I would like to obtain dihydydroxyacetone phosphate (DHAP) for a science experiment but, since I'm 15, I ...
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How does DNA damage increase the activity of p53?
I understand the steps leading up to the halting of the S-cdK checkpoint from there, but I can't find the mechanism by which DNA damage actually increases the activity of p53.
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Could trees be engineered to produce rainfall-nucleators?
Scientists are using genetic engineering to make trees produce more terpenes. Is it possible to genetically engineer trees to produce more hygroscopic volatile organic compounds? These trees could be ...
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Why does a broad-leaved evergreen (Mahonia aquifolium) has red leaves?
To my knowledge, oregon grape (Mahonia aquifolium) is purportedly an evergreen shrub? Deciduous broadleaf plants lose their leaves in autumn usually and before that as the leaves die they oxidize and ...
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Where do class 2 preservatives end up after digestion?
Do anybody know what happens to class 2 preservatives in general after they are digested - i.e details like weather they are absorbed into blood as simplest elements or excreted out or assimilated to ...
Muhammed Salih
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Does alpha-amylase from different species have different *optimal* conditions?
Do the optimal conditions for the enzyme isoforms differ between species? Specifically, do the optimal pH and temperature for alpha-amylase differ for that enzyme produced by B. lichiniformis and A. ...
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What is the function of CETP?
I read up that CETP transfers cholesterol from HDL, which collected it from tissues, to VLDL. This VLDL is then sent back to the tissues, ultimately forming LDL internalised by cells.
What is the ...
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What is the rationale behind reverse cholesterol transport?
Reverse cholesterol transport is transport of cholesterol from the tissues back to liver/VLDL. My question is why do the tissues have this extra cholesterol in the first place?
Why would you ...
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How much energy would it cost to synthesize all cholesterol requirements de novo?
Imagine a scenario in which some person is unable to absorb any dietary cholesterol because of some intestinal mutation (for example). Thus, they have no cholesterol available from their diet for ...
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What Chemical Trigger Causes Ectomycorrhiza To Change From Asexual To Sexual?
I want to know the trigger behind the change of asexual to sexual ectomycorrhiza when symbiosis with a tree root is formed. As ectomycorrhiza attaches itself to a root, it forms a relationship wherein ...
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Can I leave BL21(DE3) cells in room temperature?
I am preparing competent cells, and I finished inoculating a single colony in SOB. It has been incubating at 37 degrees Celsius for almost 16 hours since, and it's getting very late where I live. I ...
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Does blood typing still provide a use for ancient tissue analysis?
Modern techniques.
In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be ...
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How does estrogen influence collagen synthesis?
Through what mechanisms does estrogen interact with collagen synthesis? Especially in the context of elevated estrogen levels and genesis of purpura simplex .
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How to measure cytochrome P450 activity in owls?
I hope you're all doing well. I'm currently working on a research project focused on owls and their exposure to anticoagulation rodenticides such as brodifacoum. As part of my study, I need to measure ...
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Cellular respiration and membrane surface protons
The final product of cellular respiration is the proton motive force, formed by protons pumped out of the membrane and by the voltage due to all charges. While Mitchell’s original theory considered ...
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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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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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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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Thermodynamics of one directional passive membrane transporters
I have read in my biochemistry textbook, that some membrane transporters transport only in one direction, moreover, they don't require ATP energy. I wonder, why these proteins do not act as ...
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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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Does glycerol in E.coli culture media somehow inhibit the lac-operon?
I have have been taught that one should induce protein expression with IPTG at an OD of about 1.0 - 2.0 when E.coli grows it TB media (terrific broth). As a reference point, one typically induces ...
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What are the carbohydrates that are found in white rice?
From this Wikipedia page on rice, it is mentioned that 100g of rice contains 80 g of carbohydrates, of which 0.12 g is "sugar" and 1.3 g is "fibre". I believe the "fibre" ...
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How it will taste if one puts two substances on tongue simultaneously?
If we put two substances having different taste on tongue simultaneously how it will taste? Does specific part of tongue is sensitive to specific taste?
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Does it make sense to express membrane transporters as concentration?
Let's assume a situation where a molecule, S, is transported out of the cell by membrane transporter T. For simplicity we do not consider any other synthesis or production processes. Furthermore, we ...
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