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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Are stable isotopes ever used in pharmaceuticals?
Carbon has two stable isotopes, C-12 and C-13. Since they both have the same electronic structure they can both make up the same molecules, but presumably they may perform different functions in ...
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Does aerobic exercise increase the incidence of disease via free radicals?
Aerobic respiration produces ROS, atleast one of which (the hydroxyl radical) cannot be neutralized by any known antioxidant and is always damaging surrounding tissue. I know ROS plays a role in ...
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How come SSBPs in RPA don't bind primers?
I've started reading about the recombinase polymerase amplification (RPA). I'm learning that in RPA, recombinase enzyme binds to primers, then makes them anneal to the complementary target DNA strand, ...
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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 Difficult is Artificial ATP Synthesis?
One way of making ATP requires:
A membrane (would probably have to be a phospholipid bilayer)
A difference in H+ chemical potential across the membrane
ATP synthase anchored to the low-potential side ...
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max % of oxygen not harmful for breathing?
Is breathing pure oxygen bad for you?
Human blood is designed to capture oxygen and safely bind it to a molecule known as hemoglobin. However, if you breathe in a high concentration of oxygen, it will ...
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How to elute the protein that is bound to biotinylated RNA immobilized with streptavidin?
I would like to test the proteins that bind to biotinylated-RNA by mass spectrometry , I was using Dynabeads™ MyOne™ Streptavidin C1 (invitrogen) coupled with biotinylated-RNA,than mix these beads up ...
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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 many pyrophosphate groups are released during dinucleotide formation?
I can't seem to fathom how a dinucleotide is formed.
My textbook says that initially both nucleotides have 3 phosphate groups before the join but the formation releases only one pyrophosphate
If ...
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Can humans metabolize D-malate?
Only the L-isomer is produced naturally, while racemic mixtures are produced synthetically and used commercially as food additives and energy supplements.
So what happens when we consume D-malate? ...
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Validating Generative Models for 3D Conformations of Inactive Dopamine Receptors in Protein Design
Considering a dataset comprising 3D conformations of Dopamine receptors in an inactive state, we aim to train a generative model capable of capturing the distribution of these receptors and generating ...
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What role does GAPDH have on the mechanism for converting G3P to 1,3BPG?
I have reviewed the mechanism involving NAD+, G3P, and cysteine and I know the steps by memory, but what is the role of GAPDH specifically? Is the fact that the reaction is catalyzed by GAPDH simply a ...
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Can a non-pure culture be used for reliable rapid phenotypic diagnostic tests?
Can a non-pure culture be used for reliable rapid phenotypic diagnostic tests (e.g. catalase, oxidase & gram stain)?
"Slide Test Method
Obtain a pure culture of the organism to be tested. ...
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Why can mitochondria make only 34 molecules (rather than 61 molecules) of ATP ？
Why can mitochondria make only 34 molecules (not 61 molecules) of ATP from the energy obtained from the oxidation in the electron transfer system of NADH and FADH2 generated by oxidation of glucose in ...
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Induction of IFN-beta in HEK293T
I'm trying to increase expression of a protein we're attempting to study, UBL7, supposedly unregulated by Type I Interferon and particularly IFN-beta.
I've tried treating HEK293T cells (~60% ...
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Why is it desirable to couple chemical production to growth?
I have the following question in systems biology:
a) Draw a graph showing the relationship of growth (Vbio) and Vefni for the system here. (Let the horizontal axis represent Vbio and the vertical axis ...
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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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Where is the source of H+ in the matrix that will be pumped during the electron transfer system? Where does the OH generated at that time go?
In the electron transfer system, it has been mentioned in prior questions that complexes I, III, and IV are proton pumps and that these pumps pump protons from the matrix into the intermembrane space.
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Fate of GTP produced in the TCA cycle
As someone already mentioned in one of the following questions, the TCA circuit generates GTP in addition to NADH and FADH2. The fate of NADH and FADH2 is clear: they are used to pump protons in the ...
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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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Examples of mechanisms of metabolic trapping inside cells that create concentration gradient
I am looking for examples in biology in which a metabolite that can diffuse freely across a cell membrane (through passive diffusion), once inside, gets modified to a form that cannot diffuse back ...
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Why is glycine considered a nonpolar amino acid but a polar molecule?
Glycine has a dipole moment, so why is it considered a nonpolar amino acid when discussing its occurrence in proteins?
Also, is the backbone of a protein nonpolar?
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Allowed Deviations in fixed bond length and bond angles in peptides from the typical values
I am using frag builder python module to generate peptide structures to compute the interaction energy for ensemble of peptides of a given sequence for a fixed bond lengths and bong angles. However, ...
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Effects of oxygenated water on bacteria
I was curious if any of you would happen to have any experience with this but any hypotheses regarding how this would turn out would be much appreciated.
I’m wondering if water fully aerated with ...
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According to an online course, ribose and adenine can bond to make ATP. Is this true?
I recently came across this question in the MIT Open Learning Library Pre-7.01 Biology Course. It is question 2d in Problem Set 1 (archived link).
The question, as well as the correct answers and ...
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Bi-phenyl degradation pathway in lignin
I am studying lignin - and really like the bi-phenyl degradation pathway of DDVA by SYK-6, as shown below
But I can't find any literature on whether this pathway transfers from the dimer to the ...
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How does a product form from a transition state in an enzyme despite the weak interactions being at its optimal
In the book Lehninger Principles of Biochemistry, there is a metal stick analogy to explain why an enzyme being compliment to its substrate would actually make a terrible enzyme.
If the enzyme is ...
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How to convert Kilo Units (KU) to mg? [duplicate]
Im searching for AChE (Acetylcholinesterase) and on sigma-aldrich it is showing 2 KU or 2000U/mg of protein and on MedChemExpress it is showing 50mg then how can we calcute how much will be the drug ...
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Can fermentation and aerobic respiration occur at the same time?
In muscle cells during exercise, does lactic acid fermentation and aeorobic respiration occur at the same time, and does this mean the cell makes more or less ATP during this time?
The cell can't ...
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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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How can saliva neutralise acids produced by bacterial cells in our mouth if it is itself acidic in nature?
My school textbook makes the following claim:
This means that saliva must be basic. However, I learnt that the pH value of saliva is about 6.8, which would surely make it acidic. How can the above ...
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Cell biology - Resting membrane potentials
Why do we say there is an overall negative charge on the intracellular side of the plasma membrane at rest, and an overall positive charge on the extracellular side when both potassium and sodium are ...
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Question on protonation/deprotonation of amino acid side chains
I understand that actual pKa of amino acid side chains is greatly influenced by the surrounding environment. I am trying to deeply understand the equilibrium between protonated and deprotonated form ...
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How does $\ce{H2CO3}$ form in the blood with a ratio of 1:20 with $\ce{HCO3-}$ if there are not enough $\ce{H+}$ ions
I have recently been studying about the bicarbonate buffer in the blood and have a doubt regarding the concentration of carbonic acid in the blood plasma.
My understanding of the buffer system is that ...
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What's the grade of D-glucose that can be used in glucose assimilation test in bacteriology?
Background information
Carbon assimilation test is based on the ability of a bacterial species to utilize an organic compound (e.g. D-glucose) as a sole carbon source.
This means that for carbon ...
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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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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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Is Eugene Koonin's probabilistic argument for the necessity of a multiverse to explain the origin of life sound?
About Eugene Koonin
Eugene Koonin, Ph.D.
NIH Distinguished Investigator
Evolutionary Genomics Research Group
NLM/NCBI
Dr. Koonin graduated from Moscow State University, Moscow, Russia and received ...
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Minimum growing conditions of a given plant
Micro-algae are organisms that can grow in aquatic environments and use light and carbon dioxide (CO2) to create biomass. Researches showed that Micro-algae biomass can be used as bio-fertilizer.
My ...
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Pathway where carbon dioxide captured by phosphoenolpyruvate is not re-released?
I have been reading about C4 carbon fixation in which CO2 is captured by phosphoenolpyruvate (PEP) to make oxaloacetate.
Are there known pathways in plants that use substantial amounts of this ...
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Compute a melting temperature in viennaRNA?
Posting here to get views, but may be more appropriate for bioinformatics or chemistry SE.
There are a variety of utilities such as biopython or primer3 that compute melting temperatures.
However, ...
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Why is iron transported across membranes in the ferrous form?
Iron in the diet of animals is predominantly in the ferric form, but it must be reduced to the ferric form by a specific ferrireductase before it can be transported across the cell membrane into the ...
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What are major obstacles that OOL research still has to overcome in order to come to a full understanding of how life could have arisen from non-life? [closed]
Dr. James Tour recently uploaded a video titled Dr. James Tour vs Dave Farina | Are we clueless about the origin of life? #abiogenesis.
The description in the video says:
Join us for an exciting ...
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How is bio electricity modulated experimentally? [closed]
In the research performed by Micheal Levin et al, the morphological changes induced by changes in bio electricity are well demonstrated, most strikingly in his experiments in planarian worms.
Yet ...
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Aerobic respiration takes place in the mitochondria; anaerobic respiration takes place in the cytoplasm. Is there a biochemical reason for this?
According to hyperphysics.edu, and my general knowledge, anaerobic respiration occurs in the cytoplasm. ("Anaerobic respiration (both glycolysis and fermentation) takes place in the fluid portion ...
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What are the units of Q10 (temperature sensitivity)?
$Q_{10}$ is the increase in a rate (e.g. activity of an enzyme) observed with a 10° temperature increase.
According to Wikipedia:
$$Q_{10}=\left(\frac{R_2}{R_1}\right)^{{10}/\left({T_2-T_1}\...
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What is the energy of activation of uncatalyzed ATP hydrolysis reaction? Say in aquous solvent?
By ATP hydrolysis, I mean the chemical reaction: ATP + Water -> ADP + Pi. Focusing only on the reaction, this is a nucleophillic substitution reaction, most likely occuring in SN2 mechanism. But so ...
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Resazurin not turning pink
I want to add resazurin to my media as an anaerobic indicator.
To my understanding, the resazurin is blue when first added to the media, then turns pink after autoclaving, and finally it turns ...
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Why are there no organisms with metal body parts, like weapons, bones, and armour? (Or are there?)
Reading this question, Why are there no wheeled animals?, I wondered why no organisms seem to make use of the tensile and other strengths of metal, as we do in metal tools and constructions. I am ...
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Why doesn't the cell just use one messenger?
I recently learned the second messenger model, where adrenaline activates adenyl cyclase, which converts ATP into cAMP. Then cAMP acts as a second messenger which activates portein kinase enzymes. The ...
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