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 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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Biochemistry conventions in writing the coding/noncoding strand

I am taking a biochemistry lab class, we work with plasmids, ligating protein DNA sequences to clone the DNA and then performing analysis on the protein (a beta lactamase) is most of what we do during ...
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Orientation of operator and promoter in E.coli expression vector plasmids

I am a biochem student and this has almost made me pull my hair out, here is the image of the question I got wrong, and I am not sure if the question is wrong or I am, I think the operator is ...
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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 oxide is used for ...
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Why isn't the Ramachandran plot symmetric?

Since only relative position of groups along a bond is considered while calculating torsional strain and considering "+" and "-" means clockwise and anti clock wise rotation, ...
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Calculating LOD (limit of detection) of sensor

I am looking to obtain the LOD from the following data set I know that the LOD (limit of detection) is 3 x std of LOB (limit of blank) But I am limited to only using the data from different ...
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biofilm model scales

I have a question about the meaning of biofilm modelling scales: Are they microscopic, mesoscopic and macroscopic. Microscopic means individual bacteria macroscopic means large number of concentration ...
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Why do some people accumulate more diglycerides in their muscle cells?

The scientist Gerald Shulman has experimentally found that young lean adults in their early twenties that are children to people with type 2 diabetes often show muscle insulin resistance. He found ...
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What's the best way to purify my His tagged protein? Supernatant super viscous after first sonication?

I am trying to purify my his-tagged protein of interest, disulfide isomerase. It is about 40kDa and is cloned in pET28a vector, at XholI and NdelI, and expressed in BL21. I'm having issues with my ...
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What is the function of dihydrofolate reductase in humans?

According to StatPearls, synthetic folic acid — as an artificial dietary supplement — needs to be converted into the active form tetrahydrofolate (THF) by dihydrofolate reductase. In the cells, folic ...
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Is the pyruvate dehydrogenase reaction considered part of the Krebs Tricarboxylic Acid Cycle?

I’ve encountered questions where I’m asked to find out the CO2 released, the number of oxidative carboxylations etc. in the Krebs tricarboxylic acid cycle. I always include the pyruvate dehydrogenase ...
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2 answers
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Does alternative splicing contribute to the diversity of enzymes?

I understand the role of alternative splicing in generating protein diversity, but for enzymes specifically, is alternative splicing responsible for the diversity of it? My professor told me something ...
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Which animal has the smallest percentage of their body mass made up of water?

It's a "well known" and interesting "fact" that the human body is made up of "mostly water". With percentages from 65% to 90% often being repeated as if they were exact ...
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Anticoagulation of black beans extract

How many ml of lithium heparin do I need to use on 2 ml blood to prevent coagulation for over 15 minutes? I am comparing it to the 4 different dosages of black turtle bean extract that has polyphenols ...
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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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Which cancer cell lines do not increase glucose uptake in comparison with their wild type analogues?

I heard that some cell lines which already have a high glucose influx do not increase it upon altering to a cancer phenotype. However, I cannot find any supporting references.
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Mechanism of the calcium-activated protein, Aequorin

In Aequorin, coelenterazine acts as the luciferin, producing light in the presence of calcium and oxygen. It is unclear to me what part of the protein structure actually catalyses this reaction after ...
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Does a protein with a mutated binding site count as an isoform of the original protein?

im an intro level student so sorry if this doesn't make sense, but would a mutant protein whose primary binding remains functional, but whose inactivation site for a small effector molecule is mutated ...
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3 votes
1 answer
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Why do eubacterial DNA Ligases use NAD whereas eukaryotic and archaeal DNA Ligases use ATP?

DNA ligases in eukaryotes are ATP-dependent (as is the enzyme from bacteriophage T4) but in Escherichia coli the DNA ligase is NAD+-dependent. I cannot understand the reason for this. An extensive ...
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1 answer
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Please explain to me the difference of molecular weight in g/mol versus dalton

From my studies i thought so far that: 1 NA * Da = 1 * NA mu = 1 g, However since 2019 SI says that one dalton is only approximately one gram per mol 1 NA Da ≈ 1 g/mol This makes sense if I consider ...
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Does ATP get broken down naturally? [duplicate]

According to my textbook, ATP is not a good energy store becasue of the instability of the bonds. Does this imply that ATP naturally breaks down due to the unstable phosphate bonds? Over a long time, ...
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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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Why is NAD used mainly for catabolic reactions and NADP used mainly for anabolic reactions?

NADH is used mainly in cellular respiration and the NAD+ to NADH ratio inside the cell is kept high, but NADPH is mainly used in photosynthesis and the NADPH to NADP+ ratio is kept low in animal cells....
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Can distilled / deionized / demineralized water "attack" teeth?

Demineralized water is claimed by some resources to be highly aggressive (due to their lack of minerals) and to attack all sorts of materials. From the World Health Organization website: ...
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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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1 answer
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Has anyone who has ever isolated synaptosomes using subcellular fractionation before know what the 'crude/heavy membrane fraction P2' is?

I am reading a journal paper where they analyse the proteome of synaptosomes. In this paper, they isolate synaptosomes from the hippocampi of mice. I know that synaptosomes contain the complete ...
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Thermodynamics of passive transport

My question is, where does energy come from for passive translocase's conformational changes? I argue it can't be concentration gradient, as concentration is only statistical phenomenon at micro scale,...
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Can we compare the effectiveness of an inhibitor by checking how much they change Km and Vmax during a reaction?

While comparing two inhibitors, can we check how they alter the Km and Vmax of the reaction and then decide which inhibitor is more potent. I tried explaining in this way: While I think the answer ...
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Do ATP generated aerobically and anaerobically have different phosphorylation potentials?

We have recently postulated that ATP generated by substrate-level phosphorylation may have a different phosphorylation potential to the ATP generated by oxidative phosphorylation. This could be ...
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In enzyme kinetics, Can the Kp be greater than K1 in any way? [closed]

Enzyme reacts with substrate to produce a complex. And finally the products in a catalysis reaction.
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Simulate merging of two ssDNA together

I have two .pdb files with two ssDNAs, which should form some specific shape when closed together. Is it possible to model/simulate this merging somehow? I would preferably like to have a program that ...
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7 votes
2 answers
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What prevents non-aminoacylated tRNA from binding to mRNA on the ribosome and disrupting protein synthesis?

Specific aminoacyl-tRNA synthetases catalyse a reaction in which a transfer RNA molecule with a given anticodon is covalently attached to its cognate amino acid (aminoacylated). What factors favor the ...
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2 votes
1 answer
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What do the colors mean in representations of amino acids?

I've seen sequences of amino acids depicted using colors, which I imagine correspond to whether the side chain is charged, etc. I can't figure this out, though, and I'm not a biologist or biochemist. ...
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why can you avoid onions making you cry either by protecting you eyes or your breath?

i was wandering why onion makes me cry when i'm cutting them, so i tried three different things : first i tried cutting onions with swimming glasses, and it worked (i didn't cry) then i tried ...
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GDP biosynthesis

I am looking into de novo purine synthesis and was wondering which pathway creates GDP from GMP? Or does this step not exist and GTP is made from GMP with pyrophosphate, and the existing GDP comes ...
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1 answer
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effect of pH, temperature and enzyme concentration on Km

I understand that enzyme concentration does'nt affect Km since the Micaelis Menten equation is based on the steady state approximation wich requires high levels of substrate compared to enzyme (that's ...
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how to extract garlic fructan?

can anyone tell me a not complicated way to extract fructans from garlic (i have access to highschool lab). I need this to be able to make an experiment on garlic extract and just fructan from garlic ...
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Can I use the Winkler method as a way to measure the rate of photosynthesis?

I want to make an investigation where I measure how the color of light affects the rate of photosynthesis. The idea is to put an Elodea plant in a test tube and shine with different color of light ...
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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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What chemical to use to recycle microplates used to grow bacteria

We grow bacteria (Escherichia coli) in polypropylene or polystyrene microplates with an optical bottom for some experiments (liquid culture). I would like to try and recycle those microplates to be ...
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3 votes
1 answer
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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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Why can't 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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1 vote
1 answer
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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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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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