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 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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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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