Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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Where do the 2 hydrogen ions in glycolysis come from?

In the reaction for glycolysis, two hydrogen ions are produced as one of the end products. In all the ten steps, I am not able to figure out where exactly these two hydrogen ions are formed. Please ...
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Is there a non-directed way to probe proteins in a given sample?

I'm familiar with various ways to probe for specific proteins in a given sample(antibody/antigen, aptamers, etc). But these techniques seem to require an understanding of what protein you're looking ...
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What is the difference between physiology and physiological processes?

Now I do understand that physiology is the study of processes and mechanisms that make a living organism. And physiological process is understanding the ways the components in the organism work ...
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Function of SMAR in plasmids?

A few years ago, the Thought Emporium published a video (https://www.youtube.com/watch?v=aoczYXJeMY4) in which he refers to a study in which they mix plasmid DNA with Chitosan and feed it to mice to ...
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What is the correct word that subsumes all the following: gene, fusion, translocation, locus [closed]

Hi molecular biologists This is a bit of a different question, but there is no easy way to google for this. I am trying to create a data model for all somatic and germline molecular alterations. The ...
4 votes
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Can DNA replicate without polymerase?

Would it be possible for short DNA molecules to replicate, for example, if it's heated to the point where the strands separate (as far as I know, that's what happens in PCR?) and freely floating bases ...
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Receptors and their distribution over the human population

For humans it has been reported that there are three vasopressin receptors (AVPR1a) and four dopamine receptors (DRD2). (Source: UNIPROT) Question: Does every human contain all three variants of ...
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Is retinoblastoma truly an autosomal dominant condition?

I am getting, in my opinion, very conflicting information from sources about the inheritance of retinoblastoma, a type of cancer. Hereditary retinoblastoma is associated with defects in the gene ...
2 votes
2 answers
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Examples of passive membrane transport proteins that only transport in one direction and their mechanism

I would like to know about those transporters with alternating-access-type mechanism, that can only efficiently shuttle molecules in one direction but the other direction is severely kinetically ...
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1 answer
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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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Primer design for site-directed mutagenesis

In our practical course about modern cloning methods, we performed point mutations on a promotor via site-directed mutagenesis. As far as I understand that method you need forward and reverse primers ...
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Does beta-actin have to be consistent in Western Blots?

I have been running Western Blots on rat brain tissues from rats that have been subject to neurological disorders. I loaded the samples on the gel to ensure that for each tissue, I had a constant mass ...
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1 answer
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Human Evolution Chromosome 2: Fusion or Break?

I have a question regarding Chromosome 2. I've heard that there is evidence that the Human Chromosome 2 is a fusion between the two ancestral chromosomes 2a and 2b, but could it be possible that it ...
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How do you do Polymerase Chain Reaction (PCR) if you don't have a thermal cycler?

PCR has three steps: Denaturation, Annealing, and Primer extension. Let's say you do not have a thermal cycler in the lab, how would you mimic similar conditions and perform PCR?
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Length of frameworks in human antibody variable regions

Are antibody variable region's frameworks enumerated by Kabat numbering system always fixed length? Like, is FWH1 always 30 residues long?
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Endosymbiosis Probability

What is the probability of endosymbiosis occurring? I remember seeing it in my AP Biology textbook but haven't been able to find it anywhere after forgetting it. I want to say I remember it being ...
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yeast culture live cell extraction

I have been extracting samples for a gene expression assay from yeast. I would like to know how to ensure that the samples I am collecting at 48 hr. culture time, by then culture is probably saturated....
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Why does plasmid cloning efficiency go down with increased size of insert?

I am setting up a cloning experiment. Briefly, I ran PCR on a gene of interest, cloned it into a vector (pGemTeasy) and bulked it up in bacteria. I have been advised to limit the size of my fragment ...
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How does tetracycline transactivator localize to the nucleus? Where is the nuclear localization signal?

Proteins typically use a nuclear localization signal (NLS) to localize to the nucleus. Tetracycline transactivator (TTA) needs to work in the nucleus, but I did not find an NLS in the structure. ...
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Where to archive web citations for molecular biology article?

In 2013 I wrote a scientific paper in the field molecular biology. I needed to quote some webpages which I feared might disappear, e.g. amazon sales offers (it was a food related topic). So I archived ...
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Do complementary DNA sequences/codons produce the same amino acids? [closed]

I haven’t been able to confirm this anywhere. If this were not the case, when transcription occurred, if the transcription were based upon the incorrect side of the DNA molecule, a completely ...
4 votes
1 answer
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Ischemia-induced deploarization in excitable cells

I have read in many sources that ischemia-induced depolarization is due to the opening of ATP-sensitive potassium channels and inactivation of Na/K exchangers [1,2]. However, K-atp channels are inward-...
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The quality of binding sites?

Can someone please provide a human friendly explanation. to the following: RNAp binds a defined site (a specific DNA sequence) at the promoter (Fig- ure 2.2a). The quality of this site specifies the ...
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Has there been a measurement of a stalling force for myosin molecular motors?

For processive molecular motors like kinesin, in vitro assays have allowed to measure directly a stalling force beyond which they do not progress anymore or detach. As far as I know, the literature ...
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How to make predictions on genes not involved in a particular disease

I have one set of genes which counts about 100 such that every gene of that set is evidence based involved in a particular disease. Let's call this set A. For a machine learning project I need a set ...
6 votes
2 answers
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What does rescue mean in the context of biological experiments?

I have come across the term 'rescue' in biological contexts a lot recently and despite reading multiple definitions online cannot seem to get my head around what the word means on its own, and what it ...
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Plasmid Design and Integration events [Single vs Double cross over]

When linearising a vector by restriction digest within the middle of a homologous region can a single cross over integration event only occur if the plasmid is re-ligated within the cell after ...
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7 votes
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How are DNA virus cladograms actually calculated in practice? Is the procedure different for RNA viruses? Are these processes somewhat subjective?

The May 24, 2022 Bloomberg opinion piece Monkeypox Isn’t Looking Like a Covid-Sized Threat; It’s still early, but contact-tracing efforts and analysis of the virus’s genome offer hope that this ...
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Why DNA polymerases don't have helicase activity

RNA polymerases have intrinsic helicase ability, while DNA polymerases don't. I am curious why DNA polymerases evolved in such a way that they lack the ability to unwind DNA.
2 votes
1 answer
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How does non-cell autonomous work - how can a mutant cell make other non-mutant cells exhibit a mutant phenotype?

I am reading a journal paper, and I have coming across the following statement: Furthermore, although late-born neurons that take up exogenous Dcc fail to settle in the superficial layer of the ...
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2 votes
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Apparant inconsistency in DNA topology theory in formation of origin of replication [duplicate]

I'm studying an introductory course in genetics and came across something I don't fully understand. I obviously used Google to find where I'm thinking wrong, but I still can't understand it. To ...
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Why would E. coli cultures suddenly start to slow down?

My E. coli cultures used to take 13.5 hours to reach stationary phase. I have not changed any of the parameters like temperature, shaking speed, media formulation/components or inoculation volume. ...
2 votes
1 answer
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How can SNP arrays be used to detect deletions within a gene?

I am reading a journal paper where the researchers are studying the effect of disease-causing mutations in the IL1RAPL1 gene. In the first figure of this paper, they show pedigrees of families where ...
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How do refractive index (RI) matching solutions reverse tissue expansion in CLARITY tissue clearing?

I am learning about the CLARITY tissue clearing technique. I am researching this technique to understand how it works better. I know that this technique can make tissues transparent without severe ...
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What is meant by “global RNA polymerase occupancy”?

I read the following in a paper It provides base-pair resolution and strand-specific information of **global RNA polymerase** occupancy. CDK13 cooperates with CDK12 to control global RNA polymerase ...
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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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How to look for different transcripts for a protein?

I am trying to find all the different transcripts for a protein that translate into different isoforms of the protein. However, when I look it up online, there is no clear organized data on different ...
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Why don't animal cells have both mitochondria and chloroplasts? [closed]

Ancestral eukaryotes had both mitochondria and chloroplasts, why do animal cells only have mitochondria. Why did evolution allow animal cells to give up such a great circle of energy? Where the waste ...
2 votes
1 answer
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Zayed et al. (2022) "Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome"; expressed sequences or transcribed?

Phys.org's Ocean water samples yield treasure trove of RNA virus data summarizes Zayed et al. (April 7, 2022) in Science Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA ...
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3 votes
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A question about transposons

I would like to use the plasmid pXen5 (by Xenogen) for a transposon screen. It contains two inverted repeat sequences, with Luciferase, Kanamycin, and the transposase itself in between. (It's tn1409). ...
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Are introns conserved among cells?

To elaborate on the title: Among somatic, post-mitotic cells, would the same intron on a given chromosome have the same sequence among all cells descended from a progenitor cell?
4 votes
1 answer
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Use of different biotinylated GTP compounds in molecular biology

In the Cappable-seq technique 3′-Desthiobiotin-GTP can be used to label the 5′ end of mRNA. However in a commercial technical article on biotinylated-RNA affinity probes I encountered the following ...
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When a dog sniffs up organic material that contains DNA, is it possible his genome incorporates it? [closed]

I'm not kidding. Was just watching my German Shepherd sniffing away at a new Amazon box. ...realized she sniffs vast array of DNA from organic material when on a walk: millions of mammalian, plant, ...
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 ...
2 votes
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 ...
1 vote
1 answer
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What is a gain-of-function assay in neuroscience?

I am reading this paper and I have come across the following statement: "We sought to test whether exogenous Kirrel3 expression induces synapse formation via a gain-of-function assay... Because ...
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In enhanced chemiluminescence in western blots, will the horseradish peroxidase eventually get used up?

I am learning about enhanced chemiluminescence in Western blots. I have read online that in enhanced chemiluminescence that horseradish peroxidase (HRP) catalyses the oxidation of luminol to 3-...
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1 answer
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Why can SPRITE measure many simultaneous interactions?

Why is the SPRITE method not limited to a number of simultaneous interactions that can be measured, while microscopy and proximity ligation are limited to 2-3 interactions?
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Can cell adhesion molecules have intrinsic enzymatic activity?

I am learning about cell adhesion molecules (CAMs), and I know that they mediate cell-cell and cell-extracellular matrix adhesion via homophilic and heterophilic interactions. I have read that CAMs ...
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7 votes
2 answers
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How do geneticists determine if a gene mutation is pathogenic?

I am analysing information about patients with neurodevelopmental disorders using the DECIPHER genomics database. I am looking for patients who have only a specific gene deleted and no other mutations ...
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