Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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61 views

Please critique my draft for a DIY SARS-CoV-2 testing facility so that I can offer these tests for free to those people in need [closed]

I hope your quarantines are going well. A little disclaimer before I move on: I am not a biologist. I am a Business major. My knowledge of biology is equivalent to that of an earlier high school ...
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The pyruvate-dehydrogenase enzyme complex catalyzes a the formation of acetyl-CoA in 5 steps? Which of these is the most irreversible step and why?

This is my homework for a bioenergetics class. The reaction has five steps (formation of hydroxietyl-TPP, than the the acetyl-lipoamide and finally the acetyl-CoA, in the end the oxidation of ...
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What is the typical choice of the RAPD primer set?

Random Amplification of Polymorphic DNA (RAPD) is a widespread method to identify species or strains that are otherwise difficult to tell apart (microorganisms, tiny insects and the like). It includes ...
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Why there is no ELISA for SARS-CoV-2?

As far as I know, SARS-CoV-2 tests currently used worldwide are real-time RT-PCR. Why there is no ELISA for SARS-CoV-2? Compared to PCRs, ELISA is: Way cheaper; Way faster; Does not require trained ...
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Do proteins contain phosphorous? If its true then how alfred hershey and martha chase used the statement that proteins do not contain phosphorous?

I hv heard about phosphorus that it is a constituent of certain protein, although we know that no amino acids have phosphorus... and if its true then how Alfred hershey and Martha chase experiment got ...
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Why are proteins considered Informational macromolecules?

I can understand somewhat why DNA and RNA are considered Informational macromolecules, because they contain genetic information. But why are proteins considered Informational macromolecules?
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What causes the overactivity of collagen production and expression in the cells of the nail bed/ nail matrix after some traumata?

What is the cellular mechanism of traumatic(sterile) onychodystrophy(hypertrophy)? I.e one hits his toenail and has it removed twice( once after the first trauma and then 3 years after the first ...
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Relationship of RNA-binding proteins to peptidyl-prolyl cis-trans isomerase

I am studying a Plasmodium gene, known to encode an RNA-binding protein. However a BLAST search brings up mainly peptidyl-prolyl cis-trans isomerases from other species. Why would this be so?
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packaging of influenza RNA segments

How can the influenza A virus package its 8 different RNA segments? Is there is a special mechanism to ensure each virus particle gets the eight different segments? I doubt it is done at random ...
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Is there software simulating virology experiments like LTspice XVII simulating electronic circuits? [closed]

I want a software if existed to simulate what happens when a virus attacks a bacteria or other organisms. It can change a parameter of the viruses.
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How to recalibrate qpCR reading when incorrect qty of solution is added during DNA elution step?

I have 20 viral DNA samples collected for 6 time points. The DNA content varies over time My DNA extraction protocol step suggests that in the last step of the protocol during elution I had 100uL of ...
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Can virus and bacteria move on the surface? [duplicate]

Do viruses/bacteria have some motive mechanism? I mean if the virus/bacteria reach some surface by touching, can it move on that surface? Life example: suppose the cooler is not so clean and has ...
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Absent gene expression from one of two vectors co-transformed into the BL21(DE3) strain of E. coli

I've been trying to express two proteins in the BL21(DE3) strain of E. coli. One gene is in a pCR2.1 vector and the other in a pET-expression vector. When I induce with IPTG and run on an acrylamide ...
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What are some good books on basics of Cell signaling?

I think the title says it all. (self answered, although others' answers requested)
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How can I get started in molecular biology?

I have a background in computer science and math and am interested in learning molecular / synthetic biology - what resources do people recommend?
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Can I pellet DNA back from dissolved state?

I have a dissolved plasmid pellet in water. Can I pellet it again by centrifuging it at 13000 rpm? If not, why?
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Is downregulation of neurological receptors fully reversible, i.e. complete upregulation and resensitization?

Are down/upregulation truly reciprocal mechanisms? After a binding ligand or agonist is removed, such as a prescription medication, is upregulation and resensitization able to occur to a level that ...
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50 views

Open Reading Frames vs Coding Sequences (CDS), are they different?

The two terms confuse me for a long time. What is the difference between ORF and CDS. Some people say ORF could contain intron and CDS does not. The wikipedia definition of ORF does not contains ...
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Why does FADH2 exist?

If FADH2 generates less ATP then why does it exist? Could have something to do with electron energy levels? And what is the evolutionary background of this molecule?
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design and assessment of qPCR primers for COVID19

I read the False Negative of qPCR test for COVID19 is high compare to CT scans. https://pubs.rsna.org/doi/10.1148/radiol.2020200642 I was curious if experts can comment on why and what makes it ...
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85 views

Expression of eukaryotic ribosomal DNA

The Wikipedia page for rDNA says "Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA" Also, the figure next to it says "The gene segment of eukaryotic rDNA contains 18S, 5.8S, and 28S ...
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In the notch signaling pathway, what is Fringe activating?

Take a look at the notch signaling pathway in human from KEGG : https://www.genome.jp/kegg-bin/show_pathway?hsa04330 I want to know what is Fringe activating. It is not pointing to another gene or ...
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Non specific band in EMSA gel?

I am doing EMSA with Thermo LightShift Kit. I have a 150 bp biotin labeled probe which has been PCR amplified, gel eluted and sequenced. When I load samples on 5% native polyacrylamide gel, I see a ...
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Circulating Tumor Cell vs Circulating Tumor DNA

I'm a little confused about the wording of these two phrases and under which context the epithelial-mesenchymal transition occurs. For example: Is it the circulating tumor cell that releases the ...
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27 views

Swing bucket for PCR

I see a swing bucket rotor for PCR trips and don't know what step is using? What difference if I use fixed - angle? In addition, Which step I can use swing bucket instead fix - angle in molecular ...
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Peptides neither produced by the ribosome or the non-ribosomal peptide synthase complexes

I read in Wikipedia: While there exist a wide range of peptides that are not synthesized by ribosomes, the term nonribosomal peptide typically refers to a very specific set of these as ...
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From a hosts point of view, which comes first, effect of toxins on pathways or identification of toxins by immune system?

From a pure biology perspective, when a pathogen (gram-negative bacteria) affects a host by secreting toxins, what comes first, the effect of the toxin on the pathways or identification of the toxin ...
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How to analyze phosphorylation shift by western blot?

I want to see the phosphorylation shift in my protein of interest. I have created a point mutation in my protein. so that it will not able to go for the phosphorylation compare to my control. i want ...
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1answer
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How does an antisense RNA molecule restore protein function in CF patients?

I am researching a treatment for cystic fibrosis (CF) called Eluforsen and I am trying to understand the mechanism by which an RNA molecule can restore proper protein function. In many research ...
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How do I identify and then isolate a Gene that codes for a particular observable phenotype

How do I identify and then isolate a Gene that codes for a particular observable phenotype. It is a novel bacteria and I do not know the gene sequence or the protein that it codes for.
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How many metabolites are in the metabolome of (almost) all eucaryotic cells?

Which small biomolecules (up to the size of amino acids) are present in (almost) every eucaryotic cell and thus part of its biochemical network, constantly and inevitably being produced and ...
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Bimodal frequency distribution of size of protein loops

The graph of number of amino acid (AA) residues in a loop Vs the frequency of their occurrence in proteins largely follows a tending-to-zero pattern. However, there appear to be some specific number ...
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Selection marker for a cytoplasmic vector that works at low expression levels?

I need to express a selection marker on a plasmid in human cells (e.g. HEK293). However, I am using a cytoplasmic vector derived from a non-human virus with its own mechanism for transcriptional ...
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What is the difference between Molecular and Cellular tolerance?

Although I've read that there are three types of tolerance, molecular cellular and behavioural, I cannot seem to find any mechanism of cellular other than desensitization of receptors. If someone can ...
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1answer
51 views

How do enhancers induce transcription?

DNA response elements are DNA sequences that are could be found upstream, downstream of genes that regulate gene expression at the transcriptional level. One type -Enhancers- bind specific ...
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1answer
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what happens to rna length if we have a termination site in additional to the original one [closed]

if we have an RNA transcription and we add an additonal temination site in the middle , will i have two RNA molecules or just a short one ?
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How does a lymphocyte produce an antibody from an antigen?

I am studying the immune system, and I have a question about the inner workings of antibody production in lymphocytes. As I understand it now, lymphocytes are able to create antibodies based on ...
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1answer
78 views

How to design the primer when you don't have GC?

I have treated my RNA with sodium bisulfite so all my cytosine is converted into thymine. Then I used that RNA for my RT reaction. I have a cDNA template without Cs. Now I am trying to amplify that ...
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38 views

Where do methyl groups in the human body come from?

Where do methyl groups in the human body or other mammals come from? Do we synthesize them (where?) Do we get them from our diets (in what? anything beside methionine?) Do our gut microbes produce ...
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1answer
51 views

what is the princlple of using DMS (Dimethylsulphate) for structural analysis of rRNA?

I want to check the secondary structure of rRNA (PTC) in a particular position by using DMS footprinting. I have deleted the modified nucleotide (m5c) which is present in the PTC and it helps in the ...
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How does lipoid pneumonia lead to acute respiratory distress syndrome (ARDS)?

How does lipoid pneumonia lead to acute respiratory distress syndrome (ARDS)? The vaping illnesses that have been happening on the news in the United States are being caused by the federal ...
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1answer
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Trade-offs between phage and yeast displays?

If you wanted to test a peptide you designed, you can do a phage display or a yeast display experiment to assess binding affinity. What are the trade-offs between these two methods? I've heard ...
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1answer
37 views

Photolysis in the Light Reactions of Photosynthesis [duplicate]

I'm a bit confused concerning photolysis. During the light reactions, photons are used to excite the chlorophyll molecules so they are passed to the primary electron acceptor. The electrons initially ...
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1answer
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Why does opening of the Ca-channels trigger the release of neurotransmitters?

I understand that the opening of the Calcium channels trigger the release of stored neurotransmitter in granules, but what is it about the flow of positive ions that makes the vesicles fuse with the ...
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Parthenogenesis vs. Fertilization. Is a polar body different from an egg?

In Parthenogenesis that happens by automixis "the replication of an egg by meiosis and the transformation of the haploid egg to a diploid cell occur by fusion with a polar body." =https://www....
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Analysis of post transplantation lineage tags

I'm having some trouble understanding some bits of a study, mostly about the Sleeping Beauty system and TARIS model, from this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408613/ I ...
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1answer
35 views

Is p53 a cyclin dependent kinase? [closed]

I've been reading some research papers about p53 and associated tumour suppressor proteins, such as p21. I see them referred to and associated with cyclin-dependent kinases. Is p53,p63 et cetera part ...
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Prokaryotes Genome

What function of repetitive sequences of Prokaryote? I see a gap (intergenic region) between 2 coding strand. But just only a single origin region in Prokaryotes. How it can transcription coding ...
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1answer
85 views

Lab technique to distinguish between single stranded and double stranded DNA?

What lab techniques exist to differentiate between single-strand and double-stranded DNA?
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Can two proteins activate/inhibit the same gene at the same time?

Suppose there are two proteins inhibiting a particular gene. Its not necessary that both will inhibit the gene at the same time instance right? So if one protein has already inhibited that gene before ...

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