Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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Is protein intake required for the formation of new myosatellite cells?

Hypertrophy of muscle fibers requires an adequate (significant, really) intake of protein, but what about just forming new myosatellite cells as a response to a stress applied to the muscle? Does that ...
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How are new myosatellite cells formed within muscle tissue?

Can anyone break down the process of exactly how and why satellite cells in skeletal muscles are formed, and how one can deliberately generate new myosatellite cells in their muscles? Specifically: ...
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Interaction of charged triphosphates with the ATP binding region in proteins

DNA-histone interactions involve positively charged amino acid side chains groups neutralizing the negatively charged phosphate of the sugar-phosphate backbone. Is the same true for ATP binding sites ...
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How to assemble three 60mer nts by pcr?

Good morning, I am new to molecular biology. The question might be silly but i would like to know the answer. I have three 60mer single strand synthetic oligonucleotide. Namely Tag 1 - 3. My goal is ...
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Which enzymes use ATP?

It is well known that there are many enzymes which use ATP in their function, and any enzyme that work against an energy gradient need to have that energy supplied from somewhere, but just as well ...
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Electrochemical and concentration gradient confusion [closed]

I am learning membrane transport and learnt that there are 2 gradients that determine passive and active transport. If the concentration of a cation is higher in the cytoplasm side (hence ions should ...
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When does DNA transcription occur? (or what triggers it)

To be specific, I'm not looking for answer such as "when dna polymerase bind to the promoter region of the dna". The question is rather, what triggers the process in the first place? Does ...
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1answer
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DNA complementarity against reverse complementarity

I am sorry to bother with this question (i study genetics for about few hours, because I need to understand my data) and I am really confused about these two terms, because I dont know if the books ...
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Introns and miRNA

From this paper, it is stated that some introns may contain genes coding for miRNA, miRNA is essential in regulating gene expression by pairing with RNA, hence disrupting regular translation. From ...
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Dealing with heterochromatin during DNA replication

Heterochromatin are present along the chromosome (uncoiled state). With the highly-condensed structure relative to euchromatin, RNA polymerase cannot get into the DNA base pairs in heterochromatin and ...
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Flip-flopping in plasma membrane

Flip-flopping of lipids (and in proteins it is impossible) in plasma membrane is rare due to high energy barrier (video ref). However, it is an important mechanism since it allows asymmetric ...
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Why can't certain nucleoside analogs be used to label bacterial RNA?

A 2020 publication in Nucleic Acids Research 1 includes the following passage: A variety of nucleoside analogs have been developed for metabolic RNA labeling in various eukaryotic cells (9–16). Among ...
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Western blotting: what common tweaks do you make to the protocol and why would you make membrane cuts?

I'm building an app which helps researchers plan out Western blots, record protocol tweaks and receive warnings in the app if: you're trying to multiplex antibodies of similar molecular weight on the ...
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Can caffeine act as viagra

Recently I studied that cAMP which is a 2° messenger can cause various physiolocal changes under the action of proper hormones. Now cAMP is degraded by phosphodiesterase and this ceases the actions. ...
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Question on cellulose synthase

How does the rosette structure of synthase cause the cellulose synthesized to be aligned next to each other? I just cannot visualise how a rosette structure can be able to cause the celluose to be ...
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Question about : RNA interference - small-interference RNA AND about Rab-protein in vesicles

First Question : RNA interference - small-interference RNA in the textbook -Essential cell biology By Bruce Alberts, Dennis Bray, Karen Hopkin this Figure is Shown my question is : if the foreign RNA ...
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Are proton and water consumed in glycolysis?

These are the inputs and the outputs of glycolysis (1): $$\ce{C6H12O6 + 2ADP + 2Pi + 2NAD+ → 2C3H4O3 + 2H2O + 2ATP + 2NADH + 2H+}$$ but when ATP converts to ADP in the first step of glycolysis, it ...
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where can i introduce my insert in the plasmid?

I assembled three different DNA fragments together. I want to do the gibson assembly to introduce my fragments into the plasmid. Main point is i don't want to use the restriction sites. I am using ...
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Need help designing an enzyme immunoassay (EIA)

I have a FITC-labelled DNA sequence and an anti-FITC antibody, however this antibody is not conjugated with HRP or any other enzyme. I work in a lab with limited finances, so is there a way I could ...
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Which landmark paper first described the differentiation of T-cells?

T-cells are distinguished from B cells in part by their locus of differentiation/maturation (thymus). This is textbook knowledge, but I was wondering which particular person or people were responsible ...
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Blood and plucked-feather sample storage

This next field season I will be collecting both blood and feather samples and I wondered how best to store the samples. The blood samples will be used for microsatellite and/or SNP analysis. The ...
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Gibson assembley for small fragments?

I am new to the Gibson assembly, I know how I need my plasmid but main problem is I don't have short tags and linker so I wanted to do Gibson assembly? 5'-...
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101 views

How to convert cell units (c.u.) to mole?

If one has values in terms of cell units (c.u.) how may it be converted to $\mu$M? Should I think a "cell unit" as $1\;c.u.= \frac{1}{\text{cell volume}}$ and $1\;c.u.=\frac{1}{\text{cell ...
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What is the chemical structure of neca? [closed]

I heard in the YouTube video https://www.youtube.com/watch?v=m07OvPEoR6g that pearls are made from neca. What actually is the chemical structure of neca? I can't figure out an algorithm for ...
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What is the “GTP activator protein” that activates GTP-cyclohydrolase-1?

From GTP-cyclohydrolase deficiency responsive to sapropterin and 5-HTP supplementation: relief of treatment-refractory depression and suicidal behaviour (BMJ Case Reports, 2011) The metabolic profile ...
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Knockdown with non-coding target

I am studying 2 splice forms of some gene. I need to knockdown both of them. To do so I have only one choice: to use non-coding right end of one of the splices. Do you have any experience with such a ...
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sequence specific endoribonuclease

I have a viral mRNA that I want to silence with a genomic method without using RNAi.I thought of using ZFN or TALENS but they both work only on dsDNA. Basically I need an endoribonuclease that ...
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VDJ sequencing in mice, DNA or RNA?

I am wondering if anyone who is well versed with VDJ sequencing for TCR repertoire analysis (specifically CDR3) would know if DNA or RNA is a better starting material? We are looking at the effects of ...
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Exact average molecular weight of a dsDNA basepair

I am trying to calculate the exact weight of a given dsDNA. On the Internet and the literature, different values for the av. molecular weight of one basepair are given : 660 g/mol (probably wrong), ...
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What is the difference between non-coding and intergenic regions?

The initial question was about understanding what is in the downstream of a gene in a eukaryotic organism. I understand that this region is located 3' of a gene, and therefore I would expect to find ...
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31 views

Alkaline Phosphatase and Ligase Protocol for Cloning

In the image the circular molecule is a restricted vector and the linear red molecule is a DNA insert. I found this protocol in my lessons notes, but I don't understand how it is possible that ligase ...
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Are there any online resources for finding the signaling pathways that two proteins both belong to?

I am studying the proteins GSK3 and AMPK and I am trying to identify the signaling pathways that both of these proteins belong to. From reading journal papers I have found out that both of these ...
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Parameters that determines the thermal stability of DNA

Why a DNA with a high GC content more stable than one with a less GC content? Is it because of the three hydrogen bonds in GC base pair which is one more than a AT base pair or is it because of the ...
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What does ΔC and ΔN mean with regards to a protein sequence?

I am reading a paper about the regulation of the nuclear export of the protein GSK3 and I have come across the following statement: Full-length FLAG epitope-tagged mFrat1 (FLAG-Frat) and the amino-...
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Why my protein transferred but ladder did not (western blot)?

My protein of interest is about 200Kd, I ran the gel for 35 min at 95V, the protein transferred but the ladder did not, I used dual color ladder(Precision Plus Protein™ Dual Color Standards, 500 µl #...
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Potential obstacles to growing nanoelectronics within living cells? [closed]

Say there was a nanotechnology allowing to "grow" and wire up electronic components/sensors measured only a few nanometers in cross-section, though spanning in length across microns. Say ...
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1answer
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Does N1-methyl-pseudouridine occur naturally in any RNA?

Pseudouridine occurs naturally in some RNAs. But what about the methylated variant of it, N1-methyl-pseudouridine? The latter is a key ingredient in both the Pfizer and Moderna Covid-19 vaccines, ...
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Questions regarding transformation in bacterial cells

First off, in transformation the donor DNA aligns itself with the complementary bases in the recipient DNA. Now a "perfect" alignment of the donor DNA ( Sorry if my terminologies are ...
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When was peptidoglycan discovered?

I've searched for some time now, but I can't find a definitive answer. The closest I have gotten is "knowledge about peptidoglycan structures dates back to the 1970s–80s" from this paper.
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What is the difference between mutation per base pair and mutation per genome? [closed]

Isn't genome size considered to be the number of base pairs present in DNA? So what is the difference between the mutation per base pair and mutation per genome? Are they similar or different?
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Can Taq polymerase be stored with PCR primers?

I don't think it's possible for TAQ to be stored with the primers, but I'm not sure. This storage wouldn't be long-term (a few days, or a week at most). Thoughts?
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What is the significance of the phospholipid bilayer being two-dimensional?

I'm wondering about the significance of the phospholipid bilayer being a two-dimensional fluid. I found this powerpoint: I also found that thetwo-dimensional fluids have limited degrees of freedom. ...
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what books do you recommend to undstand horvath clock?

I’ve read about horvath clock, and the new theory of aging. One that describes DNA methylation as the upstream root for all age related symptoms. I want to read more, and understand this at a much ...
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Should I consider one or two DNA chains to find how many nucleotides are in a gene?

I am trying to solve an exercise. How many nucleotides does a gene contain if information about 287 amino acids is encoded in it? What is the molecular mass and length of this gene? AFAIK, I have to ...
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What is the minimum-volume : neutral-volume : maximum-volume of the molecules that make up the SARS-Cov-2 virus-fusion machine?

The "neutral-volume" is the over-lapping volume between minimum-volume & maximum-volume of the molecules that make up the SARS-Cov-2-fusion machine. Those identifying potential ...
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What does it mean to “nucleate multi-protein complexes”?

I am reading an article about the mTOR signalling pathway and I have come across the following: mTOR nucleates at least two distinct multi-protein complexes, mTOR complex 1 (mTORC1) and mTOR complex ...
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How good are the hematologic parameters (e,g, IL6 or others) in predicting which patients will develop a severe COVID-19 disease?

Clinical implications of the hematologic profile of COVID-19 patients including cytokine storm, coagulation profile and thrombophilic complications are starting to be recognized. Hypercoagulability ...
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Why we need a plasmid for r-DNA technology [closed]

Recently I was studying Biotechnology. When I went through the texts, I had a doubt: both plasmids and gene of interest are made of DNA stretches and bacteria directly absorb plasmids in a test tube (...
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How correlated is the chirality of different molecules?

In astrobiology, a proposed way of testing whether life found on another world is alien or originates from Earth is to determine the chirality of its molecules. This is of course only useful when the ...
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Do all anabolic reactions involve condensation?

I know that condensation is one example of an anabolic reaction (building macromolecules from monomers), but do all anabolic reactions involve condensation? Or is there an example of an anabolic ...

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