Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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15 views

Types of bonds in protein chains?

I'm trying to understand possible bonds on the protein backbone. There are a lot of hydrogen bonds and sometimes disulphide bridges. Are both of these non-covalent bonds? I've read that we also have ...
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How to map A single N1-methyladenosine (m1A) by primer extension?

I want to map a single N1-methyladenosine (m1A) modification by primer extension. I have silenced a gene which is responsible for guiding modification of m1A then I confirmed the silencing. My next ...
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Where to study biology on undergraduate level? [on hold]

I hope I'm asking the question on the right place and in the right format. Anyway, I am really interested in how things work, and from that perspective I want to study molecular biology and ...
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Is gluconeogenesis exothermic and is it exogenic?

Glycolysis is exothermic, but a lot of energy is released as heat. Can gluconeogenesis bypass the heat absorption and be exogenic or exothermic?
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what is minimal promoter and what is basal promoter?

what is minimal and basal promoter and what are their elements and what is the difference between the two?I'm confused. searched a lot, but didn't found any satisfactory answer. please help
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Theoretically, if one were to atomically piece together a microorganism or virus, without using any biological reproduction, would it still be alive? [closed]

I'm aware that this is likely impossible in the current state of technology, and possibly always will be, but I can't help but be curious. Say we took an extremely small virus, such as Porcine ...
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1answer
24 views

Which one is better to use for water stress experiment GWAS or RNASeq?

This is my first time in this area of research. I am working on 95 varieties of bambara groundnut. I have done the agromorphological characterization of these varieties as well as the genetic ...
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Can someone explain how a water molecule reacts to form ions? [on hold]

How does a water molecule react in order to form ions? Please explain. H20 apparently separates into H+ and OH-.
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2answers
288 views

Why is the Tm defined as the temperature at which 50% of dsDNA has changed into ssDNA?

In molecular biology, Tm is defined as the temperature at which 50% of dsDNA is converted to its single stranded form. Intuitively it would seem that the melting temperature should have been defined ...
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1answer
31 views

What causes the elongation of Genome down the evolutionary time line

Theory of natural evolution says that complex life forms arose from simpler ones e.g. starting from Eubacteria to modern day multicellular eukaryotes. {If we try to reduce these changes happening at ...
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74 views

Viral RNA to DNA

I have a question concerning reverse transcriptase. Why is it that when the viral rna is converted to viral dna( as in the case for hiv), the virus develops resistance to medicine? Under what ...
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Adenosine Triphosphate is used as energy supplier why not GTP / CTP / TTP [duplicate]

All are having Triphosphate ATP / GTP / CTP / TTP Why only ATP is used as an energy supplier?
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How to prepare for the biology olympiad? [on hold]

Is there anyone out there preparing for the biology olympiad? I am looking for great study resources, including textbooks! Many thanks!
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Invivoscribe T-Cell Testing

Invivoscribe says they are replacing their T-Cell Receptor Gamma Gene Rearrangement Assay 2.0 (one T-Cell MMix with the TCRG T-Cell Clonality Assay (two T-Cell Mmixes. Our comparison study suggests ...
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4answers
85 views

Why do mutations not take place in mRNA of higher eukaryotes?

Is it because it is too short-lived to be mutated? Both DNA and RNA are nucleic acids so how is mRNA protected? RNA viruses undergo mutations to evolve so I guess it is not immune to mutations
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1answer
32 views

Which are more beneficial: lyophilized or hydrolized collagen peptides?

Looking at two different manufacturing methods for collagen peptides: hydrolyzed vs lyophilized (freeze dried), I read that hydrolyzed results in a hydrophobic biolayer molecule collagen peptide. Re:...
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1answer
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A little help understanding DNA supercoiling

I am studying molecular biology from Lewin's Genes XII and got confused in the supercoiling topic. Since then I read from several other sources and so far understood the following. However, I can't ...
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1answer
37 views

What is the difference between protein and peptide? [closed]

On which basis do protein and peptide are divided? I mean which factors differentiate them?
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50 views

Software to model and analyse protein–ligand interactions

I am currently trying to model a certain protein (Golgi Mannosidase II) and compare the induced fit of the inhibitor swainsonine. I would like to be able to analyse the distances between bonding ...
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1answer
119 views

Why is it thought that protein folding is determined solely by amino acid sequence?

It seems that it is a generally accepted idea that protein folding is completely determined by the sequence of amino acids, but why do people believe that? Is it simply that no example of a protein ...
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Allelic dominance and recessiveness [duplicate]

What is the reason for the allelic dominance and recessiveness of a gene? Is it all about the chance or probability of getting the fusion of a particular character ? So how can be there a dominance ...
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E. coli & aspartate

I am familiar with the linkage between aspartate/ligand binding, receptor methylation, and flagellar behavior re. style of locamotion, but I do not know what the bacterium does with the aspartate it ...
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1answer
20 views

What is ApoCas9 in the CRISPR-Cas9 system?

I am currently reading an article about a particular assay of Cas9 nucleases. In one of the experiments, they have used ApoCas9 (Apo variants of other CRISPR nucleases) as some sort of control. But ...
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1answer
39 views

Non-coding DNA as a protection to deleterious mutations

We know that most part of our genome (at least 75 percent) is non-coding DNA. Can it be a way to protect the organism from mutations in important genes, such as the ones which control cellular cycle, ...
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What are the uses of Helical Wheel Projections in Structural Biology?

I have seen helical wheel projections used to illustrate amphipathic helices in proteins. Are there any other uses for these models?
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1answer
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What Ultimately Controls DNA Transcription?

Transcription of DNA and further splicing of mRNA is regulated by various transcription factors, small nuclear RNAs and so on; similarly such related mechanisms as transposition of transposons. All ...
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2answers
108 views

Why isn't the human zygote considered a human life how is a living anatomically modern human defined biologically? [closed]

It has 46 chromosomes by default when healthy(Differences almost always are pathological) and has almost every biological functions, processes a Newborn or and Adult person has. It even invades ...
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How can I improve efficiency of Ecoli transformation?

I am an intern in biology institute. I have a 17.3kbp plasmid need to transform to Ecoli. But I have tried many time but have no or very few colony on LB plate. I know large plasmid have less ...
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1answer
51 views

Can denatured GFP show fluorescence?

GFP ( green fluorescent protein) can show green fluorescence. And its fluorescence is due to the tri peptide chromophore which is given in below I was wondering, can we observe fluorescence, if we ...
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Which animals don't have pheromones?

Which animals are known to not have pheromones besides humans? I can't find any research on this. There are examples of every class that uses pheromones. However nobody seems to answer conclusively ...
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1answer
44 views

Difference Junk DNA and Pseudogenes [duplicate]

1-Are Pseudogenes and Junk DNA both Non-Coding DNA or they are different entity? How much Pseudogenes & Junk DNA do we have respectively? 2-I read that Non-Coding DNA has functions, my question ...
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Holder for 75 mm x 25 mm glass slides that can handle vibration

Hello Biology Stack Exchange, I have an application where I have cells on a glass slide (dimensions: standard 75 mm length x 25 mm width x 1 mm thick). I want to vibrate/shake the cells rapidly ...
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1answer
83 views

Does this article call into question the theory of evolution?

https://www.quantamagazine.org/neutral-theory-of-evolution-challenged-by-evidence-for-dna-selection-20181108/ The article above challenges how mutations work in evolution. Does this disprove the ...
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Why do people use J2 viruses for macrophage immortalization?

I've been trying to figure out how to go about immortalizing some primary alveolar macrophages harvested from mice. What I am seeing in the literature is that it seems like people have been using a ...
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1answer
33 views

How to do desalt reaction by passage through a Micro Bio-spin 6 column?

I want to perform the bisulfite sequencing on rRNA to detect the 5-mC. I followed this protocol • DNA-free™ DNA Removal Kit (Invitrogen) • Purified RNA, Treat RNA according to manufacturer's ...
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1answer
32 views

Does anyone know a good pancreatic-cancer metastasis cell line?

Researching about pancreatic cancer. We have mostly "main-tumor" cell lines in our lab, and I´m currently looking for cell lines originating from metastases (liver, lung, etc.). Does anyone know a ...
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2answers
70 views

What is the subcellular location of synthesis of non-essential amino-acids?

What is location of non-essential amino acids synthesis in a cell? Is it some specific organelle? And what is the gene driver behind this? I thought the whole point of DNA is coding for how to ...
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24 views

Biochemistry of pleasure of/desire for physical exercise in mammalians and humans?

Are there some known biochemical mechanisms, that induces desire for/pleasure of physical exercise in mammalians and humans? I have heard, that horses can not live without physical exercise and they ...
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1answer
36 views

What buffer should I choose for IEX chromatography for purifying IgY

I will use ion exchange chromatography with an anion exchange column to purify chicken IgY. Prior to this I did dialysis to remove salts from previous purification steps, is it possible after this ...
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Chemical inhibition of fertilization in plants

Are there any chemical compounds that inhibit fertilization in plants after gametogenesis? Simply put, I am talking about spermicide or emergency contraception for plants. Specifically, I am ...
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ATP and Muscle Contraction

I have a question regarding how molecular interactions manifest in physical actions - such as hanging from a bar. To the best of my understanding, when it comes to the contraction of muscles, ATP is ...
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1answer
29 views

Can I use a basic compound microscope to analyze the ploidy of plant chromosomes?

So, I'm not really any kind of trained botanist. But I do have two things: some dandelion seeds from France, and, collecting dust in my garage along with related accessories, this thing. Normally, ...
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How to troubleshoot in vitro formaldehyde fixation for nucleosomes?

For an experiment, I am trying to fix the mononucleosomes (100ng) using formaldehyde as crosslinking agent in HEPES buffer. I have been using 2% formaldehyde in a reaction buffer containing 1mM EDTA, ...
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28 views

How do receptors lose their sensitivity?

Recently, I learned that one of the causes of Type II diabetes is that insulin receptors on cell surfaces lose their sensitivity due to long-term high exposure to insulin (which occurs as a result of ...
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1answer
44 views

Application of molecular dynamics simulation (or alternatives) for the full pathways of protein interactions?

If one would like to control the biological system (e.g. to treat disease or aging/senescence) then one should introduce the drugs in the system, that initiate complex protein interaction pathways ...
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What is the relationship between Ca- and Na-ions and mucins and why?

According to Wikipedia https://en.wikipedia.org/wiki/Mucin#Secretion mucins (Proteins that form mucus) obtain viscoelastic properties by the Exchange of sodium and Calcium Ions. What is Happening ...
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1answer
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Can Cas13 be used with multiple crRNAs in the same reaction?

CRISPR-Cas13 equipped with crRNA (complementary to transcripts of interest) can be designed to target ssRNA transcripts in cells. Upon successful crRNA and ssRNA binding, a fluorescent domain on ...
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How are multiples transmembrane proteins translocated or embedded in the membrane?

This image is in the textbook, Molecular Biology of the Cell. I understand why the start and stop transfer sequences must alternate, but why is there 2 consecutive start transfer sequences at the N ...
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What is the typical concentration of Calcineurin (PP2B) in CA1 dendritic spines?

I am trying to find the concentration of CaN (PP2B) in dendritic spines, there is a computational model (doi:10.1073/pnas.0804672105) that uses the quantity of 1uM in the dendritic spine. I think this ...
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1answer
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What is the difference between DNA vs RNA Editing in the context of gene therapy?

As a someone with beginner knowledge on biology, I have come across the terms "RNA editing". Take this paper for example : RNA Editing with CRISPR-Cas13 From my understanding, DNA -> RNA -> Proteins ...