Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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How does RNA polymerase II CTD bind to the RNA modification proteins if the tail is flexible?

The tail of RNA polymerase II is flexible, not folded into a fixed structure , but does each repeat have more "rigid" structure (i.e. fold into a structure that has less rotation freedom ...
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211 views

CRISPR/Cas9: What are the main differences between sgRNA and the Cr:TracrRNA ?

So from what I understand, in gene editing, the CRISPR vector expresses a small RNA sequence comprised of a small guide-RNA that is complementary to your target sequence. The sgRNA comprises a 20 Bp ...
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30 views

Why are Ramachandran angles of first and the last amino acid not necessary to define the full 3D structure of a protein chain?

I have come across an online ppt slide of the bioinformatic algorithm where it is said that first and the last amino acid Ramachandran angle is not necessary to tell all its internal coordinates. Is ...
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41 views

How do ribosomes know not to translate non-coding RNA?

I'm unclear as to the molecular mechanism whereby mRNA is translated into proteins, but non-coding RNA is not similarly translated. How do ribosomes know not to translate non-coding RNA?
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combustion vs biological oxidation of glucose [duplicate]

I am a high school student and I am a little confused in cellular respiration, To represent respiration many biology text books just writes, C6H12O6 + 6 O2 --> 6 CO2 + 6 H2O But in actual ...
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What is the difference between a paralog and an isoform?

I am reading a journal paper about the protein kinase GSK3 and I have come across the following statement: Although commonly referred to as isoforms, GSK3α and GSK3β are actually paralogs, homologous ...
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Measuring the protein content using UV Vis

The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ...
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2answers
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What is a 21q21 deletion?

I am reading a journal paper about the relationship between the protein NCAM2 and autism, and I have come across the following statement: We report three patients affected with neurodevelopmental ...
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1answer
46 views

Why is this oxoglutarate dehydrogenase and not oxoglutarate decarboxylase?

I was looking at the oxoglutarate dehydrogenase complex and saw the reaction mechanism for its E1-TPP mechanism, which results in the formation of a stabilized carbanion intermediate. The mechanism ...
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Does the magnitude of gene-expression changes decrease the more downstream a gene is from the origin of change?

If I have a decrease or increase in expression in one gene, will the decrease/increase in expression in the downstream genes always be of a magnitude lower than the previous ones, or can they be ...
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Collagen, are fibrils arranged in overlapping fashion too just like tropocollagen?

Collagen molecules (tropocollagen) are interlinked into fibrils, with a banded structure showing the spaces ("lacunae") between the molecules. Do fibrils in turn also interlink in a similar ...
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Proinsulin is an 84 residue polypeptide with six cysteines. How many different disulfide combinations are possible?

Generally cysteine residues form disulfide linkages - so how many combinations are possible out of (say) six residues. Also can cysteine form bonds with all the residues?
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why does water go from high to low osmotic pressure to decrease the size of the nucleus?

I am reading this paper "Volume regulation and shape bifurcation in the cell nucleus" (linked below) https://jcs.biologists.org/content/joces/128/18/3375.full.pdf I am confused by this ...
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How do mRNAs find ribosomes?

After mRNA is released from the nucleus, the next process is its translation by ribosomes. By what physical, chemical or biochemical process does the mRNA reach the ribosome in the cytoplasm?
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43 views

What is the significance of running an uncut plasmid on electrophoresis gel?

What is the significance of running an uncut plasmid on electrophoresis gel? In this case we are talking about inserting a gene into plasmid, which then goes under PCR and then electrophoresis.
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1answer
102 views

Are the y-axis values informative when performing biolayer interferometry?

I am currently reading an this article by Alexandra C. Walls et. al. I would like to ask a question about a graph that is being used in the article and I wanted to know if my analysis was correct. I ...
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1answer
169 views

A mutation question from the Indian National Biology Olympiad

DNA was isolated from wild type (Gal+) and mutant (Gal-) E. coli cells and separated by density gradient centrifugation technique. DNA from Gal- strain acquired a lower position. This indicates that ...
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Could a mutation on neutral part of genome become deleterious?

I know that silent mutations are neutral because they dont affect function of the protein/gene, and a missense mutation would. But lets say both occur on a neutral portion, could one or the other ...
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Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?

I got my sequencing results (bisulphite treated and non treated sequences of same species Allium cepa) and now I have to do analysis in Cymate online tool. I prepared all sequences as it is written in ...
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What is mitochondrial run length?

I am reading the following journal paper and I have come across the following statement: Overexpression of GSK-3β significantly increases motile mitochondria in a Tau protein-dependent manner. ...
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What is the relationship of stimulants to hair loss?

I've noticed several topical hair loss products (ex: minoxidilmax) add caffeine to their recipes with the claim that "caffeine stimulates blood flow to the scalp" thereby improving hair ...
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2answers
44 views

What does γ mean before a gene name?

I am reading the following paper and I have come across the following statement: It has been demonstrated that the phosphorylation of histone H2AX-Ser139 to form γH2AX. I am not sure what the γ ...
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What property of water explains how sweating helps the runner continue running?

My question I have to answer is: A runner picks up pace on a warm day and starts sweating profusely. What property of water explains how sweating helps the runner continue running? The following are ...
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What does it mean for an enzyme to be “constitutively partially active”?

I am reading a paper* about the link between the enzyme GSK3 and autism, and I have come across the following statement: Unlike many kinases that require a signal to be activated, GSK3 is ...
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Why do most negatively charged phospholipids concentrate in the inner leaftlet?

Due to the asymmetry of the lipid membrane, negatively charged phospholipids such as phosphatidylserine, phosphatidylinositol are concentrated in the inner leaflet, creating a different charge ...
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109 views

Why doesnt the SARS-Cov-2 affect other animals?

Why doesn't the coronavirus affect animals like dogs and cows? I know that the SARS-CoV-2 is a zoonotic virus i.e. it can affect both humans and other animals. I also know that the DNA composition ...
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35 views

How did Rna replicate according to Rna World Hypothesis?

I was studying Rna World Hypothesis in Khan Academy, and there is a line..... The RNA world hypothesis suggests that life on Earth began with a simple RNA molecule that could copy itself without help ...
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50 views

Can Euchromatin convert into Heterochromatin?

I know that Heterochromatin can convert into Euchromatin but is the reverse possible? If yes, then How?
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Is the binding of androgen to androgen receptor in prostate cancer cells a requirement for the production of prostate-specific antigen?

The binding of androgen to the androgen receptor results in the transcription of androgen-regulated genes, which signals the proliferation of prostate cancer cells. This process also produces prostate-...
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3answers
433 views

How Incomplete dominance can be explained at molecular level?

What is exactly happening at the molecular level when two alleles constitute incomplete dominance? Whether the protein formed from each of the alleles constitute a new protein having a different ...
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1answer
62 views

How can Chronic myeloid Leukaemic drugs reduce the production of the Philadelphia genotype?

How can Chronic Myeloid Leukaemic drugs (Tyrosine kinase inhibitors, e.g. imatinib, etc.) that act by inhibiting bind of ATP to the active site of the BCR-ABL1 protein actually reduce the prevalence ...
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35 views

What is more dangerous, exotoxins or endotoxins?

Since gram- negative bacteria tends to cause disease to human and they mostly produce endotoxins. Does this mean that endotoxin is more dangerous than exotoxin? and if that so why?
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67 views

Determine similarity in percentages between species A and B, A and C, and B and C

The chart above is a graphic that shows the amino acid sequence differences between different organisms for a protein keratin. The question I am required to answer begins as, "Keratin is made up ...
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Can we apply NGS (next generation sequencing) on DNA extracted from formalin fixed paraffin embedded tissues (FFPE)?

I'm working on the microbiome and I can only use tissues which are fixed with formalin and embedded in paraffin. Is it possible to apply NGS (next generation sequencing) on FFPE (formalin fixed ...
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Can I use dATP instead of ATP (vice versa) for in vitro assay? [closed]

For example, polynucleotide synthesis reaction requires dATP which gives H on 3'end and synthesizes polynucleotide. For this reaction can I use ATP because I knew that ddNTPs are used so that ATP ...
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1answer
151 views

What does Δcys mean after a gene name?

I am reading a paper and I have come across the following statement: "Plasmids encoding full-length NCAM140 and NCAM140Δcys, intracellular domain of NCAM140, and the NCAM140ID729–750 fragment ...
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What does it mean for a protein to be dominant-negative?

I am reading this journal paper, which investigates the interaction of the NCAM protein and the Pak1 protein. In this paper I have come across the term "dominant-negative Pak1" and "...
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What is the difference (if any) between an Intrinsically Disordered Protein and an Intrinsically Disordered Region

The wikipedia definition of an Intrinsically Disordered Protein is a protein that lacks a specific 3D structure. An Intrinsically Disordered Region is similarly defined. Why are they often listed ...
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1answer
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Question in gel chromatography experiment

Here I am trying to do gel chromatography to separate vitamin B12 and Bovine Serum Albumin (BSA) in this experiment, I am using sephacryl s-100 HR gel column my question is can I use Phosphate ...
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Biochemical Mechanism behind red hibiscus flower on a cream hibiscus plant

I have two 3-4 yrs old cream hibiscus shrubs in my garden. The shrubs seemed normal enough, giving cream colored petals with a red center. But soon I noticed that there are specific branches, which ...
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Transcription of two different factors from the same transcription factor - seeking a relation between concentrations

Let's assume that: Factor $X$ enters nucleus and results in the transcription of two different factors, $A$, and $B$. $X$ $\to$ $A$ $X$ $\to$ $B$ Can it be expressed as $[A]=\alpha [X]$ or $[A]=\...
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Converting from RU/ML to AEU/ML

I'd like to know whether it is possible to convert from RU/ml to AEU/ml. I work in the ELISA department in our laboratory. We need to validate some kits by comparing results between our lab and ...
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Are Oct4 and Oct3 the same protein?

Are the transcription factors Oct4 and Oct3, who are encoded by the POU5F1 gene, actually the same protein, or alternative spliced products from said gene?
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What is a Protein contact map, and how do I read one?

Protein contact maps are symmetrical and look great, but how does one read one? I tried to underside the following source: 'Understanding contact patterns of protein structures from protein contact ...
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1answer
114 views

Horizontal gene transfer in a bacteria

I encountered an old examination question: Which of the following is not required in Bacteria for horizontal gene transfers? Infection 2. Translation 3. Transformation 4. Conjugation 5. Transduction ...
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Does anybody have an references to share or idea onhow the tumor behaviour changes as it grows from oligometastasis to polymetastasis?

I have looked at the literature and mostly scientist discuss about how a metastatic lesion is formed. But what I am interested to learn is how does a new metastatic lesion develop when there is ...
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1answer
37 views

Can viruses be deformed?

Viruses are created in their fully-formed state and do not grow. But one thing has been bugging me lately: can a virus be deformed, e.g. in order to fit into an opening slightly smaller than itself? ...
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Design rules for DNA linkers

I want to use double stranded DNA linkers to physically bind two "things" together, by grafting ssDNA on each one of them and using DNA hybridization as the locking mechanism. I do not expect the ...
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1answer
68 views

Can sperm cells penetrate the cell membrane of non-ovum cells?

Sperm cells have tiny bags of enzymes on their tip (the acrosome) which allow them to penetrate the ovum. My question is whether or not the process that allows sperm cells to penetrate the cell ...
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69 views

Gene of interest number of copies in transformed K. pastoris

When transforming a K. pastoris strain, is there a way to predict how many copies of the gene will be integrated following the homologous recombination? More specifically is it something that a ...

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