Questions tagged [molecular-biology]
The study of the molecular processes underlying life.
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How many GTPs are used in prokaryotic translation?
Here is the question: How many GTP are necessary to synthesize 2 linear peptides of 11 amino acids each using an in vitro prokaryotic system? Assume the tRNAs provided are already loaded with their ...
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Why doesn't treating neurons with a high sodium solution depolarize their membranes?
I am reading a journal paper, and in one of their experiments they treated organotypic hippocampal slice cultures with a high potassium solution to depolarize the neuronal membranes:
We found that ...
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Can a person have different sex at cellular level?
I mean like every cell has a sex chromosome.So does a male with XY chromosomes has all the cells in all the organs inside his body of XY chromosomes only? And vice versa.....
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Storing bacteria in a dry, room temperature long-term storage whilst maintaining viability
I'm quite new to biology, but I'm wondering if there are any methods of storing bacteria in long-term, dry conditions with no climate control. Perhaps they could be dormant in a powder or granule-like ...
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How come SSBPs in RPA don't bind primers?
I've started reading about the recombinase polymerase amplification (RPA). I'm learning that in RPA, recombinase enzyme binds to primers, then makes them anneal to the complementary target DNA strand, ...
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Does recombination occur in both chromatid of a chromosome with homologous chromosome? Or only 1 chromatid participate in crossing over?
A chromosome has two chromatids. In meiosis weather both chromatid participate in crossing over or just only 1 chromatid does?
So, I am asking whether 1 turquoise and 1 purple chromatid participate ...
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Can humans metabolize D-malate?
Only the L-isomer is produced naturally, while racemic mixtures are produced synthetically and used commercially as food additives and energy supplements.
So what happens when we consume D-malate? ...
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Is crossveinless in Drosophila melanogaster example of condition mutant or phenocarpy?
This is the original question -
Ques - A researcher exposed Drosophila larvae to 37°C during their growth. One of the adult flies that emerged had a crossveinless phenotype. When this crossveinless ...
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Induction of IFN-beta in HEK293T
I'm trying to increase expression of a protein we're attempting to study, UBL7, supposedly unregulated by Type I Interferon and particularly IFN-beta.
I've tried treating HEK293T cells (~60% ...
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Why is the codon size three, rather than four? [duplicate]
The genetic code consists of triplets, each of which (apart from the stop codons) yields an amino acid when the mRNA is translated.
But why did triplets evolve, rather than a longer or shorter codon ...
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Does the molecules in nerve cell membrane change 100% during the life of the nerve cell?
In their lifespan nerve cells do not divide and so they stay the same. They do get damaged sometimes and require some maintenance and change their axons a bit. They also require a lot of energy so ...
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Ubiquitous overexpression line of a gene expressed higher gene expression in leaf but not in seeds
I tried to make ubiquitous overexpression lines of a gene using a constitutive promoter vector in plant. I got multiple regenerated plants through tissue cultures.
At T0, T1, T2 leaves tissues, the ...
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Effects of oxygenated water on bacteria
I was curious if any of you would happen to have any experience with this but any hypotheses regarding how this would turn out would be much appreciated.
I’m wondering if water fully aerated with ...
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According to an online course, ribose and adenine can bond to make ATP. Is this true?
I recently came across this question in the MIT Open Learning Library Pre-7.01 Biology Course. It is question 2d in Problem Set 1 (archived link).
The question, as well as the correct answers and ...
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Transfecting cocoon or chrysalis
Do you know whether anybody tried to transfect insects during their cocoon/chrysalis stage, and if so do you have a link to such studies?
I was thinking it would be easier to do given that it's a more ...
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Migration of cut vs. non-cut plasmid on gel
As you might know there are 3 common forms of a plasmid:
ccc-form (CCC), being supercoiled.
oc-form (OC), being nicked and therefore relaxed.
linearized form (L), being cut on both strands and linear....
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What is the approx. diameter of a completely "folded up" human DNA molecule, in inches?
The human DNA molecule would be about 6ft if stretched out to a straight line.
I'm curious what the diameter of the DNA molecule normally is when it is "all scrunched up" or "bundled&...
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ddT-tailed TA cloning, and the fate of a double nicked plasmid in E. coli
In an undergraduate lab class on TA cloning, it was explained that ddNTPs are used as the substrate for terminal transferase when making the T overhangs of the vector. I was told this was to ensure ...
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Live cell imaging using confocal microscope - Question about the microscope settings and laser wavelength
I am doing some calcium imaging to measure calcium levels in HeLa cells. To do this I have expressed cameleon calcium indicator (YC3.60) in the cells and I am using confocal microscope Fluoview for ...
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Why is There a Necessity for Two Rounds of Cell Division and Four Daughter Cells in Meiosis
Why does meiosis involve two rounds of cell division instead of stopping after meiosis I, where each daughter cell would have one chromosome randomly selected from each pair of homologous chromosomes? ...
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Does blunt end have a hydrogen bond?
I am an undergraduate student of biology.
I saw a lecturer online, who said that sticky ends makes phosphodiester and hydrogen bonds cut. (also here).
But why blunt end just makes phospodiester bonds ...
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modify PCR steps to include a ligation
Imagine a multiplex PCR in which after the extension step, the dsDNA is nicked and requires a ligation reaction to repair the nick before the next denaturation step. So the steps would be:
Denature
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What should be considered a GC clamp in a qPCR primer?
Hello there!
After reading different sources regarding designing of qPCR primers, I'm a little confused regarding the concept of GC clamp.
Can you help me by telling which of these cases below is ...
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Why am I getting a large horizontal band spreading across my native gel?
On every gel of this type that I've ran so far, I'm getting this large band interfering with my gel analysis no matter how much troubleshooting I've done. This is a Novex Wedgewell 6% Tris-Glycine Gel ...
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Are all proteins translated by the RER ribosomes destined for the Golgi apparatus?
The proteins translated by the free ribosomes can fold in the cytoplasm and never go through the endomembrane system. But when the endomembrane system is described, it is always stated that the ...
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What is meant by 20 ul final concentration of polyacrylamide?
I am performing a phenol-chloroform extraction in which precipitation is enhanced by linear polyacrylamide. The SDS for linear polyacrylamide mentions that it should be used such that its final ...
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Covalent modification of Pyruvate Kinase in RBCs
Human body has 4 isozymes of PK and I am particularly interested in the RBC isozyme.
It is capable of being covalently modified through phosphorylation catalysed by Protein Kinase A which is in turn ...
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Mass Spectrometry Artefacts: R-deamidation / Oxidation?
Context: I am a student-researcher. I expressed GST-tagged protein (Pyruvate Kinase) in the yeast Saccharomyces cerevisiae on synthetic drop-out media. I then purified the GST-tagged protein, ran it ...
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Efficiency of molecular motors vs. human-made motors
On the wikipedia page for "Molecular motor", it says "In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors." without any ...
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DnaA binding energy to E coli genome
I have been told that DnaA binds strongly to DnaA boxes on the E coli genome, but binds weakly to 8 out of 11 sites near ori. I want to know more quantitatively what strongly and weekly mean. Are ...
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How did cells survive before the first appearance of topoisomerases?
How did cells operate before the first appearance of topoisomerases to relax DNA supercoils during replication? I read a recent paper on the early phase of topoisomerase evolution, but it doesn’t ...
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What is the precise definition of "cytokine"?
For example, both bone morphogenetic protein 4 and nerve growth factor are paracrine signaling proteins which promote growth of their respective tissues, and both are known to have some effect on the ...
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What is meant by the steady-state activation of a receptor?
I am reading a journal paper about the insulin-like growth factor 1 receptor. In this paper, there is the following statement:
Finally, we show that the IGF-IR and the PI3K subunit p85 and Akt are
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Allowed Deviations in fixed bond length and bond angles in peptides from the typical values
I am using frag builder python module to generate peptide structures to compute the interaction energy for ensemble of peptides of a given sequence for a fixed bond lengths and bong angles. However, ...
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Programs/software used to create illustrations and scientific paper ready figures
I am new to the field of molecular biology. I am finding the need to generate illustrative figures displaying interplay between proteins, DNA and various other molecular constructs at different scales ...
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What are the key mechanisms of control and transport of ATP from mitochondria to synapse in active firing neurons?
I am working with a group in the field of neuronal activity (in computational neuroscience), in specific the firing rates at different ensemble/population hierarchies.
It is well established that ...
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Why doesn't the cell just use one messenger?
I recently learned the second messenger model, where adrenaline activates adenyl cyclase, which converts ATP into cAMP. Then cAMP acts as a second messenger which activates portein kinase enzymes. The ...
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Confused about the transport of materials across cell membranes
I am very confused about how exactly substances are transported across cells. For example, if a cell is placed in a hypertonic solution, the cell loses water. If the cell is placed in a hypotonic ...
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Immunoprecipitation efficiency
Immunoprecipitation efficiency
Hi, I need to calculate efficiency of IP.
For that, I had 300microliter lysates containing eGFP (300microliter). I used 2 microliter to carry out BCA assay and find ...
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A DNA extraction protocol that is equipment-less for bacterial metagenomes?
I am going into the field soon to sample a very remote environment. For reasons that are unimportant here, I would like to extract bacterial DNA from these samples in the field.
I will have access to ...
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Why do the components of PCR mixture need to be added in a specific order?
I have recently been told that the components of a PCR mixture need to be added in a specific order: primers, dNTP, and finally polymerase. May I know why this is the case?
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How did birds reduce their tail and fuse the last caudual vertebrae into a pygostyle?
I was just looking at the phylogeny of Avialae and saw that birds go from having long tails made up of many caudal vertebrae (ex: Archaeopteryx, Jixiangornis, Jeholornis) to ones with very few ...
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choosing the right housekeeping gene for Western Blotting analysis for liver lysates
B- actin is used a great deal for quantitation of liver lysates. What other alternatives are there for WB analysis? should we opt for GAPDH or tubulin?
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How does ATP work? [duplicate]
I have heard many times that ATP is the basic unit of energy used by cells. People explain this by saying that energy is released when the ATP molecule breaks from its 3rd phosphate group. But what ...
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Identification of cells containing the gene of interest at a double strand break instead of undergoing recombination
If I tried to knock in a gene for example KANMX and want to swap it with say some gene "x", but, since, there can be double strand break in the DNA and KANMX may get inserted within the ds ...
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What happens exactly in the electron transport chain when there's no oxygen
what is the mechanism of hypoxia in the electron transport chain? It stops because there's no terminal electron acceptor so the IV complex become "stuck" with an electron? There's no other ...
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Immunoaffinity chromatography: avoiding damage to the antibodies from proteases
What are the possible methods to prevent the digestion of antibodies (mainly Polyclonal) by proteases during affinity chromatography?
I read some papers about doing modifications to the anitbodies:
...
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Absorption bands of chlorophyll
I am currently reading this article, which discusses the functional impact of the $Q_x$ and $Q_y$ absorption bands of chlorophyll in photosynthesis. However, the article didn't say where on the ...
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The springlike behavior of titin problem
I am currently reading a textbook (Molecular Biology of the Cell, 6th ed), and this problem on p. 170 is driving me crazy. I read through the solution given in this book but I couldn’t understand it ...
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How do I determine the direction of transfer of genes from a hfr bacterial cell to a F- bacterial cell
My Biology professor recently asked our class to determine the time taken for rec E to be transferred from the donor to the recipient cell given that the origin of transfer was located at KL96.
I was ...
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