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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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What determines if a bacteria has an F-plasmid? Are F-plasmids the only plasmids shared between bacteria?

If I’m designing an expierment to study bacterial concergation (while adding a plasmid of my choice to the bacteria), how do I know the bacteria I’m using has an F-plasmid (or can transfer my ...
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149 views

Do chaperone proteins misfold?

If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones ...
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Calories burned for each activity - is numbers true? [on hold]

I always wonder if we burn 90 calories for running a 1 km distance and the same we’ll get by consuming 5 tea spoons of sugar, How is it possible energy from that little amount of matter able to push a ...
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Must I HPLC-purify my PCR Primers? (PCR amplicon sequencing with PacBio SMRT )

I would like to order some primers for amplicon sequencing. I am using universal tag primers (unusually long 30-mers recommended by PacBio for SMRT, both F&R) + barcodes (16-mers). The resulting ...
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Are there any natural cases of direct translation of DNA to protein? [duplicate]

I'm aware direct translation of DNA to protein (without the need for RNA) has been observed in test-tubes using e-coli. (Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC219759/) I wanted to ...
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How would you use PGAl to select for mutants of beta galcodosidase gene (z-) and permease (y-)?

How would you use PGAl to select mutants of beta galcodosidase gene (z-) and permease (y-)? Or do you just use PGAL to grow these mutants after you've isolated the mutant gene and inserted it into a ...
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Histone binding [on hold]

As they don’t need access to sequence info Histones should usually bind DNAs minor groove, correct? Additionally, transcription factors ought to bind the major groove for he same reason?
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What is the overall end result of proteins and enzymes binding together? [closed]

My rudimentary understanding is... a gene gets transcribed to mRNA that mRNA is sent off to the ribosome that ribosome pumps out whatever proteins are coded by that gene each protein floats around in ...
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Naming of Secondary Structure Elements

I have 2 questions regarding the naming of secondary structure elements ($\alpha$-helix and $\beta$-sheets), like helix C or sheet 2, which are often used in publications. Example protein: CYP1A2 ...
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1answer
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Notation for repetitive nucleic acids

With regard to nucleic acids with repeating residues, could anyone provide a description of what the following sequences are, and the key differences between them: Poly(dA) Oligo(dA) Poly(A)
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What are the different types of helices in protein secondary structures and how do they differ?

What are the different types of helices in protein secondary structures and how are they differentiated? In the DSSP docs, types of helices mentioned are: Alpha-Helix, Helix-3, and Helix-5. In the ...
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What is the difference between saturated phenol and equilibriated phenol?

I was confused about phenol while searching it in the context of PCI solution (phenol:chloroform:isoamylalcohol 25:24:1) recipe. -First, what is the difference between saturated phenol and ...
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Is there a software simulator for monomeric formation, a la Miller-Urey?

At the moment, does any widely-available software exist for small-scale, programmable simulation of monomeric formation in specific conditions? Could one, for instance, recreate the Miller-Urey ...
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What happens to Bacterial Cells stored at 4 degrees?

4C is when water is most dense and is not so low as to cause ice crystal formation. For short term storage bacterial cultures are often simply kept in a fridge at 4C. I guess that this significantly ...
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plant uptake of large molecules

I have read several studies concluding that plants can indeed take up molecules with a molecular weight largar than 390 g/mol. Does this mean plants do also take up large molecules like hormones if ...
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Why do -ssRNA viruses need to do intermediate positive strand (antigenome) instead of just replicate it negative strands?

I was reading about RSV replication here https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185921/, but i cannot understand what is the reason for making a antigenome instead of just replicate it negative ...
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Human Body Electricity

Since the human body has electricity, can the human body use that energy in any possible way? Such as using it to power something in any way. As you know we can use technology because we have ...
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1answer
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How to confirm secondary structure formation of Precursor miRNA on gel?

I want to fold precursor-miRNA into its secondary structure and then confirm it on gel. At first, I heat it in annealing buffer at 95°C for 5 minutes and cool down slowly. Then I run it on gel but the ...
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How does hydrophilic and/or hydrophobic components of polysaccharides influence their 3 dimensional conformation?

It is my understanding that polysaccharides are insoluble in water. Does this mean they are hydrophobic? Beyond being insoluble in water how does this affect their 3D structure? Thanks!
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How does CRISPR/Cas9 compare to plasmid injection for editing new genes into cells?

I've heard that both of these techniques can be used to add new genes to cells, so I'm curious as to how they compare, e.g.: can plasmids be used in eukaryotes like CRISPR? are plasmids kept after ...
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do platelets cytoplasm contains DNA?

I'm a 12th-grade student and I have an entrance exam this year. I have a question in biology. I would appreciate you if you help me <3 as we thoroughly know platelets are multiple pieces of a big ...
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How is Saccharomyces cerevisiae grown on acetate and ammonium able to produce TCA intermediates?

I am working with a metabolic model of Saccharomyces cerevisiae and I am studying its growth on acetate and ammonia. I am performing Flux Balance Analysis to compute the growth rate and then I am ...
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How can I set micropipette volume with decimal separators, for example 109.5 in p200?

And how can I set: 150.1 in p200 871.3 in p1000 840.5 in p1000?
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1answer
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Size constraints on CRISPR guide RNA

I had a quick questions on the size limitations of a CRISPR guide. More specifically on the shorter end. Can I make a guide that is say 7-10bp and still have an active complex? I transfect using an ...
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1answer
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Improving DNA quality and yield from stool samples

I prepared genomic DNA from pig stools but the concentration was very low — about 3~4 ng/µl, when I measured it using nanodrop. The A260/A280 and ...
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1answer
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Why pellet and resuspend E. coli for plasmid prep

For maxipreps, cant you just add all the stuff that would be in P1 (RNase A, EDTA) then just add P2? Because if we pellet cells then resuspend theres got to be a reason, right? Is it slats and other ...
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1answer
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Is the lac operon repressed in the presence of both glucose and lactose?

In the presence of both sugars (glucose and lactose) will there be repression of the lac operon completely? I know that more glucose means less cAMP --> less CAP --> less positive regulation, and ...
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1answer
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Could deutrium oxide be used to make organic compounds with Deutrium instead of hydrogen? [closed]

I am wondering for prokaryotes if Deutrium Oxide could be made into Deutrium Glucose or other biological compounds with Deutrium.
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1answer
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How to identify whether something is in linkage disequilibrium?

If the following loci indicated the presence of an SNP in flu strains, is Locus 2 and Locus 3, which are located 10 bp apart in linkage disequilibrium? "When alleles and molecular markers are ...
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Why are higher doses of atropine required to produce central effects?

Reason given in my book is restricted entry into the brain..is it something to do with the chemisty?
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1answer
32 views

Ligation without purifying insert

I am planning to insert a 45 bp sequence in a vector. After restricting my insert to create compatible sticky ends, I am finding no way to clean it up. Is there any way for cleaning this fragment ...
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1answer
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Gene vs Protein homology

I am trying to find homologs for some proteins and I am wondering if it is better to find it by comparing the proteins or the coding genes or either is fine.
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1answer
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Why do we use different micropipette tips for different volumes? [closed]

Isn’t it easier to use a 1000 µl micropipette tip for all volumes? I don’t understand why there are different tips for smaller volumes. Does it affect the accuracy of the pipette for very small (<...
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1answer
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Melting point of animal fat and plant fat

I notice in daily life that animal fat typically has a higher melting point than plant fat does. I wonder the reason why this happens. What exactly contributes to this difference? Is it because of the ...
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1answer
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When muscles contract is the process similar to how non-newtonian fluids react?

I'm trying to understand how muscles contraction/tension works but getting loss in on the cellular level. From my understanding, when muscle tissue need to contract, the cells are flooded with calcium?...
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How to take precise/low number of cells from cell lysate? [closed]

I would like to know that how can we take low or precise number of cells from a cell lysate? (without using any protein quantification assay). Let say, If I have a cell line having cell density 5x10^...
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1answer
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Does *E. coli Dh5 Alpha* strain has the ability to degrade polyethylene?

Does E. coli Dh5 Alpha strain has the ability to degrade polyethylene? What are the bacteria that can be used as a control in the research of polyethylene degradation?
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What M9 stands for

Can anyone tell me what M9 stands for in M9 medium? I have tried googling but I still cannot find it.
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1answer
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Antigen molecular mimicry

Let us consider a situation in which the body is attacked by a microbe, and the microbe is captured by the immune system for recognition of surface antigens. The surface antigen recognized mimics one ...
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1answer
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Is studying chemical and physical properties of chemical substances that make up organisms really a task of molecular biology?

I have read in a high school textbook that (translated into English by myself): "Branch of science that concerns itself with studying chemical and physical properties of substances that make up ...
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What is the difference between a signal peptide and a transit peptide?

From what I know, the two names are used interchangeably and I haven't found any resource which says otherwise either. Is there at all any difference, is there a transit peptide that is not a signal ...
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Can we spike with a different enzyme to a SYBR Green Master Mix?

I followed the standard SYBR Green Protocol for doing a qPCR. For which I used 10 uL of 1X SYBR Green Master Mix Forward Primer and Reverse Primer (each at a final conc. = 8.5 uM) Template (unknown ...
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1answer
51 views

Barr body. How does it work? [duplicate]

Barr's body is a spiral X chromosome. If I'm not mistaken, one random chromosome (a healthy woman) is inactivated in each cell. Which X chromosome is inactivated in a given cell is random. I've heard ...
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1answer
52 views

Why is Turner's syndrome a problem?

So Turner's syndrome is a chromosomal defect where one of the X chromosomes is missing. For more details visit the [Wikipedia page] (https://en.m.wikipedia.org/wiki/Turner_syndrome). But I don't ...
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1answer
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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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Why don't the heads of phospholipid bilayers repel hydrophobic molecules?

What I Think I Know: Hydrophilic and hydrophobic things repel each other. Since the cell membrane contains hydrophobic tails, it is difficult for hydrophilic molecules to pass through the cell ...
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1answer
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What would “N” and “V” stand for in DNA barcoding?

I'm currently looking protocol for PAT-seq, and when it talks about the barcoding that's utilized, the documentation mentions there being an "N" and "NN" in the sequence, as well as a "V". For example:...
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Are redundant codons used in translation?

I am learning about redundancy in genetics and I came across this statement in my textbook: more than one codon for an amino acid means that some codons are redundant - the process of protein ...
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Will DNA nanostructures be useful for medical applications?

There is a lot of work being done on developing small nanomechanical structures and even small nanomechanical actuators built with DNA. I have heard researchers motivate this research with claims ...