Questions tagged [molecular-biology]
The study of the molecular processes underlying life.
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Why is one strand of human mitochondrial DNA designated ‘heavy’, whereas the other is designated ‘light’?
In the Wikipedia article on ‘Mitochondrial DNA’, one strand is designated ‘heavy’ and the other ‘light’. (These are the outer and inner circles, respectively, in the cartoon illustration from the ...
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How are antibodies designed?
Antibodies have the ability of recognising highly specific peptide sequences and bind it at their antigen-binding site.
This ability is harnessed as a tool in research to purify target structures in ...
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Buffer Preparation Acetate pH 4.8 for alkaline lysis
This question might sound silly to many, but here we go.
Could someone please tell me the correct way to prepare 5M Potassium Acetate buffer pH 4.8 (3M w.r.t Potassium and 5M w.r.t. Acetate) for ...
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Why is DNA antiparallel? Can it be parallel?
My biology textbook mentions that DNA is antiparallel and it got me wondering - can DNA be parallel? What would happen if it was parallel? Could DNA still replicate correctly?
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Why can’t DNA strands be parallel? [duplicate]
As the title states, why can’t it be parallel?
I will explain my questions using the image below. When you look at the two strands, for the one from 3′-5′ (on the right), the base is flipped ...
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What actually kills a plant that requires winter dormancy if it is kept indoors all year?
In bonsai practice, beginners will commonly purchase a juniper (often Juniperus procumbens 'Nana'), which is an outdoor tree, and keep it inside all year. The tree invariably dies. It is commonly ...
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Fraction of methylated sites in restriction-modification systems
Given a strain that is expressing proteins of a restriction-modification system (like EcoRI), is there data to measure the fraction of metylated target sites? I am just looking for an approximation, ...
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Are these cassettes suitable for expressing PETase mutant in E. coli?
I created two potential gene expression cassettes (constitutive and inducible) for expression of a mutant PETase gene on PeptiCloud using the version tree feature, which allows users to create ...
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Why are multiple copies of the 35S enhancer used for overexpression in plants?
I know that the CaMV 35S promoter is widely used for transgenic plants, where it acts as an enhancer element for constitutive overexpression.
I noticed that it is always used as a tandemly repeated ...
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Is lactic acid build up the cause of muscle fatigue or only a symptom?
If your body could magically instantly remove lactic acid as it is produced, would that make you immune to muscle fatigue, or is the lactic acid only a symptom of muscle fatigue and instead exists, at ...
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How many fruit flies from a single banana, and what is the bottleneck?
Suppose I start breeding a fruit fly population on a single rotting overripe banana which weights 100g, in an isolated container. The fruit flies don't have access to anything else, though ventilation ...
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Use of plasmid pXen5 for transposon screening
I would like to use the plasmid pXen5 (by Xenogen) for a transposon screen.
It contains two inverted repeat sequences, with Luciferase, Kanamycin, and the transposase itself in between. (It's tn1409).
...
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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 do I carry out an in silico PCR on a bacterial genome (target:16S rRNA)? Unable to find any bacterial genome on UCSC Genome Browser in silico PCR
I could not find any bacterial species in the drop-down list for genomes in https://genome.ucsc.edu/cgi-bin/hgPcr
Any kind of help would be appreciated. Other links for in silico PCR did not really ...
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Why does acidosis cause cells to remove hydrogen ions using the proton/potassium ion pump rather than exchange with another cation?
Many mammalian cells respond to acidosis by transferring hydrogen ions to the blood using a proton/potassium ion pump. Why is this system employed rather than one involving another cation such as ...
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Open Reading Frame problem
Problem
An mRNA of 999 bases codes for a protein with 300 amino acids and the open reading frame (ORF) starts from base 38. If the base at position 903 is deleted the length of the ORF increases by 3 ...
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Cell Signaling: What is meant by "sustained tonal induction"?
I am reading a journal paper about the insulin-like growth factor 1 receptor. I have a question about the following statement in the paper:
IGF/IGF-IR stimulates the PI3K-Akt pathway in a ...
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Why do receptor tyrosine kinases undergo constitutive endocytosis?
I am reading a journal paper about the endocytosis of receptor tyrosine kinases. I have a question about the following statement:
At the cell surface RTKs undergo constitutive endocytosis
(...
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Primer Optimization for full length gene amplification
I need your help. I have sequences of my desired gene (WRKY TF) from RNA seq data (it was a denovo assembly performed on agave sisalana). Now i need to amplify full length of that gene for which I ...
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Crick’s Central Dogma — Counter Cases
I was recently reading about non-coding RNAs being a counter example to Central Dogma of Biology. Can someone add more cases which violate the Central Dogma? Thanks!
UPDATE - Reference of lncRNAs ...
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Could you recommend literature regarding non-coding RNA and micro RNA?
I am familiar with the Alberts and Watson textbooks, but they are quite general, not specific.
I would be grateful if you wrote down books or even in-depth reviews/papers regarding the topic.
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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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Which is the best results for Plasmid dna extraction on gel electrophoresis?
I did plasmid dna extraction and uploaded on the gel.
Well 1: marker
Well 2: nicked,circular,and supercoiled bands
Well 3: linear,circular,and supercoiled bands
Well 4: circular and supercoiled bands.
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Do cells know or imagine how each part of the DNA influences body structure and function? How else would evolution happen in specific ways?
Consider how an octopus looks at a rock and it's entire body blends in to resemble the rock. Consider how insects evolved to resemble leaves or twigs. Even frogs, butterflies and other creatures ...
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How can (or did) Deinococcus radiodurans continue to evolve after developing resistance to mutation?
Deinococcus radiodurans has a remarkable ability to resist damage to its DNA due to radiation, dehydration or (to my knowledge) any other source. It keeps multiple copies of its genome and has a ...
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Can the mechanism behind changes in protein expression be inferred by the timing of those changes?
My question relates to the timing of protein expression changes, and whether there is a literature-based consensus as to how long changes in protein generally take.
For example, if protein changes 24h ...
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How to prevent small-protein smearing in SDS-PAGE?
I am doing SDS-PAGE for ubiquitin-6xhis (9.6kDa), and all my hand-cast gels produce a smeared band (see image). I typically use 5% acrylamide for stacking, 15% for resolving gel layers. I don't ...
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How do you determine the structure of a molecular recognition feature (MoRF) after it binds to itself?
I have a protein that has a roughly 10 residue chain that registers at a MoRF in MoRFPred and MoRFchibi. I have the PDB files to correlate the known structure of the protein with the site of the MoRF; ...
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Could p-loop bind fully protonated ATP?
The phosphate tail of ATP binds the p-loop motif, evolutionary conserved, going back to since forever. In the dominant model, the deprotonated hydroxyl groups are complexed with Mg2+, at least two of ...
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Why is there no Ligase in Ligation Independent Cloning?
Ligation Independent Cloning literally says no need Ligation, but it still needs ligase to anneal the fragment to vector. And the Protocol used T4 DNA Ligase for anneal process. What does this mean &...
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#Gateway Cloning How does gene of interest replace ccdB genes?
I knew that Gateway cloning used a site-specific recombination method, but I still cannot figure out how does gene of interest actually replace ccdB genes? Bacteriophage site-specific recombination
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What makes viruses like the flu and covid so tolerant of mutations compared to most other viruses?
I was curious about why we benefit from yearly flu shots and apparently will also benefit from yearly covid booster shots too, whereas this doesn't seem to be the case for most other vaccines -- even ...
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Overlapping atomic radii in data of experimentally observed protein assemblies
I am looking at experimentally observed configurations of viral capsid proteins like that of the tobacco mosaic virus. https://www.rcsb.org/structure/6R7M
When taking the atom centers of a monomer and ...
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What is H-activation vs. O-activation in the context of cellular respiration?
I was reading this article on Albert Szent-Gyorgyi and on page 7 there's this statement:
Now, I thought myself capable of tackling a biochemical problem. I
embarked on biological oxidations. At that ...
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Understanding DNA Fingerprinting
I am a high-school student learning about DNA fingerprinting. I know that satellite DNA is non-coding DNA and has a lot of repetitive sequences, and the length of each repeat can be either short or ...
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Rectangle-like structures and their folding in biology
I've heard that mathematics helps to explain some biological problem. For example gömböc, which was a well hidden body from mathematicians, explains the body structure of some tortoises in relation to ...
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Is blood typing still useful for analysis of ancient tissues?
Modern techniques.
In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be extracted ...
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What is, (and what isn't) "kinetic replication" as it applies to molecules and to living organisms?
CNN's World's first living robots can now reproduce, scientists say describes "xenobots"; clusters of stem cells that move around and by this motion occasionally push enough free stem cells ...
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Do right-handed helices bind to right-handed helices, and vice versa?
I know that B-conformation DNA is a right-handed helix, and most proteins that form helices form right-handed, not left-handed, helices (1). Furthermore, "Many transcription factors have an alpha-...
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What is the minimum Ct value that you would consider indicates no gene expression?
I am doing relative quantification to compare gene expression between a control with several mutant backgrounds using qPCR.
Looking online I find several different sources suggesting different values ...
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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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Correlation of Meselson and Stahl with “multifork” replication in E.coli
Because of the limiting value of the rate of DNA replication, rapidly dividing E.coli use multiple replication forks [1][2]. Thus, DNA replication of one generation has already begun in the previous ...
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Will diffusible protein aggregates coated in cell-free nucleic acids near a depolarizing neuron's soma diffuse along the axon to synapsing neurons?
Edit in response to feedback in comments requesting specific details, etc.: Will aqueously diffusible protein oligomers and protofibrils coated in cell-free nucleic acids in the aqueous interstitial ...
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Receptor tyrosine kinases: Clarification about what is meant by stabilization of the receptor
I am reading a journal paper. This paper focuses on how neural cell adhesion molecule (NCAM) interacts with fibroblast growth factor receptor 1 (FGFR1) and promotes its stabilization.
When FGF binds ...
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Why do we choose to use agar instead of agarose in various microbial applications?
When performing gel-electrophoresis we always use agarose. Is there a reason we can't perform it using Agar?
And in microbial culture Agar is commonly used as solidifying agent, could this be replaced ...
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Best way to predict the effects of deletion mutations on protein function?
I have the coding sequences of a WT gene and several mutants of this gene (deletion mutations varying from 5bp to 50% of the sequence deleted). What is the best method for inferring the impact of ...
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The split in Boroeutheria into Euarchontoglires and Laurasiatheria. Was this due to the opening up of the Atlantic Ocean?
I'm asking this question as a cat owner. I've seen a figure like 94 MA for the most recent ancestor of both cats and humans (this from, I guess, molecular clock arguments), and it kind of lines up ...
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How can good Shine–Dalgarno or Kozak sequences enhance translation?
In prokaryotes the Shine-Dalgarno sequence, a polypurine consensus sequence near the initiation codon (usually AUG), is required for the mRNA to bind to the small ribosomal subunit, allowing ...
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why does translation occur more frequently than transcription?
In our textbook it says that translation occurs more in a cell than transcription but I couldn't find anything that explains why it happens
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Who discovered that phage phiX174 has a single-stranded genome?
I have recently read that Erwin Chargaff has discovered that the genome of phage phiX174 (ϕχ174) is single-stranded. However I could not find the paper reporting this discovery.
Is there a link to the ...
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