Questions tagged [molecular-biology]
The study of the molecular processes underlying life.
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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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Genetically modified food
Were antibiotic resistance genes still used as markers in the current generation of genetically modified foods? Some early generations of GM products didn't remove these markers, so does this mean ...
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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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Can cancer cells be destroyed by proteins which specifically target them?
I’ve seen how destructive chemotherapy is, it destroys healthy as well as unhealthy cells. I have read about monoclonal antibody therapy and the prion. It appears that the prion is able to survive the ...
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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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What signals the corpus luteum to degenerate once the placenta is formed?
I've been trying to learn what causes the corpus luteum to finally degenerate once the placenta is ready to take over (in other words what is the trigger or signal and where is this signal produced) I'...
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Receptor tyrosine kinases: What does "tonic activation", "tonic inhibition" and "tonic brake" mean?
I am reading a journal paper about the insulin receptor (IR). The insulin receptor is a receptor tyrosine kinase, and upon ligand binding, undergoes autophosphorylation of intracellular tyrosine ...
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Sources of chlorophyll fluorescence
I have been reading this article recently, which claims that photoinhibition of photosystem II can have measurable impacts of chlorophyll fluorescence. This confused me, however, because ...
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Why is DNA not single stranded? [duplicate]
From what I have researched DNA is not single stranded, because if it was single stranded, nitrogenous bases (the 'information' of the DNA) would be exposed to the cellular environment (although, I ...
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Is there a name for this type of diagram?
Is there any commonly used name for this type of diagram / symbology? I have not been able to find them referred to by any name.
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Why is random protein selection not used more often in biotech to create proteins with desired enzymatic activity?
mRNA/cDNA display allows random libraries of up to ~ 10^13 proteins to be subject to selection for binding to arbitrary binders. In the listed studies, proteins selected for ATP binding also had ATP ...
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Is there a way to isolate bacteria and viruses without a centrifuge?
Is there a way to isolate bacteria and phages from soil samples if you do not have access to a centrifuge? The purpose for which we need to isolate bacteria is for basic phage hunting.
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TMPRSS2 Primer Design
I am trying to design a primer for TMPRSS2 PCR reaction. However, this gene is in reverse position like in the picture I'll show.
From the nucleotide sequence I got from NCBI, should I reverse the ...
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Is there any disease that is proven to originate from malfunction of alternative splicing or post translation changes in the genome?
The most common diseases with genetic origin like muscular dystrophy seem to originate from issues with the primary structure of the DNA itself. Also it seems to be somewhat controversial as to ...
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Molecular biology - Lewin's Gene Xi vs Molecular Biology of the Cell by bruce albert [closed]
I am an undergraduate and want to start reading about molecular biology. to anyone who has read both books please let me know your thoughts. which one should I go with?
Lewin's Gene Xi or Molecular ...
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Are "antibodies" and "immunoglobulins" really the same things?
Wikipedia says that NCAM (CD56) glycoprotein belongs to Immunoglobulin (Ig) superfamily.
A the same time, its article on antibodies equates them with immunoglobulins. NCAM is obviously not an antibody,...
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Can anyone recommend a paper/protocol on baculovirus in vitro DNA packaging?
I have a couple of good protocols on in vitro lambda phage DNA packaging, where you can get the empty capsid to take in the DNA without the involvement of a host organism. But now I need something ...
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Why do cells keep synthesizing and degrading transcription factors in certain signaling pathways? [duplicate]
In some signaling pathways (e.g. Wnt/β-catenin pathway, ethylene signaling pathway), transcription factors are continuously being synthesized and degraded. In these cases, transcription factors are ...
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Would a size-specific, electrophoresis-based RNA quantification kit work for ssDNA as well?
I'm using a custom library of ssDNA oligos to test the performance of some qPCR assays with mismatched bases in various primer and probe regions, and I'm trying to come up with a good way to verify ...
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Receptor tyrosine kinases: What is meant by basal phosphorylation of the receptor?
I am reading a journal paper about the insulin receptor. The insulin receptor is a receptor tyrosine kinase, and upon ligand binding, undergoes autophosphorylation of intracellular tyrosine residues.
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Cut plasmids with unknown sequence only once
Is there a way to linearize plasmids in a sequence-independent manner?
The circular plasmid should be cut ideally only once. It does not matter where. But as soon as it is linearized, it should not be ...
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What is the actual molecular mechanism for muscle relaxation?
A number of my students asked what happens to the sliding filaments when muscles relax. For example, in an individual sarcomere, do all myosin heads release all at once or one/few at a time?
More ...
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chip sequencing
I understand the concepts of steps in Chip-seq up to DNA purification, but I don't get how one can then amplify the purified DNA samples that are once bound to the proteins.... Since sequence-specific ...
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Rationale for two-components in feedback loop of circadian molecular clock
The circadian clock in humans and fruit flies involves a feedback loop in which the active components are protein heterodimers. This is illustrated for humans in the diagram below:
The nuclear ...
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Cross correlation metric in ChIP-seq experiments
I found this explanation of cross-correlation metric in ChIP-seq.
Now, the definition of Pearson's correlation coefficient between two random variables $X$ and $Y$ is $$\rho_x = \frac{Cov(X,Y)}{\...
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How bacteria respond to toxic viral proteins?
The lysis-lysogeny state of bacteriophage lambda is well known. Under certain conditions, the phage will enter the lysogenic state after infection of a bacterium. Then, after a while, the phage ...
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How does alternative splicing actually work?
How do two identical pre-mRNA molecules give rise to two different mRNA molecules after alternative splicing? They contain the same introns and exons and thus same splicing enhancers and silencers
Is ...
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How to avoid mutations when performing Gibson Assembly (or generating amplicons during PCR)
More often than desired (about 75 % of the time), when building plasmids via Gibson Assembly (~ 5 kb plasmids; from a maximum of 2 fragments) we obtain clones with several random point mutations all ...
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RNA Quantity for RT-qPCR
I isolated RNA from different surface sampling, and performed reverse transcription and then PCR. To get good results, in which range should the the quantity (concentration) at 260 nm should my RNA be?...
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Are dendrimers synthesized by living organisms?
Dendrimers are beautiful https://en.wikipedia.org/wiki/Dendrimer
They are used to deliver drugs and model branched molecules. But everywhere they are strangers to a living cell. It is hard to believe ...
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Molecular Signaling: Why is it more difficult to study membrane-bound signaling molecules compared to soluble ones?
I am reading the textbook Neuroscience (6th ed.) by Dale Purves and colleagues. In one of the chapters (Chapter 7, Molecular Signaling within Neurons), I am reading about the different types of ...
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Where do the 2 hydrogen ions in glycolysis come from?
In the reaction for glycolysis, two hydrogen ions are produced as one of the end products. In all the ten steps, I am not able to figure out where exactly these two hydrogen ions are formed. Please ...
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Is there a non-directed way to probe proteins in a given sample?
I'm familiar with various ways to probe for specific proteins in a given sample(antibody/antigen, aptamers, etc). But these techniques seem to require an understanding of what protein you're looking ...
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What is the difference between physiology and physiological processes?
Now I do understand that physiology is the study of processes and mechanisms that make a living organism. And physiological process is understanding the ways the components in the organism work ...
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Function of SMAR in plasmids?
A few years ago, the Thought Emporium published a video (https://www.youtube.com/watch?v=aoczYXJeMY4) in which he refers to a study in which they mix plasmid DNA with Chitosan and feed it to mice to ...
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Can DNA replicate without polymerase?
Would it be possible for short DNA molecules to replicate, for example, if it's heated to the point where the strands separate (as far as I know, that's what happens in PCR?) and freely floating bases ...
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Receptors and their distribution over the human population
For humans it has been reported that there are three vasopressin receptors (AVPR1a) and four dopamine receptors (DRD2). (Source: UNIPROT)
Question: Does every human contain all three variants of ...
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Is retinoblastoma truly an autosomal dominant condition?
I am getting, in my opinion, very conflicting information from sources about the inheritance of retinoblastoma, a type of cancer. Hereditary retinoblastoma is associated with defects in the gene ...
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Examples of passive membrane transport proteins that only transport in one direction and their mechanism
I would like to know about those transporters with alternating-access-type mechanism, that can only efficiently shuttle molecules in one direction but the other direction is severely kinetically ...
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What specific molecules cause the difference in spectral sensitivity in the cones?
What causes the difference in their spectral sensitivity of the S, M and L cones. I'm guessing that the opsin or photopigments are different, but haven't been able figure out conclusively from my web ...
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Primer design for site-directed mutagenesis
In our practical course about modern cloning methods, we performed point mutations on a promotor via site-directed mutagenesis.
As far as I understand that method you need forward and reverse primers ...
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Does beta-actin have to be consistent in Western Blots?
I have been running Western Blots on rat brain tissues from rats that have been subject to neurological disorders.
I loaded the samples on the gel to ensure that for each tissue, I had a constant mass ...
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Human Evolution Chromosome 2: Fusion or Break?
I have a question regarding Chromosome 2. I've heard that there is evidence that the Human Chromosome 2 is a fusion between the two ancestral chromosomes 2a and 2b, but could it be possible that it ...
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