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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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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 ...
H001O's user avatar
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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 ...
novara's user avatar
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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 ...
Damocle Damoclev's user avatar
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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 ...
donkey's user avatar
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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 ...
Vibhav Agarwal's user avatar
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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 ...
thefutureisnow's user avatar
2 votes
2 answers
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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 ...
nullspace's user avatar
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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 ...
stochastic's user avatar
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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 ...
Devin's user avatar
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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 ...
Candlebeam's user avatar
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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 ...
ceno980's user avatar
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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, ...
vigneshwaran kannan's user avatar
2 votes
1 answer
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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 ...
Zebra Fish's user avatar
1 vote
1 answer
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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 ...
al-Hwarizmi's user avatar
2 votes
1 answer
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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 ...
Bruce M's user avatar
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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 ...
Nawaz_04's user avatar
1 vote
1 answer
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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 ...
donkey's user avatar
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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?
Oakss's user avatar
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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 ...
RenaMoon's user avatar
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1 answer
190 views

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?
Stela Pap's user avatar
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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 ...
Adaintyflower's user avatar
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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 ...
lorga's user avatar
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2 votes
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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: ...
Alpha's user avatar
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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 ...
slithy-tove's user avatar
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1 answer
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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 ...
Son of Sevenless's user avatar
1 vote
1 answer
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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 ...
ceno980's user avatar
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4 votes
1 answer
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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 ...
slithy-tove's user avatar
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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.
tsj's user avatar
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1 answer
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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 ...
symmetrickittens's user avatar
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2 answers
89 views

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.
edmund shelto's user avatar
1 vote
1 answer
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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 ...
Hieronimus Adiyoga's user avatar
3 votes
1 answer
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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 ...
user2277550's user avatar
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1 answer
183 views

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 ...
Maharshi's user avatar
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4 votes
1 answer
729 views

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,...
Damocle Damoclev's user avatar
1 vote
0 answers
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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 ...
MikeyC's user avatar
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2 votes
1 answer
142 views

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. ...
ceno980's user avatar
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1 vote
1 answer
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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 ...
Michael's user avatar
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5 votes
1 answer
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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 ...
theforestecologist's user avatar
2 votes
0 answers
39 views

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 ...
uwuwubread's user avatar
2 votes
0 answers
73 views

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 ...
yoshi's user avatar
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1 answer
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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)}{\...
algebroo's user avatar
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1 vote
1 answer
45 views

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 ...
Wei Feng's user avatar
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2 votes
1 answer
64 views

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 ...
Noel Lundström's user avatar
2 votes
1 answer
264 views

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 ...
The Quark's user avatar
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1 vote
1 answer
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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 ...
ceno980's user avatar
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1 vote
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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 ...
Nisha Prakash's user avatar
1 vote
1 answer
33 views

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 ...
sam's user avatar
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3 votes
1 answer
285 views

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 ...
projective_line's user avatar
3 votes
2 answers
653 views

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 ...
Lem0n's user avatar
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2 votes
1 answer
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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 ...
SK SARIF HASSAN's user avatar

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