Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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1answer
162 views

When should you use a stringent plasmid?

I was wondering if anyone had good examples of when you would want to use a stringent plasmid vs. a relaxed plasmid in a research setting.
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813 views

Has anyone used Crispr/Cas to induce a knock-in in MEF cells?

Does anyone have experience with the CRISPR/CAS9 platform performed on MEF? Or does anyone recall any relevant articles?
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Storage of bacteria

Why are strains of bacteria stored when they are inactive (frozen)? What is the problem with storing growing cultures for long periods?
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57 views

How do biologists discover information from fossils? [closed]

I have a query about the study of fossils (palaeontology). Let me know about the study of fossils. How do biologist discover "DNA" information from dead and old fossils such as a dinosaur? (answer ...
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1answer
40 views

Why does 4-thiouracil labelling to map RNA-binding proteins cause a T-C change?

I am now reading a paper about the purification and identification of mRNAs and its RNA binding proteins by using UV crosslinking and immunoprecipitation. I came upon this sentence which puzzled me ...
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What is the structure of DNA during Interphase? Chromatin Fibre or Beads on a string(nucleosomes)?

During Interphase, does DNA predominantly exist as Chromatin Fibre (30nm fibre) or Chromatin/beads on a string structure(10nm) ?
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1answer
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Must I HPLC-purify my PCR Primers for 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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15 views

the Oxidization reaction of NADH [duplicate]

Does oxidization of NADH need H+? I've seen a reaction like this👇 NADH + H+ >>>> NAD+ + 2H+ What's the use of the proton in here?
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1answer
61 views

What chemical test can be used to tell apart meat and plant-based meat?

Long story short, I thought about this question and simple Google searches weren't enough. I know there must be some nutrient that can only be found in one of the meats but not the other, but I can't ...
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1answer
48 views

What impedes the understanding of genotype/phenotype relationship without statistics? [closed]

Most genetic research tries to establish a relationship between a certain genotype and certain phenotype. To me this is like trying to understand a system as a black box, where you try to establish ...
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1answer
22 views

Measuring transgenic gene expression with a microplate reader

I have been working on genetically engineering an E. coli strain to autotrophically oxidize arsenite into arsenate for bioremediation of arsenic contamination in groundwater. For my research, I have ...
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1answer
107 views

How to interpret this PubChem record of L-Alanine

Using the PUG service from NCBI, I am retrieving 3d structure data for a molecule. Raw data here. I am trying to understand this record, specifically for the purpose of rendering in a 3D coordinate ...
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1answer
38 views

Where do the lysines come from during ubiquitination?

I know that Ub forms an isopeptide bond with lysine, but where do the lysine come from? Are they just always available for the Ub to find to during the ubiquitination process? Is there a free lysine ...
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19 views

Why both forward and reverse primer are added in asymmetric PCR?

If the purpose of Asymmetric PCR is to amplify single targeted strand of dsDNA then instead of adding just one primer for targeted strand why do we add both forward and reverse primer? Upon addition ...
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What is the electric field strength of microalgae?

Question: What is the electric field strength of microalgae? Background: So I have been having some problems with fungi contaminating my chromera velia algae cell cultures. I haven't determined what ...
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2answers
73 views

Why are restriction sites palindromic in nature? [duplicate]

Any restriction site given in any fragment of DNA or vector molecule is a palindrome. eg restriction site for the endonuclease EcoRI is ...
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14 views

What proteins are assisted by chaperone folding?

I've been looking into a lot of papers, and most say that chaperones assisted in the folding of misfolded proteins, or Ubiquitin markers aggregates for degradation by the proteasome. Or it will say ...
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1answer
57 views

How do you dilute forward and reverse primers for a master mix?

I apologize for the very naive question, but I'm just starting out in a high school biology lab and I am very confused. If I have stocks of 100μM for forward and reverse primers separately, I can ...
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15 views

Cadmium Poisoning and Toxicity Mechanisms

Is anyone aware of the toxic mechanisms of specific instances in which cadmium ions can interfere with cellular functions resulting in acute cadmium poisoning?
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17 views

Toxic Metals and Oxidative Phosphorylation

I was reviewing the toxicity of certain toxic metals, specifically cadmium and their effect on Oxidative Phosphorylation and Cellular Respiration, I have found that metals such as cadmium inhibit ...
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3answers
118 views

Is oxygen's paramagnetism biologically relevant?

It seems our most common everyday O2 molecule happens to be a paramagnetic one (see https://en.wikipedia.org/wiki/Oxygen). But, does this have a biological relevance as well? In other words, Do any ...
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3answers
103 views

Double Digestion with Restriction Enzymes Using Different Buffers

I am currently working on preparing a 9 kb sequence of DNA for restriction digestion into the pBAD30 expression vector. There are very few restriction enzymes that do not have a restriction site ...
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2answers
237 views

How can one create images like those in the PDB ‘Molecule of the month’?

I am impressed by the illustrations for the Protein Data Bank ‘Molecule of the month’, e.g. the gorgeous image of DNA Helicase below. Does anyone know how they were made or how one might create ...
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30 views

If bacterial plasmid DNA is methylated then how do we digest it using restriction enzyme in cloning experiments? [duplicate]

So, I was reading about how bacteria protects its own DNA by methylation against restriction enzyme. But if the plasmid DNA is also methylated then we can't cut plasmid using restriction enzyme for ...
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18 views

Using expression vector to express arsenite oxidase genes in E. coli

So I am trying to express a gene cluster that can oxidize arsenite into arsenite autotrophically. The arsenite oxidase gene cluster sequence is linked here: https://www.ncbi.nlm.nih.gov/nuccore/...
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1answer
48 views

Is there a data base, tool or method I can use to find out which of my genes code for cytokine receptors?

I have a list of over 600 differentially expressed genes from my single cell RNA seq data analyses. I want to proceed to find out which of my genes code for cytokine receptors so that I can show on a ...
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How does Hayflick limit relate to cellular senescence

If the Hayflick limit says that there are a maximum of around 60 cell division before a cell becomes senescent, I assume this is because the cell looses length of telomere. But how can this be if, for ...
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1answer
209 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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3answers
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How, on a physical level, does ATP confer energy?

When ATP is used as the energy currency to make, say, reaction X + Y → Z happen, is what happens on a physical level down at the molecular scale that during the reaction ATP + H2O → ADP + Pi  &...
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1answer
29 views

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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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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2answers
1k views

Do antibiotics attenuate immune response on subsequent exposure to same bacteria?

A healthy immune response to a bacterial infection includes "memory" to permit the body to thwart subsequent exposure to same bacteria. What are the dynamics of using antibiotics on initial exposure ...
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1answer
4k views

Why AZT is selective towards HIV and doesn't impair human DNA replication?

I've found this article, which is a very old one (from the time when nucleoside analogs where researched as a possible way to prevent replication of virus genetic material, before the HIV epidemics). ...
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1answer
87 views

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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2answers
50k views

Why is SOC medium recommended for transformations?

In pretty much every transformation protocol I've seen SOC medium is used to grow the bacteria for a short while after the tranformation and before plating. I've usually substituted LB medium for ...
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0answers
300 views

How does lactic acidosis lead to pain?

I come from Physics, not biology. My understanding is that without sufficient oxygen present, the Krebs cycle terminates in lactic acid formation for the body to later continue the reaction when ...
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52 views

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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22 views

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
52 views

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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1answer
55 views

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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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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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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46 views

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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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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The GUG start codon in E. coli: identity of initiating tRNA and efficiency of translation

Translation in E. coli is usually initiated at an AUG codon, which encodes the amino acid methionine. In some cases, however, the start codon is GUG, which normally encodes valine. If GUG is used as ...
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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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1answer
411 views

Is one Short Tandem Repeat (STR) enough for a reliable identification?

The lab simulates the analysis of just one STR in the genome. Would this analysis be sufficient for a reliable identification in real life? If not, explain what could be done using DNA to identify ...
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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 ...