The study of the molecular processes of the nucleus and cell function.

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1answer
132 views

What is a mechanical cue?

I was attending a talk related to neurogenesis. So one professor was asking a question related to biochemical cues and mechanical cues (related to signaling pathways I believe). Cue as far as I ...
3
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2answers
125 views

Do transposons usually jump from one chromosome to another?

If it is usual occurrence, does it mean that my one gene can change its location from one chromosome to another?
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1answer
139 views

How will changing the concentration of a Tris buffer affect amylase enzyme activity?

For instance if you increase the amount of Tris but pH still does not change then will the enzyme activity still proceed normally? If it does change the pH will it change enzyme structure and why?
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2answers
44 views

Question about flux and changes in net flux of molecules across a membrane

I've been reading a book called Principles of Human Physiology by Stanfield 5th edition, and was reading a chapter on membrane transport when I came across a figure question which will be posted ...
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0answers
37 views

Why I obtain larger bands than expected after minipreparation?

guys! I made a "home made" minipreparation to obtain my plasmid+insert (totalizing approximately 6Kb). But, when I run a agarose gel, I saw a unique band with 10Kb. Why?
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3answers
414 views

Amplification technique for proteins similar to PCR for DNA?

I know PCR can be used to amplify a tiny sample of DNA in order to perform experiments. Is there a similar technique to use on a protein sample? More specifically, I'm not interested in "cutting" up ...
3
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2answers
216 views

How does Cro protein expressed by lambda phage kill its host?

I read that the DNA segment of lambda phage integrated in host DNA could switch between lysogenic state where cI represses the expression of Cro and lytic state where Cro expression takes over and ...
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1answer
143 views

Why do the deoxyribonucleotides use T and ribonucleotides use U? [duplicate]

We all know deoxyribonucleotides form DNA while ribonucleotides form RNA, DNA is double stranded while RNA is single stranded, and RNA can transcribe from DNA. We also know that DNA use A, G, C, T, ...
2
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1answer
115 views

Are all dipeptides synthesizable?

Probably a basic question, but are all possible dipeptides synthesizable? For 20 amino acids, there should be in principle 190 dipeptides; do they all exist or is there chemistry that makes some ...
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1answer
30 views

connect three coding sequences with IRES

To express two proteins at once in mammalian cells, expression vectors carrying an IRES (internal ribosomal entry site) are available. Does anyone know any attempt to express three proteins using two ...
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1answer
44 views

Is galvinoxyl antioxidant assay possible using NMR spectroscopy?

I would like to perform an antioxidant assay using the galvinoxyl protocol. The protocol states that we need EPR spectroscopy, but only NMR spectroscopy is available at my institution. Is there an ...
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1answer
60 views

Is T7 promotor leaky in DH5 alpha?

In my experiment I found that a GFP gene under T7 promotor in high copy number pTAC-2 vector is showing green fluorescence producing colonies of DH5 alpha under UV light. what could be the possible ...
2
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0answers
62 views

PAGE gel in EtBr

I have been using TBE-PAGE gel to see small fragments of DNA by post-staining that means gel is stained with EtBr after electrophoresis. Someone told me that you can add EtBr before polymerizing ...
2
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2answers
122 views

Extending a small fragment of DNA

Is there a way to extend a small fragment of DNA, say 150 bp, by making copies of itself and attaching each copy of that small fragment to the end of that 150 bp sequence? For example, I want a 1 ...
2
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0answers
26 views

Can mutation rate be increased for instance by mutagenesis targeting the DNA polymerase?

I am studying a non-cultivable bacterium living in an insect host, and I would like to generate some random mutants of this bacteria while preserving the insect. I am wondering if one way to do so ...
1
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2answers
64 views

If a given DNA oligo is an aptamer, will the corresponding RNA oligo with the same sequence be an aptamer aswell?

Functionality of aptamers depends upon the oligo's sequence and secondary structure. So, if I take a DNA aptamer and make an RNA oligo of the same sequence (T replaced with U obviously), will this RNA ...
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2answers
123 views

Definition of Phenotype

I'm not a biologist but, I'm trying to enter molecular biology from a perspective. I have noticed that concept of genotype is quite well defined while ...
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2answers
1k views

Why is the DNA helix anti-parallel? [duplicate]

Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.
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0answers
95 views

How can we determine the polarity of fat molecules?

I'm trying to solve a question in a biochemistry quiz, which is asking for classifying a set of lipidic derivatives, by increasing polarity. Unfortunately, we didn't cover the classification of ...
3
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0answers
248 views

How much salt [NaCl] is too much in DNA precipitation?

In DNA extractions, how much is too much salt in a CTAB extraction buffer? Protocols hover around 2.5 molar; if you go over this (e.g. 25 molar), will you saturate your solution, and precipitate the ...
2
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0answers
31 views

BSA for trouble shooting failed PCRs?

I am using PCR to amplify a 1000bp region of the CytB mt gene. Some of the samples had not amplified and I wish to change the reaction components (or use additives like BSA) to attempt at getting ...
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1answer
31 views

How is Glycophorin A and straphylococcal related to Escherichia coli and what does readily purified mean in this context?

I am reviewing the paper "Glycophorin A Dimerization Is Driven by Specific Interactions between Transmembrane Alpha-Helices." There is a statement in the abstract which I don't understand: "The ...
1
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1answer
61 views

How to synthesize and isolate single stranded cDNA from an RNA template?

I would like to have pure single stranded cDNA of my choice. I am thinking of reverse transcription from RNA (obtained by in vitro transcription), degrading RNA from RNA-DNA hybrid with RNase-H, ...
3
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0answers
90 views

L-tryptophan in mammalian cell culture

Why must the concentration of L-tryptophan be kept to a relatively low level when culturing mammalian cells? It's an essential amino acid, so I cannot fathom why low concentrations as opposed to ...
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0answers
28 views

Is a Ribonuclease Inhibitor protein the only mechanism employed by the human cell to protect cellular RNA from degradation by endoribonuclease?

Are there any other methods of protection for cellular RNA from degradation by endonuclease (specifically the Pancreatic Ribonuclease RNase II (Eosinophil-derived neurotoxin) and RNase III (Eosinophil ...
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1answer
42 views

Is there a good site or software to see if a primer pair spans an exon junction?

I am going to perform some RT-qPCR tests to validate an experiment.  I'm currently in the process of ordering primers, and I would like to get them from the Harvard Primer Bank since these have been ...
3
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1answer
180 views

What is a functional screen?

I was going through this paper, but did not understand a term. What is the meaning of functional screen? (I am not a biology student, I don't understand much, and a small simple explanation would ...
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0answers
26 views

What is the lifetime of the vasopressin receptor V2?

I was looking at the production of vasopressin receptor 2, also known as V2R or ADH-R. What I found is that it is coded by the AVPR2 gene and degraded by the Alix protein (source). But I did not get ...
3
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0answers
58 views

What Chemical Trigger Causes Ectomycorrhiza To Change From Asexual To Sexual?

I want to know the trigger behind the change of asexual to sexual ectomycorrhiza when symbiosis with a tree root is formed. As ectomycorrhiza attaches itself to a root, it forms a relationship wherein ...
2
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1answer
36 views

Finding a reaction from a KEGG map

I have come across a map and a part of it looks like this: Now I have not been able to locate the reaction that converts alpha D-Glucose to Glucono-1,5-lactone but was successfully able to locate ...
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0answers
17 views

What is the effect of the RNA 2' OH group on its structure and stability? [duplicate]

I've read that the 2'-hydroxyl group plays "fundamental roles" in both the structure and the function of RNA, and that it is a major difference between RNA and DNA. I would like to know more ...
2
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1answer
86 views

Is nuclear DNA immuno-privileged?

It is well known that if DNA occurs in the cytoplasm of eukaryotic cells, an immune response may be triggered through a myriad of DNA receptors and pathways as part of the immuno response. Yet, ...
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1answer
288 views

Operators and Enhancers/Silencers

Wikipedia has two images, of a eukaryotic gene and of a prokaryotic gene. They show the difference that the prokaryotic gene also has an operator while the eukaryotic gene does not. Both also have ...
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1answer
71 views

Primer Design with Primer-BLAST over specific site

I am trying to design primers using Primer-BLAST such that the forward primer spans a specific base pair site. I am looking at KRAS for which I believe the RefSeq ID is NG_007524.1 and the forward ...
4
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2answers
255 views

How to Extract RNA and perform RT-qPCR from very few cells ( ~5,000)?

I am currently conducting an experiment which involves FACS-sorting a specific population of cells using an antibody of interest. In order to validate the type of cells I have collected using this ...
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2answers
572 views

Does ATP hydrolysis reaction have a high or low activation energy?

I was recently studying about ATP and how it functions as an energy carrier to all biological processes; however, I came across a confusing and paradoxical statement from two sources: (at 7:36) and ...
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2answers
202 views

What happens when we re-start a PCR reaction?

Recently when my PCR reaction was running there was power fluctuation and the entire lab was blacked out for a few minutes and unfortunately PCR that I was running got switched off. So, would it be ...
0
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1answer
31 views

Presence of reaction module in bacteria but not in Eukaryotas (human)

From the statistics page, I found that the Module-M00008 is present only in bacteria and not Eukaryotes. Why so? I noticed that all the compounds necessary or the reaction are present in human body ...
1
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1answer
110 views

shRNA knockdown not showing with Western

I've recently been performing shRNA transfections and was hoping to get some advice on why I'm not seeing any knockdown via western blot I transfected by MDAMB468 breast cancer cell lines with shRNA ...
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1answer
19 views

What information does the KEGG Module statistics page show?

While browsing through the home page of KEGG Module, I clicked the button named Module statistics. Can someone tell me what does these numbers signify? What are they the statistics of?
2
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1answer
57 views

What happens to IP3 molecules after release from IP3 receptors?

IP3 molecules bind to IP3 receptors and open up the calcium channels on the endoplasmic reticulum. I am wondering what happens to IP3 molecules after they have been released from the IP3 receptor? Do ...
6
votes
1answer
133 views

What is the biochemical explanation for tingling and burning sensation in brain due to certain food?

Consumption of mustard (spicy English Mustard), wasabi and horseradish based food dressings usually result in a burning, tingling or freezing sensation in the brain/scalp and nostrils as the vapour ...
2
votes
1answer
89 views

Why does my anti-ubiquitin antibody visualization not work on my PAGE gel?

I am using 2D gel electrophoresis to visualize polyubiquitinated proteins. However, while I can see actin and heat shock protein using when appropriate antibodies, I cannot visualize them using ...
6
votes
1answer
300 views

How bad is ethidium bromide in your plasmid for downstream applications?

I want to transfect Adipose Derived stem cells using a clone of my own. My problem is that I get a lot of contamination (not only genomic, but due to the nature of the technique, I get undesired ...
5
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0answers
73 views

Why do some medicines induce sleep? [closed]

I have seen lot of people sleep or say that they are feeling sleepy after taking some medicines. Why? I mean, if a medicine acts on some cell of the body because that cell has got its receptors and ...
3
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1answer
211 views

Where do the H+ ions come from in light reactions?

In the light-dependent reactions of photosynthesis, H+ ions pass to the thylakoid space. Where do these protons come from?
6
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3answers
695 views

Mutation That Loses Stop Codon

Someone asked this in my class and my instructor wasn't sure in her answer, doesn't anyone know what happens in protein synthesis if a mutation causes mRNA to not possess a stop codon? Would the ...
0
votes
1answer
62 views

What is a selectively neutral genotypic change?

I am reading the paper "Neutral evolution of mutational robustness". Because I am new to neutral evolution, I have a few questions. Firstly, from my understanding, genotypic neutrality means the ...
3
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1answer
49 views

What makes a strong polyadenylation signal a strong signal?

I was wondering why is it that "AAUAAA" is a strong Polyadenylation signal whereas the rest of the polyadenylation signals show reduced cleavage and polyadenylation efficiency?
3
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2answers
249 views

Neomycin resistance gene in E. coli stb3 cells

We use a lentivirus packaging vector called pLenti_puro_DEST. We use puromycin to select for the cloned gene in 293T cells. However, the pLenti_Neo_Dest has been discontinued, so I'm cloning a ...