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

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29 views

Refer to Ran-GEF as a coenzyme?

Ran-GEF facilitates an exchange of GDP for GTP in the formation of Ran-GTP in the nucleus as part of gated import of proteins. Would I be correct in calling Ran-GEF or Ran-GAP coenzymes?
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54 views

Molecular weight of my 2-D gel

I am a little confuse when I try to figure out the molecular weight of the marker on my gel. I used NuPage Novex 4-12% bis-tris gel and Mark12™ Unstained Standard as a marker. Could please someone ...
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53 views

Do snRNAs exit the nucleus or not?

In Molecular Biology of The Cell (Alberts, et al., 2015), it lists the various RNAs that are trafficked through the Nuclear Pore Complex (NPC) into the cytoplasm. The list includes snRNAs, but I ...
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482 views

Evolution of endosymbionts?

Mitochondria and plastids in eukaryotes evolved through a process of endosymbiosis. How does an event like a eukaryote engulfing a bacteria, become a part of the genome? Some of these primitive ...
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3answers
859 views

Do we consume dna, proteins of other organisms?

When we eat raw meat, e.g. chicken or fish, we are actually consuming the DNA, proteins etc. which are present in their cells. Wouldn't this affect our cell functions as this DNA might enter our ...
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29 views

In vitro virus assembly

Are researchers able to assemble viruses in vitro? For example, I imagine that a phage display library may be generated by throwing in a test tube the capsid proteins (or what have you) along with ...
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18 views

Using Q solution with ready made MasterMix

I am exploring the possibility of using Q solution (5x) to get rid of non specific bands in PCR. I mostly use a MasterMix and not separate aliquots of dNTPs, Taq, buffer etc. In principle, adding Q ...
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1answer
83 views

How does Cas9 interact with CRISPR?

I read that Cas9 protein along with guided RNA binds at a specific DNA fragment of foreign organism integrated in a host organism DNA. To make the host immune to virus infection Cas9 along with gRNA ...
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1answer
70 views

How to interpret the simple sequence repeat (SSR) on the coding sequence, but not the related protein sequence?

I have predicted some SSR repeat on the gene of interest using SSRLocator program, which the result creates a question for me. Please consider the below sequence, which is part of gene sequence of ...
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48 views

How does intron retention make the alternative transcript non-coding?

I faced with a non-coding transcript that specified as one the isoform of BIN1. It sounds that this isoform generated as a result of alternative splicing with a intron retained; am I right? However, ...
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1answer
160 views

How does NHEJ cause indels?

I was reading up on CRISPR-cas9 and how it works and I am having trouble wrapping my head around how NHEJ to repair the DSB can cause indels to occur. Shouldn't the NHEJ just stick the two strands of ...
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1answer
237 views

How do DNA-binding proteins determine that they're binding to the correct DNA base pairs?

My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?" He alluded to the different arrangements of hydrogen-bond donor and acceptors in ...
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2answers
778 views

Are eukaroytic promoters located in the 5' UTR region?

I was wondering if promoter sequences are located on 5'UTR region in eukaryotic organisms?
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51 views

Was site-directed mutagenesis used to study the effects of sickle-cell anemia?

The title says it all. I am inquiring whether or not site-directed mutagenesis was used to study the effects of sickle-cell anemia/figuring out that specific amino acid mutation was the problem.
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1answer
145 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 ...
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2answers
128 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
148 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
476 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 ...
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2answers
231 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
149 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, ...
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1answer
117 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
32 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
62 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 ...
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65 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 ...
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2answers
124 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 ...
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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 ...
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2answers
67 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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125 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
2k 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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113 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 ...
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0answers
272 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 ...
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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 ...
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1answer
63 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
93 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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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
44 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
187 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 ...
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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
319 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
75 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 ...
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289 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
590 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 ...