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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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How can I clone a gene into a plasmid vector with an N-terminal his tag and TEV cleavage site between the tag and the start of the sequence?

I'm a scientist who has significant experience in chemistry but am relatively new to molecular biology and biochemical techniques. I'm trying to make an isolated domain of a protein (166 residues, 19....
magnetic's user avatar
1 vote
1 answer
246 views

Why is DNA replication not 100% accurate

I've been reading about DNA mismatch repair (MMR) and how this process improves DNA fidelity. However, I was wondering, what is stopping MMR from correcting all mistakes in the daughter DNA with 100% ...
harold__hadrada's user avatar
6 votes
3 answers
602 views

Does the term 'protein expression' refer to the production of proteins only or also their regulation?

I am learning about molecular biology and I have come across the term 'protein expression' in a research paper. I have searched the definition of this term online and on the Thermo Fisher Scientific ...
ceno980's user avatar
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How do cilia beat?

From what I have learnt, the mechanism of the beating of cilia is: movement of dynein towards the (-)-end i.e. towards the microtubule-organizing center (MTOC), causing the 2 pairs of microtubules to (...
Questions's user avatar
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When transmembrane proteins destined for the plasma membrane are in the ER membrane are they in their final folded form?

I am studying how transmembrane proteins are made and I have read that proteins that are destined for the plasma membrane are initially in the ER membrane and do not get translocated into the ER lumen ...
ceno980's user avatar
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What is meant by 'topologically continuous' in the context of cell compartmentalisation? [closed]

I am reading the textbook 'Molecular Biology of the Cell', and I am reading the chapter about the compartmentalisation of cells. I have come across the following statement: The nucleus and the ...
ceno980's user avatar
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6 votes
2 answers
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Can we dilute PureExpress Cell Free Mix to increase number of reactions?

Since the PureExpress Cell Free mix is so expensive, I was wondering if it might be possible to just dilute the mix to increase the number of reactions we need to use. From this image I found: It ...
rkrishnasanka's user avatar
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How to incerase the efficiency of co-immunoprecipitation?

immunoprecipitation recently. My main problem is i am getting very clean and my target protein only (as you see in the lane 3,4,5,6) but when i reduced the NP40 concentration to 0.05 percentage i ...
Rengaraj's user avatar
1 vote
1 answer
80 views

How broad are the conclusions that one can make from a heterologous expression experiment?

I am studying whether a neural protein regulates the activity of the protein GSK3. I am using heterologous expression systems where I am overexpressing the neural protein in CHO cells (via ...
ceno980's user avatar
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4 votes
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How can I change the payload of a bacteriophage used to transform E. coli?

I was looking at bacteriophages and how they're used to transform E.coli. While the whole process of how a bacteriophage works makes sense theoretically, I wanted to know how one goes about changing ...
rkrishnasanka's user avatar
2 votes
1 answer
386 views

Can restriction enzymes (Type II) displace single-stranded binding proteins (SSB)?

Many type II restriction enzymes have been shown to be able to cut ssDNA. If single-stranded binding proteins are bound to single-stranded DNA (ssDNA), does this prevent restriction enzymes which cut ...
etowah's user avatar
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Does anyone have a tutorial or some guide to get started with Rosetta protein modeling and design tool? (I am a Mac user) [closed]

I have been trying to get started with Rosetta protein modeling and design software bundle. I searched online but the tutorials in the Rosetta website are difficult follow. I have the binaries already ...
7V7's user avatar
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8 votes
1 answer
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Why is electroporation not the prefered choice transforming for Mammalian Cells (HEK)?

I see a lot of folks using different techniques for transforming mammalian cell (specifically HEK) instead of doing electroporation like I see with E.Coli (bacteria). Is there a reason for this ?
rkrishnasanka's user avatar
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Does the two-state gene expression model apply to constitutive genes?

Wikipedia defines constitutive genes as a gene that is transcribed continually as opposed to a facultative gene, which is only transcribed when needed. I don't have a strong theoretical background ...
pew31's user avatar
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1 answer
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Is the phrase "transmembrane segment" equivalent to the transmembrane domain of a protein?

I am reading the Handbook of Neurochemistry and Molecular Neurobiology and I am learning about the cell adhesion molecule NCAM2 and I have come across the following: The overall structure of NCAM2 ...
ceno980's user avatar
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1 vote
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What is meant by "opposing plasma membrane" with respect to cell adhesion molecules?

I am reading the Handbook of Neurochemistry and Molecular Neurobiology and I am learning about cell adhesion molecules (CAMs) and I have come across the following: CAMs are involved in homo‐ or ...
ceno980's user avatar
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11 votes
2 answers
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Can I use multiple bicistronic RBS sequences in a synthetic biological circuit?

The bicistroninc RBS sequences (BCDs) developed by Mutalik et al. [1] aim to remove context sensitivity from translation and therefore ensure more predictable gene expression. However, I have been ...
ajhfedorec's user avatar
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Does Invertase catalyse the hydrolysis of other sugars other than sucrose?

I recently did a lab where we tested out the substrate specificity of Invertase on different types of sugars such as sugar alcohols and disaccharides, measured by the absorbance of red using a ...
starry's user avatar
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Surface Plasmon Resonance (SPR) Predicting Molecular Weight Limit?

Just asking, can we predict how low molecular weight (LMW) analyte our SPR system can detect based on our LOD (limit of detection) and our sensitivity on another protein detection? So right now our ...
NexusRay's user avatar
2 votes
1 answer
56 views

Confusion regarding the Kir2.1 inward-rectifying potassium channel

I was trying to find out more about gustation and the transduction of sourness when I came across the supposed inward-rectifying potassium channel $\ce{K+_{ir} 2.1}$. Here's the thing, despite being ...
chematwork's user avatar
3 votes
1 answer
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Interaction of charged triphosphates with the ATP binding region in proteins

DNA-histone interactions involve positively charged amino acid side chains groups neutralizing the negatively charged phosphate of the sugar-phosphate backbone. Is the same true for ATP binding sites ...
KanyeWest2's user avatar
2 votes
2 answers
127 views

How to assemble three 60mer nts by pcr?

Good morning, I am new to molecular biology. The question might be silly but i would like to know the answer. I have three 60mer single strand synthetic oligonucleotide. Namely Tag 1 - 3. My goal is ...
Rengaraj's user avatar
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0 answers
231 views

Which enzymes use ATP?

It is well known that there are many enzymes which use ATP in their function, and any enzyme that work against an energy gradient need to have that energy supplied from somewhere, but just as well ...
Anthony Khodanian's user avatar
0 votes
1 answer
1k views

Electrochemical and concentration gradient confusion [closed]

I am learning membrane transport and learnt that there are 2 gradients that determine passive and active transport. If the concentration of a cation is higher in the cytoplasm side (hence ions should ...
Questions's user avatar
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1 answer
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DNA complementarity against reverse complementarity [duplicate]

I am sorry to bother with this question (i study genetics for about few hours, because I need to understand my data) and I am really confused about these two terms, because I dont know if the books ...
stanly's user avatar
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4 votes
1 answer
131 views

Introns and miRNA

From this paper, it is stated that some introns may contain genes coding for miRNA, miRNA is essential in regulating gene expression by pairing with RNA, hence disrupting regular translation. From ...
Questions's user avatar
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7 votes
1 answer
243 views

Why can't certain nucleoside analogs be used to label bacterial RNA?

A 2020 publication in Nucleic Acids Research 1 includes the following passage: A variety of nucleoside analogs have been developed for metabolic RNA labeling in various eukaryotic cells (9–16). Among ...
acvill's user avatar
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1 answer
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Can caffeine act as viagra

Recently I studied that cAMP which is a 2° messenger can cause various physiolocal changes under the action of proper hormones. Now cAMP is degraded by phosphodiesterase and this ceases the actions. ...
Chloritone_360's user avatar
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0 answers
47 views

Question about : RNA interference - small-interference RNA AND about Rab-protein in vesicles

First Question : RNA interference - small-interference RNA in the textbook -Essential cell biology By Bruce Alberts, Dennis Bray, Karen Hopkin this Figure is Shown my question is : if the foreign RNA ...
cisco_guy's user avatar
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Need help designing an enzyme immunoassay (EIA)

I have a FITC-labelled DNA sequence and an anti-FITC antibody, however this antibody is not conjugated with HRP or any other enzyme. I work in a lab with limited finances, so is there a way I could ...
Carica Rubus's user avatar
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1 answer
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Which landmark paper first described the differentiation of T-cells?

T-cells are distinguished from B cells in part by their locus of differentiation/maturation (thymus). This is textbook knowledge, but I was wondering which particular person or people were responsible ...
alghazali's user avatar
1 vote
0 answers
97 views

Blood and plucked-feather sample storage

This next field season I will be collecting both blood and feather samples and I wondered how best to store the samples. The blood samples will be used for microsatellite and/or SNP analysis. The ...
Quinn's user avatar
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0 votes
1 answer
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Gibson assembley for small fragments?

I am new to the Gibson assembly, I know how I need my plasmid but main problem is I don't have short tags and linker so I wanted to do Gibson assembly? 5'-...
PraveenKumar's user avatar
0 votes
1 answer
220 views

How to convert cell units (c.u.) to mole?

If one has values in terms of cell units (c.u.) how may it be converted to $\mu$M? Should I think a "cell unit" as $1\;c.u.= \frac{1}{\text{cell volume}}$ and $1\;c.u.=\frac{1}{\text{cell ...
confused's user avatar
2 votes
0 answers
50 views

What is the "GTP activator protein" that activates GTP-cyclohydrolase-1?

From GTP-cyclohydrolase deficiency responsive to sapropterin and 5-HTP supplementation: relief of treatment-refractory depression and suicidal behaviour (BMJ Case Reports, 2011) The metabolic profile ...
CopperKettle's user avatar
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1 vote
0 answers
62 views

VDJ sequencing in mice, DNA or RNA?

I am wondering if anyone who is well versed with VDJ sequencing for TCR repertoire analysis (specifically CDR3) would know if DNA or RNA is a better starting material? We are looking at the effects of ...
Manon Valiquette's user avatar
0 votes
1 answer
1k views

Exact average molecular weight of a dsDNA basepair

I am trying to calculate the exact weight of a given dsDNA. On the Internet and the literature, different values for the av. molecular weight of one basepair are given : 660 g/mol (probably wrong), ...
user12256545's user avatar
4 votes
2 answers
305 views

What is the difference between non-coding and intergenic regions?

The initial question was about understanding what is in the downstream of a gene in a eukaryotic organism. I understand that this region is located 3' of a gene, and therefore I would expect to find ...
Silvia VC's user avatar
0 votes
1 answer
3k views

Alkaline Phosphatase and Ligase Protocol for Cloning

In the image the circular molecule is a restricted vector and the linear red molecule is a DNA insert. I found this protocol in my lessons notes, but I don't understand how it is possible that ligase ...
Mirko's user avatar
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1 vote
1 answer
33 views

Are there any online resources for finding the signaling pathways that two proteins both belong to?

I am studying the proteins GSK3 and AMPK and I am trying to identify the signaling pathways that both of these proteins belong to. From reading journal papers I have found out that both of these ...
ceno980's user avatar
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3 votes
1 answer
221 views

Parameters that determines the thermal stability of DNA

Why a DNA with a high GC content more stable than one with a less GC content? Is it because of the three hydrogen bonds in GC base pair which is one more than a AT base pair or is it because of the ...
Nikhil Verma's user avatar
8 votes
1 answer
361 views

What does ΔC and ΔN mean with regards to a protein sequence?

I am reading a paper about the regulation of the nuclear export of the protein GSK3 and I have come across the following statement: Full-length FLAG epitope-tagged mFrat1 (FLAG-Frat) and the amino-...
ceno980's user avatar
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5 votes
2 answers
467 views

How can good Shine–Dalgarno or Kozak sequences enhance translation?

In prokaryotes the Shine-Dalgarno sequence, a polypurine consensus sequence near the initiation codon (usually AUG), is required for the mRNA to bind to the small ribosomal subunit, allowing ...
Questions's user avatar
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1 vote
0 answers
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Potential obstacles to growing nanoelectronics within living cells? [closed]

Say there was a nanotechnology allowing to "grow" and wire up electronic components/sensors measured only a few nanometers in cross-section, though spanning in length across microns. Say ...
Greendrake's user avatar
4 votes
2 answers
703 views

Does N1-methyl-pseudouridine occur naturally in any RNA?

Pseudouridine occurs naturally in some RNAs. But what about the methylated variant of it, N1-methyl-pseudouridine? The latter is a key ingredient in both the Pfizer and Moderna Covid-19 vaccines, ...
the gods from engineering's user avatar
0 votes
0 answers
54 views

Questions regarding transformation in bacterial cells

First off, in transformation the donor DNA aligns itself with the complementary bases in the recipient DNA. Now a "perfect" alignment of the donor DNA ( Sorry if my terminologies are ...
Anish Kumar's user avatar
1 vote
1 answer
142 views

When was peptidoglycan discovered?

I've searched for some time now, but I can't find a definitive answer. The closest I have gotten is "knowledge about peptidoglycan structures dates back to the 1970s–80s" from this paper.
Nold's user avatar
  • 21
-2 votes
1 answer
57 views

What is the difference between mutation per base pair and mutation per genome? [closed]

Isn't genome size considered to be the number of base pairs present in DNA? So what is the difference between the mutation per base pair and mutation per genome? Are they similar or different?
Mani's user avatar
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0 votes
1 answer
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Can Taq polymerase be stored with PCR primers?

I don't think it's possible for TAQ to be stored with the primers, but I'm not sure. This storage wouldn't be long-term (a few days, or a week at most). Thoughts?
PhetBoi's user avatar
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3 votes
2 answers
812 views

What is the significance of the phospholipid bilayer being two-dimensional?

I'm wondering about the significance of the phospholipid bilayer being a two-dimensional fluid. I found this powerpoint: I also found that thetwo-dimensional fluids have limited degrees of freedom. ...
Carlton Reid III's user avatar

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