Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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11 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 ...
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Dealing with heterochromatin during DNA replication

Heterochromatin are present along the chromosome (uncoiled state). With the super-soiled structure, RNA polymerase cannot get into the DNA base pairs in heterochromatin and starting transcription. ...
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Flip-flopping in plasma membrane

Flip-flopping of lipids (and in proteins it is impossible) in plasma membrane is rare due to high energy barrier (video ref). However, it is an important mechanism since it allows asymmetric ...
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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 ...
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Western blotting: what common tweaks do you make to the protocol and why would you make membrane cuts?

I'm building an app which helps researchers plan out Western blots, record protocol tweaks and receive warnings in the app if: you're trying to multiplex antibodies of similar molecular weight on the ...
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1answer
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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. ...
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2answers
118 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. ...
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1answer
34 views

Examining antibody - target interactions in PyMOL

I'm a student currently looking at antibody responses against a viral target protein of interest. I have my own, annotated PyMOL session of my protein and I also have .pdbs of crystallised antibody ...
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3answers
120 views

Evolution: Can the genotype frequencies change, but the allele frequencies remain constant?

If a population isn't evolving because it's in Hardy-Weinberg (HW) equilibrium, then I know that both genotype and allele frequencies must stay constant. My question is, can evolution still not occur ...
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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 ...
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weight / voulme calculation? [closed]

I know this is a simple question but i am not able solve this can anyone please help me. I have prepared the 5% of SDS (stock solution). I need to prepare the buffer for 5 ml with the final of 0.2% ...
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Question on cellulose synthase

How does the rosette structure of synthase cause the cellulose synthesized to be aligned next to each other? I just cannot visualise how a rosette structure can be able to cause the celluose to be ...
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30 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 ...
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Are proton and water consumed in glycolysis?

These are the inputs and the outputs of glycolysis (1): $$\ce{C6H12O6 + 2ADP + 2Pi + 2NAD+ → 2C3H4O3 + 2H2O + 2ATP + 2NADH + 2H+}$$ but when ATP converts to ADP in the first step of glycolysis, it ...
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You have extracted protease from culture filtrate of Termitomyces clypeatusgrown in potato dextrose broth [closed]

You have extracted protease from culture filtrate of Termitomyces clypeatusgrown in potato dextrose broth.During partial characterization, youchecked protease activity at different temperature, pH. ...
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where can i introduce my insert in the plasmid?

I assembled three different DNA fragments together. I want to do the gibson assembly to introduce my fragments into the plasmid. Main point is i don't want to use the restriction sites. I am using ...
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3answers
60 views

Book recommendation: protocols and recipes handbook for molecular biology / biochemistry

I'm a 5th-year PhD student in chemical biology. I've mostly been doing computational work, so my bench skills are rusty. To help me, I'd like a handbook of common techniques -- transformations, ELISA, ...
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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 ...
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1answer
98 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 ...
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1answer
24 views

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 ...
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51 views

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'-...
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24 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 ...
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What is the chemical structure of neca?

I heard in the YouTube video https://www.youtube.com/watch?v=m07OvPEoR6g that pearls are made from neca. What actually is the chemical structure of neca? I can't figure out an algorithm for ...
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36 views

Knockdown with non-coding target

I am studying 2 splice forms of some gene. I need to knockdown both of them. To do so I have only one choice: to use non-coding right end of one of the splices. Do you have any experience with such a ...
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1answer
163 views

How complete is the information in DNA?

Everyone talks about how DNA is the "molecule of life" and "the set of instructions for building you." How complete are the instructions, really, though? To make the question concrete, say I were to ...
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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 ...
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How do enhancers induce transcription?

DNA response elements are DNA sequences that are could be found upstream, downstream of genes that regulate gene expression at the transcriptional level. One type -Enhancers- bind specific ...
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50 views

sequence specific endoribonuclease

I have a viral mRNA that I want to silence with a genomic method without using RNAi.I thought of using ZFN or TALENS but they both work only on dsDNA. Basically I need an endoribonuclease that ...
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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 ...
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what books do you recommend to undstand horvath clock?

I’ve read about horvath clock, and the new theory of aging. One that describes DNA methylation as the upstream root for all age related symptoms. I want to read more, and understand this at a much ...
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259 views

How to write a stoichiometric matrix for a part of the Pentose phosphate pathway

maybe this is more bioengineering than biology but I didn't find any such group. So I got the following photo: And I was asked to do the following for the network inside the red area. 1) Write the ...
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1answer
49 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), ...
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2answers
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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 ...
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1answer
87 views

Ligation without purifying insert

I am planning to insert a 45 bp sequence in a vector. After restricting my insert to create compatible sticky ends, I am finding no way to clean it up. Is there any way for cleaning this fragment ...
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1answer
28 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 ...
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1answer
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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 ...
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239 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-...
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1answer
28 views

Analysis of post transplantation lineage tags

I'm having some trouble understanding some bits of a study, mostly about the Sleeping Beauty system and TARIS model, from this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408613/ I ...
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How would one track a mineral nutrient in a plant in order to prove that nutrient has been re mobilized?

Before abscission - senescence of a plant structural components that contain mineral nutrients (E.g. Magnesium, Potassium...) are re-mobilized from the senescent tissue and used in other plant tissue ...
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582 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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1answer
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How does lipoid pneumonia lead to acute respiratory distress syndrome (ARDS)?

How does lipoid pneumonia lead to acute respiratory distress syndrome (ARDS)? The vaping illnesses that have been happening on the news in the United States are being caused by the federal ...
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Why my protein transferred but ladder did not (western blot)?

My protein of interest is about 200Kd, I ran the gel for 35 min at 95V, the protein transferred but the ladder did not, I used dual color ladder(Precision Plus Protein™ Dual Color Standards, 500 µl #...
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2answers
61 views

Can Cas13 edit DNA

Can Cas13 be used to edit DNA or is it only for RNA? I have tried looking at literature and my understanding is that it can only edit RNA.
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1answer
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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, ...
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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 ...
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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 ...
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1answer
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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.
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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?
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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?
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What is the purpose of co-translational transport?

During intracellular proteins synthesis, all proteins are made by free ribosomes in the cytoplasm and some, but not all ribosomes (those which make membrane or secretory proteins) move to the ...

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