Questions tagged [molecular-biology]
The study of the molecular processes underlying life.
1,639
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ETC & Hydrogen Calculation [Need Details]
During ETC we need Protons & electrons to go throw or across membrane
Electrons makes Protons move & protons makes F0F1 Complex to produce ATP
But How many ...
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34 views
How do sequences of amino acids perform and what properties do they have? [closed]
I am learning and have a question regarding sequences of amino acids and their properties, please.
There are quite highly detailed accounts of each step of the process getting from the sequence of DNA ...
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31 views
Cloning in a large DNA fragment into a plasmid
I need to clone in a 30kb DNA fragment into my plasmid (~7kb).
Working with such a large fragment I have run into a few problems. The first was purifying it from the PCR mix used to amplify it out of ...
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1answer
26 views
can mammalian expression vector be used in e coli to produce plasmid
I would like to use this plasmid (mammalian expression Flag-HA-USP53 (Plasmid #22606) - Addgene) to produce plasmid in e coli to purify plasmid. Would this work? I am starting out with this vector ...
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Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous? [migrated]
I have a project to write in Python that requires to write a function that given an ambiguous DNA (for example: KKGTACACCAG) sequence and a molecular weight interval, returns a list of all unambiguous ...
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Recommendations for good books on bacterial genetics & molecular biology?
I'm starting a new phase of my PhD soon, and am feeling very under-prepared with respect to my general bacteriology knowledge. I was recommended to read up on basic bacterial genetics and molecular ...
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49 views
Interactive molecular machinery visualisation software?
If I want to manually feed mRNA through a ribosome to actually see what happens step by step which software can I use to do that?
I'd like to be able to see changes in geometry and orientation at an ...
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1answer
238 views
how to extract garlic fructan?
can anyone tell me a not complicated way to extract fructans from garlic (i have access to highschool lab). I need this to be able to make an experiment on garlic extract and just fructan from garlic ...
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1answer
20 views
Is Signal Transduction Unidirectional from the Stimuli to the Final Receptor?
I wonder if signal transduction in biological systems including visual, olfactory, tactile or any other biological system, is unidirectional. Suppose that $X_i$ is the $ith$ cell in the signal ...
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1answer
69 views
What has a more negative impact: Having only a partial deletion of a specific gene or the having entire gene deleted?
I am looking through a genomics database to see whether patients who have intellectual disability have deletion of only a specific gene of interest and no other mutations (e.g. deletions or copy ...
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1answer
66 views
Multicellular but uninucleate?
The "standard" biological setup is one cell-one nucleus (with one or more chromosomes and zero or more plasmids). Multinucleate cells are a thing (e.g., in fungi)--a situation wherein a ...
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Why does Meiosis produce 4 daughter cells instead of 2? Won't splitting the initial diploid cell into two haploid cells be easier?
At first, I thought it was because of crossing-over, but when I thought more about it, that didn't seem reasonable. Why don't cells just do meiosis like this? (I know that we don't understand all the ...
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1answer
33 views
How many non-pairing bases can a PCR primer have in directed mutagenesis?
I'm not including a lot of details here, because the problem I'm working with is actually more complex.
Say you have the DNA sequence
5'-...tct gcg gtg gtt ggc att ctg ctg...-3'
Could this sequence ...
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1answer
60 views
Transformation and PCR in molecular cloning
After obtaining the recombinant DNA, it is common to transform into E. coli to screen for recombinant DNA and amplify it. But I would like to ask can we amplify it using PCR?
I think there will be 3 ...
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0answers
61 views
Occurrence of the theoretical thymine enol::guanine base pair in DNA [closed]
DNA polymerase has a proofreading exonuclease activity that can remove incorrect tautomers in the DNA template or incoming base. In theory the enol form of thymine can form three hydrogen
bonds with ...
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2answers
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What is, (and what isn't) "kinetic replication" as it applies to molecules and to living organisms?
CNN's World's first living robots can now reproduce, scientists say describes "xenobots"; clusters of stem cells that move around and by this motion occasionally push enough free stem cells ...
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3answers
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Effects of mRNA vaccines on human body processes
I would like to understand the effect of an mRNA vaccine on more complex processes in the human body.
To what extent does this "artificial", external addition of mRNA interfere with the body'...
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1answer
88 views
Does DNA ligase have any role to play in replication on leading strand?
Actually I developed this doubt while solving some questions(they are poorly framed I suspect). According to my notes and my institute modules, 1 RNA primer is required on the leading strand as well ...
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1answer
80 views
DNA Design for Multi-Site Restriction Enzymes
I have to use the SacII restriction enzyme, which requires multiple recognition sites to efficiently cut DNA, for a DNA assembly. From my understanding, multiple copies of DNA holding only a single ...
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1answer
42 views
Why are IMAC and gel filtration combined?
In a practical course I used an Biorad Profina system to purify a protein with a histidine tag.
The device uses a column for IMAC and one for gel filtration. Why are these two devices combined in one? ...
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1answer
96 views
What is a downstream target?
For example, in a systems biology analysis, what is a "downstream target" and why are these significant in pathway analyses?
I have looked for answers on Google, DuckDuckGo, Wikipedia, etc. ...
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1answer
73 views
What breaks hydrogen bonds while producing sticky ends using restriction endonucleases?
I am a high school student and I am little confused about the uses of restriction endonucleases. Why do hydrogen bonds(base pairing)
break when restriction endonucleases produce sticky ends? If they ...
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1answer
67 views
Can we view the cross section of dna using electronmicroscope?
Is it possible to find how the cross section of DNA looks using without computer simulations ? All pictures I find on the internet are mainly computer simulations.
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35 views
Determine directionality of backbone from electron density map
I am given a polypeptide with three electron density maps at different resolutions; 1.85, 2.5 and 3.5Å. And from this I am to determine at which resolution you could be certain about the ...
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1answer
34 views
Where is the location of cutin or cuticle in the plant leaf [closed]
Cutin's main role is to prevent the the plant leaf from water loss, cutin is thick in shape , but I need to know where is the location of it ,for example is it in the lower epidermis or in the upper ...
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2answers
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How can you identify recessive mutations in a gene that has been disrupted by a chromosomal translocation?
I am reading a journal paper about a patient who has intellectual disability. The patient was found to have a balanced chromosomal translocation t(11;16)(q24.2;q24).
This chromosomal translocation ...
2
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1answer
64 views
Are there any online resources for visualising on which band of a chromosome a particular gene is located?
I am studying some genes that are expressed in the brain. I use the online database UniProt to get information about the proteins encoded by the genes of interest. However, I would like to know on ...
3
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1answer
54 views
How do molecules find their places? [duplicate]
In many molecular biology animations, a molecule just flies in and goes straight to the right spot. It's clearly a useful simplification, but I'm interested in learning more of the full story.
I ...
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1answer
45 views
Where in the cell does this enhancer RNA knockdown take place?
In Pneuli et al 2015, they knock down an enhancer RNA using RNAi, testing whether it is a mere byproduct or whether it has a key role in the enhancer's function. They find their system works: the ...
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1answer
120 views
Could p-loop bind fully protonated ATP?
The phosphate tail of ATP binds the p-loop motif, evolutionary conserved, going back to since forever. In the dominant model, the deprotonated hydroxyl groups are complexed with Mg2+, at least two of ...
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0answers
54 views
What are the additional considerations for primer design in ancient DNA?
I'm familiar with the principles of primer design and have previously designed primers for use in modern DNA. However, in my current project I am working with ancient DNA (nuclear gene) and need to ...
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1answer
53 views
Why is ACE 2 located on the Alveolar side of Pulmonary Epithelium?
Location and Purpose of ACE 2.
Given that the primary purpose of the transmembrane enzyme ACE 2 is ostensibly to bind Angiotensin 1 and 2 in order to convert these to derivatives such as Angiotensin [...
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1answer
57 views
Can a polymer coated with antibodies have enough attraction to wrap around a virus?
Archived source for image
Please ignore the signal release. Does anyone know if it’s possible for polymer to wrap around a virus?
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1answer
144 views
How does the hydrophobic amino acid fuse the corona virus with the host cell membrane?
I am reading the article How the coronavirus infects cells — and why Delta is so dangerous.
It describes the fusion process of the virus into the host cell as follows right above an animation ...
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1answer
80 views
Methods of investigating the occurrence of non-standard bases in nucleic acids
Recently the popular scientific press gave considerable publicity to three publications in Science (30th April 2021 — see below) relating to the substitution of the nucleic acid base, 2-amino adenine, ...
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1answer
133 views
Why doesn't RNA polymerase just rotate?
I read A little help understanding DNA supercoiling , Understanding DNA supercoiling , and Why does underwinding create topological strain of DNA? , but there's still something I don't get. ...
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Question about using primary neuronal cultures from mice to support findings from in vivo models
I am analysing synapse formation during early postnatal development using the brains of postnatal day 2 (P2) and postnatal day 10 (P10) wild-type and knockout mice. Through Western blot analysis, I ...
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0answers
41 views
Is lactic acid build up the cause of muscle fatigue or only a symptom?
If your body could magically instantly remove lactic acid as it is produced, would that make you immune to muscle fatigue, or is the lactic acid only a symptom of muscle fatigue and instead exists, at ...
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24 views
Which genes/proteins constitute the core components of the circadian clock?
What the title says.
For instance in Drosophila melanogaster and Mus musculus (see Patke et al. 2020) the CLOCK, CYCLE/BMAL, CRYPTOCHROME, PERIOD setup seems to be conserved. But other components also ...
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1answer
132 views
Is 'constitutive effect' the proper term for explaining a biological effect that occurs due to the constitutive knockout of a gene in a mouse?
I am working on an experiment involving the analysis of expression of a protein X in wild-type (+/+) and knockout mice (-/-). In the knockout mice, the gene of interest has been constitutively knocked ...
9
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2answers
449 views
Tips for longer fragment size and higher purity of insect DNA
Aim
In a pilot experiment I tested three different genomic DNA extraction methods on the non-model organism Pieris mannii (southern small white; Insecta, Lepidoptera, Pieridae). The goal was to ...
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1answer
82 views
Why are heterologous expression systems such as mammalian cell lines commonly used for studying interactions between neuronal proteins?
I am reading papers about heterologous expression systems and I have seen that they are used a lot in neuroscience to studying interactions between proteins that are normally expressed in the brain.
I ...
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1answer
50 views
How does protein knockdown allow a phenotype to be observed?
I am trying to understand how AID2 technology works.
I came across an article that says "Protein knockdown using the auxin-inducible degron (AID) technology is useful to study protein function in ...
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54 views
What is the effect of an acidic solution on hydrolytic enzymes?
I'm working on a school research project and my research question is "What is the effect of increasing concentrations of Acid X on hydrolytic enzymes, measured through the loss of mass of leaf ...
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1answer
83 views
What are the prospects in synthetic biology, especially in the introduction of biological computers? [closed]
One of the interesting areas of synthetic biology is the so-called biological computers. A biological computer refers to an engineered biological system that can perform computer-like operations. I ...
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24 views
Preventing the transcription bubble from occurring in an individual gene
I'm trying to find a way to stop the transcription bubble from occurring over a individual gene in humans. I need the act of transcription to be inhibited, siRNA knock down of the transcript does not ...
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0answers
76 views
The average of Ct values in real-time PCR
The Ct value is the number of cycles when the "PCR amplification curve with the horizontal axis as the number of cycles" and the "predetermined threshold" intersect, and is not ...
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Will a Kozak sequence within a coding sequence interfere with eukaryotic expression?
I want to make a DNA vaccine for fish by using plasmid pcDNA3.1(+) with a bacterial antigen. Unfortunately, there is a Kozak sequence in the middle of my target gene.
I am concerned that this Kozak ...
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1answer
32 views
Can Ni-NTA-Atto Conjugates bind to single His-tag
Can I label a protein with a single His-tag with Ni-NTA-Atto conjugates?
Papers generally use this technique to label 6His-tag.
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Why bananas exposed in UVC light turn brown afterwards?
We have this research, where we test if our germicidal disinfection box is working and is functional by doing the banana test, where we expose the green banana to UVC and if the exposed peel turns ...
