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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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Open Reading Frame problem

Problem An mRNA of 999 bases codes for a protein with 300 amino acids and the open reading frame (ORF) starts from base 38. If the base at position 903 is deleted the length of the ORF increases by 3 ...
Soumyojyoti Pal's user avatar
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Cell Signaling: What is meant by "sustained tonal induction"?

I am reading a journal paper about the insulin-like growth factor 1 receptor. I have a question about the following statement in the paper: IGF/IGF-IR stimulates the PI3K-Akt pathway in a ...
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Why do receptor tyrosine kinases undergo constitutive endocytosis?

I am reading a journal paper about the endocytosis of receptor tyrosine kinases. I have a question about the following statement: At the cell surface RTKs undergo constitutive endocytosis (...
ceno980's user avatar
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Primer Optimization for full length gene amplification

I need your help. I have sequences of my desired gene (WRKY TF) from RNA seq data (it was a denovo assembly performed on agave sisalana). Now i need to amplify full length of that gene for which I ...
Fizzah Zulfiqar's user avatar
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Could you recommend literature regarding non-coding RNA and micro RNA?

I am familiar with the Alberts and Watson textbooks, but they are quite general, not specific. I would be grateful if you wrote down books or even in-depth reviews/papers regarding the topic.
Ármin Horváth's user avatar
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Which is the best results for Plasmid dna extraction on gel electrophoresis?

I did plasmid dna extraction and uploaded on the gel. Well 1: marker Well 2: nicked,circular,and supercoiled bands Well 3: linear,circular,and supercoiled bands Well 4: circular and supercoiled bands. ...
Fatima Assaf's user avatar
-3 votes
1 answer
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Do cells know or imagine how each part of the DNA influences body structure and function? How else would evolution happen in specific ways?

Consider how an octopus looks at a rock and it's entire body blends in to resemble the rock. Consider how insects evolved to resemble leaves or twigs. Even frogs, butterflies and other creatures ...
Nav's user avatar
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Can the mechanism behind changes in protein expression be inferred by the timing of those changes?

My question relates to the timing of protein expression changes, and whether there is a literature-based consensus as to how long changes in protein generally take. For example, if protein changes 24h ...
Ryan Ellison's user avatar
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How to prevent small-protein smearing in SDS-PAGE?

I am doing SDS-PAGE for ubiquitin-6xhis (9.6kDa), and all my hand-cast gels produce a smeared band (see image). I typically use 5% acrylamide for stacking, 15% for resolving gel layers. I don't ...
Tom Murphy's user avatar
1 vote
1 answer
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How do you determine the structure of a molecular recognition feature (MoRF) after it binds to itself?

I have a protein that has a roughly 10 residue chain that registers at a MoRF in MoRFPred and MoRFchibi. I have the PDB files to correlate the known structure of the protein with the site of the MoRF; ...
vdg's user avatar
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Why is there no Ligase in Ligation Independent Cloning?

Ligation Independent Cloning literally says no need Ligation, but it still needs ligase to anneal the fragment to vector. And the Protocol used T4 DNA Ligase for anneal process. What does this mean &...
Gordon Chao's user avatar
7 votes
2 answers
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What makes viruses like the flu and covid so tolerant of mutations compared to most other viruses?

I was curious about why we benefit from yearly flu shots and apparently will also benefit from yearly covid booster shots too, whereas this doesn't seem to be the case for most other vaccines -- even ...
Mikayla Eckel Cifrese's user avatar
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#Gateway Cloning How does gene of interest replace ccdB genes?

I knew that Gateway cloning used a site-specific recombination method, but I still cannot figure out how does gene of interest actually replace ccdB genes? Bacteriophage site-specific recombination ...
Gordon Chao's user avatar
1 vote
1 answer
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Understanding DNA Fingerprinting

I am a high-school student learning about DNA fingerprinting. I know that satellite DNA is non-coding DNA and has a lot of repetitive sequences, and the length of each repeat can be either short or ...
Shivam Agarwal's user avatar
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Rectangle-like structures and their folding in biology

I've heard that mathematics helps to explain some biological problem. For example gömböc, which was a well hidden body from mathematicians, explains the body structure of some tortoises in relation to ...
Mikhail Gaichenkov's user avatar
3 votes
2 answers
132 views

What is H-activation vs. O-activation in the context of cellular respiration?

I was reading this article on Albert Szent-Gyorgyi and on page 7 there's this statement: Now, I thought myself capable of tackling a biochemical problem. I embarked on biological oxidations. At that ...
imrobert's user avatar
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What is the minimum Ct value that you would consider indicates no gene expression?

I am doing relative quantification to compare gene expression between a control with several mutant backgrounds using qPCR. Looking online I find several different sources suggesting different values ...
aquaporin's user avatar
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Do right-handed helices bind to right-handed helices, and vice versa?

I know that B-conformation DNA is a right-handed helix, and most proteins that form helices form right-handed, not left-handed, helices (1). Furthermore, "Many transcription factors have an alpha-...
OdinTheDO's user avatar
3 votes
1 answer
68 views

Overlapping atomic radii in data of experimentally observed protein assemblies

I am looking at experimentally observed configurations of viral capsid proteins like that of the tobacco mosaic virus. https://www.rcsb.org/structure/6R7M When taking the atom centers of a monomer and ...
Ivan Spirandelli's user avatar
2 votes
1 answer
59 views

Correlation of Meselson and Stahl with “multifork” replication in E.coli

Because of the limiting value of the rate of DNA replication, rapidly dividing E.coli use multiple replication forks [1][2]. Thus, DNA replication of one generation has already begun in the previous ...
Hdje's user avatar
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Will diffusible protein aggregates coated in cell-free nucleic acids near a depolarizing neuron's soma diffuse along the axon to synapsing neurons?

Edit in response to feedback in comments requesting specific details, etc.: Will aqueously diffusible protein oligomers and protofibrils coated in cell-free nucleic acids in the aqueous interstitial ...
OdinTheDO's user avatar
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Receptor tyrosine kinases: Clarification about what is meant by stabilization of the receptor

I am reading a journal paper. This paper focuses on how neural cell adhesion molecule (NCAM) interacts with fibroblast growth factor receptor 1 (FGFR1) and promotes its stabilization. When FGF binds ...
ceno980's user avatar
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Why do we choose to use agar instead of agarose in various microbial applications?

When performing gel-electrophoresis we always use agarose. Is there a reason we can't perform it using Agar? And in microbial culture Agar is commonly used as solidifying agent, could this be replaced ...
Jayanth Vegesna's user avatar
2 votes
1 answer
75 views

Best way to predict the effects of deletion mutations on protein function?

I have the coding sequences of a WT gene and several mutants of this gene (deletion mutations varying from 5bp to 50% of the sequence deleted). What is the best method for inferring the impact of ...
aquaporin's user avatar
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The split in Boroeutheria into Euarchontoglires and Laurasiatheria. Was this due to the opening up of the Atlantic Ocean?

I'm asking this question as a cat owner. I've seen a figure like 94 MA for the most recent ancestor of both cats and humans (this from, I guess, molecular clock arguments), and it kind of lines up ...
Emanuel Landeholm's user avatar
1 vote
2 answers
52 views

Who discovered that phage phiX174 has a single-stranded genome?

I have recently read that Erwin Chargaff has discovered that the genome of phage phiX174 (ϕχ174) is single-stranded. However I could not find the paper reporting this discovery. Is there a link to the ...
Gigiux's user avatar
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Mesh formation in the wells of SDS PAGE. How to solve it?

I casted 10% resolving gel and 4% stacking gel and every time a mesh like structure ( polymerisation) in the wells are formed.How to avoid this from happening and how do i get clear wells? If someone ...
user78810's user avatar
3 votes
2 answers
145 views

Change of DNA concentration due to restriction digest?

Assume that you perform a restriction digest in a molecular biology lab: you combine genomic DNA, a restriction endonuclease (e.g., EcoRI), and the optimal buffer for that endonuclease and are about ...
Michael Gruenstaeudl's user avatar
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Recovering DNA from an RNA-extraction/purification kit

We are extracting RNA from single insects with the later purpose of performing RNA-seq. We are using the RNeasy Plus Miniki from Qiagen, which involves the use of eliminator columns as you can see ...
CaroZ's user avatar
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1 answer
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What is meant by the stabilization of a receptor?

I am reading a journal paper, and have a question about the below statement: PSD-95 is involved in the recruitment, trafficking and stabilization of N-methyl-D-aspartic acid receptors (NMDARs) and α-...
ceno980's user avatar
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1 vote
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Is the 5% of the oxygen used in the breathing process fully transformed into CO2?

More specific, I found out that the amount of oxygen we inspire is 21% from the total amount, with 0.04% CO2. The expired amount is 16% oxygen, with 4% CO2. Where does the remaining 1% oxygen go? Or ...
me1234's user avatar
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1 vote
1 answer
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Why are camelid-derived nanobodies called VHH (variable heavy domain of heavy chain)?

Single-domain antibodies (or nanobodies) derived from camelid heavy-chain antibodies are called VHH antibodies, where VHH stands for "variable heavy domain of heavy chain". I assume the ...
mgarort's user avatar
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What is the optimal pO2 concentration for automated reactor batch mode EColi expression?

I am wondering what is the optimal pO2 level for an reactor based expression? All protocols I have found indicate for E.Coli pO2 levels just bigger 20%. So, I am wondering what is the optimal level? ...
raptorlane's user avatar
1 vote
0 answers
141 views

Can you store 5% BSA, in TBST, in -20C?

I have stock solution of 5% BSA prepared in TBST I use to make primary antibody dilutions for western blot. I'll admit I just assumed -20C, with freezing and thawing as needed, was an acceptable means ...
Tom Murphy's user avatar
0 votes
0 answers
111 views

How many GTPs are used in prokaryotic translation?

Here is the question: How many GTP are necessary to synthesize 2 linear peptides of 11 amino acids each using an in vitro prokaryotic system? Assume the tRNAs provided are already loaded with their ...
ninja_fun's user avatar
0 votes
1 answer
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Why doesn't treating neurons with a high sodium solution depolarize their membranes?

I am reading a journal paper, and in one of their experiments they treated organotypic hippocampal slice cultures with a high potassium solution to depolarize the neuronal membranes: We found that ...
ceno980's user avatar
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3 votes
1 answer
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Can a person have different sex at cellular level?

I mean like every cell has a sex chromosome.So does a male with XY chromosomes has all the cells in all the organs inside his body of XY chromosomes only? And vice versa.....
PAWAN's user avatar
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1 vote
2 answers
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Storing bacteria in a dry, room temperature long-term storage whilst maintaining viability

I'm quite new to biology, but I'm wondering if there are any methods of storing bacteria in long-term, dry conditions with no climate control. Perhaps they could be dormant in a powder or granule-like ...
Lee's user avatar
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1 answer
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How come SSBPs in RPA don't bind primers?

I've started reading about the recombinase polymerase amplification (RPA). I'm learning that in RPA, recombinase enzyme binds to primers, then makes them anneal to the complementary target DNA strand, ...
Andrew Roots's user avatar
0 votes
2 answers
152 views

Does recombination occur in both chromatid of a chromosome with homologous chromosome? Or only 1 chromatid participate in crossing over?

A chromosome has two chromatids. In meiosis weather both chromatid participate in crossing over or just only 1 chromatid does? So, I am asking whether 1 turquoise and 1 purple chromatid participate ...
Amit Kumar's user avatar
2 votes
1 answer
500 views

Can humans metabolize D-malate?

Only the L-isomer is produced naturally, while racemic mixtures are produced synthetically and used commercially as food additives and energy supplements. So what happens when we consume D-malate? ...
ManRow's user avatar
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0 answers
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Is crossveinless in Drosophila melanogaster example of condition mutant or phenocarpy?

This is the original question - Ques - A researcher exposed Drosophila larvae to 37°C during their growth. One of the adult flies that emerged had a crossveinless phenotype. When this crossveinless ...
Deepesh Bhatt's user avatar
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1 answer
39 views

Induction of IFN-beta in HEK293T

I'm trying to increase expression of a protein we're attempting to study, UBL7, supposedly unregulated by Type I Interferon and particularly IFN-beta. I've tried treating HEK293T cells (~60% ...
Tom Murphy's user avatar
2 votes
1 answer
189 views

Why is the codon size three, rather than four? [duplicate]

The genetic code consists of triplets, each of which (apart from the stop codons) yields an amino acid when the mRNA is translated. But why did triplets evolve, rather than a longer or shorter codon ...
Mathew's user avatar
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4 votes
0 answers
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Does the molecules in nerve cell membrane change 100% during the life of the nerve cell?

In their lifespan nerve cells do not divide and so they stay the same. They do get damaged sometimes and require some maintenance and change their axons a bit. They also require a lot of energy so ...
Lauri's user avatar
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0 answers
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Ubiquitous overexpression line of a gene expressed higher gene expression in leaf but not in seeds

I tried to make ubiquitous overexpression lines of a gene using a constitutive promoter vector in plant. I got multiple regenerated plants through tissue cultures. At T0, T1, T2 leaves tissues, the ...
bio's user avatar
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0 answers
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Effects of oxygenated water on bacteria

I was curious if any of you would happen to have any experience with this but any hypotheses regarding how this would turn out would be much appreciated. I’m wondering if water fully aerated with ...
Jaston's user avatar
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5 votes
1 answer
654 views

According to an online course, ribose and adenine can bond to make ATP. Is this true?

I recently came across this question in the MIT Open Learning Library Pre-7.01 Biology Course. It is question 2d in Problem Set 1 (archived link). The question, as well as the correct answers and ...
Ben Zelnick's user avatar
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0 answers
31 views

Transfecting cocoon or chrysalis

Do you know whether anybody tried to transfect insects during their cocoon/chrysalis stage, and if so do you have a link to such studies? I was thinking it would be easier to do given that it's a more ...
TheChymera's user avatar
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391 views

Migration of cut vs. non-cut plasmid on gel

As you might know there are 3 common forms of a plasmid: ccc-form (CCC), being supercoiled. oc-form (OC), being nicked and therefore relaxed. linearized form (L), being cut on both strands and linear....
Felix H.'s user avatar
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