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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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129 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 ...
-2 votes
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19 views

What could be the components of the ddPCR mix here, and what is the meaning of VIC FAM HEX?

Can someone please explain me the procedure shown in this diagram?
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20 views

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 &...
-2 votes
0 answers
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Setting up lab at home [closed]

I'm considering doing some plant bioengineering at home for fun. From what I have read, the most dangerous part is the usage of Agrobacterium. I saw another thread (Is it possible to genetically ...
13 votes
1 answer
203 views

What actually kills a plant that requires winter dormancy if it is kept indoors all year?

In bonsai practice, beginners will commonly purchase a juniper (often Juniperus procumbens 'Nana'), which is an outdoor tree, and keep it inside all year. The tree invariably dies. It is commonly ...
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How much data to expect from metabarcoding? [migrated]

I am about to conduct my first metabarcoding study. We will be using the ITS amplicon to look at fungal community composition in soil samples. I need to write a data management plan before I actually ...
1 vote
0 answers
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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 ...
7 votes
2 answers
86 views

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 ...
-1 votes
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Need help choosing a plasmid that induces increased trehalose and glycerol production in yeast

I wanted to know how I should go about choosing a plasmid that increases trehalose and glycerol production in yeast or if anyone had any ideas on suitable plasmids.
3 votes
1 answer
66 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 ...
3 votes
2 answers
124 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 ...
1 vote
1 answer
47 views

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 ...
1 vote
0 answers
44 views

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 ...
4 votes
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66 views

Is blood typing still useful for analysis of ancient tissues?

Modern techniques. In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be extracted ...
13 votes
1 answer
2k views

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 ...
1 vote
1 answer
48 views

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-...
1 vote
1 answer
33 views

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 ...
2 votes
1 answer
98 views

Why are multiple copies of the 35S enhancer used for overexpression in plants?

I know that the CaMV 35S promoter is widely used for transgenic plants, where it acts as an enhancer element for constitutive overexpression. I noticed that it is always used as a tandemly repeated ...
2 votes
1 answer
314 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 ...
3 votes
1 answer
72 views

Use of plasmid pXen5 for transposon screening

I would like to use the plasmid pXen5 (by Xenogen) for a transposon screen. It contains two inverted repeat sequences, with Luciferase, Kanamycin, and the transposase itself in between. (It's tn1409). ...
0 votes
2 answers
103 views

Can Cas13 be used with multiple crRNAs in the same reaction?

CRISPR-Cas13 equipped with crRNA (complementary to transcripts of interest) can be designed to target ssRNA transcripts in cells. Upon successful crRNA and ssRNA binding, a fluorescent domain on ...
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1 answer
82 views

What should be considered a GC clamp in a qPCR primer?

Hello there! After reading different sources regarding designing of qPCR primers, I'm a little confused regarding the concept of GC clamp. Can you help me by telling which of these cases below is ...
2 votes
1 answer
52 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 ...
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42 views

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 ...
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15 views

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 ...
0 votes
1 answer
44 views

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 ...
2 votes
1 answer
53 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 ...
1 vote
1 answer
39 views

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 ...
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 ...
3 votes
3 answers
436 views

why does translation occur more frequently than transcription?

In our textbook it says that translation occurs more in a cell than transcription but I couldn't find anything that explains why it happens
1 vote
2 answers
49 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 ...
28 votes
2 answers
10k views

What determines which strand of DNA is transcribed by RNA polymerase?

DNA has two strands. How does the machinery of RNA transcription determine which one to transcribe?
2 votes
1 answer
56 views

Protein half-life regulating gene expression

Are there any instances in real life of protein half-life regulating gene expression? For example, in a cell, Gene A produces a starting population of protein P, after which the expression of the gene ...
0 votes
1 answer
29 views

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 ...
3 votes
2 answers
132 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 ...
0 votes
1 answer
108 views

What is the approx. diameter of a completely "folded up" human DNA molecule, in inches?

The human DNA molecule would be about 6ft if stretched out to a straight line. I'm curious what the diameter of the DNA molecule normally is when it is "all scrunched up" or "bundled&...
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0 answers
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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 ...
1 vote
1 answer
54 views

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-...
2 votes
1 answer
113 views

Sucrose inhibits onion root mitosis? Why?

I am doing an experiment about the growth of onion roots. I put onion plants in different solutions of sucrose in water — 0.1M, 0.2M, 0.3M, 0.4M, 0.5M — with the root touching the water. Measurements ...
1 vote
1 answer
50 views

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 ...
0 votes
1 answer
78 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 ...
1 vote
1 answer
95 views

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 ...
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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? ...
1 vote
0 answers
87 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 ...
5 votes
2 answers
678 views

How can one create images like those in the PDB ‘Molecule of the month’?

I am impressed by the illustrations for the Protein Data Bank ‘Molecule of the month’, e.g. the gorgeous image of DNA Helicase below. Does anyone know how they were made or how one might create ...
50 votes
4 answers
9k views

What is the longest-lasting protein in a human body?

Protein life times are, on average, not particularly long, on a human life timescale. I was wondering, how old is the oldest protein in a human body? Just to clarify, I mean in terms of seconds/...
0 votes
0 answers
98 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 ...
2 votes
2 answers
3k views

What is the difference between a response element and a enhancer?

I have been confused as to the difference between a response element and an enhancer. Wikipedia has the definition of response element as the following: Response elements are short sequences of ...
3 votes
1 answer
128 views

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.....
0 votes
1 answer
43 views

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 ...

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