Questions tagged [molecular-biology]
The study of the molecular processes underlying life.
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Human Stem Cells and Disease
Can human stem cells be stored for use by future family members as a way to combat generational diseases like diabetes
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Intein Splicing
Currently I am trying to read and understand this paper on intein splicing.
https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/22001202
However, I'm a little confused with Figure 4.
Why do the ...
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RNAi termination
Can you stop an ongoing RNAi after transfection with a vector containing siRNA?
I want to experiment on gene function loss effect, using RNAi, and gene function gain, using stopping the RNAi.
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Is it possible to stop more/extra fat from being stored in the body?
I don't mean simply by restricting eating or upping the activities, but a way to basically stop the body from adding more fat on itself down on the bio level. For example, I'm not too knowledgeable on ...
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How can MMLV reverse transcriptase add cytosines to the 3'-end of cDNA
I am working on the mechanism of SMART, a kind of reverse transcription strategy.
However, I am confused about the terminal transferase activity of MMLV enzyme.
It have been reported since 1998, ...
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1answer
163 views
Why did they expect Astronaut Scott Kelley's telomere shortening to accelerate? (they got longer!)
The NPR News article and podcast Scientists Share Results From NASA's Twins Study says:
SCOTT KELLY (NASA Astronaut): You know, the symptomatic stuff is fine. I don't have any long-term negative ...
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1answer
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Spatially Encoded GPCRs?
I'm reading this paper, and I'm already lost in terms of what they mean by GPCR signaling is spatially encoded.
How can signaling be spatially encoded?
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2answers
59 views
What is a “pan-specific” antibody?
I am new to biology. I searched a lot to find an article that explains what "pan-specific" antibody is but I could not find anything substantial that would help me understand what it is.
An example ...
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Rhodamine 123 Staining Function
How does Rhodamine 123 act as a probe for Mitochondrial Staining? What is the Exact Biochemical Basis? and can it Stain Chloroplast as well?
Thanks in Advance
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Gene cluster of interest not being amplified in PCR
In a lab, I currently have a sample of Rhizobium sp. NT-26. This bacteria is a chemolithoautotrophic arsenite-oxidizer, and I want to clone the arsenite oxidase genes into another bacteria strain in ...
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Can sperm cells penetrate the cell membrane of non-ovum cells?
Sperm cells have tiny bags of enzymes on their tip (the acrosome) which allow them to penetrate the ovum. My question is whether or not the process that allows sperm cells to penetrate the cell ...
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What is a secretion target family protein?
I came across this link: https://www.genome.jp/dbget-bin/www_bget?btw:BF38_3398
What is this protein, is it a secreted effector protein or is it something else?
What is the difference between type ...
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Why are Barr Bodies usually seen along the edge of the nucleus under the light microscope?
We do a typical class exercise of aceto-orsein staining of buccal epithelial cells from female students to visualize Barr bodies under the light microscope. All the illustrations and pictures in the ...
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How to detect specific mRNA dsRNA by Northern analysis?
I silenced a gene by RNAi method, for that i chose the gene and the size of the gene is 1.5kb and my insert size is 500nts. i did the transfection and i want to confirm the silencing by northern ...
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What is the frequency of AUG near-cognates (as start codon) in ‘Leaderless’ mRNA?
In typical bacteria that use SD-dependent translation initiation, the AUG start codon may sometimes be replaced by near-cognates (GUG, UUG, etc.). The frequency of these near-cognates is somewhat ...
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Is there other unknown-compound in Blood?
Blood is made of red blood cells, platelets, plasma etc. Let's say, then, there are these $x$ known compounds in blood.
But how can one be sure that there is no other compound other than those $x$ ...
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1answer
29 views
Relationship between the ambiguity (wobble) at codon position 3 in elongation and codon position 1 in initiation
In prokaryotes the usual observed start codon frequency is AUG > GUG > UUG.
An explanation for this is that
AUG is the most common initiator codon because it forms the most stable interaction with ...
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3answers
91 views
Why are there three stop codons but only one start codon?
I was wondering whether there is any specific reason that there are three stop codons but only one start codon in prokaryotic and eukaryotic cytoplasmic mRNAs.
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1answer
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How are primary monoclonal antibodies for screening mutant cells made, physically?
I'm working with a fairly common protein expressed in a large numbers of organisms, let's say a keratin-associated beta-protein. I'm trying to develop a process which requires primary-secondary ...
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What regulates cyclic AMP?
After reading a textbook chapter on GPCRs I am still confused by what regulates cAMP.
I took in my notes that cAMP is made by adenylyl cyclase and destroyed by cAMP phosphodiesterases (also another ...
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1answer
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What is meant by “heads” and “tails” in the context of gene orientation?
I have a hard time understanding what this paper is talking about when it says:
We observed maximal cleavage at sites oriented tail-to-tail and separated by -10 bp to +30 bp (Fig. 2d). Finally, ...
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1answer
55 views
How do biologists discover information from fossils? [closed]
I have a query about the study of fossils (palaeontology). Let me know about the study of fossils. How do biologist discover "DNA" information from dead and old fossils such as a dinosaur? (answer ...
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What is the structure of DNA during Interphase? Chromatin Fibre or Beads on a string(nucleosomes)?
During Interphase, does DNA predominantly exist as Chromatin Fibre (30nm fibre) or Chromatin/beads on a string structure(10nm) ?
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1answer
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Why does 4-thiouracil labelling to map RNA-binding proteins cause a T-C change?
I am now reading a paper about the purification and identification of mRNAs and its RNA binding proteins by using UV crosslinking and immunoprecipitation. I came upon this sentence which puzzled me
...
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the Oxidization reaction of NADH [duplicate]
Does oxidization of NADH need H+?
I've seen a reaction like this👇
NADH + H+ >>>> NAD+ + 2H+
What's the use of the proton in here?
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1answer
32 views
Approximate Cell Doubling Time?
If I know it takes 12 min to occur in mitotic fibroblast cells and I count there are 32 dividing cells in the microscope slide out of a total population of 32034 cells, how do I calculate the ...
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1answer
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What chemical test can be used to tell apart meat and plant-based meat?
Long story short, I thought about this question and simple Google searches weren't enough. I know there must be some nutrient that can only be found in one of the meats but not the other, but I can't ...
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1answer
19 views
Measuring transgenic gene expression with a microplate reader
I have been working on genetically engineering an E. coli strain to autotrophically oxidize arsenite into arsenate for bioremediation of arsenic contamination in groundwater. For my research, I have ...
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1answer
44 views
What impedes the understanding of genotype/phenotype relationship without statistics? [closed]
Most genetic research tries to establish a relationship between a certain genotype and certain phenotype.
To me this is like trying to understand a system as a black box, where you try to establish ...
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20 views
Can Dpn1 digest hybrid PCR product with only one methylated strand?
In Site directed mutagenesis using PCR, after a cycle we obtain a hybrid molecule with one parental strand and other newly synthesized unmethylated strand. This is followed by Dpn1 digestion. Does ...
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1answer
99 views
How to interpret this PubChem record of L-Alanine
Using the PUG service from NCBI, I am retrieving 3d structure data for a molecule.
Raw data here.
I am trying to understand this record, specifically for the purpose of rendering in a 3D coordinate ...
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0answers
16 views
Why both forward and reverse primer are added in asymmetric PCR?
If the purpose of Asymmetric PCR is to amplify single targeted strand of dsDNA then instead of adding just one primer for targeted strand why do we add both forward and reverse primer? Upon addition ...
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What is the electric field strength of microalgae?
Question: What is the electric field strength of microalgae?
Background: So I have been having some problems with fungi contaminating my chromera velia algae cell cultures. I haven't determined what ...
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1answer
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Where do the lysines come from during ubiquitination?
I know that Ub forms an isopeptide bond with lysine, but where do the lysine come from?
Are they just always available for the Ub to find to during the ubiquitination process? Is there a free lysine ...
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What proteins are assisted by chaperone folding?
I've been looking into a lot of papers, and most say that chaperones assisted in the folding of misfolded proteins, or Ubiquitin markers aggregates for degradation by the proteasome. Or it will say ...
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2answers
63 views
Why are restriction sites palindromic in nature? [duplicate]
Any restriction site given in any fragment of DNA or vector molecule is a palindrome. eg restriction site for the endonuclease EcoRI is
...
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Cadmium Poisoning and Toxicity Mechanisms
Is anyone aware of the toxic mechanisms of specific instances in which cadmium ions can interfere with cellular functions resulting in acute cadmium poisoning?
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1answer
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How do you dilute forward and reverse primers for a master mix?
I apologize for the very naive question, but I'm just starting out in a high school biology lab and I am very confused.
If I have stocks of 100μM for forward and reverse primers separately, I can ...
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Toxic Metals and Oxidative Phosphorylation
I was reviewing the toxicity of certain toxic metals, specifically cadmium and their effect on Oxidative Phosphorylation and Cellular Respiration, I have found that metals such as cadmium inhibit ...
2
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0answers
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If bacterial plasmid DNA is methylated then how do we digest it using restriction enzyme in cloning experiments? [duplicate]
So, I was reading about how bacteria protects its own DNA by methylation against restriction enzyme. But if the plasmid DNA is also methylated then we can't cut plasmid using restriction enzyme for ...
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3answers
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Double Digestion with Restriction Enzymes Using Different Buffers
I am currently working on preparing a 9 kb sequence of DNA for restriction digestion into the pBAD30 expression vector. There are very few restriction enzymes that do not have a restriction site ...
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0answers
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Using expression vector to express arsenite oxidase genes in E. coli
So I am trying to express a gene cluster that can oxidize arsenite into arsenite autotrophically. The arsenite oxidase gene cluster sequence is linked here: https://www.ncbi.nlm.nih.gov/nuccore/...
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3answers
113 views
Is oxygen's paramagnetism biologically relevant?
It seems our most common everyday O2 molecule happens to be a paramagnetic one (see https://en.wikipedia.org/wiki/Oxygen).
But, does this have a biological relevance as well? In other words, Do any ...
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How does Hayflick limit relate to cellular senescence
If the Hayflick limit says that there are a maximum of around 60 cell division before a cell becomes senescent, I assume this is because the cell looses length of telomere. But how can this be if, for ...
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1answer
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Is there a data base, tool or method I can use to find out which of my genes code for cytokine receptors?
I have a list of over 600 differentially expressed genes from my single cell RNA seq data analyses. I want to proceed to find out which of my genes code for cytokine receptors so that I can show on a ...
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1answer
200 views
Do chaperone proteins misfold?
If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones ...
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1answer
66 views
Must I HPLC-purify my PCR Primers for amplicon sequencing with PacBio SMRT?
I would like to order some primers for amplicon sequencing. I am using universal tag primers (unusually long 30-mers recommended by PacBio for SMRT, both F&R) + barcodes (16-mers). The resulting ...
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Are there any natural cases of direct translation of DNA to protein? [duplicate]
I'm aware direct translation of DNA to protein (without the need for RNA) has been observed in test-tubes using e-coli. (Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC219759/)
I wanted to ...
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How would you use PGAl to select for mutants of beta galcodosidase gene (z-) and permease (y-)?
How would you use PGAl to select mutants of beta galcodosidase gene (z-) and permease (y-)? Or do you just use PGAL to grow these mutants after you've isolated the mutant gene and inserted it into a ...
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1answer
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What is the overall end result of proteins and enzymes binding together? [closed]
My rudimentary understanding is...
a gene gets transcribed to mRNA
that mRNA is sent off to the ribosome
that ribosome pumps out whatever proteins are coded by that gene
each protein floats around in ...
