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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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How to map the N6-dimethyladenosine by primer extension?

I am trying to map N6-dimethyladenosine on rRNA using primer extension (low dNTPs assay) method. But i am not able to detect map my position. I went through some articles they mentioned like they ...
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Insight on HPV vaccine to prevent/control reactivation of latent infections in those already infected

Some women experience reactivation of HPV infection in their 50's due to weakened immune system and weakened immune memory. Is it outside the realm of possibility that giving the HPV vaccine to those ...
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Protein misfolding

Protein misfolding is usually prevented by molecular chaperons. Rarely, the chaperons are not able to prevent the misfolding as a result of which the infectous molecules called prions will form. My ...
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Could Wobble Base Pairing ultimately yield an amino acid that was originally uncalled for or not expected?

For the purpose of this question I'm picking UGC, UGA and UGG codons (Cys, Stop and Trp aa's) so that the 3rd position of the codon really makes a difference (if it does). I know there are other ...
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In HIV-1, what produces Tat?

The Trans-activator of transcription (Tat) plays a crucial role in regulating the transcription process of HIV-1. But which state of the Long Terminal Repeat (LTR) produces Tat? Is it the "...
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Do molecular motors have a life time?

Most of the enzymes have a certain lifetime. I want to know that do molecular motors have a certain lifetime after which they degenerate? Any reference will be appreciated. Basically, I just want to ...
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If there is a list of all major bioactive compounds on the web

There are many databases of every molecule we've discovered, but I haven't seen just a list of the major bioactive compounds, which would be helpful for better understanding what chemicals have an ...
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what is ideal dose of peptide injection for mice? [closed]

What would be ideal concentration of 15 amino acidic antibacterial peptide and water (or buffer)? Injection rout is tail vein of mice and peptide is synthetic.
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57 views

Does the lack of “mirror life” tell us anything about abiogenesis?

My (extremely rudimentary) understanding of Biology is that many of the building blocks of life are chiral and that life on earth is entirely made up molecules with the same chirality. Does this ...
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Why magnesium ion is needed for activity of G-proteins?

I was studying about G-protein coupled signaling sysytem, somewhere they have mentioned about need of Mg$^{2+}$ for acticty of G-protein and related it to increase of cyclic AMP production. On further ...
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51 views

What is the difference among biochemistry, molecular biology, molecular genetics and structural biology?

I have never heard of straigthforward definitions of these fields in my college lectures, and the Internet searches were not very helpful. However, from what I have learned at different subjects, this ...
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Immunoprecipitation compared to western blotting

Immunoprecipitation and western blotting are both used to locate a specific protein within a sample and to isolate it. In immunoprecipitation, a specific antibody and agarose beads ( or other ...
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Endocytic pathway: Macropinocytosis

So I'm trying to understand this phrase: Unlike other endocytic pathways, macropinocytosis is acutely induced by growth factors From the following paper The 4 endocytic pathways I know of are ...
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why transcription error rate is high than that of dna replication

The error rate of RNA polymerase is observed to be pretty high about 1 in 10^4 than that of DNA polymerase which about 1 in 10^7, why?
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Is NMDA produced in the body?

On the wiki page for NMDA it says that NMDA is a synthetic substance that mimics glutamate. So why does the body not use glutamate instead of NMDA? Also how is it possible that our body can produce ...
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1answer
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Emergence of novel protein interactions by mutation of amino acids

Are there any examples of proteins that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other protein ...
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Does the molecular composition of human body change after a period of time?

I was discussing change in human biology over time and my two in-laws charged in saying, "we're molecularly different after x". I didn't pay attention to what time period they exactly mentioned (hence ...
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1answer
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When are neuropeptides loaded into vesicles?

It is well known that small neurotransmitters like monoamines (dopamine, serotonin, etc), acetylcholine, glutamate, etc are loaded into vesicles at the axon terminal. Stated differently, synaptic ...
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Techniques of molecular medicine/biology for aesthetic medicine?

Are there scientifically valid methods (possibly in the developmental stage) that can be used for aesthetic medicine. Usually surgical of physical therapies are used for aesthetic medicine, but ...
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What phosphorylates tau protein & and what causes tau to be phosphorylated?

I want to know what phosphorylates tau protein and its 6 isoforms. I know kinases cause phosphorylation events, and in tau it can be phosphorylated in a healthy neuron in the trans conformation, but ...
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Molecular biology [duplicate]

Does every protein start with methionine? The start codon is AUG (which corresponds to methionine),then why doesn't the methionine present in the protein after the translation has done. I have ...
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25 views

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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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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2answers
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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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2answers
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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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34 views

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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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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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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56 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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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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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
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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
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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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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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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 ...