Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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Is the lac operon repressed in the presence of both glucose and lactose?

In the presence of both sugars (glucose and lactose) will there be repression of the lac operon completely? I know that more glucose means less cAMP --> less CAP --> less positive regulation, and ...
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2answers
149 views

Why are dietary recommendations for methionine consumption combined with cysteine?

I want to understand the amino acids missing in certain vegetables. I looked up the US recommendations for amino acids (source: wikipedia). I don’t understand why they pair Methionine + Cysteine: ...
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Ligation without purifying insert

I am planning to insert a 45 bp sequence in a vector. After restricting my insert to create compatible sticky ends, I am finding no way to clean it up. Is there any way for cleaning this fragment ...
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How are multiples transmembrane proteins translocated or embedded in the membrane?

This image is in the textbook, Molecular Biology of the Cell. I understand why the start and stop transfer sequences must alternate, but why is there 2 consecutive start transfer sequences at the N ...
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3answers
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What does the gene name “lexA” stand for?

It is an important gene expressed in E. coli that represses the SOS response and also the expression of lambda lytic phase genes. UV light and damage to DNA is responsible for its breakdown and hence ...
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What is the typical concentration of Calcineurin (PP2B) in CA1 dendritic spines?

I am trying to find the concentration of CaN (PP2B) in dendritic spines, there is a computational model (doi:10.1073/pnas.0804672105) that uses the quantity of 1uM in the dendritic spine. I think this ...
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25 views

Could Wobble Base Pairing ultimately yield an amino acid that was originally uncalled for or not expected?

How does the cell choose which amino acid to attach to tRNA when there is wobble base pairing involved (not the other way around)? Consider the example below. For the purpose of this question I'm ...
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1answer
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What is the difference between DNA vs RNA Editing in the context of gene therapy?

As a someone with beginner knowledge on biology, I have come across the terms "RNA editing". Take this paper for example : RNA Editing with CRISPR-Cas13 From my understanding, DNA -> RNA -> Proteins ...
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38 views

Why do NK cells not destroy bacteria, even though bacteria don't have MHC-I?

Part of the function of NK cells is to destroy cells that are unable to bind their KIR receptors. Or in other words, cells that don't express MHC class I. This is why they can kill MHC supressed ...
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1answer
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Dna based question [duplicate]

We know that dna is an acid which is elaborated by deoxyribo nucleic acid.It has 4 nucleo bases.Now,the question arises, why dna has no uracil base?
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Can a lentivirus expressed protein that is undetectable by western blot be detected by BioID?

Cloned a single herpesviral gene into pCDH-EF!-GFP and see phenotypic effect on cells of interest and viral gene transcripts BUT unable to detect ANY protein using HRP boosted western blot. Even with ...
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Need help in identifying and understanding the origin of an expression variant

We usually denote the origin of a mutation as either somatic or germline. This information is usually available in certain databases such as CIVIC, ClinVar, COSMIC etc. But when we come to variants ...
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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 [closed]

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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3answers
550 views

Getting PCR amplification at annealing higher than Tm!

I am amplifying a gene where in a gradient pcr i am getting amplification at an annealing temperature about 5 degrees (67) higher than Tm (62.5)? What is wrong here? Also, I am getting a very strong ...
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2answers
637 views

Are all genes transcribed in differentiated cells?

My textbook tells me that it’s specific transcription factors that allow for a different set of genes to be expressed in different cells (differential gene expression). My book gives the example of ...
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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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36 views

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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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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1answer
67 views

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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1answer
59 views

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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1answer
41 views

Design rules for DNA linkers

I want to use double stranded DNA linkers to physically bind two "things" together, by grafting ssDNA on each one of them and using DNA hybridization as the locking mechanism. I do not expect the ...
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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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Can cysteine alone change pigmentation?

According to this graph (from here): cysteine contributes to pheomelanogenesis, and having a high enough concentration of cysteine makes the shift towards pheomelanin instead of eumelanin. So my ...
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4answers
277 views

How to find suitable qRTPCR reference gene for a inflammatory response experiment?

I have tried several housekeeping genes – Hprt, β-actin and GAPDH, to analyze the relative expression of a cytokine for measuring the inflammatory local response in mice ears. However, all ...
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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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Will DNA nanostructures be useful for medical applications?

There is a lot of work being done on developing small nanomechanical structures and even small nanomechanical actuators built with DNA. I have heard researchers motivate this research with claims ...
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What is an acceptable qPCR efficiency when adjust using the Pfaffl equation?

I have efficiencies of 76% and 85%. THis is clearly below what is normally acceptable. But the pfaffl equation corrects this, doesnt it? However is it acceptable to publish this data?
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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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27 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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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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1answer
2k views

Can mRNA be used by ribosomes more than once?

Can mRNA be used by ribosomes more than once? I mean can mRNA be translated more than one time? If not what will happen to it after translation?
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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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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 are some genes dominant over others? What is the mechanism behind it?

If I have a brown eye gene which encodes the protein that is responsible for the brown color and have a blue eye gene as well, what is the reason that my eye color is brown? How does one gene maintain ...
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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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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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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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1answer
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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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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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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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Why is AUG the initiation codon?

Is there any reason why AUG is the initiation codon? Can’t translation start with different codons?
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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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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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What's the difference between shotgun sequencing and clone based sequencing?

In a lecture during my undergraduate degree we were introduced to the race to complete the human genome. Celera were competing with Sanger and collaborators to sequence the human genome. Celera ...