Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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10
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3answers
31k views

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 ...
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3answers
120 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.
-1
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1answer
1k views

basic programming and bioinformatics [closed]

As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work ...
0
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0answers
36 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 ...
15
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2answers
8k views

Why is there more variation in proteins than genes?

The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular). How do ...
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0answers
6 views

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 ...
2
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1answer
60 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 ...
2
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0answers
37 views

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 $x$ ...
1
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1answer
150 views

What is the difference between a signal peptide and a transit peptide?

From what I know, the two names are used interchangeably and I haven't found any resource which says otherwise either. Is there at all any difference, is there a transit peptide that is not a signal ...
2
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1answer
56 views

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 ...
2
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1answer
86 views

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, ...
2
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0answers
46 views

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 ...
6
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2answers
141 views

Why is Turner syndrome a problem?

Turner syndrome is a chromosomal disorder where one of the X chromosomes is missing. For more details visit the Wikipedia page I don't understand why missing one X chromosome would be harmful. In ...
0
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2answers
52 views

identification of differentially expressed genes in RNA-seq analysis [closed]

I am using four different packages (viz. EBSeq, DESeq2, edgeR, LPEseq) for identification of differential genes. Now I am confused whose fold change value should I take for further downstream ...
2
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1answer
39 views

Storage DNA Condition

It is possible to store a digestion of cells with lysis buffer several days at -20 degrees and then proceed with the phenol chloroform isoamyl purification?
1
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1answer
163 views

When should you use a stringent plasmid?

I was wondering if anyone had good examples of when you would want to use a stringent plasmid vs. a relaxed plasmid in a research setting.
1
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1answer
813 views

Has anyone used Crispr/Cas to induce a knock-in in MEF cells?

Does anyone have experience with the CRISPR/CAS9 platform performed on MEF? Or does anyone recall any relevant articles?
2
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2answers
121 views

Storage of bacteria

Why are strains of bacteria stored when they are inactive (frozen)? What is the problem with storing growing cultures for long periods?
0
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1answer
57 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 ...
2
votes
1answer
42 views

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 ...
0
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0answers
13 views

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) ?
2
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1answer
78 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 ...
0
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0answers
15 views

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?
4
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1answer
61 views

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 ...
-1
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1answer
48 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 ...
0
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1answer
22 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 ...
3
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1answer
107 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 ...
1
vote
1answer
38 views

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 ...
0
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0answers
20 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 ...
0
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0answers
44 views

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 ...
1
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2answers
74 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 ...
0
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0answers
14 views

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 ...
1
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1answer
74 views

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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0answers
15 views

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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0answers
18 views

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 ...
1
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3answers
118 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 ...
5
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3answers
109 views

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 ...
5
votes
2answers
239 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 ...
2
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0answers
30 views

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 ...
2
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0answers
18 views

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/...
0
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1answer
48 views

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 ...
0
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0answers
19 views

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 ...
8
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1answer
212 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 ...
27
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3answers
1k views

How, on a physical level, does ATP confer energy?

When ATP is used as the energy currency to make, say, reaction X + Y → Z happen, is what happens on a physical level down at the molecular scale that during the reaction ATP + H2O → ADP + Pi  &...
0
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1answer
29 views

How to confirm secondary structure formation of Precursor miRNA on gel?

I want to fold precursor-miRNA into its secondary structure and then confirm it on gel. At first, I heat it in annealing buffer at 95°C for 5 minutes and cool down slowly. Then I run it on gel but the ...
3
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0answers
36 views

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 ...
0
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0answers
16 views

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 ...
11
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2answers
1k views

Do antibiotics attenuate immune response on subsequent exposure to same bacteria?

A healthy immune response to a bacterial infection includes "memory" to permit the body to thwart subsequent exposure to same bacteria. What are the dynamics of using antibiotics on initial exposure ...
6
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1answer
4k views

Why AZT is selective towards HIV and doesn't impair human DNA replication?

I've found this article, which is a very old one (from the time when nucleoside analogs where researched as a possible way to prevent replication of virus genetic material, before the HIV epidemics). ...
0
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1answer
88 views

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 ...