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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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1answer
38 views

Do different transcription factors attract different kind of RNA polymerase?

Initiation step of transcription is simply binding of RNA polymerase on the DNA strand and its activation by addition of a phosphate group onto it. Different kind of promotors are present close to ...
3
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0answers
51 views

Is there recent info about the hypothetical ancient two-codon genetic code?

Here is the latest I have found. link This is the basic idea: Evolution does not look ahead and make plans. It would not create a system of mRNA with giant ribosomes to create proteins, until ...
0
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1answer
58 views

How do Wikipedia users create the structure of proteins and peptides?

Recently I saw the structure of insulin on Wikipedia. And my question is that which software(s) or application(s) (I don't know the proper way to name it) do they use to create that picture of the ...
5
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1answer
226 views

Compare affinity to potency h1 receptor

This quote from Miller (2004) makes it clear that the affinity of drugs for the H1 receptor does not correlate to sedation: Although both dosage and affinity for histamine H1 receptors play a part ...
0
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1answer
266 views

Relative rates of migration of circular, linear and supercoiled DNA in agarous gel electrophoresis

I have read the supercoiled plasmid DNA migrates fastest when subjected to agarose gel electrophoresis and this makes sense to me because it is small and experiences the least friction because of its ...
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1answer
83 views

what is CpG coverage? DNA starting material?

referring to this quote from an article about predicting methylation states: "Because of the small amounts of genomic DNA starting material per cell, single-cell methylation analyses are ...
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0answers
30 views

How to perform TUNEL Assay for yeast?

Currently, I am working on yeast strain CEN PK and I want to carry out TUNEL Assay to detect the amount of damage upon treatment with some damaging agent. We have a kit in the name of TUNEL Assay Kit -...
2
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1answer
29 views

Expected bands in polyacrylamide gel

I have something in my notes that doesn't seem right. If I use restriction enzymes on a PCR product how many bands should I see provided I know the restriction enzimes will cut the DNA? If I use two ...
3
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0answers
48 views

Antibody staining

I am staining tissue sections and I did a mistake, I was supposed to have mixed 3 primary antibodies but I stained only with one of them. After the 1h incubation I washed 10 min with PBS and then I ...
0
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1answer
31 views

Calculation of extinction coeffcient of GFP

I want to convert the absorption of a protein into concentration. Hence ı need to calculate the extinction coefficient of the protein (GFP). ı found the formula (nTrp)5500+(nTyr)1490 on the internet ...
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0answers
30 views

Gases from breathing

It was brought to my attention my question isn't direct and simply written enough. Ok in an effort to simplify this question: Can I resuse exhaled nitrogen and supplement it with new oxygen only? ...
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0answers
17 views

How are siRNAs introduced to cells for RNAi experiments?

Specifically, can somebody explain how in-vitro transcription can synthesize siRNAs to conduct RNAi? I have been reading a number of research papers that discuss how to use siRNA and shRNA to conduct ...
1
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0answers
48 views

Can Programmable Cell Death (PCD) be engineered in a bacterium like E. coli?

I am reading a paper which says : Messages not received after a certain time can be considered lost, as bacteria carrying them will suicide. I even read some paper which says about PCD like this, but ...
0
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1answer
37 views

How do I reverse my insert within a plasmid?

I have a plasmid with: ...T7pro. -- RBS -- XBa1 cut site -- ProDpro. -- RBS -- AmilCP -- T -- Spe1 cut site -- T... How do I design primers to reverse the portion in bold, such that the T7 and ProD ...
2
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2answers
228 views

Advanced books about molecular biology and genetics

I'm finishing my third year of biochemistry and doing gene therapy practicals during the summer. I'd like to buy a book that describes flow of genetic information (transcription, translation, ...
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0answers
15 views

Preparation of DNA ladder

how to prepare working stocks of 100 bp and 1 kb DNA ladder supplied by promega? the pack that we purchased contains a 6X loading dye. thanks!
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1answer
66 views

Significance of Nissl bodies

What is the significance of Nissl bodies? How are Nissl bodies different from any other RER seen in any other cell of the body?
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0answers
29 views

Does vesicles fragmantation (fusion) during endocytosis require energy?

In the process of endocytosis, does the stage of fragmanting of the vesicle membrane to the cell membrane requires energy? I know that the disconection of the Vsnare and t-snare from the membrane ...
1
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1answer
43 views

What are the types of interactions in biological network (protein networks)?

In the KGML files, the types of relations between genes or proteins are precisely activation, inhibition, expression, repression, indirect effect, state change, binding/association, dissociation, ...
3
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1answer
45 views

Are longer and shorter DNA similarly charged?

A longer DNA molecule would have more phosphate groups, so it should have a greater negative charge, right? It was taught in my class that only terminal ends of DNA are charged and all the phosphates ...
3
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1answer
525 views

Why do bacteria use formylated methionine in the initiator tRNA, while eukaryotes do not?

Could anyone suggest an explanation for the evolution of this trait in bacteria? Does it confer any advantage? It is also exploited by immunity receptors of some eukaryotes for the recognition of ...
4
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1answer
104 views

What would be the fate of protein made from D-amino acids after ingestion by humans?

There are some natural peptides made of D-amino acids, rather than the L-amino acids normally found in nature. It is now possible to chemically synthesize artificial proteins made of D-amino acids. ...
0
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0answers
25 views

Highest yielding protein in E coli culture

Which protein can be isolated or over-expressed to the highest possible yield per liter of E coli culture. Or in other words, what is the easiest possible protein to express in a typical E coli ...
1
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1answer
152 views

We know archea and eukarya are more closely related but endosymbiotic theory says eukarya have evolved from prokaryotes, justify the statements?

I am confused if eukaryotes have evolved from prokaryotes then how are they more closely related to archea?
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1answer
75 views

Gene located on Which strand? Want reference. [duplicate]

Update: Initially my question (below) was appropriately marked as duplicate/overlapping with two other questions; This and this ; among them a specific part of an answer of the second duplicate/...
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2answers
69 views

How were genes located before the development of bioinformatics?

I would like to know the detailed procedure of how scientists in earlier time were able to locate genes like how we were able to locate Huntington gene in 1983?
2
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1answer
65 views

What does “Origin” mean in NCBI GenBank?

I'm having trouble determining what exactly is meant by the term "Origin" in this case. It is just before a 70 bp sequence that the page claims is a plasmid, but does not specify it to be what I ...
0
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1answer
447 views

Why are prokaryotic promoter sequences written 5' to 3', when transcription proceeds from 3' to 5'?

It seems that the promoter regions are written from the 5' to 3' direction. My lecture notes, for example, give the -35 and -10 promoter regions sequences like so: Wikipedia seems to agree, on their ...
0
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1answer
104 views

How are single-stranded binding proteins removed from the lagging strand during DNA replication?

The lagging strand, downstream of the Okazaki fragment, is covered in single-stranded binding proteins (SSBPs) during DNA replication. What is the mechanism which ensures that SSBPs are removed from ...
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0answers
27 views

How to relate different phospholipid structures with entropy?

Phospholipids can form different stuructures like micelles, liposomes and bilayer. How can I relate this with entropy? ie explain different these different shapes based on entropy knowledge.
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0answers
86 views

How does gram-negative bacteria use high molecular weight starch if the membrane is only permeable to small molecular weights?

So one of my question is: The outer membrane of a gram negative bacterium contains pores that allow only molecules with a molecular weight less than 1,000 to cross. What does this bacterium need in ...
2
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1answer
44 views

Why is there a carbon atom without a greek letter in protein residues?

For protein residues I know that $C\alpha$ denotes the first carbon atom attached to a functional group. Each subsequent carbon is given a corresponding greek letter ($\beta, \gamma, \delta$) except ...
0
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1answer
24 views

Mice that have been reconstituted with geneX-transduced cells

I read this article in the following: ... Mice that have been reconstituted with geneX-transduced cells Now, someone who is not familiar with animal sciences, what does this exactly mean? ...
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0answers
34 views

How can I render a protein non-functional to avoid problem during expression?

We're expressing a protein in a model organism for crystallization, however it seems the protein has some toxic effect on the cells. Is there something we can do to make it non-functional during ...
4
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3answers
177 views

Knockout and knockdown of gene

Out of curiosity, I got this question whether knocking out (deletion) of a gene on one side and knocking down (RNAi) of the same gene on the other side will affect the cell in a similar manner or not. ...
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0answers
64 views

Assignment help: Transcription and translation

I was almost sure I had the right approach to this assignment until I got a variation of answer. Please help to evaluate my approach. An E. coli promoter has the following consensus sequence (Figure ...
1
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1answer
101 views

What is the difference between alarmones and riboswitches

An Alarmone is an intracellular signal molecule that is produced due to harsh environmental factors. They regulate the gene expression at transcription level. A riboswitch is a regulatory segment of a ...
0
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1answer
49 views

Building microtubules [closed]

I have some questions regarding building microtubules: Do alpha and beta monomers always exist as dimers when they are bonding to form tubulin? When tubulin structure is destroyed, do alpha and beta ...
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1answer
31 views

Help understanding cell replication animations

I often come across these animations about molecular biology showing for example how cell replication works, how virus infection works etc. Take this video as an example https://www.youtube.com/watch?...
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What are the interactions between mtDNA and nucelus' DNA?

In an exam situation I have been presented with the following question by the teacher: What are the interactions between the mitochondrial DNA and the cell's nuclear DNA? To my knowledge there is ...
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0answers
18 views

Will the addition of 3 amino acids in the C-terminal of a membrane protein affects its properties?

I am planning to use 2A self-cleavage peptide to express my gene of interest downstream of an intrinsic gene in my model organism so that I can exploit the intrinsic promoter, instead of cloning it ...
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0answers
11 views

transcriptional modulators

Transcriptional modulators are shown to be significant in differential activation/deactivation of genes, my question is considering recent advances in molecular biology have all the specific ...
2
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2answers
153 views

Are molecular machines encoded in the DNA?

I don't know much, if anything, about molecular biology. I watched the "inner life of the cell" on Youtube which triggered my curiosity about how these molecular machines came to be. My simple ...
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0answers
46 views

Sucrose inhibit onion root mitosis? Why?

I am doing an experiment about onion root growing. I had put an onion in different solutions of $C_{11} H_{22} O_1$ in H2O —with the root touching the water—: 0,1M; 0,2M; 0,3M; 0,4M; 0,5M. The ...
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1answer
43 views

How does gene affect organs development in eukaryotic cells? [closed]

I'm totally new to biology and apologies if you find this basic. The central dogma insists that genetic information flows in this direction: DNA -> RNA -> proteins So far so good, it is very clear ...
4
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1answer
3k views

What is the role of potassium acetate in plasmid extraction?

What is the role of potassium acetate in the alkaline lysis method of plasmid extraction? Earlier I was thinking its role is to shield plasmid DNA (the same as sodium acetate in genomic DNA ...
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0answers
44 views

Yeast transformation: is it necessary to remove template plasmid from PCR?

I'm frequently transforming budding yeast with PCR fragments. Normally, after PCR I digest with DpnI to remove the template plasmid. DpnI is a restriction enzyme which cuts methylated DNA, i.e. the ...
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1answer
75 views

Why replication collapse but not stall leads to DNA break?

I have been looking into the concept of replication dynamics and was wondering why collapsing but not stalling leads to a DNA break.
3
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1answer
99 views

Is there any evidence that supports glycolysis in mitochondria or chloroplasts?

Glycolysis is known to be a part of cellular metabolism undergone by both eukaryotic and prokaryotic cells, whether under aerobic or anaerobic conditions. As the endosymbiotic theory states that ...
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0answers
25 views

Quantification of concentration from chromatogram paper [closed]

In an experiment, I recently isolated and purified calf thymus DNA, hydrolyzed it with perchloric acid, and then applied the hydrolyzate to a Whatman paper in a polar solvent and let it run overnight. ...