The study of the molecular processes of the nucleus and cell function.

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27
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4answers
521 views

Why are amino acids in biology homochiral?

Why are nearly all amino acids in organisms left-handed (exception is glycine which has no isomer) when abiotic samples typical have an even mix of left- and right-handed molecules?
23
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4answers
482 views

How are the boundaries of a gene determined?

What statistical processes and methods are used by geneticists/molecular biologists to know where one gene starts and one ends?
20
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1answer
475 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 ...
19
votes
1answer
373 views

Regulation of chromatin structure

Recently, I reviewed the different levels of chromatin structure. The primary level is nucleosomes, where DNA is bound to histones, and has structural similarity to "beads on a string." The secondary ...
17
votes
3answers
909 views

How long can I store extracted RNA?

If I extract RNA from a (leaf tissue) sample using a one-step phenol:chloroform extraction, how long can those samples be stored at -80°C? And how many times can I defrost and refreeze them before ...
16
votes
3answers
1k views

How and where, in the human brain, are memories stored?

Background I am a computer programmer who is fascinated by artificial intelligence and artificial neural networks, and I am becoming more curious about how biological neural networks work. Context ...
16
votes
1answer
639 views

ATP cost for gene expression

How would you estimate the number of ATPs required to transcribe, export and translate a single eukariotic protein?
14
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6answers
1k views

Online Molecular and Cellular Biology Video Lectures?

I am looking for video lectures to go through to guide my reading in intro molecular and cellular biology. I've had intro bio and I study evolutionary theory, but my molecule- and cell-level knowledge ...
13
votes
2answers
461 views

Intrinsically disordered proteins as potential drug targets

Intrinsically disordered proteins (IDPs) are a class of proteins that do not adopt a stable secondary or tertiary structure under physiological conditions in vitro, but still have biological ...
13
votes
1answer
193 views

What is the prehistory of amino acids in cells?

As a followup to Why 20 amino acids instead of 64? and What is the smallest number of amino acids required for life?, I am trying to understand the prehistory of amino acids in cells. All living ...
12
votes
1answer
762 views

What did Richard Feynman contribute to molecular biology?

Some time ago, I read James Gleick's "Genius: The Life and Science of Richard Feynman", a wonderful biography of Feynman and, by extension, most of modern physics. In this book, the author mentions ...
10
votes
3answers
2k views

How long can E. coli stocks be stored at -20°C?

I'm volunteering for a biohacker lab - biocurious in Sunnyvale. The have a pretty good set of equipment - gel boxes, incubators, but they don't have a -80°C freezer yet. I'd like to set up some ...
10
votes
2answers
712 views

Why are restriction enzymes not frozen?

We all know restriction enzymes are proteins, but we never freeze them. They are instead provided in high glycerol containing solutions by companies and stored at -20C. Is there a reason why this is ...
10
votes
2answers
306 views

What is the highest competency possible for E coli?

I am looking to find a highly competent E coli strain. I am making a library of a ~6.6kb plasmid and I am not getting high enough efficiency. Does anyone have a suggestion of a strain/protocol with ...
10
votes
2answers
4k views

How do I clean phenol contaminated RNA without losing any of the sample?

I recently extracted RNA from developing plant leaves for the first time, as part of a very long and intensive experiment. The samples were extremely precious because of the amount of effort that went ...
10
votes
1answer
1k views

Is the eukaryotic nucleus composed of a single or double membrane?

I know that it is usually considered a double membrane like those surrounding mitochondria and chloroplasts, but I read a review that stated "according to topological details it is actually a single ...
10
votes
1answer
311 views

What is the functional and structural distinction between core (H2A, H2B, H3,H4) and linker(H1/H5) histones?

Many explanations of histone biochemistry isn't quite elucidating for the undergraduate student. How does histone structure (dimers, octomers) relate to their specific functions as core or linker ...
10
votes
1answer
2k views

How does translational coupling work in prokaryotes?

Today I heard about a phenomenon called "translational coupling", where the translation of one protein influences the translation of another protein. The messenger RNA levels don't seem influenced. ...
10
votes
1answer
884 views

How is Taq polymerase produced?

I've seen Taq polymerase being marketed as either "native" or "recombinant". I understand that the recombinant version is produced by specially modified Escherichia coli strains that have the gene for ...
10
votes
1answer
103 views

When running a gel, what could cause a standard to run “faster” than usual?

We are running a gel on the products of a restriction digest to determine the size of an insert. We know the vector backbone size should be ~2.9kb; however, the standard appears to be running too ...
9
votes
3answers
1k views

Why some genes are dominant to each other? 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 either, what is the reason that my eye color is brown? How does one gene ...
9
votes
2answers
14k views

Why is SOC medium recommended for transformations?

In pretty much every transformation protocol I've seen SOC medium is used to grow the bacteria for a short while after the tranformation and before plating. I've usually substituted LB medium for ...
9
votes
2answers
154 views

What is the least costly method to generate sequential amino acid deletions?

I'm looking to generation sequential deletions from a gene of interest. The total size of this region is 8 amino acids. I'm trying to determine which portion of this region is necessary within the ...
9
votes
1answer
15k views

Why do we add salt when precipitating DNA?

All the DNA extraction protocols I have seen involve adding salts to the extraction buffer. What is the purpose of the salts? What happens if they aren't included?
9
votes
4answers
202 views

How can I avoid digesting protein-bound DNA?

I'm interested in sequencing and analyzing the bound DNA, and minimizing the amount of unbound DNA that gets sequenced through digestion. When digesting protein-bound DNA, is all of the unbound DNA ...
9
votes
1answer
200 views

How are there alternative initiation codons?

According to wikipedia and the original complete sequence of the K-12 genome, there are multiple non-AUG start codons such as GUG and UUG. How is this possible? I'm particularly curious about the ...
9
votes
2answers
2k views

How do I clean and calibrate pipettes, and how often should I do it?

I work in a lab where all the pipettes are shared. We often have visiting students who come and use the pipettes for a short project. So when I work with them, they might have been handled by other ...
9
votes
1answer
23k views

Absorption ratios 260/280 and 260/230 for RNA

I extracted RNA from different cell lines, an I want to perform reverse transcription and then PCR. To get good results, in which range should the absorption ratios 260/280 nm and 260/230 nm be? And ...
9
votes
2answers
493 views

What is causing my problem with very low yields when isolating a 42kb yeast plasmid?

I have to isolate a large plasmid from yeast and transform it in E. coli. After transformation, I often get no colonies. One reason for that is the yeast mini prep hasn't worked or the DNA ...
9
votes
2answers
5k views

What is the difference between SOLiD, 454, and Illumina next-gen sequencing?

I've started teaching myself about next-generation sequencing in preparation for a new job, and I'm wondering what the main differences are between the 454, SOLiD, and Illumina/Solexa machines, in ...
9
votes
2answers
191 views

bi-directional transcription experiment

We suspect a bi-directional transcription event is happening at a locus in our organism where two genes are directly adjacent to each other. The annotation data is not well established. The intergenic ...
9
votes
1answer
716 views

Can I elute my GFP-tagged protein off anti-GFP antibody using a peptide?

I would like to perform a modified co-immunoprecipitation assay using a GFP-tagged protein. We are going to bind the tagged protein to anti-GFP antibody then bind that to protein A/G beads, however ...
9
votes
2answers
4k views

Why is PEG important for efficient yeast transformation?

One way to do an yeast transformation is by using lithium acetate, a single-stranded carrier DNA, and PEG (1). I was wondering why is the polyethylene glycol important for the efficient ...
9
votes
1answer
114 views

E. coli values for [enzymes], [metabolites] and kinetic rates

In my attempt to create a metabolic model of E. coli, I have found a comprehensive list of metabolic reactions and their stoichiometry. The one I am currently using is E. coli model iJO1366 (more ...
8
votes
1answer
164 views

Is there a program that simulates biology on a molecular level?

Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?
8
votes
2answers
5k views

Agarose vs agar? Why do DNA gels use agarose only and how do you obtain agarose from agar?

Agar is a relatively cheap substance from red algae. And it contains a saccharide agarose as well as a small amount of pectin. Agar is used for culture plates as is, but for DNA gels a grade of ...
8
votes
2answers
603 views

Why is the number of PCR cycles limited?

I've been told that the maximum number of cycles in PCR is between 20 and 30. Is this true, and what are the reasons for this limitation?
8
votes
1answer
98 views

Why is propanoic acid often added to the diet of C. elegans?

And what are its effects on C. elegans? The paper is Burnett C, Valentini S, Cabreiro F, Goss M, Somogyvári M, Piper MD, Hoddinott M, Sutphin GL, Leko V, McElwee JJ, et al.. 2011. Absence of effects ...
8
votes
2answers
413 views

Has anyone tried Gibson Assembly Optimizations?

Has anyone tried the chew back-anneal in vitro DNA assembly method (known as Gibson Assembly) for difficult sequences, like GC-rich sequences? How big constructs could you efficiently assemble? Did ...
8
votes
2answers
280 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 ...
8
votes
2answers
174 views

How are antibodies designed?

Antibodies have the ability of recognising highly specific peptide sequences and bind it at their antigen-binding site. This ability is harnessed as a tool in research to purify target structures in ...
8
votes
1answer
227 views

How Antioxidants affects Human Metabolism?

I'd like to know how antioxidants affects the human metabolism and which ones are essential for metabolism processes.
8
votes
1answer
124 views

How realistic is to use DNA for long term storage?

This is mainly a followup question to the recent paper Next-Generation Digital Information Storage in DNA. Personally, while I agree about the data density of the format, I can't help point out the ...
8
votes
2answers
84 views

Is there a Reverse Transcription optimization for long, 9kb, transcripts?

Has anyone optimized RT for long transcripts (9kb)? The downstream application will be PCR amplification and Illumina library prep. It will be trivial to make internal primers sets for the PCR that ...
7
votes
2answers
1k views

why is AUG the initiation codon?

Is there any reason why AUG is the initiation codon ? Why is there a need for an initiation codon ? Can't translation start with different codons?
7
votes
1answer
386 views

How do you knockout an E. coli gene without disrupting the rest of the gene cluster?

I'm familiar with the method to build Keio collection using single-gene deletion with an antibiotic cassette. However, what happens when there are gene clusters or overlapping ORFs and you still only ...
7
votes
1answer
2k views

The effect of the start codon GTG on translation in E. coli

Translation in E. coli is initiated at the start ATG codon, which encodes for the amino acid Methionine (Met). In some cases, the start codon can be GTG, which within the open reading frame (ORF) ...
7
votes
2answers
795 views

Bacterial cell lysis - what solution to use?

I am trying to determine how quickly detergents act on bacterial cells (cell lysis). I would like to compare some detergents at difference concentrations for bacteriolytic activity. I don’t care about ...
7
votes
1answer
124 views

PDB Mining: Why Do I Find Atoms Less than 1 Angstrom Apart?

I am attempting to find potential Hydrogen bonds between Hydrogen donors and aromatic ring acceptors. I do this by predicting the location of Hydrogens on residues and then calculating how far these ...
7
votes
2answers
362 views

What exactly happens if during translation, an amino acid is not present?

Lets say that the cell wants to make a particular protein. Transcription of the appropriate gene is done and the mRNA is made. mRNA attaches to the ribosome and the translation is initiated in a ...