2
votes
1answer
33 views

Substitute 25mM dNTPs mix with 10mM dNTPs

I need to make a solution of multiple compounds, one of them is dNTPs. The recipe calls for 20 μl 25 mM dNTPs in a 1250 μL master mix. Unfortunately I do not have it available at that concentration, ...
1
vote
1answer
40 views

Missing 4$H_2O$s (per glucose) in Cellular Respiration… Where can they be?

I having trouble understanding the equation of the cellular respiration. The thing that bothers me is the number of $H_2O$ molecules. Generally, cellular respiration is written thus : $C_6H_{12}O_6 + ...
1
vote
2answers
37 views

Functioning of EDTA

I know that EDTA chelates metal ions. It weakens bacterial cell wall and inactivates the DNases. What is the reason why it can do so ? I guess it can inactivate DNases by altering the ...
2
votes
1answer
21 views

Transport of mammalian insulin in vivo

What is the mechanism for transport of insulin in mammalian cells?
0
votes
0answers
44 views

Are DNA molecular motors described by cellular automata rules?

While watching this Molecular Visualizations of DNA it struck me how much the motion resembles Conway's Game of Life. And not only visually; each molecule/atom is described by a finite set of ...
-1
votes
2answers
48 views

PAH gene mutation

Analysis of the DNA of the Phenylalanine hydroxylase (PAH) gene in a patient with phenylketonuria revealed a mutation in the protein coding region whose predicted effect would be to replace the amino ...
0
votes
0answers
16 views

How do you express and detect GLP-1 receptors?

I am currently working with a peptide which is an analogue for glp-1, but during invitro studies am not able to detect for the presence of GLP1- receptors. The cell line used is Min-6. How do I detect ...
1
vote
1answer
38 views

DNA ligase mechanism

I am unable to understand what happens to the phosphates from ATP. What are they used for ?Charging 3' end or 5'end ?
4
votes
0answers
37 views

What are the lifetimes of cellular components on organelle or molecular level?

I was thinking that even though I know how generally the cell works, I don't really have a feeling of how volatile it is. I want to know what is the lifetime/turnover rate of different constituents of ...
0
votes
1answer
36 views

Identifying mutations in a yeast strain

Cells of a triple-mutant yeast strain (leu- his- trp-) were spread either on minimal medium or on minimal medium supplemented with various combinations of histidine, leucine, or tryptophan. The ...
1
vote
1answer
61 views

Shine-Dalgarno sequence and expressing proteins

Shine-Dalgarno sequence present in the prokaryotic mRNA plays a role in initiation of translation. In eukaryotes a Shine-Dalgarno like sequence is present but does not play an important role in ...
1
vote
2answers
55 views

How does promoter sequence affect initiation?

I don't know if this might have been highlighted in recent research, but a textbook I have states that "the exact way in which promoter sequence affects [transcription] initiation is unclear" I'm ...
5
votes
1answer
309 views

Why is ATP the preferred choice for energy carriers?

Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?
3
votes
1answer
472 views

How does blue white screening work in selecting E coli that have taken up a plasmid vector?

The plasmid vector I am referring to is pCR 2.1 - TOPO. I added the vector to the E coli and plated them up onto LB+amp+X-gal plate, then incubated. After incubation the plates had two types of ...
5
votes
3answers
134 views

What does it mean for a distribution to be “consistent with a two rate-limiting stochastic steps”?

I'm reading a study (full text here) that examine the dynamic of nuclear translocation of a transcription factor in budding yeast, in response of calcium stress. They found that it occurs in bursts, ...
5
votes
4answers
771 views

Why we have no enzyme to digest cellulose?

As we know, cellulose is the most abundant polysaccharide in nature. Why don't we have any enzyme to digest cellulose?
0
votes
1answer
64 views

Why to choose a grammar from a lot of grammars that can describe structure of proteins?

Why do we choose a grammar from a lot of grammars that can describe structure of proteins? Usually, there are a lot of (maybe infinite) grammars that can describe one language. Why do we choose a ...
6
votes
2answers
324 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 ...
1
vote
1answer
153 views

How to calculate or know by experiment the entropy of enzymes or protein?

How do you calculate or experimentally determine the entropy of enzymes or protein? In particular, I am interested in Boltzmann and conformational entropy, and Gibbs free energy. Any references are ...
3
votes
1answer
161 views

Can replication occur if DNA is methylated?

Can a methylated strand of DNA be replicated without removing methylation? Does it make any difference if the strand is methylated or not (during replication)?
-4
votes
4answers
120 views

Are biological systems engineered? They are often reverse engineered at a molecular level!!

Understanding biological systems, molecular biologists need to “reverse engineer” them. Is this evidence that the systems were engineered to begin with?
2
votes
1answer
97 views

How does GTP help in the step of codon recognition?

The anticodon of an incoming tRNA base pairs with the complementary mRNA codon in the A site.Hydrolysis of GTP increases the efficiency and accuracy of this step. How does GTP do so ?
6
votes
2answers
583 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?
3
votes
1answer
345 views

What is DNA binding domain? It is not clear what the domain means

I am confused about the term DNA binding domain. Does it mean that there are some parts of the DNA that tends to coil up? Does it happen because some proteins tend to stick around that area? Also it ...
4
votes
1answer
122 views

Cloning two fluorescent proteins with different promoters in the same plasmid?

I want to clone two fluorescent proteins both driven by different promoters in a plasmid to be used to transform B. subtilis at the amyE locus. For this I want to use plasmid pSG1729 (Lewis and ...
1
vote
1answer
48 views

Isoprenoid Diphosphate Concentration in Yeast saccharomyces cerevisiae

Isoprenoid Diphosphate(IPP) is an important metabolites which is precursor in lot of secondary metabolites like Dolichol diphosphate, ubiquinone, prenylated proteins and carotenoid (not synthesized ...
1
vote
2answers
85 views

Finding a easy and cheap method for dyeing dNTP

I want to measure OD to know the concentration of dNTP. Any idea for dyeing dNTP at cheapest price and easiest way ?
2
votes
0answers
87 views

Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
1
vote
0answers
37 views

Protocol for immobilize oligo to solid

I'm learning about microarrays and understand that an oligonucleotide can be immobilized to a solid like a CD acrylic plastic by modifying the oligo. Does anyone have a good protocol for modifying a ...
0
votes
1answer
47 views

Some question about materials for PCR

I'm planning to order oligo, polymerase, nucleotide, buffer for my first diy PCR experiment (now I have nothing), so I have some questions. How and how long I can storage them? I have only a fridge ...
0
votes
1answer
42 views

Carotenoid biosynthesis in yeast

Does Budding Yeast Sacchromyces cerevisiae produces significant amount of carotenoids? Have anybody estimated the ratio of flux going in branches 1. Cholesterol synthesis(via squalene) 2. Coenzyme Q6 ...
5
votes
2answers
152 views

Can PCR tubes be made of different materials than plastic?

Does it matter if I replace the PCR tube (usually made of plastic) with another material like aluminum, glass, or something similar?
5
votes
3answers
117 views

Finding a template/oligo combination for my first PCR experiment

I'm an information technology engineer. I love biology so I research biological topics and have an interest in PCR. That's why I have decided to create a PCR machine. Everything is done now and I ...
2
votes
1answer
459 views

Why is allolactose the LacI inducer?

For what reason(s) is allolactose, instead of lactose, the "natural" inducer of lac operon repressor?
3
votes
3answers
308 views

Why do neurones use chemical signalling at synaptic junctions?

Problem. When a neurone fires, it sends an electrical signal that jumps down the axon via the nodes of Ranvier very rapidly. At a synaptic junction, chemical brownian diffusion signalling with ...
3
votes
1answer
125 views

What molecular processes are involved in pseudopodial extension?

I am curious as to the processes and mechanisms involved in the extension of pseudopodia in amoeba. How does the cell know and control the direction and extent of pseudopodia formation at a molecular ...
6
votes
2answers
880 views

Very high 260/230 absorbance ratio of an RNA sample

After my most recent RNA extraction, the RNA samples had very high 260/230 absorbance ratios, (ranging from 5 to 25). I've never gotten numbers like this and I know the ratio is supposed to be ~2 in ...
1
vote
0answers
47 views

Solid phase use in HIV rapid tests

I have another question in regards to my HIV test research. The rapid tests like Orasures Oraquick contains a strip of synthetic peptides that are used to represent proteins found in the envelope ...
7
votes
2answers
541 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 ...
10
votes
1answer
93 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 ...
4
votes
2answers
1k views

DNA as an acid? [duplicate]

Possible Duplicate: Does DNA react in all of the ways most other acids do? Even if DNA is made up of nucleotide bases, it is said to be an acid. Why is this?
2
votes
3answers
79 views

Is DNA mutation locally energetically stabilizing the DNA molecule

I am no biologist, but as a physicist, a spontaneous mutation (seen as a chemical transformation) should lower the energy of the system, at least locally. So I wonder if any research has been done ...
7
votes
1answer
189 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.
9
votes
2answers
3k 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 ...
16
votes
1answer
562 views

ATP cost for gene expression

How would you estimate the number of ATPs required to transcribe, export and translate a single eukariotic protein?
20
votes
1answer
424 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 ...
10
votes
1answer
281 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 ...
9
votes
4answers
193 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 ...