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

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3
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4answers
31 views

Enzymatic error rate

I am aware that each enzyme generate a certain amount of misproducts. This is well documented, for example, for the DNA polymerase. I am interested in enzyme involved in biochemical processes, so for ...
0
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4answers
36 views

Why are there both stop and start codons?

Based on my understanding from wikipedia, there is the (RNA) start codon AUG and the stop codons UAA, UGA, UAG. AUG can also encode Methionine, I'm assuming if it appears in the middle of a mRNA ...
1
vote
1answer
13 views

Repair of cloning vector nicks digested with antarctic phosphatase and ligated with T4 enzyme

The vector product obtained by ligation between a vector previously digested with antarctic phosphatase lacks 5' phosphate groups. T4 ligase can ligate it to an insert with complementary sticky ends ...
2
votes
1answer
42 views

Is it possible that a set of functionally related proteins in a pathway fulfill different functions?

Could it be that a given pathway of enzymes (or proteins in general) may fulfill different purposes in a cell by for shifting partners? Say protein A activates B, B activates C and C has a specific ...
0
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0answers
12 views

What are the forms of host pathogen interaction [on hold]

What are the forms of host pathogen interaction apart from the host pathogen protein protein interaction?? Or is protein protein interface is the only one way of host pathogen interaction?? I am ...
1
vote
1answer
364 views

Complementarity Determining Regions (CDR)

Complementarity determining regions (CDRs) are part of the variable chains in immunoglobulins (antibodies) and T cell receptors, generated by B-cells and T-cells respectively, where these molecules ...
5
votes
1answer
53 views

Why does high pH result in the denaturation of DNA?

In the Southern blot method, for example, a solution of NaOH is used to denature the DNA in the sample. I find this counterintuitive since I expected that $\text{Na}^+$ cations would neutralize the ...
1
vote
1answer
35 views

What are pseudoknots?

I'm trying to get my head around what a pseudoknot is and how I can identify them given some RNA string. For example, suppose I have a string s = CGUUGUGUACACGAUAGUACAU. Suppose the two longest ...
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0answers
26 views

Aspects of host pathogen interaction [on hold]

I have very simple(probably silly) question. I am a bit confused, hence asking. Does the epitope mapping fall under host pathogen interaction? What I want to know is what are the aspects of host ...
0
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1answer
32 views

Examples of how the presence or absence 2'-hydroxyl groups influence physicochemical properties of DNA and RNA

I know, for instance, that RNA is much more succetible to alkaline hydrolysis than DNA and this difference is determined by the presence of 2'-hydroxyl group in ribose. I have also heard that "DNA is ...
3
votes
0answers
27 views

Why do most organisms have negative supercoiled DNA?

It has been observed that in nature most organisms have negative supercoiled DNA and that few organisms have positive supercoiled DNA. Some of the organisms that have the positive supercoiled DNA live ...
0
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0answers
10 views

Why is carbonylation added as a fixed modification in mass spectrometry peptide analysis?

When using mass spectrometry analysis software we use carbonylation as a fixed modification. What is the significance of this modification and why doesn't it change?
2
votes
2answers
240 views

Why people fear GMOs? Can't we map a plant composition?

My main question is can we map what a fruit is made of? For instance apples are made of 0.0002% of protein X, 0.00001 of protein Y, 0.001% of amino acid Z... etc... If we can, then my next question ...
0
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0answers
12 views

Does the use of a Thiazide diuretic affect the ability of a hair follicle to absorb substances?

Thiazide diuretics are on the World Anti Doping Agency's, as well as the International Olympic Committee, list of banned substances due to it ability to mask illegal substances in urine. The rapid ...
0
votes
1answer
22 views

What does gene encoding receptor mean? [closed]

What does gene encoding receptor mean? I know what each of these of these words separately, but cant identify the exact meaning of the complete phrase, I cant visualize. Please help me!
3
votes
1answer
21 views

Authority on Microbiological Definitions

Is there an authority on definitions for molecular microbiology concepts, like an IUPAC book for chemical definitions? The particular definition I am debating is chromatin. Some say it encompasses ...
1
vote
0answers
33 views

If you are God, how would you create an efficient priming reaction? [closed]

Imagine that you are “natural selection” (or God if you prefer) and you can reconstitute replication changing the concentrations or the properties (higher/lower activity; reactivity; etc.) of the ...
3
votes
1answer
57 views

How is the type of genetic manipulation determined in CRISPR-Cas9?

I've been reading up a bit on the CRISPR-Cas9 system for gene manipulation. From what I read, it introduces double-strand breaks at specific points determined by the choice of sgRNA. But how do you ...
3
votes
2answers
170 views

In cancer, why do cells duplicate themselves?

In regards to cancer why do cells replicate themselves? If it's a mutation, what kind of mutation would this be classified as?
0
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2answers
44 views

mRNA Transcription from Nuclear DNA

How does a cell "know" the coding strand vs. the non-coding strand of DNA during transcription of mRNA?
4
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2answers
37 views

what does Pro→Glu substitution mean?

Considering the paper: A single amino acid in E-cadherin responsible for host specificity towards the human pathogen Listeria monocytogenes in the abstract portion, what does Pro→Glu mean? Does it ...
0
votes
0answers
17 views

Does DNA Ligase look for complementarity in sticky ends?

Can DNA ligase seal two non-complementary sticky ends if the reaction is incubated at the optimum conditions ? I do almost 100% double digestion in the lab. However, during ligation, when I do a ...
3
votes
3answers
59 views

Western Blot: Fischer ECL substrate 2:1 instead of 1:1?

i recently developed a b-actin-ab-incubated PVDF-WB-Membrane with the Thermo Scientific Pierce ECL Kit. According to the manufacterers orders i mixed Reagent 1 and Reagent 2 1:1. But unfortunately i ...
1
vote
0answers
32 views

Zinc and brewer's yeast

I'm hoping for some information relating to yeast nutrition (specifically Saccharomyces cerevisea) in beer fermentation. Zinc is well-known to be necessary for yeast cultures to perform successful ...
1
vote
0answers
50 views

How does estrogen influence collagen synthesis?

Through what mechanisms does estrogen interact with collagen synthesis? Especially in the context of elevated estrogen levels and genesis of purpura simplex .
0
votes
1answer
35 views

Why does the cloning scheme to shuttle GFP into a pL4440 have to be between two T7 promoter regions? [on hold]

When designing a cloning scheme, why does it have to be between the two T7 promoter regions, and what is the benefit of using one or two enzymes to perform this?
1
vote
2answers
88 views

Growing E. coli at room temperature?

If I were to do a blue/white selection of transformed E. coli on LB agar ampicillin plates at room temperature (23⁰C) for about 2 days and 18 hours, will I run into the issue of satellite colonies or ...
3
votes
1answer
98 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
2
votes
1answer
29 views

Why is the resting potential of a neuron so close to the equilibrium potential of K⁺?

I know this has something to do with the K+ leak channel. I just don't understand how. I know that 3 Na+ are pumped out for every 2 K+ pumped in. This makes the cell interior net negative. I know ...
8
votes
2answers
496 views

What is it about the housekeeping genes that makes them almost immune to gene regulation?

When it comes to eukaryotes, including ourselves, we have all different kinds of specialized cells and tissues that are so different, yet originally all came from the same single cell. And apparently ...
0
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0answers
15 views

How to engineer chromosomal duplications?

Specific genetic engineering of chromosomal aberrations like deletions, inversions and translocations are doable by using the CRISPR/Cas system or the other programmable nuclease systems. Insertions ...
6
votes
1answer
60 views

Receptors for red and far-red light in plants: Shade avoidance

Franklin (2009) describes how plants use the ratio of the red wavelength (660-670nm) over the far-red wavelength (725-735nm) (R:FR) in order to avoid shading. My question is: which receptor is ...
1
vote
1answer
59 views

Enzyme Assay - pectinase

During assaying an enzyme at high temperature, the substrate (Pectin) is degraded by the high temperature rather than by enzyme, so, how can I minimize degradation of the substrate by the temperature? ...
0
votes
0answers
17 views

Cannot conjugate Biotin-labeled DNA to Streptavidin-labeled solid surface

I have been trying to immobilize DNA by the bioconjugation of biotin and streptavidin, but I cannot get this work. I added EDC and streptavidin to COOH ...
1
vote
0answers
10 views

Gene expression for mouse feeder cells (inactivated MEFs)

I'm looking for a paper with gene expression data for mouse feeder cells, inactivated by gamma radiation or mitomycin C. Ideally I'd like RNA-seq data but I'll use microarray data if that's all there ...
2
votes
1answer
44 views

How do C. elegans manage nutrition?

If there is ample amount of food, do C. elegans worms know when to stop eating or do they store extra energy? Could they put this extra energy to use by moving faster or putting more eggs?
4
votes
1answer
223 views

RNA isolation from Drosophila head

I need to isolate RNA from Drosophila head. I basically chop the head off and first homogenize it with a homogenizer (similar to this: ...
1
vote
1answer
19 views

Why does a tumour's genome change depending on the environment?

According to the book "Primer of The Molecular Biology of Cancer" by Vincent, Theodore and Ateven, the tumour cell is changed depending on its environment. performed genome-wide analysis on three ...
2
votes
0answers
43 views

How to prevent e coli from clumping (for FACS)?

I'm performing FACS on e coli, but the cells are clumping together so each event is multiple cells. I ran a control where I had one flask of e coli expressing GFP, and one flask expressing RFP. Run ...
6
votes
1answer
182 views

why is DNA antiparallel? Can it be parallel?

My biology textbook mentions that DNA is antiparallel and it got me wondering... Can DNA be parallel? What would happen if it was parallel? could DNA still replicate right?
3
votes
0answers
40 views

Why is ATP the main nucleoside triphosphate used to exchange energy? [duplicate]

Out of all of the nucleoside triphosphates what makes ATP the most used? Is it its structure? The amount of energy it contains? Why is GTP not used as much? What is the deal with the other nucleoside ...
4
votes
3answers
309 views

How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?

How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids? The book's answer is $20^{12}$. However, I disagree. This result ...
9
votes
3answers
2k views

Does a man contain all the genes needed to make a woman?

This question is brought on by a Sci Fi novel I am thinking about writing. The plot device involves a colonist in charge of building a population on a new planet who loses his supply of embryos and so ...
3
votes
2answers
44 views

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 ...
13
votes
5answers
2k views

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 ...
4
votes
1answer
160 views

Can concentration of a protein be determined from a gel quantitatively (rough estimation)?

I've got a His-tagged protein in 6M urea, 500 mM imidazole buffer that needs to be quantified before dialysis to ensure there's enough protein worth dialysing. I ran out of my elution buffer which ...
2
votes
2answers
463 views

What is Pan for in pan-caspase?

A simple question (I could not find it on internet): What is Pan for in pan-caspase? Is it any different from the term 'caspase' ?
3
votes
1answer
114 views

Does sample buffer require EDTA for protein separation on SDS PAGE?

In sample buffer preparation we add EDTA, but if SDS-PAGE is for protein then is it necessary to add EDTA in sample buffer? What is role of EDTA in sample buffer for protein separation for SDS-PAGE.
1
vote
1answer
44 views

Protocol for checking pipette calibrations using absorbance readings of a dye in solution?

I've been looking around the net looking for a nice protocol to validate micropipette calibrations using absorbance readings of a dye in solution. Does anyone have one they can share? I'd highly ...
2
votes
1answer
33 views

What is the importance of urea in mass spectrometry?

What is the importance of urea in mass spectrometry? We use 8M urea to FASP our proteins prior to mass spectrometry. What is the significance of using 8M urea? and how does it affect the proteins?