Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

Filter by
Sorted by
Tagged with
0 votes
1 answer
33 views

Why do we choose to use agar instead of agarose in various microbial applications?

When performing gel-electrophoresis we always use agarose. Is there a reason we can't perform it using Agar? And in microbial culture Agar is commonly used as solidifying agent, could this be replaced ...
Jayanth Vegesna's user avatar
-3 votes
0 answers
13 views

How to measure protein concentration after mixing with sample buffer [closed]

After mixing the protein sample with the sample buffer, it is ok to measure protein concentration?
都都日塔哈拉's user avatar
2 votes
1 answer
38 views

Best way to predict the effects of deletion mutations on protein function?

I have the coding sequences of a WT gene and several mutants of this gene (deletion mutations varying from 5bp to 50% of the sequence deleted). What is the best method for inferring the impact of ...
aquaporin's user avatar
  • 170
1 vote
1 answer
36 views

The split in Boroeutheria into Euarchontoglires and Laurasiatheria. Was this due to the opening up of the Atlantic Ocean?

I'm asking this question as a cat owner. I've seen a figure like 94 MA for the most recent ancestor of both cats and humans (this from, I guess, molecular clock arguments), and it kind of lines up ...
Emanuel Landeholm's user avatar
1 vote
2 answers
45 views

Who discovered that phage phiX174 has a single-stranded genome?

I have recently read that Erwin Chargaff has discovered that the genome of phage phiX174 (ϕχ174) is single-stranded. However I could not find the paper reporting this discovery. Is there a link to the ...
Gigiux's user avatar
  • 561
0 votes
1 answer
27 views

Mesh formation in the wells of SDS PAGE. How to solve it?

I casted 10% resolving gel and 4% stacking gel and every time a mesh like structure ( polymerisation) in the wells are formed.How to avoid this from happening and how do i get clear wells? If someone ...
user78810's user avatar
3 votes
2 answers
112 views

Change of DNA concentration due to restriction digest?

Assume that you perform a restriction digest in a molecular biology lab: you combine genomic DNA, a restriction endonuclease (e.g., EcoRI), and the optimal buffer for that endonuclease and are about ...
Michael Gruenstaeudl's user avatar
0 votes
0 answers
27 views

Recovering DNA from an RNA-extraction/purification kit

We are extracting RNA from single insects with the later purpose of performing RNA-seq. We are using the RNeasy Plus Miniki from Qiagen, which involves the use of eliminator columns as you can see ...
CaroZ's user avatar
  • 392
1 vote
1 answer
51 views

What is meant by the stabilization of a receptor?

I am reading a journal paper, and have a question about the below statement: PSD-95 is involved in the recruitment, trafficking and stabilization of N-methyl-D-aspartic acid receptors (NMDARs) and α-...
ceno980's user avatar
  • 1,671
0 votes
1 answer
45 views

Is the 5% of the oxygen used in the breathing process fully transformed into CO2?

More specific, I found out that the amount of oxygen we inspire is 21% from the total amount, with 0.04% CO2. The expired amount is 16% oxygen, with 4% CO2. Where does the remaining 1% oxygen go? Or ...
me1234's user avatar
  • 3
1 vote
1 answer
62 views

Why are camelid-derived nanobodies called VHH (variable heavy domain of heavy chain)?

Single-domain antibodies (or nanobodies) derived from camelid heavy-chain antibodies are called VHH antibodies, where VHH stands for "variable heavy domain of heavy chain". I assume the ...
mgarort's user avatar
  • 111
0 votes
0 answers
11 views

What is the optimal pO2 concentration for automated reactor batch mode EColi expression?

I am wondering what is the optimal pO2 level for an reactor based expression? All protocols I have found indicate for E.Coli pO2 levels just bigger 20%. So, I am wondering what is the optimal level? ...
raptorlane's user avatar
1 vote
0 answers
53 views

Can you store 5% BSA, in TBST, in -20C?

I have stock solution of 5% BSA prepared in TBST I use to make primary antibody dilutions for western blot. I'll admit I just assumed -20C, with freezing and thawing as needed, was an acceptable means ...
Tom Murphy's user avatar
0 votes
0 answers
68 views

How many GTPs are used in prokaryotic translation?

Here is the question: How many GTP are necessary to synthesize 2 linear peptides of 11 amino acids each using an in vitro prokaryotic system? Assume the tRNAs provided are already loaded with their ...
ninja_fun's user avatar
0 votes
1 answer
42 views

Why doesn't treating neurons with a high sodium solution depolarize their membranes?

I am reading a journal paper, and in one of their experiments they treated organotypic hippocampal slice cultures with a high potassium solution to depolarize the neuronal membranes: We found that ...
ceno980's user avatar
  • 1,671
3 votes
1 answer
125 views

Can a person have different sex at cellular level?

I mean like every cell has a sex chromosome.So does a male with XY chromosomes has all the cells in all the organs inside his body of XY chromosomes only? And vice versa.....
PAWAN's user avatar
  • 39
1 vote
2 answers
54 views

Storing bacteria in a dry, room temperature long-term storage whilst maintaining viability

I'm quite new to biology, but I'm wondering if there are any methods of storing bacteria in long-term, dry conditions with no climate control. Perhaps they could be dormant in a powder or granule-like ...
Lee's user avatar
  • 11
0 votes
1 answer
59 views

How come SSBPs in RPA don't bind primers?

I've started reading about the recombinase polymerase amplification (RPA). I'm learning that in RPA, recombinase enzyme binds to primers, then makes them anneal to the complementary target DNA strand, ...
Andrew Roots's user avatar
0 votes
2 answers
94 views

Does recombination occur in both chromatid of a chromosome with homologous chromosome? Or only 1 chromatid participate in crossing over?

A chromosome has two chromatids. In meiosis weather both chromatid participate in crossing over or just only 1 chromatid does? So, I am asking whether 1 turquoise and 1 purple chromatid participate ...
Amit Kumar's user avatar
2 votes
1 answer
329 views

Can humans metabolize D-malate?

Only the L-isomer is produced naturally, while racemic mixtures are produced synthetically and used commercially as food additives and energy supplements. So what happens when we consume D-malate? ...
ManRow's user avatar
  • 395
0 votes
0 answers
18 views

Is crossveinless in Drosophila melanogaster example of condition mutant or phenocarpy?

This is the original question - Ques - A researcher exposed Drosophila larvae to 37°C during their growth. One of the adult flies that emerged had a crossveinless phenotype. When this crossveinless ...
Deepesh Bhatt's user avatar
0 votes
1 answer
35 views

Induction of IFN-beta in HEK293T

I'm trying to increase expression of a protein we're attempting to study, UBL7, supposedly unregulated by Type I Interferon and particularly IFN-beta. I've tried treating HEK293T cells (~60% ...
Tom Murphy's user avatar
2 votes
1 answer
162 views

Why is the codon size three, rather than four? [duplicate]

The genetic code consists of triplets, each of which (apart from the stop codons) yields an amino acid when the mRNA is translated. But why did triplets evolve, rather than a longer or shorter codon ...
Mathew's user avatar
  • 29
4 votes
0 answers
109 views

Does the molecules in nerve cell membrane change 100% during the life of the nerve cell?

In their lifespan nerve cells do not divide and so they stay the same. They do get damaged sometimes and require some maintenance and change their axons a bit. They also require a lot of energy so ...
Lauri's user avatar
  • 41
0 votes
0 answers
18 views

Ubiquitous overexpression line of a gene expressed higher gene expression in leaf but not in seeds

I tried to make ubiquitous overexpression lines of a gene using a constitutive promoter vector in plant. I got multiple regenerated plants through tissue cultures. At T0, T1, T2 leaves tissues, the ...
bio's user avatar
  • 1
0 votes
0 answers
34 views

Effects of oxygenated water on bacteria

I was curious if any of you would happen to have any experience with this but any hypotheses regarding how this would turn out would be much appreciated. I’m wondering if water fully aerated with ...
Jaston's user avatar
  • 1
5 votes
1 answer
637 views

According to an online course, ribose and adenine can bond to make ATP. Is this true?

I recently came across this question in the MIT Open Learning Library Pre-7.01 Biology Course. It is question 2d in Problem Set 1 (archived link). The question, as well as the correct answers and ...
Ben Zelnick's user avatar
0 votes
0 answers
29 views

Transfecting cocoon or chrysalis

Do you know whether anybody tried to transfect insects during their cocoon/chrysalis stage, and if so do you have a link to such studies? I was thinking it would be easier to do given that it's a more ...
TheChymera's user avatar
  • 1,316
0 votes
0 answers
177 views

Migration of cut vs. non-cut plasmid on gel

As you might know there are 3 common forms of a plasmid: ccc-form (CCC), being supercoiled. oc-form (OC), being nicked and therefore relaxed. linearized form (L), being cut on both strands and linear....
Felix H.'s user avatar
  • 318
0 votes
1 answer
107 views

What is the approx. diameter of a completely "folded up" human DNA molecule, in inches?

The human DNA molecule would be about 6ft if stretched out to a straight line. I'm curious what the diameter of the DNA molecule normally is when it is "all scrunched up" or "bundled&...
Doug Null's user avatar
  • 105
1 vote
1 answer
37 views

ddT-tailed TA cloning, and the fate of a double nicked plasmid in E. coli

In an undergraduate lab class on TA cloning, it was explained that ddNTPs are used as the substrate for terminal transferase when making the T overhangs of the vector. I was told this was to ensure ...
jettosutorimu's user avatar
0 votes
0 answers
22 views

Live cell imaging using confocal microscope - Question about the microscope settings and laser wavelength

I am doing some calcium imaging to measure calcium levels in HeLa cells. To do this I have expressed cameleon calcium indicator (YC3.60) in the cells and I am using confocal microscope Fluoview for ...
Ke Keiss's user avatar
0 votes
1 answer
122 views

Why is There a Necessity for Two Rounds of Cell Division and Four Daughter Cells in Meiosis

Why does meiosis involve two rounds of cell division instead of stopping after meiosis I, where each daughter cell would have one chromosome randomly selected from each pair of homologous chromosomes? ...
Growing6884's user avatar
1 vote
0 answers
65 views

Does blunt end have a hydrogen bond?

I am an undergraduate student of biology. I saw a lecturer online, who said that sticky ends makes phosphodiester and hydrogen bonds cut. (also here). But why blunt end just makes phospodiester bonds ...
arsy's user avatar
  • 9
1 vote
1 answer
53 views

modify PCR steps to include a ligation

Imagine a multiplex PCR in which after the extension step, the dsDNA is nicked and requires a ligation reaction to repair the nick before the next denaturation step. So the steps would be: Denature ...
Ryan's user avatar
  • 121
0 votes
1 answer
63 views

What should be considered a GC clamp in a qPCR primer?

Hello there! After reading different sources regarding designing of qPCR primers, I'm a little confused regarding the concept of GC clamp. Can you help me by telling which of these cases below is ...
H001O's user avatar
  • 1
3 votes
0 answers
52 views

Why am I getting a large horizontal band spreading across my native gel?

On every gel of this type that I've ran so far, I'm getting this large band interfering with my gel analysis no matter how much troubleshooting I've done. This is a Novex Wedgewell 6% Tris-Glycine Gel ...
novara's user avatar
  • 31
0 votes
0 answers
37 views

Are all proteins translated by the RER ribosomes destined for the Golgi apparatus?

The proteins translated by the free ribosomes can fold in the cytoplasm and never go through the endomembrane system. But when the endomembrane system is described, it is always stated that the ...
Damocle Damoclev's user avatar
1 vote
1 answer
31 views

What is meant by 20 ul final concentration of polyacrylamide?

I am performing a phenol-chloroform extraction in which precipitation is enhanced by linear polyacrylamide. The SDS for linear polyacrylamide mentions that it should be used such that its final ...
donkey's user avatar
  • 125
0 votes
0 answers
19 views

Covalent modification of Pyruvate Kinase in RBCs

Human body has 4 isozymes of PK and I am particularly interested in the RBC isozyme. It is capable of being covalently modified through phosphorylation catalysed by Protein Kinase A which is in turn ...
Vibhav Agarwal's user avatar
0 votes
0 answers
23 views

Mass Spectrometry Artefacts: R-deamidation / Oxidation?

Context: I am a student-researcher. I expressed GST-tagged protein (Pyruvate Kinase) in the yeast Saccharomyces cerevisiae on synthetic drop-out media. I then purified the GST-tagged protein, ran it ...
thefutureisnow's user avatar
2 votes
2 answers
113 views

Efficiency of molecular motors vs. human-made motors

On the wikipedia page for "Molecular motor", it says "In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors." without any ...
nullspace's user avatar
0 votes
0 answers
18 views

DnaA binding energy to E coli genome

I have been told that DnaA binds strongly to DnaA boxes on the E coli genome, but binds weakly to 8 out of 11 sites near ori. I want to know more quantitatively what strongly and weekly mean. Are ...
stochastic's user avatar
1 vote
0 answers
48 views

How did cells survive before the first appearance of topoisomerases?

How did cells operate before the first appearance of topoisomerases to relax DNA supercoils during replication? I read a recent paper on the early phase of topoisomerase evolution, but it doesn’t ...
Devin's user avatar
  • 39
0 votes
0 answers
29 views

What is the precise definition of "cytokine"?

For example, both bone morphogenetic protein 4 and nerve growth factor are paracrine signaling proteins which promote growth of their respective tissues, and both are known to have some effect on the ...
Candlebeam's user avatar
0 votes
0 answers
31 views

What is meant by the steady-state activation of a receptor?

I am reading a journal paper about the insulin-like growth factor 1 receptor. In this paper, there is the following statement: Finally, we show that the IGF-IR and the PI3K subunit p85 and Akt are ...
ceno980's user avatar
  • 1,671
4 votes
1 answer
56 views

Allowed Deviations in fixed bond length and bond angles in peptides from the typical values

I am using frag builder python module to generate peptide structures to compute the interaction energy for ensemble of peptides of a given sequence for a fixed bond lengths and bong angles. However, ...
vigneshwaran kannan's user avatar
2 votes
1 answer
98 views

Programs/software used to create illustrations and scientific paper ready figures

I am new to the field of molecular biology. I am finding the need to generate illustrative figures displaying interplay between proteins, DNA and various other molecular constructs at different scales ...
Zebra Fish's user avatar
1 vote
1 answer
49 views

What are the key mechanisms of control and transport of ATP from mitochondria to synapse in active firing neurons?

I am working with a group in the field of neuronal activity (in computational neuroscience), in specific the firing rates at different ensemble/population hierarchies. It is well established that ...
al-Hwarizmi's user avatar
2 votes
1 answer
74 views

Why doesn't the cell just use one messenger?

I recently learned the second messenger model, where adrenaline activates adenyl cyclase, which converts ATP into cAMP. Then cAMP acts as a second messenger which activates portein kinase enzymes. The ...
Bruce M's user avatar
  • 151

1
2 3 4 5
36