Questions tagged [proteins]
Biopolymers consisting of amino acids that fold into 3D shapes and perform a large number of functions in living organisms.
944
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Is alternative splicing possible in the same cell?
I know alternative splicing is possible in different cell types of an organism, or within the same cell at different developmental stages. There are several examples like this. But are there any ...
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In phospho/pan analysis in Western blots, what is best way to normalise to an internal loading control?
I am analysing the expression of a protein kinase X that is a phosphoprotein through Western blots. I have labelled the membrane for both the phosphorylated form of the protein and also for the total ...
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When analysing phosphoproteins via Western blot, why is total protein level of the target protein recommended as an internal loading control?
I am analysing the expression of a protein kinase via Western blots, and it is a phosphoprotein. I have labelled my membrane with antibodies against the phosphorylated form of the protein (using ...
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Can you use images taken at different exposure times in western blot image analysis?
I am doing Western blot data analysis where I have images from a number of experiments (where the samples in the experiments are biological/technical replicates). For each experiment, I labelled the ...
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Why do you need to calculate the lane normalisation factor when doing western blot data analysis?
I am learning about western blot data quantification from some online resources. I have read about methods to normalise the data.
I have seen in a number of resources, such as this handbook and this ...
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How many times is a single strand of mRNA translated into a protein?
In other words, is the mRNA damaged or somehow "marked completed" in the translation process? Or does it pop out the other side of a ribosome ready to be translated again? If the latter, how ...
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Is the kinase domain of a protein kinase the same as the catalytic domain?
I am learning about protein kinases and I have read that the protein kinase domain is a structurally conserved protein domain containing the catalytic function of protein kinases. I am wondering ...
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Is sonic hedgehog a gene or a protein or both?
Is sonic hedgehog a gene or a protein or both?
I think sonic hedgehog is okay as a name for a chemical.
Having said that, I am a little bit concerned about the way sonic hedgehog seems to mean the ...
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SARS-CoV - relative size of the spike protein
I was given the task of determining the percentage of the S-protein of the SARS-CoV relative to the total of its proteins from the attached image. However, I have been given no explanation of the ...
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Can a constitutively active kinase be highly regulated?
I am studying the protein kinase GSK3 and I am learning about the regulation of its activity. Many journal papers that I have read have stated that GSK3 is unique because it is a constitutively active ...
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Are there any online resources that have a list of post-translational modifications and their molecular weight?
I am studying a protein and I am interested in learning about all the post-translational modifications that it has (as I am analysing it via Western blot). I have found a list of the post-...
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Does the mRNA of the covid19 spike protein contain any nuclear localization signals
Does the covid19 spike protein amino acid sequence, as used in the covid19 vaccines, contain a nuclear localization signal. Because if they do, isn't there a chance that the RNA can find its way to ...
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147
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Can Western Blots be used to quantify the activity of a protein?
I am new to Western Blot analysis and I have recently done my first two. I am studying a phosphoprotein (a protein kinase) that can be both activated and inactivated via phosphorylation at a specific ...
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241
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How can I clone a gene into a plasmid vector with an N-terminal his tag and TEV cleavage site between the tag and the start of the sequence?
I'm a scientist who has significant experience in chemistry but am relatively new to molecular biology and biochemical techniques. I'm trying to make an isolated domain of a protein (166 residues, 19....
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Does the term 'protein expression' refer to the production of proteins only or also their regulation?
I am learning about molecular biology and I have come across the term 'protein expression' in a research paper. I have searched the definition of this term online and on the Thermo Fisher Scientific ...
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How do G proteins move?
G proteins consist of an alpha subunit and a beta/gamma subunit. These proteins are involved in various cellular signalling process.
From what I have understood, the alpha and gamma subunits have ...
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63
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What is background signal in a Western blot?
I have done a western blot and I want to remove the background signal when doing densitometry analysis of my protein bands of interest. I have read some articles online such as this one regarding high ...
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What is the best way from remove background signal from a band when doing Western blot image analysis?
I am doing image analysis of a Western Blot in Image J. I have calculated the total intensity of my protein bands of interest through outlining each band using the rectangle tool in ImageJ, and ...
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Do phagocytes need antibodies to be able to engulf pathogens (to function)?
I recently saw a question about monoclonal antibodies, that are specific to a certain virus, being split (into their constant and variable regions via an enzyme), and the question asked whether some ...
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Would the amino acid profile of lab-grown human meat perfectly match the dietary nutritional amino acid requirements for humans?
Whey protein is the food which has the most ideal (yet not perfect) amino acid profile for humans, whereas gelatin for example has a very poor and incomplete amino acid profile for humans. Would human ...
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Compatibility between spytag/spycatcher versions
Background
SpyTag and SpyCatcher are peptides which can associate via a spontaneous amide bond. Because of this, they can be fused to proteins of interest as tags to cause the proteins to bind. There ...
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What are the units of the band intensities in a western blot image?
I have done a Western blot and I am measuring the band intensities in Image J. Using the rectangle tool, I have outlined the band and then calculated the area and the mean intensity of the band. I ...
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In western blots, do loading controls have to be proteins that are in equal amounts in each lane?
I have recently done a Western Blot and I am doing data analysis on my blots. I am studying the protein GSK3, which is a phosphoprotein.
I have labelled my membrane against active GSK3 and inactive ...
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Is the phrase "transmembrane segment" equivalent to the transmembrane domain of a protein?
I am reading the Handbook of Neurochemistry and Molecular Neurobiology and I am learning about the cell adhesion molecule NCAM2 and I have come across the following:
The overall structure of NCAM2 ...
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What is meant by "opposing plasma membrane" with respect to cell adhesion molecules?
I am reading the Handbook of Neurochemistry and Molecular Neurobiology and I am learning about cell adhesion molecules (CAMs) and I have come across the following:
CAMs are involved in homo‐ or ...
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Does Invertase catalyse the hydrolysis of other sugars other than sucrose?
I recently did a lab where we tested out the substrate specificity of Invertase on different types of sugars such as sugar alcohols and disaccharides, measured by the absorbance of red using a ...
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47
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How to find a model organism's standard data about proteome size and genome size?
I want to know proteome size(the number of proteins not length) and genome size(length) of model organisms like Caenorhabditis elegans, Saccharomyces cerevisiae etc.
I found www.uiprot.org
and I made ...
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What does q stands for in Gq/11 alpha subunit?
Sorry for asking, I am not capable to find what does the q stands for in Gq/11 alpha subunits.
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Confusion regarding the Kir2.1 inward-rectifying potassium channel
I was trying to find out more about gustation and the transduction of sourness when I came across the supposed inward-rectifying potassium channel $\ce{K+_{ir} 2.1}$. Here's the thing, despite being ...
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What is the thickness of the membrane if only alpha helixes are embedded of a transmembrane protien?
Given is the representation of a transmembrane protein. Calculate the thickness of the membrane if only alpha helixes are embedded in it. One turn = 5.4Å
Please read:
The reason I didn't submit my ...
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Which enzymes use ATP?
It is well known that there are many enzymes which use ATP in their function, and any enzyme that work against an energy gradient need to have that energy supplied from somewhere, but just as well ...
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201
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Calculating sequence divergence score for a protein from identity or similarity score?
I have % identity and % similarity scores for ~50K protein alignments, that I fetched from Ensembl Compara database. The issue ...
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What are the effect of radioactivity on grey wolves in Chernobyl?
I am doing some research about the effects that radioactivity has and is having on grey wolves in Chernobyl and more particularly on their genetics, but maybe also looking at the populations in the ...
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Question about : RNA interference - small-interference RNA AND about Rab-protein in vesicles
First Question :
RNA interference - small-interference RNA
in the textbook -Essential cell biology By Bruce Alberts, Dennis Bray, Karen Hopkin
this Figure is Shown
my question is : if the foreign RNA ...
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Does hydrolysis of carbohydrates, proteins, and fats occur in the small intestine?
Does the hydrolysis of carbohydrates, proteins, and fats occur in the small intestine? I have researched this and just cannot seem to get a clear-cut answer. Perhaps I am misunderstanding something?
...
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Why can't plain water be used in dialysis? Why is buffer used?
I read that buffer is used in dialysis because usage of water could cause precipitation of proteins but I don't really understand why and how water can cause precipitation of proteins and buffer ...
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Are there any online resources for finding the signaling pathways that two proteins both belong to?
I am studying the proteins GSK3 and AMPK and I am trying to identify the signaling pathways that both of these proteins belong to. From reading journal papers I have found out that both of these ...
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What does ΔC and ΔN mean with regards to a protein sequence?
I am reading a paper about the regulation of the nuclear export of the protein GSK3 and I have come across the following statement:
Full-length FLAG epitope-tagged mFrat1 (FLAG-Frat) and the
amino-...
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1
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139
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Do we find protein not of cellular origin in nature?
I read once that we have two sources for proteins:
Protein that is made in cells
Protein that is made in labs
However, based on Miller–Urey experiment, it's argued that amino acids can be made from ...
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Did Mendel believe that proteins are hereditary substances?
Scientists first thought that proteins, which are found in chromosomes along with DNA, would turn out to be the sought-after genetic material. Proteins were known to have diverse amino acid sequences, ...
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Is there any commercial vector technology platform for boosting recombinant protein production?
I am a novice in biomedical industry. Our team would like to search new vector technology for boosting recombinant protein production. It's difficult to google a firm that provide those plasmids.
Dose ...
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Predicting how proteins will be cleaved
Is it possible to predict how proteins coded from mRNA will be cleaved?
The reason I was interested in this is because I did some initial work to translate the raw Coronavirus RNA sequences, which you ...
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How does the eukaryotic cell synthesize all of the proteins of a protein complex (like ETC complex I) at stoichiometric ratios/numbers? [closed]
(eg synthesize all proteasome proteins at the appropriate ratios to which they are used)
How often are proteins of the same complex (eg all the proteins of the 20S/19S parts of the proteasome or ...
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Speed of protein conformational change?
Although the speed may vary a lot based on factors like protein size/scale of conformational change/type of changes (small block change/arm movement,etc), are there examples of experimental results of ...
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Why can't C1r cleave C4 proteins?
I am researching the complement system, and have ran into something I'm not really sure about. In the past, the C1r2s2 complex was thought to be an 8-like structure tucked inside C1q's collagenous ...
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Why did the protein structure prediction accuracy in terms of GDT-TS decrease from 2008 (CASP 8) to 2014 (CASP 11)?
I read on https://doi.org/10.1038/d41586-020-03348-4:
Why did the protein structure prediction accuracy in terms of GDT-TS (Global Distance Test — Total Score) decrease from 2008 (CASP 8) to 2014 (...
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How does the order of the pairs of cross-links in DNA determine the arrangement of the amino acids?
Quoting Richard Feynman from Chapter 3 of his book Six Easy Pieces, when he talks about DNA:
Attached to each sugar along the line, and linking the two chains together, are certain parts of cross-...
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2
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Why do large, aromatic residues prefer beta-pleated sheets?
I read in many journals that amino acids with branched and large aromatic R-groups have higher beta pleated sheet propensities. However, none really go in depth into the significance or reasoning ...
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Measuring the protein content using UV Vis
The experiment is to determine the protein content of the solution. I followed the procedure of the Bradford assay but the reagent needed is unavailable and so we use an alternative by using cold pure ...
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What makes a protein structure discernible? [closed]
In Lehninger's Principles of Biochemistry, Pg. 116 states that "parts of proteins lack discernable structure." What exactly makes this protein not readable? Is it the complexity of the shape ...
