Questions tagged [proteins]

Biopolymers consisting of amino acids that fold into 3D shapes and perform a large number of functions in living organisms.

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Protein crashing [closed]

I'm an undergrad trying to write a research proposal. I just found out that the protein I want to study is extremely prone to crashing and that the grad students + postdocs in my lab are all afraid of ...
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If an animal eats protein will it be fuller protein or will it have protein like other animals? [closed]

If for example we have 2 fish, one eats a lot of protein and the other barely eats protein. Will a fish that has eaten a lot of protein be fuller of protein when we eat it than one that has eaten ...
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Intelligence of nervous system vs other human intelligence? [closed]

Viral proteins are shown to be used in intelligence such as for memory: https://www.sciencedaily.com/releases/2018/01/180111141450.htm I wondered since proteins able to form prions are the most ...
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115 views

Why would this viral strain-specific antiserum fail to immunoprecipitate the same (98% identical protein) from another strain?

I'm reading this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC392475/ and I can't work out why a certain immune serum didn't work on the same viral protein but from different strains. The serum ...
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52 views

Predicting protein folding with Alphafold

I’m trying to figure out how to use Alphafold, which is a biological analysis software for predicting the folding of amino acid sequences. I’ve been trying to follow the directions on the creators’ ...
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Do muscle fibres/tissues have any such property that with equal amount of food/exercise, they show different amounts of hypertrophy?

We have two subjects (two humans or one human and one animal), we feed the same amount of food (protein) and exact the same amount of exercise from both. Will both undergo similar amount of ...
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Ways to predict the preservation of functional domains in fusion proteins

My lab is synthetically creating fusion proteins consisting of an enzyme attached to a zinc finger through a linker. We can attach the zinc finger to the enzyme at either its N-terminus or its C-...
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141 views

Meaning of ‘motif’ in molecular biology

I would like to understand the meaning of the term motif as used in molecular biology. In an article in Nature Biotechnology, Patrik D’haeseleer states: Sequence motifs are short, recurring patterns ...
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How does the shape of a protein determine its function?

There is currently much interest in protein folding and the problems in predicting how the sequence of amino acids determines how proteins fold into specific shapes. Accounts of this generally mention ...
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What is 'protein' in food?

I know that proteins perform a lot of functions and as a result there are a lot of different types of proteins in our bodies. When I eat food that has x grams of 'protein', what is this? A homogenous ...
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Which genes/proteins constitute the core components of the circadian clock?

What the title says. For instance in Drosophila melanogaster and Mus musculus (see Patke et al. 2020) the CLOCK, CYCLE/BMAL, CRYPTOCHROME, PERIOD setup seems to be conserved. But other components also ...
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1answer
103 views

Has life on Earth explored the entire space of genomes?

Recently I came across a 2008 article, the authors of which argue that in fact the space of protein sequences is not as large as it might seem, and that life on Earth has most likely already explored ...
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1answer
54 views

What is the point of calculating extinction coefficients of a protein without Cys residues?

ProtParam computes various physico-chemical properties that can be deduced from a protein sequence. One of these parameters are "Extinction coefficients". They provide two values. One value ...
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510 views

Why can't H3O+ ions pass through aquaporins?

Aquaporins are proteins that facilitate the movement of water (and related molecules) through cell membranes. (Also, these transport proteins are very specific about what they transport.) ...
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308 views

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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When subtracting background from a Western blot image, does the method of subtracting background signal have to be the same for all blots analysed?

I am analysing some Western blot images and I want to subtract the background signal for my protein bands of interest. Previously, the way that I subtracted background was to draw a rectangle (that ...
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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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1answer
30 views

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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1answer
41 views

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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19 views

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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1answer
120 views

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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1answer
39 views

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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1answer
166 views

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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1answer
60 views

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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1answer
39 views

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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147 views

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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1answer
54 views

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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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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388 views

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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1answer
105 views

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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How to combine data points from different western blots into one graph?

I am doing Western blot data analysis and I have data from two different western blots. In my two Western blots, I have labelled for the same proteins. I am comparing knockout (KO) samples against ...
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Question about total protein normalisation in western blot image analysis

I am analysing western blot data and I am using total protein normalisation using Ponceau S. My supervisor and I have agreed to use total protein normalisation for my western blots instead of using ...
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1answer
39 views

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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1answer
28 views

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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In Western blot, is Ponceau S a valid loading control if band intensities vary between lanes?

I have done a Western blot and I am using Ponceau as a loading control to normalise my measurements against a protein of interest. For my Western blot I have a number of wild-type and knockout samples ...
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1answer
42 views

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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2answers
290 views

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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209 views

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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1answer
45 views

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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1answer
37 views

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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1answer
15 views

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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How are integral monotopic proteins synthesized? Is it the same process as a transmembrane integral protein or are they different?

In a book I was reading, they state that secretory proteins and integral transmembrane proteins are synthesized in the same manner. But, they don't mention how integral monotopic proteins are ...
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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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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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1answer
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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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