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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33 views

How does the immune system recognize harmful proteins?

How does the human immune system detect whether a protein happens to be a protein found in the body that is supposed to be there, a bacterial toxin that should be inactivated, an already inactivated ...
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What is a secretion target family protein?

I came across this link: https://www.genome.jp/dbget-bin/www_bget?btw:BF38_3398 What is this protein, is it a secreted effector protein or is it something else? What is the difference between type ...
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Are there only a few alleles or groups of many alleles impacting protein structure and function?

I'm in the first year of Medicine and I'm studying Genetics and Evolution. I have this doubt in the back of my mind and I'm not being able to move forward without someone explaining me what's wrong ...
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164 views

What is the difference between a signal peptide and a transit peptide?

From what I know, the two names are used interchangeably and I haven't found any resource which says otherwise either. Is there at all any difference, is there a transit peptide that is not a signal ...
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How do cells relocate transmembrane proteins from one side of the cell to the other? Is it possible?

Is there a process by which cells can relocate proteins residing on the cell membrane in areas of low demand to that of a high demand location somewhere else in on the cell? What's that process called?...
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How does the body detect irreversible binding to receptors?

I have read an article on Wikipedia about irreversible agonists and antagonists. These permanently bind to a target receptor on a cell. However, the receptor protein is then internalized and recycled ...
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765 views

What's the difference between physical (direct) and functional (indirect) protein interaction?

I read that the Protein-Protein interactions one can consider are generally of two types, namely physical and functional, but I cannot get the difference between the two. I was just thinking that if ...
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119 views

Why do BRAF mutations appear more in skin cutaneous melanoma?

When looking at the tissue expression of the BRAF protein it seems that BRAF is regularly expressed in almost all of the tissues. There is elevated expression in tissues like the Testis and the ...
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241 views

Plasma Membrane Proteins and Cytoskeletal Attachment

Regarding membrane protein functions, which of the following statements is CORRECT? a. Membrane proteins are responsible for both cell to cell recognition and cell anchoring and are ...
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protein size range for ultrafiltration or nanofiltration

I am hoping to concentrate mixed proteins in homogenized leafy vegetables such as kale, spinach etc (after removing pulp and fibers) as a first step in further investigations (second step using size ...
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1answer
38 views

Where do the lysines come from during ubiquitination?

I know that Ub forms an isopeptide bond with lysine, but where do the lysine come from? Are they just always available for the Ub to find to during the ubiquitination process? Is there a free lysine ...
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1answer
118 views

Is it possible for human body to convert carbohydrates to protein? [closed]

Is it possible for human body to convert carbohydrates to protein to build muscle for example? EDIT: I read in many articles that you should eat more than 1.5 gram protein for each 1 kg weight of ...
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What is the fastest way to crystallise lysozyme (for student course)?

High school sudents are going to visit my university and I plan to demonstrate crystallisation of lysozyme. I ordered pure lysozyme from VWR. I can easily crystallise this within 15 min in batch (4% w/...
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How can one create images like those in the PDB ‘Molecule of the month’?

I am impressed by the illustrations for the Protein Data Bank ‘Molecule of the month’, e.g. the gorgeous image of DNA Helicase below. Does anyone know how they were made or how one might create ...
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212 views

Do chaperone proteins misfold?

If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones ...
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1answer
21 views

Can someone help me interpret these charts on fluorescent polarization?

I have to present an article about binding designed proteins to fentanyl for my biochem class; I understand everything except how to interpret these charts on fluorescence at the very top of Figure 2a:...
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93 views

Etymology of PAX proteins

What is the reasoning behind naming proteins first found in Drosophila as paired box? All I could find on internet is that it was first found in Drosophila as a protein with paired domain, but I ...
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How do scientists determine the nature of ions passing through a channel/carrier/pump?

The NCE (Sodium Calcium Exchanger) transports 3 Na+ inside the cell for 1 Ca2+ outside. How did we figure this out, and other mechanisms of this sort? If it were a protein, we could tag it with GFP. ...
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38 views

Obtaining protein atomic co-ordinates from dihedral angles

https://en.wikipedia.org/wiki/Dihedral_angle#/media/File:Protein_backbone_PhiPsiOmega_drawing.svg I've been reading on Protein Amino Acid Sequences and their 3D structure. It seems that the 3D ...
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1answer
544 views

What is the importance of alkaline condition in biuret test?

Biuret test aims to quantify the amount of protein in a given unknown sample. Biuret agent contains copper sulphate, sodium potassium tartrate and Sodium hydroxide. Coppper ions form the complex of ...
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93 views

When does protein folding begin?

I had always assumed that protein folding is an independent activity that occurs after translation is complete. However, recently, I learned that intermolecular forces begin shaping the peptide bonds ...
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81 views

What are the different types of helices in protein secondary structures and how do they differ?

What are the different types of helices in protein secondary structures and how are they differentiated? In the DSSP docs, types of helices mentioned are: Alpha-Helix, Helix-3, and Helix-5. In the ...
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How does DNA code for the actual *shape* of individual body parts/areas (NOT segments or Hox genes)?

Just to save the trouble - I am not asking for general information on how DNA codes for proteins and definitely not how Hox genes work. I have a very good understanding of the evolutionary process and ...
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How many proteins are common to all species? [duplicate]

Are there any proteins that are common to every Species in Earth's biosphere? If so, how many? If not, are there any proteins common to every species of an entire Kingdom? If so, how many? If not, ...
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118 views

How does DNA determine all of our hereditary traits?

It's my understanding that DNA codes only for protein synthesis. Does that mean that hereditary traits, like the shape of our nose, are determined only by the proportions in which various proteins are ...
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366 views

Will new proteins incorporating new amino acids trigger an immune response?

This article reported that scientists have succeeded in adding two new bases to the quartet of A, C, G and T, resulting in non-canonical amino acid. Additionally, the bacteria in which this was done ...
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Given ATP synthase's structure, how can 3.33 protons ultimately synthesize one and only one ATP?

I am familiar with the structure and function of ATP synthase, but one small detail doesn't seem to make sense. It also happens to be a detail that seems very hard to express. Depending on the ...
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What created the first ribosome

If a ribosome is made of protein, yet is used in protein sysnthesis, what created the first ribosome? What created the ribosomal RNA?
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What does ubiquitination between 2 genes mean?

I have come across the Hedgehog signaling pathway. In this pathway, the genes Cul3 and ptc have an interaction of ubiquitination (The information is available from the KGML file). What does this ...
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Amino acid substitutions near the receptor binding site HA protein in type A H3N2 influenza strains?

I have read the scientific paper, "Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution" by Björn F. Koel et al (http://science.sciencemag.org/...
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How does one predict how large of an effect on antigenic drift a substitution in the amino acid sequence of a surface protein of influenza has?

I know that some amino acid substitutions are more effective in causing antigenic drift than other substitutions based on their location in the 3d structure of the HA protein (proximity to the ...
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How to take precise/low number of cells from cell lysate? [closed]

I would like to know that how can we take low or precise number of cells from a cell lysate? (without using any protein quantification assay). Let say, If I have a cell line having cell density 5x10^...
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does Trichloroacetic acid remove fats from milk

I am trying to detect melamine in milk. As a part of preprocessing, I add 200 ul of TCA to 1 mL milk,and after filtration I get a clear solution. Does the filtrate contain fat. I feel I am having ...
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Are all enzymes proteins?

So throughout my education and research career I have been taught that all enzymes are proteins. This makes sense when you consider enzyme denaturing and folding/shape etc. However, I was recently ...
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58 views

How do people measure how many calories or proteins/fats/сarbohydrates are in some food?

How is the composition (in fats, proteins or carbohydrates) of a certain food estimated and how is the amount of calories provided by the food calculated?
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39 views

How is the activation energy lowered in an enzyme by just orientating the reactants closer to one another?

If the activation energy is lowered, bond strength has decreased. How does purely orientating the reactants closer to one another lower the activation energy in a protein? The only thing I can think ...
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Quantify Protein Denaturation with Change in Solubility

I plan to run a lab which compares the impacts of ethanol and methanol, in varying concentrations, on the denaturation of whey protein. Change in water solubility is a good indicator of the degree ...
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What is the longest-lasting protein in a human body?

Protein life times are, on average, not particularly long, on a human life timescale. I was wondering, how old is the oldest protein in a human body? Just to clarify, I mean in terms of seconds/...
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1answer
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False positives in TAP - MS experiments

Is anyone aware of a website where they show common false positives often found when doing a TAP-MS experiment to find protein-protein interaction experiments? Particularly the Acs1 protein (Acetyl-...
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94 views

Centrifuge after sonication

I follow a protocol to get protein from E.coli cells after sonication. I used to grow 6 litres of large cultures and add IPTG to express the protein. I centrifuge for 10 mins at 8,000 rpm and get the ...
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Is tyrosine hydrophobic or hydrophilic?

I’ve seen tyrosine classified as a hydrophobic amino acid due to its aromatic ring in some textbooks and as hydrophilic due to its hydroxyl group in other textbooks. How does tyrosine actually ...
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Are there any enzymes without aromatic amino acids?

I'd like to try a new spectroscopic technique to study enzymatic reactions (which reaction doesn't especially matter, something simple and with fast kinetics like catalase would do fine - I'm just ...
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1answer
84 views

How to characterize stability of a protein from Trp fluorescence vs [denaturant] curves?

A colleague of mine has taken Trp fluorescence measurements from a dimer in combination with various ligands, over a range of denaturant concentrations. The idea is that ligands which bind more ...
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How can we quantify the effect of pancreatin (biological enzyme) on the clarification of milk powder

Alright so I'm trying to quantify the rate at which casein (protein constituent of milk powder) is converted into a product (I am unaware of) by pancreatin (a biological enzyme that speeds up the ...
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Which server to use for volume and accessible surface area calculation of proteins

I want to find the accessible surface area and the volume of a protein, giving PDB file as the input for the protein. I used two servers, 3vee and Vadar. For the PDB id, 1LTM, the websites are giving ...
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1answer
95 views

Why is gel used in electrophoresis?

In analysing amino acids content in a protein through gel electrophoresis, What's the purpose of the gel? Wouldn't putting the amino acid in the gel prohibit the amino acid from dissolving into the ...
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Molecular animations of, say, protein synthesis, are simplified, but how exactly?

In several animations of biological processes (eg protein synthesis (go to frame 1.20mins), DNA replication, etc), molecules such as amino acids are shown heading straight to the replicating protein ...
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Does every protein encoding gene necessarily have a transcription factor?

For instance, transcription factor gene A is responsible for activating gene B that encodes protein 1. However, it is possible for genes like gene B to encode proteins without having transcription ...
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596 views

What does the acronym ‘PIN’ stand for referring to PIN proteins in plants?

There are so called PIN proteins, or PIN-formed proteins, in plants. What does this acronym mean? Wikipedia briefly explains the function of the protein but not the origin of the name. It's not ...
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Net electrical load of a peptide

I have to determine the electrical charge of the next peptide chain: C - E - H - P I know that this page is not there to raise doubts about this style, but I have looked for resources on the ...