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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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42 views

Backbone hydrogen bonds between adjacent amino acids in a protein?

Is it possible for two adjacent amino acids in a peptide to form hydrogen bonds between the backbone NH and CO? Are there any examples of such situations in proteins and how common are they? If ...
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21 views

Intein Splicing

Currently I am trying to read and understand this paper on intein splicing. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/22001202 However, I'm a little confused with Figure 4. Why do the ...
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32 views

Does digestion require hydrochloric acid?

Would our digestion function any differently if we secreted something else, like sulfuric or nitric acid, instead? I'd assume an acidic environment may be required, but not sure if chloride is also ...
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37 views

If overcooked hard boiled eggs show these green sulfide rings, why do scrambled/fried eggs not show this?

In the image above, the dark green rings are ferrous sulfide rings, caused when the sulfur from the egg white reacts with the iron in the egg yolk when the egg is overcooked. I was wondering, given ...
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42 views

is a-keratin a fully functional protein?

is a-keratin before it coils with another polypeptide, makes chains, and build intermediate fillaments a fully functioal protein? I mean, is the single monomer of a-keratin a protein or it has to ...
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47 views

What's a good reference for learning about recombinant proteins?

I'm looking for books and articles that can bring me up to speed on the design, expression, and purification of mammalian proteins in recombinant systems, both in E. coli and in more complex systems ...
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14 views

How do you interpret the resulting bands of gel zymography?

I would like to clear up some things for gel zymography. I understand that bright bands show proteolytic activity. But which molecular weight do these bands correspond to? Is it the weight of the ...
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24 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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5 views

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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2answers
51 views

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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1answer
110 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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2answers
161 views

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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72 views

Why are dietary recommendations for methionine consumption combined with cysteine?

I want to understand the amino acids missing in certain vegetables. I looked up the US recommendations for amino acids (source: wikipedia). I don’t understand why they pair Methionine + Cysteine: ...
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1answer
45 views

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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1answer
645 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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36 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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2k views

What inactivates pepsin in infants?

In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach. Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk ...
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176 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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27 views

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
34 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
115 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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49 views

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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2answers
234 views

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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1answer
200 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
17 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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2answers
89 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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23 views

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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1answer
31 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
144 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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1answer
43 views

What does “PDPN+ cells” means?

Are they podoplanin positive cells (cells that tested positive for podoplanin)? "...though it has been shown that podoplanin (PDPN+) cells analogous to mouse FRCs are found in human secondary ...
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2answers
79 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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1answer
40 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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0answers
121 views

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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23 views

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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75 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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2answers
262 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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2answers
10k views

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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1answer
49 views

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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1answer
35 views

How to convert enrichment/depletion to frequency for comparing deep sequencing to sequence profile?

I have two datasets, from different sources, that I need to compare. The first set is deep sequencing results of a directed evolution experiment, where I have the naive library and selected library ...
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14 views

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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1answer
28 views

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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1answer
25 views

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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1answer
164 views

What are the secondary structure requirements for cell-penetrating peptides AKA protein transduction domains

Cell penetrating peptides. Cell penetrating peptides (CPPs) are a class of short amino acid sequences which are sufficient for crossing cell membranes and delivering themselves along with any ...
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0answers
19 views

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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16 views

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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3answers
485 views

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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1answer
53 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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1answer
34 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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45 views

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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4answers
8k views

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/...