Questions tagged [proteins]

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

Filter by
Sorted by
Tagged with
1
vote
0answers
12 views

what is the relation between protein domain and disease? [on hold]

I am computer science student, and I am interested in bioinformatics. Thus, I am just at the beginning of learning some biology concepts. I am asking about the relation between protein domains and ...
0
votes
1answer
27 views

Is the chitin in an insect's exoskeleton cross-linked?

This answer to the question How to clean and preserve a cicada's molted exoskeleton (exuvia)? states: The exuvia is made of cross-liked chitin, and will not decay. You don't need any special ...
-2
votes
0answers
13 views

I have an 4 grid clustalw matrix result please help me decode it [on hold]

Percent Identity Matrix - created by Clustal2.1 # # ...
-1
votes
0answers
17 views

Which is actually better for you - lyophilized vs hydrolyzed collagen peptides?

From my research and the common selling feature of hydrolyzed proteins and collagen peptides that they offer the highest absorption rate. This however does not relate to amino acid synthesis, as ...
1
vote
0answers
33 views

Can genetic circuit alone alter protein structure? [on hold]

I would like to know if there are examples of genetic circuits, that usually appear in synthetic biology, can modify aspects of protein structure (allosteric sites, regiospecificity, and so on) i.e. ...
0
votes
1answer
39 views

Why is the amount of protein variants in a human genome higher than gene variants? [on hold]

Why does the human genome have more protein variants than gene variants? Is this because of PTMs?
0
votes
0answers
13 views

Iterative macrocyclic design in drug design [closed]

Suppose that I have some proteins (for example, kinase) that their structures are completely determined (cryo-EM, crystal structure from X-ray crystallography). Given that I have raw peptides, I want ...
0
votes
0answers
47 views

Can protein/codon chirality be described in tRNA molecules? [closed]

Is left-handed chiral protein and right-handed chiral RMS factored in to the tRNA molecuar structure? If so, how.
0
votes
0answers
25 views

What aggregates can be seen in reduced SDS-PAGE? [closed]

Can dimers and trimers of a Ig's heavy chain and light chain be seen in SDS-PAGE reduced with heat and 2-ME? Or will they be reduced to monomers? Thanks in advice!
0
votes
0answers
23 views

Dipeptide approximations for making Ramachandran plot [closed]

How did Ramachandran arrived at his plot? Did he consider only the nearest neighbor amino acids and their steric clashes? In general all those interactions in protein are electrostatic in nature which ...
2
votes
1answer
40 views

Lysozyme amino acid sequence: N-terminal extension

I looked up the amino acid sequence of lysozyme here: http://www.biology-pages.info/L/Lysozyme.html Then I crossed referenced that with the lysozyme sequence on UniProt: https://www.uniprot.org/...
2
votes
1answer
63 views

What is the function of spongin in sea sponges?

Sea sponges (Porifera) use different types of skeletons to support their structures. Some skeletons are built from minerals, some are built from proteins like spongin, and some use both. My question ...
3
votes
1answer
48 views

Can denatured GFP show fluorescence?

GFP ( green fluorescent protein) can show green fluorescence. And its fluorescence is due to the tri peptide chromophore which is given in below I was wondering, can we observe fluorescence, if we ...
2
votes
2answers
51 views

Why does it matter to predict protein structure?

And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ? Moreover, I've read that knowing the ...
0
votes
0answers
10 views

Relationship between Communication Proteins and Gap Junctions

What is the relation between communication proteins and gap junctions? Do the communication proteins make up gap junctions or something?
1
vote
2answers
63 views

What is the subcellular location of synthesis of non-essential amino-acids?

What is location of non-essential amino acids synthesis in a cell? Is it some specific organelle? And what is the gene driver behind this? I thought the whole point of DNA is coding for how to ...
1
vote
1answer
34 views

How can I get the yield of my purified immunoglobulins?

In order to get the yield of IgY through a set of purification steps, what method can I use? Thanks in advice!
4
votes
4answers
331 views

How can I change my buffer system for protein purification?

I have a protein that I purified in PBS buffer, pH 7. I will do dialysis to remove salt and will then further purify the protein with ion exchange chromatography. I will need to use another buffer (...
3
votes
1answer
35 views

What buffer should I choose for IEX chromatography for purifying IgY

I will use ion exchange chromatography with an anion exchange column to purify chicken IgY. Prior to this I did dialysis to remove salts from previous purification steps, is it possible after this ...
0
votes
1answer
40 views

What does “count in gene set” mean?

I am trying to understand the analysis generated by STRING. In analysis for biological processes table, there is a column titled "count in gene set." This gives a value for example "68 of 498". What ...
0
votes
0answers
7 views

What is the relationship between Ca- and Na-ions and mucins and why?

According to Wikipedia https://en.wikipedia.org/wiki/Mucin#Secretion mucins (Proteins that form mucus) obtain viscoelastic properties by the Exchange of sodium and Calcium Ions. What is Happening ...
0
votes
0answers
17 views

Why does the ratio type III collagen:type I collagen increase after a tendon injury?

I read on {1}: Type III collagen has accumulated at the rupture site [of human Achilles tendon] probably due to microtraumas and the subsequent healing process. […] The increased content of type ...
0
votes
0answers
10 views

How are multiples transmembrane proteins translocated or embedded in the membrane?

This image is in the textbook, Molecular Biology of the Cell. I understand why the start and stop transfer sequences must alternate, but why is there 2 consecutive start transfer sequences at the N ...
1
vote
0answers
28 views

Genes of the electron transport chain

Where are the genes of proteins that make the electron transport chain of mitochondria?(are they in in the nucleus or they are in the dna of the mitochondria itself?) Thanks for this answering system ...
0
votes
0answers
30 views

conversion of distance matrices to pdb/coordinates

I am currently facing two transformational issues. Suppose I am given a protein's residue sequence and calpha distance matrix; is there a way to generate the 3d coordinates of the protein's residues ...
5
votes
2answers
190 views

Why do protein solutions have to be alkalised in biuret test?

I’ve read that CuSO4 solution reacts with peptide bonds that connect amino acids to create a violet colour, but the instructions always tell me to add NaOH solution to the protein solution before I ...
2
votes
2answers
215 views

How do organophosphates actually work?

The common explanation as to what the primary mechanism of action for organophosphates (and carbamates) is is the inhibition of the enzyme acetylcholinesterase and resulting buildup of acetylcholine ...
3
votes
1answer
59 views

Immunoprecipitation compared to western blotting

Immunoprecipitation and western blotting are both used to locate a specific protein within a sample and to isolate it. In immunoprecipitation, a specific antibody and agarose beads ( or other ...
0
votes
2answers
43 views

Preparing sample for SDS PAGE

I have more than 10 cell lysate samples (70 µL each) whose concentration varies from 1.9 mg/mL to 4.8 mg/mL. I have 5X and 2X SDS sample buffers. I would like to prepare SDS PAGE samples in such a way ...
37
votes
1answer
5k views

Why are prions in animal diets not destroyed by the digestive system?

According to CBC: Mad cow disease is the common name for a condition known technically as bovine spongiform encephalopathy, or BSE. [...] The only known source of mad cow disease is from animal-...
1
vote
0answers
17 views

Where can I find and download HMMTOP training set?

I would like to perform redundancy reduction for my test set for membrane topology prediction. I checked the 1998 paper and website of the HMMTOP server but haven't found any download links for the ...
5
votes
1answer
68 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 ...
0
votes
0answers
29 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 ...
1
vote
1answer
82 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 ...
1
vote
1answer
51 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 ...
1
vote
0answers
17 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 ...
0
votes
0answers
32 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 ...
0
votes
0answers
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 ...
-1
votes
2answers
66 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 ...
2
votes
1answer
47 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 ...
2
votes
0answers
118 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 ...
1
vote
0answers
29 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 ...
4
votes
2answers
149 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: ...
1
vote
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 ...
0
votes
1answer
116 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 ...
6
votes
0answers
54 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/...
8
votes
1answer
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 ...
2
votes
1answer
20 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:...
4
votes
0answers
26 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. ...
2
votes
1answer
422 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 ...