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

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38 views

What effects would be caused by exposure to common life forms with opposite enantiomer biology?

Pretend a human had their body "reflected": heart on the wrong side, etc.; but also at the biochemical level: proteins, sugars, cells, DNA, everything. What would the effects be of that human's ...
7
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1answer
92 views

What is peptide mapping?

After searching online for peptide mapping to my understanding it can be treated as the fingerprint of the protein. It is obtained at the end of several chemical processes and it helps to understand ...
9
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2answers
65 views

How can we predict protein folding in silico?

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.). The question that I have is: How do you know ...
5
votes
2answers
101 views

Proteins that give color (without fluorescence)

Is there proteins that have strong color, that could be seen without the need of UV and with naked eyes (with white light) - in mammalian cells? Searching for reporter, something like GFP, but that ...
0
votes
1answer
16 views

Using Jpred to predict secondary structure

I'm trying to use Jpred to predict secondary structure for a protein sequence. When I run J-pred, I get a bunch of hits from PDB. I've also noticed these 'hits' are the same name as the templates i ...
0
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1answer
26 views

One Gene and many proteins [closed]

Imagine a gene with $n$ exons and $m$ introns. How many proteins are possible from that gene? Would all the proteins be isoforms?
1
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1answer
39 views

Which protein complex is composed of the greatest number of different kinds of proteins, and how many types are involved?

Why are some protein complexes composed of many different types of proteins? How many different types are they composed of? In particular, which protein complex has the greater number of different ...
4
votes
1answer
29 views

Are all protein composed of all the amino acid (in animal) or are there less diverse protein?

I have a question about amino acid composition of proteins: Are there proteins in animals that are made up only from a small subset of amino acids? So instead of all 20 amino acids let's say only 6-14 ...
3
votes
1answer
49 views

Why do some proteins “use” a beta barrel structure instead of alpha helices in transmembrane space?

Most proteins are fixed in the membrane by alpha helices. But some use beta barrels. Wikipedia describes beta barrels as used for porins, preprotein translocases, and lipocalins. To me, a coiled coil ...
5
votes
2answers
988 views

What has caused life to choose this unfathomably tiny subset of all possible proteins?

I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever ...
6
votes
2answers
147 views

What is the purpose of using two layers of gel in SDS- PAGE?

I just made a SDS-PAGE with a top layer of stacking gel and a bottom layer of separating gel with different pH values of 0.5M Tris-HCl. The stacking was 6.8 and the separating gel was 8.8. What about ...
0
votes
1answer
40 views

What is a complex?

In my text book it says that "Troponin" is a complex of Troponin C, I and T. In this sense, what is the relation between Troponin complex and C, I, T?
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0answers
13 views

About post translational modifications

A secreted monomeric protein of 132 amino acids, lets say protein XY, has two N-linked glycosylated Asparagine residues, at position 10 and 67, and act as a ligand for a XY-Receptor (XYR). I want to ...
3
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0answers
19 views

Is there a cellular mechanism that detects Ribosomal damage?

What kinds of options, if any, do cells (Eukary and Prokary) have for detecting, and repairing damage in Ribosomes (of all types)? I am curious as to what happens when a cell sustains damage of some ...
0
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0answers
35 views

Best software for protein in electric field modeling?

I'm trying to find a free, or cheap, software program to model the movement of a heterotrimeric protein in an alternating electric field. The dipole and crystal structure of the trimer are known. ...
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0answers
24 views

How does a cell create/gain its initial ribosomes for protein synthesis?

I did some quick google searches for how a cellular organism generates or acquires its first ribosomes, but I found nothing. For instance, do the organisms initiating replication form extra Ribosomes ...
4
votes
1answer
39 views

How can human infants express chymosin with only a pseudogene at their disposal?

I read on the Wikipedia article about Chymosin http://en.m.wikipedia.org/wiki/Chymosin It stated that chymosin is produced by gastric chief cell in human infants. But it also stated that human only ...
1
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0answers
30 views

Compare Proteins - Structural / Sequence parameters

I have been working on algorithms that extract co evolutionary signatures from protein sequence. As a result of my work I got some evolutionary information which possibly explains cotranslational ...
1
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0answers
19 views

Question about cytoskeleton coordination

I am trying to study for a biology and I am having some confusion over the following topic. Can anyone help explain/ shed some light on the concepts of Rho family GTPases. Is it true that we have Rho ...
0
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0answers
19 views

Where does the oxygen and water produced from the decomposition of hydrogen peroxide by catalase enzyme go?

How are they disposed of by the body, or are they disposed of at all? Since our body needs water and oxygen anyway, I'm speculating that these "waste product" will be reused/recycled by the body in ...
5
votes
1answer
152 views

Where do amino acids get attached to tRNA and where is it synthesized?

Some very basic parts of transcription/translation seem to be left out in various literature. I can't find the answer to this anywhere: How exactly is tRNA synthesized? I realize that mRNA is ...
0
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0answers
23 views

How to do Sliding 80mer Window search against a database with fasta

I know how to do a 80-mer window search against a single protein ...
5
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4answers
83 views

Any good website/book to understand protein folding and enzymes?

I'm looking for a good, understandable and simple explanation about protein folding, mechanisms and function, and their relationship with enzymes. I understand that the protein is a polypeptidic ...
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0answers
22 views

Incremental denaturation of protein mixtures

When a protein solution is heated above the denaturation temperature, it seems that denaturation does not happen at the time the temperature is reached, but it takes some time. I assumed that ...
4
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2answers
79 views

Why proteins are not visible on my membrane after ponceau staining?

I have a problem in western blot that I can't resolve by myself. When I am use to add 100 microgram of proteins for each sample but after running and transfer its impossible to me to see bands of ...
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0answers
24 views

How do BCAA's promote faster muscle recovery?

I am aware that ingesting Branched chain amino acids (BCAA's) prior, during, and after workouts has an effect on muscle recovery due to their difficulty of metabolism. However, how much more ...
5
votes
2answers
62 views

What percentage of a cell's volume is occupied by protein?

I was looking at one of David Goodsell's illustrations of a cell: And it seems to suggest a very crowded picture of the intracellular environment. Just how crowded are cytoplasms? What percentage ...
3
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0answers
39 views

Can't resolve protein with native PAGE

This is a native gel. Let's call the left 2 lanes protein A and the right 2 lanes protein B. B is the same as A except it has a FLAG tag. They are both homotetramers of about 65 kDa. After ...
4
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3answers
83 views

Amino acid compatibility

The (human) genetic code encodes 20 amino acids. They form a protein using peptide bonds. Each amino acid has a carboxyl group (COOH) and an amino group (NH2) that can potentially form a peptide bond. ...
2
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0answers
39 views

Are there sterilisation methods that do not denature proteins as heat does?

Context: Most countries require milk to be sterilised through radiation or heat to remove possible harmful bacteria. Both of these processes denature the proteins in the milk (ref). Are there methods ...
2
votes
1answer
42 views

Edman method to identify peptides with Phenylisothiocyanate (PTH)

We all know that in this method the PTH reacts with the first amino acid (aa) from the N-terminal to the peptide and separates from it giving PTH-aa so that we can know the amino acids sequence in the ...
3
votes
1answer
55 views

Proteins in Milk, Oat , Eggs and Soy

I have read that there are proteins in oat which are similar to those in soy, milk and eggs. I know nothing about biochemistry, and I'm struggling to decipher the info i find.. the closest Ive got to ...
0
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0answers
48 views

Medical Uses of toxic venom

One interesting thing I recently learned is that venom has medical uses that can actually save lives! But from what I see so far this either applies to venoms from creatures that are not fatal to ...
3
votes
1answer
88 views

What happens to the precursor protein's signal sequence after it is cleaved?

Where does this signal sequence "go" after it has been cleaved by signal peptidase and what is its next function?
5
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1answer
60 views

Is consuming proteins different vs. consuming amino-acids and how?

Yesterday I had a discussion with a friend. He said that consuming proteins and amino-acids is different. He said that those who grow muscles would agree on that. I wanted to argue against that ...
2
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0answers
24 views

Is it possible to isolate and analyse intermediates of protein folding?

I would like to know if there is an assay which could allow us to analyse a protein before it has assumed its 3D functional form. While studying structural biology, I only came to know the forces that ...
6
votes
3answers
203 views

Proteins folding

Some of us are involved in the folding@home project, spending time, money and resources. I would like to know an answer to two main questions: how do we know we fold it right? I mean these models ...
2
votes
1answer
30 views

Protein PTM site prediction

Is there any in silico analysis method to predict post-translational modification sites on a given protein?
3
votes
1answer
37 views

Divalent cation binding to calmodulin

I have carried out a native PAGE with 4 reaction mixtures. To each I had added an equal volume of EDTA (1 µl/1mM) to sequester any divalent ions and an equal volume of calmodulin (5 µl/0.5 mg/ml). I ...
2
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0answers
48 views

How do I identify the protein with the highest Disulfide bond density? i.e protein with highest ratio of Disulphide bonds per Peptide bond? [closed]

I want to list all proteins in the protein database and list them by the ratio of number of disulphide bonds per peptide bond. I am not particular about the reliability of identification of ...
1
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0answers
42 views

Nutritious protein substance for vitamin enhanced crop?

I am not a bio or science major, but we have a subject, like an elective on biotechnology and we were tasked to think of a product that hasn't been invented yet. My groupmates and I thought of a ...
1
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3answers
74 views

What is the relationship between protein-protein interaction networks and metabolic networks? [closed]

I am trying to find out how these networks can be linked together. I know that Protein-protein interaction networks and metabolic networks both fall under the Intra-cellular type of biological ...
3
votes
1answer
32 views

IPTG and lac operator with e coli for foreign gene question

We did an experiment were we have e coli with a plasmid with a gene from another bacteria in it, and we put in IPTG in for induction. Will after looking up more about IPTG online I see it's related to ...
6
votes
1answer
39 views

Has the protein composition (with identification) in honey and other honeybee byproducts been studied?

I am interested in studying honey and other honeybee byproducts. I have not been able to find sequence or structure records for any of the contents of honey. In particular, I want to study the ...
2
votes
1answer
154 views

Proteins: Post translational modification

I am a physicist and trying to understand some protein chemistry for a small project. Basically, amino acids combine to form proteins and after forming the primary structure, some chemical ...
1
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0answers
36 views

Which method would more accurately help to identify the unknown concentration of a protein sample between the A280 and the Bradford methods?

I quantified my protein using the standard Bradford method and the A280 methods and obtained values that were far off from the theoretical value of the protein of interest, and therefore was wondering ...
3
votes
1answer
132 views

Do these things contain amylase? [closed]

I have 10 samples of some food or other things and I need to know, if it contains amylase. I already ran an experiment with storch and iodine, but I have to make it right and my experiment must not be ...
1
vote
2answers
37 views

How do I find a protein from this DNA sequence?

I have a DNA sequence from a sequencer. How can I determine what protein is it? I tried some translator but it didn't help. What protein is this and how can I determine it? The sequence: ...
6
votes
1answer
75 views

Is using Hidden Markov Models to find homologues sensible in abstract, short sequences?

HMM alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss. I am only looking at a small ...
8
votes
2answers
59 views

All UniprotIDs of a cancer pathway

I need to download all uniprotIDs of a cancer pathway, say the AKT Signaling. It may be super easy, but I don't know which resource to look at since it is a new field. How/where do I find these?