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

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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 ...
0
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1answer
19 views

Will tagging a protease with HlyA for secretion inactivate the protease?

We are looking to secrete the protease proline iminopeptidase by attaching the secretion signal HlyA to the protease in a gene circuit. Since the natural HlyA secretion sequence in Escherichia coli ...
4
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1answer
43 views

Proline Iminopeptidase v Proline Aminopeptidase

We're an undergraduate independent research team and we are having trouble purchasing commercial proline iminopeptidase as it is unavailable on Sigma Aldrich and very expensive on other websites. We ...
1
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0answers
47 views

aluminum sulfate vs (NH4)2SO4 in Colloidal Coomassie Staining Sol

I have been interested in Colloidal Coomassie Staining to detect proteins in PAGE gel. I found 2 different recipes: one of them uses aluminium sulfate, the other, (NH4)2SO4. I am wondering about ...
0
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0answers
56 views

How do I select the sequence identity threshold in cd-hit to cluster proteins for core genome comparative analysis?

Can anyone suggest a method for selecting the sequence identity threshold for protein clustering in cd-hit? If I use too high of a threshold, then the number of protein clusters shared between three ...
9
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1answer
157 views

Circular mRNA to produce long proteins

Ribosomes can read mRNA and produce proteins, if we somehow make a circular mRNA for the ribosome to bind onto, it will make infinitely long "proteins", (since ribosomes can make very big proteins, I ...
2
votes
1answer
39 views

In protein-protein interactions what is the difference between a binding site and an interface?

I see binding site and interface used almost interchangeably in the literature, but I'm not sure if it is exactly the same thing or not - what is the difference?
1
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2answers
30 views

T7 Tagging Next to Met

Will a T7 tag still work if it is placed next to a start codon? Meaning, will it still work with a Met attached to it in the amino acid sequence? Thank you!
2
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1answer
107 views

Why does the inhibition of translation initiation cause the accumulation of 80S ribosomal monosomes?

As I have read in (1), inhibition of translation initiation will increase the number of 80S ribosomes while decreasing the fraction of polysomes due to the polysome-runoff. The net effect is to ...
2
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0answers
55 views

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

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
190 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 ...
5
votes
4answers
335 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 ...
4
votes
3answers
215 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. ...
6
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2answers
666 views

Solvent Accessibility, the 20% cut-off method

I'm reading the papers linked below and all three of them mention a 20% cut-off for buried/exposed residues, by calculating a relative solvent accessibility (RSA) value. I understand how the RSA is ...
4
votes
2answers
197 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
99 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
votes
1answer
39 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
vote
1answer
56 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 ...
3
votes
1answer
194 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 ...
4
votes
1answer
35 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 ...
5
votes
2answers
1k 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 ...
14
votes
4answers
1k views

How many human proteins have a solved 3D structure?

I was wondering how many human proteins have a solved 3D structure. Is there a database with only human proteins? I looked at pdb but couldn't find a filter.
6
votes
2answers
2k 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
160 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?
0
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0answers
51 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. ...
0
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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
23 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 ...
4
votes
1answer
85 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 ...
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0answers
45 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 ...
1
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0answers
60 views

Compare Proteins - Structural / Sequence parameters [closed]

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 ...
7
votes
3answers
19k views

Why are 3 nucleotides used as codons for amino-acid mapping in DNA?

DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length? A related question can be ...
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0answers
32 views
0
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0answers
40 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
519 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 ...
5
votes
2answers
369 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 ...
2
votes
1answer
59 views

Is it possible that a set of functionally related proteins in a pathway fulfill different functions? [closed]

Could it be that a given pathway of enzymes (or proteins in general) may fulfill different purposes in a cell by for shifting partners? Say protein A activates B, B activates C and C has a specific ...
1
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0answers
68 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 ...
1
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0answers
23 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 ...
5
votes
2answers
459 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 ...
0
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0answers
77 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 ...
2
votes
0answers
98 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 ...
3
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0answers
286 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 ...
2
votes
1answer
96 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 ...
6
votes
3answers
247 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 ...
3
votes
1answer
96 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 ...
3
votes
1answer
238 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?
4
votes
0answers
34 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 ...
2
votes
1answer
68 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
56 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 ...
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3answers
134 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 ...