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

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1answer
26 views

Evolution of robustness towards mutations

Did some proteins evolve to be robust to detrimental mutations, i.e. to not just function well, but to be far away (many steps away) in "mutation space" (sequence space, where the metric is based on ...
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0answers
7 views

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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votes
0answers
25 views

Why don't we have cancer despite defected p53 protein?

In my textbook, I found that p53 protein controls the mitotic cell division. Also a defective p53 is a cause of tumour and cancer. It is also written that half p53 in our body is defected. Then ...
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0answers
12 views

What are the differences between etioplast and chloroplast? [closed]

What are the differences between etioplast and chloroplast.
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0answers
26 views

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 ...
2
votes
1answer
20 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 ...
3
votes
1answer
230 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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votes
1answer
56 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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0answers
28 views

Questions to protein folding

I have some questions regarding the process of Protein folding. These are the following: Are there existing Protein folding processes, where only a few seconds after completed folding a Protein ...
1
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1answer
30 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 ...
2
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0answers
21 views

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 ...
2
votes
1answer
23 views

Fluorescent protein tags and colocalisation

We want study if 2 proteins A and B are co-located, for that we use 2 FTP(Fluorescent tag proteins) for each protein?and after the expirement these 2 FTP are co-located. Does that mean necessarily ...
0
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0answers
31 views

What are the limits on gluconeogenesis from proteins?

The liver and kidneys can transmute certain molecules into glucose. What I'm interested in - how much could they make, at most per day, given nothing but unlimited amounts of complete (animal) ...
1
vote
1answer
23 views

How many different chains exist within a specific pdb file?

More specifically, if we want to understand the different chains within a protein, is it enough to look at the fourth column of all the lines that start with "ATOM" in a pdb file, and see how many ...
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0answers
25 views

Why are the hydrogen bonds between the backbones not straight down in a parallel B-sheet?

I am not sure why the hydrogen bond patterns in a parallel beta sheet are not straight down and why they are offset by about ~0.5 Angstroms. Is there any significance to this difference?
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votes
1answer
50 views

Homology modelling of protein with two identical subunits in its quaternary structure

I am using homology modelling to assign the 3D structure of Torpedo acetylcholine receptor (Unwin 2004, 2bg9 in RCSB) to human muscle nAChR. The problem is, both Torpedo receptor, and human receptor ...
0
votes
1answer
18 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 ...
1
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0answers
21 views

Tensile strength of collagen?

Really specific question, but what is the average tensile strength of human collagen, type I? I've tried looking for it online, and either my google-fu skills are weak, or I'm just unlucky. Also, is ...
0
votes
1answer
28 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 ...
4
votes
5answers
128 views

Why analyse transcriptome instead of proteome?

Analysing the transcriptome (RNA-Seq, microarrays, qPCR etc) is probably the most widely used technology to assess gene expression and dynamic cellular processes. The results are then extrapolated (...
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votes
1answer
59 views

Why do ADULTS need protein in their diet, if they are not growing? [duplicate]

Why do ADULTS need protein in their diet, assuming they are not growing? What happens to the amino acids already present in the body? Why don't our bodies conserve them?
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1answer
57 views

What does 'half life' of a protein mean?

Why do we use the term 'half life' for proteins? Here is a link to some information regarding this question, but I am unable to infer it.
3
votes
2answers
73 views

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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0answers
19 views

Proline flexibility

I was reading about the role of proline-rich domains in proteins. There seem to be two schools of thought. One is that proline has 2 degrees of freedom instead of 4, making it more rigid. This makes ...
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0answers
17 views

How did self-replicating molecules distinguish between regular nucleic acid and the first codons?

I've read that the first protein synthesis has likely included translation by readily formed tRNA-like adapters. The other alternative is that primordial 'mRNA's didn't need adapters and instead ...
1
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1answer
38 views

Glucose Carrier Proteins in Cell Membranes

I'm using Campbell's Biology textbook, and it states that certain carrier proteins transport glucose across the cell membrane much faster than would occur normally. It states that the "glucose ...
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votes
1answer
24 views

What is the difference between spidroin-1 and spidroin-2?

So I'm doing a research project for my school and I'm trying to decide on the exact nature of the project. My current plan is to try to genetically engineer E. coli or Yeast to produce spider silk ...
1
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1answer
16 views

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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votes
0answers
18 views

Removing signal peptide enough to prevent protein from going to membrane?

I am trying to perform a yeast two hybrid and one of my proteins of interest has a single peptide and several transmembrane domains. Now for the yeast two hybrid it is of course better that the ...
2
votes
1answer
50 views

When in Ampicillin degraded (gone) in liquid TB-media? Concerns about selectivity

Question: Specifically regarding Ampicillin; When growing cells in TB (terrific broth) for protein expression - when should I expect the ampicillin to be gone due to degradation by b-lactamases? (and ...
2
votes
3answers
239 views

Can the central dogma work in reverse?

Theoretically, is it possible to obtain the original gene from the protein’s amino acid sequence as its “template”, as in, the reverse of how gene’s codons were “templates” for the amino acid sequence ...
2
votes
1answer
69 views

What proportion of proteins require chaperone-assisted folding?

I am new to the field of biochemistry (I am a chemist, actually). I have long known the process of folding as the process that leads to the minimum energy conformation of a protein. Now, I am ...
2
votes
2answers
66 views

What is protein secondary structure?

Could someone please clarify what is protein secondary structure: https://en.wikipedia.org/wiki/Protein_secondary_structure I believe I understand the primary structure, I am not sure what's the ...
1
vote
0answers
168 views

Are microtubules in centrioles helical, like they are when in isolation?

Microtubules tend to be of a helical structure, do microtubules in centrioles also have a helical structure? The centriole is composed of nine circularly arranged triplet microtubules, one complete ...
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0answers
11 views

how long do chaperone proteins take to fold a protein? [closed]

how long do chaperone proteins take to fold a protein?
2
votes
1answer
23 views

Will the interaction of two proteins vary across different tissues? [closed]

Suppose protein A and B is both abundant in tissue X an tissue Y. Will A and B interact in X but not interact in Y? I guess A and B could be biomarkers of a certain disease, and in the pathological ...
2
votes
0answers
31 views

How are animal patterns encoded in the dna?

After seeing the patterns on the feathers of a argusianus argus pheasant (shown below), I am curious where is the information that encodes a pattern for a particular bird, and what form is this ...
5
votes
2answers
1k views

Is Tyrosine considered hydrophobic or hydrophilic?

I’ve seen Tyrosine classified as a hydrophobic amino acid due to its benzene ring in some textbooks and as hydrophilic due to its hydroxyl group in other textbooks. How does Tyrosine actually ...
2
votes
1answer
30 views

How do metal ions acting as enzyme cofactors “find” their respective enzymes?

Metalloproteins are metal-dependent proteins, i.e. they require certain metal ions (copper, magnesium, zinc, etc.) for their correct function in the body. Since proteins are manufactured inside cells ...
5
votes
4answers
101 views

Program (on Mac) to show 3D protein structures?

I have an assignment for 6th grade biology. I have to look at a 3D structure of a protein and manipulate it so it only shows the AA I’m interested in currently. what I already did I already looked up ...
1
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1answer
31 views

Is there a notion of RMSD for two different molecules?

The (least) Root Mean Square Deviation is used for comparing different conformations of the same molecule. However one may be interested in comparing the conformations of two different molecules e.g. ...
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votes
1answer
12 views

How does chemical shift assignment from NMR spectroscopy is translated to three dimensional structure of protein?

I am currently involved in determination of protein structure using NMR spectroscopy. As part of structure determination I have finished the chemical shift assignment. The chemical shift information ...
3
votes
2answers
1k views

Why is pepsin able to operate at low pH?

Pepsin is a protease that operates in the acid pH of the stomach. Many proteins are denatured at low pH, and most enzymes — whether or not they denature — require a higher pH for activity. Why is ...
-1
votes
1answer
30 views

How to estimate the amount of protein that are going to be synthesized?

I'm studying protein synthesis to understand how the body use the different amino acids to build proteins. In particular I would like to learn how to (roughly) calculate the total amount of protein ...
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0answers
37 views

How to calculate the amount of protein synthesized knowing the amount of essential amino acids ingested?

I'm studying protein synthesis to understand how the body use the different amino acids to build proteins. In particular I would like to learn how to (roughly) calculate the total amount of protein ...
3
votes
0answers
35 views

How can I differentiate between polysaccharide bands and protein bands on SDS-PAGE? [closed]

I tried to extract bacterial polysaccharide but after running a SDS-PAGE I couldn't differentiate between the polysaccharide band and protein ones. I face a problem of moving up of the samples from ...
1
vote
2answers
66 views

mRNA and Protein relation [closed]

A and B are two different proteins: 1- can they have same mrna 2- is it possible that the gene types which encoding the synthase are same ? my answer is yes to both . because after protein synthased ...
0
votes
0answers
25 views

Can a frameshift mutation into the open reading frame not affect the stop codon?

I'm having trouble understanding a practice test question that is as follows: https://imgur.com/a/AeXPK#yXx9W8G So they insert a nucleotide to the mRNA of an open reading frame (so it starts with ...
1
vote
0answers
19 views

What prevents a density gradient made of sucrose from mixing through diffusion?

Based on what I've read, density gradients are used to facilitate separation in ultracentrifugation and prevent convective mixing of the molecular species from different locations in the gradient. But ...
2
votes
1answer
74 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 ...