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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4answers
1k views

What is the difference between a protein and a factor?

In terms of nomenclature/semantics, why are some proteins named proteins, and some named factors? I've been revising on eukaryotic DNA, and I've come across some proteins that seem to serve roughly ...
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2answers
375 views

What is C-terminal tryptic peptide?

A biologist wrote to me: ... C- or N-terminus,... For example, a C-terminal tryptic peptide like AGWRGSDSHSR, would be... I don't have any idea what that is. When ...
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1answer
99 views

Proteins in water vs proteins in crystal

I am not very familiar with the experimental procedure of x-ray crystallography except that it involves the very delicate matter of producing crystal that contain proteins and then diffracting rays ...
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1answer
160 views

Ribosomes producing proteins, but need proteins to be produced?

So according to my textbook: RNA is used to create ribosomal RNA (known as rRNA) which is then combined with proteins to form the ribomsomes necessary for protein synthesis. I'm a bit confused ...
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1answer
26 views

Is it possible to induce protein activation via frequency-specific mechanical waves? [closed]

Would it be possible to induce shape changes in specific proteins by providing specific frequencies of mechanical waves in a thermostatically controlled environment such that those proteins may be ...
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3answers
73 views

Why structures of many proteins are still unknown? [closed]

https://www.learner.org/courses/biology/textbook/proteo/proteo_3.html Despite advances in techniques for determining protein structure, the structures of many proteins are still unknown... My ...
3
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1answer
72 views

Filter proteins by domain with InterProScan

I have a bunch of proteins (over 300000) in fasta format, and I want to find the ones that contain a specific domain (using a specific InterPro accession). I can run InterPro on the proteins and get ...
3
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0answers
246 views

Plant vs animal protein digestibility?

The protein scoring methodologies ( https://en.wikipedia.org/wiki/Protein_Digestibility_Corrected_Amino_Acid_Score) rate plant proteins of a lower quality than animal proteins. Now I can understand ...
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0answers
73 views

Do cells store information other than permanent (chromosome) information

The brain stores information in neurons (i.e. neural networks), and cells store information in DNA. But with DNA, this is permanent information. There is a lot of potential temporary information in ...
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0answers
69 views

Proteins folds: relation to splicing and post-translational modification?

Is the secondary structure pattern of protein folds related in any way to alternative splicing and post-translational modification?
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1answer
80 views

Blackgram leaves. SDS page. Phosphate buffer method

I am doing protein analysis in blackgram leaves by using phosphate buffer method. But I cannot get proper bands on my SDS-PAGE. What should I do to get proper bands?
3
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1answer
2k views

Clarify pre-column pressure vs. system pressure vs. backpressure for prepacked columns used with the äkta purification system

Background: I am using the Äkta pure system for protein purification, with prepacked columns from GE-healthcare. Just to take one example, I use the HisTrap 5 mL column (IMAC: immobilized metal ...
3
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3answers
115 views

What are the applications of predicting the structure of proteins?

Protein molecules are very important as they are used for catalyzing almost all the chemical reactions in the cell, regulation of gene activity and provide cellular structure. However, in predicting ...
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1answer
332 views

Laemmli-SDS-PAGE problems [closed]

I did Laemmli-SDS-PAGE for my Ammonium sulphate precipitate but I had very weak band and have very weird part at the end of gel. Please help me to solve that problem. Thanks
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92 views

How a biologist attempts to explain the structure of the ribosomal proteins?

I have a Computer Science background and a minimal biology knowledge. This is the question I am asked to answer in one of the biology courses: What would be the structure of ribosomal proteins when ...
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1answer
1k views

What is the structural difference between beta and gamma globin chains of Hb?

Hemoglobins are tetramers composed of pairs of two different polypeptide subunits. The subunit composition of the principal hemoglobins are α2β2 (HbA; normal adult hemoglobin), α2γ2 (HbF; fetal ...
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2answers
4k views

More proteins from diet when common cold and flu?

My coach says that I need to eat 1.2 - 1.5 grams of proteins per kilogram when I have a common cold and flu. I normally eat one gram of proteins per kilogram, while double it when doing my exercise ...
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1answer
105 views

Generate mesh surface from protein structure

What tools are most widely used for generating a mesh surface of a protein from an x-ray crystallographic structure (from the PDB)? Pros and cons would be appreciated. I'd prefer the output to be a ...
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1answer
824 views

What are the characteristics of a promising drug?

The drug development industry is a multi-billion dollar economy powered by a multitude of research bodies from industry and academia. A big risk is that drug development costs are in the tens of ...
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4answers
116 views

Why do food items expire?

Why do food items and medicines expire after sometime?
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2answers
431 views

Can VMD change its cartoon representation for secondary structure according to trajectories?

I am using VMD to visualise the secondary structure of protein. The trajectories are from my Gromacs simulation. Firstly I use ...
5
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1answer
3k views

Effect of 2,3-bisphophoglycerate (2,3-BPG) on haemoglobin

When 2,3-bisphophoglycerate (2,3-BPG) binds to haemoglobin, a higher partial pressure of oxygen is needed to bring about 50% saturation of with oxygen. What is the physiological significance of this ...
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1answer
74 views

What is the “mucin net”?

From Giulia Enders, Gut: The Inside Story of Our Body’s Most Underrated Organ Mucins are proteins that form the main constituent of mucus. They help provide hours of fascination and fun for young ...
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2answers
1k views

Why and how does uniprot list around 150,000 proteins in the human genome?

Using organism:"Homo sapiens (Human) [9606]" as a query in uniprot returns about 146,000 proteins. I was under the impression that there were only 20-25,000 protein ...
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1answer
428 views

Why do raw prawns turn red after sitting in vinegar?

Yesterday morning I put some raw prawns (shell removed) into vinegar (more specific this one), and put them in fridge. When I came back at night all of them turned red, which looks cooked, except ...
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1answer
41 views

Assays for detecting RNA binding with protein

In a project I'm working on, we are designing a system where specific RNAs bind to proteins - an important part of this is to test whether the RNA binds when we modify the proteins in some way. What ...
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2answers
425 views

Are peanut proteins similar to chicken meat proteins?

I'm studying amino acids content in vegetable food. I was looking at peanut protein and noticed its similarity with chicken meat, as you can see in the table below (quantities are measured in grams). ...
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1answer
2k views

What is the difference between gene expression and protein synthesis? [closed]

I have no idea what I'm supposed to do. Can someone please help me? What is the difference between gene expression and protein synthesis?
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101 views

Do non-pathogenic organism not have PAMPs? Are there any research paper which proves that a certain microbe is non-pathogenic?

According to this PAMPs are delivered along with additional information that can be used by the host to distinguish pathogenic from nonpathogenic microbes and thereby guide the ensuing innate ...
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1answer
259 views

Can I dry digested protein sample over weekend in a vacuum concentrator?

I have digested with trypsin the tissue protein extract for mass spectrometry, and forgot to transfer the sample from the SpeedVac to the -80C freezer. As I did this on Friday, I can transfer the ...
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1answer
26 views

Will a sandwich assay work with a GST 26 antibody/protein?

I have a GST 26 kda antibody, and want to use it in a sandwich lateral flow assay. Are there enough epitope regions for both antibodies to bind to the protein?
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1answer
54 views

Is Ellman's reagent specific for low molecular weight proteins and thiols?

Is it still possible to quantify cystein rich low molecular weight proteins such as Metallothionein in a given sample using Ellman's reagent if the sample is contaminated with some high molecular ...
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1answer
101 views

Do non-functional (‘junk’) protein sequences exist?

For DNA one can distinguish between protein-coding DNA sequences, i.e. nucleic acid sequences inside DNA (vs. non-coding sequences) DNA sequences that do not code for proteins but are transcribed ...
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1answer
40 views

Are there differences between the activation proteins of Eukaryotes and those of Prokaryotes

I'm in BIO 203 (for reference to my skill level), and I noticed the textbook makes a whole section out of transcriptional activator proteins, their function and applications in eukaryotes, but in ...
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2answers
11k views

Why does Edema occur in Kwashiorkor?

Edema in lower leg and face is a symptom of Kwashiorkor. It is the most distinguishing feature of it which distinguishes it from Marasmus. Why would decrease in amount of proteins cause Edema? Why ...
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1answer
2k views

How do DNA-binding proteins recognize the correct DNA base pairs?

My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?" He alluded to the different arrangements of hydrogen-bond donor and acceptors in A-...
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2answers
103 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
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1answer
80 views

How does radiolabeling work?

Protein turnover can be measured by calculating the "decay" or loss of radio-labeled proteins in the blood, for example, but I am confused at how this calculation works. Wouldn't the radioactive ...
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1answer
49 views

Protein molar mass from Uniprot ID?

I have a long list of uniprot IDs. How can I get the mass of the "canonical" isoform for each? Ideally from some Python library.
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0answers
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Is osteoid an uncalcified substance?

I recently learned about Osteoid (the substance secreted by osteoblasts during intramembranous ossification), and I read that it was an "unmineralized organic component of bone." Now, does this mean ...
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2answers
196 views

How do membrane proteins find their target locations?

The question might be asked for any kind of "bound" proteins, but I'd like to restrict it to membrane proteins. Assuming membrane proteins (or their main parts) don't (or aren't) build in situ but at ...
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1answer
148 views

Is there any way to make protein pass through cell membrane?

Protein cannot pass cell membrane because it's a large molecule. Until now, is there any technique that can make protein pass through the cell membrane in vivo? I want to create a protein-drug that ...
3
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1answer
460 views

What is the shortest mRNA the ribosome can read to produce a peptide?

This question came as a comment on a previous question regarding non-ribosomal peptide synthesis, and why Glutathione cannot be synthesized by the ribosome. In general, Glutathione has a "gamma" ...
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2answers
2k 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 ...
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1answer
113 views

How would one go about identifying unknown cell cycle checkpoint proteins (i.e., cyclins)?

No this is not 'homework'. I'm a PhD student, and this was something brought up at the end of a journal club recently, and one of the PIs posed this question and told us to think about it. It sounds ...
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1answer
648 views

Does pepsin digest plant protein?

This may sound trivial, but... Protein is sourced from plants and animals. Pepsin and HCl digest meat (animal protein). Does pepsin also digest plant-based proteins? I took a look at few articles ...
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1answer
2k views

What is a complex? [closed]

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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1answer
81 views

Since the matter in the brain is recycled every few days how does consciousnesses work?

Since parts of the brain are recycled every few days does that mean that materialistic theories of consciousness don't work?
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1answer
702 views

Life cycle of proteins

I try to get a picture of the life cycle of a protein (considered as a specific molecule). This is how I can imagine it: After the cell is born a protein molecule is synthesized by gene expression ...
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1answer
95 views

Etymology of vimentin [closed]

What is the etymology of the intermediate filament , Vimentin?