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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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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 ...
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4answers
121 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 ...
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1answer
32 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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1answer
14 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 ...
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2answers
2k 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 ...
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1answer
33 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
41 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
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0answers
44 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 ...
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2answers
71 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 ...
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0answers
32 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 ...
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0answers
26 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
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1answer
77 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 ...
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2answers
62 views

NAG, FUC molecules in PDB files

In some proteins (such as 4ZXB, 6CE9 which are respectively apo and halo forms of insulin receptors), I see ligands such as FUC (ALPHA-L-FUCOSE) and NAG(N-Acetylglucosamine). No matter which paper I ...
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1answer
583 views

What is the difference between Integrin to Cadherin?

My question is probably very basic but i couldnt get it in lecture and not from looking in the net. What is the difference between Integrin to Cadherin. By difference I am looking for say: ...
2
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1answer
79 views

How is the urea cycle regulated with respect to protein deficit?

Proteins cannot be stored in the body. Excess proteins from the diet are deaminated in the urea cycle that takes place in the liver. The liver is the first contact since these amino acids are ...
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1answer
41 views

What are the types of interactions in biological network (protein networks)?

In the KGML files, the types of relations between genes or proteins are precisely activation, inhibition, expression, repression, indirect effect, state change, binding/association, dissociation, ...
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1answer
45 views

Can two proteins have equal primary structure but different secondary structure?

I've been reading lately about primary (which I understand completely) and secondary (which I do not understand that well since I'm not very good at chemistry) structure of proteins. My question is: ...
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1answer
56 views

Is protein folding symmetric with respect to reversing the sequence order?

Suppose that I have two proteins, protein A and protein B, and suppose that the sequence of amino acids of protein B is exactly the reverse of the sequence of protein A. For example (these are made-...
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0answers
21 views

Which among the seven secretion systems in gram-negative bacteria are pathogenic?

Among the 7 secretion systems of a gram-negative bacteria, do all the systems secrete pathogenic proteins that harm the host into which the protein is secreted? Or is it the type 3, type 4 and type 6 ...
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1answer
33 views

gel band contrast

Is there any way to increase the contrast of my SDS PAGE gel. I want to increase the coomassie stained gel contrast of my gel bands a little bit as it looks little less for my thesis. Ive heard that ...
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1answer
43 views

Where different types of proteins can be found in food?

According to https://www.youtube.com/watch?v=KSKPgaSGSYA (created by one of the largest supermarket chains in the UK), different proteins have different roles in human body: (Group 1) They’re like ...
8
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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 ...
3
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2answers
332 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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2answers
86 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
24 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
68 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 ...
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0answers
41 views

MHC-II molecules and Erythrocytes

I am doing an essay which focuses on the MHC Class II deficiency and hemolytic anaemia, however I cannot seem to figure out why the deficiency of MHC-II would cause hemolytic anaemia, I could only ...
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1answer
564 views

How exactly is casein digested?

I mean it seems first step is rennin or pepsin digestion in stomach - then what happens with remaining peptides? I am interested in the whole process from casein to amino acids. Is there brush border ...
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1answer
60 views

Could the protein dystrophin be artificially synthesised?

Could the protein dystrophin be artificially synthesised and if so could patients with DMD (Duchenne Muscular Dystrophy) benefit from it? //Now I don't have much scientific background other than a ...
4
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1answer
51 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 ...
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0answers
40 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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1answer
65 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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0answers
65 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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3answers
100 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
176 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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0answers
21 views

Caffeine metabolism

Can you tell me the physiological difference between the following two cases: 80mg caffeine is taken 201.6mg caffeine is taken 6 hours ago by a half life of 4.5h for caffeine (equals 80mg caffeine ...
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0answers
68 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 ...
2
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1answer
856 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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38 views

Are fMLP/C5a required for the respiratory burst to occur?

So in Janeway's Immunobiology 9th edition, it mentions about fMLP (fMet-Leu-Phe) as a chemotactic factor for phagocytes as well as also inducing a respiratory burst through downstream activation of ...
4
votes
2answers
118 views

How do cells relocate transmembrane proteins from one side of the cell to the other? Is it possible?

Is there a process by which cells can relocate proteins residing on the cell membrane in areas of low demand to that of a high demand location somewhere else in on the cell? What's that process called?...
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0answers
19 views

Do all E. coli Express OmpC Membrane-Protein?

In a lot of papers I am reading, people are amplifying the OmpC gene (which codes for the OmpC membrane protein), from 'E. coli' but they do not specify the strain they used. According to my ...
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0answers
48 views

What is the meaning of protein dimerisation in SDS-Gel?

I purified a virus protein and I got 2 bands on the SDS-Gel. My teacher said it might be protein dimerization.. What does it mean? and what is the reason of getting another band?
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2answers
278 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 ...
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1answer
43 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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1answer
39 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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0answers
42 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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2answers
166 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
1k 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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1answer
52 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
39 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 ...