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

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What is the process of degradation of proteins into amino acids inside living cells?

Just like beta oxidation does our cells have a distinct mechanism for degradation of proteins? There are processes for degradation of amino acids but where does these amino acids come from, is it all ...
3
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1answer
64 views

What is the lower temperature limit for ion channels function?

What is the cold-block temperature of ion channels? (not of nerves or axons)
0
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1answer
45 views

A molecular marker for global protein synthesis

I know that protein synthesis is governed by a lot of factors (I'm mostly studying the mTOR pathway), but I'm looking for some kind of marker that will indicate the global protein synthesis rates. I ...
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1answer
70 views

Electrophoresis of hemoglobin from a carrier for sickle cell anemia shows two bands - why not three?

Electrophoresis of hemoglobin from a carrier for sickle cell anemia shows two bands - why not three? Since there are two beta chains in each hemoglobin, it seems to me they should have three types of ...
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0answers
31 views

How hydrophilic is human mucus?

I am interested in the stability of virus particles in human mucus, and how this may bias the evolution of surface amino acids in respiratory viruses. For instance if the mucus environment were more ...
10
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2answers
149 views

Protein tertiary Structure formation

As we know that coils and loops are evolutionary variable regions where mutations,deletions, and insertions frequently occur. So does it mean that they don't have much role in the structure of protein?...
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1answer
66 views

Can exhaustive algorithms produce MSAs that are suitable for 3D structure modelling?

While predicting 3D structure of a protein through homology modelling, the most important step is Multiple Sequence Alignment of template sequences with the target protein whose 3D model is to be ...
0
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0answers
11 views

Are receptors integral membrane proteins or peripheral membrane proteins?

In tegral membranes serve as transporters. Peripheral protiens serve as cell adhesion molecules, antigens and enzymes. So what about receptors? Which protiens carry out the duty of receptors?
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26 views

mRNA extraction from mice ears.

I am trying to extract RNA from mice ears and for some reason I don't have RNA when I perform the electrophoresis. I directly cut the ears and I put it in a tube with a bead and trizol. then I place ...
2
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0answers
28 views

Lifeforms concentrations of the categories of macromolecules, and Lipids

Lifeforms are formed of large, modular, organic molecules called macromolecules, large organic molecules called Lipids, and simpler molecules such as H2O. Macromolecules are commonly grouped into the ...
0
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1answer
39 views

How does protein enter bloodstream?

If a hemophiliac patient injects his factor 8 through the veins directly into the bloodstream to provide the body with clotting factor... Why don't they just make the drug as a pill and have the liver ...
0
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1answer
71 views

Will dissolved proteins pass through a 0.2 micron filter?

Given that there may be exceptions, can you usually expect protein to pass through?
2
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1answer
72 views

Why does heating kidney beans at a low temperature potentiate the toxicity of phytohaemagglutinin?

I recently found out that red kidney beans contain a relatively high amount of the toxic lectin, phytohaemagglutinin. An article on phytohaemagglutinin on the FDA website states: Several ...
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0answers
8 views

Is there a deblocking aminopeptidase without normal aminopeptidase activity?

The deblocking aminopeptidase is a unique exo-type aminopeptidase that liberates blocking groups (formyl, acetyl, and myristyl) from proteins and peptides. However, according to this paper, it has two ...
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0answers
63 views

Which of the three is true for insulin receptors?

I have seen the following question in a Cell Biology exam: Which of the following is true" Insulin has an hydrophobic Signal Peptide and the insulin receptor does not have an hydrophobic ...
0
votes
1answer
62 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 ...
0
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0answers
24 views

SDS-Page-Concentration confusion

So I purified some a protein, purified it using two different types of resins (comparing resins for cost efficiency). Ran a Bradford Assay to find concentrations of each. Unsure of SDS-Page protocol ...
2
votes
1answer
52 views

How do proteins perform their function [closed]

I have asked a question on physics stackexchange, but was redirected here. I copy the entire question word for word. The original is here. Let's, for example, take a ribosome. It is an enzyme that ...
2
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1answer
63 views

What is membrane-partitioning free energy? Can it be simulated?

Firstly, is there a strict definition of the "membrane-partitioning free energy"? It is banded around in membrane biology, but I have never seen it strictly defined. The only non-scholarly site that ...
1
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1answer
35 views

A question involving immunoprecipitation to identify interacting proteins?

Using recombinant Flag-tagged Dcr-2 and His-tagged protein X, pull-down assays were performed to determine whether protein X and Dcr-2 interact directly. The recombinant proteins (either alone or in ...
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0answers
11 views

Which fractions are enriched for siRNA cleavage activity by comparing electrophoresis?

Size exclusion column chromatography was used to separate the proteins in a Drosophila cell lysate to attempt to identify the protein complex responsible for processing long dsRNA into siRNAs. SDS-...
3
votes
1answer
124 views

Does urea at different concentrations (5 or 0.5M) have different effects on proteins?

The problem is to explain why each additive gives rise to the distribution of the protein (RMAS) as shown in the Western blow below: In each case, the homogenates were subjected to high-speed ...
3
votes
1answer
50 views

Resolution of X-ray crystallography

A structure determined by X-ray crystallography has a resolution of 1.5 Å. When I look at the coordinates, I find every backbone C-N distance is 1.32 Å.i.e. Accurately predicted. If resolution is not ...
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1answer
42 views

Stabilizing forces between the protein sequences?

we know that Protein structures from secondary to Quaternary are maintained by noncovalent or weak interactions including electrostatic interactions,van der Waals forces & hydrogen bonding. What ...
2
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1answer
773 views

Difference between protein channels, protein carriers and protein pumps?

I'm revising for my biology exam and I don't fully comprehend the difference between protein channels, carriers and pumps. I know that: Protein channels do not require ATP (passive transport) The ...
4
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1answer
741 views

Is ATP Synthase a channel or an enzymatic protein?

Today in a biology lecture about plasma membranes and functions of proteins, we learned about channel and enzymatic proteins along other kinds of proteins. ATP synthase is considered an enzyme that ...
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0answers
17 views

Determination of hyaluronic acid hydrolysis

I have a protein that I am reasonably sure hydrolyzes hyaluronic acid, and I'm trying to design an experiment to test that. I was told that a dye binding plate assay where clear zones will indicate ...
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5answers
234 views

Why do asparagine and glutamine have two different abbreviations? [closed]

I'm looking at amino acid abbreviations and on every site I visit, asparagine and glutamine have two different abbreviations. Is there a reason for this? Do they represent different forms of the amino ...
2
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2answers
115 views

How to build a trimeric protein structure from monomeric PDB file?

Problem: I have a PDB file, with a monomer, but I would like to show the entire structure - which is trimeric - but I don't understand how to merge/build or combine the monomeric units to its full ...
2
votes
1answer
125 views

Why do bacteria need messenger RNA?

Why do bacteria need mRNA? Isn't the DNA free floating without nuclear membrane so why doesn't the tRNA read the code directly off of the split DNA strands? (ofcourse after helicase splits them). ...
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1answer
32 views

How do you calculate the charge on a polypeptide chain with changing pH?

I understand the charge placement on the N & C-terminus and also the utilization of the R-side groups in the amino acids. For example, What is the overall charge for a chain Glu-Cys-Arg-Asp with ...
0
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0answers
15 views

Which ligands bind to (are sensed by) these Odorant Binding Proteins (OBPs)?

Question I have a list of 69 odorant binding protein (OBP) IDs, belonging to the malarial mosquito Anopheles gambiae, and I would like to know which ligands/molecules they bind to. I would greatly ...
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2answers
867 views

How much ATP is consumed during protein synthesis?

I'm trying to find out how many molecules of nucleoside triphosphates (ATP, GTP, UTP and/or CTP) it takes to release enough energy to link two amino acid monomers together with a peptide bond, ...
2
votes
2answers
73 views

How important is non-binding site of protein?

Just a curious question: What will happen if i remove most protein sequence that encoded for non-binding site of Restriction Enzyme to make a new enzyme, can the new restriction enzyme still work?
6
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1answer
417 views

Lac operon: How can lactose enter the cell in the absence of lactose permease?

My textbook states that lactose permease...transports lactose into the cell and When lactose is added to the growth medium, the lactose molecules bind to the other site on the repressor ...
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1answer
76 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 ...
0
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0answers
20 views

Will a metalloenzyme bind to its substrate in the absence of its metal ion cofactor?

A metalloenzyme is an enzyme using a specific metal ion as its cofactor. Their activity is dependent on this metal ion. For example, the T4 DNA ligase requires Mg2+ to ligate DNA strands; The ...
0
votes
1answer
156 views

How can I tell if a protein has been denatured?

So i recently done an experiment using egg albumin, and we had 5 test tubes. the goal was to see if they have been denatured. 1- heat 2-acid (HNO3) 3-base (NaOH) 4- Alchol (ethanol) 5- heavy metal ...
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1answer
47 views

Can we create custom gene/protein?

Does it possible to create any custom gene or protein we want with current technology? I have a protein sequence or a gene sequence about 4000 bp write down on my computer, is there anyway to "print" ...
2
votes
1answer
47 views

Conserved acetylation sites in a given protein

I want to identify potential conserved Acetylation sites in protein X. As it is known, acetylation happens in Lysines (K), thereby I would like to identify conserved K residues for protein X during ...
2
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0answers
45 views

Determine secondary structure (per residue pair) from a protein contact map

Given a protein map contact map (which for this particular case is a matrix of all Ca-Ca atoms in protein 1a3a that are less than 8 Angstroms): Question: For ...
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2answers
61 views

yeast protein secondary structure

i have a fasta file of yeast orfs (from the SGD database) and i need to find out(predicted) secondary structure/classification for all of them (so ~6K queries and doing this by hand on numerous ...
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34 views

Wash adsorbed protein without destroying Biotin-Avidin-Mechanism

I am looking for reliable protocols to wash protein (e.g. Fibronectin) adsorbed onto glass surfaces. According to Protein immobilization literature, people usually use 1% SDS and some incubation time. ...
3
votes
1answer
91 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" ...
3
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0answers
58 views

Relative densitometry from SDS PAGE

I'd like to perform densitometry on a Coomassie stained SDS PAGE gel to compare a recombinant protein's expression levels under two conditions. I'm using BioRad's Image Lab software. My questions are ...
5
votes
2answers
145 views

Non-ribosomal peptide synthesis: why Glutathione cannot be produced by the ribosome?

Case: I am writing a summary for a class in protein structure and function, and was asked to describe some different ways that peptides are synthesized (that does not involve the ribosome). I ...
2
votes
1answer
58 views

Difference between the P4 and P5 subtypes of P-type ATPases in plants

In plants there are various kinds of P-type ATPases. What is difference between P4-ATPase and P5-ATPase?
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0answers
26 views

How do molecular recognition features work?

The occurrence of relatively short (10–70 residues), loosely structured protein regions bind within longer, largely disordered sequences that were characterized as bound to larger proteins. These ...
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0answers
22 views

Effects of Acids and Bases on protozoa

Why is it that when you pour acid (HCl) on a culture of Euglena gracilis in an aqueous environment the protozoa begins to swell and when you pour a base (NaOH), it maintains its shape? I feel like ...
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27 views

Why would the addition of whey protein to oatmeal make the oatmeal more runny?

So, at the suggestion of a friend I added some protein to my morning oatmeal. While I do feel better for it, I noticed a few things it did to the oatmeal I didn't expect, the primary is that the ...