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

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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 ...
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3answers
474 views

Amplification technique for proteins similar to PCR for DNA?

I know PCR can be used to amplify a tiny sample of DNA in order to perform experiments. Is there a similar technique to use on a protein sample? More specifically, I'm not interested in "cutting" up ...
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1answer
644 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 ...
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1answer
35 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 ...
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1answer
49 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?
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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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57 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 ...
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23 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 ...
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1answer
85 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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1answer
51 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 ...
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1answer
33 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 ...
3
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1answer
48 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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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. ...
3
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1answer
106 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 ...
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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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2answers
71 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?
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1answer
85 views

What is a detailed chemical explanation for describing how an enzyme may lower the activation energy of a reaction?

If you can provide some sound reasoning that touches on tertiary structures of proteins and does not use a lot of advanced chemistry jargon that might be really helpful, especially for an intro ...
2
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2answers
130 views

Have proteins been observed to come into existence through mutations and natural selection?

A protein that catalyzes one reaction can theoretically be modified by mutations and natural selection and eventually catalyze another reaction completely unrelated to the original. Has this been ...
5
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5answers
213 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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1answer
123 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). ...
2
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2answers
105 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 ...
4
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1answer
640 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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1answer
31 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 ...
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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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1answer
331 views

What are the characteristics of a promising drug?

Generally speaking, what makes a good drug for research?
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2answers
608 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, ...
5
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1answer
369 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
74 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 ...
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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 ...
3
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2answers
793 views

Why does the 'Positive-inside Rule' exist?

Gunnar von Heijne's Positive-inside Rule seems to have been around for a couple of decades and underpins a lot of what we know about transmembrane topology. It is used to predict the topology of a ...
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1answer
133 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
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43 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
60 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 ...
5
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2answers
136 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
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1answer
975 views

Using DTNP to find free thiol groups on a protein

I've been tasked with using DTNB to find the number of thiol groups on a molecule of Bovine Serum albumin (BSA). After measuring the absorbance, finding the concentration of TNB and calculating the ...
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0answers
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. ...
4
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1answer
188 views

What equation to compare protein isoforms in a Western Blot?

The protein isoforms I am interested in comparing appear as distinct bands on the gel I have already run. I have an Excel sheet with optical density measurements I obtained using ImageJ; it looks ...
3
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0answers
51 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 ...
4
votes
1answer
297 views

How can a polar molecule pass through polar channels of proteins in the cell membrane?

To transport a polar molecule through the nonpolar cell membrane, a protein with a polar channel is needed to allow it to diffuse. However, if the molecule is polar and the channel is polar, wouldn't ...
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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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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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0answers
25 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 ...
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1answer
92 views

How protein denaturation affects digestion?

Which one of these is a) easier to digest, b) more nutritious (in whatever sense): 1. scrambled egg, 2. raw egg. Bascially is "denatured protein are worse than not denatured" a myth, or not?
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53 views

How is the volume of the dialysis buffer decided?

Is there a specific ratio between the volume of enzyme solution in semipermeable membrane bag and the volume of the buffer outside the membrane bag? I have been looking for a specific formula or ...
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0answers
47 views

Protein modification and ATP consumption

According to wikipedia there exists a lot of ways to modify a protein (post-translationally). Just to mention few: phosphorylation, dephosphorylation, glycosylation... While phosphorylation requires ...
0
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1answer
18 views

C-myc/anti-myc Ab Interaction with Fusion Proteins

I am going to prepare a c-myc fusion protein with the following configuration: (28-residue signal sequence)-(c-myc)-(GGSGGGSG Linker)-(Protein of Interest (POI)) POI is a transmembrane protein and ...
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1answer
48 views

What are the key differences in giant and large unilamellar vesicle preparation processes?

I have to study my peptide's folding on membrane mimetic (model membrane) by circular dichroism spectra. Now I'm looking for suitable methods for preparation of vesicles: LUV, SUV, GUV- large, small ...
3
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2answers
83 views

What signals a ribosome to stop production when the cell is out of available amino acids?

In the production of a protein molecule, there have to be a ready supply of free-floating amino acids. When a given codon for adjoining, say, serine comes up, how are the serine molecules found out of ...