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

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851 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, ...
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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 ...
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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 ...
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2answers
879 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
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" ...
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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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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 ...
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1answer
992 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
202 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 ...
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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 ...
4
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1answer
324 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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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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0answers
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 ...
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1answer
107 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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65 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 ...
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1answer
19 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
49 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
85 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 ...
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47 views

Question about Collagen and Glycosylation

Just curious, I know that collagen typically undergoes O type glycosylation. However, can you say that this type of glycosylation is essentially like putting a mailing address for proteins to be ...
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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 ...
3
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1answer
105 views

Difficulty in finding protein inhibition drugs

I was reading an article on a recent identification of a PARP-14 protein in cancer cells that is responsible for production of additional glucose which keeps cancer cells from dying, and that a PARP-...
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1answer
54 views

Molecular weight of my 2-D gel

I am a little confuse when I try to figure out the molecular weight of the marker on my gel. I used NuPage Novex 4-12% bis-tris gel and Mark12™ Unstained Standard as a marker. Could please someone ...
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45 views

Western blot extrange band

I performed a WB using plasma rats and monkeys samples with anti ubiquitin K-48 antibody. In every sample the antibody binds something and it appears a specific band that seems to be 71kDa. When I ...
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1answer
269 views

How do DNA-binding proteins determine that they're binding to 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-...
2
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1answer
119 views

Are all dipeptides synthesizable?

Probably a basic question, but are all possible dipeptides synthesizable? For 20 amino acids, there should be in principle 190 dipeptides; do they all exist or is there chemistry that makes some ...
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30 views

Consumption of different type of energy when one is inactive

I'm wonder if there is any study done on this and what are the results? how much of each type of energy one's body(healthy normal person) uses when inactive(seating down) I know there are alot of ...
3
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1answer
248 views

What is the significance in an alpha-helix being right-handed or left-handed?

Why is that often when alpha-helices are discussed, it is also mentioned their direction - right-handed (clockwise) or left-handed (anti-clockwise)? I have heard that left-handed alpha-helices are ...
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2answers
49 views

Properties that can be derived from amino acid sequences [closed]

What are the properties that can be derived from an amino acid sequence apart from those mentioned in the website? In the mentioned website, the properties that can be calculated from amino acid ...
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2answers
60 views

Are multi-chain proteins synthesized as one biological unit?

Are multi-chain proteins (especially homo/hetero-dimers) synthesized together as one overall unit or are they separate monomers which bind together at some point after synthesis, and are there any ...
2
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1answer
327 views

Do the enzymes and compounds in saliva help with stain removal?

Does spitting on stains help with removal? Saliva is high in amylase that should help with the breakdown of protein rich stains like blood and semen. It also contains antimicrobial enzymes and ...
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1answer
89 views

How does the structure of the pancreatic acinar cell relates to its function?

So the pancreatic acinar cell synthesizes, stores and secretes digestive enzyme precursors called zymogens e.g. pepsinogen. The structure of the acinar cell shows that there is an apical and basal ...
2
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1answer
89 views

Why are VAL, MET and ALA substitutions commonly used for protein behaviour and function studies?

I have seen that amino acids are commonly replaced with VAL, MET or ALA to study the effects of these specific substitutions. Why are these specific amino acids used in particular, what are the ...
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1answer
526 views

Doubts regarding definition of upstream/downstream genes and cognate protein

With respect to the research paper, there are a few things I didn't understand: 1. What is upstream and downstream gene 2. This paper identifies proteins that help in secretion, but does not identify ...
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52 views

Proteins and Blood Acidification

Is there evidence to suggest that excessive consumption of Whey, or similar proteins will lead to acidification of the blood?
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17 views

Interaction study of oligomeric proteins

I'm dealing with two different protein(say, protein_a and protein_b) which stays in an interacting-oligomeric form in biological system. I have so far successfully been able to purify both the ...
6
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1answer
7k views

Is consuming proteins different vs. consuming amino-acids and how?

Yesterday I had a discussion with a friend. He said that consuming proteins and amino-acids is different. He said that those who grow muscles would agree on that. I wanted to argue against that ...
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15 views

How are split inteins joined?

Do they form a peptide bond? Or is it just some affinity/van der Waals interaction? Is the mechanism enzyme catalized? Are the residues/moieties at the join site known? Could they be introduced to ...
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1answer
50 views

How does the MET gene work and what happens when the promoter region gets mutated?

I am doing research on inherited risk of Autism Spectrum Disorders(ASD) due to common Copy Number Variants(CNVs) One of the mutations is the 'CC' variant of Rs1858830 in the promoter region of the MET ...
10
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1answer
774 views

Did not understand a small excerpt from a research paper

Was going through this paper, among multiple things that i did not understand, I came across this part: Each amino acid residue of a single window was encoded into a unitary bit string of length ...
2
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0answers
94 views

Multiple transcripts encoding for one protein

Trying to get a better understanding of the process of DNA to proteins. So when we have a gene, it is read from the 5' to 3' end, only translating the exons to mRNAs. A single gene can have multiple ...
7
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1answer
303 views

Why is leucine amino acid used the most in proteins and tryptophan the least?

The amino acid leucine, is used in proteins more than others. Leucine with 9.1 percent (its average in more than 1.150 different proteins) is used most and tryptophan with 1.4 percent is used less ...
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1answer
236 views

Gene and Protein isoform

What is the relationship between term "Gene isoform" and "Protein isoform"? Say a gene can make 3 isoforms, will it produce only (maximum) 3 isoform protein?
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2answers
41 views

Protein that exit from the cell - as marker

Searching for some protein, that I could use as extracellular marker for mammalian cells. I need to insert mRNA to cell, and to detect the protein outside the cell (not on membrane) if the mRNA ...
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67 views

How are membrane and extracellular proteins delivered to the target membrane?

In bacteria, either folded or unfolded proteins can be trafficked to the membrane or the extracellular space provided that they have the appropriate signal sequences. Once the chaperones or Signal ...
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1answer
42 views

Phosphorylation capacity of an enzyme [closed]

Let's think ProteinA can phosphorylate proteinB, proteinC and proteinD. Condition1: All proteins are expressed and proteinA phosphorylates proteinB, proteinC and proteinD. Condition2: Only proteinA ...