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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9
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1answer
155 views

Peptides neither produced by the ribosome or the non-ribosomal peptide synthase complexes

I read in Wikipedia: While there exist a wide range of peptides that are not synthesized by ribosomes, the term nonribosomal peptide typically refers to a very specific set of these as ...
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1answer
99 views

How to analyze phosphorylation shift by western blot?

I want to see the phosphorylation shift in my protein of interest. I have created a point mutation in my protein. so that it will not able to go for the phosphorylation compare to my control. i want ...
0
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1answer
48 views

If a gene is missing from an operon that structures a protein, then would that protein not be made properly?

From my understanding, operon is a series of genes that are regulated by a single promotor. In many cases genes in an operon form subunits of a protein. I obtained a genome in my study and looked for ...
6
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1answer
195 views

Statistics: How are protein species distributed over cell types?

There are roughly 10,000 to 20,000 protein species in the human proteome (while I've seen also numbers of 500,000 to 1,000,000). Furthermore, there are roughly 200 different cell types in the human ...
3
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1answer
48 views

Bimodal frequency distribution of size of protein loops

The graph of number of amino acid (AA) residues in a loop Vs the frequency of their occurrence in proteins largely follows a tending-to-zero pattern. However, there appear to be some specific number ...
1
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1answer
107 views

How are proteins reused in the body? [duplicate]

Part of what we eat are proteins, and our body is in part build of proteins. Are the proteins of the body build based on proteins in food at all? Are proteins in food directly reused in the body, or ...
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0answers
29 views

What difference in proteins radius of gyration can be considered significant?

In molecular dynamics simulations of proteins, the radius of gyration is often used to assess the compactness of a protein. When comparing two protein radius of gyration, what difference can be ...
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1answer
79 views

Why is dimethylmercury so poisonous? [closed]

According to the Wikipedia article Karen Wetterhahn, Karen Wetterhahn died after only a very small amount of dimethylmercury got absorbed through the gloves. What is it about the way the body works ...
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37 views

Is brewer's yeast a good source of protein for humans?

I read that brewer's yeast protein is not a "real protein" and is not usable by non-ruminants. Is that true? If yes, how can I know what kind of protein is good for humans (especially athletes)
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1answer
48 views

KRAS gene and K-Ras Mutations

This question pertains to the KRAS wikipedia page, and I just want to double check and clarify my own understanding of how this mutation works in cancer. It states: K-Ras protein acts like a switch ...
2
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0answers
88 views

Appropriate regeneration of StrepTrap HP columns for FPLC

My question is related to protein purification using a ÄKTA FPLC. We used StrepTrap HP Columns (1 ml column Volume (CV)) from GE Healthcare Life Sciences to purify a strep-tagged protein. In the first ...
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1answer
42 views

What happens to embedded membrane proteins after a vesicle is formed?

When an animal cell is going through endocytosis it cell surrounds a food particle, and the membrane swallows it, creating a vesicle within the cell. However, what happens to the embedded ...
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0answers
21 views

Are Hsp70 proteins only activated in response to heat shock?

Hsp70 proteins are chaperones that assist in protein folding in my plant physiology textbook it says the Hsp70 proteins were discovered by inducing heat shock. But do they only work in response to ...
3
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1answer
25 views

How to get a list of kinases that phosphorylated a particular protein?

I am analysing the protein SF2 (also named as SRSF1). In the database, it is shown that this protein is often phosphorylated at the 189th tyrosine residue. I want to know which proteins could have ...
1
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1answer
23 views

Is mucus significantly affected by the presence of ions?

In mucus, there is besides water and the mucins (Proteins for mucus), there are Ions like $Ca^{2+},Na^{+}$, etc. I have read that These Ions can Control the mucus swelling, i.e. the volume that the ...
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1answer
52 views

Why does the structure for cellular retinol binding protein show interactions with cadmium ions?

A structure of cellular retinol binding protein (1CRB) contains two cadmium ions as ligands. Is Cd2+ a ligand of CRBP and, if so, is that interaction necessary for protein function or is the protein a ...
0
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1answer
73 views

Protein folding

I've two questions 1. Is free ATP available in the cytoplasm of the cell? 2. In the protein folding funnel, prions and other misfolded proteins are located at the local minima of the graph. If ATP ...
2
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0answers
37 views

Do carrier proteins constantly open and close or do they only work when a substance binds to them?

What causes carrier proteins to change shape ? Do they need energy to change shape? If that is true, how are they involved in Facilitated diffusion ? By changing shape, do we always mean opens from ...
0
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1answer
72 views

Which lipoprotein has the highest protein content?

I know that HDLs have the highest protein/lipid ratio but know that the HDLs are very small molecules too and I couldn’t find the exact answer for this question. I mean, by amounts which of these ...
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0answers
55 views

Can two proteins activate/inhibit the same gene at the same time?

Suppose there are two proteins inhibiting a particular gene. Its not necessary that both will inhibit the gene at the same time instance right? So if one protein has already inhibited that gene before ...
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0answers
77 views

Can enzymes be modeled using classical mechanics?

When enzymes interact with substrates (i.e. a small ADP molecule and the much larger ATP synthase), does quantum mechanics play a significant role? Or can the interactions be relatively accurately be ...
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1answer
64 views

Why is sickle cell trait expressed in half of all cells rather than all cells containing half-sickled haemoglobin

If sickle cell trait is due to be heterozygous with respect to a single gene mutation on the haemoglobin β-globin chain, why is it the case that ~50% of RBCs are sickled rather than half of the ...
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0answers
59 views

Fluorescence assays to identify protein concentration without adding a large peptide sequence?

I'm trying to find a way of tagging a protein with something visually quantifiable to track protein concentration through potential purification steps and screen for the most efficient such steps. ...
5
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4answers
156 views

Why does protein folding not depend on the order in which it is synthesized?

I read an article recently, written by researcher from Department of Biochemistry, University of Washington, which stated that: Similarly, success in de novo protein design bears on the question I ...
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2answers
90 views

How do mutations and protein synthesis link to cancer?

How do mutations and protein synthesis link to cancer? I know that a mutation in DNA can cause the triplet code on the mRNA to change so different amini acids are made and a different order means a ...
2
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2answers
96 views

Which proteins are most sensitive to electric fields?

Many Proteins have ionic charges that can attract each other (e.g. Formation of salt bridges) or repel each other. On the other Hand, Proteins are mostly immersed in water that screens most of the ...
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3answers
112 views

Are there any proteins not found in the brain that are affected by prions?

A prion is an abnormally folded protein that is capable of causing otherwise normal proteins to also misfold and become prions. They are responsible for causing diseases such as Kuru and Creutzfeldt–...
2
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1answer
150 views

Why spider's web don't burn when electricity touches it?

I saw and spider on it's web at an electrical cable and thinked: If the web is made of proteins, why dont burn. Sorry, the photo is dark because is night in Ecuador
2
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1answer
53 views

Formation of disulfide bonds in protein expressed after transduction

Say I transduce a nucleic acid sequence using a viral vector that encodes a protein having at least one disulfide linkage. For simplicity, let’s assume that there are only two cysteines in the protein ...
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0answers
36 views

Estimating diffusion constant of a protein based on number of amino acids

Is there a way to estimate the diffusion constant of a protein based on the number of amino acids it is comprised of. I know that the shape of the protein has an influence on the diffusion constant, ...
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4answers
4k views

Do all humans have an identical nucleotide sequence for certain proteins, e.g haemoglobin?

All humans have the same sort of proteins in our bodies. Take haemoglobin for example. Is the gene coding for haemoglobin in my body identical to everyone else's gene or is there slight variations ...
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17 views

The Collagen Triple Helix

In the amino acid sequence X-Hyp-Gly (where X can be any amino acid) of the triple helix can the Hyp residue be both hydroxyproline and hydroxylysine? In our textbook it says that the Hyp residue is ...
2
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1answer
69 views

Does the arrangement of amino acids in a protein matter for nutrition?

Let's say there are two diets, consisting of entirely different proteins. If you split up all of the proteins from one day of each diet, you'll get the same set of amino acids and the same count of ...
2
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1answer
161 views

Can any one explain me the structural difference between Proteins and Peptides? [closed]

I have read in books that Proteins and Peptides are fundamental components of cells which carryout important biological functions.Can any one explain me the structural difference between Proteins and ...
4
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1answer
387 views

Why is sorbitol used in buffers?

Many protocols in my lab use sorbitol in buffers. For instance, in co-immunoprecipitation, we include it at a final concentration of 200 mM in our lysis buffer. I'm not entirely sure why though. I ...
0
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1answer
95 views

Is the chitin in an insect's exoskeleton cross-linked?

This answer to the question How to clean and preserve a cicada's molted exoskeleton (exuvia)? states: The exuvia is made of cross-liked chitin, and will not decay. You don't need any special ...
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1answer
56 views

Lysozyme amino acid sequence: N-terminal extension

I looked up the amino acid sequence of lysozyme here: http://www.biology-pages.info/L/Lysozyme.html Then I crossed referenced that with the lysozyme sequence on UniProt: https://www.uniprot.org/...
2
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1answer
512 views

What is the function of spongin in sea sponges?

Sea sponges (Porifera) use different types of skeletons to support their structures. Some skeletons are built from minerals, some are built from proteins like spongin, and some use both. My question ...
3
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1answer
62 views

Can denatured GFP show fluorescence?

GFP ( green fluorescent protein) can show green fluorescence. And its fluorescence is due to the tri peptide chromophore which is given in below I was wondering, can we observe fluorescence, if we ...
2
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3answers
216 views

Why does it matter to predict protein structure?

And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ? Moreover, I've read that knowing the ...
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2answers
98 views

What is the subcellular location of synthesis of non-essential amino-acids?

What is location of non-essential amino acids synthesis in a cell? Is it some specific organelle? And what is the gene driver behind this? I thought the whole point of DNA is coding for how to ...
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1answer
34 views

How can I get the yield of my purified immunoglobulins?

In order to get the yield of IgY through a set of purification steps, what method can I use? Thanks in advice!
4
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4answers
459 views

How can I change my buffer system for protein purification?

I have a protein that I purified in PBS buffer, pH 7. I will do dialysis to remove salt and will then further purify the protein with ion exchange chromatography. I will need to use another buffer (...
3
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1answer
57 views

What buffer should I choose for IEX chromatography for purifying IgY

I will use ion exchange chromatography with an anion exchange column to purify chicken IgY. Prior to this I did dialysis to remove salts from previous purification steps, is it possible after this ...
0
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1answer
165 views

What does “count in gene set” mean?

I am trying to understand the analysis generated by STRING. In analysis for biological processes table, there is a column titled "count in gene set." This gives a value for example "68 of 498". What ...
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0answers
33 views

Genes of the electron transport chain

Where are the genes of proteins that make the electron transport chain of mitochondria?(are they in in the nucleus or they are in the dna of the mitochondria itself?) Thanks for this answering system ...
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0answers
67 views

conversion of distance matrices to pdb/coordinates

I am currently facing two transformational issues. Suppose I am given a protein's residue sequence and calpha distance matrix; is there a way to generate the 3d coordinates of the protein's residues ...
4
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2answers
375 views

Why do protein solutions have to be alkalised in biuret test?

I’ve read that CuSO4 solution reacts with peptide bonds that connect amino acids to create a violet colour, but the instructions always tell me to add NaOH solution to the protein solution before I ...
2
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2answers
266 views

How do organophosphates actually work?

The common explanation as to what the primary mechanism of action for organophosphates (and carbamates) is is the inhibition of the enzyme acetylcholinesterase and resulting buildup of acetylcholine ...
3
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1answer
131 views

Immunoprecipitation compared to western blotting

Immunoprecipitation and western blotting are both used to locate a specific protein within a sample and to isolate it. In immunoprecipitation, a specific antibody and agarose beads ( or other ...

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