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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2
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1answer
95 views

Etymology of vimentin [closed]

What is the etymology of the intermediate filament , Vimentin?
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1answer
242 views

The difference between the beta-sheets and the quaternary structure of proteins

My biochemistry book says that beta-pleated sheets is a form of secondary structure of proteins, and it is formed between two or more polypeptide chains. I wonder why the sentence in bold doesn't ...
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1answer
243 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 Signal ...
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1answer
59 views

What do you call mRNAs that translate to the same protein?

For example AUAACC and AUCACG in distinct mRNAs may both be translated to the same dipeptide Ile-Thr.
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2answers
159 views

What are some examples of non-homologous sequences having similar functions?

I am trying to find some proteins that are non-homologous but functionally similar. However, I cannot seem to find concrete examples. Can someone please point out any resources or provide examples?
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1answer
379 views

Are proteins a different shape in space?

Is the shape of a protein affected by gravity? In space, will the shape of a protein be different to what it is on Earth? If the structure and shape is in fact affected, then would it be enough of a ...
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0answers
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What attaches plant cells to the cell wall?

In animal cells integrins span the plasma membrane and attach the cell membrane to the extracellular matrix. I was wondering how are plant cells attached to the cell wall? Is it just the middle ...
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1answer
94 views

The insulin protein of apes & chimpanzees [closed]

How many amino acids do the insulin protein of apes and chimanpzees compose of?!
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1answer
30 views

Can you say “screening for a” in English?

I know this is not a "Correct Use of English Forum" but I'm afraid that people from outside the field won't be able to properly answer my question. Would it be correct to say "screening for a long ...
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0answers
38 views

Do GPCRs have 7TMHs?

I've screened a non-redundant set of GPCRs acquired from UniProt. I found a handful of examples of record IDs that contain more than the 7 TMHs. For example Q89609 and P20905, both of which have been ...
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1answer
57 views

How big is the change in proteins due to alternative splicing?

How different can the proteins be that are coded from the same DNA-sequence but undergoe alternative splicing? What I am trying to wrap my head around is why we are so fixated with the DNA-sequences ...
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36 views

Indicators of Ras binding domain (RBD) activity in Ras effector proteins?

Ras family based small GTPase proteins usually have a Ras binding domain (RBD) in their effector downstream proteins like Raf. Roughly Ras proteins cycle between active(GTP-bound situation) and ...
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56 views

Visual maps of the neuronal membrane

There are lots of visual maps of the brain as a whole, especially the cortex, that show the distribution of "features" over a two-dimensional map, e.g. the Brodman areas (their morphology and their ...
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34 views

Can one refer to pieces of proteins produced by enzymatic digestion as “enzymatic lysates”?

A Russian text I'm translating says this: The location of post-translational modification (PTM) sites was determined using the “bottom-up” approach commonly used in this field. In accordance with ...
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43 views

Will a polyclonal antibody attach to proteins of different kDA?

If I have a GST 26kDa polyclonal antibody, will it bind to the GST 28kDa protein as well?
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538 views

What is the function of cystine, cysteine, and cysteine protease?

I am not a biologist, and I have a probably dumb biological question. For some purpose, I need to understand the function of the CTNS gene, and here is the definition of it: "This gene encodes a ...
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1answer
795 views

Effect of mutation on phenotype

Is there a type of mutation that changes the phenotype of an organism, but not the protein sequence?
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23 views

Multi-protein drug treatments

Apologies if this an obvious question - I am very new to this. I am, as of now, under the impression that multiple SNP variations interact to create multiple mutated proteins, which ultimately results ...
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1answer
7k views

What is the meaning of “E-value” in the BLAST search?

After reading many pages, I still do not understand the definition. Can someone use simple words to explain me that? https://en.wikipedia.org/wiki/BLAST This expectation or expect value "E" (often ...
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360 views

What are the causes of abortive initiation?

I was reading more about DNA transcription, and it mentioned abortive initiation. The article gave no explanation as to why the phenomenon occurs. The only explanation I can think of is that it is ...
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1answer
660 views

Pros and cons of amino acid structure vs DNA sequences for evolutionary comparison [closed]

This is an analysis question for a lab on the amino acid differences in beta globin amongst different primates, and using such differences to construct a cladogram and infer evolutionary relationships ...
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2answers
100 views

Is there a hypernym for enzymes that “cut” other molecules?

I have searched on Google for a hypernym/umbrella term that encompasses all enzymes whose function is to cut other molecules, but I have yet to find such a term. The term I am looking for would ...
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4answers
63k views

Why are 3 nucleotides used as codons for amino-acid mapping in DNA?

DNA is made of 4 unique nucleotides. When coding for a protein, a sequence of 3 nucleotides is used to code for each amino acid. Why are codons 3 nucleotides in length? A related question can be ...
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1answer
1k views

What is the distinction between deoxyribonucleases and restriction enzymes?

Both deoxyribonucleases (DNases) and restriction enzymes are endonucleases (some DNases can be exonucleases). They both break the bonds between nucleotides. Therefore, what is the difference between ...
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1answer
179 views

Why do humans cook animal meat

Why do humans "need" to cook animal meat? It seems there's an aspect of safety to it: are other animals (eg, house cats, dogs) not vulnerable to the same diseases we get from modern food processing ...
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2answers
298 views

Dissolving cell pellet after sonication

I was doing a protein prep and I made a mistake. After sonicating my cells, I was supposed to centrifuge and collect the supernatant (my protein is soluble and comes in the supernatant). I however, ...
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1answer
33 views

Can a protein go outside of nucleus after go inside with nuclear localization signal (NLS)

To make a protein (for example Cas9, GFP...) able to enter the nucleus, we need to add a NLS tag for it. So will it able to go outside the nucleus after get inside ?
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1answer
785 views

What happens to the enzymes produced by the digestive system?

Our digestive system produces a lot of enzymes and they help to catabolize the food, and after completing their work are they excreted out or as they are also made up of proteins are they catabolized ...
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1answer
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Does cocaine bind competitively or non competitively to DAT?

I was just wondering whether cocaine, once reaching a synapse, binds to a DAT (Dopamine transporter) competitively or non competitively, or neither of them?
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555 views

Why do fully grown organisms need protein intake?

If proteins are building blocks of an organism then it makes sense why a growing organism would need an intake of them, but why would a fully grown organism need proteins (aside from those lost by ...
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1k views

When does histone synthesis occur in relation to DNA replication?

Do histones have to be synthesized before DNA is replicated to allow the DNA to coil around histones?
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1answer
2k views

Why are transmembrane proteins difficult to crystallise?

I know that in vivo there are a lot fewer transmembranous proteins in general, and that they are produced at a lower rate than their free counterparts. This is mainly because transmembrane proteins ...
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1answer
135 views

In myosin II are regulatory and essential light chains calcium binding proteins or sites of phosphorylation?

According to my medical physiology by Rhodes and Bell their description is as follows: the essential light chain is necessary for myosin stability, and the other chain called the regulatory light ...
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2answers
908 views

How does hypochlorous acid inactivate viruses?

I was reading how bleach was used very widely as a disinfecting agent during the 2014 West Africa ebola outbreak and am interested in the mechanisms with which hypochlorous acid inactivates viruses. ...
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0answers
33 views

To which SCOP Class corresponds the following secondary structure?

I need to classify this protein into one of the SCOP class (all $\alpha$, all $\beta$, $\alpha +\beta$, $\alpha/\beta$, or small protein). I'm having difficulties understanding the difference ...
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1answer
10k views

Do proteins generally contain phosphorus and sulfur?

I've heard that proteins generally contain six main elements - carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. I know that proteins are made from amino acids. Amino acids are composed of ...
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1answer
246 views

Does terminology for changes in membrane potential refer to additive or multiplicative change?

Is the membrane potential just the number of mV, or is it to what extent it differs from 0? For example: If the mV goes from -40 to -60, can you say that: The membrane potential decreases, because ...
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3answers
438 views

Why do bacteria eat enamel?

What causes tooth decay bacteria or acids? I've been told that it is a combination of both but why would bacteria eat enamel? There are much easier supplies of protein for bacteria to munch through (...
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1answer
160 views

Kidney failure → Inhibition of Na+/K+ pump → Heart failure

I read in my biology book: Due to kidney failure, the concentration of K+ in the body increases. This can lead to heart failure too. But there wasn't any explanation to the mechanism of this ...
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2answers
4k views

Why are proteins always made in N to C direction?​

Why are proteins always synthesized from the N-terminus to the C-terminus? Can there be any “reverse” peptide-bond formation to synthesize proteins in the C-terminal to the N-terminal direction?
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Size of the glycan chain in a glycosylated protein

I would like to know where I can find the (experimental/estimated) distribution of glycan sizes attached to proteins.
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1answer
467 views

What characteristics of the protein folding process ensure that the energy landscape is a funnel?

The folding funnel hypothesis states that the energy landscape that proteins observe when they fold is funnel shaped with a single global optima. This ensures that no matter what sequence of folds the ...
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1answer
329 views

What's the difference between prions and prion-like proteins?

If I added a prion domain to a protein, does that make the protein a prion-like protein or would it be considered a prion at that point? I'm trying to understand what prions are, how they aggregate ...
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2answers
140 views

Database of known human proteins

Is there an up-to-date database of known human proteins that is easily accessible using Python libraries?
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0answers
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Protein/ligand affinity databases?

Is there any database that contain binding affinities reported in litterature for different proteins and ligands? I have checked uniprot already and it does not seem to included any binding affinity ...
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1answer
36 views

Retrieve the associated annotation from Uniprot

I have a dataset that I extracted using Cytoscape and STRINGAPI Hoz can I retreive the annotation of that network from uniprot as it has more than 1k proteins . and doing it manually is not possible
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1answer
350 views

If bortezomib, a cancer drug, inhibits cell proteasomes, wouldn't resulting protein aggregate in normal cells further increase the risk of cancer?

Bortezomib is an anti-cancer drug that inhibits the proteasomes of cancer cells, allowing proteins that stop cell growth to fold and perform their function. However, wouldn't bortezomib also affect ...
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3answers
2k views

Is prion a term used to describe the normal form of the protein as well as the disease causing form?

I've been reading my textbook and it refers to prions as a normal protein with a helpful function but it can turn into a disease causing form. However, I look in my other textbook and it refers to the ...
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0answers
56 views

String-db locally downloaded

I need a ppi network of cancer and it should have 200k to 300k proteins (nodes) As the web inteface don't allow more than 2000 ...
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2answers
80 views

Predicting DNA nucleotide bases sequence from fully formed protein

I know there are many algorithms (and a lot of different implementations) that allow predicting the outcome of protein synthesis given a set of nucleotide bases present in the DNA. In other words, ...