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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What is the longest-lasting protein in a human body?
Protein life times are, on average, not particularly long, on a human life timescale.
I was wondering, how old is the oldest protein in a human body? Just to clarify, I mean in terms of seconds/...
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Why are prions in animal diets not destroyed by the digestive system?
According to CBC:
Mad cow disease is the common name for a condition known technically as bovine spongiform encephalopathy, or BSE. [...] The only known source of mad cow disease is from animal-...
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What is 'protein' in food?
I know that proteins perform a lot of functions and as a result there are a lot of different types of proteins in our bodies. When I eat food that has x grams of 'protein', what is this? A homogenous ...
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Do all proteins start with methionine?
Start codon AUG also codes for methionine and without start codon translation does not happen. And even the ambiguous codon GUG codes for methionine when it is first. So does this mean that all ...
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How do proteins 'know' where to go?
I've just found once again this famous animation I've been curious about for many years:
https://youtu.be/WFCvkkDSfIU?t=213
Here's a screenshot from the animation:
The green blobs (proteins, I ...
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What inactivates pepsin in infants?
In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach.
Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk ...
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What is the difference between HPLC and FPLC and why is FPLC preferable for protein purification?
I've used HPLC (high performance liquid chromatography) before (once, so I'm barely even qualified to know what it stands for) so I was surprised when my labmate told me she would be using an ...
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Given ATP synthase's structure, how can 3.33 protons ultimately synthesize one and only one ATP?
I am familiar with the structure and function of ATP synthase, but one small detail doesn't seem to make sense. It also happens to be a detail that seems very hard to express.
Depending on the ...
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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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Why are sushi proteins called "sushi"? What are the origins of this name?
Does anybody know why complement control proteins (also short consensus repeats) are called "sushi" proteins? Is there any special reason for their name?
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Do gene expression levels necessarily correspond to levels of protein activation?
I have seen a lot of research into molecular mechanisms of diseases/phenotypes use measures of RNA as a 'proxy' for the level of protein available in the cell. Is this actually valid?
My problem ...
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What is the significance and method behind Ramachandran plots?
My PI showed a Ramachandran plot in class today with minimal explanation, but I'm interested in finding out more. I understand that the Ramachandran plot shows the relation between the omega phi and ...
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Intrinsically disordered proteins as potential drug targets
Intrinsically disordered proteins (IDPs) are a class of proteins that do not adopt a stable secondary or tertiary structure under physiological conditions in vitro, but still have biological functions....
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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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How can computer predictions of protein folding be verified computationally?
Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.).
The question that I have is: How do you know ...
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What effect has changing pH and salt concentration on protein complexes?
I'm struggling to find peer reviewed literature that explains the effect of changing the pH and the salt concentration on protein/protein complexes in solution. What effect does the pH and the salt ...
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Can two protein secondary structures "overlap" in the PDB?
I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file:
...
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Can any protein be phosphorylated?
I am working with an Arabidopsis mutant with an F-box protein knocked out. It has been shown that F-box proteins targets must first be phosphorylated (Skowrya et al., 1997). I have heard of ...
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Are there any examples of proteins with no or minimal sequence identity, but highly similar structure?
What are they, and do they share a common ancestor? How far back in evolutionary time must we go to find them?
If none are known, what computational tools might be used to search for such examples?
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How many human proteins have a solved 3D structure?
I was wondering how many human proteins have a solved 3D structure. Is there a database with only human proteins? I looked at pdb but couldn't find a filter.
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What are the benefits of elucidating the three-dimensional structure of a protein?
I have spent months as a student working on trying to form a tricky protein crystal. But I have never actually had explained to me why the structure will be useful. Once elucidated, what can we ...
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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 ...
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Does the recent concern over several papers about Aβ*56 call into question the association of Alzheimers Disease with any amyloyd beta oligomer forms?
The news item by Charles Piller just published in Science BLOTS ON A FIELD? A neuroscience image sleuth finds signs of fabrication in scores of Alzheimer’s articles, threatening a reigning theory of ...
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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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Differences Between Protein Motifs and Protein Domains?
I am in a 300-level molecular biology class and am unclear about this concept and how to delineate motifs versus domains of proteins. Any suggestions would be much obliged.
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Why are restriction enzymes not frozen?
We all know restriction enzymes are proteins, but we never freeze them. They are instead provided in high glycerol containing solutions by companies and stored at -20C. Is there a reason why this is ...
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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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Can you get enough water by eating only fish?
Scenario: In a boat in the middle of the sea, no freshwater or food stores, no desalination equipment, no rain, but you can catch fish and eat it raw. Can you get enough water this way to survive, let'...
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What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?
First definition.
Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly ...
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What is "irrational" drug/molecule design?
Both the papers "Directed evolution: the 'rational' basis for 'irrational' design" by Tobin et al. and "Rational and 'Irrational' Design of Proteins and Their Use in Biotechnology" ...
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Why can't H3O+ ions pass through aquaporins?
Aquaporins are proteins that facilitate the movement of water (and related molecules) through cell membranes. (Also, these transport proteins are very specific about what they transport.) ...
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What is the purpose of using two layers of gel in SDS- PAGE?
I just made a SDS-PAGE with a top layer of stacking gel and a bottom layer of separating gel with different pH values of 0.5M Tris-HCl. The stacking was 6.8 and the separating gel was 8.8. What about ...
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How would I explain different properties of the same protein in different species?
I recently finished an experiment where I analyzed the rate of ATP hydrolysis of Heat shock protein 104 in three species of fungi. They have shown to all have different rates of ATPase activity. How ...
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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 ...
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What is the difference between a protein and a factor?
In terms of nomenclature/semantics, why are some proteins named proteins, and some named factors?
I've been revising on eukaryotic DNA, and I've come across some proteins that seem to serve roughly ...
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Why is protein turnover necessary or important for cells to function?
Cells constantly create new proteins in order to maintain their normal function, this is called protein turnover.
Why is that? Do the old molecules wear out as time passes, so that they need a ...
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Can protein structure be determined by X-Ray Diffraction in a single image?
I'm reading about the use of x-ray crystallography to determine protein structure. According to my book, data is collected at 30-360 angles (dependent on the symmetry of the protein). An illustration ...
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How do we know if the folding@home project results are right?
Some of us are involved in the folding@home project, spending time, money, and resources.
I would like to know the answer to two main questions:
How do we know we fold it right? I mean, these models ...
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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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What role does a protein's size have on protein-protein interactions?
Protein-protein interactions are when two or more proteins bind together, possibly for some important biological function. Recently, I'm starting to look more into proteins, and in particular, ...
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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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Do chaperone proteins misfold?
If molecular chaperone proteins assist in the folding process of other proteins and misfolded proteins, can chaperone themselves misfold since they are also proteins? What would happen if chaperones ...
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How does Yeast-two-hybrid detect interactions between several proteins in one experiment?
I am trying to understand the Y2H screening method. I can understand how we can check if two specific proteins interact with each other. For example, if we want to check whether protein A and protein ...
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How does the enzyme ATP Synthase use a proton concentration gradient to make ATP?
I understand what the enzyme ATP synthase does, but I'm not exactly sure how it does it. I've heard that it uses rotary catalysis, but how exactly does this work? How is the energy from the H+ ion ...
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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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Circular mRNA to produce long proteins
Ribosomes can read mRNA and produce proteins, if we somehow make a circular mRNA for the ribosome to bind onto, it will make infinitely long "proteins", (since ribosomes can make very big proteins, I ...
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What are the secondary structure requirements for cell-penetrating peptides AKA protein transduction domains
Cell penetrating peptides.
Cell penetrating peptides (CPPs) are a class of short amino acid sequences which are sufficient for crossing cell membranes and delivering themselves along with any attached ...
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Why don't membrane proteins move?
I understand that based on their tertiary structure, intrinsic proteins have hydrophobic non-polar R-groups on their surface and that they 'interact with the hydrophobic core of the cell membrane to ...
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Why is glycine considered a nonpolar amino acid but a polar molecule?
Glycine has a dipole moment, so why is it considered a nonpolar amino acid when discussing its occurrence in proteins?
Also, is the backbone of a protein nonpolar?
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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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