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Crystallin proteins are found in the eye lens (where their main job is probably to define the refractive index of the medium); they are commonly considered to be non-regenerated. So, your crystallins are as old as you are! Because of this absence of regeneration, the accumulate damage over time, including proteolysis, cross-linkings etc., which is one of ...


49

Proteases are enzymes in your digestive system that help break down food, acting like molecular-sized scissors that cut up proteins. Proteases have clefts, or subpockets, into which proteins fit, where the substrate (protein) gets cut. Infectious or pathogenic prions are resistant to proteases, because of their three-dimensional conformation, or shape, ...


33

It is highly unlikely that there exist any protein that is made from completely identical nucleotide sequences across the entire human population. There will certainly be regions within a gene that are highly conserved, but there is little evolutionary pressure to conserve an entire gene's nucleotide sequence across the population. This is in part due to ...


22

I like Mowgli's answer, because it is a non-obvious example. However I would also point out that there are many, many protein-based structural components in the body that we know do not regenerate due to associated pathologies; so presumably these structural proteins are as old as from when they first arose in developemnt. Take the stereocilia on hair cells ...


22

Humans have many variants There is variation. The project I use to help understand this natural variation is gnomAD. Using VarMap and a slightly out of date gnomAD file, I counted 16007805 protein-coding variants across the human genome. This number will only go up over time. Indeed, the 1000 Genome project found that on average each person has between ...


9

A very interesting example are the cohesin molecules holding sister chromatids together in the oocytes (so only applicable to females, sorry!). Cohesion is established in utero, and these molecules are not recycled throughout life (AFAIK only shown directly for mice, not humans - https://www.ncbi.nlm.nih.gov/pubmed/20971813, https://www.ncbi.nlm.nih.gov/...


9

Chaperone proteins are still proteins and they can certainly misfold just like any other. If that happens, it will either be assisted by another chaperone and given time to fold successfully or it will be destroyed. If this is happening too often and the amount of chaperones drops too low or the number of unfolded or incorrectly folded proteins becomes ...


8

The situation you ask about was originally part of the 27 ribbon and 2.27 helix structures considered as possibilities by protein chemists (Linus Pauling?) in the 50s or 60s. The diagram below, showing the ribbon, is from the classic text (long out of print) The Structure and Action of Proteins by Dickerson and Geis. This turns out to be very rare in ...


8

At the whole-gene level, there is likely no absolute conservation of any human protein-coding gene at the population level, though there might be complete conservation between individuals. Keep in mind that most human genes are on the order of tens of thousands of base pairs long, and only a portion of that length encodes functional motifs. There are, ...


7

Until the late 1980's all enzymes* were believed to be proteins, and were often defined as protein catalysts, often in textbooks which are often not perfect representations of science. At that point every macromolecular biological catalyst known was a protein so they thought all macromolecular catalysts were proteins. But the discovery of ribozymes (RNA ...


5

When does protein folding begin? With reference to time you have asked, it can be after the translation has occurred (called Translational protein folding) or while translation is still occuring (called Co-Translational protein folding). Here is the link to an article for basic understanding of co-translational protein folding. There is a lot of debate on ...


5

Like many genes and gene products, PIN proteins were named for a mutant phenotype and PIN is not actually an acronym; the source in your link does actually explain this (emphasis mine): The significance and function of AtPIN1 was discovered through the phenotype generated by the loss-of-function mutation in the gene: mutant plants fail to develop floral ...


5

In humans, cysteine can be synthesized from methionine and tyrosine from phenylalanine (note that the reverse pathways do not occur). Because their synthesis requires essential amino acids and the biosynthetic capacity of the organism does not always meet its need, they have been labelled conditionally essential. Under normal circumstances, an adult human ...


5

The two techniques serve different purposes: IP: purifies a protein WB: visualizes or quantifies a protein Most often when I have done IPs (in the hazy past) I have turned around and run the protein out on a WB, so one will frequently combine both techniques. Sometimes a protein is very low abundance so you will not see it in a small volume of crude cell ...


5

Assuming that your protein can handle being in the new buffer, you have multiple options. Dialysis will work although you might want to consider using a centrifuge spin filter with a suitable MW cutoff to gradually switch buffer and concentrate the sample. Be aware that some of your protein will stick to the filter, giving a loss of sample. Alternatively ...


5

There are a number of ways to address this, and the other answers are certainly correct. Another strategy, especially if you already have the sample in PBS, is just to dilute it in the low salt ion exchange buffer. This works because you don’t need to completely remove the phosphate or salt, just get it low enough so that it doesn’t interfere with binding to ...


4

Introduction This question has two components. The first is the near rhetorical question whether proteins with unnatural amino acids will be considered by the immune system as ‘non-self’. Unless, by chance, the unnatural amino acid resembles some normal macromolecular component, the answer is obviously that it will be regarded as ‘non-self’. The second ...


4

This DSSP page makes it clear that: Helix-3 = 3-10 helix Helix-5 = π-helix The α-helix) is described in every biochemistry text book and widely on the web. It has 3.6 residues per helical turn and has 13 atoms in the ring formed by the hydrogen bond and so can also be called a 3.6-13 helix. The 3-10 helix is less common than the α-helix, but is ...


4

This is probably to prevent precipitation of copper hydroxide (see Itzhaki & Gill, 1964 - they suggest adding dilute copper sulfate slowly to the NaOH solution to avoid this). If you have the protein already alkalized and ready to react you'll get the color reaction before precipitate forms. Commercial premixed solutions, like @canadianer mentioned in a ...


4

If you scroll down through the uniprot entry you will come to a section with the heading PTM/Processing. From this you can see that the first 18 amino acids are a signal peptide. You can learn more about signal peptides from any good introductory textbook covering cell-biology — alternatively Khan Academy is a good source for learning the basics.


3

In the Biuret reaction, copper forms a complex with the nitrogen of the peptide bond, that looks like this (Structure 61 from the paper below): A strong base is necessary to provide the conditions for deprotonating these nitrogen atoms and have the conditions to form the complex. If you want to read this in detail, have a look at this publication: ...


3

Signal peptides are typically located at the N terminus of a protein. The signal peptides are processed by the translocon machinery and are cleaved off after sorting through the membranes of organelles in the secretory system: endoplasmic reticulum Golgi apparatus ER-Golgi transition vesicles plasma membrane lysosomes Transit peptides ...


3

In gel electrophoresis, the gel is the mechanism by which macromolecules of different sizes are separated. By loading the gel with amino acids (or proteins or DNA), you start all of the samples equally, and then push them through a gel using a salty buffer solution that is electrified. The gel has a certain concentration of a polymer (commonly agarose or ...


3

I don’t actually consider these pictures either “gorgeous” or “cool” — they are not to my taste — and I’m not really sure that the question is about biology, but as it has resurfaced after almost 5 years I thought I’d give an answer which explained how one might create something similar, rather than how they were actually made. The original 3D-graphics ...


3

It depends on how you define "enzyme". Wiktionary says an enzyme is: A globular protein that catalyses a biological chemical reaction. Wikipedia says: Enzymes are macromolecular biological catalysts. So the first definition excludes anything but proteins and the second also allows other large biological molecules which catalyze reactions. The ...


3

The activation energy is not only lowered by orientating the substrate but by stabilizing the transition state. According to the induced fit model many enzymes show a higher binding affinity to the transition state of a substrate.


3

In terms of the common/abundant proteins, the answer would have to be elastin. The turnover is extremely slow, with a half-life of 74 years (https://www.elastagen.com/media/The_Science_of_Elastin.pdf) or "decades" according to other sources. In any case it is very slow - slow enough that most of it lasts a lifetime. Elastin is a major constituent of the ...


3

The Wikipedia article on Ubiquitin gives a pretty good answer to your questions. Look at the referenced articles if you want to get more detailed answers. Are they just always available for the Ub to find to during the ubiquitination process? Yes, This [Ubiquitination] process most commonly binds the last amino acid of ubiquitin (glycine 76) to a lysine ...


3

The process of downregulating a receptor by internalizing and degrading it in response to (sometimes prolonged) activation or (sometimes prolonged) failure to activate is what pharmacologists call desensitization (in either context). You can read about this generally in Goodman and Gilman's Pharmacological Basis of Therapeutics, Chapter 3, under the ...


3

Scrambled eggs can change color, but you perhaps haven't run into a batch that shows discoloration. It is the same chemical reaction: Why Scrambled Eggs Turn Green When serving a large group, a buffet can provide enough food for everyone without the need to spend all of your time in the kitchen. Breakfast is a fairly simple buffet to set up, but ...


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