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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 ...


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 ...


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/...


6

There are a large number of ways a protein variant can be produced by post translational modification. The question may seem obvious, but its really quite broad. I can start this out. I doubt I know all the ways a single transcript can produce variant proteins. A detailed description might be more like a review article than an answer here. First, ...


6

Heterologous promoters often express genes that are toxic to the organism when expressed in too high quantities. When the genes are expressed constitutively, the organism will either grow slowly or die before they reach a high density suitable for production of the protein. As such, it is not about expressing the genes all the time, but expressing the ...


5

Proteasome inhibitors do affect normal cells to some extent, but the whole point of using them as cancer treatments is that (some) cancer cells are far more sensitive to proteasome inhibitors than are normal cells. For example, multiple myeloma cells (the first clinical targets of Bortezomib) that overproduce immunoglobulins are dependent on proteasome ...


5

The answer is not simple - @shigeta mentioned a few mechanisms leading to single gene-to-multi protein relationships - and the answer is certainly not short (there are thousands of these genes). But anyway "alternative splicing" seems to be the primary mechanism according to this article, so rather than listing all alternatively splicing genes, here are the ...


4

Just for balance, here is an example of a single protein being constructed from two primary gene products (two separate genes involved) via protein splicing.


4

Are multi-chain proteins synthesized as one biological unit? Sometimes yes but mostly not. Some proteins are synthesized as one long polypeptide pre-protein which is cleaved by some proteases to yield multiple chains. After cleavage the intramolecular interactions become inter-molecular or inter-chain interactions. Insulin is a good example of this (See ...


4

I am not aware of anything precisely corresponding to your diagram, but the somewhat related behaviour of inteins may be of interest in this respect. They are defined in Wikipedia as: An intein is a segment of a protein that is able to excise itself and join the remaining portions (the exteins) with a peptide bond in a process termed protein splicing. So,...


3

Does splicing of peptides in the proteasome count? Proteasomes normally degrade proteins into small peptides, but the process is conceptually reversible -- peptide bonds can be generated as well as broken -- which leads to splicing of two smaller peptides into one longer one. There is some evidence that this is a fairly common event: Reports of ...


3

If you're expressing the gene in E. coli, then you're almost certain to be using a plasmid or other ectopic gene vector. There are a wide variety of plasmids available, with many different promoters. With a commercial plasmid, you're not adding in the promoter sequence, but the gene sequence. You pick the promoter you want and then clone your gene sequence ...


3

You can induce the lac operon by two things: Lactose (or more precisely Allolactose a metabolite of it) and lactose analogons which are not metabolized by the bacteria. Lactose induces the expression and is metabolized while IPTG is not a target of the $\beta$-Galactosidase and will give you a strong and permanent induction. Sucrose will not have any ...


3

I think that enzyme-linked immunosorbent assay (or ELISA) is the best way to do so, given you have an antibody against the protein to coat the sample wells with... You could use mice to create polyclonal antibodies against your protein by injecting the protein and collecting the serum and purifying it...as long as there isn't similar proteins to the ...


3

Not sure that I have ever come across trace metals in recipes (I assume that you aren't referring to the Ca/Mg salts component of M9), but it is certainly the case that many K12 strains (e.g. C600, DH5α) require thiamine because they are thi mutants. This doesn't apply to BL21 since it is from a different lineage (it is a B strain). In a lab where ...


3

Dominance is defined based on the phenotype Dominance is defined based on a phenotype of interest. Pick a phenotype, say coat color for example. If genotypes AA and Aa have the same coat color while aa has another coat color, then A is domiant over a. The concept hold even for sequence that do not produce proteins The concept of dominance can be applied ...


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

Nonambiguity refers to the fact that codon X will always code for the same amino acid. Degeneracy refers to the fact that an amino acid can be coded for by many codons. I rephrase the question to get to the gist of things: Why do certain mutations cause no difference for protein synthesis, while others make a big difference? Certain mutations can ...


2

The sequences you have posted seem to be (protein) amino acid sequences. The stop codon are present in DNA sequences and in mRNA sequences. In DNA, the bases are A, G, C and T; stop codons are TAG, TGA and TAA. In RNA, the bases are A, G, C and U; stop codons are UAG, UGA and UAA. In DNA and RNA, other letters are used to specify degeneracy. What you have ...


2

The exact numbers depend on the protein. In my hands, I would say between the pAraBAD and a pLac-T5 you can expect some fold improvement and pAraBAD and a pT7 promoters you can expect about an order of magnitude… but there are two big caveats. First, pET and other T7 driven plasmids do not work in K-12 strains (without the pTARA) so BL21 is generally used. ...


2

Yes. In principle you will have a vastly increased ability to customize the boundaries of each protein domain with a primer and PCR based approach. It is not obvious to me that the Gateway Cloning System is required, or necessarily the best choice for this approach, but that is likely subjective. Are you familiar with, or aware of, the efforts of the SGC (...


2

Gene expression is the production of a functional gene product from a gene. So protein expression is a functional read-out of gene expression for gene loci that encode proteins. However, gene expression is frequently, and erroneously, used to refer to measures of mRNA levels. The production of mRNA is a prerequisite step for the production of protein from ...


2

Why people still die after eat them even boiled to 100 oC, but why? Well not all toxins are protein based. Some are just small molecules that fit into some vital protein in your body, causing it to stop and death not long later. Some are cyclic peptides and are not denatured by heat. The peptide is simple, and has many carbon bonds to stablize its ...


2

No, if you use only centrifugation to separate proteins from other parts of the (bacterial) cell, you need very high centrifugal forces. The actual speed (in rpm) you need to separate soluble proteins from the rest of the cell is mostly dependent on the rotor of the centrifuge, because both together determine the acceleration you get, which should be in the ...


2

How do you want to predict function and binding partners without knowing how your protein looks like? The sequence itself contains only limited information. Similar sequences might fold into similar structures with similar functions. These motifs can be used to transfer your knowledge from one protein to another, which might have similar e.g. binding ...


1

There are a couple of things that are strange here. First, you have low expression in the presence of galactose. The GAL1 promoter is really strong, so that strikes me as odd. Even if it was leaky, induced vs uninduced should be night and day. However, you should keep in mind you still may not be able to see it by eye. Second, it is weird that it would be ...


1

There are two questions being asked here. 1) When DNA was used to encode RNA via DNA dependent RNA polymerase It is uncertain if the Last Universal Common Ancestor (LUCA) had this enzyme. There is some debate. Also some DNA polymerases of family A, B are structurally related to RNA polymerases https://www.ncbi.nlm.nih.gov/books/NBK6360/. So DNA may have ...


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