Proteins are way cooler than cookies and cakes, but a more fun analogy the cake does make! So how do you open, manage, & shut down protein bakeries? Explaining GENE REGULATION the bumbling biochemist way! Which I think could make a great “Inside Out 2” that, instead of taking you into a brain, takes you inside a cell making proteins.
adapted from past post
Proteins are cellular “workers” made up of amino acid building blocks. I like to think of them as “baked goods” like cookies & cakes. Cells are constantly dealing w/different demands, to which they have to be able to adapt their supply to meet. There are many different ways in which they do this & the further down the protein production pipeline, the more quickly effects can be seen, but the less efficient the process (like turning off a faucet vs cleaning up the mess)
The cellular nucleus is like the corporate headquarters that directs the opening of franchise bakeries by issuing messenger RNA (mRNA) copies of recipes for various protein “baked goods.” Cells can regulate how many bakeries in each chain they open (transcriptional control); how many bakers each chain hires & how efficient those bakers are (translational control); how long the bakery stays open (mRNA regulation); and how “well the product sells” and when it expires (post-translational control)
The original recipes are written in DNA in the form of genes, bound together into “cookbook volumes” called chromosomes housed in a membrane-bound room in your cells called the nucleus. To make a protein, the cells make an messenger RNA (mRNA) copy of the gene-encoded recipe in a process called TRANSCRIPTION, then (if it passes the security check) the mRNA recipe gets sent out into the general part of the cell (CYTOPLASM) where they’re used to start “bakeries” where “bakers” called ribosomes turn it into a protein in a “baking” process called TRANSLATION.
These “bakeries” are called mRNPs – messenger RNA containing ribonucleoprotein complexes. Short acronym for long words which tell you you have a group of proteins & RNAs bound to a protein recipe (mRNA). The only “constant” in the bakery is the recipe (mRNA) – binding partners vary throughout the mRNA’s lifetime depending on what needs to be done (e.g. swap out proteins that help w/start-up construction phase to ones that specialize in maximizing productivity to ones that help w/shutting down the bakery).
The mRNA sequence is also the only “unique” part about the bakery, so the other components can be reused. So they have to be “cross-compatible” → they often bind to the “generic parts” of mRNAs. Most of the text in the mRNA is “templated” meaning that it comes word-for-word from the DNA version. But mRNA also has extra “generic” words put on in the form of a polyadenylate (poly-A) tail & a 7mG at the beginning. In addition to offering generic “latch-on” points for proteins, the cap & tail serve as a kind of “watermark” that tells the cell they’re legit. more here: http://bit.ly/mRNAbiochemistry & https://bit.ly/mrnalife
The “bakers” are called RIBOSOMES & they’re complexes of proteins & ribosomal RNA (rRNA) molecules that read the recipe and link together the corresponding amino acids (protein letters). They know what to add because 3-letter RNA words (codons) spell one amino acid letter. The baker moves along the recipe & “calls out” the next amino acid to be added → biochemically, what’s happening is the ribosome is translocating along the mRNA (taking 3-nt-long steps) & as it does so it exposes the next codon in its A site. Then a tRNA “servant” brings it the corresponding amino acid. more here: https://bit.ly/proteintranslationwedding & https://youtu.be/XFNg6OlKWvw
There are 4 RNA letters (A, U, C, & G) so 64 codons – 1 (AUG) spells start (& methionine) & 3 spell stop → When a stop codon shows up, instead of tRNA binding, release factors bind (proteins pretending to be tRNA that come with scissors) → cut off growing chain and free the baker which can then start making another protein (either at this bakery or a different one)
But before you can get to translation, you have to go through TRANSCRIPTION (making the mRNA copy of the DNA recipe you can take out of the nucleus). And this provides an opportunity for…
TRANSCRIPTIONAL CONTROL: how many recipes do you make? → each copy can become a bakery so how many recipes you make determines how many bakeries of the chain you open. regulation at this level is largely dependent on proteins called transcription factors (TFs). These are kinda like “lobbying groups” which influence what chains do or don’t get opened. Biochemically, TFs are proteins &/or regulatory RNAs that bind to regulatory regions on the gene & recruit or keep away transcriptional machinery (the DNA to RNA “Xerox machines”).
This level of control is the slowest because it’s furthest removed from the user & it only effects new the opening of new bakeries – doesn’t affect all of the existing bakeries. But, in terms of future production, it’s the most efficient because you don’t waste resources making proteins you then have to destroy
POST-TRANSCRIPTIONAL CONTROL – a nice thing about controlling at this level is you don’t risk harming the “original copy”. When it comes to problems in the protein production pipeline, problems w/the DNA version of the gene are the scariest because they can get passed down to future cells. Since 1 mRNA can be used to make lots of copies of a protein, problems with 1 copy of the mRNA can lead to lots of faulty protein copies, but if you can detect & get rid of the typo-ed recipe, you’re safe
And your cells have multiple pathways to detect typos, starting in the nucleus. To get out of the nucleus, recipes have to undergo processing and a security check to make sure they got processed correctly and the regulatory information got “redacted” – mature mRNA is an edited version of the DNA version of the gene – some of the information in the gene is regulatory information that’s “for upper-management eyes only.” Parts of the gene that have protein-making instructions are called EXONS &, in DNA, they’re interspersed w/“margin notes” called INTRONS that are important for transcription but not translation.
The exons are stitched back together & the only “extra” info is at the ends – before the start codon is the 5’ untranslated region (5’ UTR) & after the stop codon is the 3’ UTR. These offer latching on points for bakery workers to help w/post-transcriptional regulation. You control from the ends because if you put things on the coding part they’d get shoved off by the ribosomes.
They also have the cap & tail added. Splicing factors help recruit the tail-adders. And cap-binding proteins bind the 7mG cap & help escort it out. Once out, it’s handed over to cytoplasmic security guards that protect it from exonucleases (RNA end-chewers). Now that you’re in the cytoplasm…
mRNA REGULATION – Are the bakeries open? You want to shut down any bakeries that fail inspections or don’t have enough demand to be worth keeping open. Shutting down a bakery usually involves removing the tail (deadenylation) & the cap (decapping) and letting the exonuclease have at it.
About those inspections… Nuclear security can tell if the mRNA’s been processed, but not if there are any “typos,” which is where TRANSLATION-COUPLED mRNA PROCESSING comes to the rescue. It relies on bakers to “beta test” recipes & report problems – you don’t want to sell defective products so the proteins are sent to the proteasome for degradation, the recipe is chewed up so it doesn’t happen again, & the baker is relocated to another bakery
different typos are handled differently: https://bit.ly/rqcontrol
There are also pathways to shut down bakeries even though nothing’s technically “wrong” with them. RNA interference (RNAi)/micro-RNA (miRNA)-mediated regulation is a sequence-directed way to silence specific mRNA’s http://bit.ly/microRNARNAi & https://youtu.be/7XHXF0x2uKA
and less-specific RNA binding proteins (RBPs) like ones that recognize “a couple letters” can work together to bring in decay machinery.
TRANSLATIONAL CONTROL: How many chefs does the chain employ & how efficiently do they work? Each bakery can only make one product because it only has 1 recipe, but multiple bakers can read from it at the same time (polyribosomes). You can let some of the bakers take a vacation when demand’s low, then ramp up production when demand grows. This is a good, reversible, way to control protein production. but it doesn’t address the action of the existing proteins. for that you need post-translational control, which involves changes to the proteins themselves that aren’t spelled-out in the recipe
POST-TRANSLATIONAL control: How well does the product sell? Is it expired? Unlike baked goods, proteins don’t usually get “consumed” but rather used – they’re usually “multi-use” but eventually they get damaged or they just aren’t needed any more. Proteins can be modified by adding groups like phosphate (phosphorylation) or sugar chains (glycosylation) which can alter their functioning, and they can get degraded.
When proteins are no longer wanted they can be tagged with chains of a small protein called ubiquitin & sent to the proteasome, which is like a protein paper shredder. ubiquitin is like mold growing on your cake – it signals it needs to gets tossed. But that mold doesn’t grow itself & it doesn’t just appear when a protein’s gone bad. It gets added by enzymes called ubiquitin ligases so something has to tell it it’s gone bad (for example, ribosome stalling leads to recruitment of ubiquitin ligases to tag the partial proteins produced in failed translation): https://bit.ly/ubiquitinylation
This is the fastest way to get a detectable response because you destroy the protein – but it’s the least efficient because you have to destroy each one individually – if you keep making more protein you’ll have to keep doing it → but can serve as a good “stop-gap” measure. And, in terms of “badness” problems that just effect the protein level are the “safest” (single bad apple) as long as your quality control’s working
There are a lot of different ways to measure “gene expression” and each can tell you different things. more here: https://bit.ly/expression_measurement & https://youtu.be/aTbJAnF4nqI
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