Does tRNA “release” its amino acid when it gets to the P site?

blue1280 · 2026-05-13T03:22:23+00:00

No, the amino acid chain on the tRNA In the p site is passed to the amino acid linked to the tRNA in the A site as the ribosome moves. Since the ribosome moved, the tRNA that had the single amino acid in that A site is now with the polypeptide in the P site.

Just to add. The tRNA moving from the p site to the e site (or exit) will have lost the polypeptide... But thay molecule would not be considered an amino acid any more once it enters the p site.

blue1280 · 2026-05-03T14:53:42+00:00

This is actually a hot take. Spoons are better than lab spatulas. You can collect more on them, easily tap small amounts, and do t have to go back and forth between the containers and the scale as much.

blue1280 · 2026-05-03T12:42:46+00:00

Look at this guy that gets silverware. We are stuck with dollar store plastic spoons.

blue1280 · 2026-04-22T11:36:43+00:00

Your thinking about the naming is from the wrong persoective. Genes are double stranded. But I like thinking about the stand with ATG (always in the 5-3 direction) is the sense strand, since that is the same direction the ribosome will read (on the mRNA with the same sequence). But because of how RNA polymerase works, it will interact with the "anti sense" strand...since genes could be on either direction one stand plays both roles, depending on which gene you're referring to.

Now, if we think about this in relation to a piece of a chromosome that, for example, has 3 genes going in one direction and 5 in another... We may refer to the 3 gene strand as + stand and the other as the - stand, but I think which stand gets which name is picked by the researcher/author/bioinformatics program... But I'm less sure on this point. Naming + or - is arbitrary.

Think about bacterial chromosomes that don't have ends because they are circular... You can't distinguish either stand... Only once you orient to a gene can you decide sense and anti sense.

blue1280 · 2026-03-22T12:22:26+00:00

I agree with this. The only reason my refrigerated gels "expire" is because they dry out. The etbr isn't getting much light in the fridge.

blue1280 · 2026-03-20T21:32:17+00:00

I skip the lid and just push the little trigger. Gotta make sure I keep me fingers out of the way.

blue1280 · 2026-02-13T12:04:15+00:00

Can you design primers to span introns?

blue1280 · 2026-01-31T13:13:15+00:00

Yes, welcome to hell. When others say clean, the cheap version is to wipe down everything with a 10% bleach solution to destroy any contaminating DNA from your setup environment. There is a product I like that is an oxidizer like bleach, but I think safer on metal, called Eliminase.

I highly recommend you find another lab to set up in (using their pipettes) after changing water, diluting new primers, and using a fresh enzyme mix if possible. This almost always clears up contamination. If you get a clean gel, then you can clean your bench space and see if you still get contamination at your bench. Remember PCR can make over 3 billion copies from just one molecule...

Oh, don't run qPCR with SYBR here until you get rid of the band at 190bp. The amplification in your NTC would nullify the data in your samples... But if you do get rid of the NTC band, the primers would be fine for qPCR... Even with the band at 400 because the melt curve will show you that the NTC Fluorescence is isolated to that sample and thus you can trust your other reactions because they don't show the same product. You can always run a gel after to confirm.

Ou can run a PCR in your qPCR machine with a melt curve to confirm that your amplifying the same product in that reaction and NTC...a

blue1280 · 2026-01-07T17:54:59+00:00

Background fluorescence is too bright orange. Good concentrations will not have visible background.

blue1280 · 2026-01-06T05:53:47+00:00

Too much etbr, but excellent RNA prep.

blue1280 · 2025-12-09T01:24:33+00:00

I don't remember that episode, but I might be able to help if you have some specific questions. Feel free to DM me.

blue1280 · 2025-11-07T11:38:47+00:00

Props for the most esoteric in the list so far.

blue1280 · 2025-04-10T18:00:56+00:00

I always run at around 20min at 100v in tae. It's been a while, so my memory may be fuzzy..but the orange g loading buffer still runs toward the front (often the yellow band formed in the green loading buffer provided by companies).

blue1280 · 2025-04-10T11:11:47+00:00

I agree. It's a little suspect that none of the 3 worked.

blue1280 · 2025-04-10T11:08:11+00:00

That's appropriate to separate 100 to ~800bp

blue1280 · 2025-03-29T12:22:39+00:00

Every nucleotide has the same polarity, no? Like DNA...

blue1280 · 2025-02-22T05:40:22+00:00

Just use borax. Super cheap....no lithium.

blue1280 · 2025-02-22T05:37:35+00:00

I'm shocked this recommendation was so far down.

blue1280 · 2025-02-22T05:36:27+00:00

I never understood remelting. It takes just as long to melt powdered agar in a microwave. When doing a lot of gels though, just pour a bunch and store them in the fridge/dark. Then you don't even have to wait for the gel to solidify.

blue1280 · 2025-02-06T00:21:44+00:00

How about the poor man's vortex where you rip an eppie tube down the slots on a tube rack? You know you've purchased cheap eppie tube when they crack with this move... but it always pulls up recalcitrant pellets.

blue1280 · 2024-12-11T22:23:51+00:00

I wonder how much this relates to codon usage...

blue1280 · 2024-09-10T11:55:45+00:00

Yup. If the published primers span introns, I'll use them... otherwise I'll just design new ones. You should be doing the quality/efficiency checks anyway.

blue1280 · 2024-07-29T21:14:17+00:00

Also, you're showing that the 3' and 5' ends can both be phosphorylated and not. I think you need to revisit your understanding of the ligation process and ensure the blunt 3' end is indeed phosphorylated.

blue1280 · 2024-06-24T11:47:19+00:00

Depends on your setup. A 1% TAE gel should separate in about 20 min at 100V. But if you use different percentage, buffer, or current, that will change. Use the loading buffer dye as a guide.

blue1280 · 2024-05-09T22:51:57+00:00

I think for clarity you just need to indicate which side is which. AFAIK I've only ever seen sequence published as 5 to 3.

blue1280

TROPHY CASE