Beautiful Things

This is something I've been wanting to write about but was afraid I wouldn't have time or motivation to. Not so much motivation. More of a time factor. The first couple of times you learn about protein synthesis and ribosomes in high school, you kind of just get brainwashed that the ribosome is the site of protein synthesis. But what does that mean?

After the mRNA strand finds its way to the ribosome, some really fucking beautiful things happen. Translation requires some amino acid activating enzymes that are really important and some soluble protein factors (friends of ribosomes as I call them).

The way that translation works is that basically the ribosome walks downt he mRNA strand creating a polypeptide chain that is formed by tRNAs bringing amino acids to the ribosome. tRNAs with amino acids attached are aminoacylated tRNAs (we'll talk about how they are "charged" later). The new tRNA that comes into the ribosome receives the growing peptide chain and the tRNA that was holding onto it before leaves the ribosome. When a stop codon is reached, we get releasing factors binding and the protein/mRNA are both released.

A "codon" has three bases it it that are going to code for some amino acid to be brought in, but sometimes in special cases, it may not mean what it says it means. For example, a codon coding for amino acid arginine to be brought in may actually code for tryptophan in some cases in plant mitochondria. There seems to be a lot of this in mitochondria of different creatures.

In this case, the three codons that code for stop/chain termination may be used alternatively in some situations. 

The first tRNA to bring the first amino acid into the chain that's going to form is typically methionine or a modified version - formylated. 

In prokaryotes, sometimes mRNA is polycistronic, meaning it carries more than one gene. The lac operon is an example of this...we learned more about this in microbio, really. Basically it's a combination of three genes that certain microorganisms can turn on to let them ferment lactose if no glucose is present in the cell. The presence of lactose takes some stuff that blocks transcription of the lac operon off of the site and RNA polymerase can transcribe, letting the organism ferment lactose. Since there's three genes, there's 3 open reading frames, each with its own start and stop codons. In the 5' end, the very beginning of the mRNA, there's a thing called a Shine-Delgarno Sequence which is rich in AG bases, helping to align the ribosome and the mRNA properly.

This is something that I maybe should have said something a while ago, but now it doesn't fit that well anywhere, so i'm going to secretly stick in here (that's what she said)

The wobble hypothesis is basically an explanation for why sometimes only the first two bases in a codon "matter", and it's what gives the genetic code some degree of redundancy. 

tRNA looks kind of...not like this. This is ugly. It's actually L shaped in reality but it does have these loopy regions. 

In translation, what needs to happen first is that the tRNA has to become charged with an amino acid. This is done by ATP hydrolysis on the enzyme Aminoacyl tRNA Synthetase. What we get is the esterification of the alpha-carboxy end of an amino acid with the 3'OH of the tRNA

There's 64 codons but you don't need that many tRNAs since some tRNAs can understand multiple codons. So E. coli has about 40 tRNAs. tRNAs have about 70-80 nucleotides in them, some of which are somewhat weird and/or modified. On the ribosome, when the mRNA and tRNA codon and anticodon "pair up", it actually is formation of double-stranded RNA, which is antiparallel. 

Describing the charging of a tRNA.. With guidance of aminoacyl tRNA synthetase, the amino acid is going to attack an ATP, which is going to serve to make the Amino Acid more reactive when we're gonna put it onto the tRNA. There you make an aminoacyl adenylate.

While everything's still bound to the synthetase enzyme, the aminoacyl adenylate reacts with the tRNA, forms a covalent bond, and releases AMP. You then get these two classes of things possible depending on whether it's attached to the 2' or 3' OH on the last sugar of the base of the tRNA. 

This is pretty fancy. So....the tRNA that has to transport Q to the peptide chain does things a bit weirdly. First, the tRNA gets charged with an E (the thing Q is the amide of) at the cost of ATP hydrolysis. Then, the E is kind of replaced by the Q. 

Identity elements are kind of important to bind the right tRNA to the right amino acid. Here's the placement of four amino acids' tRNA's identity elements. The acceptor stem, D Loop, and Anticodon area are pretty important.

RIBOSOMES 

Ribosomes have three groups of friends that help them complete translation. Initiation factors, elongation factors, and release factors.

IF's 1 & 3 help the full units of the ribosome dissociate and IF2 attaches the initiator tRNA.

Elongation factors deliver the charged tRNAs to the ribosome and help the ribosome slide down the mRNA strand.

Release factors will bind to a stop codon and promote release of the newly formed protein and the mRNA strand from the ribosome.

This is basically a bad illustration of what it all looks like together.

At the start of initiation, IF1 and 3 bind to the 30s to dissociate the 70s ribosome. The mRNA strand with the initiating tRNA on IF2 comes next and the ribosome settles on the mRNA. The first tRNA binds to the AUG codon, creating an initiation complex that has a high affinity for the reassembly of the full ribosome. The 50s comes back and the first tRNA with the first fmet amino acid settles in the Peptidyl Site (P Site)

In Elongation, tRNAs bring amino acids to the aminoacyl site of the ribosome one by one.

The newly arrived amino acid then grabs the growing chain from the tRNA in the peptidyl site.

First, the NH3+ end is deprotonated. That gives you a better nucleophile with which to attack the amino acid on the tRNA in the peptidyl site.

The NH2 of the newly arrived amino acid attacks the carbonyl carbon of the amino acid on the tRNA in the peptidyl site

You get some proton transfers

Finally the chain is on the tRNA that's in the aminoacyl site, one amino acid longer.

Peptidyl transferase catalyzes this whole thing.

It requires GTP hydrolysis for the ribosome to then slide down the mRNA strand, and then it releases the empty tRNA from the Exit site, with the strand now again in the peptidyl site.

Role of the elongation factor with GTP...

Some more stuff about the proton transferer

For termination, we've got a stop codon coming into the A site, which tRNA don't recognize. You get binding of release factors tot he ribosome and stimulation for release of the protein.

Whereas the elongation allowed the NH2 to act as a nucleophile, here, hydrolysis lets water act as the nucleophile that attacks the protein. Then there's dissociation of the ribosome for all this shit to start again.

And some interesting tidbits.

DRUGS