[Music] this next section is on protein synthesis procaryotic cells are going to need proteins just like you carotic cells if you've learned about protein synthesis and the process with eukaryotic cells in other classes it's basically the same process it's just that the ribosomes the enzymes are a little different because they are going to be in a procaryotic Cell rather than a eukaryotic cell but the process is B basically the same so what I wanted to do first was to introduce some of the players in protein synthesis so we just talked about DNA replication DNA contains all of the codes to make a protein so DNA is number one that's where we're getting the codes from then because DNA is too important it's also too big to link up with a ribosome we're going to need to make a copy of that g which will code for the protein and we're going to keep it in a form of RNA and that form is messenger RNA so messenger RNA is single stranded much shorter than DNA because it's only containing a copy of that Gene then we're going to need a ribosome and I call ribosomes the decoding assembly station because that's where the protein is put together so what makes a ribosome are different proteins and ribosomal RNA so that's another player then we're going to need something to carry the amino acids over to build that polypeptide and that is where TNA comes in so those are some of the players so to delve into ribosomes a little bit more one of the things that we talked about are that procaryotic ribosomes are a little different than eukariotic ribosomes they both have a small and large subunit but the proteins and the ribosomal RNA is a little different if you take a look at the procaryotic ribosome it's a 70s ribosome the small soup unit is 30s and the large subunit is 50s now I know that 50 and 30 don't add to 70 that s has to do with the sediment coefficient so how they actually settle out in solution if we were to centrifuge these things by comparison the eukariotic ribosome is 8s so the small subunit is 40s the large subunit is 60s here you can see the different ribosomal rnas and proteins I would never ask you to know those but what you should know is that the procaryotic ribosome is a little different than the eukaryotic ribosome one of the things that you'll probably notice about the small subunit is it's made up of that 16s RI romal RNA and we talked a little bit about that with identifying different species and I talked about how with my bacteria from the desert we actually had that analyzed to tell us the identification of our bacteria so here is a picture of a ribosome this is actually a procaryotic ribosome you can see the large subunit and you can see the small sub unit and this is a procaryotic ribosome and you can see on the bottom picture where that messenger RNA is fitting and then we have that growing polypeptide what you're seeing on the first picture in a little more detail is that a p and E site that's how the transfer RNA actually jumps through the ribosome and drops off the amino acid um I'm not going to hold you to knowing those different sites but if you see pictures and you're wondering what those sites are it has to do with the way that transfer RNA drops off that amino acid so this part is going to be in Translation as that cell is building that polypeptide so making a protein is a twostep process first we need to make a copy of the gene remember DNA is too big it's too important to link up with the ribosome so we need to make a copy of that one gene DNA contains all of the genes to make all of the proteins so if the cell is needing to make a protein we're only interested in that code for that one specific protein so the first step is transcription and with transcription this is making a copy so just like you would make copies of a note and copy has a c just like um transcription has a c in it so that's how I always remember that transcription is making a copy translation is like you're translating a language so you're translating from the language of nucleic acids and nucleotides to the language of proteins and amino acids so we're going to translate from one form to another so if you take a look at this picture that I've drawn we're always going to start with DNA because DNA contains the codes for the protein and the first step is is to make a copy of that Gene so we're going to make a copy of that Gene and that Gene only and that copy is going to be retained as messenger RNA it's containing that code containing that message the second part is translation so that is taking that message the copy and translating it turning it into a protein something three-dimensional and usable for the cell so we're going from the language of nucleotides and nucleic acids to the language of amino acids and proteins both of these processes are a three-step process so just like a story or like a movie there's always a beginning a middle and an end because this is science of course you know that we have to give it fancy names so the start of the story is initiation the middle of the story is elongation and the end of the story is termination and that happens for both transcription and translation so we're going to go through the steps of transcription so I know this slide is a little wordy um I'm a visual person so it's a little easier for me to actually describe and see from a picture but what you're going to notice in the slide is that it mentions the start the middle and the end of the story initiation elong ation and termination and we're also going to need an enzyme to build that messenger RNA if you remember in DNA replication the enzyme that built DNA was DNA polymerase in this case because we're building RNA the enzyme is RNA polymerase now we're going to have to get at the DNA and if you remember in DNA replication that enzyme that unwind DNA is helicase so we're actually going to see helicase in transcription because that's what's going to help to unwind DNA so helicase is something that is common in both DNA replication and transcription now remember as the cell is building that copy of the code in messenger RNA we are going to have to build it one nucleotide at a time so just as a reminder a nucleotide is made up of a sugar phosphate and nitrogenous base in the case of RNA the sugar is ribos so that's actually where RNA gets its name from ribonucleic acid and if you remember there is that base substitution there are no T's in RNA we have that base substitution of uracil so remember my little Valentine's Day riddle I'd rather be RNA than DNA because RNA has you in it so a clue to you as you're taking quizzes and exams if I'm asking you about the code in messenger RNA if any of those choices have a te have a thigh Meine then you know that we're not in the language of RNA we're in the language of DNA now we're also going to need a stop part so there's actually termination sequence on the DNA that will actually stop the process from happening this is really important because we don't want to continue on and end up with more nucleotides than we need because then when we go into translation and we build the polypeptide one amino acid at a time we could end up with extra amino acids or if we stop too soon we could end up with fewer amino acids that means that that polypeptide is not going to be able to fold right it's not going to be able to function so here is my drawing of transcription so remember there is a start of the story there is a middle of the story and then there's an end of the story so this first picture here is actually initiated ation then we have elongation and then the end of the story we have termination so the first step of initiation is that we need to unwind the DNA so thanks to that enzyme helicase helicase will unwind the DNA and this exposes sort of a start here button that start here Button as I call it it's kind of like a neon sign that's blinking start here this is where transcription is going to start it's actually a sequence of thines and adenines they actually call it the Tata box this is what is called the promoter region so that promoter region is going to promote The Binding of the enzyme that is going to transcribe that Gene and build messenger RNA that's RNA polymerase so helicase unwinds the DNA exposes the promoter region and RNA polymerase hops on and starts to build that messenger RNA in the next picture elongation now we're going to build that code so every place that we see a nucleotide with a c on the messenger RNA we're going to see a nucleotide with a G don't forget those nitrogenous bases are attached to a sugar and a phosphate if we see a g then we're going to see a c if we see an a then we're going to see a u if we see a t then we're going to see an A so we're having that corresponding code I kind of call it the flip you're kind of doing that that corresponding code not forgetting that that nitrogenous base is attached to a phosphate and a sugar and so our RNA polymerase is going to continue to build that messenger RNA now we have to have the end of the story the end of the story is then going to be termination this is when there are stop sequences termination sequences on the DNA that say okay this is the end of the gene n RNA polymerase hops off so that is transcription so here you can see a picture of that building we've got RNA polymerase reading the code don't forget I know that we talk about the code in terms of nitrogenous bases so a g c t but don't forget they're attached those nucleotides as we build that messenger RNA are going to be attached to a sugar and a phosphate so if you notice on the first picture there is an Adine so RNA polymerase is going to be bringing in a uracil remember no T's in RNA and you can see that nitrogenous base is attached to a sugar and a phosphate and so RNA polymerase is going to go down the line and it's going to build that Messer RNA I know that we spend a lot of time I'm talking about procaryotic cells this is actually something that we talk about with UK carotic cells now these are introns and exons now procaryotic cells do not have introns and exons only eukariotic cells do so introns are pieces that don't code for anything so I like to call the introns kind of the junk where the exons that's the good stuff and exons are going to be expressed procaryotic cells do not have introns so we're going to talk a little bit about these exons and introns that we would see in a eukariotic Cell so this is a picture of translation that you're seeing in a UK carotic cell you notice that it's actually in a nucleus remember procar itic cells don't have a nucleus so transcription in a eukaryotic cell will happen in the nucleus so at the very top you see that eukaryotic DNA and you'll see that it has codes so there's the E and the I's so the E are the exons the good stuff the things that will be expressed where the introns that's the stuff that doesn't really code for anything I kind of call it the junk then we go through transcription so now the cell has made that messenger RNA transcript so what the cell can do with this is that it can bring in these molecular scissors these enzymes to basically cut out those introns and then splice those exons together this allows that cell to have one transcript that can actually get multiple products so one transcript the way that it's sliced and diced and put together together can actually result in different polypeptides so it's just sort of an efficient way of doing things I often compare this to going to the store and getting a box of cake mix so you could take a box of cake mix and you could do a lot of different things with it you could make cupcakes you can make a sheet cake you can make a layer cake you can throw some chocolate chips in you can take it home and you can make tons of different products with it that's what the cell is doing so it's taking that one transcript and the way that it's spliced and diced it can actually get different products so an a very efficient way of taking that same transcript and getting multiple products all right so now that we've got our transcript so we've got our code we've got our message housed and messenger RNA now we're going to need to turn that code into something usable three-dimensional that protein that the cell can use now we're going to need a few more players now we already talked about messenger RNA that was a result of transcription so at the end of transcription the product that the cell gets is messenger RNA so that messenger RNA then has to go link up with the ribosome so remember the ribosome is going to be made of proteins and the ribosomal RNA so we're bringing in one of those first players that we talked about then we're going to need something to actually carry the amino acid over to that ribosome to build that polypeptide here's where Transfer RNA comes in so I often call the ribosome the decoding assembly station and that's because the cell has to dissect that code how does it know what that code corresponds to in terms of the amino acids so on the messenger RNA the code is actually read in a sequence of three nucleotides we call those codons and codons are going to code for amino acids now remember just like transcription translation is a three-part story a beginning a middle and an end so that means there's going to be a start codon there's going to be codons that code for the amino acids and then there's going to be a stop codon that says okay we've reached the end of the line now Transfer RNA that carries the amino acid does not have a code on it actually has the corresponding anti-codon like we saw with transcription that flip that I talked about that's what we're going to see with our Transfer RNA so just to show you a little bit on these codons this is a codon table now I would never ask you to memorize the code on table that's just crazy I've talked about this for years and I don't even know all of these codons but I wanted to show you this table just to point out a few things first of all there's 20 different amino acids if you look at this table there's more than 20 codons so you will notice that some of these codons have multiple or these amino acids have multiple codons so if you take a a look at the middle of the table Proline so it's abbreviated P there's actually four codons that will get Proline this is sort of a little insurance policy so if there's a mutation that happens we're still going to get that amino acid so if you take a look at the middle of the table CCU is a codon that should get us Proline if there was a mutation where that U was changed to a c you notice that that codon C CCC will also get Proline so it's just a little insurance policy that if there is a mutation there's a good chance that we can actually get the amino acid that we needed now remember there's a start a middle and an end to the story so if you take a look at the AUG which is highlighted in blue that's actually a star codon that start codon is going to be the first one in sequence on that messenger RNA you notice that Aug corresponds to me that's short for methionine there's another star code on gug which corresponds to veiling but the one that we see most often is Aug what that means is that most proteins the very first amino acid in sequence is actually methionine so that's the start of our story and then we would actually dissect the code three nucleotides at a time and build that polypeptide and at the end of the story we have to have a stop codon so this is going to be our termination sequence so if you take a look at the codons in pink UAA is a stop codon u a and UGA are also stop codons I always remember those as you are away you are gone you go away and that is that message to the cell to the ribosome that okay we're done that's the end of the line and then translation ends so we're going to take a look at how translation works so just as a little reminder proteins are polymers they're big biomolecules and they are made of monomers which are amino acids as we saw from that codon table a codon which is a set of three nucleotides will correspond to an amino acid so we have that sequence from transcription in the form of messenger RNA so now messenger RNA is going to link up with the ribosome and we're going to go through the steps of translation so just like with transcription there's a start a middle and the end to our story so we're going to talk about initiation elongation and termination remember with our Transfer RNA we have a corresponding anti diodon so what that means is that transfer RNA is going to carry over that corresponding amino acid so with the start of our story initiation our messenger RNA is going to link up with our decoding assembly station the ribosome and we're going to start with the very beginning that start codeon Aug now remember Aug corresponds to methionine so the transfer RNA with the appropriate corresponding anti-codon and that anti-codon if we were to actually do the flip would be u a c so a is going to correspond to u u is going to correspond to A and G is going to correspond to C so the TRNA is going to have that anti-codon UAC with that methine and then it's going to come in and it's going to drop off that methine that's going to be the start of our story elongation is when we continue to read that code three nucleotides at a time by way of codon so the next three in sequence we're going to have the appropriate TRNA with the corresponding anti-codon and then it's going to come in and it's going to drop off the amino acid now this can actually take quite a while because some of these proteins can be really big like 40,000 amino acids long so we're going to need a lot of trnas and this is going to take a little bit of time to actually build that polypeptide we finally have the end of our story termination this is when we have those stop codons so remember my little phrases UAA u a UGA you are away you are gone you go away once we encounter those we know we're at the end of the line protein is released from the ribosome ribosome kind of falls apart messenger RNA is released and now the cell has that three-dimensional product the protein so here is my little picture so just like we saw with transcription we've got initiation we have got elongation and then we've got termination so if you take a look at the first picture this is initiation so that is my kind of strange drawing of a ribosome I'm no artist that is for sure so here's our messenger RNA in initiation linking up with that ribosome you can see that I've tried to draw a large and small subunit and we've got our start code on remember our start code on is Aug so here comes our Transfer RNA that's that U looking thing and it has the anti- code on that corresponding code that's UAC notice that that TRNA is carrying methionine so it's going to come in it's going to see if it matches with Aug it comes in bing bing bing we've got a match and it's going to drop off methionine with elongation we're going to continue to read the code and again this could take a while because a polypep could have thousands of amino acids so if you take a look at our next codon CCC from our table that corresponds to Proline there is our TRNA with our corresponding anti-codon this one's kind of easy g g g it's going to come in bing bing bing we've got a match let's drop off Proline so you can see where that polypeptide is building if you think back to biochemistry learning about biomolecules remember what's going to hold those monomers together those are going to be Cove valent Bonds in proteins we kind of give it a special name those are going to be peptide bonds so where we have these anabolic reactions and we have those coent peptide bonds forming is going to be at the ribosome the last picture is termination so the end of our story we're going to encounter our stop codon you go away you U now we're done and what's going to happen is the ribosome is going to fall apart messenger RNA will fall apart and the polypeptide is going to fold into a protein and now that cell has that three-dimensional usable product so here is a bigger more much fancier picture than my drawing and here you can see where we've got the building of that polypeptide so those codons are going to be red one at a time and we've got the appropriate Transfer RNA coming in with the code bing bing bing we've got a match we're going to drop off those amino acids connect those amino acids together with those peptide bonds and that cell is building that protein and here you can see another picture of that growing polypeptide the next thing that we're going to talk about is when does the cell know when to make protein and that has to do with gene expression and regulation I have posted a couple of videos on protein synthesis I know that it's really abstract to kind of look at these two-dimensional pictures so I really encourage you to look at some of those videos just so that you can see all of those moving parts