Cell Biology | Translation: Protein Synthesis 🧬

what's up ninja nerds in this video today we're going to be talking about translation or protein synthesis but before we get started if you guys do like this video if you guys benefit from this video the best way that you guys can support us to continue to keep making free videos for you guys enjoyment is by subscribing to us as well as hitting that like button and commenting down in the comment section that it really helps us to continue to grow as a channel also down in the description box we're linked to our patreon if you guys go to our patreon there we'll have access to illustrations and notes that we are continuously adding and growing every single day but there is a limited amount at this time but go check it out and to see if it can help you in your academic journey all right ninja so let's start translation when we talk about translation we have to have a basic definition of what the heck it is and that is you're taking rna in this case what type of rna we really is our primary one that we're going to focus on mrna we're taking that mrna that we made from dna what was that process called transcription so we're taking the mrna that we got from dna and now we're going to make proteins that is the process of translation taking rna and making proteins there's so many different types of rna the three main ones that i need you guys to remember that are crucial for translation is mrna trna and rrna and we'll go through these as well as a couple other things before we get into the phases of translation the first thing that we need to talk about is this concept of the genetic code okay it's really simple it's not as like scary as it seems a little boring but we're gonna make it fun the first thing you need to know is here we have a molecule of mrna right so this is our mrna now mrna is very very important for this translation process right messenger rna messenger rna it has a very specific sequence of nucleotides if you will that are in these triplet forms you see how this is a there's three little lines there that line is a nucleotide that's a nucleotide that's a nucleotide so there's three nucleotides there and we have a couple of these spanned along the length of this mrna molecule right and the other thing you need to know is the orientation right so a little bit about the topology of the mrna on this end i'm going to have a five prime cap do you guys remember that whole process we talked about in post transcriptional modification this is the five prime end on this end you have the three primate and we had on this side do you guys remember what happened here in the transcription process we've added the poly a tail on that end right so on the mrna you have a five prime end a three prime end and sequences of nucleotides within it these sequences of nucleotides that are in these triplet forms along the mrna are given a very special name that you need to remember and these are called codons so let's write that down so these things these triplets let's put down triplets triplets of what triplets of nucleotides okay and you guys need to remember the nucleotides and rna are different than the nucleotides in dna let's write down primarily the nitrogenous bases that are associated with rna what are they we'll represent that by kind of just the single letter abbreviation one is you have adenine right that's one of the nitrogenous bases in rna then you have guanine cytosine and uh what else if you guys said thymine i'm gonna be really upset with you it's not thymine it's uracil in rna it's uracil that's the big difference between dna it has thymine in rna it has uracil okay so we have codons are triplets of nucleotides what type of nucleotides nucleotides that contain these four nitrogenous bases okay now here's the next thing i need you guys to know we know what they are how many are there let's take this let's do a little bit of math i know it's a little boring let's take and do a little bit of math here we have the triplets we described that what those triplets are made up of and let's talk about how many of these triplets of these four nucleotides you can have well there's four total nucleotides right so let's put a four here four different types of combinations of nucleotides each one of there's three of these nucleotides in a codon so if i take four raise it to the third power what does that give me 64. 64 possible codons based upon the four nucleotides i have and that there's three nucleotides in that codon so that means that there are 64 different possibilities of codons okay so what do we need to know here that there's 64 different types of codons now we've got to talk a teensy little bit about the different types we're not going to go through every single one of them that's unnecessary you'll have these if you guys don't go into the back of your textbook like an appendix you'll have the entire genetic code that you guys can look at there's no need to memorize them but need to know a couple things about these 64 different types of codons and what should you know the next thing you should know is that when you take these 64 codons okay that are triplets and we'll kind of talk about them 61 of those codons read you read them right and we'll give you an example here for an example let's give you an example now let's say i take a codon right which is a triplet and it contains one of these three of those nucleotides let's use the example a u g that's a codon if i look in the back of the textbook at that genetic code kind of thing and i see aug it's going to code for an amino acid and that amino acid is very specific to that codon and so what type would it be this one's an easy one to remember and this is probably one of the few that you should remember and memorize but this is methionine and methionine is an amino acid so out of the 64 codons 61 of them right in this kind of form three nucleotides which there's so many different types of possibilities will code for an amino acid i'm just giving you an example so out of these 61 codons they code for an amino acid so very important to remember that okay out of the remaining how many are remaining 61 there's three codons left that we have to talk about these other three codons do not code for an amino acid they code for terminating the translation process and these are called stop codons and we'll get into these a little bit more in detail when we go through the phases of translation but you can remember these by the mnemonic or kind of like the phrase if you will a little memory trick which is you go away you are away you are gone these do not code for an amino acid so in other words if i were to look in the genetic code in the back of the textbook these would not give you a particular amino acid they would stop the translation process so that's important and we'll go over what that kind of looks like a little bit later so basic concept i want you guys to get out of the genetic code particularly is mrna contains codons codons are made up of nucleotides how many three what are the particular types of nucleotides they have to contain adenine guanine cytosine and uracil there's how many different types of codons so many 64. do you need to know all of them no out of those 64 61 of them code for amino acids you can look at all those up in the textbook three of them do not code for amino acids they stop the translation process that's all i want you to know about that the other aspect of the genetic code is that we need something that's going to carry so we said that these codons code for amino acids how the heck do they do that you guys should be asking that question there's another molecule called trna right what is it called t rna transfer rna transfer rna if you guys kind of look at the structure of it it contains what's called anticodons let's write that down so it contains anti codons okay that's the first thing what the heck are anticodons it's really simple anticodons are a triplet all right so three nucleotides that are complementary to the codons in mrna that's it so what are they they are a triplet of nucleotides that are complementary to codons in the mrna that is it the other aspect of this is there's some enzymes we'll talk about a little bit later so there's a funky little enzyme that'll come in it's kind of like a little bit it's a little gropy grabs the anticodon portion reads it says okay i got the anticodon there all right so i know what it is i need to find an amino acid that is very specific right to the codons that this anticodon is complementary to so let's give the example here let's say the codon that you have an anticodon complementary to is this one aug okay so let's give the example here that you have a codon we're going to use this example here so let's say here we have a codon and the codon is aug what would the anticodon be has to be complementary to this so the anticodon for this example would be u a c right because that are copper complementary to each other right you guys remember that that if it's a that's complementary with u that g is complementary with c and technically these should be triple bonds right so this would be a is complementary with u u is complementary with a and g is complementary with c so we'll go u a c what will happen is the trna enzyme that'll come in we'll talk about later it'll say oh uac that's complementary to aug if i go into my genetic code because it's got all of it in its head this enzyme it says aug is specific for what amino acid methionine so then this enzyme takes and we use a particular amino acid domain we'll call it there's a specific amino acid domain on this trna that we'll talk about and that is going to carry the amino acid specific to this codon what was the amino acid methionine so it'll carry the methionine in this example now let's talk a little bit about this kind of like anatomy or structure of the trna that kind of coincides with what we just talked about if we take the trna the first thing is where are the anticodons the anticodons if you look at a trna kind of has the shape of a t in a way right on this portion this bottom loopy portion this right here is where you'll have your anti-codons on this portion so this is the part of the trna that'll interact with the codons in the mrna the next portion here is you have another loop i'm not really too worried about you knowing about these loops this portion here though okay this is called the five prime end of the trna so what would be on that end what group hydroxyl group or phosphate group engineers phosphate group this end over here which has like the little copper loopy thing is the three prime end three priming contains what oh phosphate group contains the hydroxyl group or the oh group but there's also a very specific sequence of nucleotides that are in this area of the three prime end which hold on to the amino acid this is the amino acid holding domain and this is containing c c a so we'll put the three prime c c a domain or region on the trna what is this portion the little cup that holds on to what we'll bind in here so here we have c c a it'll bind on to the amino acid in this case it was what the finding if the anticodon is uac which is complementary to aug holy crap we went through all of that all right so the next thing we're going to talk about is the characteristics of the genetic code i don't want to go too long into this let's just breeze over really quick but it's things that can be asked in your exam so you should know it when we talk about the genetic code all the stuff we talked about with the codons the anticodons the mrna tr and all that good stuff when we take the mrna and we read it right from five prime end to three prime end for the most part there's a couple exceptions you start at the five prime end and you go to the three prime end continuously you don't like have any stops or anything like that so in that way when we talk about the genetic code this translation process understanding the genetic code is what's referred to as kamalas so what does that mean here's a codon right i'm going to read this codon utilizing the trna and the ribosomes and i'm going to give an amino acid then i'm going to go to the next codon read that make amino acids and i'll keep going down this way going through each sequence of three nucleotides are a triplet now what does this mean that it's homolos let's say that i read this codon read this codon and there's a couple nucleotides in between to between this next codon that i want to read i don't skip these nucleotides and go to the next codon okay so this this thing does not happen you don't go three nucleotides read through nucleotides next and then skip a couple nucleotides and go to the three next nucleotides it's consistent this does not happen in the genetic code or the translation process the only exception to this is viruses they're the only exception so we'll put exception to this where they can have some type of translation process that does have commas in it or you kind of skip a couple nucleotides okay the next thing that we need to know about the genetic code is that not only is it kamalis but it's non-overlapping what does that mean that means that when i read these again five prime to three prime i'm gonna read it all the way down continuously i'm gonna read this codon give an amino acid read this codon give an amino acid what i'm not going to do is read this codon give an amino acid but then let's do a different color start here at the second nucleotide read these three and give an amino acid now let's do one more color start at this third nucleotide after and read here and give an amino acid that does not happen in the translation process according to the genetic code there is one exception and again that exception is that this overlapping process can occur in viruses that is the only exception okay so the when someone says can you give me characteristics of the genetic code you will say it is comless it occurs continuously from five to three and non-overlapping continuous from five to three the only exceptions are viruses that's it the next thing that you need to know is a little bit more important than this gibberish up here and that is that the genetic code is what's called redundant so it's redundant and it's degenerate okay so it has degeneracy or it's degenerate so let me explain what that means let's say i have a couple codons and i'm going to actually give specific nucleotide sequences to i'm going to give this a nucleotide sequence of a u a a u c and a u u okay now here's what's really interesting about these i have three different codons these three codons you would probably say each one of them codes for you know a different amino acid but you'd be wrong and that's where redundancy or degeneracy comes in if you guys look in the back of your textbooks or the appendix where the genetic code is if you were to look there is a amino acid called isoleucine and if you take isoleucine and you try to track back to its codon you'll find that it has three different types of codons that can actually code for it and that is a u a a u c and a u u that's really interesting so that tells me that i could know the amino acid that i'm making but i won't be able to track it back to one to the specific codon there's two exceptions to that and that is um if you truly want to know it the only exceptions to this concept of redundancy or degeneracy the exceptions are methionine so we'll put here methionine and what's called tryptophan and here and let's i want you guys to think about why these would be exceptions because it actually does help methionine there was only one codon what was it aug tryptophan only has one codon you know you don't need to know this but it's ugg there's no other codons that code for these amino acids they're just one so they're the only exceptions all the other amino acids have multiple codons that code for it so that's the concept of redundancy now here's the thing you guys are like how the heck does that happen i asked this question when i was learning it so let's take an example here let's say here i have my mrna right and again this is my five prime end this is my three prime end of the mrna let's say i start here and i'm going to go in sequence here so the sequence is which one let's kind of keep these colors we'll do red here for the mrna so this is going to be which ones a u a a u c and the next one is a u u how the heck does the trna do that in a particular way does each anticodon have to be different because i thought they have to know the trna the enzyme that we talked about kind of like a little bit said it has to read the anticodon and it has to be complementary to the codon to give me this amino acid how does it do that here's the way it does it there's something called the wobble effect wobble baby wobble baby wobble right and it's called the wobble effect or the wobble phenomena let's write that down and let's talk about what the heck that is so let's take and this is particularly for the trna that kind of allows this process to occur it's pretty cool so where's the anticodon on the trna here's our trna where would it be on this bottom loop what would it have to be specifically you would say oh complementary to a is u complementary to u is a complementary to a is u but here's where it's different on this position what was this point here on the trna at this point here this was the five prime end right what's this portion here the three prime end so going from five prime of the trna to the three prime of the trna right because if you kind of follow this down like that so you start five prime this would be the first position this would be the second this would be the third position and then you continue to work your way back up on this first position on the five prime end it's actually containing a something called inocine you're like what the heck believe me i thought that too so the same thing we'll talk about what that does in a second but let's go to the next one same thing you'll read this here you have your five prime three prime and it'll have come down the first one will be ionosine and then what will you have what's complementary to you a what's complementary to a u do the same thing over here start at 5 three prime for the trna work your way down first one has to be i next one will be what a and the next one will be u let's explain what happens with all this do you notice a difference here remember i told you that the enzyme has to read that anticodon it has to be complementary to the codons in the mrna to pick the correct amino acid well do you notice how all these are dif they all differ in that third position on their codon and they differ on this kind of like first position in the anticodon here's how this happens ionosine okay that i i'm representing with is actually called ionosine ionosine is not talked about too often in the watson and crick model you know in your dna stuff the interactions complementary stuff ionosine is complementary to adenine ionosine is complementary to uracil ionosine is complementary to cytosine so whenever you have something like this where the third position is a c and u on the trna they can have an ionosine that can be complementary to a complementary to you and complementary to c and still give you the same amino acid which would be what i already told you this will be isoleucine isoleucine isoleucine okay so that's called the wobble effect you're probably like why the heck do we do this why don't we just make it specific to each of these types of um you know codons why don't we just make it u a u u a g uaa why don't we do that the reason why is the wobble effect reduces the risk it decreases the risk of mutations so what do i mean by it can decrease the risk of mutation it can and specifically it can decrease the risk of mutations how does it do that it's all based upon this fact that if i have any mutations in the dna that'll lead to mutations in the mrna and if there's mutations in the mrna i'm going to have changes like substitutions or things like that in the codons and if i kind of substitute or switch up some of the nucleotides i'll code for a different amino acid particularly so if i have a little bit of that wobble effect i have a little bit of you know wiggle room in that that first position on the trna i may reduce the risk of giving a wrong amino acid leading to a abnormally structured protein so that's kind of the big effect here is when we talk about redundancy or degeneracy it's that one amino acid can have multiple codons with just these two exceptions and how does that work via the wobble effect in trna where on that first position on the five prime end of the anticodon it is an ionoscene which has multiple complementarities with a uc whole purpose of this is to decrease the risk of mutations so when we're talking about when i'm mentioning all this stuff about the genetic code and you can look in your textbooks i use marieb kind of a human anatomy physiology book and again you can find the in the appendix all the information about that genetic code but you can find this in various textbooks campbell's biology as well but again i'm just referring to in any book you'll have that appendix to talk about the genetic code so that you guys know what i'm talking about here all right so we got a pretty decent idea about the genetic code right i'm talking about codons anticodons and some of the features of it our characteristics the next thing i want to talk about is trna a little bit and i want to go through something called trna charging we'll review the structure of the trna really briefly as a nice like little review but we're going to talk about this process called trna charging which is very important when we talk about the translation process so here we have our trna molecule right so this is our trna transfer rna tiny little guy right again what is this end here it doesn't have the little kind of like little socket or pocket there where the amino acids bind what is this end this is your five prime end what's this end this is your three prime end which contains the oh group but particularly what nucleotide sequence cca what binds here this is the amino acid kind of like binding domain if you will so this is where an amino acid will bind correct now this arm was the one i really wanted you to focus with we had the three loops we'll briefly talk about these other two loops not super worried if you guys know it but here in this bottom loop what do we have down here on this bottom loop you contain the anticodons and the anticodons will be in a triplet form and these triplets can be in the form of again containing nitrogenous bases like what adenine you know adenine guanine uracil and the cytosine okay so again this portion here will be what this will be the anti-codon portion okay the last thing here is these two little arms or loops and this little thing that's kind of like sticking out the side this portion here near that three prime end this is called the t arm so what is this portion here called nor the three prime end this is called the t arm the t arm what you really need to know about this is that it tethers the trna to the ribosome that's all i want you guys to know is that it tethers the trna to the ribosome so it kind of is one of the big things that allows for interaction between the trna to the ribosome okay that's it this other arm over here this loop near the five prime end this is called the d-arm and the d-arm is what allows for the identification of the trna by the enzyme called trna the aminoacyl trna synthetase so it allows for identification identification of the trna by what's called the uh we'll just a br we'll kind of a basic thing trna synthetase enzyme okay so basic concept here you have the five prime end then you have the first arm which is the d arm it allows for the identification of the trna by the trna synthetase anticodons on the bottom loop t arm is near the three prime end that allows for the trna to interact with the ribosome three prime end has the cca domain which allows for it to interact with amino acids this last thing here i'm not really concerned if you guys truly know it it's the invariable domain it's uh it can i mean it can actually it's the variable domain it can change from trna to trna nothing too big to know about that portion okay so if the basic structure of the trna the next thing i need you guys to know about is called charging so this is really simple it's basically talking about how do we get the amino acid to bind on to that three prime end that's all it is and it's really simple here i have an amino acid okay so here's my amino acid and let's let's use this example that we've continuously been using a lot let's say that we're con we're going to start the translation process and let's just pretend for example here's my mrna okay let's use this example that this is a u g what would the anticodons be if we were to kind of write them in here if it was aug it would be u a c what is that aug code for methionine we've already said that multiple times right so let's say here's our here's our example this is our methionine we'll just abbreviate it as met okay what we're going to do is the first step we're going to do in this process is we're going to add an atp molecule onto it we're going to add an atp molecule onto the methionine so let's say that here i use an atp and i add it into this process here okay then what i'll have here is i'll have my amino acid and what happens is when atp gets added in it actually we break two of the phosphate groups off of the atp okay so if we break two phosphate groups off that gives you what's called a pyrophosphate and so the only thing that's kind of hanging onto this amino acid is an amp they want you to know these kinds of names of it right so when i take this amino acid and add on an amp it's called i know it's annoying it's called the amino acyl amp molecule okay then here's the next thing we have this aminoacyl amp and we have that three prime kind of amino acid domain with the cca portion imagine we draw a big old enzyme here so here's this enzyme okay here's this enzyme this enzyme has in one end is holding the trna right so it's holding that trna molecule so we're just gonna we're gonna draw a very generic structure of it here's gonna just be this process here okay so here's the generic structure and we'll just kind of show that this is our three prime end right there okay just generic it's holding in one pocket this trna molecule in the other pocket it's holding the amino acid with what bound to it the amp then what it does is it basically just says hey let me make sure that this anticodon is appropriate is it appropriate to the mrna codon that we need oh it is good clicks them together and so it takes and adds that amino acid with the amp onto the three prime cca region so let's draw the little cup what was that little cup thing the cca portion it'll add on this reaction will occur so we're going to just fuse these two things together and when we fuse these two things together what do you get you'll get this structure where all you'll have the trna with the little cup and what will be kind of sitting in that little pocket there the amino acid and what amino acid was this in this example methionine in the process though do you see amp still bound to it no so what are we going to do we're going to release the amp during that process okay what you need to know is what the heck is this enzyme this enzyme is called the amino acyl trna synthetase i kind of quickly abbreviated it for you like a shorthand version of it when we talked about with the d arm that's the enzyme i'm really referring to is the amino acyl trna synthetase and if you really wanted to remember what part of the tna is keeping it kind of like identified the d arm of the trna will allow for it to be identified okay so to recap really quickly i want to take the amino acid put on the three prime end what do i have to do first thing take the amino acid add an atp onto it i'll pop off a pyrophosphate so i'm truly only adding a amp that's called an aminoacyl amp a amino acyl trna synthetase will come in have two pockets in one pocket it will hold the amino acyl amp in the other pocket it will bind the trna with no amino acid it will read make sure that it's the proper anticodon that is complementary to the codon of mrna click them together when it clicks them together it puts the amino acid on the three prime in and spits out the amp now what do i have a charged trna so what is this thing here called this is called a charged t rna okay that's the process that's all i really want you to know out of this okay so let's now move on to the next thing which is saying okay we've already talked about mr now we talked about codons anticodons some features we talked about trna charging now we need to get into these things called ribosomes a little bit all right so now let's talk a little bit about ribosomes and what are their kind of significance because we're going to go into all these phases of translation it's all going to make sense it might seem a little bit scattered right now but i promise we're really building our foundation so we truly understand the translation process so the next thing we need to talk about is these ribosomes ribosomes are definitely very very crucial for translation as well as the mrna and the trna but some of the things that you guys need to know particularly is the difference in ribosomes between eukaryotic and prokaryotic cells and there is a very brief clinical significance that we'll talk about with that so let's say here i have ribosomes and they're interacting with the mrna they will interact with the trna but we're going to talk about these specific differences between eukaryotes and prokaryotes because this is something that you guys will be asked eukaryotic cells when we talk about ribosomes they have two subunits okay we're going to say this subunit up here is bigger than this one down here right so it's pretty straightforward this is the large subunit or ribosomal subunit and then this one down here is the small ribosomal subunit okay now these have different ways that we can kind of like describe their size okay large and small according to a zved zvedberg unit and eukaryotic cells that zvedberg unit for large rebels almost sub units are called 60s large ribosomal subunits and the small and eukaryotic cells are called 40s ribosomal subunits but we sometimes generally in textbooks refer to them as ads ribosomes and eukaryotic cells you're probably like zach that those numbers do not make any sense 60 plus 40 is a hundred zach what are you losing your brain i promise you the there the way that they do this via this vedburg unit gives you an ads ribosomal subunit for eukaryotic cells and prokaryotic cells it's the same concept again we're not going to write these down but this is your large here we'll put large ribosomal sabine small ribosomal subunit and prokaryotic cells the large one is a 50s ribosome and then in prokaryotics the small is a 30s ribosomal subunit and you're probably like oh that's going to give you 80. nope according to this vedburg units it gives you a 70s ribosomal sub ribosomes in prokaryotic cells you're probably like okay is that cool i'm glad that i know that now why do i need to know that before we talk about why you need to know that the next thing i need you guys to remember is what are ribosomes made up of you guys need to remember this ribosomes contain a very specific kind of molecule if you will that's kind of a sitting and a part of it very integral to its structure what is this it's got little like nucleotides on it it's rrna so ribosomes contain two different types of things that make them up it's equal to r rna and what else proteins so proteins so when we're talking about remember when i said in the beginning translation requires three types of rna mrna trna and rrna we usually just say ribosomes but ribosomes contain rrna and proteins now why did i spend the time talking about all this stuff a common clinical relevance here is that they love to say when you're talking about prokaryotic cells prokaryotic cells okay we can use different types of antibiotics to target these ribosomal subunits and prokaryotic cells for example if i give someone an antibiotic like an aminoglycoside and there's so many different types of these but the commonly one that you need to know is like gentamicin and another one called tetracyclines and there's a bunch of different types of these doxycycline tetracycline minocycline all those these love to target and inhibit the translation process by affecting the 30s ribosomal subunits so they inhibit the activity of the 30s ribosomal subunit in prokaryotic cells the other antibiotics is going to be particularly not the aminoglycosides and the tetracyclines but let's say that we're talking particularly about something called macrolides and these are things like azithromycin clarithromycin erythromycin these love to target and inhibit the activity of the 50s ribosomal subunit and prokaryotes which inhibits protein synthesis think about this prokaryotic cells like bacteria let's use this example like bacteria need proteins in order for them to function if you give an antibiotic if a bacteria is infecting a particular tissue you give them an antibiotic something like an aminoglycoside a tetracycline or a macrolide it's going to inhibit these ribosomal subunits you can't now use them to make proteins if you can't make proteins the bacteria will die so you see how there's a clinical relevance to something at the molecular level okay we've gone through all the players that we really need to understand and know for translation we went through the mrna we went through the trna we went through the ribosomes and the rrna now let's head home and talk about the phases of translation all right so we're going to talk about the phases of translation we've really built up our foundation to understand translation now so there's three phases of translation the first phase that we're going to go through is called initiation so what's the first that we're going to talk about here called the first phase we're going to discuss is called initiation of translation and it's probably like it's really it's it's not that hard it's a really simple step we have to kind of discuss though the differences between prokaryotic initiation and translation and eukaryotic initiation and translation so let's first talk about prokaryotes because they're easier so here's our mrna right and on the mrna again what do you have you'll have a five prime end and you'll have a three prime and let's just kind of uh write here now that this is specific for prokaryotes okay we're talking about this for prokaryotes right now let's say here on the prokaryote is my start codon and what are your start codons we didn't talk about that yet did we but there is a particular star codon we kind of talked about a little bit what i want you to remember is that your start codons we talked about there were 64 different types of codons 61 code for amino acids and three don't they're stop a star codon we did kind of talk about it is aug do you guys remember what aug coded for methionine right so methionine but here's the difference this is an important thing to talk about and they'll probably throw this on an exam for prokaryotic cells it's technically not methionine it's called informal methionine so what is it called in formal methionine okay we'll put met so again the start codon is aug in prokaryotic cells same as it is for in eukaryotic cells but what it codes for is not methionine like it is in eukaryotic cells it's called informal methionine sometimes it's even abbreviated as f met okay either way that's my start codon so we're going to put here a u g on this mrna there is a sequence of nucleotides particularly like purines that are a couple nucleotide bases upstream towards the five prime end from that start codon and for whatever reason they love to give this a particular name because this is where your ribosomes a lot of initiation factors things like that bind and recognize the mrna and the prokaryotic cells and bind it helps to start the translation process and this sequence that's like eight nucleotides upstream from the aug is called the shine delgarno sequence okay and if you really want to know it contains a lot of a's adenines and guanines okay so it contains a lot of adenine and guanines or your purine nucleotides in that region okay so there's a shine delgarno sequence it's kind of like an identifier on the mrna and what happens is a couple things first thing is you have your small ribosomal subunit okay your small ribosomal subunit will come and bind to this area right and what happens is when it binds to the area here on the mrna it uses a very special type of protein let's represent these in brown actually no let's do it in pink so it's kind of different here there's these things called initiation factors and there's these initiation factors that recognize the shine delgarno sequence that are in the small ribosomal subunit are bound to the small ribosomal subunit and so what happens is the initiation factors in the small ribosomal subunit will bind the shine delgarno sequence then once it does that it starts kind of moving towards the start codon so two things happen these pink things called initiation factors that are associated with the small ribosomal subunit will identify the shine delgarno sequence when they bind they then move down about eight nucleotides until they hit the start codon which is aug that's the first thing okay so if we wanted to kind of show that that's the first event to happen let's put one here first to event event to happen is initiation factors and small ribosomal subunits bind shine delgarno move down until they hit the aug the second thing to happen here is that there is a molecule called trna right and trna is going to have to have anticodon specific to this aug which is u a c and it'll be carrying with it an amino acid what is that amino acid specific we already kind of talked about it we're going to abbreviate it called f met now when the trna comes what is this called this is your trna containing the fmet when it comes in as its anticodons interact with the codons here there's something that help to bring it or drag it into this area what do you think that is this represents another little pink color there's a pink protein that kind of helps to yank that trna the initiator trna right which contains the fmet and bring it into where the start codon is what is that pink protein called it's called an initiation factor that's it so first step initiation factor small ribosomal subunit bind shine delgarno move down until they hit the start codon second step initiator trna in the prokaryotes which contains trna and n-formal methionine with a initiation factor come to the area where the start codon is and bind that's the second step third step there is a molecule bound to this initiation factor and that molecule is called let's bring it over here a gtp this gtp is a high energy molecule what's going to happen is this initiation factor will break down the gtp into gdp and an inorganic phosphate and that'll create a lot of energy and what happens is at the same time the gtp gets broken down into gdp and inorganic phosphate the large ribosomal subunit will represent it like this the large ribosomal subunit will come over and bind to this area and so what would it look like if we had kind of like showing all of this happen here this process and the large ribosomal subunit coming in here this would be in your third step so third step here is gtp gets broken down to gdp and inorganic phosphate and the large robot is almost up and it comes and gets added in what would be the final thing that it would look like if we drew it down here if we drew it all down here at the end product here you would have what large ribosomal subunit small ribosomal subunit bound here then what else would we have we would have the trna kind of sitting in here with the f informal methionine bound with the codon in this case it would be aug and then what would we have released during this process we would have released gdp in an inorganic phosphate and what else would we release we don't need this thing anymore we don't need this pink protein anymore the initiation factors we can just spit those out as well so we can spit out the initiation factors as well what are these things called we're just going to abbreviate them initiation factors so to recap really quick because i know it's a lot of crap and one thing shine dog arnold sequence identifier of the mrna small ribosomal sub being it's initiation factors bind to it identify it move down till they hit the start second thing trna which contains the fmet right which is particularly based upon the anticodons complementary to the codons and mrna it gets brought to this area by the initiation factors they bring it to the area and bind the trna then third step there's a gtp associated with the initiation factors it gets broken down into gdp and inorganic phosphate at the same time a large ribosomal subunit will bind and what will you get at that process you'll get the large and small bound to the mrna with the trna sitting in the ribosome in what site we didn't talk about this yet but there's three sites in a ribosome one of them if we start them here this first one is called the a site that's the kind of the arrival site this one is called the p site and this one is called the e site and we'll go through these all in detail but that trna is going to be sitting right smack dab in the middle which is going to be the p site okay so that covers the initiation and prokaryotic cells thank goodness in eukaryotic cells it's pretty much the same we just give different names for stuff so this step here in initiation this is for particularly what eukaryotic cells they still have a five prime end and a three prime end but guess what they don't have a shine delgarno sequence they just have this start codon what happens is first thing that happens is you have a molecule called a eukaryotic initiation factor so a eukaryotic initiation factor will come and bind to this five prime end and we call this eukaryotic initiation factor type four it'll bind to this five prime end okay that's the first thing that will happen the second thing that will happen is that you'll have your small ribosomal subunit and other you know initiation factors that we're not too concerned with just yet that'll come in interact with this mrna so let's draw here your small ribosomal subunit that'll come in bind that's the second thing that will happen and then what else is happening you're having some initiation factors some small little initiation factors that'll help that small ribosomal subunit to bind to the mrna this the third thing that happens okay so so far we've had two things happen eukaryotic initiation factor type 4 identifies the mrna second thing is the small ribosomal subunit with the initiation factors bind to the mrna the third thing to happen is that you have a eukaryotic initiation factor type 2 eukaryotic initiation factor type 2 that will bind your trna right it'll bind the trna that contains anticodons that are complementary to the codons and mrna which is uac it'll have an amino acid that'll be based off of that start codon what is it in eukaryotic cells what is the start codon in eukaryotic cells it's the same one we talked about in prokaryotes right aug what's the difference aug and eukaryotes codes for methionine not in formal methionine that's all that's different so this is just methionine eukaryotic initiation factor type 2 will bring with it the trna with the methionine and bind it to this portion on the start codon the fourth thing to happen here is that you have a gtp molecule that is going to be bound to the eukaryotic initiation factor type two this is the fourth thing it's going to get broken down into gdp and an inorganic phosphate and the other event to happen here is that the large ribosomal subunit which contains the e site p site a site will come and bind to the mrna and what will it look like if all of this stuff kind of happens accordingly you'll have here your large ribosomal subunit with the e site p site a site small ribosomal subunit you'll have the trna which will have its anticodons complementary to the codons of the mrna and you'll have your methionine sitting there and what would be of release because we don't need them anymore in this process we would release the gdp and the inorganic phosphate and we would also release the eukaryotic initiation factors right like type 2 and type 4. do you see how it's pretty much the same in prokaryotic cells the only difference is is that in order to start this you have a shine delgarno sequence that's identified by initiation factors and eukaryotes it's a eukaryotic initiation factor that binds the five prime end okay the other thing is you still have a trna that's coming in and binding with initiation factors to where that star codon is the only difference is is that's informal methionine and eukaryotic cells it's called methionine and these are just called initiation factors this one's called eukaryotic initiation factor type 2. they just wanted to be annoying but the same thing happens in the remaining steps which is the large ribosomal subunit has to bind and you have to break down gtp into gdp and inorganic phosphate and you have to release the initiation factors all of it's the same with just some minor changes in it that's it we finished initiation thank the lord now let's move on to the next step which is called elongation so what's the next step that we're going to talk about here the next step is probably one of the more difficult ones to kind of visualize but this is called elongation this is the second phase in translation so let's pick up where we left off we initiated the translation process let's pretend this is the same thing thank goodness this is the same and eukaryotic cells and prokaryotic cells but we're going to use a lot of the examples here in eukaryotic cells so this is primarily going to be used in eukaryotic cells that we're going to be using this as an example and it's because we're going to be using particular types of factors okay so in this example just so you know it's the same and prokaryotes and eukaryotes just in this example i'm going over it in eukaryotes because i'm going to use specific factors and you'll see what i mean so to see if you guys remember everything we just talked about up here you had to initiate it right small ribosomal large ribosomal have to bind initiation factors help that process break down gtp into inorganic phosphate and bring a trna which contains a amino acid the initiator trna which is going to be informal with ionine and prokaryotes and methionine and eukaryotes in this example what was our start codon aug what would be the anticodons that are complementary to that on the trna uac okay that's where we are we just finished the initiation now we're gonna do is okay we have to quickly review what is this site here the a site now if you really want to know the a site is called the acyl site p site is called the peptidyl site and e is called the exit site you can remember ape in that order okay because that's the order we're gonna have things coming in and leaving so a site is i like to remember the arrival site piece i like to think about as the synthesis site and e i like to think about is the exit site that's how i remember them okay so the first thing we have to do with this elongation process is we have to bring something into the a site let's just make up we use isoleucine as an example over there let's bring them back let's put here a u a as the next codon that i'm going to read if that's the case then what do i need to bring into this area a trna in order for me to bring a trna that is has anticodon specific to that let's draw that in bringing him in here so we're going to have him come into this step here so we're going to bring in what are the anticodons to this u a u right if you really wanted to be specific according to the wobble effect what would it be the ionosine but just in this example we're going to put uau okay this is going to be containing what an amino acid and that amino acid in this example doesn't really matter but it's called isoleucine since we talked about that one before now in order to bring this trna into this a site we need something to help bring it to that area and that is going to be called an elongation factor so it's called a elongation factor it's called eukaryotic elongation factor type 1. eukaryotic elongation factor type 1 will bind this trna which is going to have anticodons complementary to these codons on the mrna and the a site now once that happens let's show what that would look like so here we're still going to have that same initiator trna right here right which contains the methionine and if you really wanted to know here this would be uac and then what would these codons be a u g this is the p site in the a site what does it look like a uua is my codons and with the help of the eukaryotic elongation factor type 1 he brings in the trna that's complementary to this one so that's going to have trna which is uau and again if you really wanted to be specific according to that wobble effect it would technically be ua i if you really wanted to but it's going to contain the isoleucine in the a site who helped to bring him into this area the eukaryotic elongation factor type one but guess what else this eukaryotic elongation factor on its back it's got a gtp molecule and really in order for this guy to get in there and to bind what do i need to have enabling this process energy so on the back of this molecule we have gtp when we add him in here and he finally gets added in what do i spit out i spit out gdp in an inorganic phosphate and what else do i spit out my eukaryotic elongation factor type one okay and now i have my trna in this spot here's where it gets a little interesting because now what do i need to do i need to take this amino acid that is bound to the trna in the p site and transfer it onto the amino acid of the trna and the a site and then i need to shift this one that's in the a site into the p site and shift the one that's in the p site into the e site you're probably holy crabs act that's too much we're going to go through it so how does this work it's really cool i'm going to show you in a very generic way and then we're going to show it in a zoomed in way because it is important that you understand this what happens is there is a a little kind of like uh nitrogen on this amino acid here and what was this one if you really wanted to remember isoleucine that nitrogen comes over and attacks the carbon end on this amino acid that's in the p site and you know those like little things when you were a kid there were like the little sticky things with the hands on the end of it and you can throw it it could stick to something and kind of like suck it back in that's kind of what this guy is doing it's going and it's grabbing the amino acid and the p site and sucking it back onto it in the a site and then what it would look like if we kind of did that process so let's say that we did this process here what would that look like if this were to be if this were to occur that amino acid would be gone because i transferred it over to this guy in the egg site isn't that cool so now in the a site i'm going to have the amino acids two amino acids the one that was originally coming from the uh the isoleucine right which was brought in in this step and the amino acid methionine that came in from the initiation step in the a site now what does that look like kind of in a zoomed in view we were to really take these and zoom in on them in a really kind of like zoomed in view here is my isoleucine and on this end it has a interminus the same thing over here from methionine it has a interminus and then on this end if you really wanted to know it has a carboxy terminus same thing here it has a carboxy terminus the interminus of the isoleucine nucleophilically attacks the carboxy group on the methionine and then again sucks it back into where that area is like the little kind of like hands the sticky hands that yank it back in in order for this process to occur the ribosome has an enzyme kind of intrinsically associated with it and this enzyme is called uh a peptidyl transferase pretty ironic right so the peptide transferase which is kind of like imagine here that the that's kind of associated in this kind of uh ribosome it's the one that's going to be helping to perform this process taking and catalyzing it so this step that we just talked about is catalyzed by an enzyme intrinsic to the ribosome which is called the peptidal transferase okay so we brought in a new trna into the a site we used the peptide transferase to catalyze this step where this amino acid and the p site gets added onto the amino acid and the a site all right so now we've already kind of done this little peptidal reaction where we transfer to this amino acid from the trna and the p site onto the amino acid of the trna and the a site what would that look like over here then after this process occurred which was catalyzed by the peptidyl transferase in the ribosome it would look like this so here we'd have our trna and would it have a here let's just represent by an x does it have an amino acid no it's gone because we transferred it then over here and that's in the p site here in the a site what would it look like well now we would have that trna and it would have the amino acid isoleucine first and then it would have the next amino acid that was added onto it which is the methionine right that's it now what did i say that we had to do that was the first thing i said we had to do in this kind of elongation process the second thing that we have to do is something called so we did kind of this like peptidal reaction now we have to do something called translocation so the next step here is called translocation and that's basically just kind of like moving things along moving whatever was in the p site into the e site moving what was in the a site into the p site that's all it is but in order for this to happen i need energy to generate this process so what happens is i have this in the not an enzyme but a kind of a factor here called a eukaryotic elongation factor type 2. and this eukaryotic elongation factor type 2 contains a molecule called gtp we need that energy baby so it brings in this gtp and puts the gtp into this reaction which breaks it into gdp and inorganic phosphate so this guy brings them the eukaryotic elongation factor type 2 brings the gtp to this area where the ribosome and mrna are interacting creates energy and then shifts what was in the a site into the p site what was in the p site into the e site what would that look like then come over here this should be in the e site which is my trna with no amino acid bound to it and the p site what i have i'd have my trna which contains the isoleucine and the methionine what would i have an a site nothing all right so now that we've kind of moved and shifted or translocated the trna that was in that site into the e site eventually because of that energy i generated i'm also just going to spit it out right i'm going to spit it out of the e site and so now this is no longer going to be associated with the mrna and the ribosomes it's going to be spit out and it'll go back up remember in the trna charging it'll go back up and it'll get charged get a new amino acid added on to it and then it'll come back into the a site eventually but after we spit that trna out that we have finished what does it look like we'll come up here right if so what do we do we spit out the trna out of the e site come back to this point here we now have if we were to take from this point what was the difference from when we started we just added on an amino acid so now the only difference here is that i have a amino acid added on to a trna in the p site then what would i do i'd have another eukaryotic elongation factor bring another amino acid into the a site i'd have that then do what have that amino acid and the a site attack the amino acids in the p site pull them over when they pull them over that's catalyzed by the peptide transferase then i'll use gtp to shift the amino acids at this point which would be now what three in the a site into the p site then after i do that i'd spit the trna that i already used out of the e site and i'd come back and i'd have three amino acids and then i would just keep doing this process and going and going and going as i continue to elongate my peptide eventually though you hit a certain point so let's pretend this trna has been going ham and you've just been bringing in tons and tons and tons of uh amino acids and by this time it's it'll start to look like this because you've gone through that elongation step like you know a thousand times at this point and you got a nice long peptide at this point okay because you've gone through this step multiple times eventually again we're in the p site here e site a site eventually you come to the third phase of translation which is called termination termination eventually you hit a stop codon okay and let's say that we used any of the three stop guns do you guys remember the thing that the memory trick you go away you are away you are gone if at any point in time you get a u r away you all go away you are gone in that a site am i going to have a trna come in and interact no no trna will be coming into this step sir so no trna with an amino acid will be brought into this step instead what am i going to bring in i'm going to bring in something called a release factor so i'm going to bring in something called a release factor a release factor has like a little pocket if you will that'll come in and interact with that uag that stop codon it'll then prevent the ribosome from continuing to move along the mrna continuing to translate it so it'll bind to the stop codon stop the translation process and then what xing cleaved shiatsu that peptide away from the trna that's in the p site so what else will it do it does three things what i want you to remember binds the stop codon second thing is it stops translation third thing is it cuts peptide in p site so then from here that release factor would then use its little shiatsu and cut that bond right there separating the trna from the peptide and then what will happen this peptide will then get released and then from there once we've released this peptide it can go and do whatever it needs to do maybe it's going to get incorporated into the cell membrane maybe it's going to be in the cytosol maybe it's going to be secreted we don't really care at this point we just know that we terminated the translation process utilizing a release factor to identify the stop codon stop the ribosome from moving along the mrna and then cleaving the peptide from the trna and stopping the translation process but now what i want to talk about is that this translation process can occur on what's called free ribosomes or it can occur on the rough endoplasmic reticulum so we have to understand the differences between those two processes so let's go talk about that now all right engineer so we've gone through we've built up the foundation talking about mrna tr and arrna ribosomes we talked about the genetic code we went through the phases of translation and we talked about particularly how translation is occurring on ribosomes right with the mrna the trna we talked about all that stuff but here's the thing translation or protein synthesis can occur on ribosomes that are just kind of like freely circulating in our cytosol our cytoplasm or it can occur on membrane-bound ribosomes which are bound to what's called the rough endoplasmic reticulum and you guys should be asking when do i do it on the rough er when do i do it on the cytoplasm and we'll answer that because it's a good question for the most part the simple answer is that when it occurs on the rough endoplasmic reticulum that is for proteins that are either going to be secreted from the cell incorporated into the cell membrane or proteins that are going to become incorporated into lysosomes so three reasons why it would occur on the rough er and not in the free ribosomes is secreting the protein embedding it into the membrane and becoming a part of lysosomes so now let's talk about the difference between the translation process that occurring on a free ribosome and when it has to bind or translocate from that cytosol where it's a free ribosome to a membrane-bound ribosome there's a very important process that we have to talk about so let's pretend here that we're covering this it's the same thing that we've already gone over you've taken dna and you transcribed it when you transcribed it you made it into mrna right so we took and you made mrna the mrna was then gone through its modification got sped out of the nucleus and came into the cytosol and bound with a ribosome starts getting translated we've already gone through it goes through the initiation elongation process and it's making these peptides that are coming out of what site the p site right as it's synthesizing these peptides there's about a sequence of amino acids about maybe nine to ten amino acids that become an identifier on this peptide and this is represented by the orange portion so we can we're translating it just like we did over here we're just continuing to go through the elongation steps and making a long peptide there's a sequence of amino acids on that peptide that is recognizable by a very specific protein that is kind of floating around in our cytosol this sequence here it's not hard is called the signal sequence okay but it's important to remember the signal sequence is what amino acids so let's make sure that we understand this is amino acids it's not any type of nucleotides or anything like that it's amino acids we're making proteins peptides amino acids make up peptides or proteins and you make a very specific sequence of them that is recognizable by a protein what is that protein that's going to be kind of floating around out here let's do it here in purple there's a protein that's kind of just floating around out here and it is going to come and recognize that signal sequence what is this called this is called a signal recognition particle or protein that's all it is so this is the signal sequence the signal recognition protein or particle will bind to the signal sequence that's it once it binds it then has a high affinity for these receptors that are located on the rough endoplasmic reticulum a very very high affinity for these receptors that are located on the rough endoplasmic reticulum so what is this here called signal recognition particle will identify the signal sequence on the growing peptide from the translation process that occurring on the ribosomes once it identifies it it binds it and then starts dragging it towards what this membrane here what is this membrane here this membrane is the rough endoplasmic reticulum membrane right so if i were to kind of show that here like a general way let's say here if i took a cell i took a cell for example here's my nucleus here's my dna i make my mrna comes out here's your ribosome the mrna will interact with the ribosomes and then the translation process that we talked about over here was just basically occurring on that free ribosome but if we wanted it to occur on the rough endoplasmic reticulum that would be kind of like over here and we'll just kind of represent this by these like lines over here we're not going to get too fancy what would happen is we're going to move this ribosome mrna and the growing peptide towards the rough endoplasmic reticulum membrane which we're just zooming in on right here okay so if we zoom in on it this is what we're going to get on that membrane are two proteins that i need you guys to know two proteins that's it this one right here is the pink protein and this is called the signal recognition particle receptor not hard that's it so what do you think the signal recognition particle receptor is going to bind onto the signal recognition particle or peptide so now let's draw that purple protein here kind of binding here with the signal recognition particle which is then bound to what bound to the signal sequence and the signal sequence is from the growing peptide so here we're going to show kind of like our ribosome here here's the large here's the small and then what's going to be kind of in between here sandwich between it that's getting red right now the mrna and if we were to just kind of show this here here's our protein that's being kind of synthesized out of here and there's one particular thing that's on the end of it which is what the signal sequence and the signal sequence is bound to the signal recognition particle which is bound to the signal recognition protein receptor that's it okay after that process occurs this molecule right here this protein that we haven't talked about yet this black protein here is called the translocon this protein is called the trans locon now in this state right the translocon is closed nothing has kind of triggered it to open yet it is closed so signal recognition particle binds the signal sequence brings it towards the rough er binds it with the receptor and the translocon is still closed how do i get that translocon to open let me explain how here's my signal recognition protein or particle receptor i know this is a lot and we're going to just keep it's going to be a good review here bound to it is going to be the signal recognition particle bound to that is going to be the what the signal sequence from the growing peptide chain so here we will kind of just represent the growing peptide chain and then what's going to be over here my ribosome right and my ribosome is going to have my large my small and then what's sandwiched in between it the mrna good now the signal recognition particle and the signal recognition protein receptor particle receptor contain gtp molecules bound to them okay they contain gtp molecules that are bound to them when this is bound nice and snug with each other the gtp molecules get broken down into gdp and inorganic phosphate so how many gtps are we actually going to break down in this process two that's important because they're each one are associated with the particle and the receptor i'm gonna break these down into gdp and inorganic phosphate bake this one down to gdp inorganic phosphate that's breaking down two total gtps in order for this process to occur when i break that down what happens to the translocon you guys see the translocon was closed it was still closed here so the translocon was still closed in these two states but once i broke down the gtp into gdp and inorganic phosphate i created energy and what happens to the translocon once this happens the translocon opens because it was dependent upon breaking down the gtp into gdp and what in inorganic phosphate okay now the translocon is opened what do you think i'm going to do i'm not going to draw all this stuff here again because we don't really need to know that we opened the whole thing that we talked about is the same i'm just going to continue to keep taking that ribosome here we'll just draw the ribosome the ribosome is going to kind of really line up perfectly like this it's going to line up perfectly with the translocon and now that peptide that was growing is just going to kind of get pushed right through the translocon into what this whole thing this whole thing right here is the lumen of the rough endoplasmic reticulum all that it's just going to start getting pushed into the lumen of the rough endoplasmic reticulum so i'm going to have this peptide getting pushed in here and what was at the end of that peptide what was there the signal recognition i'm sorry the signal sequence so here i'm going to have that signal sequence now since the signal sequence is kind of inside the lumen at this point do i need my signal recognition particle anymore no so what can i do spit him off go back and bind another ribosome and bring him here to you know to another site so while i spit off right here i'm going to spit off also in this step my signal recognition particle i don't need him once i start have this growing peptide line up with the translocon the peptide gets pushed into the lumen there's another little freaky little enzyme in here that loves to identify the signal sequence and cut him off so that we don't have him in there anymore because we don't need him he was primarily needed just to bring the peptide the ribosome to the rough er we don't need him for anything else so this enzyme beautiful cute little enzyme that's inverted is called a signal peptidase thank goodness that's an easy name right and he comes over here and he cuts off the signal sequence and when he cuts off the signal sequence that signal sequence will just kind of get spit off over here and there's going to be some enzymes that'll come and degrade that signal sequence into amino acids because we don't need them but what happens is that peptide is just going to continue to keep going and being translated and translated and translated through the elongation process until what happens till we hit a stop codon you go away you are away you are gone right remember that little trick once you hit that stop code on translation ceases and what do you do this was once lined up continuing to push the peptide in continuing to push the peptide into the cell we already broke off the signal sequence so we don't have that anymore more once you hit the translation process that stop codon the translation will stop occurring the translocom will close and the ribosomal subunits and the mrna will disassociate away from this site so what happens the translocon closes the peptide is released into what into the rough endoplasmic reticulum's lumen into rough er lumen and then the ribosomes and the mrna will disassociate okay and they'll actually go and get degraded as well that is because why does this happen because at this point you hit a stop codon and once you hit that stop code on it terminates the translation process closes the translocon releases the peptide with no signal sequence on it into the rough er lumen and then the ribosomes and mrna will disassociate and that's covered the ribosomal translocation process now really quickly when you have this process ribosomal translocation coming and binding with the rough er i want you to know why we already talked about the three reasons why this would occur it's proteins that are going to be secreted proteins and that's why because they need to go to the rough er then to the golgi make a vesicle and then go and get excreted or get incorporated into the membrane second thing is they're going to be a membrane protein and the last reason is that they'll become lysosomal proteins okay these are the three reasons why it would be rough er ribosomes okay i need you guys to know that and it's a really simple process because whenever if you guys know come back to this diagram over here if i take a protein it gets synthesized in the rough er then where does it have to go to the golgi then from the golgi it has to get packaged into vesicles and those vesicles can either go to the cell membrane get incorporated go to the cell membrane get excreted or they can become a lysosome okay so that's the whole purpose of why we go through that process with the rough er what about the other ones i know you guys are probably like well zack what about all that free ribosomes that don't bind to the rough er what what how do where do they go what do they do if we talked about let's say that we kind of use a line here and say that these structures are where the proteins are going to be incorporated into these are going to come from free ribosomes and the ones that we already talked about these proteins that will be either be incorporated cell membranes secreted or become lysosomes are going to be rough er ribosomes we already know the ones for the rough er secretive proteins membrane proteins lysosomal proteins what about the free ribosomes where are those proteins going to go if it's just in the free ribosomes these proteins will be for cytosolic proteins what are the reasons that we have cytosolic proteins just use a very simple example a lot of the metabolic processes that occur in the cell glycolysis that occurs in the cytoplasm some other steps that occur in the cytoplasm we need those proteins to catalyze things that are in the cytosol the second one proteins that are incorporated into the nucleus different types of enzymes that are involved in things that are involved in dna transcription things that are involved in replication and modification of things so we also need them for nuclear proteins proteins that are actually going to be involved in the mitochondrial processes certain metabolic processes that are involved there so mitochondrial enzymes and the last one is enzymes that are very very important catalases and a bunch of other enzymes that are involved within peroxisomes so peroxisomal enzymes okay very very important to remember those things okay so free ribosomes gives ways to cytosol nuclear mitochondrial peroxisomal proteins and rough vr gives way to membrane-bound proteins lysosomes and excreted proteins simple as that we've now made the protein we've either got it we've either made the protein via the free ribosomes or we've made the proteins from the rough endoplasmic reticulum now what do we got to do we got to modify the protein a couple different ways let's talk about that very briefly all right guys so at this point in time we have gone from dna we transcribed it we made mrna then we translated and made proteins in this case we made a protein we went through all of these stages in sequence of videos transcription and then translation in this video now what we're going to do is we've got to take this protein that we've synthesized whether it was via the free ribosomes or whether it was via the rough endoplasmic reticulum ribosomes and we have to modify them a little bit in other words we add things on or cut things off that's it add on cut off let's give some examples we're not going to go too ham let's say on one of these i add a sugar residue i'm just going to represent that with a g what does this call when you add a sugar residue onto a protein like oscillation so that could be a reaction called glycosylation and we'll talk about a couple examples of these very briefly a little bit later but that's one thing i add a sugar residue onto these proteins the next thing i could do is i could add a lipid onto these proteins what do you think that's called lipidation here we'll just kind of represent like this little thing called lipidation and we'll talk about reasons that this is important the next thing we could do is we could add on a phosphate groups so we could add on phosphate groups so we'll just kind of show here phosphate groups what is this called phosphorylation we could add on hydroxyl groups what is this called hydroxylation okay what else could i do i could add on like a methyl group here let's put down a couple of methyl group i could add acetyl group or i could cut some some of the amino acids off so let's put cut or trim some of the amino acids off so what would this be called if i add a methyl group on this is called methylation what would it be called if i added an acetyl group on not hard right an acetyl group you would call that acetylation and the last thing is i could cut so here i would just represent maybe i'm going to cut some of these amino acids out of the reaction if i cut some of these amino acids off okay what is that called that's called trimming we actually specifically we call that trimming now these are the basic kind of most important types of modifications that you truly need to know when you're taking a protein and doing things to it but glycosylation lipidation phosphorylation hydroxylation methylation acetylation and trimming what are examples of those that's kind of the big thing that you really should know not going to go ham on it but just think about examples if i took a protein and i added a sugar residue onto it what would be a reason that i would want to do that the best example that i can think of is antigens okay so you know like your red blood cells your red blood cells you have different antigens like a antigens b antigens rh antigens those have sugar residues on them they're proteins with sugar residues on them and they help to identify what's what type of protein that this has on it which can determine your blood type right so that's an example so it can be good for identifying particular proteins or antigens specific to a cell also good for transporters you know transporters different types of channels like glut channels that we talked about in this membrane transport or other different types of voltage-gated ion channels those can sometimes have some sugar residues on them lipidation these are good for proteins that are going to be incorporated into the cell membrane so these are going to be lipid proteins are good for cell membrane as well as organelle membranes for example the rough endoplasmic reticulum that's a that's a phospholipid bilayer which we could use some proteins with sugar lipid residues on them the golgi the smooth endoplasmic reticulum things like that or the cell membrane itself phosphorylation this is a really big one i really need you guys to remember these use the example that we've talked about like a million times like protein kinase a or cyclin-dependent kinases things like that we've talked about a lot in other videos these guys add phosphate groups right so if you had a protein here and we added a phosphate group that could either activate the protein or it could inhibit the protein and that's important in a lot of cells like you know your cell cycle when you go from your g1 to your s phase to your g2 phase through mitosis we phosphorylate particular proteins that modulate that activity or modulate cellular signaling pathways so this is very very important hydroxylation is very very key for making collagen collagen synthesis collagen is extremely important because it's incorporated into our bones our cartilage our connective tissue our basement membranes and hydroxylation is one of the biggest ways that we make collagen okay methylation acetylation this is best talked about and i know you ninja nerds know this we've literally just talked about it in dna structure and organization if i methylate a histone protein what do you do if you add a methyl group onto it does it decrease transcription or increase it keeps the interaction tight so is it can an rna polymerase fit between that no so that would decrease transcription if i put an acetyl group onto it it relaxes the dna increases the space the rna polymerase can come in read it and does what increases the transcription so something as simple as modifying our protein in that way can make a huge difference and my favorite example is trimming i like to think about this as let's say that you just worked worked out you got yourself some gains you're going to go home and eat chicken breasts you know it tastes like a bike tire you know because you know sometimes chicken isn't that good but anyway you're getting trying to get your gains you're getting your protein and when you do that the protein gets into your small intestine and you have a particular enzyme called trypsinogen you know enzyme called trypsinogen trypsinogen it's kind of like the precursor it's not active but if i take and i use an enzyme that cuts the trypsinogen and turns him into trypsin i'm going to cut a piece of it this is the inactive protease this is the active protease if i activate him by cutting some pieces off of him now he can go and shiatsu the proteins that i ate from the chicken so that i can absorb it that's kind of the simple examples of how we can modify proteins that they can either become activated deactivated be incorporated into a membrane be particularly an antigen all these different things so that's taking proteins and modifying it away for particular cellular examples and that concludes our video on translation of protein synthesis all right ninjas in this video today we talk about translation or protein synthesis i hope it made sense and i hope that you guys enjoyed it alright engineers as always until next [Music] [Music] time [Music] you

Channel: Ninja Nerd

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Keywords: Ninja Nerd Lectures, Ninja Nerd, Ninja Nerd Science, education, whiteboard lectures, medicine, science, DNA, biology, cell biology, translation 🧬, genetics, dna replication, transcription, replication, lesson

Id: 80kxa1zApUM

Length: 93min 2sec (5582 seconds)

Published: Tue Apr 06 2021