D1.2 Protein Synthesis [IB Biology SL/HL]

this video is for the standard level content from D 1.2 on protein synthesis protein synthesis will happen in two major steps transcription and translation we'll talk about transcription first so transcription is the process of using a strand of DNA as a template to create a strand of RNA now we only want to do this for the gene that is being expressed okay so we're only going to transcribe a segment of DNA called a gene genes code for proteins and in order to do this we'll need this enzyme called RNA polymerase so RNA polymerase is shown

here in green it's this big green blob looking thing and it does a couple of things first it's going to separate the strands in DNA replication that was done by heala case in this case it's done by RNA polymerase and then I love the name for RNA polymerase because it tells you what the function is it is an enzyme that synthesizes a polymer of RNA so how does it do that well it uses one of the strands of DNA as a template to put RNA nucleotides together and it knows what sequence to put together because

it follows the rules of complementary base pairing it also connects the RNA nucleotides together by um creating those sugar phosphate bonds those phosphodiester bonds to create one continuous strand of mRNA and then one important thing to notice is that um when we think about the rules of complimentary base pairing in RNA um a does not pair with t adenine does not pair with thyine instead adenine pairs with uracil so RNA won't have any T's it won't have thyine it still has cytosine and it is complementary to guanine but this is one difference we want to

keep an eyon RNA is single stranded and we're only going to use one of the strands of DNA of one of those parent strands as a template to synthesize that RNA so how do we know which strand actually gets transcribed well these strands can be renamed into the S Strand and the anti sense strand the sense strand actually contains the genetic material to be copied so I have that up here you'll notice that that is complimentary to the anti-sense Strand so this does not include the genetic information to be copied however it is the one

that is used as a template during transcription and here's why so I'm going to do my RNA in green here and I'm going to use the anti-sense Strand as a template and I'm going to follow the rules of complimentary base pairing whoops um so me remembering to replace and I see an error here here we go remembering that RNA does not have thy means it has uracil instead okay so here's my RNA strand by using the anti-sense Strand as the template you'll notice that my RNA is actually identical to the DNA in the sense strand

minus of course this exception that Ur ail replaces thyine but otherwise they are identical so this complimentary base pairing and the use of the antisense Strand helps to ensure that the genetic information on that sense strand is actually represented by the MRNA molecule so if I'm looking at this picture down here this sense strand is not being utilized as the template The anti-sense Strand is being used as the template to make this strand of mRNA and it's really the hydrogen bonding between that comp those complimentary base pairs that ensure that that continuity of genetic information

persists so here's what we mean adenine can only pair with thyine because their molecular Arrangement is just so that when they line up they can form two hydrogen bonds between them cytosine and guanine their molecular structure aligns so that they can form three hydrogen bonds if you try to form a hydrogen bond between let's say guanine and adenine their molecular structures are not compatible for hydrogen bonding so this continuity of genetic information being being you know Rewritten onto mRNA is all because of this complimentary base pairing rule when DNA is in its double stranded form

it is incredibly stable and this stability really prevents any changes um or mutations from happening in that base sequence however when this DNA is temporarily separated um that complimentary BAS pairing those hydrogen bonds don't exist and so we have a decrease in the stability so that instable form in DNA allows mutations to occur more frequently so um something to keep an eye on there in terms of this theme of continuity and change continuity persists in replication and transcription change can occur when there are mutations and those mutations are usually going to to occur when the

strands of DNA have been separated now we said that transcription is only going to occur along a small segment of DNA and that small segment is a gene genes code for proteins okay so gene expression is the production of a protein using the sequence of bases in a gene so your cell or a single cell in your body has lots and lots of gen but different cells will express some genes and turn other genes off or not express them cells will only express the genes that are needed at that time when we say that genes

are expressed what we really mean is that they are transcribed and then later translated into proteins so for example in a human cell in a liver cell liver cells are going to turn on all of the genes that they need in order to be a liver cell okay and do what liver cells do they are not going to express the genes for how to be a muscle cell or for the functions of a skin cell so it's important to note that all of the cells in an organism contain the full genome just that not all

genes are expressed that control of genetic expression um is further developed in another topic but we want to be able to relate gene expression with transcription if you need to express a gene then you need transcription to take place first now we've already talked about transcription so transcription is using DNA as a template to make RNA and then the next step that we'll talk about is something called translation and then in Translation we're going to be taking that RNA and and translating it into a polypeptide so it's important to kind of maybe add some more

detail here when we say RNA we mean mRNA the m stands for Messenger it is literally a message being carried from the DNA to the ribosomes where that polypeptide will be produced okay now when we say polypeptide remember polypeptides are long chains of amino acids so whereas here we're making an mRNA strand using nucleotides during translation we're going to be making a polypeptide by connecting many amino acids so this mRNA code gets translated into a polypeptide sequence of amino acids in the cytoplasm on a ribosome so here I've got a picture of the full process

we'll talk about all the parts so this big kind of BL blue blob here this is the ribosome and then this strand is the MRNA mRNA is going to have many base sequences and they are read in groups of three at a time these groups of three bases are called codons on each strand of DNA there will be a start codon that tells the ribosome where to actually start transl in and there will be a stop Caton that will be at the end where translation should be terminated and this molecule right here this is something

called TRNA so it's a strand of RNA guys it's still single stranded I know it doesn't look like it but it's one strand that's looped in on itself so still RNA the T stands for transfer it is literally transferring amino acids to the ribosome and it's got two important structures that we want to pay attention to it carries a specific amino acid at the top and it also has a group of three bases that kind of stick out from the bottom called an anti-codon so on mRNA the groups of three bases are called codons TRNA

has an anti-codon and of course codons and anti-codons are matched together follow foll in the rules of complementary base pairing now we kind of mentioned that the ribosome looks like one Big Blob it's not it's actually made of two subunits so the small subunit is this part on the bottom here okay where the RNA the MRNA is going to bind okay so this is our small subunit the large subunit is exactly what it sounds like it's this larger part up here here on the top and this part of the ribosome is going to contain binding

sites for TRNA and also a catalytic site to help create these peptide bonds between the amino acids that the tRNA molecules are carrying in Let's do an overview of this process we'll go in and add some more details later but translation starts like this the MRNA is going to attach to the small sub unit of the ribosome and then a TRNA molecule that has remember an anti-codon that is complimentary to the start codon will attach okay so these anti-codons when they're complimentary to the MRNA codons will attach the ribosome is then going to slide down

to the next codon and the next TRNA molecule will attach the amino acids from the TRNA molecule are joined together so we can see that happening here that the TRNA molecule carrying this amino acid um is right next to this TRNA molecule and we're going to form a peptide bond between them and eventually this TRNA molecule will be holding this big long chain so this continues until a stop codon is reached at which point all of the parts will disassemble the large and the small subunit the ribosome will come apart the MRNA will detach and

this peptide or this polypeptide um will detach as well now let's zoom and see how this would work okay so again we're going to read these codons on mRNA in groups of three right so a codon has three base sequences and on TRNA so that's going to look a little bit something like this we'll have TRNA that's a single continuous loop but kind of sticking out here are going to be be three base sequences okay so something like this and those will of course be complementary to the three bases on this mRNA now each TRNA

carries a specific amino acid okay and so this TRNA that has this anti-codon happens to carry the amino acid called methionine then the next TRNA molecule with an anti-codon that is complimentary to the codon on mRNA will attach and again it has a unique anti-codon and it carries a unique amuno acid and finally my third TRNA with its complimentary anti-codon carries a different amino acid this time it would be Arginine so again what we're going to need is a peptide bond okay to connect these amino acids together and that is eventually how we will get

our polypeptide now there are are some really cool features of the genetic code that are going to have applications both within this topic and to other topics first of all the genetic code is read in triplets that's groups of three so let's back up for a moment there are only four possible bases right in DNA a t g and C or if we're talking about RNA a u g and C if we read these one at a time that would only mean that there's only four combinations an a a g or a c a t

that's not very much okay there's not a lot of variety there but when you read things in groups of three okay and I have four possible bases that means that there are 64 different combinations of those four bases so that 64 is a lot greater than just four that's going to give me a lot wider variety and I'm going to have um a lot more opportunity to produce unique amino acid sequences the DNA code or the genetic code is also Universal and that means that the same codons will make the same amino acids in all

organisms and viruses so I want to show you how to read this codon chart down here so codons again are read in groups of three let's just say I have a codon that reads u a c okay so UAC I'm going to find the first letter which is you and so that's right here and that tells me I'm looking for something in this row okay all right so that's the first letter we can check that off then I'm going to find my second letter which is a and the second letter is right here it's across

the top and I'm looking for a so that means I'm looking for something something in this column all right well what that really means is that I'm looking for something in the intersection of where that row and where that column are I'm finally going to find the third letter okay and it's important that I'm using my mRNA code on here my third letter is C so I'm going to find that third letter over here and I'm going to follow it this way and I'm going to double check this says UAC and so that means that

I am making this amino acid tyene so UAC let's try that again so we can actually read it UAC is right here and this is the amino acid tyene UAC codes for tyrosine in your cells in the cells of a tiger in the cells of a yeast okay in the cell or I shouldn't say the cell but even in a virus right so that means that the genetic code is Universal it is also degenerate now in English we often use this word degenerate to mean something bad but in this case it's actually very good this

means that different codons can code for the same amino acid for example if I have the Cod on uu U that is going to make pheny alanine u u and then u i see it right here if I have a different amino acid like let's say I have a mutation and I that changes to u u see okay U see also makes phenol alanine so degenerate means different codons can code for the same amino acid and this is actually a huge advantage in case you have a mutation it means that that mutation might not actually

result in a change in the amino acid sequence so I've made this table a little bit bigger I recommend that you pause this video and use this codon chart to try to figure out what amino acid sequence would be translated by this mRNA sequence so my suggestion is that the first thing that you do is to separate these into codons codons are groups of three and if I look at a u and then C Au U is right here and that codes for isoline a a codes for lysine CCA codes for Proline and ug codes

for one of those stop codons so if you're doing this on an exam and you get a stop codeon you must stop you can write the word stop but if there are additional codons after that do not translate them okay that literally means to stop now put yourself to this test okay if I give you an mRNA sequence can you work backwards and see what DNA was used to transcribe and make it can you figure out what the TRNA anti-codons are and can you figure out what amino acids that would code for well how did

you do this mRNA if I'm working backwards to get my DNA noticed that these are all complementary based pairs if I want to know what the TRNA anti-codons are again they are also complementary and then I can use this chart to find the amino acid sequence again to find that amino acid sequence I want to be using the MRNA split this up into threes okay into those codons you can then use that chart and we should be finding that this codes for Proline cysteine and veine now that we have the basics down let's dive into

a little little bit more detail on how this process occurs on the large subunit of the ribosome we're going to have three binding sites the a site the P site and the E site and trnas will move through them in that order at the a site this is the initial binding site for the each TRNA and this is also where the peptide bond is going to be formed so this TRNA right here is in the a site okay that a site is Again part of the large subunit at this as site okay this TRNA has

um bound with the MRNA and this polypeptide that's already in existence is going to get transferred to this TRNA molecule through the formation of the peptide bond so this TRNA is going to let go of this amino acid and that chain will be passed to this TRNA molecule at the P site so this one is right here at the P site this is where this empty tRNA molecule um is going to be so again what's happening here is that this TRNA or sorry this ribosome is sliding down the MRNA and it's forcing these tRNA molecules

into these sites so once this TRNA molecule has passed the polypeptide chain to the one in the a site it is now empty and then again as that ribosome continues to move down tRNA molecules will find themselves in this last binding site called the E site and this is literally um where these tRNA molecules are going to exit this process they are empty um and they are no longer carrying amino acids so they will be moved through that eite and then I say like ejected okay or they exit and so this will continue to happen

as this ribosome slides down the MRNA it is a repeating cycle and it will end with the elongation of this polypeptide chain theme D is all about continuity and change those rules of complimentary base pairing ensure that there is continuity of that genetic sequence but what about change well this happens with mutations mutations are changes to the base sequence of a gene one of the types of mutations that you have to know is something called a base substitution and this is the change to one base in a gene so it might look a little something

like this where I have three DNA base letters and I'm noticing that there's a change in the base sequence now this might change the amino acid sequence or it might not if I were to transcribe and translate these my original sequence well let's see what would the MRNA read it would read GAA now GAA makes glutamic acid let's then create an mRNA sequence with my mutated DNA so this would be g a g g a also makes glutamic acid so in this case the mutation has not caused a change in my amino acid sequence let's

imagine another scenario where it's not this letter that experiences a mutation but this one and instead of a t there's an a there well let's go ahead and transcribe this into mRNA so again this would be GAA and GAA makes glutamic acid if I transcribe this mutated be base sequence that would make Gua and Gua makes veine so in this case the amino acid has been changed and if you change the amino acid in a polypeptide that may change the way that that polypeptide folds into the protein and so you may find that that protein's

shape and function um have changed quite a bit this is exactly what happens um in the hemoglobin Gene one of the genes for hemoglobin that results in sickle cell anemia that is caused by a base substitution mutation that um eventually ends up with glutamic acid being substituted by veiling so again theme D all about continuity and change we want to be thinking about complimentary base pairs transcription translation and the effective mutations