hello bisque 130 this is the beginning of recorded lecture 42 uh continuing on with this genes and proteins chapter so last time I had introduced the central dogma of molecular biology and we had talked about transcription uh coming up is translation but before that uh I actually want to outline uh the three main types of RNA so yeah we we talked about transcription how RNA is made uh but we need to understand that not all RNA has the same fate not all RNA has the same job uh there are three different types of RNA and they do very different things so one of these is called R RNA lowercase R before the capital r capital n capital a the little r stands for ribosomal uh because this type of RNA forms the ribosomes as the name implies uh which again is uh kind of this one's kind of unint inuitive you know we RNA is supposed to be translated into protein it's supposed to be a blueprint well this is kind of an exception to that our RNA is not a blueprint it's not a message it's not instructions our RNA is a structural component of these ribosomes it it plays a a physical enzymatic role in these structures so uh in summary R RNA ribosomal RNA a structural component of rib ribosomes we'll see ribosomes in action soon enough but yeah this type of RNA is a structural component of these things another atypical uh but very important type of RNA uh is T RNA a little lowercase T RNA the T stands for transfer and I'm honestly not going to say much about these here just kind of introducing this term we're going to see these in action when we talk about translation and once again these are not a message they're not a blueprint these are playing a structural role that we will see later in this chapter so TRNA the T Stander transfer these things play a structural role in the process of translation and finally it's the one I've been saying the others are not our third type of RNA is mRNA it it is messenger RNA it is the blueprint it is an instruction mRNA is not playing some structural role in a process it's just the information it's just the message so mRNA messenger RNA uh its information directs protein synthesis just like a blueprint directs the building of the house the information the code within this messenger RNA is going to tell the cell uh how the protein is supposed to be made it's the message the other ones are structural rnas okay so now we can move to translation well not quite yet before we talk about the process of translation we have to talk about something called the genetic code so little background um how many different nucleotides are there hopefully you know this one off the top of your head the number of different building blocks that are used to build DNA uh it's it's four uh adenine guanine thyine and cytosine not uracil that one's used in RNA but yeah there there are only four different nucleotides uh that are used to build DNA what about RNA how many building blocks does RNA have well also four it's adenine guanine cytosine and instead of thymine we've got uracil so there are four different building blocks in uh in RNA what about amino acids this one's a little trickier we haven't talked about amino acids in a while but if you've got a sharp memory you may remember a table like this from several chapters ago and you may remember even if you didn't memorize the names of all of these things that there were 20 so this is a pretty big disparity when we were doing transcription and we were going from a piece of DNA to a piece of RNA it was a pretty easy one to one you know uh one nucleotide in DNA corresponded to one nucleotide in RNA that worked out pretty easily because yeah they have the same number of of letters in these two alphabets if you want to think about it like that uh but if we try to do one to one if we try to have one you know as we move to translation if we try to have one RNA nucleotide code for one amino acid uh clearly that's not going to be enough we're going to be missing 16 codes here if if the genetic code was one: one that's not enough four is nucleotides four letters is not enough to somehow encode 20 different amino acids so the genetic code is not going to be one: one what about 2: one though so what if uh we have two nucleotides in code one amino acids so by two nucleotides now I'm talking about a code something like AA or GC or uu or UC or CU or you all of these um I did not list all the possible combinations of two uh if you're a math person though you'll be able to to understand that the number of possible combinations of two nucleotides is four to the second power um because there are four possibilities for each position and there are two positions if you don't follow the math don't worry about it but there are 16 possible combinations of two nucleotides which is cool um but it's still not good enough uh again we need 20 for our 20 amino acids so the genetic code whatever it is is not 2:1 what about 3: one well can follow the same kind of math uh if three nucleotides encode a single amino acid don't know why I said one up here but single down here whatever uh the number of possible combinations of three nucleotides is 4 to the3 power which means 64 there are 64 comb possible combinations of you know CCU and U and ggu and things like that uh which is more than enough for our 20 amino acids so I could have just told you that the genetic code is based on sets of three I went through this so we could understand why it can't be one: one 2: one's not good enough three is the simplest code that gives us what we need need so the take-home here the genetic code is going to be based on sets of three nucleotides there's a very important term that refers to these sets of three these things are called codons I'm going to move to a table now that you do not need to memorize uh but it's important to be able to look at and interpret uh here here's our genetic code these are the 64 different possible combinations of three nucleotides RNA nucleotides you know ACU AAU Gau ggu yeah it's all 64 of them in this big old table now there are a couple of things that you may notice about this table one of these should be the redundancy so we have 20 amino acids and 60 codons that is as I've noted more than enough so instead of having codons that just do nothing we have redundancy so if we look at this uh if we want to encode the amino acid Proline for example CCU codes for Proline but so does CCC and so does CCA and so does ccg uh in fact almost all of these amino acids are encoded by two four sometimes even six different codons the term for this redundancy and this is this is kind of a strange term but I didn't make this up this is the term that's used in the world of um code making um the term for this redundancy is to say that the genetic code is degenerate and again that doesn't imply it has bad morals or something like that uh the degeneracy of the genetic code means that there is redundancy in the genetic code most amino acids are encoded by multiple codons that's what this means the other thing that you should hopefully notice if you you know pause and stare at this for a second is you know most of these codons are encoding amino acids that's with these threel all all 20 of these amino acids have you know a cute little three-letter code they also have cute little onlet codes if you take biochemistry you'll probably have to memorize all of them but for here don't even begin to worry about it uh but yeah that's what these things are Proline threonine Lucine isol leucine uh that are a few codons here that seem a little abnormal um there are in fact two different types of what we call special codons one of these is the one in red right here the AUG red codon right here is called the start codon uh so this codeon there is there's only one start codeon it is a type of special codeon and there's only one of them the start codeon signals the start of the protein we're going to see this in action when we finally start talking about translation uh but yeah that's the the job of the the start codeon it says translation start here this is the beginning of the protein it's going to put in the first amino acid uh importantly it it does two things actually not only does it say start here it also says methionine that's one of those 20 amino acids so the start codon also encodes the methionine amino acid the other type of special codon is over here it's called the stop codeon it's actually not the stop codon it's the stop codons because there are three of these all three of these codons do the same thing they say translation stop end of the line end of the protein in contrast to the start codon which encoded an amino acid the stop codons do not encod Cod and amino acid they just say stop so there are three different stop codons again you don't need to memorize their sequences but you do need to know that there are three of them uh there are three different stop codons they signal for the end of translation and they do not encode an amino acid one other important thing about this code so this this code that we've been looking at here I should more appropriately you know uh label this this is the human genetic code we've been looking at so this is how our bodies uh our cells go through the process of translation uh but let me switch to I think I have cat coming up next so for for Keen eyed viewers keep an eye out for this I'm about to switch over this is this is a Spot the Difference moment so this is human I'm going to switch to cat now did you see it let me do another one coming up next is earthworm coming up next is Oak Tree coming up next is eoli bacterium I'm screwing with you they're all the same the genetic code is almost completely Universal among all living things it the 64 codons and what they encode did not change at all in any of these examples there are a couple of weird primitive bacteria that have a couple of codons that are different but other than those weird exceptions with it's even then it's only small differences uh it's all Universal among you know certainly all ukar certainly all animals and and mammals it's almost completely Universal the genetic code is almost completely Universal is the just the blanket statement to make um concerning this uh there's an an interesting uh example or demonstration of this from the textbook showing this glowing kitten so um well this is cool uh but there's a reason for this this kitten is glowing green because it is transcribing and translating a protein this protein is called Green fluorescent protein and it fluoresces green it does exactly what the name says uh This Is Not A protein that kitten normally has it's actually a protein that's found in nature in in some species of jellyfish but because the jellyfish genetic code is exactly the same as the cat genetic code you can take the gene for this protein from one organism put it into a different organism it's going to get transcribed and translated faithfully and they're going to make the same protein that the jellyfish make so yeah this is just demonstrating the the universality of the genetic code and if you're curious this is not just mad scientist to make M mad science to make glowing cats uh this is proof of concept for being able to introduce genes into higher vertebrates like mammals this is proof of concept for uh gene therapy to try to cure uh genetic disorders in humans if we can introduce a gene into a cat it's green just because it's easy to see whether it's succeeded or not uh maybe we can fix um genetic issues in humans so yeah looks adorable but there's a reason behind this madness uh and I'm just using this experiment for you uh to illustrate this universality okay so now that we know a bit about the genetic code we can finally start talking about translation so translation is carried out by structures called ribosomes um these are not just structures these are actually enzymes they they carry out enzimatic reactions one of the few enzymes that doesn't end in eight but it's kind of a special one cuz they're massive massive structures so translation carried out by ribosomes in three phases the first phase is called initiation this begins when we have the small subunit of the ribosome oh by the way yeah the ribosome consists of two subunits a small one and a big and they come together so uh initiation starts with the small part of the ribosome binding to our messenger RNA small ribosomal subunit binds to mRNA from there a TRNA I told you that I would come to these a TRNA which specifically holds the methionine amino acid binds to the start codeon I know I I told you you didn't have to memorize this and that's still true but if we want to double check this Au uh yep Aug there's there's our start code on so it's exactly what I what I I said it was uh this special TRNA is called the initiator TRNA carries meing binds to this start codon um from there the large ribosomal subut is going to bind sorry I blocked out some text that's uh confusing at the moment the large ribosomal subunit is going to bind and now we're ready to start building protein so after this initiation of everything sort of coming together we move to our second phase called elongation now to talk about elongation we kind of have to go back to these trnas and uh talk a little bit more about their actual structure uh trnas have two important bits to them one end is the end that holds the amino acid the other end down here is called the anti-codon so trnas have an amino acid attached at one end and an anti-codon at the other the anti-codon is exactly what it sounds like it's it's like the reverse of a codon anti-codons are complementary to codons that are present in the MRNA so if we go back to this initiator TRNA just to use this as an example the codon was a that's the start codon therefore if we have a TRNA if we want it to bind to this start codon this initiator TRNA must have an anti-codon complementary to the start codon which would be UAC it's just a a is complimentary to U because again we're talking about rnas here there's no thyine there's uracil um U is complimentary to a g is complimentary to C bam there we go that's why this initiator TNA binds the way it does it's anti-codon matches up with the start codon that's why it comes into place because there are tons of different trnas floating around in the cell uh only the ones that match up with the exposed codon are the ones that are going to enter the ribosome so actually let's move to the next step here we see our next codon is u u c so u c is complementary to a a g so there should be a TRNA floating around with a a g and which TRNA would it have well we're going to have to go back to the genetic code which again we don't memorize what is U supposed to encode h u is supposed to encode phenyalanine so that means in the cell there should be a TR a floating around with pheny alanine attached at one end and an a a anticodon skip to this there we go fenel alanine a a this of all the trnas in the cell is going to enter the ribosome because it's the one TNA that fits correctly it's anti-codon matches up with this exposed codon in the ribosome so to summarize in text tras enter the ribosome one at a time during elongation according to the MRNA sequence uh if we want to do another step of this moving next our looks like our next exposed codon is CGA a going to the genetic code let's see CGA what is CGA supposed to encode ah there we go CGA Arginine so there is going to be a TRNA floating around with Arginine attached to one end and an anti-codon of g c u let's double check this as we go back GCU Arginine this is the next TRNA that's going to enter the ribosome and this is where my figure ends but the cell is going to go through this exercise again and again because there's going to be another code on and another code on and another code on another code on it's going to they're all going to enter the ribosome one at a time according to the MRNA sequence one TRNA at a time now we kind of skipped over an important part here yeah enter one at a time according to the sequence we kind of skipped over an important part here uh the attachment of this first amino acid to the second amino acid remember in order to build a protein we have to connect amino acids to one another we have to create if you remember this term from several chapters ago a peptide bond so the T as part of elongation the T rna's amino acid is passed to the next trna's amino acid peptide bond created and yes this costs Energy building protein costs a lot of energy every single amino acid that you ATT attach to the next one is going to take energy to form this kind of bond so we're going to pass the amino acid to the next amino acid from there the empty tRNA this one has lost its amino acid it gave its methionine to the next one this empty tRNA is going to exit the ribosome and the next TRNA is going to come in so empty tRNA um exists uh exits sorry for that typo exits the ribosome uh as the MRNA slides along and the next TRNA comes in um Etc again this is just showing the first three but there will be a fourth a fifth a sixth and so on with every um TRNA coming in according to the MRNA sequence mRNA sequence anti-codon carrying the appropriate amino acid this is going to continue on for I mean depends on how long the protein is most proteins are dozens hundreds of amino acids long this will keep happening until we reach our third phase called termination during termination there is a stop codeon that is exposed in the ribosome one of these three there is no TRNA floating around that corresponds to the stop codeon instead there is a protein called release factor that recognizes the stop codon this is not a TRNA it looks like a TRNA it has the same shape as a TRNA it would have to it's fitting into the little pocket that TRNA is normally nor Al occupy but this is a this is a protein the release Factor protein upon recognizing a stop Caton and entering the ribosome is going to cause the whole thing to fall apart the two halves of the ribosome fall apart the MRNA uh is released and the protein is released as well this string of amino acids it's going to fold up into its complicated three-dimensional structure if it hasn't started doing that already and so yeah this this termination happens because a stop codeon pops up so to summarize a stop codeon in the MRNA causes release Factor protein to come into the ribosome the two ribosomal subunits dissociate or come apart the protein is released and the MRNA is released and importantly so yeah this mRNA if you think about what happened to this mRNA throughout this entire process the MRNA is not altered by this at all it's it's just sort of looked at it's just sort of read and then it's going to slide down the next TRNA comes in but nothing is nothing is permanently happening to this mRNA and so once this mRNA is released there's absolutely nothing stopping that mRNA from just going right back to the beginning and becoming translated a second time a third time a fourth time um mRNA doesn't have the best shelf life so it doesn't last forever eventually it'll start to break apart and it'll be scrapped for energy and uh spare nucleotides but yeah that mRNA is is going to be translated um again after it has been released so importantly I I know it's confusing that the three stages of transcription uh were initiation elongation and termination which are the same stages as translation uh but it really is important to remember the difference between transcription and translation and and what is actually doing what importantly translation starts at the start codeon and ends at a stop code on transcription if I can go back to this is just a a means of uh of compare and contrast transcription started at the promoter and ended with either row factor or an RNA hair pin so even though they both have beginning middle and end phases it's very important to not get them mixed up and remember what starts and stops and does transcription remember RNA polymerase does transcription and not get that mixed up with the things that start stop and you know perform translation ribosome does translation starts with a start code on on uh and ends with a stop coat on it's all just that's all just review so termination there's my piece for translation now once again UK carots VPR carots so how how how are they different when it comes to translation well there's really one kind of minor difference that kind of has a big impact and that has to do with where all of this is happening so there's a lot going on here uh let's let's look at this left half first so this is a procaryotic cell and if you'll recall procaryotic cells do not have a nucleus so we're watching the process of transcription right here this is our big molecule of DNA again a circular DNA chromosome and here's the creation of mRNA from that DNA transcription is occurring right here because this is just floating around in the cytoplasm the cell actually doesn't have to wait for transcription to finish before ribosomes can come in and start Translating that mRNA and building protein so these two steps are happening simultaneously transcription is still ongoing it hasn't even finished reading uh the DNA yet uh and yet translation has already begun so in Pro Pro carots we have simultaneous transcription and translation however we don't in ukar ukar do have a nucleus the nucleus is where transcription happens and the cytoplasm or the rough ER is where translation happens so we can't do them at the same time in a UK carote we have to fully transcribe this mRNA we've got to do our processing our splicing our additions for stability then it gets exported from the nucleus to where it needs to go then we can do translation on this mRNA so yeah simultaneous in procaryotes but in ukar uh transcriptions of the nucleus translations of the cytoplasm uh so again that's the the biggest difference between these two everything else that I had said about translation uh applies to both procaryotes and ukar now finally we're coming back to this so this was in the last chapter it's technically a chapter 14 topic I told you we would come back to it later well we're coming back to it now to talk about the different types of mutations the first category of mutation I want to talk about uh is called point mutations and you can see there are three of these four three different types of mutations fall under this category atory of point mutations point mutations are changes in a single base pair so whatever has changed in the in the sequence is just a single change just one base pair has changed uh there are three different types of point mutations because it it kind of depends on how it has been changed uh let's take a look at the first type of point mutation called a silent mutation so you can see the mutation here it's within this codon GTA it looks like the a has been mutated again A mutation is a stable change in the DNA sequence this GTA uh the the a has been changed to a t so instead of being the GTA codeon it is the gtt codon now that we've learned about the genetic code we can investigate what effect that's going to have on the protein well GT oh so sorry if this is confusing uh this is showing mutations not in the RNA strand but in the coding strand of the DNA so remember the coding Strand and the RNA have the same sequence it's just used instead of T's so we won't be looking for GTA in the genetic C code we will be looking for Gua and comparing that to guu just a call back to those uh different strands and a template and coding and all of that stuff so G UA encodes veiling whereas guu encodes veiling oh so remember the genetic code is redundant so sometimes you can have a mutation that actually doesn't change the amino acid sequence at all the DNA sequence has been changed this is a mutation but the protein that comes as a result of this is exactly the same it's not going to change the protein sequence that's why this is called a silent mutation no effect on the amino acid sequence the new codon encodes the same amino acid uh that the old codon did so that's a silent mutation a type of point mutation next up we have something called a Mis sense mutation in this example we've we're looking at this codon here CC C uh and the mutation is right there at the first position instead of a c it's an A so the CCC codon has been changed into an AC codon if we consult the genetic code there's our CCC uh which encodes the amino acid Proline and there's ACC which encodes something different again this is not silent mutation we're actually changing the sequence of this protein instead of a proline amino acid there is going to be a threonine amino acid in this position so in a Mis sense mutation the amino acid one of the amino acids of the protein is actually changed now this might not seem like a big deal uh again there are dozens hundreds of amino acids in a protein is changing one of them really going to affect the protein's function well absolutely can uh sickle cell anemia is a genetic disease for example that is caused by a single amino acid changed from one to another so missense mutations one little amino acid change can have a very profound effect on the functionality of a cell third type of point mutation is called a nonsense mutation looks like we're over here now T is now t a g remember this is a sequence in the coding strand of the DNA so we won't be looking for TAC in our genetic code table we will be looking for UAC UAC contain uh encodes tyrosine we've changed UAC to U A and it looks like UAG encodes ooh a stop codon so instead of just swapping one amino acid for a different amino acid in this type of mutation a nonsense mutation we cause an amino acid uh in coding codon to become a stop codon so protein is just going to end here uh doesn't matter whether it was near the beginning or in the middle or wherever it is you're just going to stop prematurely and you're going to have a protein that is shorter than it is supposed to be uh so nonsense mutation this is where an amino acid in coding codon is changed to a stop codon uh and yeah this can also have catastrophic effects on the functionality of that uh that protein cystic fibrosis for example is caused by a nonsense mutation now all three of these were examples of point mutations one am or one nucleotide was changed to another nucleotide the other category of mutations is called Fram shift mutations in a Fram shift mutation we are not changing one nucleotide to another we are adding or removing entire nucleotides from this sequence here's an example of a frame shift so we've got AGC GTA CCC in this example the TA has been moved what and and so yeah then instead of GTA CCC it's just gccc Ta A C T and you know the rest of the sequence what this does I'm not even going to track this it screws everything up every single codon after this point is is going to be is going to be messed up is is not going to be read correctly again the reading frame of codons is sets of three if you add or remove one or two nucleotides it messes up the frame of reading so my example of what this would look like here's a normal looking sentence the sentence reads would this make sense if I shifted each space and here I'm going to introduce uh a shift here in the reading frame just moving that little space over one point now the sentence reads needs would Tois a en Fe hid Ox pace and obviously resulting in total nonsense uh it well okay don't get it mixed up with with actual nonsense that was a that was a different type of thing resulting in everything being wrong so a frame shift mutation like I said a few nucleotides are inserted or removed if that is not a multiple of three if it's a multiple of three you're just get get a new amino acid or you're going to lose an entire amino acid but if this addition or removal is not a multiple of three it's going to completely change the further amino acid sequence in this protein again it this is only showing a couple Downstream Proline tyrosine becomes Lucine Lucine but yeah it's going to mess up everything that comes after that so again to summarize we had point mutations which came in three varieties silent missense and nonsense and then we have this frame shift mutation and hopefully you understand why I moved this to chapter 15 I really don't understand how they expect students to understand these before we've introduced the genetic code and how this works so yeah that's why I moved it over to chapter 15 I think you need to understand this first before you can understand the effects of these mutations but anyway that's uh that's the mutation stuff now I do briefly want to start start in on the next chapter within this recorded lecture I know it's kind of long already but I'm just briefly beginning on this so the textbook calls this chapter 16 gene expression uh I'm going to just quickly change the name of this uh to call this chapter regulating gene expression this this just makes more sense in my opinion so what is gene expression well the phrase gene expression refers to everything that we've just talked about in the last chapter the process of a gene in the DNA being transcribed into Mna being translated into protein and then those proteins doing stuff in the cell you know all of this business uh we just refer to that as gene expression and if a gene is expressed and it's going through transcription and translation and its proteins are doing stuff that Gene is said to be on if a gene is not expressed and for whatever reason at whatever point it is not going through this entire process that Gene is said to be off now this leads to kind of an interesting question why would we need to turn genes off what's the point of having these instructions if you're not going to use them why would you waste space in the chromosome on something that you're not going to transcribe and translate well an important thing to point out here in the overall process of gene expression is we've got a lot of genes but we don't need all of them at all the time not all genes need to be expressed at all times a good justification for this statement comes when we look just at our own bodies so here's a slide I stole from bis 132 but yeah these are some of the internal organs of the human body and every single one of the cells in all of these organs has the same chromosomes they have the same sets of genes they have the same instructions your neurons have the instructions for how to build muscle proteins do your brain cells need to be constructing muscle proteins no you're you know and your muscles have all the genes required for making liver proteins and you know metabolizing things do your muscles do your muscle cells need to be expressing those genes absolutely not so even though uh we have you know all these cells have the exact same genetic instructions most of these genes are going to be turned off in most of these cells for them to do their jobs um in summary and sorry this is kind of an awkward sentence it's the best I can come up with different cell types Express different genes in order to fulfill different functions that's why we don't need everything on all the time we have different cells with different sets of genes on and off because they're doing different jobs and need different genes that's true for multi-cellular organisms yeah so for multicellular organisms that statement is true but for every organism this is also an answer to the question of why we have genes that we're not going to use in order to respond to the environment some genes are only necessary under certain circumstances and so we don't need them to be on all the time we want to have them on hand if needed but we need to be able to switch them on or off in order to respond to the world changing around us that's why I want to call this chapter regulating gene expression because this chapter is not just the process of gene expression we kind of did that in the last chapter this process is about how we control this or this chapter is about how we control gene expression how we switch things on or off now there are different ways to switch things on and off in procaryotes most of this control is right here at the beginning at the transcriptional stage in procaryotes uh if you want to control whether a gene is expressed or not usually it's right here at the beginning controlling whether the gene is transcribed into mRNA or not to do this things called transcription factors are used couple of key terms here transcription factor is defined in the key terms as a protein that binds to DNA and influences transcription of a gene or genes in other words a transcription factor is a protein that controls this switch there are two different flavors of transcription factors ones that turn things on and ones that turn things off um based on the names you could maybe guess which one is which uh but they're defined in the key terms if you if you want that spelled out for you repressors are a type of transcript let me read the key terms repressor a transcription factor that prevents or reduces levels of transcription an activators are to read from the key terms a transcription factor that increases levels of transcription so yeah these are types of transcription factors ones that switch off ones that switch on these can be used by procaryotes to regulate transcription uh UK carots do use transcription factors we do have repressors we do have activators but in addition to that we also control stuff everywhere else uh we also control at the translational stage regulating whether the MRNA is translated or not and we control things at this stage as well we've already made the protein we're going to control whether it does stuff or doesn't do stuff so procaryotes mostly regulate things transcriptionally ukar regulate at every stage now if this sounds a little abstract like what does how what does this look like how do you switch on how does how does an off switch work that's just fine because what's going to come next in this chapter is uh an example of each of these so again I I said I was just briefly getting started on this regulating gene expression chapter in the next recorded lecture we'll pick up here and I will give you an extended example of transcription regulation involving both repressors and activators so yeah just introducing the terms now we'll see more of it next time so that's it for recorded lecture 42 more gene expression regulation in the next one