RNA and the Genetic Code

hello everybody my name is Iman welcome back to my YouTube channel today we&#39;re going to be discussing RNA and the genetic code what we&#39;re going to start with is this an organism must be able to store and preserve its genetic information and then pass that information down along to Future Generations they also have to be able to express that information as it carries out all of the processes of life we know that DNA and RNA share the same language the language of nitrogenous bases which we covered last chapter they both code using nitrogenous bases proteins however are composed of amino acids which constitute a different language altogether therefore we have to use the genetic code to translate this genetic information into proteins and the major steps involved in the transfer of genetic information are Illustrated in in the central dogma of molecular biology so classically a gene is a unit of DNA that&#39;s going to encode a specific protein or RNA molecule and through transcription and translation that Gene can be expressed it&#39;s useful then for us to develop a working definition and understanding of processes like DNA replication transcription and translation now we discussed DNA we discussed DNA replication in the last chapter but we&#39;re going to continue learning more about gene expression in the rest of this chapter and so the theme of this chapter that we&#39;re going to delve into is this messenger RNA is going to be synthesized in the five Prime to three prime Direction and it&#39;s complementary and it&#39;s anti-parallel to the DNA template strand the ribosomes translate mRNA in the five Prime to three prime direction as it synthesizes the protein from the amino acid Terminus to the carbox carboxyl Terminus and we&#39;re going to see the central dogma of molecular biology going from DNA to RNA through transcription and then going from RNA to a protein through translation now we&#39;re going to start by discussing RNA and the three main types of RNA found in cells our mRNA is going to be the the most abundant followed by TRNA and finally rrna so let&#39;s go ahead and discuss these all right RNA or ribonucleic acid it&#39;s a nucleic acid That&#39;s essential to the synthesis of proteins all right there are three main types we&#39;re going to start with mRNA mRNA or messenger RNA carries genetic information from your DNA to the ribosome where it&#39;s going to be used as a template for protein synthesis mRNA is transcribed in the nucleus and then is transported out to the cytoplasm where it&#39;s translated into proteins mRNA is relatively unstable is relatively stable allowing for the regulation of gene expression sorry about that it is stable now fun fact um in eukaryotes mRNA is um monocystronic meaning that each mRNA molecule translates into only one protein product in prokaryotics mRNA can be polycystronic so it can actually translate into more than one protein a product all right so mRNA messenger RNA message from DNA in the nucleus to transcription of a gene in the cytoplasm what about TRNA all right TRNA or transfer RNA is responsible for bringing the correct amino acid to the ribosome during protein synthesis TRNA has an anticodon that is complementary to the codon to the codon on the MRNA and it&#39;s going to allow it to recognize the correct amino acid TRNA is also responsible for catalyzing the formation of the peptide bonds between the amino acids as the as protein synthesis occurs all right so that&#39;s TRNA brings in those amino acids helps us form a peptide chain three is RNA or rrna or ribosomal RNA this is the component of the ribosome it&#39;s essential for protein synthesis the ribosome is composed of two subunits one large one one small one and each subunit contains rrna our RNA catalyzes the formation of peptide bonds between the amino acids and it helps to position the MRNA and the TRNA into the ribosome now together these three types of RNA they play a really crucial role in the synthesis of proteins mRNA provides a template for protein synthesis it&#39;s the messenger of genetic information TRNA is going to bring the correct amino acid by translating or converting the language of nucleic acids to the language of amino acids and peptides and rrna catalyzes the formation of peptide bonds between the amino acids and it&#39;s an integral part of the ribosomal Machinery that&#39;s used in the cytoplasm during protein assembly now something else that we have to Define and understand that we&#39;ve made mention here several times are codons if a gene sequence is a sentence that describes a protein then its basic unit is a three-letter word that&#39;s known as a codon and it translates into an amino acid genetic code table serves as a easy way as an easy way to determine the amino acid that&#39;s translated from each mRNA codon we&#39;re going to see a genetic code table here in a second each codon is going to consist of three bases all right so there are 64 codons and note how all codons are written in the five Prime to three prime Direction and the code is unambiguous in that each codon is specific for one and only one amino acid all right now we&#39;re going to look at this table really quickly 61 of the codons are going to code for one of the 20 amino acids all right while three codons are going to encode for the termination of translation and this code is universal across species all right these three codons they code for stop all right and so um translation will stop all right now also during translation the codon of the MRNA is recognized by a complementary anticodon on the TR T RNA the anticodon sequence allows the TRNA to pair with the codon in the MRNA every pre-processed eukaryotic protein starts with the same exact amino acid you guessed it methio methio9 all right that&#39;s going to be this right here all right this is the only three letter codon that codes for for method methion9 all right so this is known as the start codon all right fantastic because every protein begins with this the codon for it is Aug it&#39;s considered the start codon all right so we have RNA we have RNA rrna form it makes the ribosomes all right it forms it&#39;s the structural RNA that&#39;s fine that&#39;s found in ribosomes all right mRNA it&#39;s an RNA copy this is the messenger RNA all right that is gonna go move from the nucleus to the cytoplasm all right it&#39;s gonna move through your ribosome to carry the message and as the ribosomes and the RNA read your messenger RNA ill let it it will read the three letter codons and then that those three letter codons specify for a specific TRNA these trnas are going to hold amino acids that are appropriate for the three letter codons they just read and then bring in that TRNA bring in that amino acid into the ribosome all right and then as we continue to do this we&#39;ll bring in all the amino acids we need and form peptide bonds between them all right this is our initiation code and anyone any one of these three are termination codes all right notice that for the TRNA this is a TRNA it has an anticodon and it will pair properly with the codon of the messenger RNA all right and that&#39;s how it brings in the appropriate amino acid that we need and I&#39;ll continue to do this as the MRNA is red and then we eventually connect all the amino acids to form the peptidal protein that we need all right now the genetic and now the genetic code is is degenerate because more than one codon can specify a single amino acid all right for example here are four and over here another two six total I think let me see if there&#39;s any more yeah six total codons that specify for serine all right so notice that the genetic code is degenerate because more than one codon can specify in a single amino acid but the degeneracy of the genetic code the thing with it is that it allows for mutations in DNA that do not always result in Altered protein structures or functions so let&#39;s talk about mutations all right that&#39;s going to be really important for us to understand all amino acids except for methionine and tryptophan are encoded by multiple codons if we look back at this codon figure we can see that for the amino acid with multiple codons the first two paces are usually the same all right we&#39;re still going to take our serine example all right all four of these that code for serine have the same two amino acids uh sorry they have the same two nucleotides you see your cell and thymine uh uracilyn cytosine oh my God what&#39;s wrong with me um uracil and cytosine all right now there&#39;s two more here for serine and they also have the same um first two nucleotides adenine and guanine all right now let&#39;s look at something like the I mean the the codons that code for Proline notice how they have the same two nucleotides for all four of these codons that can signal Proline all right so they&#39;re all encoded by multiple codons and if we look at this table some of these amino acids that have multiple codons the first two bases are usually the same and it&#39;s the third base in the codon that&#39;s variable all right we refer to that third base in the in the codon as a wobble position wobble is an evolutionary development that&#39;s designed to protect against mutations in the coding region of our DNA mutations in the wobble position tend to be called Silent or degenerate which means there&#39;s no effect on the expression of the amino acid and therefore no real adverse effects on the poly peptide sequence all right so things like silent point mutations all right they have no effect on the protein sequence notice how we change GTA to gtt but both of these GTA and gtt both all right they both are codons that signal for valence valine so it doesn&#39;t matter that the a was changed to a t it didn&#39;t affect it because both of these codons signal for the same amino acid all right now within the same realm let&#39;s talk also about other kinds of mutations like Miss sense and nonsense if a mutation occurs and it affects one of the nucleotides in a codon all right we said it&#39;s known as a point mutation like this one all right this is a silent mutation I mean it&#39;s known as a point mutation one is a silent mutation the one that we just discussed all right now although we&#39;ve discussed this silent point mutation in the wobble position other point mutations can have can happen and they can have severe detrimental effects depending on where the mutation occurs in the genome because these mutations can affect the primary amino acid sequence of the peptide they are called expressed mutations and expressed point mutations so they fall into two categories you have Miss sense and you have nonsense all right these are two examples of expressed mutations expressed point mutations so let&#39;s write that down beautiful missense mutation is a mutation where one amino acid substitutes for another all right so for example here we have CCC which codes for Proline all right but if this C was replaced to an a then we have ACC that that is a codon for 309 so that&#39;s completely two different amino acids a mutation where one amino acid is substituted for another because of a change in the codon because of a result in an amino acid substitution nonsense mutation well this is a mutation where the codon now encodes for a premature stop codon all right look how t-a-c this signals for tyrosine but if that c was was mutated to a g now we have t a g this is one of our stop codons all right all right and so now we&#39;ve stopped reading the MRNA maybe a little too early all right and this results in a nonsense mutation all right or also it&#39;s also called by the way a truncation mutation fantastic so we talked about three point mutations one is silent this has no effect on the protein sequence the two others are expressed point mutations missense and nonsense and they both affect um they both affect the amino acid um the peptides that are formed or can be formed now there&#39;s also frame shift mutations all right frame shift mutations now there the three nucleotides of a codon are referred to as the reading coton reading frame point mutations occur when one nucleotide is changed but a frame shift mutation occurs when some number of nucleotides are added or deleted from the MRNA sequence and this insertion or deletion of nucleotides what is it going to do it&#39;s going to shift the reading frame and that usually results in changes in the amino acid sequence or premature truncation of the protein and this can be this can be much more serious than a point mutation all right so for example let&#39;s say we&#39;ve deleted two amino acids all right they have been removed from the MRNA sequence now the way we read it is this is three and then suddenly these are three and then suddenly these are three and now notice how everything is shifted and notice how many changes in amino acids there already are all right so frame shift mutations can have some serious negative consequences and it can result in some serious mutations all right so these are a couple of mutations that can occur now we can take all this information and the previous chapters that we&#39;ve learned especially the last chapter where we learned DNA replication and we can move into talking about translation and transcription all right and we&#39;re going to start by talking about transcription now although DNA contains the actual coding sequence for a protein the Machinery to generate that proteins actually located in the cytoplasm not the nucleus but DNA cannot leave the nucleus all right so it will be quickly degraded if it does and instead it we will use RNA we have to use RNA to transmit genetic information so that we can use the coding sequence in DNA that code for proteins to actually make said proteins and so what happens is the creation of mRNA the creation of mRNA from a DNA template that is known as transcription and while RNA is on while mRNA is only one type of RNA that carries information while mRNA is only one type of RNA it is this type of mRNA that carries information from DNA directly into the cytoplasm so that it can be translated into proteins all right there are of course other RNA during this process of going from DNA all the way to proteins that help in the process of course we&#39;ve talked about TRNA and rrna and we&#39;re going to our RNA we&#39;re going to see how they play a role in the transcription translation now we create mRNA from a DNA template that&#39;s known as transcription transcription produces a copy of only one of the two strands of DNA during initiation of transcription several enzymes like helicases and Topo and topoisomerases are involved in unwinding the double-stranded DNA and obviously preventing formation of super coils all right the Strand this step is important in allowing the transcriptional Machinery to access to the DNA in particular um translated transcription of a gene of Interest all right so transcription results in a single strand of M RNA synthesized from one of the two nucleotide strands of DNA called the template strand and this newly synthesized mRNA strand is going to be both antiparallel and complementary to the DNA template strand all right so we see it here right we&#39;re gonna unwind the DNA all right and then we&#39;re going to create a RNA transcript from the template strand of DNA all right in eukaryotes there are three types of RNA polymerases but only one is actually involved in the transcription of mRNA all right RNA polymerase 1 is located in the nucleolus and synthesizes rrna RNA polymerase II is located in the nucleus and it synthesizes hrna which is pre-processed mRNA and also some other small nuclear RNA called snrna RNA polymerase 3 is located in the nucleus and it synthesizes TRNA and some rrna now RNA polymerase travels along the template strand in the three to five Prime Direction which allows for the constructed um the the construction of transcribed MRA in the five Prime to the three prime Direction now Unlike DNA polymerase RNA polymerase actually does not proofread its work so the synthesized transcript is not going to be edited whatsoever the coding strand of DNA is not used as a template during transcription why because the coding strand is also complementary to the template strand it&#39;s identical to the MRNA transcript except that all the thymine nucleotides in DNA have now been replaced with uracil in the MRNA molecule all right now in the vicinity of a gene a numbering system is used to identify the location of important bases in the DNA strand so the first base that&#39;s transcribed all right the first base that&#39;s transcribed from DNA to RNA is identified as the plus one base of the gene region anything to the left of the starting point upstream or towards the five Prime is given a negative number everything to the right with positive numbers and transcription will continue along the DNA coding region until the RNA polymerase reaches a termination sequence or stop signal and then that results in a termination of transcription the DNA Helix then reforms and that primary transcript form is termed heterogeneous nuclear RNA or hnrna and then mRNA is derived from that through Prost through post-transcriptional modification so we unwind our DNA we use one we use the template strand to make our RNA sequence complementary RNA sequence all right that&#39;s done now we have our now we have that RNA sequence it&#39;s not rmrna just yet it&#39;s actually called h n RNA or heterogeneous nuclear RNA then it has to go through a couple of post-transcriptional modifications to become mRNA and we&#39;re going to go over those post-transcriptional modifications what are those transcriptional modifications that can happen well there&#39;s a couple before the hn RNA can leave the nucleus and be translated to a protein it has to undergo it has to undergo three specific processes to allow it to interact with the ribosome and survive the conditions of the cytoplasm all right you can think of the nucleus as the happy home of the cell the DNA strands are the parents and the hn RNA is their child but the child has to mature before they let it go out into the wild and survive all right one post-transcriptional process is splicing of introns and extra and exons all right introns and extra exons they&#39;re written right here introns exons so one Prince one post-transcriptional process is the splicing of these so maturation of the H and RNA is going to include splicing of the transcript to remove non-coding regions which one of these is the non-coding regions introns introns are non-coding regions all right so Sometimes some post-transcriptional processes involve removing non-coding sequences and then ligating coding sequences or exons together splicing is accomplished by slicesomes and in the spliceosome small nuclear RNA molecules coupled with proteins known as small nuclear ribonucleoproteins also known as snerps and they together the complex recognize both the five Prime and three prime spliceites of the introns these non-coding sequences are then cut and and remove and then everything else is um kind of like pasted back together all right so they cut out parts of the H and RNA that have that don&#39;t code for anything they remove them they cut them away and then we put together back all the exons the regions that code for something all right so that&#39;s one post-transcriptional process another is called a five Prime cap at the five Prime end of H and RNA molecule we can add a 7-methyl um gunalate triphosphate Cap all right this cap is added and it is actually added during the process of transcription it&#39;s recognized by the ribosome as The Binding site and what it does is it protects the MRNA from degrading in the cytoplasm another thing that we can add is a three prime poly a tail all right this is this is a poly adenosine tail that&#39;s added to the pre three prime end of mRNA transcript and it protects the message also against rapid degradation it&#39;s really just composed of a dining bases um and they&#39;re added to help prevent degradation also increases the stability of mRNA and it facilitates binding of the ribosome to the MRNA in the cytoplasm all right so those are just a couple of um post-transcriptional modifications that convert the H and RNA that transcribed RNA into mRNA that is ready to go out into the cytoplasm and attach and bind to ribosomes so that the protein synthesis process can begin all right let&#39;s reiterate just a few points really quickly going from DNA to DNA all right to replicate all right let&#39;s just make a few notes really quickly before we move on to translation all right whenever you&#39;re going from DNA to DNA what are you doing you&#39;re replicating how does that work well we have new DNA synthesized in the five Prime to three prime Direction all right do not forget that then when you have DNA to RNA that&#39;s called transcription all right we just talked about that that&#39;s transcription all right we have new RNA and the RNA is going to be also synthesized in the five Prime two three prime direction that means the template is read from the 3 Prime to the five Prime Direction and then we&#39;re also going to see here in one second we&#39;re going to see how we can go from RNA to protein and that is called some and that&#39;s something called translation translation all right mRNA is going to be red in the five Prime to three prime Direction all right notice the consistency that&#39;s going to help in Remembering this with this reminder now we can actually officially move into translation once the MRNA transcript is created and processed it&#39;s going to exit the nucleus through nuclear pores all right and it&#39;s going to make it to the cytoplasm once in the cytoplasm mRNA finds a robot ribosome to begin the process of translation which is converting the MRNA transcript into a functional protein translation is a complex process it&#39;s going to require mRNA TRNA ribosomes rrna amino acids and energy so first before we even get to all the juicy stuff let&#39;s talk about the structure of ribosomes because the MRNA is going to have to bind to a ribosome to even begin the process of translation all right the anti the anticodon of the Tiana TRNA is going to bind to the codon on the mature mRNA in the ribosome the ribosome is composed of proteins and rrna in both prokaryotes and eukaryotes there&#39;s a large and small subunit and those subunits only bind together during protein synthesis the structure of the ribosome dictates its main function and that function is to bring the MRNA message together with TRNA to generate the protein in prokaryotes ribosomes are composed of a small 30s unit and a large 50s subunit which combined to form the 70s ribosome that&#39;s what that&#39;s what you see right here prokaryotic ribosomes you have a 50s subunit 30s subunit they come together they form a 70s and eukaryots they&#39;re composed of a small subunit called a 40s subunit and a larger subunit called the 60s unit and they combine to form the ads ribosome all right the small subunit is responsible for binding to the MRNA transcript while the large subunit is responsible for catalyzing the formation of peptide bonds between the amino acids that are brought to the ribosome by TRNA now that we have that understanding of ribosomes and we know that we can take the MRNA that we transcribe from drna and we can use it to translate let&#39;s talk about how translation is the process of translating or converting the transcript mRNA into a specific sequence of amino acids that will grow into a chain of polypeptides there are three steps that we&#39;re going to cover in Translation those are initiation elongation and termination all right let&#39;s go step by step all right initiation is the first step initiation begins when the small ribosomal subunit binds to the MRNA molecule and then it moves along the molecule until it reaches the Stark codon what&#39;s the start codon again a-u-g Ugg all right the start codon is recognized by the initiator TRNA which carries methio9 the initiated TRNA binds to the start codon and then the large ribosomal subunit finally joins the complex and we have now formed the initiation complex all right easy small subunit binds to mRNA looks for the starting codon found starting codon TRNA comes in because it has the same complementary codon to the start codon it binds to it all right bringing in an amino acid this is our first amino acid to start our protein protein formation and of course the large subunit also joins the party now because the large subunit will help in this this alignment of of the TRNA to the right codon and bringing in that right amino acid then during elongation the ribosome moves along the MRNA molecule and it adds amino acids to the growing polypeptide chain so we have trnas that come they bind to their correct codons and they continue to bite bind to their correct codons bringing in amino acid after amino acid that will form a polypeptide chain all right now um the TN TRNA molecule brings these amino acids to the ribosome and they&#39;re added together to the growing polypeptide chain the peptide bonds form between the amino acids as they&#39;re added to the chain all right and the ribosomes are going to move along the MRNA in the five Prime to three prime Direction something that is important to understand in this step is that there are three very important binding sites here there is the a site P site and then there is an e site as well all right there&#39;s an e site as well it&#39;s somewhere here probably all right the a side the a site it holds the incoming amino acid TRNA complex this is the next amino acid that is being added to the growing chain and it&#39;s determined obviously by the MRNA codon within the a site the P site holds the TRNA that carries the growing polypeptide chain all right so the a is the next up amino acid and the P site is already whatever polypeptide chain we have and the a side holds the next amino acid that will be added to the polypeptide chain sitting in the P site all right and then there&#39;s the east side it&#39;s where the now inactivated TRNA pauses transiently before exiting the ribosome and that&#39;s near the end all right it&#39;s like the exiting site and then we have our third and final step of translation that&#39;s termination it occurs when the ribosome reaches a stop codon release factors recognize the saw up codon and they caused the ribosome to release the polypeptide chain and dissociate from the MRNA molecule all right that polypeptide chain then can fold into its final three or three or four dimensional structure and the protein is ready to carry out whatever specific function it needs to carry out all right and that is translation all right small subunit binds to mRNA looks for start codon we bring in our amino acid to um to the a site that&#39;s the next upcoming amino acid all right and then we bring in the next one all right and we&#39;re forming bonds between the amino acids that are all held together in the P site and then when we reach a stop codon all right then we stop translating the MRNA the final form of the polypeptide is released and translation ends all right now just like there is post-transcriptional processing there is also post-translational processes all right there are things like phosphorylation which is the addition of phosphates by protein kinases to activate or deactivate the protein that we&#39;ve made there&#39;s carboxylation addition of carboxylate acid groups that usually are there to serve as calcium bindings spots there&#39;s glycosylation addition of oligosaccharides as proteins pass through the ER or the Golgi apparatus there&#39;s many other things that can happen um post translationally to the protein to either activate or inactivate it whatever is needed all right now with that understanding of transcription and translation we want to understand how prokaryotes and eukaryotes control gene expression and we&#39;re actually going to start first with control of gene expression in prokaryotes all right we&#39;re going to start by defining operons operons are a cluster as there are a cluster of genes transcribed as a single mRNA and we have this model called the Jacob monad model it&#39;s a model that&#39;s used to describe the structure and function of operons and prokaryotic cells the model proposes that operons consist of a regular a regulatory Gene called a promoter and one or more structural genes and the regulatory Gene codes for a protein known as a repressor which binds to the operator region of the operon and it prevents transcription of the structural gene the promoter is the region of DNA to which RNA polymerase binds initiating transcription of the structural genes in the presence of specific inducers the repressor is activated and the transcription of structural genes can then occur and this model actually helps us explain how prokaryotic cells regulate gene expression in response to in to changes in their environment now there are two types of operons there are inducible systems and there&#39;s repressible systems in inducible systems the repressor is bonded tightly to the operator system and therefore thereby acts as a roadblock so RNA polymerase is actually unable to get from the promoter to the structural gene all right because the repressor is in the way to remove that block an inducer has to bind to the repressor protein so that the RNA polymerase can move down the Gene and a good example of this is the Lac operon all right this is one way of controlling what is transcribed and when it is transcribed a repressible system allows constant production of a protein product the repressor made by the regulatory Gene is inactive until it binds to a compressor and this complex then binds to the operator site to then prevent further transcription so it creates it transcribes until it&#39;s told not to a good example of this is the trip operon all right that&#39;s a good example now what about eukaryotes for eukaryotes it&#39;s obviously much more complicated we have transcript transcription factors that search for promoter and enhance the regions in DNA promoters are usually within 20 base pairs of the transcription um start site and enhancers are usually they&#39;re more than 25 base pairs away from the start the transcription start site all right so those are ways for controlling so transcription factors they&#39;re transcription activating proteins that search the DNA looking for specific DNA binding motives and they can bind to a specific nucleotide sequence in the promoter region or to a DNA response element um and um and there&#39;s promoters that are within 20 base pairs of transcription um and then there are enhancers which are within 25 base pairs away from the transcription site and those allow for the control of one Gene&#39;s expression by multiple signals all right that&#39;s all I have for review for this chapter next video we&#39;re going to do some practice problems let me know if you have any questions or comments down below other than that good luck happy studying and have a beautiful beautiful day future doctors

hello everybody my name is Iman welcome back to my YouTube channel today we&amp;#39;re going to be discussing RNA and the genetic code what we&amp;#39;re going to start with is this an organism must be able to store and preserve its genetic information and then pass that information down along to Future Generations they also have to be able to express that information as it carries out all of the processes of life we know that DNA and RNA share the same language the language of nitrogenous bases which we covered last chapter they both code using nitrogenous bases proteins however are composed of amino acids which constitute a different language altogether therefore we have to use the genetic code to translate this genetic information into proteins and the major steps involved in the transfer of genetic information are Illustrated in in the central dogma of molecular biology so classically a gene is a unit of DNA that&amp;#39;s going to encode a specific protein or RNA molecule and through transcription and translation that Gene can be expressed it&amp;#39;s useful then for us to develop a working definition and understanding of processes like DNA replication transcription and translation now we discussed DNA we discussed DNA replication in the last chapter but we&amp;#39;re going to continue learning more about gene expression in the rest of this chapter and so the theme of this chapter that we&amp;#39;re going to delve into is this messenger RNA is going to be synthesized in the five Prime to three prime Direction and it&amp;#39;s complementary and it&amp;#39;s anti-parallel to the DNA template strand the ribosomes translate mRNA in the five Prime to three prime direction as it synthesizes the protein from the amino acid Terminus to the carbox carboxyl Terminus and we&amp;#39;re going to see the central dogma of molecular biology going from DNA to RNA through transcription and then going from RNA to a protein through translation now we&amp;#39;re going to start by discussing RNA and the three main types of RNA found in cells our mRNA is going to be the the most abundant followed by TRNA and finally rrna so let&amp;#39;s go ahead and discuss these all right RNA or ribonucleic acid it&amp;#39;s a nucleic acid That&amp;#39;s essential to the synthesis of proteins all right there are three main types we&amp;#39;re going to start with mRNA mRNA or messenger RNA carries genetic information from your DNA to the ribosome where it&amp;#39;s going to be used as a template for protein synthesis mRNA is transcribed in the nucleus and then is transported out to the cytoplasm where it&amp;#39;s translated into proteins mRNA is relatively unstable is relatively stable allowing for the regulation of gene expression sorry about that it is stable now fun fact um in eukaryotes mRNA is um monocystronic meaning that each mRNA molecule translates into only one protein product in prokaryotics mRNA can be polycystronic so it can actually translate into more than one protein a product all right so mRNA messenger RNA message from DNA in the nucleus to transcription of a gene in the cytoplasm what about TRNA all right TRNA or transfer RNA is responsible for bringing the correct amino acid to the ribosome during protein synthesis TRNA has an anticodon that is complementary to the codon to the codon on the MRNA and it&amp;#39;s going to allow it to recognize the correct amino acid TRNA is also responsible for catalyzing the formation of the peptide bonds between the amino acids as the as protein synthesis occurs all right so that&amp;#39;s TRNA brings in those amino acids helps us form a peptide chain three is RNA or rrna or ribosomal RNA this is the component of the ribosome it&amp;#39;s essential for protein synthesis the ribosome is composed of two subunits one large one one small one and each subunit contains rrna our RNA catalyzes the formation of peptide bonds between the amino acids and it helps to position the MRNA and the TRNA into the ribosome now together these three types of RNA they play a really crucial role in the synthesis of proteins mRNA provides a template for protein synthesis it&amp;#39;s the messenger of genetic information TRNA is going to bring the correct amino acid by translating or converting the language of nucleic acids to the language of amino acids and peptides and rrna catalyzes the formation of peptide bonds between the amino acids and it&amp;#39;s an integral part of the ribosomal Machinery that&amp;#39;s used in the cytoplasm during protein assembly now something else that we have to Define and understand that we&amp;#39;ve made mention here several times are codons if a gene sequence is a sentence that describes a protein then its basic unit is a three-letter word that&amp;#39;s known as a codon and it translates into an amino acid genetic code table serves as a easy way as an easy way to determine the amino acid that&amp;#39;s translated from each mRNA codon we&amp;#39;re going to see a genetic code table here in a second each codon is going to consist of three bases all right so there are 64 codons and note how all codons are written in the five Prime to three prime Direction and the code is unambiguous in that each codon is specific for one and only one amino acid all right now we&amp;#39;re going to look at this table really quickly 61 of the codons are going to code for one of the 20 amino acids all right while three codons are going to encode for the termination of translation and this code is universal across species all right these three codons they code for stop all right and so um translation will stop all right now also during translation the codon of the MRNA is recognized by a complementary anticodon on the TR T RNA the anticodon sequence allows the TRNA to pair with the codon in the MRNA every pre-processed eukaryotic protein starts with the same exact amino acid you guessed it methio methio9 all right that&amp;#39;s going to be this right here all right this is the only three letter codon that codes for for method methion9 all right so this is known as the start codon all right fantastic because every protein begins with this the codon for it is Aug it&amp;#39;s considered the start codon all right so we have RNA we have RNA rrna form it makes the ribosomes all right it forms it&amp;#39;s the structural RNA that&amp;#39;s fine that&amp;#39;s found in ribosomes all right mRNA it&amp;#39;s an RNA copy this is the messenger RNA all right that is gonna go move from the nucleus to the cytoplasm all right it&amp;#39;s gonna move through your ribosome to carry the message and as the ribosomes and the RNA read your messenger RNA ill let it it will read the three letter codons and then that those three letter codons specify for a specific TRNA these trnas are going to hold amino acids that are appropriate for the three letter codons they just read and then bring in that TRNA bring in that amino acid into the ribosome all right and then as we continue to do this we&amp;#39;ll bring in all the amino acids we need and form peptide bonds between them all right this is our initiation code and anyone any one of these three are termination codes all right notice that for the TRNA this is a TRNA it has an anticodon and it will pair properly with the codon of the messenger RNA all right and that&amp;#39;s how it brings in the appropriate amino acid that we need and I&amp;#39;ll continue to do this as the MRNA is red and then we eventually connect all the amino acids to form the peptidal protein that we need all right now the genetic and now the genetic code is is degenerate because more than one codon can specify a single amino acid all right for example here are four and over here another two six total I think let me see if there&amp;#39;s any more yeah six total codons that specify for serine all right so notice that the genetic code is degenerate because more than one codon can specify in a single amino acid but the degeneracy of the genetic code the thing with it is that it allows for mutations in DNA that do not always result in Altered protein structures or functions so let&amp;#39;s talk about mutations all right that&amp;#39;s going to be really important for us to understand all amino acids except for methionine and tryptophan are encoded by multiple codons if we look back at this codon figure we can see that for the amino acid with multiple codons the first two paces are usually the same all right we&amp;#39;re still going to take our serine example all right all four of these that code for serine have the same two amino acids uh sorry they have the same two nucleotides you see your cell and thymine uh uracilyn cytosine oh my God what&amp;#39;s wrong with me um uracil and cytosine all right now there&amp;#39;s two more here for serine and they also have the same um first two nucleotides adenine and guanine all right now let&amp;#39;s look at something like the I mean the the codons that code for Proline notice how they have the same two nucleotides for all four of these codons that can signal Proline all right so they&amp;#39;re all encoded by multiple codons and if we look at this table some of these amino acids that have multiple codons the first two bases are usually the same and it&amp;#39;s the third base in the codon that&amp;#39;s variable all right we refer to that third base in the in the codon as a wobble position wobble is an evolutionary development that&amp;#39;s designed to protect against mutations in the coding region of our DNA mutations in the wobble position tend to be called Silent or degenerate which means there&amp;#39;s no effect on the expression of the amino acid and therefore no real adverse effects on the poly peptide sequence all right so things like silent point mutations all right they have no effect on the protein sequence notice how we change GTA to gtt but both of these GTA and gtt both all right they both are codons that signal for valence valine so it doesn&amp;#39;t matter that the a was changed to a t it didn&amp;#39;t affect it because both of these codons signal for the same amino acid all right now within the same realm let&amp;#39;s talk also about other kinds of mutations like Miss sense and nonsense if a mutation occurs and it affects one of the nucleotides in a codon all right we said it&amp;#39;s known as a point mutation like this one all right this is a silent mutation I mean it&amp;#39;s known as a point mutation one is a silent mutation the one that we just discussed all right now although we&amp;#39;ve discussed this silent point mutation in the wobble position other point mutations can have can happen and they can have severe detrimental effects depending on where the mutation occurs in the genome because these mutations can affect the primary amino acid sequence of the peptide they are called expressed mutations and expressed point mutations so they fall into two categories you have Miss sense and you have nonsense all right these are two examples of expressed mutations expressed point mutations so let&amp;#39;s write that down beautiful missense mutation is a mutation where one amino acid substitutes for another all right so for example here we have CCC which codes for Proline all right but if this C was replaced to an a then we have ACC that that is a codon for 309 so that&amp;#39;s completely two different amino acids a mutation where one amino acid is substituted for another because of a change in the codon because of a result in an amino acid substitution nonsense mutation well this is a mutation where the codon now encodes for a premature stop codon all right look how t-a-c this signals for tyrosine but if that c was was mutated to a g now we have t a g this is one of our stop codons all right all right and so now we&amp;#39;ve stopped reading the MRNA maybe a little too early all right and this results in a nonsense mutation all right or also it&amp;#39;s also called by the way a truncation mutation fantastic so we talked about three point mutations one is silent this has no effect on the protein sequence the two others are expressed point mutations missense and nonsense and they both affect um they both affect the amino acid um the peptides that are formed or can be formed now there&amp;#39;s also frame shift mutations all right frame shift mutations now there the three nucleotides of a codon are referred to as the reading coton reading frame point mutations occur when one nucleotide is changed but a frame shift mutation occurs when some number of nucleotides are added or deleted from the MRNA sequence and this insertion or deletion of nucleotides what is it going to do it&amp;#39;s going to shift the reading frame and that usually results in changes in the amino acid sequence or premature truncation of the protein and this can be this can be much more serious than a point mutation all right so for example let&amp;#39;s say we&amp;#39;ve deleted two amino acids all right they have been removed from the MRNA sequence now the way we read it is this is three and then suddenly these are three and then suddenly these are three and now notice how everything is shifted and notice how many changes in amino acids there already are all right so frame shift mutations can have some serious negative consequences and it can result in some serious mutations all right so these are a couple of mutations that can occur now we can take all this information and the previous chapters that we&amp;#39;ve learned especially the last chapter where we learned DNA replication and we can move into talking about translation and transcription all right and we&amp;#39;re going to start by talking about transcription now although DNA contains the actual coding sequence for a protein the Machinery to generate that proteins actually located in the cytoplasm not the nucleus but DNA cannot leave the nucleus all right so it will be quickly degraded if it does and instead it we will use RNA we have to use RNA to transmit genetic information so that we can use the coding sequence in DNA that code for proteins to actually make said proteins and so what happens is the creation of mRNA the creation of mRNA from a DNA template that is known as transcription and while RNA is on while mRNA is only one type of RNA that carries information while mRNA is only one type of RNA it is this type of mRNA that carries information from DNA directly into the cytoplasm so that it can be translated into proteins all right there are of course other RNA during this process of going from DNA all the way to proteins that help in the process of course we&amp;#39;ve talked about TRNA and rrna and we&amp;#39;re going to our RNA we&amp;#39;re going to see how they play a role in the transcription translation now we create mRNA from a DNA template that&amp;#39;s known as transcription transcription produces a copy of only one of the two strands of DNA during initiation of transcription several enzymes like helicases and Topo and topoisomerases are involved in unwinding the double-stranded DNA and obviously preventing formation of super coils all right the Strand this step is important in allowing the transcriptional Machinery to access to the DNA in particular um translated transcription of a gene of Interest all right so transcription results in a single strand of M RNA synthesized from one of the two nucleotide strands of DNA called the template strand and this newly synthesized mRNA strand is going to be both antiparallel and complementary to the DNA template strand all right so we see it here right we&amp;#39;re gonna unwind the DNA all right and then we&amp;#39;re going to create a RNA transcript from the template strand of DNA all right in eukaryotes there are three types of RNA polymerases but only one is actually involved in the transcription of mRNA all right RNA polymerase 1 is located in the nucleolus and synthesizes rrna RNA polymerase II is located in the nucleus and it synthesizes hrna which is pre-processed mRNA and also some other small nuclear RNA called snrna RNA polymerase 3 is located in the nucleus and it synthesizes TRNA and some rrna now RNA polymerase travels along the template strand in the three to five Prime Direction which allows for the constructed um the the construction of transcribed MRA in the five Prime to the three prime Direction now Unlike DNA polymerase RNA polymerase actually does not proofread its work so the synthesized transcript is not going to be edited whatsoever the coding strand of DNA is not used as a template during transcription why because the coding strand is also complementary to the template strand it&amp;#39;s identical to the MRNA transcript except that all the thymine nucleotides in DNA have now been replaced with uracil in the MRNA molecule all right now in the vicinity of a gene a numbering system is used to identify the location of important bases in the DNA strand so the first base that&amp;#39;s transcribed all right the first base that&amp;#39;s transcribed from DNA to RNA is identified as the plus one base of the gene region anything to the left of the starting point upstream or towards the five Prime is given a negative number everything to the right with positive numbers and transcription will continue along the DNA coding region until the RNA polymerase reaches a termination sequence or stop signal and then that results in a termination of transcription the DNA Helix then reforms and that primary transcript form is termed heterogeneous nuclear RNA or hnrna and then mRNA is derived from that through Prost through post-transcriptional modification so we unwind our DNA we use one we use the template strand to make our RNA sequence complementary RNA sequence all right that&amp;#39;s done now we have our now we have that RNA sequence it&amp;#39;s not rmrna just yet it&amp;#39;s actually called h n RNA or heterogeneous nuclear RNA then it has to go through a couple of post-transcriptional modifications to become mRNA and we&amp;#39;re going to go over those post-transcriptional modifications what are those transcriptional modifications that can happen well there&amp;#39;s a couple before the hn RNA can leave the nucleus and be translated to a protein it has to undergo it has to undergo three specific processes to allow it to interact with the ribosome and survive the conditions of the cytoplasm all right you can think of the nucleus as the happy home of the cell the DNA strands are the parents and the hn RNA is their child but the child has to mature before they let it go out into the wild and survive all right one post-transcriptional process is splicing of introns and extra and exons all right introns and extra exons they&amp;#39;re written right here introns exons so one Prince one post-transcriptional process is the splicing of these so maturation of the H and RNA is going to include splicing of the transcript to remove non-coding regions which one of these is the non-coding regions introns introns are non-coding regions all right so Sometimes some post-transcriptional processes involve removing non-coding sequences and then ligating coding sequences or exons together splicing is accomplished by slicesomes and in the spliceosome small nuclear RNA molecules coupled with proteins known as small nuclear ribonucleoproteins also known as snerps and they together the complex recognize both the five Prime and three prime spliceites of the introns these non-coding sequences are then cut and and remove and then everything else is um kind of like pasted back together all right so they cut out parts of the H and RNA that have that don&amp;#39;t code for anything they remove them they cut them away and then we put together back all the exons the regions that code for something all right so that&amp;#39;s one post-transcriptional process another is called a five Prime cap at the five Prime end of H and RNA molecule we can add a 7-methyl um gunalate triphosphate Cap all right this cap is added and it is actually added during the process of transcription it&amp;#39;s recognized by the ribosome as The Binding site and what it does is it protects the MRNA from degrading in the cytoplasm another thing that we can add is a three prime poly a tail all right this is this is a poly adenosine tail that&amp;#39;s added to the pre three prime end of mRNA transcript and it protects the message also against rapid degradation it&amp;#39;s really just composed of a dining bases um and they&amp;#39;re added to help prevent degradation also increases the stability of mRNA and it facilitates binding of the ribosome to the MRNA in the cytoplasm all right so those are just a couple of um post-transcriptional modifications that convert the H and RNA that transcribed RNA into mRNA that is ready to go out into the cytoplasm and attach and bind to ribosomes so that the protein synthesis process can begin all right let&amp;#39;s reiterate just a few points really quickly going from DNA to DNA all right to replicate all right let&amp;#39;s just make a few notes really quickly before we move on to translation all right whenever you&amp;#39;re going from DNA to DNA what are you doing you&amp;#39;re replicating how does that work well we have new DNA synthesized in the five Prime to three prime Direction all right do not forget that then when you have DNA to RNA that&amp;#39;s called transcription all right we just talked about that that&amp;#39;s transcription all right we have new RNA and the RNA is going to be also synthesized in the five Prime two three prime direction that means the template is read from the 3 Prime to the five Prime Direction and then we&amp;#39;re also going to see here in one second we&amp;#39;re going to see how we can go from RNA to protein and that is called some and that&amp;#39;s something called translation translation all right mRNA is going to be red in the five Prime to three prime Direction all right notice the consistency that&amp;#39;s going to help in Remembering this with this reminder now we can actually officially move into translation once the MRNA transcript is created and processed it&amp;#39;s going to exit the nucleus through nuclear pores all right and it&amp;#39;s going to make it to the cytoplasm once in the cytoplasm mRNA finds a robot ribosome to begin the process of translation which is converting the MRNA transcript into a functional protein translation is a complex process it&amp;#39;s going to require mRNA TRNA ribosomes rrna amino acids and energy so first before we even get to all the juicy stuff let&amp;#39;s talk about the structure of ribosomes because the MRNA is going to have to bind to a ribosome to even begin the process of translation all right the anti the anticodon of the Tiana TRNA is going to bind to the codon on the mature mRNA in the ribosome the ribosome is composed of proteins and rrna in both prokaryotes and eukaryotes there&amp;#39;s a large and small subunit and those subunits only bind together during protein synthesis the structure of the ribosome dictates its main function and that function is to bring the MRNA message together with TRNA to generate the protein in prokaryotes ribosomes are composed of a small 30s unit and a large 50s subunit which combined to form the 70s ribosome that&amp;#39;s what that&amp;#39;s what you see right here prokaryotic ribosomes you have a 50s subunit 30s subunit they come together they form a 70s and eukaryots they&amp;#39;re composed of a small subunit called a 40s subunit and a larger subunit called the 60s unit and they combine to form the ads ribosome all right the small subunit is responsible for binding to the MRNA transcript while the large subunit is responsible for catalyzing the formation of peptide bonds between the amino acids that are brought to the ribosome by TRNA now that we have that understanding of ribosomes and we know that we can take the MRNA that we transcribe from drna and we can use it to translate let&amp;#39;s talk about how translation is the process of translating or converting the transcript mRNA into a specific sequence of amino acids that will grow into a chain of polypeptides there are three steps that we&amp;#39;re going to cover in Translation those are initiation elongation and termination all right let&amp;#39;s go step by step all right initiation is the first step initiation begins when the small ribosomal subunit binds to the MRNA molecule and then it moves along the molecule until it reaches the Stark codon what&amp;#39;s the start codon again a-u-g Ugg all right the start codon is recognized by the initiator TRNA which carries methio9 the initiated TRNA binds to the start codon and then the large ribosomal subunit finally joins the complex and we have now formed the initiation complex all right easy small subunit binds to mRNA looks for the starting codon found starting codon TRNA comes in because it has the same complementary codon to the start codon it binds to it all right bringing in an amino acid this is our first amino acid to start our protein protein formation and of course the large subunit also joins the party now because the large subunit will help in this this alignment of of the TRNA to the right codon and bringing in that right amino acid then during elongation the ribosome moves along the MRNA molecule and it adds amino acids to the growing polypeptide chain so we have trnas that come they bind to their correct codons and they continue to bite bind to their correct codons bringing in amino acid after amino acid that will form a polypeptide chain all right now um the TN TRNA molecule brings these amino acids to the ribosome and they&amp;#39;re added together to the growing polypeptide chain the peptide bonds form between the amino acids as they&amp;#39;re added to the chain all right and the ribosomes are going to move along the MRNA in the five Prime to three prime Direction something that is important to understand in this step is that there are three very important binding sites here there is the a site P site and then there is an e site as well all right there&amp;#39;s an e site as well it&amp;#39;s somewhere here probably all right the a side the a site it holds the incoming amino acid TRNA complex this is the next amino acid that is being added to the growing chain and it&amp;#39;s determined obviously by the MRNA codon within the a site the P site holds the TRNA that carries the growing polypeptide chain all right so the a is the next up amino acid and the P site is already whatever polypeptide chain we have and the a side holds the next amino acid that will be added to the polypeptide chain sitting in the P site all right and then there&amp;#39;s the east side it&amp;#39;s where the now inactivated TRNA pauses transiently before exiting the ribosome and that&amp;#39;s near the end all right it&amp;#39;s like the exiting site and then we have our third and final step of translation that&amp;#39;s termination it occurs when the ribosome reaches a stop codon release factors recognize the saw up codon and they caused the ribosome to release the polypeptide chain and dissociate from the MRNA molecule all right that polypeptide chain then can fold into its final three or three or four dimensional structure and the protein is ready to carry out whatever specific function it needs to carry out all right and that is translation all right small subunit binds to mRNA looks for start codon we bring in our amino acid to um to the a site that&amp;#39;s the next upcoming amino acid all right and then we bring in the next one all right and we&amp;#39;re forming bonds between the amino acids that are all held together in the P site and then when we reach a stop codon all right then we stop translating the MRNA the final form of the polypeptide is released and translation ends all right now just like there is post-transcriptional processing there is also post-translational processes all right there are things like phosphorylation which is the addition of phosphates by protein kinases to activate or deactivate the protein that we&amp;#39;ve made there&amp;#39;s carboxylation addition of carboxylate acid groups that usually are there to serve as calcium bindings spots there&amp;#39;s glycosylation addition of oligosaccharides as proteins pass through the ER or the Golgi apparatus there&amp;#39;s many other things that can happen um post translationally to the protein to either activate or inactivate it whatever is needed all right now with that understanding of transcription and translation we want to understand how prokaryotes and eukaryotes control gene expression and we&amp;#39;re actually going to start first with control of gene expression in prokaryotes all right we&amp;#39;re going to start by defining operons operons are a cluster as there are a cluster of genes transcribed as a single mRNA and we have this model called the Jacob monad model it&amp;#39;s a model that&amp;#39;s used to describe the structure and function of operons and prokaryotic cells the model proposes that operons consist of a regular a regulatory Gene called a promoter and one or more structural genes and the regulatory Gene codes for a protein known as a repressor which binds to the operator region of the operon and it prevents transcription of the structural gene the promoter is the region of DNA to which RNA polymerase binds initiating transcription of the structural genes in the presence of specific inducers the repressor is activated and the transcription of structural genes can then occur and this model actually helps us explain how prokaryotic cells regulate gene expression in response to in to changes in their environment now there are two types of operons there are inducible systems and there&amp;#39;s repressible systems in inducible systems the repressor is bonded tightly to the operator system and therefore thereby acts as a roadblock so RNA polymerase is actually unable to get from the promoter to the structural gene all right because the repressor is in the way to remove that block an inducer has to bind to the repressor protein so that the RNA polymerase can move down the Gene and a good example of this is the Lac operon all right this is one way of controlling what is transcribed and when it is transcribed a repressible system allows constant production of a protein product the repressor made by the regulatory Gene is inactive until it binds to a compressor and this complex then binds to the operator site to then prevent further transcription so it creates it transcribes until it&amp;#39;s told not to a good example of this is the trip operon all right that&amp;#39;s a good example now what about eukaryotes for eukaryotes it&amp;#39;s obviously much more complicated we have transcript transcription factors that search for promoter and enhance the regions in DNA promoters are usually within 20 base pairs of the transcription um start site and enhancers are usually they&amp;#39;re more than 25 base pairs away from the start the transcription start site all right so those are ways for controlling so transcription factors they&amp;#39;re transcription activating proteins that search the DNA looking for specific DNA binding motives and they can bind to a specific nucleotide sequence in the promoter region or to a DNA response element um and um and there&amp;#39;s promoters that are within 20 base pairs of transcription um and then there are enhancers which are within 25 base pairs away from the transcription site and those allow for the control of one Gene&amp;#39;s expression by multiple signals all right that&amp;#39;s all I have for review for this chapter next video we&amp;#39;re going to do some practice problems let me know if you have any questions or comments down below other than that good luck happy studying and have a beautiful beautiful day future doctors

Transcript for:RNA and the Genetic Code

Transcript for:
RNA and the Genetic Code