D1.2 HL Protein Synthesis [IB Biology HL]

this is the video for the higher level content from D 1.2 on protein synthesis just like with replication transcription and translation can only happen in a five Prime to thre Prime Direction so let's blow up this picture of transcription for a moment shall we what we'll see is that the five Prime end and the three prime end of the RNA molecule are situated to where the growing end of mRNA is the three prime end new RNA nucleotides can only be added to that three prime end that directionality of five Prime to 3 Prime also applies

to translation in Translation the ribosome is going to move in this direction from the five Prime end of the MRNA to the thre Prime end of the MRNA transcription and translation produce proteins and proteins are coded for by genes genes again are segments of DNA that code for a specific protein at the beginning of a gene we will find a short segment of Base sequences called the promoter so this serves as a binding site for either RNA polymerase or other factors that control transcription this is again at the beginning of the gene so if transcription

were going to take place then RNA polymerase would bind here and start using the anti-sense Strand as a template for transcription transcription factors are proteins that can regulate genetic expression and the way that they do that is they bind to the promoter so I'll do these in blue and the promoter in yellow these transcription factors are molecules that are going to regulate transcription by either promoting transcription like saying hey let's transcribe this gene or inhibiting it and so it can inhibit transcription by preventing RNA polymerase from binding so these again are called transcription factors the

promoter itself does not get transcribed again it's just the starting point and it's also a great example of a non-coding region so noncoding means that it does not code for a polypeptide and therefore is not a gene genes code for polypeptides we have lots of Base sequences in fact most of our base sequences in our genome are not genes they are non-coding regions base sequences that code for something else and this might include base sequences for how to produce TR RNA or R RNA even though those are important they are not polypeptides this could include

those promoters again they don't get transcribed the telr teirs are these very cool struct pieces of structural DNA at the ends of chromosomes so chromosomes kind of look like this right um in their replicated form you might be more I don't know you might recognize them more in the replicated form this classic X shape telr and let's do them in let's say green telr are like these little caps at the end of a chromosome okay and those telome are structural DNA that prevents damage especially during like mitosis and then introns introns do not get translated

into a polypeptide they're actually edited out after transcription and keep your eye on that one we'll go into more detail here in a bit let's take a look at this procario in this Pro carot transcription and trans translation are actually happening simultaneously so as that mRNA is being synthesized the part that's already built is getting translated by the ribosomes this is super efficient but it does not allow for post transcriptional modification so remember transcription is going to produce mRNA in posttranscriptional modification we will modify that mRNA and this can only happen in ukar because ukar

are compartmentalized that means that there is a nucleus separating the area where transcription is happening and the area where translation is happening out here in the cytoplasm on the ribosomes now why do we care because editing that mRNA allows us to make lots of different versions of a protein using the same gene let's use the alphabet as an example here so let's say I have all the letters of the alphabet and I cut out all of the letters except for c o and W okay so I have just spelled the word cow I can take

the exact same sequence of letters the exact same alphabet and by eliminating a different combination of letters I can make an entirely different word and I can continue this pattern in this example I could even I've just been making three-letter words you could even make words of different lengths so again much like this alphabet when we take mRNA and we cut out different sections we can make different versions of that mRNA which will be translated into different amino acid sequences even though they were all transcribed from the same Gene so the MRNA that is made

from transcription contains both exons and introns introns are going to be removed before this mRNA leaves the nucleus to be translated so just like we were removing letters of the alphabet these introns are also going to be removed they are edited out of that mRNA and the exons are spliced together so this is an important um bit here again if you take out different introns you're going to create a very different sequence okay so introns I know this is hard it sounds like introns should stay in the MRNA but don't think of it like that

think of it as this mRNA eventually once to exit the nucleus and only the exons can exit with it the introns w w they get cut out and they have to stay in the nucleus that's how I think of it so once that splicing has taken place we're also going to see the addition of a five Prime cap this is going to help protect the MRNA as it's moving through the nucleus and a poly a tail and it's exactly what it sounds like it's this very long string of nucleotides that all have adenine as their

um nitrogenous base this can vary in length so I often won't actually draw it like that I will just say that it is a poly a tail so a meaning addine poly meaning many so our poly a tail will go on the three prime end of our mRNA molecule and this is what we now call mature mRNA so mature mRNA is splicing out those exons um adding sorry getting rid of those introns splcing together the exons adding that five Prime cap and the poly a tail and again if you remove different introns then you're going

to end up with different sequences in your mature mRNA and this is called alternative spacing okay it allows you to produce different versions of a protein all from the same gene because you edited the MRNA in different ways all right and so we see this a lot in how um cells make different antibodies and there are lots of applications here all resulting in a wide variety of polypeptides or proteins being able to um be synthesized from a single Gene now that we've added a bit more detail to the process of transcription let's do the same

with translation in the standard level portion of this topic you learned that tRNA molecules bring their amino acids to the ribosome right they're transferring that amino acid but we need to have a good understanding of how that TRNA attaches to its amino acid in the first place and this is all due to an enzyme called the TRNA activating enzyme you are allowed to call it by that name however you will also notice that some sources call it the amino AAL TRNA synthetase enzyme don't be afraid of that it's exactly what it sounds like it is

an enzyme that is going to attach an amino acid to a TRNA molecule so it attaches the correct amino acid you will notice that there is a different TRNA activating enzyme for each amino acid here is the one that is specific to the amino acid called methionine when the TRNA activating enzyme attaches this amino acid to the TRNA this is going to require ATP so let's take a more simplistic view TRNA like all RNA molecules is single stranded it's just kind of looped in on itself but it's still one strand and just like any other

nucleotide it has a five Prime end and a thre Prime end and just like nucleotides amino acids can only attach to the three prime end so we need this amino acid to attach up here to the TRNA molecule now I can redraw this line here we like this we need that attachment to take place but that's going to require two things it's going to require that TRNA activating enzyme and it will require ATP so the amino acid ATP and the TRNA will all sit in on the active sites of this enzyme and the enzyme will

catalyze the reaction that results in the attachment of the amino acid and it will cleave these phosphate groups from the ATP in order to get the energy needs to make that attachment when the amino acid is attached we say that the TRNA is activated you may also see it written as charged it doesn't mean charge is in positive or negative it just means it's ready it's activated it has the amino acid attached once that TRNA activation has happened we can begin translation in Earnest so the TRNA carrying methionine is going to attach to the small

subunit of the ribosome methionine corresponds to this start codon it will always be the first amino acid in that chain that small subunit of the ribosome that again has this TRNA is going to slide down the MRNA molecule until that complimentary anticodon is attached to the codon on mRNA so we have a start codon reading Aug and once it finds that complimentary anti-codon the ribosome will stop right there at that point the ribosome will finish assembling by adding the large subunit so the large subunit of the ribosome will bind with the small one and we

are now ready to begin notice for this first TRNA it's sitting not in the a site but the pite site okay so that will be important but this is how translation begins and we call this phase initiation and you already know the rest of the story from the standard level content again then the next TRNA will bind with the as site we'll get a transferring of this polypeptide chain through the synthesis of a peptide bond and this cycle will repeat again moving down the MRNA in a five Prime to three prime Direction until a stop

codon is reached so far in this video we've talked about more details in transcription more details in Translation and now we're going to look at what happens to these polypeptides after they've been translated a polypeptide becomes a protein when it is modified and folded into its final functional shape and this can include lots of different things it could include the removal of that methine or even whole sections of amino acids which we'll look at in a moment it could entail the modification of some of the r groups on the amino acids folding into tertiary structure

or creating quinary structure by combining with other polypeptides we see that here in this example of hemoglobin right where I have 1 2 3 four polypeptides combined together or we could add non-polyp tide components um and that's a process called conjugation so like I see these heem groups here there's a whole other topic on proteins which I suggest you take um a look at if you want to know more about things like tertiary structure um or folding into functional shapes the production of insulin is a great example of modification of poly peptides into their functional

State now insulin is a polypeptide hormone produced by the beta cells of the pancreas but when it's first translated it's we don't call it insulin it's preproinsulin and it's not insulin until it is modified the insulin Gene actually codes for 110 amino acids and you can see them here in this chain in the modification procedure the ruar is going to remove 24 amino acids okay and this is going to form proinsulin so we re we've removed this poly this part of the polypeptide it then folds into tertiary structure by forming disulfide bonds okay so these

are our group interactions and so this change is going to fold into a three-dimensional structure some amino acids are going to be removed from the middle so these amino acids here are going to be edited out okay and we're going to be left with two linked chains so these two right here mature insulin has these two chains held together by the disulfide bridges and now we're left with only 51 amino acids so we've covered two of those modification steps removal of some of the amino acids and folding into tertiary structure and this is how you

get mature insulin proteins do not tend to last very long inside of cells they're very quickly transformed either they're denatured and we need to make a new one or they're just not needed anymore and so they need to kind of get recycled and for that we rely on a structure called a proteosome proteosomes are an enzyme complex that are going to take proteins and break them into short polypeptides okay so these shorter poly peptides can then be further broken down into individual amino acids and then what's really cool is they get recycled right because when

the cell needs to build a different protein it needs those amino acids so we're taking small amino acids putting them together to make a functional protein when we're done with that protein we take them apart we create amino acids again and it all Cycles through of course like anything else in biology this requires enzymes and ATP so we want to keep our eye on that um and that'll conclude this video on protein synthesis