what's up ninja nerds in this video today we're going to be talking about translation or protein synthesis but

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academic journey all right ninja so let's start translation when we talk about

translation we have to have a basic definition of what the heck it is and that is you're taking rna in this

case what type of rna we really is our primary one that we're going to focus on mrna we're taking that mrna

that we made from dna what was that process called transcription so we're taking the mrna

that we got from dna and now we're going to make proteins that is the process of translation

taking rna and making proteins there's so many different types of rna the three main ones that i need you guys

to remember that are crucial for translation is mrna trna and rrna and we'll go through these

as well as a couple other things before we get into the phases of translation the first thing that we need to talk

about is this concept of the genetic code okay it's really simple it's not as like

scary as it seems a little boring but we're gonna make it fun the first thing you need to know is here

we have a molecule of mrna right so this is our mrna now mrna is very

very important for this translation process right messenger rna messenger rna it has a very specific

sequence of nucleotides if you will that are in these triplet forms you see how this is a

there's three little lines there that line is a nucleotide that's a nucleotide that's a nucleotide so

there's three nucleotides there and we have a couple of these spanned along the length

of this mrna molecule right and the other thing you need to know is the orientation

right so a little bit about the topology of the mrna on this end i'm going to have a five

prime cap do you guys remember that whole process we talked about in post

transcriptional modification this is the five prime end on this end you have the three primate and we

had on this side do you guys remember what happened here in the transcription process we've added

the poly a tail on that end right so on the mrna you have a five prime end a three prime end

and sequences of nucleotides within it these sequences of nucleotides that are in these

triplet forms along the mrna are given a very special name that you need to remember

and these are called codons so let's write that down so these things these triplets let's put down

triplets triplets of what triplets of nucleotides okay and you guys need to remember the

nucleotides and rna are different than the nucleotides in dna

let's write down primarily the nitrogenous bases that are associated with rna

what are they we'll represent that by kind of just the single letter abbreviation one is

you have adenine right that's one of the nitrogenous bases in rna then you have guanine

cytosine and uh what else if you guys said thymine i'm gonna be really upset with you it's not thymine

it's uracil in rna it's uracil that's the big difference between dna it has thymine in rna it has

uracil okay so we have codons are triplets of nucleotides what

type of nucleotides nucleotides that contain these four nitrogenous bases okay now here's the next thing i need

you guys to know we know what they are how many are there let's take this let's do a little bit of

math i know it's a little boring let's take and do a little bit of math here we have the triplets we described that what

those triplets are made up of and let's talk about how many of these triplets

of these four nucleotides you can have well there's four total nucleotides right so let's put a four here four

different types of combinations of nucleotides each one of there's three of these

nucleotides in a codon so if i take four raise it to the third power

what does that give me 64. 64 possible codons based upon the four nucleotides i have

and that there's three nucleotides in that codon so that means that there are 64

different possibilities of codons okay so what do we need to know here that there's 64 different types of

codons now we've got to talk a teensy little bit about the different types we're not

going to go through every single one of them that's unnecessary you'll have these if you guys don't go

into the back of your textbook like an appendix you'll have the entire genetic code that

you guys can look at there's no need to memorize them but need to know a couple things about

these 64 different types of codons and what should you know the next thing you should know is that when you take

these 64 codons okay that are triplets and we'll kind of talk about them

61 of those codons read you read them right and we'll give you an example here for an example

let's give you an example now let's say i take a codon right which is a triplet and it contains

one of these three of those nucleotides let's use the example a u g that's a codon

if i look in the back of the textbook at that genetic code kind of thing and i see aug it's going to code for an

amino acid and that amino acid is very specific to that codon

and so what type would it be this one's an easy one to remember and this is probably one of the few that

you should remember and memorize but this is methionine and methionine is an amino acid

so out of the 64 codons 61 of them right in this kind of form three nucleotides which there's so many

different types of possibilities will code for an amino acid i'm just giving you an example

so out of these 61 codons they code for an amino acid so very important to remember that

okay out of the remaining how many are remaining 61 there's three codons left that we

have to talk about these other three codons do not code for an amino acid they

code for terminating the translation process and these are called stop codons and

we'll get into these a little bit more in detail when we go through the phases of translation but

you can remember these by the mnemonic or kind of like the phrase if you will a little memory trick

which is you go away you are away you are gone these do not code for an amino acid

so in other words if i were to look in the genetic code in the back of the textbook these would

not give you a particular amino acid they would stop the translation process so that's important and we'll go over

what that kind of looks like a little bit later so basic concept i want you guys to get

out of the genetic code particularly is mrna contains codons codons are made up of

nucleotides how many three what are the particular types of nucleotides they have to contain adenine guanine

cytosine and uracil there's how many different types of codons so many 64. do you need to know

all of them no out of those 64 61 of them code for amino acids you can look at all

those up in the textbook three of them do not code for amino acids they stop the translation process

that's all i want you to know about that the other aspect of the genetic code is that we need something that's going

to carry so we said that these codons code for amino acids how the heck do they do that

you guys should be asking that question there's another molecule called trna right what is it called

t rna transfer rna transfer rna if you guys kind of look at the structure of it

it contains what's called anticodons let's write that down so it contains anti

codons okay that's the first thing what the heck are anticodons it's really simple anticodons

are a triplet all right so three nucleotides that are complementary to the codons in

mrna that's it so what are they they are a triplet of nucleotides

that are complementary to codons in the mrna that is it

the other aspect of this is there's some enzymes we'll talk about a little bit later

so there's a funky little enzyme that'll come in it's kind of like a little bit it's a little gropy

grabs the anticodon portion reads it says okay i got the anticodon there all right so i

know what it is i need to find an amino acid that is very specific right to the codons that this anticodon is

complementary to so let's give the example here let's say the codon that you have an anticodon

complementary to is this one aug okay so let's give the example here that you have a codon

we're going to use this example here so let's say here we have a codon and the codon is aug

what would the anticodon be has to be complementary to this so the anticodon

for this example would be u a c right because that are copper complementary to each other right

you guys remember that that if it's a that's complementary with u that g is complementary with c and

technically these should be triple bonds right so this would be a is complementary with

u u is complementary with a and g is complementary with c so we'll go u

a c what will happen is the trna enzyme that'll come in we'll talk about later it'll say oh uac

that's complementary to aug if i go into my genetic code because it's got all of it in its head this enzyme

it says aug is specific for what amino acid methionine so then this enzyme takes and we use a

particular amino acid domain we'll call it there's a specific amino acid domain

on this trna that we'll talk about and that is going to carry the amino acid specific to this

codon what was the amino acid methionine so it'll carry the methionine in this example

now let's talk a little bit about this kind of like anatomy or structure of the trna that kind of

coincides with what we just talked about if we take the trna the first thing is where are the anticodons

the anticodons if you look at a trna kind of has the shape of a t in a way right

on this portion this bottom loopy portion this right here is where you'll have your anti-codons

on this portion so this is the part of the trna that'll interact with the codons in the mrna the

next portion here is you have another loop i'm not really too worried about you knowing about

these loops this portion here though okay this is called the

five prime end of the trna so what would be on that end what group hydroxyl group or phosphate group

engineers phosphate group this end over here which has like the little copper loopy thing

is the three prime end three priming contains what oh phosphate group contains the hydroxyl

group or the oh group but there's also a very specific sequence of

nucleotides that are in this area of the three prime end which hold on to the amino acid this is the amino acid

holding domain and this is containing c c a so we'll put the three prime c c a

domain or region on the trna what is this portion the little cup that holds on to what

we'll bind in here so here we have c c a it'll bind on to the amino acid in this case it was what

the finding if the anticodon is uac which is complementary to aug holy crap we went through all of

that all right so the next thing we're going to talk about is the characteristics of the genetic code i

don't want to go too long into this let's just breeze over really quick but it's things that can be asked in

your exam so you should know it when we talk about the genetic code all the stuff we talked about with the

codons the anticodons the mrna tr and all that good stuff when we take the mrna and we read it

right from five prime end to three prime end for the most part there's a couple

exceptions you start at the five prime end and you go to the three prime end continuously

you don't like have any stops or anything like that so in that way when we talk about the

genetic code this translation process understanding the genetic code

is what's referred to as kamalas so what does that mean here's a codon right

i'm going to read this codon utilizing the trna and the ribosomes and i'm going to give an amino acid then

i'm going to go to the next codon read that make amino acids and i'll keep going down this way going

through each sequence of three nucleotides are a triplet now

what does this mean that it's homolos let's say that i read this codon read this codon and there's a couple

nucleotides in between to between this next codon that i want to read i don't

skip these nucleotides and go to the next codon okay so this this thing does not happen

you don't go three nucleotides read through nucleotides next and then

skip a couple nucleotides and go to the three next nucleotides it's consistent this does not happen in

the genetic code or the translation process the only exception to this is viruses they're the only

exception so we'll put exception to this where they can have some type of translation

process that does have commas in it or you kind of skip a couple nucleotides okay

the next thing that we need to know about the genetic code is that not only is it

kamalis but it's non-overlapping what does that mean that means that when i read these

again five prime to three prime i'm gonna read it all the way down continuously

i'm gonna read this codon give an amino acid read this codon give an amino acid what i'm not going to do is read this

codon give an amino acid but then let's do a different color start here at the second nucleotide read

these three and give an amino acid now let's do one more color start at this third nucleotide after and

read here and give an amino acid that does not happen

in the translation process according to the genetic code there is one exception and again that exception

is that this overlapping process can occur in viruses that is the only

exception okay so the when someone says can you give me characteristics of the genetic code you

will say it is comless it occurs continuously from five to three and non-overlapping continuous

from five to three the only exceptions are viruses that's it the next thing that you need to know

is a little bit more important than this gibberish up here

and that is that the genetic code is what's called redundant so it's redundant

and it's degenerate okay so it has degeneracy or it's degenerate so let me explain what that means let's

say i have a couple codons and i'm going to actually give specific nucleotide sequences to i'm going to

give this a nucleotide sequence of a u a a u c and a u

u okay now here's what's really interesting about these i have three different codons these

three codons you would probably say each one of them codes for you know a different amino acid but you'd be wrong

and that's where redundancy or degeneracy comes in if you guys look in the back of your

textbooks or the appendix where the genetic code is if you were to look there is a amino

acid called isoleucine and if you take isoleucine and you try to track back to

its codon you'll find that it has three different types of codons that can actually code for it

and that is a u a a u c and a u u that's really interesting so that

tells me that i could know the amino acid that i'm making but i won't be able to track

it back to one to the specific codon there's two exceptions to that and that is um

if you truly want to know it the only exceptions to this concept of redundancy or degeneracy

the exceptions are methionine so we'll put here methionine and what's called tryptophan

and here and let's i want you guys to think about why these would be exceptions because it actually does help

methionine there was only one codon what was it aug tryptophan only has one codon

you know you don't need to know this but it's ugg there's no other codons that code for

these amino acids they're just one so they're the only exceptions all the other amino acids

have multiple codons that code for it so that's the concept of redundancy now here's the thing

you guys are like how the heck does that happen i asked this question when i was learning it

so let's take an example here let's say here i have my mrna right and again this is my five prime

end this is my three prime end of the mrna let's say i start here and i'm going to

go in sequence here so the sequence is which one let's kind of keep these colors

we'll do red here for the mrna so this is going to be which ones a u a a

u c and the next one is a u u how the heck does the trna do that in a particular way does each

anticodon have to be different because i thought they have to know the trna the enzyme

that we talked about kind of like a little bit said it has to read the anticodon and it

has to be complementary to the codon to give me this amino acid how does it do that

here's the way it does it there's something called the wobble effect wobble baby wobble baby wobble right and

it's called the wobble effect or the wobble phenomena let's write that down and let's talk about what the heck that

is so let's take and this is particularly for the trna that kind of allows this

process to occur it's pretty cool so where's the anticodon on the trna here's our trna

where would it be on this bottom loop what would it have to be specifically

you would say oh complementary to a is u complementary to u is a complementary to a is u but here's where

it's different on this position what was this point here on the trna at this point here

this was the five prime end right what's this portion here the three prime end so going from five prime of the trna to

the three prime of the trna right because if you kind of follow this down like that

so you start five prime this would be the first position this would be the second this would be

the third position and then you continue to work your way back up on this first position on the five prime

end it's actually containing a something called inocine

you're like what the heck believe me i thought that too so the same thing we'll talk about what

that does in a second but let's go to the next one same thing you'll read this here you have your five

prime three prime and it'll have come down the first one will be ionosine

and then what will you have what's complementary to you a what's complementary to a u do the same

thing over here start at 5 three prime for the trna work your way down first one has to be

i next one will be what a and the next one will be u let's explain what happens with all this do you notice

a difference here remember i told you that the enzyme has to read that anticodon it

has to be complementary to the codons in the mrna to pick the correct amino acid

well do you notice how all these are dif they all differ in that third position on their codon and they differ on this

kind of like first position in the anticodon here's how this happens ionosine okay that i

i'm representing with is actually called ionosine ionosine is not talked about too often in the watson and crick model

you know in your dna stuff the interactions complementary stuff ionosine is complementary to

adenine ionosine is complementary to uracil ionosine is complementary to cytosine so whenever you have something

like this where the third position is a c and u on the trna they can have an ionosine

that can be complementary to a complementary to you and complementary to c

and still give you the same amino acid which would be what i already told you this will be

isoleucine isoleucine isoleucine okay so that's called the wobble effect

you're probably like why the heck do we do this why don't we just make it specific to each

of these types of um you know codons why don't we just make it u a u u a g

uaa why don't we do that the reason why is the wobble effect reduces the risk

it decreases the risk of mutations so what do i mean by it can decrease the

risk of mutation it can and specifically it can decrease the risk of mutations

how does it do that it's all based upon this fact that if i have any mutations in the dna

that'll lead to mutations in the mrna and if there's mutations in the mrna i'm going to have changes like substitutions

or things like that in the codons and if i kind of substitute or switch up

some of the nucleotides i'll code for a different amino acid particularly

so if i have a little bit of that wobble effect i have a little bit of you know wiggle room in that that first position

on the trna i may reduce the risk of giving a wrong amino acid

leading to a abnormally structured protein so that's kind of the big effect here

is when we talk about redundancy or degeneracy it's that one amino acid can have multiple codons

with just these two exceptions and how does that work via the wobble effect in trna where on that first

position on the five prime end of the anticodon it is an ionoscene which has multiple

complementarities with a uc whole purpose of this is to decrease the risk of

mutations so when we're talking about when i'm mentioning all this stuff about the genetic code and you can look in

your textbooks i use marieb kind of a human anatomy physiology book and again you can find

the in the appendix all the information about that genetic code but you can find this in various

textbooks campbell's biology as well but again i'm just referring to in any book you'll have that appendix to talk

about the genetic code so that you guys know what i'm talking about here all right so we got a

pretty decent idea about the genetic code right i'm talking about codons anticodons and some of the features of

it our characteristics the next thing i want to talk about is trna a little bit

and i want to go through something called trna charging we'll review the structure of the trna

really briefly as a nice like little review but we're going to talk about this process called trna charging which

is very important when we talk about the translation process

so here we have our trna molecule right so this is our trna transfer rna tiny little guy right

again what is this end here it doesn't have the little kind of like little socket or pocket there where the

amino acids bind what is this end this is your five prime end what's this end

this is your three prime end which contains the oh group but particularly what nucleotide

sequence cca what binds here this is the amino acid kind of like binding domain if you

will so this is where an amino acid will bind correct now this arm was the one i really wanted you

to focus with we had the three loops we'll briefly talk about these other two loops not

super worried if you guys know it but here in this bottom loop what do we have down here

on this bottom loop you contain the anticodons and the anticodons will be in a triplet

form and these triplets can be in the form of again containing nitrogenous bases like

what adenine you know adenine guanine uracil and the cytosine okay so again this

portion here will be what this will be the anti-codon portion okay the last thing here is

these two little arms or loops and this little thing that's kind of like sticking out the side

this portion here near that three prime end this is called the t arm so what is this

portion here called nor the three prime end this is called the t arm

the t arm what you really need to know about this is that it tethers the trna to the

ribosome that's all i want you guys to know is that it tethers

the trna to the ribosome so it kind of is one of the big things that allows for interaction between the trna

to the ribosome okay that's it this other arm over here this loop near the five prime end

this is called the d-arm and the d-arm is what allows for the identification of the trna by

the enzyme called trna the aminoacyl trna synthetase so it allows for

identification identification of the trna by what's called the uh we'll just a br

we'll kind of a basic thing trna synthetase enzyme okay so basic concept here you have the five

prime end then you have the first arm which is the d arm it allows for the identification of

the trna by the trna synthetase anticodons on the bottom loop t arm is near the three prime end that

allows for the trna to interact with the ribosome three prime end has the

cca domain which allows for it to interact with amino acids this last thing here i'm not really

concerned if you guys truly know it it's the invariable domain it's uh it can i mean it can

actually it's the variable domain it can change from trna to trna nothing too big to know about that

portion okay so if the basic structure of the trna the next thing i need you guys to know

about is called charging so this is really simple it's basically talking about

how do we get the amino acid to bind on to that three prime end that's all it is and it's really simple here i have an

amino acid okay so here's my amino acid and let's let's use this example that we've

continuously been using a lot let's say that we're con we're going to start the translation process

and let's just pretend for example here's my mrna okay let's use this example that this is

a u g what would the anticodons be if we were to kind of write them in here

if it was aug it would be u a c what is that aug code for methionine we've already said that multiple times

right so let's say here's our here's our example this is our methionine we'll

just abbreviate it as met okay what we're going to do is the first step we're going to do in this process

is we're going to add an atp molecule onto it we're going to add an atp molecule onto the methionine

so let's say that here i use an atp and i add it into this process here okay then what i'll have here is i'll have my

amino acid and what happens is when atp gets added in it actually we break two of the

phosphate groups off of the atp okay so if we break two phosphate groups off that gives you

what's called a pyrophosphate and so the only thing that's kind of hanging onto this amino acid

is an amp they want you to know these kinds of names of it right so when i take this

amino acid and add on an amp it's called i know it's annoying it's called the

amino acyl amp molecule okay then here's the next thing

we have this aminoacyl amp and we have that three prime kind of amino acid domain with the cca portion

imagine we draw a big old enzyme here so here's this enzyme okay here's this enzyme

this enzyme has in one end is holding the trna right so it's holding that trna molecule

so we're just gonna we're gonna draw a very generic structure of it here's gonna just be this process here okay so

here's the generic structure and we'll just kind of show that this is our three prime end right there

okay just generic it's holding in one pocket this trna molecule in the other pocket

it's holding the amino acid with what bound to it the amp then what it does is it basically just

says hey let me make sure that this anticodon is appropriate

is it appropriate to the mrna codon that we need oh it is good clicks them together

and so it takes and adds that amino acid with the amp onto the three prime cca region

so let's draw the little cup what was that little cup thing the cca portion it'll add on this reaction will occur so

we're going to just fuse these two things together and when we fuse these two things together what

do you get you'll get this structure where all you'll have the trna

with the little cup and what will be kind of sitting in that little pocket there

the amino acid and what amino acid was this in this example methionine in the process though do you

see amp still bound to it no so what are we going to do

we're going to release the amp during that process okay what you need to know is what the

heck is this enzyme this enzyme is called the amino acyl trna

synthetase i kind of quickly abbreviated it for you like a shorthand version of it when we

talked about with the d arm that's the enzyme i'm really referring to is the amino acyl trna synthetase

and if you really wanted to remember what part of the tna is keeping it kind of like identified

the d arm of the trna will allow for it to be identified okay so to recap really quickly

i want to take the amino acid put on the three prime end what do i have to do first thing take the amino acid add an

atp onto it i'll pop off a pyrophosphate so i'm truly only adding a amp

that's called an aminoacyl amp a amino acyl trna synthetase will come in have two pockets in one pocket it will

hold the amino acyl amp in the other pocket it will bind the trna with no amino acid

it will read make sure that it's the proper anticodon that is complementary to the codon of mrna

click them together when it clicks them together it puts the amino acid on the three prime in and

spits out the amp now what do i have a charged trna so what is this thing here called

this is called a charged t rna okay

that's the process that's all i really want you to know out of this okay so let's now move on to the next thing

which is saying okay we've already talked about mr now we talked about codons anticodons some features we

talked about trna charging now we need to get into these things called ribosomes a little bit all right

so now let's talk a little bit about ribosomes and what are their kind of significance because we're going to go

into all these phases of translation it's all going to make sense it might seem a little bit scattered right now

but i promise we're really building our foundation so we truly understand the translation

process so the next thing we need to talk about is these ribosomes ribosomes are

definitely very very crucial for translation as well as the mrna and the trna

but some of the things that you guys need to know particularly is the difference in ribosomes between

eukaryotic and prokaryotic cells and there is a very brief clinical significance that we'll

talk about with that so let's say here i have ribosomes and they're interacting with the mrna

they will interact with the trna but we're going to talk about these specific differences between

eukaryotes and prokaryotes because this is something that you guys will be asked

eukaryotic cells when we talk about ribosomes they have two subunits okay we're going to say this subunit up

here is bigger than this one down here right so it's pretty straightforward this

is the large subunit or ribosomal subunit and then this one down here is the small

ribosomal subunit okay now these have different ways that we can kind of like describe

their size okay large and small according to a zved zvedberg unit

and eukaryotic cells that zvedberg unit for large rebels almost sub units are called 60s large ribosomal subunits

and the small and eukaryotic cells are called 40s ribosomal subunits but we sometimes

generally in textbooks refer to them as ads ribosomes and eukaryotic cells you're probably like zach

that those numbers do not make any sense 60 plus 40 is a hundred zach what are you losing your brain

i promise you the there the way that they do this via this vedburg unit gives you an ads ribosomal subunit for

eukaryotic cells and prokaryotic cells it's the same concept again we're not going to write

these down but this is your large here we'll put large ribosomal sabine small ribosomal

subunit and prokaryotic cells the large one is a 50s ribosome

and then in prokaryotics the small is a 30s ribosomal subunit and you're probably like oh that's going

to give you 80. nope according to this vedburg units it gives you a 70s

ribosomal sub ribosomes in prokaryotic cells you're probably like okay is that cool

i'm glad that i know that now why do i need to know that before we talk about why you need to know that the

next thing i need you guys to remember is what are ribosomes made up of you guys need to remember this

ribosomes contain a very specific kind of molecule if you will that's kind of a sitting and

a part of it very integral to its structure what is this it's got little like nucleotides on it

it's rrna so ribosomes contain two different types of things that make them up

it's equal to r rna and what else proteins so proteins so when we're talking about remember

when i said in the beginning translation requires three types of rna mrna trna and rrna we usually just say

ribosomes but ribosomes contain rrna and proteins now why did i spend the time talking about all this

stuff a common clinical relevance here is that they

love to say when you're talking about prokaryotic cells prokaryotic

cells okay we can use different types of antibiotics to target these ribosomal subunits and prokaryotic

cells for example if i give someone an antibiotic like an aminoglycoside and there's so many

different types of these but the commonly one that you need to know is like gentamicin

and another one called tetracyclines and there's a bunch of different types of these doxycycline

tetracycline minocycline all those these love to target and inhibit the translation process by affecting the

30s ribosomal subunits so they inhibit the activity of the 30s ribosomal subunit in prokaryotic cells

the other antibiotics is going to be particularly not the aminoglycosides and the tetracyclines

but let's say that we're talking particularly about something called macrolides

and these are things like azithromycin clarithromycin erythromycin these love to target and inhibit the

activity of the 50s ribosomal subunit and prokaryotes which inhibits protein synthesis think

about this prokaryotic cells like bacteria let's use this example like bacteria need

proteins in order for them to function if you give an antibiotic if a bacteria is infecting a particular tissue you

give them an antibiotic something like an aminoglycoside a tetracycline or a macrolide

it's going to inhibit these ribosomal subunits you can't now use them to make proteins if you can't

make proteins the bacteria will die so you see how there's a clinical relevance to something at the molecular

level okay we've gone through all the players that we

really need to understand and know for translation we went through the mrna we went through the trna we went through

the ribosomes and the rrna now let's head home and talk about the phases of

translation all right so we're going to talk about the phases of translation we've really built up our foundation to

understand translation now so there's three phases of translation the first phase that

we're going to go through is called initiation so what's the first that we're going to

talk about here called the first phase we're going to discuss is called initiation of translation and

it's probably like it's really it's it's not that hard it's a really simple step

we have to kind of discuss though the differences between prokaryotic initiation and translation

and eukaryotic initiation and translation so let's first talk about prokaryotes

because they're easier so here's our mrna right and on the mrna again what do you have

you'll have a five prime end and you'll have a three prime and let's just kind of uh write here now

that this is specific for prokaryotes okay we're talking about this for prokaryotes right now

let's say here on the prokaryote is my start codon and what are your start codons

we didn't talk about that yet did we but there is a particular star codon we kind of talked about a little bit

what i want you to remember is that your start codons we talked about there were 64 different

types of codons 61 code for amino acids and three don't they're stop a star codon

we did kind of talk about it is aug do you guys remember what aug coded for methionine right so methionine but

here's the difference this is an important thing to talk about and they'll probably throw this on an

exam for prokaryotic cells it's technically not methionine

it's called informal methionine so what is it called in formal

methionine okay we'll put met so again the start codon is aug in prokaryotic cells same as it is for

in eukaryotic cells but what it codes for is not methionine like it is in eukaryotic cells it's

called informal methionine sometimes it's even abbreviated

as f met okay either way that's my start codon so we're going to put here

a u g on this mrna there is a sequence of nucleotides

particularly like purines that are a couple nucleotide bases upstream towards the five prime end from

that start codon and for whatever reason they love to give this a particular name

because this is where your ribosomes a lot of initiation factors things like that

bind and recognize the mrna and the prokaryotic cells and bind it helps to start the translation process

and this sequence that's like eight nucleotides upstream from the aug is called the shine

delgarno sequence okay and if you really want to know it contains a lot of a's

adenines and guanines okay so it contains a lot of adenine and guanines or your purine

nucleotides in that region okay so there's a shine delgarno sequence it's kind of like an identifier on the mrna

and what happens is a couple things first thing is you have your small ribosomal subunit

okay your small ribosomal subunit will come and bind to this area

right and what happens is when it binds to the area here on the mrna it uses

a very special type of protein let's represent these in brown actually no let's do it in pink so

it's kind of different here there's these things called initiation factors

and there's these initiation factors that recognize the shine delgarno sequence that are in the small ribosomal

subunit are bound to the small ribosomal subunit and so what happens is the initiation

factors in the small ribosomal subunit will bind the shine delgarno sequence then

once it does that it starts kind of moving towards the start codon so two things happen

these pink things called initiation factors that are associated with the small ribosomal subunit will identify

the shine delgarno sequence when they bind they then move down about eight nucleotides until they hit the

start codon which is aug that's the first thing okay so if we wanted to kind of show that

that's the first event to happen let's put one here first to event event to happen is

initiation factors and small ribosomal subunits bind shine delgarno move down until they hit the aug the

second thing to happen here is that there is a molecule called trna right and trna is going to have to have

anticodon specific to this aug which is u a c and it'll be carrying with it an amino

acid what is that amino acid specific we already kind of talked about it we're going to abbreviate it called

f met now when the trna comes what is this called this is your trna

containing the fmet when it comes in as its anticodons interact with the codons here

there's something that help to bring it or drag it into this area what do you think that is this

represents another little pink color there's a pink protein that kind of helps to yank that

trna the initiator trna right which contains the fmet and bring it into

where the start codon is what is that pink protein called it's called an initiation factor that's

it so first step initiation factor small ribosomal subunit bind shine delgarno move down until they hit the start codon

second step initiator trna in the prokaryotes which contains

trna and n-formal methionine with a initiation factor come to the area

where the start codon is and bind that's the second step third step there is

a molecule bound to this initiation factor and that molecule is called

let's bring it over here a gtp this gtp is a high energy molecule what's going to happen is this

initiation factor will break down the gtp into gdp and an inorganic phosphate and

that'll create a lot of energy and what happens is at the same time the gtp gets broken down

into gdp and inorganic phosphate the large ribosomal subunit will represent it like this

the large ribosomal subunit will come over and bind to this area and so what would it look like if we had

kind of like showing all of this happen here this process and the large ribosomal

subunit coming in here this would be in your third step

so third step here is gtp gets broken down to gdp and inorganic phosphate and the large robot

is almost up and it comes and gets added in what would be the final thing that it

would look like if we drew it down here if we drew it all down here at the end product here

you would have what large ribosomal subunit small ribosomal subunit bound here then what else would

we have we would have the trna kind of sitting in here

with the f informal methionine bound with the codon in this case it would be

aug and then what would we have released during this process we would have released gdp in an

inorganic phosphate and what else would we release we don't need this thing anymore we don't need this

pink protein anymore the initiation factors we can just spit those out as well

so we can spit out the initiation factors as well what are these things called we're just

going to abbreviate them initiation factors so to recap really quick because i know

it's a lot of crap and one thing shine dog arnold sequence identifier of the mrna small ribosomal sub being it's

initiation factors bind to it identify it move down till they hit the start

second thing trna which contains the fmet right which is particularly based upon

the anticodons complementary to the codons and mrna it gets brought to this area by the

initiation factors they bring it to the area and bind the trna then

third step there's a gtp associated with the initiation factors it gets broken down

into gdp and inorganic phosphate at the same time a large ribosomal subunit will bind

and what will you get at that process you'll get the large and small bound to the mrna with the

trna sitting in the ribosome in what site we didn't talk about this yet but

there's three sites in a ribosome one of them if we start them here this first one is called the a site

that's the kind of the arrival site this one is called the p site and this one is called the

e site and we'll go through these all in detail but that trna is going to be sitting right smack dab in the middle

which is going to be the p site okay so that covers the initiation and prokaryotic cells thank

goodness in eukaryotic cells it's pretty much the same we just give different names for

stuff so this step here in initiation this is for particularly what

eukaryotic cells they still have a five prime end and a three prime end but guess what

they don't have a shine delgarno sequence they just have this start codon what

happens is first thing that happens is you have a molecule called a eukaryotic initiation factor

so a eukaryotic initiation factor will come and bind to this five prime end and we call this eukaryotic initiation

factor type four it'll bind to this five prime end okay that's the first thing that will happen

the second thing that will happen is that you'll have your small ribosomal subunit and other

you know initiation factors that we're not too concerned with just yet that'll come in interact with this

mrna so let's draw here your small ribosomal subunit that'll come in bind that's the second

thing that will happen and then what else is happening you're having some initiation factors some

small little initiation factors that'll help that small ribosomal subunit to bind

to the mrna this the third thing that happens okay so so far we've had two things

happen eukaryotic initiation factor type 4 identifies the mrna second thing is the small ribosomal

subunit with the initiation factors bind to the mrna the third thing to happen

is that you have a eukaryotic initiation factor type 2 eukaryotic initiation factor type

2 that will bind your trna right it'll bind the trna that contains anticodons that are complementary to the

codons and mrna which is uac it'll have an amino acid that'll be based off of that start codon

what is it in eukaryotic cells what is the start codon in eukaryotic cells it's the same one we talked about

in prokaryotes right aug what's the difference aug and eukaryotes codes for methionine

not in formal methionine that's all that's different so this is just methionine eukaryotic

initiation factor type 2 will bring with it the trna with the methionine

and bind it to this portion on the start codon the fourth thing to happen here

is that you have a gtp molecule that is going to be bound to the eukaryotic initiation factor type two

this is the fourth thing it's going to get broken down into gdp and an inorganic phosphate and the other

event to happen here is that the large ribosomal subunit which contains the

e site p site a site will come and bind to the mrna and what will it look like if all of

this stuff kind of happens accordingly you'll have here your large ribosomal subunit with the e site

p site a site small ribosomal subunit you'll have the trna which will have its anticodons complementary to the codons

of the mrna and you'll have your methionine sitting there and what would be of release

because we don't need them anymore in this process we would release the gdp

and the inorganic phosphate and we would also release the eukaryotic initiation factors

right like type 2 and type 4. do you see how it's pretty much the same in prokaryotic cells

the only difference is is that in order to start this you have a shine delgarno sequence that's identified

by initiation factors and eukaryotes it's a eukaryotic initiation factor that binds the five prime end okay

the other thing is you still have a trna that's coming in and binding with initiation factors

to where that star codon is the only difference is is that's informal methionine and eukaryotic cells

it's called methionine and these are just called initiation factors this one's called

eukaryotic initiation factor type 2. they just wanted to be annoying but the same thing happens in the

remaining steps which is the large ribosomal subunit has to bind and you have to break down gtp into gdp

and inorganic phosphate and you have to release the initiation factors all of it's the same with just

some minor changes in it that's it we finished initiation

thank the lord now let's move on to the next step which is called elongation so what's the next step that

we're going to talk about here the next step is probably one of the more difficult ones to kind of visualize

but this is called elongation this is the second phase in translation so let's pick up where we

left off we initiated the translation process let's pretend this is the same thing

thank goodness this is the same and eukaryotic cells and prokaryotic cells but we're going to

use a lot of the examples here in eukaryotic cells so this is primarily going to be used

in eukaryotic cells that we're going to be using this as an example and it's because we're going to be using

particular types of factors okay so in this example just so you know it's the same and prokaryotes and

eukaryotes just in this example i'm going over it in eukaryotes because i'm going to use specific

factors and you'll see what i mean so to see if you guys remember everything we just talked about up here

you had to initiate it right small ribosomal large ribosomal have to bind initiation factors help that process

break down gtp into inorganic phosphate and bring a trna which contains a amino acid the initiator trna which is

going to be informal with ionine and prokaryotes and methionine and eukaryotes

in this example what was our start codon aug what would be the anticodons that are complementary to that on the

trna uac okay that's where we are we just finished the initiation

now we're gonna do is okay we have to quickly review what is this site here the a site now if you really want to

know the a site is called the acyl site p site is called the peptidyl site and e is called the

exit site you can remember ape in that order okay because that's the order we're

gonna have things coming in and leaving so a site is i like to remember the arrival site

piece i like to think about as the synthesis site and e i like to think about is the exit

site that's how i remember them okay so the first thing we have to do with this elongation process is we have to

bring something into the a site let's just make up we use isoleucine as an example over there

let's bring them back let's put here a u a as the next codon that i'm going to read if that's the case then what do i

need to bring into this area a trna in order for me to bring a trna that is has anticodon specific to

that let's draw that in bringing him in here so we're going to have him come into

this step here so we're going to bring in what are the

anticodons to this u a u right if you really wanted to be specific according to the wobble effect

what would it be the ionosine but just in this example we're going to put uau

okay this is going to be containing what an amino acid and that amino acid in this example doesn't really matter but

it's called isoleucine since we talked about that one before now in order to bring this trna into

this a site we need something to help bring it to that area

and that is going to be called an elongation factor so it's called a elongation factor it's

called eukaryotic elongation factor type 1. eukaryotic elongation factor type 1

will bind this trna which is going to have anticodons complementary to these

codons on the mrna and the a site now once that happens let's show what that would look like so here

we're still going to have that same initiator trna right here right which contains the methionine and

if you really wanted to know here this would be uac and then what would these codons be

a u g this is the p site in the a site what does it look like a uua is my codons

and with the help of the eukaryotic elongation factor type 1 he brings in the trna that's

complementary to this one so that's going to have trna which is uau

and again if you really wanted to be specific according to that wobble effect it would technically be

ua i if you really wanted to but it's going to contain the isoleucine in the a site

who helped to bring him into this area the eukaryotic elongation factor type one but guess what else

this eukaryotic elongation factor on its back it's got a gtp molecule and really in order for this guy to get

in there and to bind what do i need to have enabling this process

energy so on the back of this molecule we have gtp when we add him in here

and he finally gets added in what do i spit out i spit out gdp in an inorganic phosphate

and what else do i spit out my eukaryotic elongation factor type one okay and now

i have my trna in this spot here's where it gets a little interesting because now what do i need

to do i need to take this amino acid that is bound to the trna in the p

site and transfer it onto the amino acid of the trna and the a site and then i need to shift this one that's