Understanding Translation: The Process of Protein Synthesis Made Simple
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Introduction
Translation, or protein synthesis, is a fundamental process in cellular biology where messenger RNA (mRNA) is converted into a sequence of amino acids, forming proteins essential for life. This process is crucial in understanding how genetic information is expressed within organisms, and it involves several types of RNA, particularly mRNA, transfer RNA (tRNA), and ribosomal RNA (rRNA). In this article, we will delve into the mechanics of translation, discussing the various stages and critical components involved in this biological phenomenon.
What is Translation?
Translation is the process by which ribosomes synthesize proteins using the information encoded in mRNA. It occurs in the cytoplasm and involves the following key steps:
- Initiation: Assembly of the translation machinery at the start codon.
- Elongation: Amino acids are sequentially added to the growing polypeptide chain.
- Termination: The finished protein is released once a stop codon is reached.
Overview of RNA Types in Translation
Before diving into the translation phases, it is essential to understand the key RNA molecules involved:
- mRNA (messenger RNA): Carries genetic information from DNA and contains codons that specify the amino acid sequence.
- tRNA (transfer RNA): Brings amino acids to ribosomes during protein synthesis, with each tRNA having an anticodon that pairs with the corresponding mRNA codon.
- rRNA (ribosomal RNA): Essential component of ribosomes, facilitating the translation process by providing a site for mRNA and tRNA interactions.
The Genetic Code
The genetic code consists of triplet codons (three nucleotide sequences) that specify which amino acids will be inserted into a protein. The codons are recognized by tRNA, decoded during translation:
- There are 64 possible codons formed from four nucleotides: adenine (A), guanine (G), cytosine (C), and uracil (U).
- 61 codons specify amino acids, while 3 codons (UAA, UAG, UGA) are stop signals, indicating the end of protein synthesis.
Codons and Anticodons
Codons in mRNA are recognized by complementary sequences in tRNA called anticodons. For example, if the mRNA codon is AUG (which codes for methionine), the corresponding tRNA anticodon would be UAC.
Phases of Translation
1. Initiation
The initiation phase sets the stage for protein synthesis.
- In prokaryotes, the small ribosomal subunit binds to the Shine-Dalgarno sequence upstream of the start codon (AUG) in mRNA. This binding is assisted by initiation factors.
- In eukaryotes, the process begins when the small ribosomal subunit binds to the 5' cap of mRNA, with the help of several initiation factors. This machinery scans the mRNA for the start codon (AUG).
Once the ribosome is assembled and the initiator tRNA is bound to the mRNA's start codon, the large ribosomal subunit joins to form a complete ribosome. Energy from GTP hydrolysis assists this process.
2. Elongation
During elongation, tRNA molecules sequentially bring the appropriate amino acids to the ribosome, facilitated by elongation factors:
- The ribosome moves along the mRNA in the 5' to 3' direction, facilitating the addition of amino acids to the growing polypeptide chain.
- Within the ribosome, the A site (arrival), P site (peptidyl), and E site (exit) play crucial roles in positioning tRNA molecules and peptide bonds formation.
- The peptide bond formation is catalyzed by the enzyme peptidyl transferase, facilitating the transfer of the growing peptide from the tRNA in the P site to the tRNA in the A site.
3. Termination
Translation concludes when a stop codon is encountered:
- A release factor recognizes the stop codon, binding to the A site, and catalyzes the release of the newly synthesized polypeptide from the tRNA in the P site.
- Following termination, the ribosome subunits, mRNA, and release factor dissociate, allowing the protein to fold and perform its biological functions.
Translation on Ribosomes: Free vs. Membrane-bound
Translation can occur on free ribosomes in the cytoplasm or on ribosomes attached to the rough endoplasmic reticulum (rough ER).
- Free Ribosomes: Synthesize proteins primarily involved in cytoplasmic functions, such as glycolysis enzymes and nuclear proteins.
- Rough ER-bound Ribosomes: Synthesize proteins destined for secretion, incorporation into the cell membrane, or delivery to lysosomes. This is initiated by a signal recognition particle (SRP) that recognizes a signal sequence on the growing polypeptide chain, guiding it to the rough ER.
Post-Translational Modifications
Once proteins are synthesized, they often undergo post-translational modifications (PTMs) such as:
- Glycosylation: Addition of carbohydrate chains, important for cell recognition.
- Phosphorylation: Adding phosphate groups to activate or deactivate proteins.
- Acetylation: Modifying proteins to regulate transcription.
- Methylation: Another regulatory modification affecting gene expression.
- Trimming: Cleaving particular amino acids to activate certain proteins, like digestive enzymes.
Conclusion
Translation is a vital process in cellular function, translating genetic code into functional proteins. Understanding the stages of translation and how proteins are synthesized provides insight into the fundamental biochemical processes sustaining all life forms. By exploring translation, we enhance our knowledge of genetics, molecular biology, and the underlying mechanisms of life itself.
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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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
scary as it seems a little boring but we're gonna make it fun the first thing you need to know is here
very important for this translation process right messenger rna messenger rna it has a very specific
there's three little lines there that line is a nucleotide that's a nucleotide that's a nucleotide so
right so a little bit about the topology of the mrna on this end i'm going to have a five
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 these are called codons so let's write that down so these things these triplets let's put down
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
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
of these four nucleotides you can have well there's four total nucleotides right so let's put a four here four
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
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
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
and so what type would it be this one's an easy one to remember and this is probably one of the few that
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
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
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
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
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
you guys should be asking that question there's another molecule called trna right what is it called
codons okay that's the first thing what the heck are anticodons it's really simple anticodons
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
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
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
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
on this trna that we'll talk about and that is going to carry the amino acid specific to this
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
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
five prime end of the trna so what would be on that end what group hydroxyl group or phosphate group
is the three prime end three priming contains what oh phosphate group contains the hydroxyl
nucleotides that are in this area of the three prime end which hold on to the amino acid this is the amino acid
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
you don't like have any stops or anything like that so in that way when we talk about the
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
what does this mean that it's homolos let's say that i read this codon read this codon and there's a couple
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
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
in the translation process according to the genetic code there is one exception and again that exception
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
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
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
its codon you'll find that it has three different types of codons that can actually code for it
tells me that i could know the amino acid that i'm making but i won't be able to track
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
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
u c and the next one is a u u how the heck does the trna do that in a particular way does each
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
process to occur it's pretty cool so where's the anticodon on the trna here's our trna
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
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
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
and then what will you have what's complementary to you a what's complementary to a u do the same
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
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
you're probably like why the heck do we do this why don't we just make it specific to each
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
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
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
mutations so when we're talking about when i'm mentioning all this stuff about the genetic code and you can look in
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
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
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
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
these two little arms or loops and this little thing that's kind of like sticking out the side
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
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
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
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
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
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
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
it's holding the amino acid with what bound to it the amp then what it does is it basically just
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
the amino acid and what amino acid was this in this example methionine in the process though do you
we're going to release the amp during that process okay what you need to know is what the
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
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
that's called an aminoacyl amp a amino acyl trna synthetase will come in have two pockets in one pocket it will
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
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
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
eukaryotic cells when we talk about ribosomes they have two subunits okay we're going to say this subunit up
and eukaryotic cells that zvedberg unit for large rebels almost sub units are called 60s large ribosomal subunits
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
and then in prokaryotics the small is a 30s ribosomal subunit and you're probably like oh that's going
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 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
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
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
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
proteins in order for them to function if you give an antibiotic if a bacteria is infecting a particular tissue you
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
really need to understand and know for translation we went through the mrna we went through the trna we went through
translation all right so we're going to talk about the phases of translation we've really built up our foundation to
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
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
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
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
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
particularly like purines that are a couple nucleotide bases upstream towards the five prime end from
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
nucleotides in that region okay so there's a shine delgarno sequence it's kind of like an identifier on the mrna
a very special type of protein let's represent these in brown actually no let's do it in pink so
and there's these initiation factors that recognize the shine delgarno sequence that are in the small ribosomal
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
acid what is that amino acid specific we already kind of talked about it we're going to abbreviate it called
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
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
let's bring it over here a gtp this gtp is a high energy molecule what's going to happen is this
that'll create a lot of energy and what happens is at the same time the gtp gets broken down
the large ribosomal subunit will come over and bind to this area and so what would it look like if we had
so third step here is gtp gets broken down to gdp and inorganic phosphate and the large robot
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
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
so we can spit out the initiation factors as well what are these things called we're just
it's a lot of crap and one thing shine dog arnold sequence identifier of the mrna small ribosomal sub being it's
and what will you get at that process you'll get the large and small bound to the mrna with the
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
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
happen eukaryotic initiation factor type 4 identifies the mrna second thing is the small ribosomal
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