D1.2 HL Protein Synthesis [IB Biology HL]
Summary
TLDRThis educational video script delves into the intricate processes of protein synthesis, including transcription and translation, emphasizing the 5' to 3' directionality. It explains the role of promoters, transcription factors, and non-coding regions in gene regulation. The script further explores post-transcriptional modifications, such as splicing, capping, and polyadenylation, leading to mature mRNA. It also covers the activation of tRNA by specific enzymes, the initiation of translation, and the subsequent folding and modification of polypeptides into functional proteins. Finally, it touches on protein degradation by proteosomes and the recycling of amino acids.
Takeaways
- 🔬 Transcription and translation in protein synthesis occur in a 5' to 3' direction, which is a fundamental rule in molecular biology.
- 📜 The 5' end and 3' end of an RNA molecule are crucial for the directionality of transcription and translation processes.
- 🧬 Genes, which are segments of DNA, code for specific proteins and have promoters that serve as binding sites for RNA polymerase and other transcription factors.
- 🔄 Transcription factors regulate genetic expression by binding to the promoter, either promoting or inhibiting transcription.
- 🧬 Non-coding regions of DNA, such as promoters and telomeres, play essential roles in the structure and regulation of the genome, despite not coding for polypeptides.
- 📝 Prokaryotic cells perform transcription and translation simultaneously, which is efficient but lacks post-transcriptional modifications.
- 🧬 Eukaryotic cells have a nucleus that separates transcription from translation, allowing for post-transcriptional modifications like mRNA editing.
- 📑 mRNA undergoes post-transcriptional modifications, including the removal of introns, addition of a 5' cap, and a poly-A tail, to become mature mRNA.
- 🔠 The process of alternative splicing allows for the creation of different protein versions from the same gene by editing the mRNA in various ways.
- 🧬 tRNA activating enzymes (aminoacyl-tRNA synthetases) are responsible for attaching the correct amino acid to a tRNA molecule, which is essential for translation.
- 📚 Translation begins with the initiation phase, where the ribosome assembles and the first tRNA carrying methionine binds to the start codon on the mRNA.
- 🛠 Post-translational modifications, such as folding and the removal of certain amino acids, are crucial for a polypeptide to become a functional protein.
Q & A
What is the directionality of both transcription and translation processes in molecular biology?
-The directionality of both transcription and translation processes is from the 5' end to the 3' end.
What is the role of the promoter in gene transcription?
-The promoter is a short segment of base sequences at the beginning of a gene that serves as a binding site for RNA polymerase or other factors controlling transcription.
How do transcription factors influence the transcription process?
-Transcription factors are proteins that can regulate genetic expression by binding to the promoter, either promoting transcription or inhibiting it by preventing RNA polymerase from binding.
What is the difference between coding and non-coding regions in DNA?
-Coding regions in DNA are segments that code for a specific polypeptide, whereas non-coding regions do not code for a polypeptide and may have other functions, such as producing tRNA or rRNA, or serving as structural elements like telomeres.
Why is the process of transcription and translation simultaneous in prokaryotes?
-In prokaryotes, transcription and translation occur simultaneously because it is more efficient, although it does not allow for post-transcriptional modifications that can occur in eukaryotes due to compartmentalization.
What is the purpose of post-transcriptional modifications in eukaryotes?
-Post-transcriptional modifications in eukaryotes allow for the editing of mRNA, enabling the production of different versions of a protein using the same gene, thus increasing the diversity of proteins that can be synthesized.
How does alternative splicing contribute to protein diversity?
-Alternative splicing contributes to protein diversity by allowing the removal of different introns and the splicing together of exons in various ways, resulting in different mRNA sequences that are translated into different amino acid sequences.
What are the roles of the 5' cap and poly(A) tail in mature mRNA?
-The 5' cap helps protect the mRNA as it moves through the nucleus, while the poly(A) tail, a long string of adenine nucleotides, is added to the 3' end of the mRNA molecule and aids in mRNA stability and translation efficiency.
How does the tRNA activating enzyme (aminoacyl-tRNA synthetase) function in protein synthesis?
-The tRNA activating enzyme attaches the correct amino acid to its corresponding tRNA molecule, using ATP for energy. This process activates or charges the tRNA, preparing it to carry the amino acid during translation.
What is the significance of the proteasome in protein synthesis and degradation?
-The proteasome is an enzyme complex that breaks down proteins into short polypeptides, which can then be further degraded into individual amino acids for recycling, thus playing a crucial role in protein turnover and cellular homeostasis.
Outlines
🧬 DNA Transcription and Translation
This paragraph discusses the fundamental processes of DNA transcription and translation, emphasizing the 5' to 3' directionality. It explains that transcription, like replication, can only occur from the 5' end to the 3' end. The paragraph also details the role of the promoter in gene transcription, serving as a binding site for RNA polymerase or other transcription factors. These factors can either promote or inhibit transcription. The concept of non-coding regions in DNA is introduced, highlighting that while genes code for proteins, most DNA sequences are non-coding and serve other functions, such as producing tRNA or rRNA, or as structural elements like telomeres. The paragraph also touches on the simultaneous transcription and translation in prokaryotes, which is efficient but limits post-transcriptional modifications that are possible in eukaryotes due to compartmentalization.
🐄 Post-transcriptional Modifications
The second paragraph delves into post-transcriptional modifications in eukaryotes, using the alphabet as an analogy to explain how different mRNA sequences can be produced from the same gene. It discusses the removal of introns and the splicing together of exons to form mature mRNA, which includes the addition of a 5' cap and a poly-A tail. This process allows for the creation of different protein versions from a single gene through alternative splicing. The paragraph also covers the concept of tRNA activation, where an enzyme attaches an amino acid to a tRNA molecule, requiring ATP. The specificity of tRNA activating enzymes for each amino acid is highlighted, setting the stage for translation.
🌟 Translation Initiation and Protein Synthesis
This paragraph focuses on the initiation of translation, where the tRNA carrying methionine, the start codon, binds to the small subunit of the ribosome. It describes how the ribosome assembles and begins the process of translation by moving along the mRNA in a 5' to 3' direction. The paragraph explains the role of the ribosome in linking amino acids together to form a polypeptide chain, which is the first step in protein synthesis. It also touches on the subsequent steps of protein synthesis, including the elongation and termination phases, leading to the formation of a polypeptide chain that will eventually fold into a functional protein.
🔄 Protein Modification and Degradation
The final paragraph explores the post-translational modifications that a polypeptide undergoes to become a functional protein. It uses the example of insulin, detailing how the preproinsulin is modified to mature insulin through the removal of certain amino acids and the formation of disulfide bonds. The paragraph also discusses the general process of protein degradation, where proteosomes break down proteins into shorter polypeptides, which can then be further broken down into individual amino acids for recycling. The importance of enzymes and ATP in these processes is highlighted, emphasizing the cyclical nature of protein synthesis and degradation within the cell.
Mindmap
Keywords
💡Protein Synthesis
💡Transcription
💡Translation
💡Directionality (5' to 3')
💡Promoter
💡Transcription Factors
💡Non-coding Regions
💡Introns and Exons
💡Post-transcriptional Modification
💡tRNA (Transfer RNA)
💡Proteosome
💡Insulin
Highlights
Directionality of transcription and translation is from 5' to 3'.
Transcription factors regulate genetic expression by binding to the promoter.
Proteins are coded by genes, which are segments of DNA.
The promoter is a non-coding region that serves as a binding site for RNA polymerase.
Most base sequences in the genome are non-coding and do not code for polypeptides.
Telomeres are structural DNA at the ends of chromosomes that prevent damage.
Introns are edited out after transcription and do not translate into a polypeptide.
Prokaryotic transcription and translation occur simultaneously without post-transcriptional modifications.
Post-transcriptional modifications allow for the creation of different protein versions from the same gene.
tRNA activating enzymes attach amino acids to tRNA molecules using ATP.
Translation begins with the initiation phase where the first tRNA binds to the ribosome.
Polypeptides are modified and folded into their final functional shape to become proteins.
Insulin production involves the modification of preproinsulin into its functional state.
Proteins are broken down by proteosomes into short polypeptides for recycling.
Protein synthesis involves a cycle of creation, modification, and recycling of amino acids.
Alternative splicing allows for the production of different protein versions from the same mRNA.
Mature mRNA is formed after splicing, capping, and adding a poly-A tail.
Transcripts
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
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