D1.2 HL Protein Synthesis [IB Biology HL]

Summary

This 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

00:00

🧬 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.

05:00

🐄 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.

10:02

🌟 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.

15:05

🔄 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.

Keywords

💡Protein Synthesis

Protein synthesis is the process by which cells generate new proteins. It is central to the video's theme as it encompasses transcription, translation, and post-translational modifications. The script explains that this process is essential for cell function and involves multiple steps, starting from the genetic code in DNA to the formation of functional proteins.

💡Transcription

Transcription is the first step in protein synthesis, where the genetic information from DNA is copied into mRNA. The script describes how this occurs in the 5' to 3' direction and involves the binding of RNA polymerase to the promoter region of a gene, highlighting the importance of transcription in gene expression.

💡Translation

Translation is the process where the mRNA sequence is used to assemble a polypeptide chain during protein synthesis. The video script explains that translation occurs in the cytoplasm and involves the ribosome moving along the mRNA from the 5' to 3' end, adding amino acids to form a polypeptide.

💡Directionality (5' to 3')

Directionality refers to the specific direction in which biological processes occur, such as the synthesis of RNA and proteins. The script emphasizes that both transcription and translation proceed in the 5' to 3' direction, which is a fundamental aspect of understanding how genetic information is read and used.

💡Promoter

A promoter is a DNA sequence that marks the starting point of transcription. The script mentions that transcription factors bind to the promoter, which can either promote or inhibit transcription, making it a crucial regulatory element in gene expression.

💡Transcription Factors

Transcription factors are proteins that regulate the transcription process by binding to the promoter region. The video script explains their role in either enhancing or preventing the binding of RNA polymerase, thereby controlling which genes are transcribed.

💡Non-coding Regions

Non-coding regions are parts of the DNA that do not code for proteins but have other functions. The script describes examples such as promoters and telomeres, emphasizing that a significant portion of the genome consists of non-coding sequences that play essential roles in cellular processes.

💡Introns and Exons

Introns and exons are parts of a gene that are involved in the processing of mRNA. The script explains that introns are removed, and exons are spliced together during post-transcriptional modification. This process is crucial for generating mature mRNA that will be translated into proteins.

💡Post-transcriptional Modification

Post-transcriptional modification refers to the changes made to mRNA after transcription but before translation. The script describes how these modifications, such as splicing out introns and adding a 5' cap and a poly-A tail, are essential for the mRNA's stability and translation efficiency.

💡tRNA (Transfer RNA)

tRNA is a type of RNA molecule that plays a critical role in translation by carrying specific amino acids to the ribosome. The video script explains how tRNA is activated by aminoacyl-tRNA synthetase enzymes, which attach the correct amino acid to the tRNA, ensuring accurate protein synthesis.

💡Proteosome

A proteosome is a complex of enzymes that degrade proteins into smaller polypeptides and then into individual amino acids. The script mentions proteosomes in the context of protein turnover, where proteins are broken down and their components recycled for the synthesis of new proteins.

💡Insulin

Insulin is a hormone produced by the pancreas and is used in the script as an example of post-translational modification. The script explains that the initial translation product, preproinsulin, undergoes modifications such as the removal of certain amino acids and folding into its functional tertiary structure to become mature 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