Post Translational Modifications

Summary

The video script delves into the complexity of the human proteome, highlighting that it contains over a million proteins,远超 the 20,000 to 25,000 genes in the human genome. It explains how mechanisms like alternative splicing and post-translational modifications (PTMs) contribute to this complexity. PTMs, such as phosphorylation and acetylation, are crucial for protein function, affecting activity, localization, and interactions. The script also illustrates how specific modifications, like the removal of methionine in collagen and the acetylation of microtubules, impact protein activity and cellular processes, emphasizing the importance of understanding these modifications for studying diseases.

Takeaways

• 🧬 The human proteome is significantly more complex than the genome, with over 1 million proteins compared to 20,000-25,000 genes.
• 🔑 Single genes can encode multiple proteins through mechanisms like alternative splicing and post-translational modifications (PTMs).
• 🔄 PTMs are crucial for regulating protein function, including activity, localization, and interactions with other cellular molecules.
• 🔬 Two main types of protein modifications are co-translational, occurring while the protein is still attached to the ribosome, and post-translational, occurring after the protein is released.
• ✂️ Collagen is an example of a protein that undergoes post-translational modification, where the initial methionine is removed by proteases.
• 📈 Signal sequences are removed from proteins like insulin to activate them and allow them to perform their functions.
• 🔗 Covalent modifications such as phosphorylation, acetylation, and methylation can alter protein structure and function.
• 🥛 Casein in milk is an example of a protein that undergoes phosphorylation, which helps it bind calcium for bone strength.
• 🧵 Microtubule acetylation is crucial for maintaining their structure during cell division and preventing breakage.
• 🧬 Histone protein methylation regulates gene transcription by either activating or inhibiting the process.
• 🩸 Post-translational modifications are reversible and play a critical role in the study of human diseases and cellular activity regulation.

Q & A

What is the estimated number of proteins in the human proteome?

The estimated number of proteins in the human proteome is over 1 million.

How does the complexity of the human proteome compare to the human genome?

The human proteome is vastly more complex than the human genome, with the genome comprising between 20,000 and 25,000 genes, while the proteome has over 1 million proteins.

What are the mechanisms that generate different mRNA transcripts from a single gene?

The mechanisms that generate different mRNA transcripts from a single gene include genomic recombination, transcription initiation at alternative promoters, differential transcription, termination, and alternative splicing of the transcript.

What is the role of protein post-translational modifications (PTMs) in the proteome?

Protein post-translational modifications (PTMs) play a key role in functional proteomics by regulating activity, localization, and interaction with other cellular molecules such as proteins, nucleic acids, lipids, and cofactors.

What is the difference between co-translational and post-translational modifications?

Co-translational modifications occur while amino acids are still attached to the ribosome, whereas post-translational modifications occur after the protein is no longer attached to the ribosome.

Why is the removal of the initial methionine from a protein important in some cases?

The removal of the initial methionine from a protein like collagen is important because it allows the protein to undergo further processing to form an active, functional protein.

What is the significance of the trimming of signal sequences in protein function?

The trimming of signal sequences is significant because it allows a newly synthesized protein to become active and perform its function after being localized to its destination.

Can you provide an example of a covalent modification and its effect on protein function?

Phosphorylation of serine amino acids in casein helps the protein bind calcium ions, which is crucial for bone strength.

How do disulfide bonds in Immunoglobulin G (IgG) contribute to its function?

Interconnected disulfide bonds in IgG help maintain its shape, which is essential for its function in protecting against bacteria or viral infections.

What is the purpose of carboxylation in pro-thrombin?

Carboxylation of the glutamate residue at the end terminal of pro-thrombin allows binding of calcium ions, which is necessary to initiate blood clotting.

How do post-translational modifications contribute to the study of human diseases?

Post-translational modifications are crucial for studying human diseases because they regulate cellular activity and can be reversible, affecting protein function and biological processes.

Outlines

00:00

🧬 Complexity of the Human Proteome

The paragraph delves into the complexity of the human proteome compared to the genome. It mentions that while the human genome consists of 20,000 to 25,000 genes, the proteome is estimated to contain over 1 million proteins. This complexity arises from mechanisms such as genomic recombination, alternative transcription, and splicing. The paragraph also explains protein modifications, distinguishing between co-translational and post-translational modifications. Co-translational modifications occur while the protein is still attached to the ribosome, like folding, whereas post-translational modifications happen after the protein is detached, such as the removal of methionine in collagen or the trimming of signal sequences. Examples of covalent modifications like phosphorylation, acetylation, and methylation are also discussed.

05:02

🔬 Impact of Covalent Modifications on Protein Function

This paragraph explores the impact of covalent modifications on the function of various proteins. It uses real-life examples to illustrate how modifications affect protein activity. Casein in milk is highlighted for its role in calcium ion binding, facilitated by serine phosphorylation. The acetylation of microtubules is discussed in terms of their structural integrity during cell division. Histone protein methylation is explained as a regulator of gene transcription. The importance of hydroxylation in collagen's structural integrity and the role of disulfide bonds in maintaining the shape and function of immunoglobulin G are also covered. The paragraph further discusses the significance of carboxylation in pro-thrombin for blood clotting, the role of glycoproteins and lipoproteins in cell membrane attachment, and the function of metalloproteins like hemoglobin. Lastly, it touches on protein folding and degradation, emphasizing the dynamic nature of the proteome and the importance of post-translational modifications in cellular regulation.

10:07

🛠️ Post-Translational Modifications and Cellular Activity

The final paragraph summarizes the dynamic nature of the human proteome and the role of post-translational modifications (PTMs) in cellular activity. It emphasizes that PTMs occur at distinct sites on amino acids or peptide linkages and are often mediated by enzymatic activity. The paragraph notes that PTMs can be reversible, with examples such as kinases and phosphatases that can add or remove phosphate groups, respectively. The analysis of proteins and their modifications is highlighted as crucial for understanding human diseases. The paragraph concludes by stressing the importance of studying these modifications for insights into disease mechanisms and potential therapeutic targets.

Keywords

💡Proteome

The human proteome refers to the entire set of proteins that are produced and can exist in human cells. It is more complex than the genome because a single gene can encode multiple proteins through various mechanisms. The video emphasizes the complexity of the proteome, which is estimated to contain over 1 million proteins, highlighting its vastness and diversity compared to the genome's 20,000 to 25,000 genes.

💡Genome

The human genome is the complete set of genetic information, including all of the genes on the chromosomes. It serves as the blueprint for the proteome, but the video script explains that the number of proteins (proteome) far exceeds the number of genes (genome), indicating the complexity introduced post-transcriptionally.

💡Post-translational modifications (PTMs)

Post-translational modifications are chemical alterations that occur to proteins after they have been synthesized by translation. PTMs play a critical role in regulating protein function, including activity, localization, and interaction with other molecules. The video script details various types of PTMs, such as phosphorylation and acetylation, and explains their significance in functional proteomics.

💡Co-translational modification

Co-translational modification refers to the process where a protein is modified while it is still being synthesized on the ribosome. This type of modification includes folding into the tertiary and quaternary state, which is essential for the protein's function. The video script uses the example of chaperones assisting in folding to illustrate co-translational modifications.

💡Alternative splicing

Alternative splicing is a mechanism that increases protein diversity from a single gene. It involves the selective inclusion or exclusion of different segments of the pre-mRNA transcript during the process of mRNA formation. The video script mentions this as one of the ways that a single gene can produce multiple mRNA transcripts, contributing to the complexity of the proteome.

💡Signal sequence

A signal sequence is a short amino acid sequence at the N-terminus of a protein that directs the protein to its proper cellular location. The video script explains that after a protein reaches its destination, the signal sequence is often removed to activate the protein, using insulin as an example where the signal peptide is cleaved to produce active insulin.

💡Covalent modifications

Covalent modifications are chemical reactions that involve the formation or breaking of covalent bonds, leading to changes in protein structure and function. Examples given in the video script include phosphorylation, acetylation, and methylation, which are all crucial for regulating various cellular processes.

💡Phosphorylation

Phosphorylation is a covalent modification where a phosphate group is added to a protein, usually at serine, threonine, or tyrosine residues. This modification is highlighted in the video script as a way to regulate protein activity, with kinases adding phosphate groups and phosphatases removing them to control biological activity.

💡Acetylation

Acetylation is a covalent modification where an acetyl group is added to a lysine residue in a protein, often affecting its stability, localization, or interaction with other molecules. The video script uses the example of microtubules, where acetylation at lysine 40 helps in the repair process and prevents breakage.

💡Disulfide bonds

Disulfide bonds are covalent linkages formed between cysteine residues in a protein, contributing to its structural stability and shape. The video script mentions that these bonds are crucial for the function of antibodies like immunoglobulin G (IgG), which rely on disulfide bonds for their structure and immune response function.

💡Protein degradation

Protein degradation is the process by which proteins are broken down into their constituent amino acids. The video script explains that this process is essential for removing damaged or improperly synthesized proteins, often involving the attachment of ubiquitin chains as a signal for degradation by proteasomes.

Highlights

The human proteome is more complex than the genome, with over 1 million proteins compared to 20,000-25,000 genes.

Single genes can encode multiple proteins through mechanisms like alternative splicing and post-translational modifications.

Protein post-translational modifications (PTMs) play a key role in regulating protein activity, localization, and interactions.

Co-translational modifications occur while amino acids are still attached to the ribosome, including folding into tertiary and quaternary structures.

Post-translation modifications happen after the protein is detached from the ribosome, involving changes to amino acids or attachment of non-protein parts.

Collagen lacks methionine due to proteases cutting it off during maturation into an active protein.

Signal sequence trimming is crucial for protein localization and activation, as seen with insulin's conversion from preproinsulin to active insulin.

Covalent modifications such as phosphorylation, acetylation, and disulfide cross-linking alter protein function.

Phosphorylation of serine in casein aids in calcium ion binding for bone strength.

Acetylation of microtubules helps in their structural integrity and repair during cell division.

Histone protein methylation acts as a regulator for gene transcription processes.

Hydroxylation of collagen is essential for its structural formation and function in connective tissues.

Disulfide bonds in immunoglobulin G (IgG) maintain its shape and function in immune response.

Carboxylation of pro-thrombin enables calcium ion binding for blood clotting initiation.

Glycoproteins and lipoproteins have carbohydrate and lipid attachments, respectively, for specific cellular interactions.

Metalloproteins like hemoglobin carry metal ions for functions like oxygen transport.

Protein folding, assisted by chaperones, is crucial for protein structure and function.

Protein degradation, signaled by ubiquitin chains, is a key process for maintaining cellular protein homeostasis.

Post-translational modifications are reversible and play a significant role in the regulation of cellular activity.

Analysis of protein PTMs is vital for understanding human diseases and their impact on protein function.

Transcripts

Within the last few decades, scientists have discovered that the human proteome is vastly

more complex than the human genome.

While it is estimated that the human genome comprises between 20,000 and 25,000 genes,

the total number of proteins in the human proteome is estimated at over 1 million.

These estimations demonstrate that single genes encode multiple proteins.

Genomic recombination, transcription initiation at alternative promoters, differential transcription

termination, and alternative splicing of the transcript are mechanisms that generate different

mRNA transcripts from a single gene.

The increase in complexity from the level of the genome to the proteome is further facilitated

by protein post-translational modifications (PTMs).

PTMs are chemical modifications that play a key role in functional proteomic because

they regulate activity, localization, and interaction with other cellular molecules

such as proteins, nucleic acids, lipids and cofactors.

In general, protein modifications can be of two different types.

One is called as co-translational modification and another is called as post-translation

modification.

The difference between the two is that, if the process of modification or changing of

one or more amino acid in a protein starts while they are still attached to the ribosome,

that is called as co-translation modification.

As you can see in this picture that this protein is still attached to the ribosome and the

ribosome is still moving along the mRNA, but these chaperones start attaching themselves

with this protein and start folding it into the tertiary and quaternary state.

Folding is considered a category of modification, so this type of protein modification is called

co-translational modification.

On the other hand, post-translation modification means that once the process of translation

is ended and the protein is no longer attached itself to the ribosome, and now the process

of changing of one or more amino acid or attachment of a non-protein part occurs to this protein,

this type of modification is called post-translation modification.

As we know that when the process of translation start, the first start codon, AUG, codes for

methionine in a eukaryotic organism or N-formyl methionine in a prokaryotic organism.

In both situations, methionine is the first amino acid that is generated in a protein.

However, a protein like collagen, there is no methionine.

In collagen protein, there are only three amino acids, that is glycine, proline, and

lysine.

It means that the terminal amino acid, methionine, is cut off from that protein by the enzymes

called proteases.

The proteases will cut out the methionine from procollagen and undergo further process

to form tertiary and quaternary protein in order to make be active.

The second type of modification is called the trimming of signal sequence.

When the newly synthesized protein is fully translated, it can be inactive.

The first 15 to 30 amino acid that is present at the N-terminal of the protein is called

a signal sequence.

This signal sequence dictates where the protein goes, whether it is going to the nucleus,

remained in the cytosol, going into the mitochondria, or being secreted to extracellularly.

Once the protein is localized at its destination, the signal sequence needs to be removed to

make the protein active and perform its function.

One good example is the hormone insulin.

At first, preproinsulin is translated as a 110 amino acid chain.

Removal of the signal peptide produces Proinsulin.

Formation of disulfide bonds between the A- & B-chain components, and removal of the intervening

C-chain, produces a biologically active Insulin molecule comprising 51 amino acids, less than

half of the original translation product.

Proteins can also undergo the process of covalent modifications.

These modifications include phosphorylation, acetylation, disulfide cross-linking, carboxylation,

methylation and hydroxylation.

Let's take a look at this polypeptide and see how some of the major covalent modifications

are occurring on it.

Starting from the N-terminal chain of this polypeptide, we can see that the phosphorylation

is occurring on serine amino acid, followed by the acetylation at the lysine residue with

the addition of the acetyl group.

Next, we will find cysteine is making disulfide crosslinking with another cysteine molecule

in this polypeptide chain.

Further on, we can see a proline that is attached with hydroxy group and this process is called

hydroxylation.

When we move forward, we can see arginine is attached with methyl groups that is called

methylation.

Note that methylation can be di- or trimethylation depending on two or three methyl group are

attached to that amino acid.

At the last amino acid, glutamine is attached with the carboxyl group and the process of

modification is called carboxylation.

The function of each covalent modification is different depending on the type of protein

it has.

Let's take the real-life example of all these type of modifications and see how this modification

is affecting their function.

For example, casein is a protein that is present in the milk and it usually helps the attachment

of calcium ions within our bone.

If we look closely at this protein, we can see that it has a lot of serine amino acid.

The serine amino acid is usually phosphorylated.

Serine phosphorylation of casein help the protein to bind calcium ions and deliver it

to the bones and make us stronger.

Another example is the acetylation of microtubules.

Microtubule is present in every cell.

They have numerous functions.

The main function is present during mitosis and meiosis where the chromosome attached

themselves with the spindle fiber.

If a crack or damage occur at one part of the microtubule, acetylation will occur on

the lysine residue at the position 40.

The lysine 40 acetylation prevent the microtubule to bend and allow the repair process to take

place.

On the other hand, if there is no acetylation occur, the crack will go bigger and results

in the breakage of the microtubule.

Histone proteins are present inside the chromosome in the form of a nucleosome in which eight

histone proteins are surrounded by DNA molecule.

Histone proteins play a major role in the process of transcription regulation.

The histone proteins tails can be modified with methyl group.

In this picture, the green modifications shown here are methylations that activate gene transcription.

If the methylation is occurring on the red areas or the red positions of lysine residue,

it will halt the process of transcription.

So, the major function of histone protein methylation is to act as a regulator for the

process of transcription.

As we mentioned earlier, collagen is the main protein in our body.

It is present in our nails, cartilage, bone and connective tissue such as skin.

Collagen have three different type of amino acid that is highly modified with the hydroxyl

group.

When hydroxy group is attached to each polypeptide chain, collagen can convert itself into the

cross-linked tropocollagen in order to perform its function.

In the absence of hydroxylation, they will not form the tropocollagen.

They will get degrade.

If it gets degraded, it will affect our skin, nails, hair, or any part of the body where

collagen plays its function.

Immunoglobulin G or IgG is a type antibody that is present in our immune system to protect

us against bacteria or viral infection.

If we look closely at the structure of this antibody, we will find a lot of inter cross-linked

disulfide bonds.

These interconnected disulfide bond held IgG to be in its shape and perform its function.

Pro-thrombin is a protein in our blood vessel that helps in blood clotting.

The glutamate residue at the end terminal of the pro-thrombin is usually carboxylated

to allow binding of calcium ion that is necessary to initiate blood clotting.

Glycoproteins are proteins that has a carbohydrate attached to it.

There are two different type of linkages.

One is called the O-linkage that usually observed on the serine and threonine residue, and N-linkage

that usually occur on asparagine residue.

Carbohydrate is a very big family of molecules.

This include mannose, galactose and glucose and many more.

Another type of post-translational modified protein is lipoprotein.

Lipoprotein consist of a lipid group that allow the protein to attach themselves onto

the cell membrane.

Because lipids are hydrophobic in nature, the attachment of protein to cell membrane

is not possible without the attachment to the lipid family.

There are three different types of protein-lipid linkages.

First, there is the linkage of palmitoyl group on the internal cysteine or serine residue.

Second, the myristoyl group can also attach to the glycine residue.

And third, the binding of the farnesyl group on the carboxy terminal of cysteine.

With these three different types of attachments with the lipid, the protein can anchor itself

with the cell membrane and plays it functions.

Metalloproteins are protein that have a metal ion attached to it as a cofactor.

An example of metalloprotein is hemoglobin.

As we know, the hemoglobin has iron attached to it in the form of a heme group to carry

oxygen.

Because the binding of the iron to the protein changes the color of the protein, hemoglobin

is also referred as chromoproteins.

Protein folding is another type of protein modifications.

After the protein is translated, there are two different types of protein folding.

One is done by itself and another one needs a helper protein called chaperone.

Chaperone attach themselves with the newly translated protein and help it to fold in

a correct form.

Finally, protein degradation.

Protein degradation is also happening when the protein is translated.

Sometimes, the protein translation is not done properly and sometimes the external factors

are damaging that protein.

In such cases, the protein will undergo the process of degradation.

Most protein degradation will be carried out when a ubiquitin chain attach to the protein,

giving signals to the proteasome to recognize the protein that needs to be degraded.

Once the attachment of ubiquitin chain happened, the proteasome will come and degrade the ubiquitinated

protein into the amino acid and that protein will lose its function.

In summary, the human proteome is dynamic and changes in response to a legion of stimuli,

and post-translational modifications are commonly employed to regulate cellular activity.

Post-translational modification occur at distinct amino acid side chains or peptide linkages,

and they are most often mediated by enzymatic activity.

Post-translational modifications can occur at any step in the "life cycle" of a protein.

Of note, Protein post-translational modification can also be reversible depending on the nature

of the modification.

For example, kinases phosphorylate proteins at specific amino acid side chains, which

is a common method of catalytic activation or inactivation.

Conversely, phosphatases hydrolyze the phosphate group to remove it from the protein and reverse

the biological activity.

Consequently, the analysis of proteins and their post-translational modifications is

particularly important for the study of human diseases.