Name: how cells tag proteins for breakdown
Uploaded: 2023-06-23T15:38:53.000Z
Duration: 1 min 17 s
Channel: JoVE

The 26S proteasome, is a large protein complex that degrades misfolded proteins through the ubiquitin-proteasome pathway.
Each proteasome consists of two major types of subunits&#8212;the 19S caps and the 20S core.
The 19S subunits are large protein caps attached at one or both ends of the core that act to regulate proteasome activity.
The cap recognizes a small protein called ubiquitin and only allows the entry of proteins with covalently-linked ubiquitin into the core.
Deubiquitinase is an enzyme in the cap that removes ubiquitin from the protein substrate before it enters the 20S core.&#160;
Additionally, the cap contains an ATPase enzyme that helps unfold the target protein using the energy from ATP hydrolysis.
The 20S core particle is a hollow cylinder composed of multiple alpha and beta protein subunits assembled as a stack of rings.
Some of the proteins in the rings are proteases, enzymes responsible for the break down of proteins that enter the proteasome core.

the proteasome structure

The Proteasome Structure

The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, the protein that needs to be eliminated undergoes a process called ubiquitination, where a chain of ubiquitin molecules is attached to the 48th lysine residue of the target protein. This ubiquitin modification helps the proteasome distinguish between a target protein and a healthy protein.
The proteasome is an ATP-driven, large multi-subunit protease (26S) found in the nucleus and cytoplasm of all eukaryotes. The 26S proteasome comprises a central hollow cylindrical core (the 20S) and ring-shaped protein caps (19S). The 20S core particle is barrel-shaped, containing stacked rings with proteolytic active sites lined inside. The 19S caps act as gatekeepers and regulatory units of the proteasome. They are present at one or both ends of the core.
Caps have ubiquitin receptors, ubiquitin hydrolase, and unfoldase, each with a unique function. The ubiquitin receptor recognizes and allows ubiquitin-tagged proteins into the core, the hydrolase deubiquitinase cleaves ubiquitin from the substrate, and the unfoldase protein unfolds target proteins as they enter the protein core.
The hexameric unfoldases create a ring structure in the proteasome cap and belong to a large class of AAA proteins. Their mechanistic action is similar to other ATP-dependent helicases that cause DNA unwinding. The ATP-bound unfoldase ring binds a folded target protein held in place by its ubiquitin tag at the proteasomal cap. Next, a conformational change, driven by ATP hydrolysis, pulls the target protein substrate into the 20S core and strains the ring structure. As a result, when a protein is subjected to pulling forces, it can undergo two possible outcomes&#8212; it may either undergo partial unfolding and enter the cylindrical core, or it can retain its structure while partially retracting.
Highly stable substrates generally require hundreds of cycles of ATP hydrolysis before being pulled through the AAA ring. Once de-ubiquitylated and unfolded, the target protein is exposed to proteases inside the proteasomal core for digestion. In contrast to free cellular proteases, which quickly dissociate after their action on the target protein, the proteasome core holds the target protein until it is fully digested into smaller peptides. These small peptides are then released into the cytosol for further processing.&#160;

The ubiquitin-proteasome pathway is a well-known mechanism utilized by eukaryotic cells to remove cytoplasmic proteins that are misfolded, damaged, or no ...

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Anatomy and Physiology

Unit 1

Cells and their Components

KEY TERMS AND CONCEPTS

how cells tag proteins for breakdown

Cells use the ubiquitin-proteasome pathway to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, a protein is first tagged with ubiquitin, a small protein marker. This ubiquitination usually adds a chain of ubiquitin molecules to the 48th lysine residue on the target protein. The tag helps the proteasome tell a protein that should be removed from a healthy one.

The proteasome is a large, ATP-driven protease called the 26S proteasome. It is found in the nucleus and cytoplasm of eukaryotic cells. The 26S complex has a hollow central core called the 20S particle and ring-shaped protein caps called 19S particles. The 20S core is barrel-shaped and contains stacked rings with proteolytic active sites lined on the inside.

The 19S caps act as gatekeepers and regulatory units. They can sit on one or both ends of the core. Each cap contains a ubiquitin receptor, a ubiquitin hydrolase, and an unfoldase. The receptor recognizes ubiquitin-tagged proteins and allows them into the core. The hydrolase, also called a deubiquitinase, removes ubiquitin from the substrate. The unfoldase then starts to unfold the target protein as it enters the protein core.

The unfoldase forms a hexameric ring and belongs to the AAA protein family. Its action is similar to other ATP-dependent helicases that unwind DNA. The ATP-bound ring binds a folded target protein that is held by its ubiquitin tag at the proteasomal cap. ATP hydrolysis drives a shape change that pulls the substrate into the 20S core and strains the ring.

As the protein is pulled, it may partially unfold and enter the cylindrical core, or it may keep its shape and partially slip back. Very stable substrates can need hundreds of ATP hydrolysis cycles before they move through the AAA ring. After deubiquitylation and unfolding, the protein is exposed to proteases inside the proteasomal core and is broken down into smaller peptides. These peptides are then released into the cytosol for further processing. Unlike free cellular proteases, the proteasome keeps hold of the target protein until digestion is complete.

How Cells Tag Proteins for Breakdown

what are cells?

Cells as the Basic Unit of Life

Cells are the basic unit of life. They are the smallest structures that make up living things, and they carry out the jobs needed to stay alive. Many organisms are made of one cell, while others are made of many cells working together. Cells share a few common features, but not all cells are the same. Some cells have a nucleus, which holds the genetic material, and other cells do not. Cells also differ in size, shape, and the specific work they do in an organism. Understanding cells helps...

cell diversity

How Cells Become Specialized

Cells are the basic units of life, and they can become specialized for different jobs in the body. The idea of the cell began in 1665, when Robert Hooke looked at dead cork tissue under a microscope and named the small boxlike spaces "cells" because they reminded him of monks' rooms. About ten years later, Antonie van Leeuwenhoek became the first person to see living, moving cells under a microscope. Over the next century, scientists developed the theory that cells are the fundamental unit of...

cytoplasm

Cytoplasm: The Cell’s Internal Fluid

Cytoplasm is the internal fluid of the cell. It fills the space inside the cell membrane and surrounds the cell’s structures. This fluid helps support the cell and gives organelles a place to stay suspended. It is an important part of cell structure because many cell activities happen within it. In many cells, the cytoplasm also helps move materials around the cell. Its fluid nature allows substances to travel where they are needed and helps keep the cell organized.

the nucleus

Nucleus Structure and Cell Control

The nucleus is the cell’s control center. It helps direct how a cell works and supports the cell’s genetic material. In many eukaryotic cells, the nucleus is the most obvious internal organelle. The nucleus is surrounded by a nuclear envelope. This envelope separates the nucleus from the rest of the cell. It also helps protect the DNA inside. Inside the nucleus, the genetic material is organized as chromatin. Chromatin contains DNA and proteins. When a cell prepares to divide, this material...

the nucleosome

DNA Packing with Histones

DNA packing with histones allows human DNA to fit inside the cell nucleus. Human DNA is almost two meters long, but the nucleus is only a few microns wide. To fit this amount of DNA into such a small space, it is organized into several levels of compaction. The most compact form of DNA is the chromosome, which can be seen under a microscope in a dividing cell. Inside a chromosome, DNA wraps twice around a histone octamer core. This core is made of eight histone proteins. The DNA and histone...

the nucleosome core particle

Histone Tails and DNA Packing

Nucleosomes help pack and protect DNA inside the cell. They are made when DNA wraps around a histone core. That core is an octamer, or eight-part protein complex, with two copies each of H2A, H2B, H3, and H4. Nucleosomes must do two jobs at once. They protect fragile DNA from physical damage and help DNA fit into a smaller space. They also must let polymerase enzymes reach histone-bound DNA during replication and transcription. To solve this, the DNA can partially unfold when needed, while...

chromatin packaging

How DNA Fits Inside the Nucleus

Chromatin is the DNA-protein material that helps human DNA fit inside the nucleus. A human somatic cell contains about 6 billion base pairs of DNA, and each base pair is 0.34 nm long. That means a diploid cell holds about 2 meters of DNA inside a nucleus that is only 10 to 20 microns wide. Histones make this packing possible. These specialized DNA-binding proteins help organize DNA into a compact chromatin structure. Chromatin is then folded into higher-order forms, and it reaches its highest...

the endoplasmic reticulum

Endoplasmic Reticulum: Cell Transport Network

The endoplasmic reticulum is a major membrane network inside the cell. It helps move materials and supports cell function. Its structure gives the cell a large internal surface for important processes. The endoplasmic reticulum has two main forms. Rough endoplasmic reticulum has ribosomes attached to its surface, while smooth endoplasmic reticulum does not. These forms help the cell handle different tasks. The rough endoplasmic reticulum is linked to protein production. The smooth endoplasmic...

golgi apparatus

Golgi Apparatus in Cell Transport

The Golgi apparatus is a cell structure that helps sort and move materials inside the cell. It works with membrane traffic, which is the movement of substances in small membrane-bound packages. The Golgi apparatus receives materials from other parts of the cell and processes them before they are sent to their next destination. It plays an important role in helping the cell organize what it makes and where those materials go. In many cells, the Golgi apparatus is part of a larger system of...

lysosomes

Lysosomes and Cell Recycling

Lysosomes are cell organelles that help break down worn-out materials and recycle useful parts. They contain digestive enzymes that work inside a membrane-bound compartment. This makes them important for keeping cells clean and organized. Lysosomes use hydrolytic enzymes to digest large molecules, cell debris, and other unwanted material. Their membrane helps protect the rest of the cell from these enzymes. When digestion is complete, the cell can reuse some of the released building blocks. <br...

mitochondria

Mitochondria in Cellular Energy Production

Mitochondria are cell structures linked to energy production. They help cells convert energy from nutrients into a usable form. In many cells, they are important for keeping energy supply steady. Mitochondria also have their own DNA. This sets them apart from many other parts of the cell. Their structure and genetic material help scientists study how they function in cells. Understanding mitochondria is important in biology because energy use affects how cells work. These structures play a...

mitochondrial membranes

Mitochondrial Membranes in Energy Production

Mitochondrial membranes help cells make energy. They form the outer boundary of the mitochondrion and also create the inner folds inside it. These membranes give the organelle its structure and support its role in energy production. The outer membrane surrounds the mitochondrion. The inner membrane is folded into many cristae, which increase surface area. This extra surface gives more space for the steps that help the cell produce usable energy. Together, the mitochondrial membranes separate...

peroxisomes

Peroxisome Functions in Cells

Peroxisomes are small organelles in cells that help manage chemical reactions. They are known for breaking down fatty acids and for handling harmful byproducts made during metabolism. These roles help keep the cell functioning normally. Peroxisomes also contain enzymes that use and break down hydrogen peroxide. Hydrogen peroxide is a reactive molecule, so cells must control it carefully. By processing it, peroxisomes support the cell's chemical balance. In cell biology, peroxisomes are...

ribosomes

Ribosomes and Protein Assembly

Ribosomes are the cell structures that build proteins. They read the instructions carried by messenger RNA, or mRNA, and join amino acids together in the correct order. This process is called translation. Ribosomes are made of ribosomal RNA and proteins. They work as the site where genetic information is turned into a protein. As the ribosome moves along the mRNA strand, it helps match each code in the message with the right amino acid. Protein assembly by ribosomes is a key step in how cells...

Cells use the ubiquitin-proteasome pathway to remove cytoplasmic proteins that are misfolded, damaged, or no longer needed. In this pathway, a protein is first tagged with ubiquitin, a small protein marker. This ubiquitination usually adds a chain of ubiquitin molecules to the 48th lysine residue on the target protein. The tag helps the proteasome tell a protein that should be removed from a healthy one. The proteasome is a large, ATP-driven protease called the 26S proteasome. It is found in...

the proteasome

How Cells Remove Damaged Proteins

Eukaryotic cells use the ubiquitin-proteasome pathway to remove damaged, misfolded, or unwanted cytoplasmic proteins. This selective cleanup helps protect the cell and keep protein levels under control. In this pathway, target proteins are tagged with ubiquitin, a small protein label. Three enzymes work together to attach ubiquitin to the target: E1, the ubiquitin-activating enzyme; E2, the ubiquitin-conjugating enzyme; and E3, the ubiquitin ligase. After tagging, the ubiquitinated proteins...

introduction to cytoskeleton

Cytoskeleton: Cell Support and Movement

The cytoskeleton gives cells shape, support, and the ability to move. It is a network of protein fibers inside the cell. These fibers help organize the cell and keep its parts in place. The cytoskeleton includes microfilaments, intermediate filaments, and microtubules. Microfilaments are made of actin. They help the cell change shape and move. Intermediate filaments provide strength. Microtubules are larger fibers that help with cell organization and transport. Together, these structures...

centrioles and centrosomes

Centrosomes in Cell Division

Centrosomes help organize cell division in animal cells. Most animal cells contain a pair of centrioles that together make a centrosome. Before division begins, the cell copies its centrosome so that two centrosomes sit side by side. During prophase, these centrosomes start moving toward opposite sides of the cell. As the centrosomes separate, microtubules grow outward from each one. These fibers and the centrosomes form the mitotic spindle. Near the end of prophase, also called prometaphase...

microtubules in cell motility

Microtubules and Cell Movement

Microtubules help cells move and change shape. They are part of the cell’s internal support system, called the cytoskeleton. In moving cells, microtubules work with other cell parts to guide motion. These structures are built from tubulin, a protein that joins together to form long, hollow tubes. Their shape makes them strong and flexible enough to support cell activity. In many cells, microtubules also help organize movement inside the cell. Cell motility means the ability of a cell to move.

mechanism of ciliary motion

How Cilia Create Movement

Cilia create movement by bending in a coordinated way. These tiny, hairlike structures help cells and fluids move in specific directions. The mechanism of ciliary motion explains how this repeated motion works. Cilia beat through a controlled motion that depends on their internal structure. Their movement is not random. It follows a set pattern that allows the cilia to push material across a surface or help a cell move. Understanding ciliary motion is important in cell biology. It shows how...

microvilli

Microvilli and Cell Surface Area

Microvilli are tiny finger-like projections on the surface of certain cells. They increase the surface area of the apical surface, which helps cells absorb or secrete substances more effectively. These structures are common in cells lining the small intestine, kidney tubules, and some cells in the respiratory and reproductive systems. Each microvillus has a core made of actin filaments. Actin is a structural protein that helps support cell shape. Other proteins, including villin and fimbrin,...

key terms and concepts

Learn how ubiquitin tags mark damaged or unneeded proteins for the proteasome, and how the 19S cap and 20S core break them into peptides.

How Cells Tag Proteins for Breakdown | JoVE K12

anatomy and physiology

JoVE Core Anatomy and Physiology showcases the anatomical and physiological details of the human body in comprehensive, clear, and engaging video animations. This collection of lessons focuses on the structures, components, functions, and requirements of the human body. It is complemented by scientist-in-action videos that demonstrate the application of this knowledge in real-world medical and research settings.

How Cells Tag Proteins for Breakdown

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