This document summarizes different classes of proteolytic enzymes (proteases) including serine, cysteine, aspartic acid, and metallo proteases. It describes their catalytic mechanisms and examples of each class. Key points are that serine proteases use a catalytic triad of serine, histidine, and aspartate residues in their mechanisms, while cysteine proteases employ a catalytic cysteine and histidine. Aspartic and metallo proteases also have distinct catalytic residues and mechanisms. The roles of proteases in digestion, lysosomes, and other cellular processes are overviewed.
This document summarizes different classes of proteolytic enzymes and their mechanisms of action. There are several classes of proteases including serine, aspartate, cysteine, and metalloproteases. Serine proteases like trypsin and chymotrypsin cleave peptides using a catalytic triad of serine, histidine, and aspartate residues. Aspartate proteases also use acid/base catalysis, while cysteine and metalloproteases employ cysteine and zinc residues respectively in their catalytic mechanisms. Proteases are regulated by activation, localization, and inhibition by endogenous protease inhibitors. Lysosomes contain many hydrolytic enzymes including proteases that degrade macromolecules through autophagy and other
I apologize, as an AI assistant I do not actually use or perform laboratory work. I do not have personal experience working with different classes of proteases.
This document provides an overview of post-translational events. It discusses various post-translational modifications including protein folding, proteolytic cleavage, and chemical modifications such as phosphorylation, acetylation, glycosylation, lipidation, and ubiquitination. These modifications influence the structure, stability, activity, and interactions of proteins and play an important role in cellular functions and signaling pathways. The document also examines specific post-translational modifications in depth, including the processes of protein folding, proteolytic cleavage, and various chemical modifications of proteins.
Unit III covers enzymes, proteases, carbonic anhydrase, restriction enzymes, and nucleoside monophosphate kinases. It then discusses photosynthesis and biological energy production. Enzymes are proteins that act as catalysts to accelerate reactions without being permanently changed. Proteases are enzymes that cleave proteins. Carbonic anhydrase catalyzes the reversible reaction between carbon dioxide and bicarbonate. Restriction enzymes recognize and cut DNA at specific sequences. Nucleoside monophosphate kinases phosphorylate purine monophosphates as part of converting them to their triphosphate forms for use in DNA synthesis.
Post-translational modifications (PTMs) are chemical changes that occur to proteins after translation. PTMs are essential for normal protein function. The document defines key PTMs like phosphorylation, glycosylation, and acetylation. It explains that after translation in the cytosol, many proteins are directed to the endoplasmic reticulum for modification and protein folding. PTMs increase proteome complexity compared to the genome by altering protein structures from the gene sequence. Common PTMs like phosphorylation and glycosylation are catalyzed by specific enzymes and influence protein interactions.
Enzymes are biological molecules (typically proteins) that significantly speed up the rate of virtually all of the chemical reactions that take place within cells. They are vital for life and serve a wide range of important functions in the body, such as aiding in digestion and metabolism
Chemistry of prostaglandins, leukotrienes and thromboxanesAbhimanyu Awasthi
The document summarizes a presentation on the chemistry of prostaglandins, leukotrienes, and thromboxanes. Prostaglandins, leukotrienes, and thromboxanes are oxygen metabolites of arachidonic acid that form a family of lipid substances with intrinsic biological activities. They are involved in processes like inflammation, platelet aggregation, and vascular homeostasis. The presentation covers their biosynthesis from arachidonic acid, sub-families, properties, and biologically important examples like prostacyclin, thromboxane A2, and leukotriene B4. It also discusses the enzymes and pathways involved in their synthesis.
This document summarizes different classes of proteolytic enzymes and their mechanisms of action. There are several classes of proteases including serine, aspartate, cysteine, and metalloproteases. Serine proteases like trypsin and chymotrypsin cleave peptides using a catalytic triad of serine, histidine, and aspartate residues. Aspartate proteases also use acid/base catalysis, while cysteine and metalloproteases employ cysteine and zinc residues respectively in their catalytic mechanisms. Proteases are regulated by activation, localization, and inhibition by endogenous protease inhibitors. Lysosomes contain many hydrolytic enzymes including proteases that degrade macromolecules through autophagy and other
I apologize, as an AI assistant I do not actually use or perform laboratory work. I do not have personal experience working with different classes of proteases.
This document provides an overview of post-translational events. It discusses various post-translational modifications including protein folding, proteolytic cleavage, and chemical modifications such as phosphorylation, acetylation, glycosylation, lipidation, and ubiquitination. These modifications influence the structure, stability, activity, and interactions of proteins and play an important role in cellular functions and signaling pathways. The document also examines specific post-translational modifications in depth, including the processes of protein folding, proteolytic cleavage, and various chemical modifications of proteins.
Unit III covers enzymes, proteases, carbonic anhydrase, restriction enzymes, and nucleoside monophosphate kinases. It then discusses photosynthesis and biological energy production. Enzymes are proteins that act as catalysts to accelerate reactions without being permanently changed. Proteases are enzymes that cleave proteins. Carbonic anhydrase catalyzes the reversible reaction between carbon dioxide and bicarbonate. Restriction enzymes recognize and cut DNA at specific sequences. Nucleoside monophosphate kinases phosphorylate purine monophosphates as part of converting them to their triphosphate forms for use in DNA synthesis.
Post-translational modifications (PTMs) are chemical changes that occur to proteins after translation. PTMs are essential for normal protein function. The document defines key PTMs like phosphorylation, glycosylation, and acetylation. It explains that after translation in the cytosol, many proteins are directed to the endoplasmic reticulum for modification and protein folding. PTMs increase proteome complexity compared to the genome by altering protein structures from the gene sequence. Common PTMs like phosphorylation and glycosylation are catalyzed by specific enzymes and influence protein interactions.
Enzymes are biological molecules (typically proteins) that significantly speed up the rate of virtually all of the chemical reactions that take place within cells. They are vital for life and serve a wide range of important functions in the body, such as aiding in digestion and metabolism
Chemistry of prostaglandins, leukotrienes and thromboxanesAbhimanyu Awasthi
The document summarizes a presentation on the chemistry of prostaglandins, leukotrienes, and thromboxanes. Prostaglandins, leukotrienes, and thromboxanes are oxygen metabolites of arachidonic acid that form a family of lipid substances with intrinsic biological activities. They are involved in processes like inflammation, platelet aggregation, and vascular homeostasis. The presentation covers their biosynthesis from arachidonic acid, sub-families, properties, and biologically important examples like prostacyclin, thromboxane A2, and leukotriene B4. It also discusses the enzymes and pathways involved in their synthesis.
Digestion and absorption of proteins for Medical SchoolRavi Kiran
This document summarizes the digestion and absorption of proteins in the human body. It discusses:
1) The proteolytic enzymes that break down proteins into peptides and amino acids in the stomach and small intestine, such as pepsin, trypsin, and chymotrypsin.
2) The categories of proteases (protein-digesting enzymes) including exopeptidases, endopeptidases, and their examples.
3) The absorption of amino acids in the small intestine and their transport to various organs in the body like the brain, kidneys, and liver.
4) The intracellular breakdown of proteins by cathepsins, the ubiquitin pathway, and proteasomes.
Post-translational modifications are important biochemical mechanisms that regulate protein function. Common types of post-translational modifications include phosphorylation, hydroxylation, glycosylation, and methylation. These modifications occur on amino acid side chains or termini and are catalyzed by specific enzymes. For example, phosphorylation regulates enzyme activity, while hydroxylation and glycosylation of amino acids are required for collagen assembly and function. Overall, post-translational modifications expand the functional diversity of the proteome.
This document discusses enzymes and their structure and function. It begins by describing the history of the discovery of enzymes and defines them as biological catalysts. It then discusses various topics related to enzymes, including their catalytic mechanisms, structural classifications, active sites, cofactors, nomenclature systems like EC numbers, and factors that influence their activity such as temperature, pH, and substrate concentration. Regulatory mechanisms of enzyme activity are also briefly mentioned.
This document discusses proteins and their structure and functions. It covers the following key points in 3 sentences:
Proteins are large, complex biomolecules formed from amino acids that are essential components of living cells and tissues. They perform a wide variety of important functions, including providing structure, acting as enzymes and transporters, and controlling gene expression. Proteins are classified based on their chemical properties, solubility, functions, and nutritional importance; some of the major protein types discussed are globular and fibrous proteins, enzymes, hormones, membrane proteins, and complete and incomplete proteins.
Enzymes are biological catalysts that accelerate chemical reactions without being consumed. They achieve this by lowering the activation energy of reactions. The document discusses the definition, mechanism of action, classification, and properties of enzymes. It also examines factors that affect enzyme activity such as temperature, pH, and inhibitors. Important clinical enzymes are mentioned for diagnosing conditions like heart attacks and liver disease. Key applications of enzymes include disease diagnosis, therapeutics, and use in laboratory reactions.
This document discusses enzymes and their properties. It defines enzymes as biocatalysts that are proteins synthesized by living cells. Enzymes lower the activation energy of chemical reactions and catalyze the formation of products. Enzymes can exist as single peptides or complexes of multiple subunits. They are classified based on the type of reaction catalyzed and have specific active sites that bind substrates. Many factors influence enzyme activity such as temperature, pH, substrate and inhibitor concentrations. The mechanisms of enzyme action and inhibition are also described.
This document discusses lysosomes and chaperone-mediated autophagy (CMA). It provides background on the discovery of lysosomes and their structure and functions. Lysosomes contain hydrolytic enzymes and digest macromolecules, cellular debris, and foreign material. CMA selectively degrades cytosolic proteins through binding to a chaperone and lysosomal membrane protein LAMP-2A. Disruption of CMA is implicated in diseases like Parkinson's and cancer. CMA activity declines with age.
COVALENT MODIFICATION AND ZYMOGEN ACTIVATIONMariya Raju
1) Covalent modifications, both reversible and irreversible, play important roles in regulating enzyme function. Reversible modifications like phosphorylation fine-tune enzyme activity, while irreversible proteolysis activates zymogens into active enzymes.
2) Digestive enzymes like trypsinogen are synthesized as inactive zymogens to avoid unwanted catalysis, then activated through limited and specific proteolysis. This proteolysis removes inhibitory peptide sequences and allows catalytic activity.
3) Activation of zymogens through proteolytic cascades amplifies hormonal signals, allowing a small stimulus to elicit a large response. This cascade activation greatly increases the potency and efficiency of regulation compared to direct hormone binding.
This document discusses enzymes and provides definitions, explanations of their mechanisms of action, and classifications. It describes how enzymes lower the activation energy of reactions, form enzyme-substrate complexes, and use induced fit and cofactors/coenzymes. Enzymes are classified based on the type of reaction they catalyze. Key properties include specificity, inhibition, and factors like temperature, pH, and inhibitors that influence enzyme activity. Important clinical enzymes are discussed.
Intracellular trafficking and protein sortingapeksha40
This document discusses intracellular protein trafficking and sorting. It describes how proteins contain signal sequences that target them to different organelles like the endoplasmic reticulum, mitochondria, peroxisomes and nucleus. It explains the roles of the signal recognition particle, translocon complex and chaperones in transporting proteins into the ER. The Ran GTPase system and importins/exportins are also summarized in their role in nuclear transport. Clinical implications of defects in peroxisome biogenesis are mentioned.
The document discusses the structure and functions of the cell membrane. It describes how the phospholipid bilayer is semipermeable and contains integral and peripheral proteins that facilitate transport. There are three main types of membrane transport: passive diffusion, active transport using ATP, and vesicular transport using exocytosis and endocytosis. Passive diffusion includes simple diffusion, facilitated diffusion through channels and carriers, and osmosis. Active transport includes the sodium-potassium pump and secondary active transport via symporters and antiporters.
The document discusses the structure and functions of the cell membrane. It describes how the phospholipid bilayer is semipermeable and contains integral and peripheral proteins that facilitate transport. There are three main types of membrane transport: passive diffusion, active transport using ATP, and vesicular transport using exocytosis and endocytosis. Passive diffusion includes simple diffusion, facilitated diffusion through channels and carriers, and osmosis. Active transport includes the sodium-potassium pump and secondary active transport via symporters and antiporters.
Physiological And Pathological Systems Within The...Deb Birch
Redox signalling is an important electron transfer process that regulates many physiological and pathological systems in the circulatory system. It is usually induced by reactive oxygen species and can alter cell processes. Redox signalling involves thiol-based redox couples that regulate imbalances in redox potentials and are linked to changes in redox potentials. Cysteine is an amino acid that can undergo oxidative modifications to perform different functions as part of redox signalling.
This document discusses enzymes and their clinical applications. It describes the general properties of enzymes, noting that they are protein catalysts that increase the rate of chemical reactions without changing themselves. It also discusses the nature, types, cofactors and coenzymes of enzymes. The mechanisms of enzyme action including the lock and key and induced fit models are described. The document also covers enzyme classification, regulation, zymogens, isoenzymes and the catalytic properties of enzymes including substrate specificity and active sites.
enzymes and it's clinical applications.pptxAlyaaKaram1
This document discusses enzymes and their properties. It defines enzymes as protein catalysts that increase the rate of chemical reactions without being used up. Enzymes can exist as simple enzymes made of only protein, or as holoenzymes which contain both a protein component (apoenzyme) and a non-protein component (cofactor). Coenzymes are cofactors that are vitamin derivatives essential for enzyme function. Metal ions are also required by many enzymes and can promote enzyme action in various ways. The document further describes enzyme properties such as active sites, specificity, regulation and isoenzymes. It outlines the classification system for enzymes and discusses factors that affect enzyme activity like temperature, pH and substrate concentration.
The plasma membrane is selectively permeable due to its structure of phospholipids and proteins. It contains transport proteins that selectively move molecules into and out of the cell, including ion channels, carriers, and pumps. Ion channels come in many varieties but generally involve selective permeability to ions and gating mechanisms. Transport proteins also include carriers that move molecules via symport, antiport, or uniport mechanisms, as well as ATP-dependent pumps and ABC transporters that use ATP to actively transport substances against gradients. Regulation of transport involves controlling expression and gating of specific transport proteins.
Organelles interact to carry out important cellular processes like material uptake/release, protein synthesis, and digestion.
(1) Endocytosis and exocytosis allow cells to take in and release material through vesicle trafficking between the plasma membrane and endosomes/lysosomes. (2) The ER and Golgi apparatus work together to synthesize, modify, and transport proteins, with the ER producing proteins and the Golgi processing and packaging them. (3) Lysosomes digest material through phagocytosis, autophagy, and other pathways, while the proteasome degrades unwanted cytosolic proteins. Defects in these organelle interactions can cause diseases.
This document provides information about enzymes, including their chemistry, structure, cofactors, mechanism of action, kinetics, and classification. It discusses that enzymes are proteins that act as biological catalysts, speeding up biochemical reactions. They have an active site that binds to substrates. Cofactors such as metal ions and organic molecules are required for some enzyme activities. The mechanism of action involves lowering the activation energy of reactions. Enzyme kinetics examines how factors like temperature, pH, and substrate concentration influence reaction rates. Enzymes are classified based on the type of reaction they catalyze.
Enzymes are protein catalysts that speed up biochemical reactions without being consumed. They achieve high reaction rates through substrate binding and shape complementarity. Enzyme activity is affected by factors like temperature, pH, and salt concentration that can alter protein structure. Most enzymes exhibit high specificity for their substrate. Inhibition studies provide information about enzyme mechanisms and active sites. Regulation of enzyme activity occurs through feedback inhibition, allosteric regulation, covalent modification like phosphorylation, and conversion of inactive zymogens to active forms.
This document discusses lipids, which are concentrated energy molecules that serve several functions in biology. Lipids include fats, oils, waxes, and hormones. They are used for energy storage and provide twice the energy of carbohydrates. Lipids also make up cell membranes and help cushion and insulate organs. Saturated fats from animals are solid at room temperature and contribute to heart disease, while unsaturated fats from plants and fish are liquid and are a healthier choice. Cell membranes contain phospholipids that form a barrier for the cell, with hydrophilic heads on the outside and hydrophobic tails on the inside.
This document discusses lipids and membranes. It describes the basic structures of lipids like fatty acids, glycerophospholipids, sphingolipids, and cholesterol. These lipids can assemble into structures like micelles and bilayers in aqueous environments due to their amphipathic nature. Bilayers allow for the formation of cell membranes. Membranes contain proteins that can be integral, peripheral, or lipid-anchored. Lipid composition and proteins influence membrane properties like fluidity.
Digestion and absorption of proteins for Medical SchoolRavi Kiran
This document summarizes the digestion and absorption of proteins in the human body. It discusses:
1) The proteolytic enzymes that break down proteins into peptides and amino acids in the stomach and small intestine, such as pepsin, trypsin, and chymotrypsin.
2) The categories of proteases (protein-digesting enzymes) including exopeptidases, endopeptidases, and their examples.
3) The absorption of amino acids in the small intestine and their transport to various organs in the body like the brain, kidneys, and liver.
4) The intracellular breakdown of proteins by cathepsins, the ubiquitin pathway, and proteasomes.
Post-translational modifications are important biochemical mechanisms that regulate protein function. Common types of post-translational modifications include phosphorylation, hydroxylation, glycosylation, and methylation. These modifications occur on amino acid side chains or termini and are catalyzed by specific enzymes. For example, phosphorylation regulates enzyme activity, while hydroxylation and glycosylation of amino acids are required for collagen assembly and function. Overall, post-translational modifications expand the functional diversity of the proteome.
This document discusses enzymes and their structure and function. It begins by describing the history of the discovery of enzymes and defines them as biological catalysts. It then discusses various topics related to enzymes, including their catalytic mechanisms, structural classifications, active sites, cofactors, nomenclature systems like EC numbers, and factors that influence their activity such as temperature, pH, and substrate concentration. Regulatory mechanisms of enzyme activity are also briefly mentioned.
This document discusses proteins and their structure and functions. It covers the following key points in 3 sentences:
Proteins are large, complex biomolecules formed from amino acids that are essential components of living cells and tissues. They perform a wide variety of important functions, including providing structure, acting as enzymes and transporters, and controlling gene expression. Proteins are classified based on their chemical properties, solubility, functions, and nutritional importance; some of the major protein types discussed are globular and fibrous proteins, enzymes, hormones, membrane proteins, and complete and incomplete proteins.
Enzymes are biological catalysts that accelerate chemical reactions without being consumed. They achieve this by lowering the activation energy of reactions. The document discusses the definition, mechanism of action, classification, and properties of enzymes. It also examines factors that affect enzyme activity such as temperature, pH, and inhibitors. Important clinical enzymes are mentioned for diagnosing conditions like heart attacks and liver disease. Key applications of enzymes include disease diagnosis, therapeutics, and use in laboratory reactions.
This document discusses enzymes and their properties. It defines enzymes as biocatalysts that are proteins synthesized by living cells. Enzymes lower the activation energy of chemical reactions and catalyze the formation of products. Enzymes can exist as single peptides or complexes of multiple subunits. They are classified based on the type of reaction catalyzed and have specific active sites that bind substrates. Many factors influence enzyme activity such as temperature, pH, substrate and inhibitor concentrations. The mechanisms of enzyme action and inhibition are also described.
This document discusses lysosomes and chaperone-mediated autophagy (CMA). It provides background on the discovery of lysosomes and their structure and functions. Lysosomes contain hydrolytic enzymes and digest macromolecules, cellular debris, and foreign material. CMA selectively degrades cytosolic proteins through binding to a chaperone and lysosomal membrane protein LAMP-2A. Disruption of CMA is implicated in diseases like Parkinson's and cancer. CMA activity declines with age.
COVALENT MODIFICATION AND ZYMOGEN ACTIVATIONMariya Raju
1) Covalent modifications, both reversible and irreversible, play important roles in regulating enzyme function. Reversible modifications like phosphorylation fine-tune enzyme activity, while irreversible proteolysis activates zymogens into active enzymes.
2) Digestive enzymes like trypsinogen are synthesized as inactive zymogens to avoid unwanted catalysis, then activated through limited and specific proteolysis. This proteolysis removes inhibitory peptide sequences and allows catalytic activity.
3) Activation of zymogens through proteolytic cascades amplifies hormonal signals, allowing a small stimulus to elicit a large response. This cascade activation greatly increases the potency and efficiency of regulation compared to direct hormone binding.
This document discusses enzymes and provides definitions, explanations of their mechanisms of action, and classifications. It describes how enzymes lower the activation energy of reactions, form enzyme-substrate complexes, and use induced fit and cofactors/coenzymes. Enzymes are classified based on the type of reaction they catalyze. Key properties include specificity, inhibition, and factors like temperature, pH, and inhibitors that influence enzyme activity. Important clinical enzymes are discussed.
Intracellular trafficking and protein sortingapeksha40
This document discusses intracellular protein trafficking and sorting. It describes how proteins contain signal sequences that target them to different organelles like the endoplasmic reticulum, mitochondria, peroxisomes and nucleus. It explains the roles of the signal recognition particle, translocon complex and chaperones in transporting proteins into the ER. The Ran GTPase system and importins/exportins are also summarized in their role in nuclear transport. Clinical implications of defects in peroxisome biogenesis are mentioned.
The document discusses the structure and functions of the cell membrane. It describes how the phospholipid bilayer is semipermeable and contains integral and peripheral proteins that facilitate transport. There are three main types of membrane transport: passive diffusion, active transport using ATP, and vesicular transport using exocytosis and endocytosis. Passive diffusion includes simple diffusion, facilitated diffusion through channels and carriers, and osmosis. Active transport includes the sodium-potassium pump and secondary active transport via symporters and antiporters.
The document discusses the structure and functions of the cell membrane. It describes how the phospholipid bilayer is semipermeable and contains integral and peripheral proteins that facilitate transport. There are three main types of membrane transport: passive diffusion, active transport using ATP, and vesicular transport using exocytosis and endocytosis. Passive diffusion includes simple diffusion, facilitated diffusion through channels and carriers, and osmosis. Active transport includes the sodium-potassium pump and secondary active transport via symporters and antiporters.
Physiological And Pathological Systems Within The...Deb Birch
Redox signalling is an important electron transfer process that regulates many physiological and pathological systems in the circulatory system. It is usually induced by reactive oxygen species and can alter cell processes. Redox signalling involves thiol-based redox couples that regulate imbalances in redox potentials and are linked to changes in redox potentials. Cysteine is an amino acid that can undergo oxidative modifications to perform different functions as part of redox signalling.
This document discusses enzymes and their clinical applications. It describes the general properties of enzymes, noting that they are protein catalysts that increase the rate of chemical reactions without changing themselves. It also discusses the nature, types, cofactors and coenzymes of enzymes. The mechanisms of enzyme action including the lock and key and induced fit models are described. The document also covers enzyme classification, regulation, zymogens, isoenzymes and the catalytic properties of enzymes including substrate specificity and active sites.
enzymes and it's clinical applications.pptxAlyaaKaram1
This document discusses enzymes and their properties. It defines enzymes as protein catalysts that increase the rate of chemical reactions without being used up. Enzymes can exist as simple enzymes made of only protein, or as holoenzymes which contain both a protein component (apoenzyme) and a non-protein component (cofactor). Coenzymes are cofactors that are vitamin derivatives essential for enzyme function. Metal ions are also required by many enzymes and can promote enzyme action in various ways. The document further describes enzyme properties such as active sites, specificity, regulation and isoenzymes. It outlines the classification system for enzymes and discusses factors that affect enzyme activity like temperature, pH and substrate concentration.
The plasma membrane is selectively permeable due to its structure of phospholipids and proteins. It contains transport proteins that selectively move molecules into and out of the cell, including ion channels, carriers, and pumps. Ion channels come in many varieties but generally involve selective permeability to ions and gating mechanisms. Transport proteins also include carriers that move molecules via symport, antiport, or uniport mechanisms, as well as ATP-dependent pumps and ABC transporters that use ATP to actively transport substances against gradients. Regulation of transport involves controlling expression and gating of specific transport proteins.
Organelles interact to carry out important cellular processes like material uptake/release, protein synthesis, and digestion.
(1) Endocytosis and exocytosis allow cells to take in and release material through vesicle trafficking between the plasma membrane and endosomes/lysosomes. (2) The ER and Golgi apparatus work together to synthesize, modify, and transport proteins, with the ER producing proteins and the Golgi processing and packaging them. (3) Lysosomes digest material through phagocytosis, autophagy, and other pathways, while the proteasome degrades unwanted cytosolic proteins. Defects in these organelle interactions can cause diseases.
This document provides information about enzymes, including their chemistry, structure, cofactors, mechanism of action, kinetics, and classification. It discusses that enzymes are proteins that act as biological catalysts, speeding up biochemical reactions. They have an active site that binds to substrates. Cofactors such as metal ions and organic molecules are required for some enzyme activities. The mechanism of action involves lowering the activation energy of reactions. Enzyme kinetics examines how factors like temperature, pH, and substrate concentration influence reaction rates. Enzymes are classified based on the type of reaction they catalyze.
Enzymes are protein catalysts that speed up biochemical reactions without being consumed. They achieve high reaction rates through substrate binding and shape complementarity. Enzyme activity is affected by factors like temperature, pH, and salt concentration that can alter protein structure. Most enzymes exhibit high specificity for their substrate. Inhibition studies provide information about enzyme mechanisms and active sites. Regulation of enzyme activity occurs through feedback inhibition, allosteric regulation, covalent modification like phosphorylation, and conversion of inactive zymogens to active forms.
This document discusses lipids, which are concentrated energy molecules that serve several functions in biology. Lipids include fats, oils, waxes, and hormones. They are used for energy storage and provide twice the energy of carbohydrates. Lipids also make up cell membranes and help cushion and insulate organs. Saturated fats from animals are solid at room temperature and contribute to heart disease, while unsaturated fats from plants and fish are liquid and are a healthier choice. Cell membranes contain phospholipids that form a barrier for the cell, with hydrophilic heads on the outside and hydrophobic tails on the inside.
This document discusses lipids and membranes. It describes the basic structures of lipids like fatty acids, glycerophospholipids, sphingolipids, and cholesterol. These lipids can assemble into structures like micelles and bilayers in aqueous environments due to their amphipathic nature. Bilayers allow for the formation of cell membranes. Membranes contain proteins that can be integral, peripheral, or lipid-anchored. Lipid composition and proteins influence membrane properties like fluidity.
The document discusses the evolution of cell membranes from early RNA molecules clinging to clay particles to the modern fluid mosaic model. Key events include the formation of lipid bilayers that separated internal and external chemistry, allowing more efficient reactions. Experiments showed lipids spontaneously forming enclosed compartments and lipid bilayers with integral membrane proteins that gave membranes a mosaic-like structure. The fluid mosaic model proposes membranes are fluid with lipids and proteins able to diffuse freely within the plane of the bilayer. Transport proteins like channels and carriers allow selective permeability while pumps use ATP to transport molecules against gradients.
This document provides information about lipids and fatty acids. It defines lipids as biomolecules that contain fatty acids or a steroid nucleus and are soluble in organic solvents but not water. There are different types of lipids containing fatty acids, including waxes, fats and oils (triacylglycerols), glycerophospholipids, and prostaglandins. Fatty acids are long-chain carboxylic acids that can be saturated or unsaturated. Fats and oils are esters of glycerol and three fatty acids called triacylglycerols. Unsaturated fatty acids have kinks that prevent close packing, giving oils and unsaturated fats lower melting points than saturated fats. Hydrogen
The octapeptide contains the amino acids A, C, D, G, L, M, S. Enzyme digestion and mass spectrometry identify the fragments D-C-M, A-S, C-M-A, S-G-A, and L-D. This information determines the primary structure is L-A-G-S-D-C-M-A. Secondary structure is based on bond rotations forming elements like alpha helices and beta pleated sheets. Tertiary structure describes the overall shape from peptide chain folding while quaternary structure involves interactions of multiple protein subunits.
This chapter discusses protein therapeutics including recombinant proteins and monoclonal antibodies. It provides examples of recombinant proteins approved for human use to treat disorders like hemophilia, diabetes, and cystic fibrosis. The chapter outlines different expression systems used to produce recombinant proteins, including bacteria, yeast, insect, and mammalian cells. It also describes the structure of antibodies and the development of monoclonal antibodies as therapeutic agents, from mouse antibodies to humanized antibodies to reduce immunogenicity.
Proteins are made up of chains of amino acids and are essential to many bodily functions. Amino acids link together through peptide bonds and proteins fold into complex three-dimensional shapes that determine their specific roles. Both insufficient and excessive protein intake can be harmful, so a balanced diet containing moderate protein is recommended.
This document provides an overview of amino acids, peptides, and proteins. It discusses the 20 standard amino acids, including their structures, properties, and classifications. Peptide bond formation between amino acids is described. Peptides are defined as short chains of amino acids, with examples of peptide functions. Proteins are introduced as longer polymers made up of amino acids that may also contain cofactors or modifications. The learning goals cover the key aspects of amino acid and peptide structures and properties.
Protein folding is the process by which a protein goes from an unfolded state to its biologically active three-dimensional structure. It is important to understand protein folding to help predict protein structures from sequence alone and to understand diseases caused by protein misfolding. Proteins typically fold through progressive formation of native-like structures rather than through a random search. Molecular chaperones help other proteins fold within cells. Misfolded proteins can form amyloid fibrils associated with diseases. Computational methods aim to predict protein structures from sequence using fragment libraries and modeling protein energy landscapes. Protein design techniques aim to computationally modify protein sequences to achieve desired stabilities, functions, and binding properties.
This document discusses protein classification and structure. It defines protein classification as grouping proteins based on structure, function or size. Proteins can have domains and subunits. They come in globular, fibrous, and other shapes. Proteins are linked within and between polypeptide chains using covalent bonds. Proteins bind other molecules specifically through interactions like ionic bonds. Binding allows proteins to regulate activity and form complexes with other molecules like opsins.
Heat shock proteins (HSPs) help other proteins properly fold and function. HSP90 and HSP70 are molecular chaperones that work sequentially to fold proteins in the cytoplasm. Misfolded proteins can cause disease. HSP90 helps buffer hidden genetic variations but under stress these variations are expressed and can lead to morphological changes. HSP90 is highly conserved across species and plays a role in evolution by allowing traits to change in response to stress. Current research studies HSP90 to better understand protein misfolding diseases.
1. Enzymes are biological catalysts that lower the activation energy of reactions and increase reaction rates. They are often proteins that contain cofactors.
2. Enzymes are classified based on the type of reaction they catalyze, such as oxidation-reduction, hydrolysis, or transfer of chemical groups. Common enzyme names end in "-ase".
3. The lock and key model describes how enzymes bind specifically to substrates in their active sites to form enzyme-substrate complexes. In the induced fit model, the enzyme structure changes to better fit the substrate.
Protein structures are classified to generate overviews of structure types and detect evolutionary relationships. Major classification schemes include SCOP, CATH, and FSSP. SCOP classifies proteins into classes, folds, superfamilies, and families based on structural and sequence similarities. CATH also uses a hierarchical system of classes, architectures, topologies, and superfamilies. FSSP provides fully automated and updated structural alignments and classifications.
This document discusses proteins from a chemist's perspective. It describes how proteins are made of amino acids, with 20 standard types but only 9 being essential. The unique side groups of each amino acid determine their individual properties. Protein structure and function depend on the specific amino acid sequence. Amino acids are linked through peptide bonds to form proteins. The document also covers protein digestion and roles of proteins in the body.
This document discusses protein structure and synthesis. It begins by describing the primary, secondary, tertiary, and quaternary structures of proteins. This includes the structures of alpha helices, beta sheets, turns, and domains. It then discusses protein translation, noting that proteins begin folding as they emerge from the ribosome in a co-translational manner. The final section discusses protein folding and some of the challenges of the folding process.
The document discusses heat shock proteins (Hsps), Hsp90 inhibitors, and protein degradation. It provides background on protein degradation mechanisms and heat shock proteins. Hsp90 plays a key role in cancer cell survival by regulating oncogenic signaling proteins. Hsp90 inhibitors like geldanamycin and 17-AAG bind Hsp90's ATP binding site, altering its function and inducing degradation of client proteins, stopping cancer cell growth. The paper found that tumor Hsp90 exclusively exists in active multichaperone complexes, conferring higher binding affinity for 17-AAG compared to normal cell Hsp90. This activated conformation in tumor cells represents a unique drug target.
This document summarizes protein therapeutics and provides a pharmacological classification. It notes that the human genome contains 25,000-40,000 genes that can undergo alternative splicing and post-translational modifications, resulting in a very high number of functionally distinct proteins. Protein therapeutics are classified into 4 groups based on their function: group I includes proteins with enzymatic or regulatory activity, group II targets specific molecules or organisms, group III are protein vaccines, and group IV are protein diagnostics. The document outlines some advantages of protein therapeutics but also challenges including solubility, immune response, stability, and costs.
1. Proteins are made up of amino acids and take on specific three-dimensional structures that dictate their function. Determining a protein's structure is important for understanding its role in biological processes.
2. There are several methods for determining and predicting protein structure, including X-ray crystallography, NMR, and computational methods like homology modeling or ab initio structure prediction.
3. Protein structure is hierarchical, ranging from secondary structure like alpha helices and beta sheets to the overall fold classified in databases like SCOP and CATH. Predicting secondary structure is easier than predicting a protein's full three-dimensional structure.
Amino acids are organic compounds that contain an amino group and a carboxyl group. There are 20 different amino acids that serve as the building blocks of proteins. Amino acids link together through peptide bonds to form polypeptide chains that fold into complex three-dimensional protein structures. Proteins serve essential functions and 10 of the 20 amino acids must be obtained through diet as humans cannot synthesize them. Common protein tests identify the presence of proteins using reactions that detect peptide bonds, amino acid side chains, or disulfide bridges.
- Proteins are made up of amino acids, which are the building blocks. There are 20 different amino acids, some are essential and must be obtained through diet.
- The specific sequence of amino acids determines the 3D shape of a protein and its function. Denaturation occurs when proteins lose their shape due to heat, acid, etc.
- Proteins serve many important functions in the body including structure, enzymes, transport, hormones, antibodies, and more. An inadequate intake can result in the body breaking down its own proteins to obtain energy.
Integrating Ayurveda into Parkinson’s Management: A Holistic ApproachAyurveda ForAll
Explore the benefits of combining Ayurveda with conventional Parkinson's treatments. Learn how a holistic approach can manage symptoms, enhance well-being, and balance body energies. Discover the steps to safely integrate Ayurvedic practices into your Parkinson’s care plan, including expert guidance on diet, herbal remedies, and lifestyle modifications.
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There is increasing confidence that cell therapies will soon play a role in the treatment of autoimmune disorders, but the extent of this impact remains to be seen. Early readouts on autologous CAR-Ts in lupus are encouraging, but manufacturing and cost limitations are likely to restrict access to highly refractory patients. Allogeneic CAR-Ts have the potential to broaden access to earlier lines of treatment due to their inherent cost benefits, however they will need to demonstrate comparable or improved efficacy to established modalities.
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2. There are several classes of
proteolytic enzymes.
Serine proteases include digestive
enzymes trypsin, chymotrypsin, & elastase.
Different serine proteases differ in substrate specificity.
For example:
Chymotrypsin prefers an aromatic side chain on the
residue whose carbonyl carbon is part of the peptide
bond to be cleaved.
Trypsin prefers a positively charged Lys or Arg
residue at this position.
H3N+
C COO
CH2
OH
H
serine (Ser, S)
3. During catalysis, there is nucleophilic attack of the
hydroxyl O of a serine residue of the protease on the
carbonyl C of the peptide bond that is to be cleaved.
An acyl-enzyme intermediate is transiently formed.
In this diagram a small peptide is shown being cleaved,
while the usual substrate would be a larger polypeptide.
+
H3N C
H
C
R
N
H
C
H
O
C
R
C
H
C
R
N
H
C
H
O
C
R
O
N
H
O
HO CH2 Enz
+
+
H3N C
H
C
R
N
H
C
H
O
C
R O
C
H
C
R
N
H
C
H
O
C
R
H2N O
O CH2 Enz +
O
O
serine residue
acyl-enzyme intermediate
4. Hydrolysis of the ester linkage yields the second peptide
product.
+
H3N C
H
C
R
N
H
C
H
O
C
R
C
H
C
R
N
H
C
H
O
C
R
O
N
H
O
HO CH2 Enz
+
+
H3N C
H
C
R
N
H
C
H
O
C
R O
C
H
C
R
N
H
C
H
O
C
R
H2N O
O CH2 Enz +
+
H3N C
H
C
R
N
H
C
H
O
C
R O
OH HO CH2 Enz
O
O
+
serine residue
acyl-enzyme intermediate
H2O
5. During attack of the serine hydroxyl oxygen, a proton is
transferred from the serine hydroxyl to the imidazole
ring of the histidine, as the adjacent aspartate carboxyl is
H-bonded to the histidine.
The active site in each
serine protease includes
a serine residue, a
histidine residue, & an
aspartate residue.
Asp102
His57
Ser195
Catalytic residues in trypsin
PDB 3BTK
6. Aspartate proteases include
the digestive enzyme pepsin
Some proteases found in lysosomes
the kidney enzyme renin
HIV-protease.
Two aspartate residues participate in acid/base catalysis
at the active site.
In the initial reaction, one aspartate accepts a proton
from an active site H2O, which attacks the carbonyl
carbon of the peptide linkage.
Simultaneously, the other aspartate donates a proton to
the oxygen of the peptide carbonyl group.
H3N+
C COO
CH2
COO
H
aspartate (Asp)
7. Zinc proteases (metalloproteases) include:
digestive enzymes carboxypeptidases
matrix metalloproteases (MMPs), secreted by cells
one lysosomal protease.
Some MMPs (e.g., collagenase) are involved in
degradation of extracellular matrix during tissue
remodeling.
Some MMPs have roles in cell signaling relating to
their ability to release cytokines or growth factors
from the cell surface by cleavage of membrane-bound
pre-proteins.
8. During catalysis, the Zn++ promotes nucleophilic attack
on the carbonyl carbon by the oxygen atom of a water
molecule at the active site.
An active site base (Glu in Carboxypeptidase) facilitates
this reaction by extracting H+ from the attacking H2O.
zinc
water oxygen
Carboxypeptidase
PDB 1YME
A zinc-binding motif at
the active site of a
metalloprotease includes
two His residues whose
imidazole side-chains are
ligands to the Zn++.
Colors in Carboxypeptidase
image at right: Zn, N, O.
9. Cysteine proteases have a
catalytic mechanism that involves
a cysteine sulfhydryl group.
Deprotonation of the cysteine SH by an adjacent
His residue is followed by nucleophilic attack of
the cysteine S on the peptide carbonyl carbon.
A thioester linking the new carboxy-terminus to the
cysteine thiol is an intermediate of the reaction
(comparable to acyl-enzyme intermediate of a serine
protease).
H3N+
C COO
CH2
SH
H
cysteine
10. Cysteine proteases:
Papain is a well-studied plant cysteine protease.
Cathepsins are a large family of lysosomal cysteine
proteases, with varied substrate specificities.
Caspases are cysteine proteases involved in activation &
implementation of apoptosis (programmed cell death).
Caspases get their name from the fact that they cleave
on the carboxyl side of an aspartate residue.
Calpains are Ca++-activated cysteine proteases that
cleave intracellular proteins involved in cell motility &
adhesion.
They regulate processes such as cell migration and
wound healing.
11. Activation of proteases:
Most proteases are synthesized as larger pre-proteins.
During activation, the pre-protein is cleaved to remove
an inhibitory segment.
In some cases activation involves dissociation of an
inhibitory protein.
Activation may occur after a protease is delivered to a
particular cell compartment or the extracellular milieu.
Caspases involved in initiation of apoptosis are
activated by interaction with large complexes of
scaffolding & activating proteins called apoptosomes.
See diagram of apoptosome in a Univ. London website.
12. Protease Inhibitors:
Most protease inhibitors are proteins with domains
that enter or block a protease active site to prevent
substrate access.
13. IAPs are proteins that block apoptosis by binding to
& inhibiting caspases.
The apoptosis-stimulating protein Smac antagonizes
the effect of IAPs on caspases.
TIMPs are inhibitors of metalloproteases that are
secreted by cells.
A domain of the inhibitor protein interacts with the
catalytic Zn++.
Cystatins are inhibitors of lysosomal cathepsins.
Some (also called stefins) are found in the cytosol,
and others in the extracellular space.
Cystatins protect cells against cathepsins that may
escape from lysosomes.
14. Serpins use a unique suicide mechanism to inhibit serine
or cysteine proteases.
• A large conformational change in the serpin
accompanies cleavage of its substrate loop.
• This leads to disordering of the protease active site,
preventing completion of the reaction.
• The serpin remains covalently linked to the protease
as an acyl-enzyme intermediate.
• Movie depicting the conformational changes.
(University of Cambridge website)
• Serpins are widely distributed within & outside of cells,
and have diverse roles, including regulation of blood
clotting, fibrin cleavage, & inhibition of apoptosis.
15. plasma membrane may be processed first in an endosomal
compartment and then delivered into the lumen of a
lysosome by fusion of a transport vesicle.
Solute transporters embedded in the lysosomal
membrane catalyze exit of products of lysosomal digestion
(e.g., amino acids, sugars, cholesterol) to the cytosol.
H+
Lysosome
ATP ADP + Pi
Vacuolar ATPase
low
internal
pH
Lumen
contains
hydrolytic
enzymes.
Lysosomes contain
a large variety of
hydrolytic enzymes
that degrade proteins &
other substances taken
in by endocytosis.
Materials taken into a
cell by inward budding
of vesicles from the
16. Lysosomal proteases include many cathepsins (cysteine
proteases), some aspartate proteases & one zinc protease.
Activation of lysosomal proteases by cleavage may be
catalyzed by other lysosomal enzymes or be autocatalytic,
promoted by the internal acidic pH.
H+
Lysosome
ATP ADP + Pi
Vacuolar ATPase
low
internal
pH
Lumen
contains
hydrolytic
enzymes.
Lysosomes have a
low internal pH due to
vacuolar ATPase, a H+
pump homologous to
mitochondrial F1Fo
ATPase.
All intra-lysosomal
hydrolases exhibit
acidic pH optima.
17. In autophagy, part of the cytoplasm may become
surrounded by two concentric membranes.
Fusion of the outer membrane of this autophagosome
with a lysosomal vesicle results in degradation of
enclosed cytoplasmic structures and macromolecules.
Genetic studies in yeast have identified unique
proteins involved in autophagosome formation.
autophagosome autophagic
vacuole
(lysosome)
One model
for autophagic
vacuole
formation
18. Protein turnover; selective degradation/cleavage
Individual cellular proteins turn over (are degraded and
re-synthesized) at different rates.
E.g., half-lives of selected enzymes of rat liver cells range
from 0.2 to 150 hours.
N-end rule: On average, a protein's half-life correlates
with its N-terminal residue.
Proteins with N-terminal Met, Ser, Ala, Thr, Val, or Gly
have half lives greater than 20 hours.
Proteins with N-terminal Phe, Leu, Asp, Lys, or Arg
have half lives of 3 min or less.
PEST proteins having domains rich in Pro (P), Glu (E), Ser
(S), Thr (T), are more rapidly degraded than other proteins.
19. Most autophagy is not a mechanism for selective
degradation of individual macromolecules.
However, cytosolic proteins that include the sequence
KFERQ may be selectively taken up by lysosomes in a
process called chaperone-mediated autophagy.
This process, which is stimulated under conditions of
nutritional or oxidative stress, involves interaction of
proteins to be degraded with:
• Cytosolic chaperones that unfold the proteins.
• A lysosomal membrane receptor (LAMP-2A) that
may provide a pathway across the membrane.
• Chaperones in the lysosomal lumen that may assist
with translocation across the membrane.
20. Intramembrane-cleaving proteases (I-CLiPs) cleave
regulatory proteins such as transcription factors from
membrane-anchored precursor proteins.
E.g., precursors of SREBP (sterol response element
binding protein) transcription factors are integral proteins
embedded in endoplasmic reticulum membranes.
21. The released SREBP can then translocate to the cell
nucleus to regulate transcription of genes for enzymes
involved, e.g., in cholesterol synthesis.
S2P (site 2 protease, an I-CLiP) is a membrane-
embedded metalloprotease that cleaves an a-helix of
the SREBP precursor within the transmembrane domain.
N
C
membrane
cytosol
lumen
S2P cleavage
releasing
SREBP
SCAP-activated
S1P cleavage
Activation of SREBP
involves its translocation
to golgi membranes
where sequential
cleavage by 2 proteases
releases to the cytosol a
domain with transcription
factor activity.
22. Ubiquitin:
Proteins are usually tagged for
selective destruction in proteolytic
complexes called proteasomes
by covalent attachment of
ubiquitin, a small, compact,
highly conserved protein.
ubiquitin PDB 1TBE
However, some proteins may be degraded
by proteasomes without ubiquitination.
An isopeptide bond links the terminal
carboxyl of ubiquitin to the e-amino
group of a lysine residue of a "condemned"
protein.
H3N+
C COO
CH2
CH2
CH2
CH2
NH3
H
lysine
23. The joining of ubiquitin to a condemned protein is
ATP-dependent.
Three enzymes are involved, designated E1, E2 & E3.
Initially the terminal carboxyl group of ubiquitin
is joined in a thioester bond to a cysteine residue on
Ubiquitin-Activating Enzyme (E1). This is the
ATP-dependent step.
The ubiquitin is then transferred to a sulfhydryl
group on a Ubiquitin-Conjugating Enzyme (E2).
24. A Ubiquitin-Protein Ligase (E3) then promotes transfer of
ubiquitin from E2 to the e-amino group of a Lys residue of a
protein recognized by that E3, forming an isopeptide bond.
There are many distinct Ubiquitin Ligases with differing
substrate specificity.
• One E3 is responsible for the N-end rule.
• Some are specific for particular proteins.
ubiquitin C S
O
Cys E2 H2N Lys protein to be degraded
ubiquitin C
O
HS Cys E2
N Lys protein to be degraded
H
+
E3
+
(Ubiquitin-Protein Ligase)
25. H2N COO
destruction
box
chain of
ubiquitins
Primary structure of a protein
targeted for degradation
More ubiquitins are added to form a chain of ubiquitins.
The terminal carboxyl of each ubiquitin is linked to the
e-amino group of a lysine residue (Lys29 or Lys48) of
the adjacent ubiquitin.
A chain of 4 or more ubiquitins targets proteins for
degradation in proteasomes. (Attachment of a single
ubiquitin to a protein has other regulatory effects.)
26. H2N COO
destruction
box
chain of
ubiquitins
Primary structure of a protein
targeted for degradation
Some proteins (e.g., mitotic cyclins involved in cell cycle
regulation) have a destruction box sequence recognized
by a domain of the corresponding Ubiquitin Ligase.
27. Ubiquitin Ligases (E3) mostly consist of two families:
Some Ubiquitin Ligases have a HECT domain
containing a conserved Cys residue that participates in
transfer of activated ubiquitin from E2 to a target
protein.
Some Ubiquitin Ligases contain a RING finger domain
in which Cys & His residues are ligands to 2 Zn++ ions.
A RING (Really Interesting New Gene) finger is not
inherently catalytic. It stabilizes a characteristic globular
domain conformation that serves as a molecular scaffold
for residues that interact with E2.
28. Regulation of ubiquitination:
Some proteins regulate or facilitate ubiquitin conjugation.
Regulation by phosphorylation of some target proteins has
been observed.
E.g., phosphorylation of PEST domains activates
ubiquitination of proteins rich in the PEST amino acids.
Glycosylation of some PEST proteins with GlcNAc has
the opposite effect,
prolonging half-life
of these proteins.
GlcNAc attachment
increases with elevated
extracellular glucose,
suggesting a role as
nutrition sensor.
H O
OH
O
H
HN
H
OH
CH2OH
H
C CH3
O
-D-N-acetylglucosamine
CH2 CH
C
NH
O
H
serine
residue
29. A ubiquitin-like protein called Nedd8 may be attached
to ubiquitin ligases (E3) that have a "cullin" subunit
including a RING finger domain.
De-neddylation (removal of the Nedd8 protein),
catalyzed by a metalloprotease subunit of a complex
called the COP9 signalosome, activates the E3 ligases.
Some disease-causing viruses target host cell proteins
for degradation in the proteasome.
They either activate a host cell Ubiquitin Ligase to
ubiquitinate host proteins, or encode their own
Ubiquitin Ligase.
30. The proteasome core complex, with a 20S sedimentation
coefficient, contains 2 each of 14 different polypeptides.
7 a-type proteins form each of the two a rings, at the
ends of the cylindrical structure.
7 -type proteins form each of the 2 central rings.
Proteasomes:
Selective protein
degradation occurs
in the proteasome,
a large protein
complex in the
nucleus & cytosol
of eukaryotic cells.
20 S Proteasome
(yeast) closed state
two views PDB 1JD2
a
a
31. The 20S proteasome core complex encloses a cavity with
3 compartments joined by narrow passageways.
Protease activities are associated with 3 of the subunits,
each having different substrate specificity.
20 S Proteasome
(yeast) closed state
two views PDB 1JD2
a
a
32. 1. One catalytic -subunit has a chymotrypsin-like
activity with preference for tyrosine or phenylalanine
at the P1 (peptide carbonyl) position.
2. One has a trypsin-like activity with preference for
arginine or lysine at the P1 position.
3. One has a post-glutamyl activity with preference for
glutamate or other acidic residue at the P1 position.
Different variants of the 3 catalytic subunits, with
different substrate specificity, are produced in cells of the
immune system that cleave proteins for antigen display.
33. The proteasome hydrolases constitute a unique family of
threonine proteases. A conserved N-terminal threonine is
involved in catalysis at each active site.
The 3 catalytic subunits are synthesized as pre-proteins.
They are activated when the N-terminus is cleaved off,
making threonine the N-terminal residue.
Catalytic threonines are exposed at the lumenal surface.
H3N+
C COO
CH OH
CH3
H
threonine (Thr)
34. Proteasomal degradation of particular proteins is an
essential mechanism by which cellular processes are
regulated, such as cell division, apoptosis, differentiation
and development.
E.g., progression through the cell cycle is controlled in
part through regulated degradation of proteins called
cyclins that activate cyclin-dependent kinases.
35. Several subunits of the proteasome are glycosylated with
GlcNAc when extracellular glucose is high, leading to
decreased intracellular proteolysis.
Conversely, under conditions of low nutrition, decreased
modification by GlcNAc leads to increased proteolysis.
Thus protein degradation is responsive to nutrition via
glycosylation of Ubiquitin Ligase & the proteasome itself.
36. Many inhibitors of proteasome protease activity are
known, some of which are natural products and others
experimentally produced.
E.g., TMCs are naturally occurring proteasome inhibitors.
They bind with high affinity adjacent to active site
threonines within the proteasome core complex.
TMCs have a heterocyclic ring structure derived from
modified amino acids.
Proteasome inhibitors cause cell cycle arrest and
induction of apoptosis (programmed cell death) when
added to rapidly dividing cells.
The potential use of proteasome inhibitors in treating
cancer is being investigated.
37. Proteasome evolution:
Proteasomes are considered very old.
They are in archaebacteria, but not most eubacteria,
although eubacteria have alternative protein-degrading
complexes.
The archaebacterial proteasome has just 2 proteins,
a & , with 14 copies of each.
The eukaryotic proteasome has evolved 14 distinct
proteins that occupy unique positions within the
proteasome (7 a-type & 7 -type).
38. The ends of the cylindrical complex are blocked by
N-terminal domains of a subunits that function as a gate.
Interaction with a cap complex causes a conformational
change that opens a passageway into the core complex.
Regulatory cap
complexes:
In crystal
structures of the
proteasome core
alone, there is no
apparent opening
to the outside.
20 S Proteasome
(yeast) closed state
two views PDB 1JD2
a
a
39. The 19S regulatory cap complex recognizes
multi-ubiquitinated proteins, unfolds them, removes
ubiquitin chains, and provides a passageway for
threading unfolded proteins into the core complex.
The 19S cap is a 20-subunit 700 kDa complex, also
referred to as PA700. When combined with a 20S core
complex, it yields a 26S proteasome.
Only low-resolution structural information, obtained
by electron microscopy, is available for the 19S cap.
Location and roles of some constituent proteins have
been established.
40. The outermost "lid" of the 19S cap is a ring of eight
proteins.
The innermost "base" of the 19S cap includes a ring of
six members of the AAA family of ATPases.
These are chaperones that carry out ATP-dependent
unfolding of proteins prior to their being threaded into
the core complex.
It is typical of AAAATPases that they assemble into
hexameric rings
Isopeptidases in the 19S cap disassemble ubiquitin
chains. Ubiquitins can then be re-used.
At least one deubiquitylating enzyme is located
between the lid & base regions of the 19S cap.
41. A simpler archaebacterial cap complex called PAN
consists only of a hexameric ring of AAAATPases,
comparable to the base of the 19S regulatory cap.
PAN, in the presence of ATP, was found to cause opening
of a gate at the end of the 20S proteasome through which
an unfolded protein could enter.
The base of the 19S cap is assumed to do the same,
although high resolution structural evidence is still lacking.
A high resolution structure has been achieved for a complex
of the 20S proteasome with an 11S regulatory cap.
The 11S cap is a heptameric complex of a protein PA28.
42. The 11S cap allows
small, non-ubiquitinated
proteins & peptides to
pass into the core
complex.
This does not require
ATP hydrolysis.
The 11S cap is dome-
shaped, with a wide
opening at each end.
20 S Proteasome
(yeast), with
11S Regulator
(Trypanosome)
two views
PDB 1FNT
Binding of the 11S cap alters conformation of N-terminal
domains of core complex a subunits, opening a gate into
the proteasome core. For images see a website.
43. There have been many
structural studies of
isolated core complex
with 19S or 11S cap.
Formation of mixed
complexes of
proteasome core
sandwiched between
19S & 11S caps has
been shown by EM.
20 S Proteasome
(yeast), with
11S Regulator
(Trypanosome)
two views
PDB 1FNT
In vivo a 19S cap may recognize, de-ubiquitinate, unfold &
feed proteins into a core complex, while an 11S cap at the
other end may provide an exit path for peptide products.
See an animation.
44. Compare with Chime the yeast 20S proteasome core
complex, with and without the 11S regulatory cap.
11S-20S-11S
complex
20 S Proteasome
a
a