10. Skeleton and Cell movement, actin - cell biology
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This document discusses actin filaments and their role in cell movement. It describes how actin monomers polymerize to form actin filaments, with ATP hydrolysis driving the treadmilling cycle of monomers adding and dissociating from the barbed and pointed ends. Various actin-binding proteins regulate filament assembly and organization, including ADF/cofilin which enhances depolymerization and can sever filaments, and profilin which enhances polymerization. Actin filaments associate with the cell membrane and form the cell cortex, protrusions, and attachments to the extracellular matrix through focal adhesions, determining cell shape and enabling cell movement.
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Secondary Structure Of Protein (Repeating structure of protein)
This document discusses the structure of proteins at various levels. It describes the primary, secondary, tertiary, and quaternary structures. The secondary structures discussed in detail include the alpha helix, beta pleated sheet, random coil, collagen helix, and beta turn. The alpha helix and beta pleated sheet are stabilized by hydrogen bonding between amino acids. The collagen helix structure provides strength and is the main component of connective tissues. Genetic disorders like Ehlers-Danlos syndrome and osteogenesis imperfecta result from defects in collagen structures. Ramachandran plots are used to visualize allowed backbone dihedral angles in protein structures.
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The document summarizes Ramachandran plots, which visualize backbone dihedral angles ψ against φ of amino acid residues in protein structures. Ramachandran plots show sterically allowed and disallowed conformations based on calculations using van der Waals radii and bond angles. Specific regions of the plot correspond to different secondary structures like alpha helices and beta sheets. The plots can also be used to validate protein structures by comparing observed dihedral angles to expected allowed regions.
The Ramachandran plot
The document discusses protein backbone flexibility and the Ramachandran plot. It provides information on:
1) The phi and psi torsion angles that describe rotations around peptide bonds in the protein backbone and allow for different protein conformations.
2) How the Ramachandran plot maps allowed and disallowed phi-psi angle combinations based on steric clashes, and observed combinations in real proteins.
3) The plot serves as an indicator of protein structure quality by showing if residues fall in allowed regions. Understanding phi-psi angles helps predict protein folding.
Enzyme catalysis mechanisms involved
Enzymes use several catalytic mechanisms to lower the free energy of transition states and greatly increase reaction rates, including acid-base catalysis, covalent catalysis, metal ion catalysis, and bringing substrates into close proximity and proper orientation. Acid-base catalysis involves proton transfer from catalytic amino acid side chains. Covalent catalysis transiently forms covalent bonds between enzyme and substrate. Metal ion catalysis uses transition metals to orient substrates, mediate redox reactions, or stabilize charges. Proximity and orientation align substrates for reaction, while catalysis by approximation brings two substrates together for reaction.
Regulation of gene expression...
This document discusses the regulation of gene expression in prokaryotes and eukaryotes. It notes that in eukaryotes, gene expression can be regulated at the transcriptional, post-transcriptional, and translational levels. In prokaryotes, regulation primarily occurs at the transcriptional level through interactions between repressor proteins and operator sequences near promoters. A key example discussed is the lac operon in E. coli, which regulates genes for lactose metabolism through binding of the lac repressor protein to the lac operator. When lactose is present, it acts as an inducer by causing the repressor to dissociate from the operator and allowing transcription.
Protein motif. by KK Sahu sir
Introduction:
Protein
Protein motif.
2. History:
3. A brief overview of protein structure.
4. The Structural Classification of Protein(SCOP):
All α.
All β
α/β
α+β
5.The super secondary structure.
6. Rules for formation of Protein Motifs.
7. Structural motifs.
8. Some Common Protein Motifs:
β-hairpin.
β-meander.
Alpha-alpha corner.
Helix-turn-helix motif.
β-α-β motif.
β-sandwich.
β-barrel.
Greek key.
The Jellyroll topology.
Omega loop.
Zinc finger motif.
9. Conclusion.
10. References.
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Chargaff's rule on DNA & RNA
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The document summarizes Ramachandran plots, which visualize backbone dihedral angles ψ against φ of amino acid residues in protein structures. Ramachandran plots show sterically allowed and disallowed conformations based on calculations using van der Waals radii and bond angles. Specific regions of the plot correspond to different secondary structures like alpha helices and beta sheets. The plots can also be used to validate protein structures by comparing observed dihedral angles to expected allowed regions.
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The document discusses protein backbone flexibility and the Ramachandran plot. It provides information on:
1) The phi and psi torsion angles that describe rotations around peptide bonds in the protein backbone and allow for different protein conformations.
2) How the Ramachandran plot maps allowed and disallowed phi-psi angle combinations based on steric clashes, and observed combinations in real proteins.
3) The plot serves as an indicator of protein structure quality by showing if residues fall in allowed regions. Understanding phi-psi angles helps predict protein folding.
Enzyme catalysis mechanisms involved
Enzymes use several catalytic mechanisms to lower the free energy of transition states and greatly increase reaction rates, including acid-base catalysis, covalent catalysis, metal ion catalysis, and bringing substrates into close proximity and proper orientation. Acid-base catalysis involves proton transfer from catalytic amino acid side chains. Covalent catalysis transiently forms covalent bonds between enzyme and substrate. Metal ion catalysis uses transition metals to orient substrates, mediate redox reactions, or stabilize charges. Proximity and orientation align substrates for reaction, while catalysis by approximation brings two substrates together for reaction.
Regulation of gene expression...
This document discusses the regulation of gene expression in prokaryotes and eukaryotes. It notes that in eukaryotes, gene expression can be regulated at the transcriptional, post-transcriptional, and translational levels. In prokaryotes, regulation primarily occurs at the transcriptional level through interactions between repressor proteins and operator sequences near promoters. A key example discussed is the lac operon in E. coli, which regulates genes for lactose metabolism through binding of the lac repressor protein to the lac operator. When lactose is present, it acts as an inducer by causing the repressor to dissociate from the operator and allowing transcription.
Protein motif. by KK Sahu sir
Introduction:
Protein
Protein motif.
2. History:
3. A brief overview of protein structure.
4. The Structural Classification of Protein(SCOP):
All α.
All β
α/β
α+β
5.The super secondary structure.
6. Rules for formation of Protein Motifs.
7. Structural motifs.
8. Some Common Protein Motifs:
β-hairpin.
β-meander.
Alpha-alpha corner.
Helix-turn-helix motif.
β-α-β motif.
β-sandwich.
β-barrel.
Greek key.
The Jellyroll topology.
Omega loop.
Zinc finger motif.
9. Conclusion.
10. References.
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Protein folding is a complex multi-step process whereby a protein folds from a random coil into its functional three-dimensional structure. It begins with the rapid formation of alpha helices and beta sheets within milliseconds. These initial elements then interact and collapse into a molten globule structure driven by hydrophobic interactions. Over the next few seconds, the protein undergoes rearrangements to attain its stable tertiary structure and expel water from its hydrophobic core. The folding process is directed by the interior residues and proceeds through a folding funnel from a high-energy random state to the native low-energy conformation.
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Cell adhesion molecules (CAMs) help cells bind to other cells and to the extracellular matrix. There are five major families of CAMs: cadherins, Ig superfamily CAMs, selectins, integrins, and mucins. Cadherins are calcium-dependent adhesion molecules that form desmosomes and bind cells together through homophilic or heterophilic adhesion. Integrins exist as alpha and beta subunits and bind to extracellular matrix proteins via outside-in and inside-out signaling to connect cells and regulate processes like adhesion, migration, differentiation, and apoptosis. CAMs play important roles in development by mediating cell-cell interactions and signals that direct tissue formation and gene expression.5.ER2+Golgi apparatus - cell biology
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1) Porphyrins are biomarkers that can identify toxicity to the heme biosynthesis pathway. Disturbances can cause accumulations of porphyrin intermediates in urine.
2) Testing porphyrin levels can identify biochemical damage from toxic exposures like mercury and monitor chelation therapy. Abnormal levels also correlate with conditions like chemical sensitivities and neurological disorders.
3) Case studies show porphyrin testing identified arsenic exposure from an elevated ratio and confirmed mercury toxicity in an autistic child with challenges excreting heavy metals.
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The document discusses protein folding, which is the process by which a polypeptide chain folds into its characteristic and functional three-dimensional structure. It describes the four levels of protein structure: primary, secondary, tertiary, and quaternary. Key drivers of folding are the hydrophobic effect and formation of hydrogen bonds. Chaperone proteins assist in protein folding in vivo. Factors such as mutations, errors in synthesis, environmental stresses, and aging can cause proteins to misfold and aggregate, which is associated with various diseases. Cells use molecular chaperones and protein degradation systems to prevent aggregation, but these become less effective with age.
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There are 5 major antibody isotypes - IgM, IgD, IgG, IgE, and IgA - which differ based on their heavy chain. The heavy chain determines the isotype and can be mu, delta, gamma, epsilon, or alpha. Light chains can be either kappa or lambda with any isotype. IgG is the most abundant in humans while IgE is the least. Isotypes are located in the constant region of the heavy and light chains. Allotypes are specified by allelic forms of immunoglobulin genes and are also in the constant regions. Idiotypes are unique epitopes located in the variable regions of individual antibody molecules.
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This document provides an overview of immunology and the immune system. It discusses the history of immunology including the discoveries of Metchnikoff, Behring, and Fleming. It also describes the innate and adaptive immune systems. The main cells of the immune system are B cells, T cells (including T helper cells, T cytotoxic cells, and T suppressor cells), and natural killer cells. Primary lymphoid organs that support immune cell development include the bone marrow and thymus. Secondary lymphoid organs where immune responses occur include lymph nodes, spleen, Peyer's patches, and mucosa-associated lymphoid tissue.
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More than half of all proteins interact with membranes.
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The document summarizes genome organization in prokaryotes and eukaryotes. In prokaryotes like E. coli, the genome is packed into the nucleoid region through supercoiling, facilitated by histone-like proteins that introduce bends and loops in the DNA. This allows the 1.5mm of DNA to fit inside the small cell. In eukaryotes, the 6 feet of DNA is packaged into chromosomes through a multi-step process involving wrapping around histones to form nucleosomes, which further condense into solenoids, super solenoids, rosettes, coils and finally chromosomes.
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I have tried to make a precise presentation on protein transport, targeting and sorting into organelle's other than nucleus. Hope this might help you. Comments are welcome.
Tryptophan operon
The tryptophan operon regulates the biosynthesis of tryptophan in E. coli through transcriptional attenuation and repression. It contains five genes encoding the enzymes needed to synthesize tryptophan. When tryptophan levels are high, the tryptophan repressor binds to the operator site, preventing transcription. Additionally, a regulatory region can form a terminator stem-loop structure to halt transcription if tryptophan tRNA levels are high during translation of the leader mRNA sequence. However, if tryptophan levels are low, the terminator structure does not form and transcription of the operon proceeds.
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the ionophores are the a part of membrane transport system. these slides include general concept of ionophores. useful for the paramedical, medical students.
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The document discusses protein folding, which is the process by which proteins achieve their functional three-dimensional structure from their linear amino acid sequence. It describes the different levels of protein structure, including primary, secondary, tertiary, and quaternary structure. The folding process depends on factors like temperature, pH, and molecular chaperones, which assist in protein folding. Proper folding is required for proteins to carry out their functions in the cell.
cell adhesion molecules
This document discusses cell adhesion molecules (CAMs), which are glycoproteins located on cell surfaces that help cells stick to each other and their surroundings. CAMs are classified into five major families: cadherins, Ig superfamily CAMs, selectins, integrins, and mucins. Cadherins are calcium-dependent and form connections between cells called desmosomes. Selectins help with inflammation and lymphocyte homing. Integrins facilitate cell-cell and cell-extracellular matrix adhesion and are composed of alpha and beta subunits. Malfunctions in CAMs can lead to conditions like breast cancer and leukocyte adhesion deficiency syndrome.
12.protein folding
Protein folding is a complex multi-step process whereby a protein folds from a random coil into its functional three-dimensional structure. It begins with the rapid formation of alpha helices and beta sheets within milliseconds. These initial elements then interact and collapse into a molten globule structure driven by hydrophobic interactions. Over the next few seconds, the protein undergoes rearrangements to attain its stable tertiary structure and expel water from its hydrophobic core. The folding process is directed by the interior residues and proceeds through a folding funnel from a high-energy random state to the native low-energy conformation.
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Prokaryotic and eukaryotic cells differ in their structural organization. Prokaryotic cells lack membrane-bound organelles and have bacterial chromosomes not associated with histones, while eukaryotic cells have organelles like the nucleus, mitochondria and chloroplasts enclosed in membranes. Another key difference is that prokaryotic cells like bacteria are typically smaller than eukaryotic cells and lack internal compartmentalization. However, both cell types share basic chemical and metabolic similarities as living organisms.
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Cell adhesion molecules (CAMs) help cells bind to other cells and to the extracellular matrix. There are five major families of CAMs: cadherins, Ig superfamily CAMs, selectins, integrins, and mucins. Cadherins are calcium-dependent adhesion molecules that form desmosomes and bind cells together through homophilic or heterophilic adhesion. Integrins exist as alpha and beta subunits and bind to extracellular matrix proteins via outside-in and inside-out signaling to connect cells and regulate processes like adhesion, migration, differentiation, and apoptosis. CAMs play important roles in development by mediating cell-cell interactions and signals that direct tissue formation and gene expression.What's hot (20)
Cell Adhesion Molecules(cams) and its types, Cadherins and Integrins and inte...
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Cytoskeleton & Extracellular matrix
The cytoskeleton and extracellular matrix are essential components of eukaryotic cells. The cytoskeleton is made up of three main types of protein filaments - actin filaments, microtubules, and intermediate filaments. These filaments help establish cell shape, provide mechanical strength, and enable intracellular transport. Actin filaments are assembled from globular actin subunits and play roles in cell motility and structure. Microtubules are hollow polymers of tubulin that nucleate from microtubule organizing centers and help separate chromosomes during cell division. Accessory proteins tightly regulate the dynamics of both filament types. The extracellular matrix provides structural support outside the cell and influences cellular behavior.
Cell bio7
This document provides an overview of a lecture on cytoskeleton. It discusses the three main components of the cytoskeleton - microfilaments, microtubules, and intermediate filaments. It focuses on actin and microfilaments, describing their roles in cell motility, cytokinesis, phagocytosis, vesicle transport, and asymmetric cell division. It explains how actin polymerizes to form microfilaments and the roles of actin nucleators like Arp2/3 and formins in determining filament structure. It also discusses actin regulatory proteins involved in polymerization, capping, depolymerization, and monomer binding.
Ctyoskeleton.pptx
The cytoskeleton is composed of three main components - actin filaments, microtubules, and intermediate filaments. Actin filaments are made up of actin monomers that polymerize to form double helical structures. They play important roles in cell shape, movement, division, and intracellular transport. Microtubules are composed of tubulin dimers that assemble into hollow rods. They are involved in determining cell shape, movement, and transport of organelles. Both actin and microtubules undergo dynamic instability, rapidly assembling and disassembling in response to cellular signals.
Msc thesis
The document provides an overview of cytoskeletal proteins and their functions, as well as how bacterial pathogens interact with and manipulate the host cytoskeleton during infection. It discusses the major cytoskeletal components microfilaments and microtubules. It also reviews how bacteria can alter host actin and microtubule dynamics through various mechanisms to facilitate infection of both phagocytic and non-phagocytic cells. The complex pathways regulating cytoskeletal dynamics are targeted by pathogenic bacteria through different strategies to subvert the host cytoskeleton for their own benefit during the infection process.
Estructura Celular
The document discusses actin filaments and their assembly into various cellular structures. It focuses on structures at the plasma membrane, including sheet-like protrusions like lamellipodia and finger-like protrusions like filopodia. There are three known classes of actin nucleation factors - Arp2/3 complex, formins, and spire - that initiate actin filament assembly. The Arp2/3 complex produces a branched network of filaments near the leading edge of lamellipodia that drives protrusion, while formins and spire produce unbranched filaments throughout the lamellipodia and lamella.
Many Faces Of Actin
The document reviews actin filament assembly factors and the cellular structures they assemble. It discusses three classes of actin assembly factors - Arp2/3 complex, formins, and spire. Arp2/3 complex nucleates branched networks while formins and spire nucleate linear filaments. It focuses on sheet-like protrusive structures at the cell membrane like lamellipodia, ruffles, and phagocytic cups, which are assembled through Arp2/3, and finger-like protrusions like filopodia and microvilli, assembled by formins. Adherens junctions and the immunological synapse are also mentioned.
Cytoskelet Plus Matrix Deel 1
The document discusses the cytoskeleton and cell junctions. It describes how actin polymerizes to form microfilaments through the addition of G-actin monomers. Microtubules also dynamically polymerize from tubulin. Intermediate filaments like keratins form coiled-coil structures. The document further explains how actin polymerization at the leading edge of cells is regulated in time and space, and the roles of proteins like profilin, Arp2/3 complex, and Rho GTPases in nucleating and branching actin networks. It also describes how actin networks anchor to the plasma membrane and how cell junctions like tight junctions and adherens junctions connect cells and regulate permeability and polarity.
Rocket Launcher Mechanism of Collaborative Actin Assembly Defined by Single-M...
This document summarizes a presentation on Adenomanous Polypolis Coli (APC) and its role in the Wnt signaling pathway and actin assembly. APC is a main component of the Wnt signaling pathway that regulates β-catenin levels and target gene expression. Mutations in APC are associated with colorectal cancers. The presentation shows that APC can directly nucleate actin assembly through its C-terminal basic domain, without sequence homology to known actin binding domains. APC and mDia1 synergistically promote actin assembly in the presence of profilin and capping protein. While the formin mDia1 remains processively bound to actin filament bar
Microfilaments and intermediate filaments
The document summarizes key aspects of the cytoskeleton, focusing on actin filaments. It describes how actin filaments: 1) maintain cell shape and generate force for cell movements through polymerization and depolymerization; 2) integrate cells through attachments to cell adhesions; and 3) produce movements within cells and at the cell membrane through interactions with myosin motor proteins. Accessory proteins regulate actin dynamics by capping, bundling, severing, and crosslinking filaments.
Microfilaments and intermediate filaments
The document summarizes key aspects of the cytoskeleton, focusing on actin filaments. It describes how actin filaments: 1) maintain cell shape and generate force for cell movements through polymerization and depolymerization; 2) integrate cells through attachments to cell adhesions; and 3) produce movements within cells and at the cell membrane through interactions with myosin motor proteins. Accessory proteins regulate actin dynamics by capping, bundling, severing, and crosslinking filaments.
Aug 26 2011
The document discusses several key topics regarding proteins and enzymes:
1. It describes the primary structure of proteins and how their amino acid sequence determines their function. It also discusses polymorphic proteins and early protein sequencing methods.
2. Protein folding and the factors that influence a protein's three-dimensional structure are summarized, including non-covalent bonds, domains, and common structural motifs like alpha helices and beta sheets.
3. The roles of different protein types like globular, fibrous, and assembly proteins are highlighted. Key fibrous proteins like collagen and elastin are also mentioned.
Structural Basis of Actin Nucleation
VopL is a bacterial actin nucleator protein that utilizes a unique C-terminal dimerization domain (VCD) to robustly nucleate actin filament formation. Single molecule studies show that VopL generates new actin filament seeds and rapidly dissociates from the filaments. The VCD domain is required for dimerization of VopL and binding to actin filaments. Crystallization of VCD proved challenging due to sensitivity of the crystals. SAXS and the crystal structure revealed that VCD forms a coiled-coil dimer that can bind two actin subunits, suggesting it acts as a platform for actin nucleation. Dimerization of actin nucleators may
Protein Structure, Post Translational Modifications and Protein Folding
Post-translational modifications (PTMs) are covalent processing events that change the properties of a protein by proteolytic cleavage or by addition of a modifying group to one or more amino acids.
Protein post-translational modification (PTM) plays an essential role in various cellular processes that modulates the physical and chemical properties, folding, conformation, stability and activity of proteins, thereby modifying the functions of proteins
Protein chemistry by Dr. Anurag Yadav
protein chemistry, Biochemistry
the different level of organisation of the protein .
detail on individual structure and the bonds stabilising the structure of the protein.
ATP-Synthase Presentation
The crystal structure of the c-ring subunits of yeast ATP synthase was determined. It revealed 10 c-subunits forming a symmetrical ring, in contrast to previous models suggesting 12 subunits. The c-ring associates closely with the γ and δ subunits, supporting the idea that it forms part of the rotary motor. Understanding the interaction between the c-ring and other F0 subunits will provide insights into how proton translocation generates rotational motion.
BT631-4-peptide_bonds
The peptide bond forms spontaneously via a condensation reaction that releases a small molecule like water. It has partial double bond character that restricts rotation, resulting in planar geometry. The phi and psi angles of the peptide backbone determine its conformation within allowed regions of the Ramachandran plot, avoiding steric clashes. While most peptide bonds adopt the trans configuration, proline favors cis. Protein function arises from its precise three-dimensional structure.
The International Journal of Engineering and Science (IJES)
The International Journal of Engineering & Science is aimed at providing a platform for researchers, engineers, scientists, or educators to publish their original research results, to exchange new ideas, to disseminate information in innovative designs, engineering experiences and technological skills. It is also the Journal's objective to promote engineering and technology education. All papers submitted to the Journal will be blind peer-reviewed. Only original articles will be published.
Protein Structure Lesson for College Students
Proteins are major components of cellular systems and are composed of linear chains of amino acids called polypeptides. Proteins vary greatly in size, ranging from just 9 amino acids to over 25,000 amino acids, and adopt complex three-dimensional structures essential to their diverse functions. Protein structures are determined by their amino acid sequences and stabilized through interactions between residues as well as post-translational modifications. Common protein structures include alpha helices, beta sheets, and domains that enable functions such as enzymatic catalysis, oxygen transport, molecular recognition, and mechanical movement.
BT631-27-Membrane_proteins
ATP synthase is an enzyme that generates ATP from ADP and inorganic phosphate using energy from the proton gradient across the inner mitochondrial membrane. It consists of two main parts - F0, which forms a channel for protons to pass through, and F1, which contains the catalytic sites to synthesize ATP. The passage of protons through F0 powers the rotation of F1, which facilitates the formation of ATP from ADP and phosphate at three catalytic binding sites. The overall reaction catalyzed by ATP synthase couples proton translocation across the membrane to ATP synthesis, and is essential for energy production in cells.
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- 1. Molecular & Cell Biology S. Rahgozar,PhD University of Isfahan Faculty of Science 2. Cytoskeleton and Cell Movement 2.1. Actin Filaments 1389-90
- 2. Assembly and disassembly of actin filaments Actin FilamentsActin monomer (G actin) Barbed end Pointed end
- 3. Assembly of actin monomers
- 7. ADP-bound actin, which is primarily at the pointed end of the filament, dissociates more readily from the filament than ATP-bound actin. In contrast, actin bound to ATP associates more readily with the rapidly growing barbed ends. ATP binding and hydrolysis play a key role in the dynamic behavior of actin filaments.
- 8. A number of different types of actin binding proteins remodel or modify existing filaments.
- 9. ADF/cofilin proteins bind to actin filaments and enhance the rate of dissociation of ADP-actin monomers from the pointed end. Profilin enhances the rate of association of ATP-actin monomers to the barbed ends. 1- ADF/cofilin and Profilin o Depolimerization/ polymerization
- 10. ADF/cofilin can sever actin filaments. ADF/cofilin binds to ADP-actin , severing the filaments and creating new barbed and pointed ends. o Filament severing
- 11. 2- Formin
- 12. 3- Arp2/3
- 13. Regulation of actin filament organization by actin-binding proteins
- 14. Organization of actin filaments
- 15. Actin – bundling proteins Actin binding domain 14nm 40 nm
- 17. Protrusions of the cell surface
- 19. Association of actin filaments with the plasma membrane The network of actin filaments and associated actin-binding proteins is called the cell cortex. Cell cortex determines cell shape and is involved in a variety of cell surface activities, including movement.
- 20. (fodrin) Association of the erythrocyte cortical cytoskeleton with the plasma
- 21. Attachment of stress fibers to the plasma membrane at focal adhesions Stress fibers and focal adhesions in a cultured human fibroblast
- 22. Attachment of actin filaments to adherens junctions