What is a Cell? By Benjamin Lewin

What is a Cell? By Benjamin Lewin
Chapter 1 What is a Cell? By Benjamin Lewin

1.1 Introduction Cells arise only from preexisting cells.
Every cell has genetic information whose expression enables it to produce all its components. The plasma membrane consists of a lipid bilayer that separates the cell from its environment.

1.2 Life began as a self-replicating structure
The first living cell was a self-replicating entity surrounded by a membrane.

1.3 A prokaryotic cell consists of a single compartment
The plasma membrane of a prokaryote surrounds a single compartment. The entire compartment has the same aqueous environment. Genetic material occupies a compact area within the cell. Bacteria and archaea are both prokaryotes but differ in some structural features.

1.4 Prokaryotes are adapted for growth under many diverse conditions
Prokaryotes adapted to many extreme environmental conditions This highlights the variations that are possible in constructing living cells.

1.5 A eukaryotic cell contains many membrane-delimited compartments
The plasma membrane of a eukaryotic cell surrounds the cytoplasm.

The nucleus is often the largest compartment within the cytoplasm
1.5 A eukaryotic cell contains many membrane-delimited compartments Within the cytoplasm there are individual compartments, each surrounded by a membrane. The nucleus is often the largest compartment within the cytoplasm It contains the genetic material.

1.6 Membranes allow the cytoplasm to maintain compartments with distinct environments
Organelles that are surrounded by membranes can maintain internal milieus that are different from the surrounding cytosol.

1.7 The nucleus contains the genetic material and is surrounded by an envelope
The nucleus is the largest organelle in the cell. It is bounded by an envelope consisting of a double membrane.

Genetic material is concentrated in one part of the nucleus.
1.7 The nucleus contains the genetic material and is surrounded by an envelope Genetic material is concentrated in one part of the nucleus. Nuclear pores provide the means for transport across the envelope for large molecules to enter or leave the nucleus.

1.8 The plasma membrane allows a cell to maintain homeostasis
Hydrophilic molecules cannot pass across a lipid bilayer. The plasma membrane is more permeable to water than to ions.

1.8 The plasma membrane allows a cell to maintain homeostasis
Osmotic pressure is created by ionic differences between the two sides of a membrane. The plasma membrane has specific systems for transporting ions and other solutes into or out of the cell.

Ion channels are proteinaceous structures embedded in membranes.
1.8 The plasma membrane allows a cell to maintain homeostasis The transport systems allow the cell to maintain a constant internal environment that is different from the external milieu. Ion channels are proteinaceous structures embedded in membranes. They allow ions to cross the membrane while remaining in an aqueous environment.

1.9 Cells within cells Organelles bounded by envelopes probably originated by endosymbiosis of prokaryotic cells.

1.10 DNA is the cellular hereditary material, but there are other forms of hereditary information
DNA carries the genetic information that codes for the sequences of all the proteins of the cell. Information can also be carried in cellular structures that are inherited.

1.11 Cells require mechanisms to repair damage to DNA
The genetic material is continually damaged by: environmental forces errors made by cellular systems Repair systems to minimize damage to DNA are essential for the survival of all living cells.

1.12 Mitochondria are energy factories
All living cells have a means of converting energy supplied by the environment into the common intermediate of ATP.

1.13 Chloroplasts power plant cells
Plastids are membrane-bounded organelles in plant cells. They can develop into chloroplasts and other specialized forms.

1.14 Organelles require mechanisms for specific localization of proteins
All organelles import proteins from the cytosol.

1.15 Proteins are transported to and through membranes
Proteins are transported into organelles through receptor complexes embedded in the organelle’s membrane.

Proteins are released into the cytosol after synthesis.
1.15 Proteins are transported to and through membranes Proteins are released into the cytosol after synthesis. For the endoplasmic reticulum, proteins are transferred into the receptor complex on the ER membrane during synthesis. Proteins then associate with the nucleus, or an organelle, such as: Mitochondria Chloroplasts

1.16 Protein trafficking moves proteins through the ER and Golgi apparatus
All proteins that are localized in the ER Golgi apparatus plasma membrane initially associate with the ER during synthesis. Proteins are transported from one compartment to another by membranous vesicles.

The vesicles bud from one membrane surface and fuse with the next.
1.16 Protein trafficking moves proteins through the ER and Golgi apparatus The vesicles bud from one membrane surface and fuse with the next. Proteins are transported into the cell from the exterior by vesicular transport in the reverse direction.

1.17 Protein folding and unfolding is an essential feature of all cells
Protein conformation is a consequence of primary sequence. But often it cannot be achieved by spontaneous folding. It requires assistance from chaperones.

1.18 The shape of a eukaryotic cell is determined by its cytoskeleton
The eukaryotic cell cytoskeleton is an internal framework of filaments, including: Microtubules Actin filaments Intermediate filaments It provides an organizing template for many activities, including anchoring organelles in place.

1.19 Localization of cell structures is important
Localization of certain structures at specific positions in a cell may be part of its hereditary information. Positional effects are important in early development.

1.20 Signal transduction pathways execute predefined responses
Events on the outside of the cell can trigger actions inside the cell by using receptor proteins embedded in the membrane. A receptor spans the membrane and has domains on both the exterior and interior.

The receptor is activated when a ligand binds to the exterior domain.
1.20 Signal transduction pathways execute predefined responses The receptor is activated when a ligand binds to the exterior domain. Ligand binding causes a change in the structure or function of the interior domain.

1.21 All organisms have cells that can grow and divide
The simplest form of division is shown by some organelles where the membrane is pinched inward.

During mitosis, eukaryotic cells are extensively reorganized.
1.21 All organisms have cells that can grow and divide Bacteria often divide by growing a rigid septum across the cell as an extension of the cell wall. During mitosis, eukaryotic cells are extensively reorganized. They form the specialized structure of the spindle. It partitions the chromosomes to daughter cells.

1.22 Differentiation creates specialized cell types, including terminally differentiated cells
A multicellular organism consists of many different cell types that are specialized for specific functions.

1.22 Differentiation creates specialized cell types, including terminally differentiated cells
Many differentiated cells have lost the ability to divide and/or to give rise to cells of different types. Stem cells have the potential to divide to generate the many different types of cells required to make: an organism or a tissue of an organism

Membrane targeting of proteins
Chapter 3 Membrane targeting of proteins By D. Thomas Rutkowski & Vishwanath R. Lingappa

3.1 Introduction Cells must localize proteins to specific organelles and membranes. Proteins are imported from the cytosol directly into several types of organelles.

The endoplasmic reticulum (ER):
3.1 Introduction The endoplasmic reticulum (ER): is the entry point for proteins into the secretory pathway is highly specialized for that purpose Several other organelles and the plasma membrane receive their proteins by way of the secretory pathway.

3.2 Proteins enter the secretory pathway by translocation across the ER membrane (an overview)
Signal sequences target nascent secretory and membrane proteins to the ER for translocation. Proteins cross the ER membrane through an aqueous channel that is gated.

Secretory proteins translocate completely across the ER membrane;
3.2 Proteins enter the secretory pathway by translocation across the ER membrane Secretory proteins translocate completely across the ER membrane; transmembrane proteins are integrated into the membrane. Before leaving the ER, proteins are modified and folded by enzymes and chaperones in the lumen.

3.3 Proteins use signal sequences to target to the ER for translocation
A protein targets to the ER via a signal sequence, a short stretch of amino acids that is usually at its amino terminus. The only feature common to all signal sequences is a central, hydrophobic core that is usually sufficient to translocate any associated protein.

3.4 Signal sequences are recognized by the signal recognition particle (SRP)
SRP binds to signal sequences. Binding of SRP to the signal sequence slows translation so that the nascent protein is delivered to the ER still largely unsynthesized and unfolded.

3.4 Signal sequences are recognized by the signal recognition particle (SRP)
The structural flexibility of the M domain of SRP54 allows SRP to recognize diverse signal sequences.

3.5 An interaction between SRP and its receptor allows proteins to dock at the ER membrane
Docking of SRP with its receptor brings the ribosome and nascent chain into proximity with the translocon. Docking requires the GTP binding and hydrolysis activities of SRP and its receptor.

3.6 The translocon is an aqueous channel that conducts proteins
Proteins translocate through an aqueous channel composed of the Sec61 complex, located within the ER membrane. Numerous accessory proteins that are involved in: Translocation Folding Modification associate with the channel

3.7 Translation is coupled to translocation for most eukaryotic secretory and transmembrane proteins
An interaction between the translocon and the signal sequence causes the channel to open and initiates translocation. The exact mechanism of translocation may vary from one protein to another.

3.8 Some proteins target and translocate posttranslationally
Posttranslational translocation proceeds independently of both ribosomes and SRP. Posttranslational translocation is used extensively in yeast but is less common in higher eukaryotes.

3.8 Some proteins target and translocate posttranslationally
The posttranslational translocon is distinct in composition from the cotranslational translocon, but they share the same channel.

3.9 ATP hydrolysis drives translocation
The energy for posttranslational translocation comes from ATP hydrolysis by the BiP protein within the ER lumen. The energy source for cotranslational translocation is less clear, but might be the same as for posttranslational translocation.

3.9 ATP hydrolysis drives translocation
Most translocation in bacteria occurs posttranslationally through a channel that is evolutionarily related to the Sec61 complex.

3.10 Transmembrane proteins move out of the translocation channel and into the lipid bilayer
The synthesis of transmembrane proteins requires that transmembrane domains be recognized integrated into the lipid bilayer

3.10 Transmembrane proteins move out of the translocation channel and into the lipid bilayer
Transmembrane domains exit the translocon by moving laterally through a protein-lipid interface.

3.11 The orientation of transmembrane proteins is determined as they are integrated into the membrane Transmembrane domains must be oriented with respect to the membrane. The mechanism of transmembrane domain integration may vary considerably from one protein to another especially for proteins that span the membrane more than once

3.12 Signal sequences are removed by signal peptidase
Nascent chains are often subjected to covalent modification in the ER lumen as they translocate. The signal peptidase complex cleaves signal sequences.

3.13 The lipid GPI is added to some translocated proteins
GPI addition covalently tethers the C-termini of some proteins to the lipid bilayer.

3.14 Sugars are added to many translocating proteins
Oligosaccharyltransferase catalyzes N-linked glycosylation on many proteins as they are translocated into the ER.

3.15 Chaperones assist folding of newly translocated proteins
Molecular chaperones associate with proteins in the lumen and assist their folding.

3.16 Protein disulfide isomerase ensures the formation of the correct disulfide bonds as proteins fold Protein disulfide isomerases catalyze disulfide bond formation and rearrangement in the ER.

3.17 The calnexin/calreticulin chaperoning system recognizes carbohydrate modifications
Calnexin and calreticulin escort glycoproteins through repeated cycles of chaperoning. The cycles are controlled by addition and removal of glucose.

3.18 The assembly of proteins into complexes is monitored
Subunits that have not yet assembled into complexes are retained in the ER by interaction with chaperones.

3.19 Terminally misfolded proteins in the ER are returned to the cytosol for degradation
Translocated proteins can be exported to the cytosol. There they are: ubiquitinated degraded by the proteasome —a process known as ER-associated degradation.

3.19 Terminally misfolded proteins in the ER are returned to the cytosol for degradation
Proteins are returned to the cytosol by the process of retrograde translocation. This is not as well understood as for translocation into the ER.

3.20 Communication between the ER and nucleus prevents the accumulation of unfolded proteins in the lumen The unfolded protein response: monitors folding conditions in the ER lumen initiates a signaling pathway that increases the expression of genes for ER chaperones The protein Ire1p mediates the unfolded protein response in yeast by becoming activated in response to conditions of cellular stress.

Activated Ire1p splices HAC1 mRNA.
3.20 Communication between the ER and nucleus prevents the accumulation of unfolded proteins in the lumen Activated Ire1p splices HAC1 mRNA. It results in the production of the Hac1 protein, a transcription factor that: localizes to the nucleus binds to the promoters of genes with a UPR response element The unfolded protein response in higher eukaryotes has evolved more layers of control beyond those seen in yeast.

3.21 The ER synthesizes the major cellular phospholipids
The major cellular phospholipids are synthesized predominantly on the cytosolic face of the ER membrane.

3.21 The ER synthesizes the major cellular phospholipids
The localization of enzymes involved in lipid biosynthesis can be controlled by the cell to regulate the generation of new lipids. Cholesterol biosynthesis is regulated by proteolysis of a transcription factor integrated into the ER membrane.

3.22 Lipids must be moved from the ER to the membranes of other organelles
Each organelle has a unique composition of lipids. This requires that lipid transport from the ER to each organelle be a specific process. The mechanisms of lipid transport between organelles are unclear. They might involve direct contact between the ER and other membranes in the cell. Transbilayer movement of lipids establishes asymmetry of membrane leaflets.

3.23 The two leaflets of a membrane often differ in lipid composition
Movement of lipid molecules between the leaflets of a bilayer is required to establish asymmetry. Enzymes (“flippases”) are required for movement of lipids between leaflets.

3.24 The ER is morphologically and functionally subdivided
The ER is morphologically subdivided into specialized compartments, including: the rough ER for protein secretion the smooth ER for steroidogenesis and drug detoxification the sarcoplasmic reticulum for calcium storage and release

3.24 The ER is morphologically and functionally subdivided
The functions of the smooth ER can be specialized according to the needs of the particular cell type. The ER may also be subdivided at the molecular level, in ways not morphologically evident.

3.25 The ER is a dynamic organelle
The extent and composition of the ER change in response to cellular need. The ER moves along the cytoskeleton.

3.25 The ER is a dynamic organelle
The mechanisms by which the ER expands and contracts and forms tubules have yet to be discovered. The signaling pathways that control ER composition are not yet understood but may overlap with the unfolded protein response.

3.26 Signal sequences are also used to target proteins to other organelles
Signal sequences are used for targeting to and translocation across the membranes of other organelles. Mitochondria and chloroplasts are enclosed by a double membrane, with each bilayer containing its own type of translocon. Two distinct pathways target matrix proteins to peroxisomes.

3.27 Import into mitochondria begins with signal sequence recognition at the outer membrane
Mitochondria have an inner and an outer membrane, each of which has a translocation complex. Import into mitochondria is posttranslational.

3.27 Import into mitochondria begins with signal sequence recognition at the outer membrane
Mitochondrial signal sequences are recognized by a receptor at the outer membrane.

3.28 Complexes in the inner and outer membranes cooperate in mitochondrial protein import
The TOM and TIM complexes associate physically, and the protein being imported passes directly from one to the other. Hsp70 in the mitochondrial matrix and the membrane potential across the inner membrane provide the energy for import.

3.29 Proteins imported into chloroplasts must also cross two membranes
Import into chloroplasts occurs posttranslationally. The inner and outer membranes have separate translocation complexes that cooperate during the import of proteins.

3.30 Proteins fold before they are imported into peroxisomes
Peroxisomal signal sequences are: recognized in the cytosol targeted to a translocation channel Peroxisomal proteins are imported after they are folded.

Peroxisomal membranes originate by budding from the ER.
3.30 Proteins fold before they are imported into peroxisomes The proteins that recognize peroxisomal signal sequences remain bound during import and cycle in and out of the organelle. Peroxisomal membranes originate by budding from the ER.

Chapter 2 Transport of ions and small molecules across membranes By
Stephan E. Lehnart & Andrew R. Marks

2.1 Introduction Cell membranes define compartments of different compositions. The lipid bilayer of biological membranes has a very low permeability for most biological molecules and ions.

Most solutes cross cell membranes through transport proteins.
2.1 Introduction Most solutes cross cell membranes through transport proteins. The transport of ions and other solutes across cellular membranes controls: electrical functions metabolic functions

2.2 Channels and carriers are the main types of membrane transport proteins
There are two principal types of membrane transport proteins: Channels Carriers

Transporters and pumps are carrier proteins.
2.2 Channels and carriers are the main types of membrane transport proteins Ion channels catalyze the rapid and selective transport of ions down their electrochemical gradients. Transporters and pumps are carrier proteins. They use energy to transport solutes against their electrochemical gradients. In a given cell, several different membrane transport proteins work as an integrated system.

2.3 Hydration of ions influences their flux through transmembrane pores
Salts dissolved in water form hydrated ions. The hydrophobicity of lipid bilayers is a barrier to movement of hydrated ions across cell membranes.

2.3 Hydration of ions influences their flux through transmembrane pores
By catalyzing the partial dehydration of ions, ion channels allow for the rapid and selective transport of ions across membranes. Dehydration of ions costs energy, whereas hydration of ions frees energy.

2.4 Electrochemical gradients across the cell membrane generate the membrane potential
The membrane potential across a cell membrane is due to: an electrochemical gradient across a membrane a membrane that is selectively permeable to ions

The Nernst equation is used to calculate the membrane potential as a function of ion concentrations. • E: equilibrium potential (volts) • R: the gas constant (2 cal mol–1 K–1) • T: absolute temperature (K; 37°C = °K) • z: the ion’s valence (electric charge) • F: Faraday’s constant ( cal volt–1 mol–1) • [X]A: concentration of free ion X in compartment A • [X]B: concentration of free ion X in compartment B

Cells maintain a negative resting membrane potential with the inside of the cell slightly more negative than the outside. The membrane potential is a prerequisite for electrical signals and for directed ion movement across cellular membranes.

2.5 K+ channels catalyze selective and rapid ion permeation
K+ channels function as water-filled pores that catalyze the selective and rapid transport of K+ ions. A K+ channel is a complex of four identical subunits, each of which contributes to the pore.

2.5 K+ channels catalyze selective and rapid ion permeation
The selectivity filter of K+ channels is an evolutionarily conserved structure. The K+ channel selectivity filter catalyzes dehydration of ions, which: confers specificity speeds up ion permeation

2.6 Different K+ channels use a similar gate coupled to different activating or inactivating mechanisms Gating is an essential property of ion channels. Different gating mechanisms define functional classes of K+ channels.

The K+ channel gate is distinct from the selectivity filter.
2.6 Different K+ channels use a similar gate coupled to different activating or inactivating mechanisms. The K+ channel gate is distinct from the selectivity filter. K+ channels are regulated by the membrane potential.

2.7 Voltage-dependent Na+ channels are activated by membrane depolarization and translate electrical signals The inwardly directed Na+ gradient maintained by the Na+/K+-ATPase is required for the function of Na+ channels.

2.7 Voltage-dependent Na+ channels are activated by membrane depolarization and translate electrical signals Electrical signals at the cell membrane activate voltage-dependent Na+ channels. The pore of voltage-dependent Na+ channels is formed by one subunit, but its overall architecture is similar to that of 6TM/1P K+ channels. Voltage-dependent Na+ channels are inactivated by specific hydrophobic residues that block the pore.

2.8 Epithelial Na+ channels regulate Na+ homeostasis
The epithelial Na+ channel/degenerin family of ion channels is diverse. The epithelial Na+ channels and Na+/K+-ATPase function together to direct Na+ transport through epithelial cell layers. The ENaC selectivity filter is similar to the K+ channel selectivity filter.

2.9 Plasma membrane Ca2+ channels activate intracellular functions
Cell surface Ca2+ channels translate membrane signals into intracellular Ca2+ signals.

2.9 Plasma membrane Ca2+ channels activate intracellular functions
Voltage-dependent Ca2+ channels are asymmetric protein complexes of five different subunits. The α1 subunit of voltage-dependent Ca2+ channels forms the pore and contains pore loop structures similar to K+ channels.

The Ca2+ channel selectivity filter forms an electrostatic trap.
2.9 Plasma membrane Ca2+ channels activate intracellular functions The Ca2+ channel selectivity filter forms an electrostatic trap. Ca2+ channels are stabilized in the closed state by channel blockers.

2.10 Cl– channels serve diverse biological functions
Cl– channels are anion channels that serve a variety of physiological functions. Cl– channels use an antiparallel subunit architecture to establish selectivity.

2.10 Cl– channels serve diverse biological functions
Selective conduction and gating are structurally coupled in Cl– channels. K+ channels and Cl– channels use different mechanisms of gating and selectivity.

2.11 Selective water transport occurs through aquaporin channels
Aquaporins allow rapid and selective water transport across cell membranes. Aquaporins are tetramers of four identical subunits, with each subunit forming a pore.

2.11 Selective water transport occurs through aquaporin channels
The aquaporin selectivity filter has three major features that confer a high degree of selectivity for water: size restriction electrostatic repulsion water dipole orientation

2.12 Action potentials are electrical signals that depend on several types of ion channels
Action potentials enable rapid communication between cells. Na+, K+, and Ca2+ currents are key elements of action potentials. Membrane depolarization is mediated by the flow of Na+ ions into cells through voltage-dependent Na+ channels.

2.12 Action potentials are electrical signals that depend on several types of ion channels
Repolarization is shaped by transport of K+ ions through several different types of K+ channels. The electrical activity of organs can be measured as the sum of action potential vectors. Alterations of the action potential can predispose for arrhythmias or epilepsy.

2.13 Cardiac and skeletal muscles are activated by excitation-contraction coupling
The process of excitation-contraction coupling, which is initiated by membrane depolarization, controls muscle contraction. Ryanodine receptors and inositol 1,4,5-trisphosphate receptors are Ca2+ channels. Ca2+ ions are released from intracellular stores into the cytosol through them.

2.13 Cardiac and skeletal muscles are activated by excitation-contraction coupling
Intracellular Ca2+ release through ryanodine receptors in the sarcoplasmic reticulum membrane stimulates contraction of the myofilaments. Several different types of Ca2+ transport proteins, including the Na+/Ca2+-exchanger and Ca2+-ATPase are important for decreasing the cytosolic Ca2+ concentration controlling muscle relaxation

2.14 Some glucose transporters are uniporters
To cross the blood-brain barrier, glucose is transported across endothelial cells of small blood vessels into astrocytes.

2.14 Some glucose transporters are uniporters
Glucose transporters are uniporters that transport glucose down its concentration gradient. Glucose transporters undergo conformational changes that result in a reorientation of their substrate binding sites across membranes.

2.15 Symporters and antiporters mediate coupled transport
Bacterial lactose permease functions as a symporter. It couples lactose and proton transport across the cytoplasmic membrane. Lactose permease uses the electrochemical H+ gradient to drive lactose accumulation inside cells. Lactose permease can also use lactose gradients to create proton gradients across the cytoplasmic membrane.

2.15 Symporters and antiporters mediate coupled transport
The mechanism of transport by lactose permease likely involves inward and outward configurations. They allow substrates to: bind on one side of the membrane and to be released on the other side The bacterial glycerol-3-phosphate transporter is an antiporter that is structurally related to lactose permease.

2.16 The transmembrane Na+ gradient is essential for the function of many transporters
The plasma membrane Na+ gradient is maintained by the action of the Na+/K+-ATPase. The energy released by movement of Na+ down its electrochemical gradient is coupled to the transport of a variety of substrates. The Na+/Ca2+-exchanger is the major transport mechanism for removal of Ca2+ from the cytosol of excitable cells.

Na+/Mg2+-exchangers transport Mg2+ out of cells.
2.16 The transmembrane Na+ gradient is essential for the function of many transporters The gastrointestinal tract absorbs sugar through the Na+/glucose transporter. The Na+/K+/Cl–-cotransporter regulates intracellular Cl– concentrations. Na+/Mg2+-exchangers transport Mg2+ out of cells.

2.17 Some Na+ transporters regulate cytosolic or extracellular pH
Na+/H+ exchange controls intracellular acid and cell volume homeostasis. The net effect of Na+/HCO3–-cotransporters is to remove acid by directed transport of HCO3–.

2.18 The Ca2+-ATPase pumps Ca2+ into intracellular storage compartments
Ca2+-ATPases undergo a reaction cycle involving two major conformations, similar to that of Na+/K+-ATPases. Phosphorylation of Ca2+-ATPase subunits drives: conformational changes translocation of Ca2+ ions across the membrane

2.19 The Na+/K+-ATPase maintains the plasma membrane Na+ and K+ gradients
The Na+/K+-ATPase is a P-type ATPase that is similar to the Ca2+-ATPase and the H+-ATPase. The Na+/K+-ATPase maintains the Na+ and K+ gradients across the plasma membrane. The plasma membrane Na+/K+-ATPase is electrogenic: it transports three Na+ ions out of the cell for every two K+ ions it transports into the cell.

2.19 The Na+/K+-ATPase maintains the plasma membrane Na+ and K+ gradients
The reaction cycle for Na+/K+-ATPase is described by the Post-Albers scheme. It proposes that the enzyme cycles between two fundamental conformations.

2.20 The F1Fo-ATP synthase couples H+ movement to ATP synthesis or hydrolysis
The F1Fo-ATP synthase is a key enzyme in oxidative phosphorylation. The F1Fo-ATP synthase is a multisubunit molecular motor. It couples the energy released by movement of protons down their electrochemical gradient to ATP synthesis.

2.21 H+-ATPases transport protons out of the cytosol
Proton concentrations affect many cellular functions. Intracellular compartments are acidified by the action of V-ATPases. V-ATPases are proton pumps that consist of multiple subunits, with a structure similar to F1Fo-ATP synthases.

V-ATPases in the plasma membrane serve specialized functions in:
2.21 H+-ATPases transport protons out of the cytosol V-ATPases in the plasma membrane serve specialized functions in: acidification of extracellular fluids regulation of cytosolic pH

Supplement: Most K+ channels undergo rectification
Inward rectification occurs through voltage-dependent blocking of the pore.

Supplement: Mutations in an anion channel cause cystic fibrosis
Cystic fibrosis is caused by mutations in the gene encoding the CFTR channel. CFTR is an anion channel that can transport either Cl– or HCO3–. Defective secretory function in cystic fibrosis affects numerous organs.

Protein trafficking between membranes By Graham Warren & Ira Mellman
Chapter 4 Protein trafficking between membranes By Graham Warren & Ira Mellman

4.1 Introduction Eukaryotic cells have an elaborate system of internal membrane-bounded structures called organelles. Each organelle: has a unique composition of (glyco)proteins and (glyco)lipids carries out a particular set of functions

An organelle comprises one or more membrane-bounded compartments.
4.1 Introduction An organelle comprises one or more membrane-bounded compartments. Organelles may act autonomously or in cooperation to accomplish a given function. In the endocytic and exocytic pathways, cargo proteins are transferred between compartments by transport vesicles.

The vesicles form by budding from an organelle’s surface.
4.1 Introduction The vesicles form by budding from an organelle’s surface. They subsequently fuse with the target membrane of the acceptor compartment.

Transport vesicles can selectively:
4.1 Introduction Transport vesicles can selectively: include material destined for transfer exclude material that must remain in the organelle from which they bud Selective inclusion into transport vesicles is ensured by signals in a protein’s amino acid sequence or carbohydrate structures. Transport vesicles contain proteins that target them specifically to their intended destinations with which they dock and fuse.

4.2 Overview of the exocytic pathway
All eukaryotes have the same complement of core exocytic compartments: the endoplasmic reticulum the compartments of the Golgi apparatus post-Golgi transport vesicles

Each organelle in the exocytic pathway has a specialized function.
4.2 Overview of the exocytic pathway The amount and organization of exocytic organelles varies from organism to organism and cell type to cell type. Each organelle in the exocytic pathway has a specialized function. The endoplasmic reticulum is the site for the synthesis and proper folding of proteins.

In the Golgi apparatus, proteins are:
4.2 Overview of the exocytic pathway In the Golgi apparatus, proteins are: Modified Sorted carried by the post-Golgi transport vesicles to the correct destination. Cargo transport to the plasma membrane occurs: directly by a constitutive process or indirectly by a regulated process. This involves temporary storage in secretory granules until the cell receives an appropriate stimulus.

4.3 Overview of the endocytic pathway
Extracellular material can be taken into cells by several different mechanisms. The low pH and degradative enzymes in endosomes and lysosomes are important in processing some endocytosed material.

4.4 Concepts in vesicle-mediated protein transport
Transport vesicles move proteins and other macromolecules from one membrane-bounded compartment to the next along the exocytic and endocytic pathways. Coats formed from cytoplasmic protein complexes help to: generate transport vesicles select proteins that need to be transported

4.4 Concepts in vesicle-mediated protein transport
Proteins destined for transport to one compartment are sorted away from: resident proteins proteins that are destined for other compartments Transport vesicles use tethers and SNAREs to dock and fuse specifically with the next compartment on the pathway. Retrograde (backward) movement of transport vesicles carrying recycled or salvaged proteins compensates for anterograde (forward) movement of vesicles.

4.5 The concepts of signal-mediated and bulk flow protein transport
Soluble secretory proteins, especially those secreted in large amounts, may not require specific signals to traverse the exocytic pathway.

4.5 The concepts of signal-mediated and bulk flow protein transport
Sorting signals may be restricted to membrane proteins and endocytosed receptors; particularly those that are targeted to some intracellular destinations, such as lysosomes. Some soluble proteins have signals that allow them to interact with receptors that mediate their transport to lysosomes.

4.6 COPII-coated vesicles mediate transport from the ER to the Golgi apparatus
COPII vesicles are the only known class of transport vesicles originating from the endoplasmic reticulum. Assembly of the COPII coat proteins at export sites in the endoplasmic reticulum requires a GTPase and structural proteins.

4.6 COPII-coated vesicles mediate transport from the ER to the Golgi apparatus
Export signals for membrane proteins in the endoplasmic reticulum are usually in the cytoplasmic tail. After scission, COPII vesicles may cluster, fuse, and then move along microtubule tracks to the cis-side of the Golgi apparatus.

4.7 Resident proteins that escape from the ER are retrieved
Abundant, soluble proteins of the endoplasmic reticulum (ER) contain sequences (such as KDEL or a related sequence). These sequences allow them to be retrieved from later compartments by the KDEL receptor.

4.7 Resident proteins that escape from the ER are retrieved
Resident membrane proteins and cycling proteins are retrieved to the ER by a dibasic signal in the cytoplasmic tail. The ER retrieval signal for type I transmembrane proteins is a dilysine signal. Type II transmembrane proteins have a diarginine signal.

4.8 COPI-coated vesicles mediate retrograde transport from the Golgi apparatus to the ER
COPI coat assembly is triggered by a membrane-bound GTPase called ARF.

4.8 COPI-coated vesicles mediate retrograde transport from the Golgi apparatus to the ER
ARF recruits coatomer complexes, and disassembly follows GTP hydrolysis. COPI coats bind directly or indirectly to cargo proteins that are returned to the endoplasmic reticulum from the Golgi apparatus.

4.9 There are two popular models for forward transport through the Golgi apparatus
Transport of large protein structures through the Golgi apparatus occurs by cisternal maturation. Individual proteins and small protein structures are transported through the Golgi apparatus either by cisternal maturation or vesicle-mediated transport.

4.10 Retention of proteins in the Golgi apparatus depends on the membrane-spanning domain
The membrane-spanning domain and its flanking sequences are sufficient to retain proteins in the Golgi apparatus. The retention mechanism for Golgi proteins depends on the ability to form oligomeric complexes and the length of the membrane-spanning domain.

4.11 Rab GTPases and tethers are two types of proteins that regulate vesicle targeting
Monomeric GTPases of the Sar/ARF family are involved in generating the coat that forms transport vesicles. Another family, the Rab GTPases, are involved in targeting these vesicles to their destination membranes.

4.11 Rab GTPases and tethers are two types of proteins that regulate vesicle targeting
Different Rab family members are found at each step of vesicle-mediated transport. Proteins that are recruited or activated by Rabs (downstream effectors) include: tethering proteins such as long fibrous proteins large multiprotein complexes Tethering proteins link vesicles to membrane compartments and compartments to each other.

4.12 SNARE proteins likely mediate fusion of vesicles with target membranes
SNARE proteins are both necessary and sufficient for specific membrane fusion in vitro, but other accessory proteins may be needed in vivo. A v-SNARE on the transport vesicle interacts with the cognate t-SNARE on the target membrane compartment.

4.12 SNARE proteins likely mediate fusion of vesicles with target membranes
The interaction between v- and t-SNAREs is thought to bring the membranes close enough together so that they can fuse. After fusion: the ATPase NSF unravels the v- and t-SNAREs the v-SNAREs are recycled to the starting membrane compartment

4.13 Endocytosis is often mediated by clathrin-coated vesicles
The stepwise assembly of clathrin triskelions may help provide the mechanical means to deform membranes into coated pits. Various adaptor complexes provide the means of selecting cargo for transport by binding both to: sorting signals clathrin triskelions

4.13 Endocytosis is often mediated by clathrin-coated vesicles
GTPases of the dynamin family help release the coated vesicle from the membrane. Uncoating ATPases remove the clathrin coat before docking and fusion.

4.14 Adaptor complexes link clathrin and transmembrane cargo proteins
Adaptor complexes bind to: the cytoplasmic tails of transmembrane cargo proteins clathrin Phospholipids Adaptors of the AP family are heterotetrameric complexes of two adaptin subunits and two smallerproteins.

4.14 Adaptor complexes link clathrin and transmembrane cargo proteins
The AP adaptors bind to sorting signals in the cytoplasmic tails of cargo proteins. The best-characterized of these signals contain tyrosine or dileucine residues. Adaptor complexes allow for the selective and rapid internalization of receptors and their ligand.

4.15 Some receptors recycle from early endosomes whereas others are degraded in lysosomes
Early endosomes are mildly acidic and lack degradative enzymes, so: internalized ligands can be dissociated without degradation of their receptors. Many receptors are recycled to the cell surface in transport vesicles that bud from the tubular extensions of early endosomes.

Receptors that are not recycled:
4.15 Some receptors recycle from early endosomes whereas others are degraded in lysosomes Dissociated ligands are transferred from early endosomes to the more acidic and hydrolase-rich late endosomes and lysosomes for degradation. Receptors that are not recycled: are segregated into vesicles within multivesicular bodies move to late endosomes and lysosomes for degradation

Recycling endosomes are found adjacent to the nucleus.
4.15 Some receptors recycle from early endosomes whereas others are degraded in lysosomes Recycling endosomes are found adjacent to the nucleus. They contain a pool of recycling receptors that can be transported rapidly to the cell surface when needed.

4.16 Early endosomes become late endosomes and lysosomes by maturation
Movement of material from early endosomes to late endosomes and lysosomes occurs by “maturation.” A series of ESCRT protein complexes sorts proteins into vesicles that bud into the lumen of endosomes. This forms multivesicular bodies that facilitate the process of proteolytic degradation.

4.17 Sorting of lysosomal proteins occurs in the trans-Golgi network
All newly synthesized membrane and secretory proteins share the same pathway up until the TGN. There they are sorted according to their destinations into different transport vesicles. Clathrin-coated vesicles transport lysosomal proteins from the trans-Golgi network to maturing endosomes.

In the Golgi apparatus, mannose 6-phosphate is covalently linked to soluble enzymes destined for lysosomes. The mannose 6-phosphate receptor delivers these enzymes from the trans-Golgi network to the endocytic pathway.

Lysosomal membrane proteins are transported from the trans-Golgi network to maturing endosomes. But, they use different signals than the soluble lysosomal enzymes.

4.18 Polarized epithelial cells transport proteins to apical and basolateral membranes
The plasma membrane of a polarized cell has separate domains with distinct sets of proteins. This necessitates a further sorting step. Depending on the cell type, sorting of cell surface proteins in polarized cells can occur at: the TGN endosomes one of the plasma membrane domains Sorting in polarized cells is mediated by specialized adaptor complexes and perhaps lipid rafts and lectins.

4.19 Some cells store proteins for later secretion
Some cargo molecules are stored in secretory granules, which: fuse with the plasma membrane release their contents only upon stimulation Storage of proteins for regulated secretion often involves a condensation process. Cargo self-associates, condensing to form a concentrated packet for eventual delivery to the outside of the cell.

Condensation of proteins for regulated secretion often
4.19 Some cells store proteins for later secretion Condensation of proteins for regulated secretion often begins in the endoplasmic reticulum continues in the Golgi apparatus is completed in condensing vacuoles that finally yield secretory granules Condensation is accompanied by selective membrane retrieval at all stages of exocytosis.

4.19 Some cells store proteins for later secretion
Fusion of synaptic vesicles with the plasma membrane involves SNARE proteins. But it is regulated by calcium-sensitive proteins such as synaptotagmin.

Nuclear structure and transport By Charles N. Cole & Pamela A. Silver
Chapter 5 Nuclear structure and transport By Charles N. Cole & Pamela A. Silver

5.1 Introduction The nucleus contains most of the cell’s DNA, allowing for sophisticated regulation of gene expression. The nuclear envelope is a double membrane that surrounds the nucleus.

The nucleus contains subcompartments that are not membrane-bounded.
5.1 Introduction The nucleus contains subcompartments that are not membrane-bounded. The nuclear envelope contains pores used for: importing proteins into the nucleus exporting RNAs and proteins from the nucleus

5.2 Nuclei vary in appearance according to cell type and organism
Nuclei range in size from about one micron (1 μm) to more than 10 μm in diameter. Most cells have a single nucleus, but some cells contain multiple nuclei, and a few cell types lack nuclei. The percentage of the genome that is heterochromatin varies among cells and increases as cells become more differentiated.

5.3 Chromosomes occupy distinct territories
Although the nucleus lacks internal membranes, nuclei are highly organized and contain many subcompartments. Each chromosome occupies a distinct region or territory. This prevents chromosomes from becoming entangled with one another.

5.3 Chromosomes occupy distinct territories
The nucleus contains both chromosome domains and interchromosomal regions.

5.4 The nucleus contains subcompartments that are not membrane-bounded
Nuclear subcompartments are not membrane-bounded. rRNA is synthesized and ribosomal subunits are assembled in the nucleolus. The nucleolus contains DNA that encodes rRNAs and that is present on multiple chromosomes.

mRNA splicing factors:
5.4 The nucleus contains subcompartments that are not membrane-bounded mRNA splicing factors: are stored in nuclear speckles move to sites of transcription where they function Other nuclear bodies can be identified with antibodies, but the functions of most of these are unknown.

5.5 Some processes occur at distinct nuclear sites and may reflect an underlying structure
The nucleus contains replication sites where DNA is synthesized. The nucleus may contain a nucleoskeleton that could help to organize nuclear functions.

5.6 The nucleus is bounded by the nuclear envelope
The nucleus is surrounded by a nuclear envelope consisting of two complete membranes. The outer nuclear membrane is continuous with the membranes of the endoplasmic reticulum (ER). The lumen of the nuclear envelope is continuous with the lumen of the ER. The nuclear envelope contains numerous NPCs. They are the only channels for transport of molecules and macromolecules between the nucleus and the cytoplasm.

5.7 The nuclear lamina underlies the nuclear envelope
The nuclear lamina is constructed of intermediate filament proteins called lamins. The nuclear lamina is located beneath the inner nuclear membrane. They are physically connected by lamina-associated integral membrane proteins. The nuclear lamina plays a role in nuclear envelope assembly and may provide physical support for the nuclear envelope.

5.7 The nuclear lamina underlies the nuclear envelope
Proteins connect the nuclear lamina to chromatin; this may allow the nuclear lamina to organize DNA replication and transcription. Yeast and some other unicellular eukaryotes lack a nuclear lamina.

5.8 Large molecules are actively transported between the nucleus and cytoplasm
Uncharged molecules smaller than 100 daltons can pass through the membranes of the nuclear envelope. Molecules and macromolecules larger than 100 daltons cross the nuclear envelope by moving through NPCs.

5.8 Large molecules are actively transported between the nucleus and cytoplasm
Particles up to 9 nm in diameter (corresponding to globular proteins up to 40 kDa) can pass through NPCs by passive diffusion. Larger macromolecules are actively transported through NPCs and must contain specific information in order to be transported.

5.9 Nuclear pore complexes are symmetrical channels
NPCs are symmetrical structures that are found at sites where the inner and outer nuclear membrane are fused. Each NPC in human cells has a mass of ~ daltons (40 times that of a ribosome). It is constructed from multiple copies of ~30 proteins.

NPCs contain: fibrils that extend into the cytoplasm
5.9 Nuclear pore complexes are symmetrical channels NPCs contain: fibrils that extend into the cytoplasm a basket-like structure that extends into the nucleus

5.10 Nuclear pore complexes are constructed from nucleoporins
The proteins of NPCs are called nucleoporins. Many nucleoporins contain repeats of short sequences, which are thought to interact with transport factors during transport. Such as: Gly-Leu-Phe-Gly X-Phe-X-Phe-Gly X-X-Phe-Gly

All of the nucleoporins of yeast NPCs have been identified.
5.10 Nuclear pore complexes are constructed from nucleoporins Some nucleoporins are transmembrane proteins that are thought to anchor NPCs in the nuclear envelope. All of the nucleoporins of yeast NPCs have been identified. NPCs are disassembled and reassembled during mitosis. Some nucleoporins are dynamic: they rapidly associate with and dissociate from NPCs.

5.11 Proteins are selectively transported into the nucleus through nuclear pores
Mature nuclear proteins contain sequence information required for their nuclear localization. Proteins selectively enter and exit the nucleus through nuclear pores. Information for nuclear import lies in a small portion of the transported protein.

5.12 Nuclear localization sequences target proteins to the nucleus
A nuclear localization sequence (NLS) is often a short stretch of basic amino acids. NLSs are defined as both necessary and sufficient for nuclear import.

5.13 Cytoplasmic NLS receptors mediate nuclear protein import
Receptors for nuclear import are cytoplasmic proteins that bind to the NLS of cargo proteins. Nuclear import receptors are part of a large family of proteins often called karyopherins.

5.14 Export of proteins from the nucleus is also receptor-mediated
Short stretches of amino acids rich in leucine act as the most common nuclear export sequences. A nuclear export receptor: binds proteins that contain nuclear export sequences (NESs) in the nucleus transports them to the cytoplasm

5.15 The Ran GTPase controls the direction of nuclear transport
Ran is a small GTPase that is common to all eukaryotes and is found in both the nucleus and the cytoplasm. The Ran-GAP promotes hydrolysis of GTP by Ran. The Ran-GEF promotes exchange of GDP for GTP on Ran.

5.15 The Ran GTPase controls the direction of nuclear transport
The Ran-GAP is cytoplasmic, whereas the Ran-GEF is located in the nucleus. Ran controls nuclear transport by binding karyopherins and affecting their ability to bind their cargoes.

5.16 Multiple models have been proposed for the mechanism of nuclear transport
Interactions between karyopherins and nucleoporins are critical for translocation across the nuclear pore. Directionality may be conferred in part by distinct interactions of karyopherins with certain nucleoporins.

5.17 Nuclear transport can be regulated
Both protein import and export are regulated. Cells use nuclear transport to regulate many functions, including: transit through the cell cycle response to external stimuli The movement of the transcription factor NF-κB illustrates how nuclear transport is regulated.

5.18 Multiple classes of RNA are exported from the nucleus
mRNAs, tRNAs, and ribosomal subunits produced in the nucleus are exported through NPCs to function during translation in the cytoplasm.

The same NPCs used for protein transport are also used for RNA export.
5.18 Multiple classes of RNA are exported from the nucleus The same NPCs used for protein transport are also used for RNA export. Export of RNA is receptor-mediated and energy-dependent. Different soluble transport factors are required for transport of each class of RNA.

5.19 Ribosomal subunits are assembled in the nucleolus and exported by exportin 1
Ribosomal subunits are assembled in the nucleolus where rRNA is made. Ribosomal proteins are imported from the cytoplasm for assembly into the ribosomal subunits. Export of the ribosomal subunits is carrier-mediated and requires Ran.

5.20 tRNAs are exported by a dedicated exportin
Exportin-t is the transport receptor for tRNAs. tRNA export requires Ran. tRNA export may be affected by modifications of the tRNAs. tRNAs may be re-imported into the nucleus.

5.21 Messenger RNAs are exported from the nucleus as RNA-protein complexes
Proteins that associate with mRNAs during transcription help to define sites of pre-mRNA processing. They are also thought to package mRNAs for export.

Signals for mRNA export may be present in proteins bound to the mRNA.
5.21 Messenger RNAs are exported from the nucleus as RNA-protein complexes Most proteins that associate with mRNA in the nucleus are removed after export and returned to the nucleus. A few are removed immediately prior to export. Signals for mRNA export may be present in proteins bound to the mRNA. The export of mRNA can be regulated, but the mechanism for this is unknown.

5.22 hnRNPs move from sites of processing to NPCs
mRNAs are released from chromosome territories into interchromosomal domains following completion of pre-mRNA processing. mRNAs move to the nuclear periphery by diffusion through interchromosomal spaces.

5.23 mRNA export requires several novel factors
Many factors required uniquely for mRNA export have been identified. Factors able to bind to both the mRNP and nuclear pore complex help to mediate mRNA export.

5.23 mRNA export requires several novel factors
One factor, Dbp5, is an ATPase and may use energy from ATP hydrolysis to remove mRNP proteins during transport.

5.24 U snRNAs are exported, modified, assembled into complexes, and imported
U snRNAs produced in the nucleus are exported modified packaged into U snRNP RNA-protein complexes imported into the nucleus to function in RNA processing

5.25 Precursors to microRNAs are exported from the nucleus and processed in the cytoplasm
MicroRNAs are produced by: transcription in the nucleus partial processing to generate a hairpin precursor export of the precursor by exportin-V final processing in the cytoplasm

Chromatin and chromosomes By Benjamin Lewin
Chapter 6 Chromatin and chromosomes By Benjamin Lewin

6.2 Chromatin is divided into euchromatin and heterochromatin
Individual chromosomes can be seen only during mitosis. During interphase, the general mass of chromatin is in the form of euchromatin. Euchromatin is less tightly packed than mitotic chromosomes. Regions of heterochromatin remain densely packed throughout interphase.

6.3 Chromosomes have banding patterns
Certain staining techniques cause the chromosomes to have the appearance of a series of striations called G-bands. The bands are lower in G • C content than the interbands. Genes are concentrated in the G • C-rich interbands.

6.4 Eukaryotic DNA has loops and domains attached to a scaffold
DNA of interphase chromatin is negatively supercoiled into independent domains of ~85 kb. Metaphase chromosomes have a protein scaffold to which the loops of supercoiled DNA are attached.

6.5 Specific sequences attach DNA to an interphase matrix
DNA is attached to the nuclear matrix at specific sequences called MARs or SARs. The MARs are A • T-rich but do not have any specific consensus sequence.

6.6 The centromere is essential for segregation
A eukaryotic chromosome is held on the mitotic spindle by the attachment of microtubules to the kinetochore that forms in its centromeric region. Centromeres often have heterochromatin that is rich in satellite DNA sequences.

6.7 Centromeres have short DNA sequences in S. cerevisiae
CEN elements are identified in S. cerevisiae by the ability to allow a plasmid to segregate accurately at mitosis. CEN elements consist of short conserved sequences CDE-I and CDE-III that flank the A • T-rich region CDE-II.

6.8 The centromere binds a protein complex
A specialized protein complex that is an alternative to the usual chromatin structure is formed at CDE-II. The CBF3 protein complex that binds to CDE-III is essential for centromeric function. The proteins that connect these two complexes may provide the connection to microtubules.

6.9 Centromeres may contain repetitious DNA
Centromeres in higher eukaryotic chromosomes contain large amounts of repetitious DNA. The function of the repetitious DNA is not known.

6.10 Telomeres are replicated by a special mechanism
The telomere is required for the stability of the chromosome end. A telomere consists of a simple repeat where a C+A-rich strand has the sequence C>1(A/T)1-4.

6.11 Telomeres seal the chromosome ends
The protein TRF2 catalyzes a reaction in which: the 3 repeating unit of the G+T-rich strand forms a loop by displacing its homologue in an upstream region of the telomere.

6.12 Lampbrush chromosomes are extended
Sites of gene expression on lampbrush chromosomes show loops that are extended from the chromosomal axis.

6.13 Polytene chromosomes form bands
Polytene chromosomes of Dipterans have a series of bands that can be used as a cytological map.

6.14 Polytene chromosomes expand at sites of gene expression
Bands that are sites of gene expression on polytene chromosomes expand to give “puffs.”

6.15 The nucleosome is the subunit of all chromatin
Micrococcal nuclease releases individual nucleosomes from chromatin as 11S particles. A nucleosome contains: ~200 bp of DNA two copies of each core histone (H2A, H2B, H3, and H4) one copy of H1 DNA is wrapped around the outside surface of the protein octamer.

6.16 DNA is coiled in arrays of nucleosomes
Greater than 95% of the DNA is recovered in nucleosomes or multimers when micrococcal nuclease cleaves DNA of chromatin. The length of DNA per nucleosome varies for individual tissues in a range from bp.

6.17 Nucleosomes have a common structure
Nucleosomal DNA is divided into the core DNA and linker DNA depending on its susceptibility to micrococcal nuclease. The core DNA is the length of 146 bp that is found on the core particles produced by prolonged digestion with micrococcal nuclease.

6.17 Nucleosomes have a common structure
Linker DNA is the region of bp that is susceptible to early cleavage by the enzyme. Changes in the length of linker DNA account for the variation in total length of nucleosomal DNA. H1 is associated with linker DNA and may lie at the point where DNA enters and leaves the nucleosome.

6.18 DNA structure varies on the nucleosomal surface
1.65 turns of DNA are wound around the histone octamer. The structure of the DNA is altered so that it has: an increased number of base pairs/turn in the middle but a decreased number at the ends

6.18 DNA structure varies on the nucleosomal surface
Approximately 0.6 negative turns of DNA are absorbed by the change in bp/turn from 10.5 in solution to an average of 10.2 on the nucleosomal surface. This explains the linking number paradox.

6.19 Organization of the histone octamer
The histone octamer has a kernel of a H32 • H42 tetramer associated with two H2A • H2B dimers. Each histone is extensively interdigitated with its partner.

All core histones have the structural motif of the histone fold.
6.19 Organization of the histone octamer All core histones have the structural motif of the histone fold. The histone N-terminal tails extend out of the nucleosome.

6.20 The path of nucleosomes in the chromatin fiber
10-nm chromatin fibers are unfolded from 30-nm fibers and consist of a string of nucleosomes. 30-nm fibers have 6 nucleosomes/turn, organized into a solenoid. Histone H1 is required for formation of the 30-nm fiber.

6.21 Reproduction of chromatin requires assembly of nucleosomes
Histone octamers are not conserved during replication; However, H2A • H2B dimers and H32 • H42 tetramers are conserved. There are different pathways for the assembly of nucleosomes during replication and independently of replication. Accessory proteins are required to assist the assembly of nucleosomes.

6.21 Reproduction of chromatin requires assembly of nucleosomes
CAF-1 is an assembly protein that is linked to the PCNA subunit of the replisome; it is required for deposition of H32 • H42 tetramers following replication. A different assembly protein and a variant of histone H3 may be used for replication-independent assembly.

6.22 Do nucleosomes lie at specific positions?
Nucleosomes may form at specific positions as the result either of: the local structure of DNA proteins that interact with specific sequences The most common cause of nucleosome positioning is when proteins binding to DNA establish a boundary. Positioning may affect which regions of DNA are in the linker and which face of DNA is exposed on the nucleosome surface.

6.23 Domains define regions that contain active genes
A domain containing a transcribed gene is defined by increased sensitivity to degradation by DNAase I.

6.24 Are transcribed genes organized in nucleosomes?
Nucleosomes are found at the same frequency when transcribed genes or nontranscribed genes are digested with micrococcal nuclease. Some heavily transcribed genes appear to be exceptional cases that are devoid of nucleosomes.

6.25 Histone octamers are displaced by transcription
RNA polymerase displaces histone octamers during transcription in a model system; Octamers reassociate with DNA as soon as the polymerase has passed. Nucleosomes are reorganized when transcription passes through a gene.

6.26 Nucleosome displacement and reassembly require special factors
Ancillary factors are required both: for RNA polymerase to displace octamers during transcription for the histones to reassemble into nucleosomes after transcription

6.27 DNAase hypersensitive sites change chromatin structure
Hypersensitive sites are found at the promoters of expressed genes. They are generated by the binding of transcription factors that displace histone octamers.

6.28 Chromatin remodeling is an active process
Chromatin structure is changed by remodeling complexes that use energy provided by hydrolysis of ATP. The SWI/SNF, RSC, and NURF complexes all are very large; there are some common subunits.

The factor may be released once the remodeling complex has bound.
6.28 Chromatin remodeling is an active process A remodeling complex does not itself have specificity for any particular target site; it must be recruited by a component of the transcription apparatus. Remodeling complexes are recruited to promoters by sequence-specific activators. The factor may be released once the remodeling complex has bound.

6.19 Histone acetylation is associated with genetic activity
Histone acetylation occurs transiently at replication. Histone acetylation is associated with activation of gene expression. Deacetylated chromatin may have a more condensed structure.

The remodeling complex may recruit the acetylating complex.
6.19 Histone acetylation is associated with genetic activity Transcription activators are associated with histone acetylase activities in large complexes. The remodeling complex may recruit the acetylating complex. Histone acetylases vary in their target specificity.

Deacetylation is associated with repression of gene activity.
6.19 Histone acetylation is associated with genetic activity Acetylation could affect transcription in a quantitative or qualitative way. Deacetylation is associated with repression of gene activity.

Deacetylases are present in complexes with repressor activity.
6.19 Histone acetylation is associated with genetic activity Deacetylases are present in complexes with repressor activity. Acetylation of histones may be the event that maintains the complex in the activated state.

6.30 Heterochromatin propagates from a nucleation event
Heterochromatin is nucleated at a specific sequence. The inactive structure propagates along the chromatin fiber. Genes within regions of heterochromatin are inactivated.

The length of the inactive region varies from cell to cell.
6.30 Heterochromatin propagates from a nucleation event The length of the inactive region varies from cell to cell. Inactivation of genes in this vicinity causes position effect variegation. Similar spreading effects occur at: telomeres the silent cassettes in yeast mating type

6.31 Heterochromatin depends on interactions with histones
HP1 is the key protein in forming mammalian heterochromatin. It acts by binding to methylated H3 histone. RAP1 initiates formation of heterochromatin in yeast by binding to specific target sequences in DNA.

6.31 Heterochromatin depends on interactions with histones
The targets of RAP1 include telomeric repeats and silencers at HML and HMR. RAP1 recruits SIR3/SIR4, which interact with the N-terminal tails of H3 and H4.

6.32 X chromosomes undergo global changes
One of the two X chromosomes is inactivated at random in each cell during embryogenesis of eutherian mammals. In exceptional cases where there are >2 X chromosomes, all but one are inactivated.

Xic includes the Xist gene.
6.32 X chromosomes undergo global changes The Xic (X inactivation center) is a cis-acting region on the X chromosome. It is necessary and sufficient to ensure that only one X chromosome remains active. Xic includes the Xist gene. Xist codes for an RNA that is found only on inactive X chromosomes.

6.32 X chromosomes undergo global changes
The mechanism that is responsible for preventing Xist RNA from accumulating on the active chromosome is unknown.

6.33 Chromosome condensation is caused by condensins
SMC proteins are ATPases that include: the condensins the cohesins A heterodimer of SMC proteins associates with other subunits.

Condensins are responsible for condensing chromosomes at mitosis.
6.33 Chromosome condensation is caused by condensins The condensins cause chromatin to be more tightly coiled by introducing positive supercoils into DNA. Condensins are responsible for condensing chromosomes at mitosis. Chromosome-specific condensins are responsible for condensing inactive X chromosomes in C. elegans.

Microtubules By Lynne Cassimeris
Chapter 7 Microtubules By Lynne Cassimeris

7.1 Introduction The cytoskeleton is made up of protein polymers.
Each polymer contains many thousands of identical subunits that are strung together to make a filament.

Cells have three types of cytoskeletal polymers:
7.1 Introduction The cytoskeleton: generates cell movements provides mechanical support for the cell Cells have three types of cytoskeletal polymers: actin filaments intermediate filaments microtubules

All cytoskeletal polymers are dynamic;
7.1 Introduction All cytoskeletal polymers are dynamic; they continually gain and lose subunits. Microtubules are polymers of tubulin subunits. Microtubules almost always function in concert with molecular motors that: generate force move vesicles and other complexes along the microtubule surface

Cilia and flagella are specialized organelles composed of:
7.1 Introduction Cilia and flagella are specialized organelles composed of: microtubules motor proteins that: propel a cell through fluid or move fluid over the surface of a cell Drugs that disrupt microtubules have medicinal and agricultural uses.

7.2 General functions of microtubules
Cells use microtubules to provide structural support. Microtubules are the strongest of the cytoskeletal polymers. Microtubules resist compression. Cells also rely on the dynamic assembly and disassembly of microtubules to allow them to quickly reorganize the microtubule cytoskeleton.

Cells can make their microtubules more or less dynamic.
7.2 General functions of microtubules Cells can make their microtubules more or less dynamic. This allows them to take advantage of: the adaptability of microtubules (when dynamic) or the strength of microtubules (when stable) Different cells can have unique organizations of microtubules to suit specific needs.

7.3 Microtubules are polar polymers of α- and β- tubulin
Microtubules are hollow polymers of tubulin heterodimers. Thirteen linear chains of subunits, called protofilaments, associate laterally to form the microtubule.

Lateral bonds between protofilaments:
7.3 Microtubules are polar polymers of α- and β- tubulin Lateral bonds between protofilaments: stabilize the microtubule limit subunit addition and subtraction to microtubule ends Microtubules are polarized polymers. The plus end is crowned by β-tubulin and assembles faster. The minus end is crowned by α-tubulin and assembles slower.

7.4 Purified tubulin subunits assemble into microtubules
Microtubule polymerization begins with the formation of a small number of nuclei (small polymers). Microtubules polymerize by addition of tubulin subunits to both ends of the polymer.

7.4 Purified tubulin subunits assemble into microtubules
A critical concentration of tubulin subunits always remains in solution. The concentration of tubulin must be above the critical concentration for assembly to occur.

7.5 Microtubule assembly and disassembly proceed by a unique process termed dynamic instability
Microtubules constantly switch between phases of growth and shortening; this process is termed dynamic instability. The transition from growing to shortening states is called a catastrophe. The transition from shortening to growing states is called a rescue.

A population of microtubules grows and shortens asynchronously;
7.5 Microtubule assembly and disassembly proceed by a unique process termed dynamic instability A population of microtubules grows and shortens asynchronously; at any instant in time, most are growing and a few are shortening. The structures of growing and shortening microtubule ends are different: growing ends have extensions of protofilaments shortening ends have curling protofilaments that bend back away from the microtubule lattice

7.6 A cap of GTP-tubulin subunits regulates the transitions of dynamic instability
Growing microtubules have a cap of GTP-tubulins at their tip. Because the GTP associated with β- tubulin is hydrolyzed to GDP shortly after a subunit adds to a microtubule. The bulk of the microtubule is made up of GDP-tubulins.

GTP-tubulins form straight protofilaments.
7.6 A cap of GTP-tubulin subunits regulates the transitions of dynamic instability Hydrolysis of GTP is coupled to a structural change in the tubulin dimers. GTP-tubulins form straight protofilaments. These maintain contacts with subunits in adjacent protofilaments. They allow these protofilaments to continue growing.

GDP-tubulins curve away from the microtubule.
7.6 A cap of GTP-tubulin subunits regulates the transitions of dynamic instability GDP-tubulins curve away from the microtubule. This breaks lateral bonds with adjacent subunits. This causes protofilaments to peel apart.

7.7 Cells use microtubule-organizing centers to nucleate microtubule assembly
In cells, microtubule-organizing centers (MTOCs) nucleate microtubules. The position of the microtubule-organizing center determines the organization of microtubules within the cell.

The centrosome is the most common MTOC in animal cells.
7.7 Cells use microtubule-organizing centers to nucleate microtubule assembly The centrosome is the most common MTOC in animal cells. Centrosomes are made up of a pair of centrioles surrounded by a pericentriolar matrix.

The pericentriolar matrix contains γ-tubulin.
7.7 Cells use microtubule-organizing centers to nucleate microtubule assembly The pericentriolar matrix contains γ-tubulin. it is γ-tubulin, in complex with several other proteins, that nucleates microtubules. Motile animal cells contain a second MTOC, the basal body.

7.8 Microtubule dynamics in cells
Dynamic instability is the major pathway of microtubule turnover in cells. Microtubule plus ends are much more dynamic in cells than they are in vitro.

Free minus ends never grow;
7.8 Microtubule dynamics in cells Free minus ends never grow; they either are stabilized or depolymerize. Cells contain a subpopulation of nondynamic, stable microtubules.

7.9 Why do cells have dynamic microtubules?
Dynamic microtubules can search intracellular space and quickly find targets, regardless of their location. Dynamic microtubules: are adaptable can be easily reorganized

Growing and shortening microtubules:
7.9 Why do cells have dynamic microtubules? Growing and shortening microtubules: can generate force can be used to move vesicles or other intracellular components The ability of microtubules to generate force allows the entire array of microtubules to organize itself into a starlike pattern.

7.10 Cells use several classes of proteins to regulate the stability of their microtubules
Microtubule-associated proteins (MAPs) regulate microtubule assembly by stabilizing or destabilizing microtubules. MAPs determine how likely it is that a microtubule will grow or shorten

MAPs can bind to different locations on the microtubule.
7.10 Cells use several classes of proteins to regulate the stability of their microtubules MAPs can bind to different locations on the microtubule. Some MAPs bind along the sides of the microtubule. Others bind only at the tips of microtubules. Still others bind only to the tubulin dimers and prevent them from polymerizing.

Changing the balance between active stabilizers.
7.10 Cells use several classes of proteins to regulate the stability of their microtubules Changing the balance between active stabilizers. Destabilizers regulates microtubule turnover. The activity of MAPs is regulated by phosphorylation. MAPs can also link membranes or protein complexes to microtubules.

7.11 Introduction to microtubule-based motor proteins
Almost every cell function that depends on microtubules requires microtubule-based motors. Molecular motors are enzymes that: generate force “walk” along microtubules toward the plus or minus ends

The motor “head” domain binds microtubules and generates force.
7.11 Introduction to microtubule-based motor proteins The motor “head” domain binds microtubules and generates force. The “tail” domain typically binds membrane or other cargo.

Most kinesins “walk” toward the plus ends of microtubules.
7.11 Introduction to microtubule-based motor proteins Most kinesins “walk” toward the plus ends of microtubules. Dyneins “walk” toward the minus ends of microtubules.

7.12 How motor proteins work
Motor proteins use ATP hydrolysis to power movement. The nucleotide (ATP, ADP, or no nucleotide) bound to a motor’s head domain determines how tightly the head binds to the microtubule.

ATP hydrolysis also changes the shape of the head.
7.12 How motor proteins work ATP hydrolysis also changes the shape of the head. This shape change is amplified to generate a larger movement of the motor molecule.

By this mechanism the motor steps along the microtubule.
7.12 How motor proteins work Cycles of ATP hydrolysis and nucleotide release couple microtubule attachments with changes in the shape of the motor’s head domain. By this mechanism the motor steps along the microtubule. It takes one step for each ATP hydrolyzed.

7.13 How cargoes are loaded onto the right motor
Binding of motors to specific cargoes is mediated by the motor tail domain. Adaptor proteins associate with motors to regulate motor activity and to link motors to cargo.

7.13 How cargoes are loaded onto the right motor
Coordination of plus end- and minus end-directed motor activities is used to generate bidirectional movement of organelles.

7.14 Microtubule dynamics and motors combine to generate the asymmetric organization of cells
Dynamic microtubules and motors work together to generate cell asymmetries. Microtubules work together with the actin cytoskeleton during processes such as: cell locomotion mitotic spindle positioning

7.15 Interactions between microtubules and actin filaments
Microtubules and actin filaments function together during cell locomotion and cell division. In general, microtubules direct where and when actin assembles or generates contractile forces. Microtubules influence the actin cytoskeleton through: direct binding indirect signaling

7.15 Interactions between microtubules and actin filaments
The two cytoskeletal systems can be bound together by linker proteins that attach microtubules to actin filaments. The dynamic growth and shortening of microtubules can activate a subset of G proteins. These activated G proteins control actin assembly and cell contraction.

7.16 Cilia and flagella are motile structures
Cilia and flagella contain a highly ordered core structure called an axoneme. The axoneme is composed of nine outer doublet microtubules surrounding a pair of central microtubules.

7.16 Cilia and flagella are motile structures
Radial spokes, a complex of several polypeptides, link each outer doublet to the center of the axoneme. Dyneins are bound to each outer doublet and extend their motor domains toward the adjacent outer doublet.

Dynein slides the outer doublets past each other.
7.16 Cilia and flagella are motile structures Dynein slides the outer doublets past each other. The structural links between outer doublets converts the sliding motion into a bending of the axoneme. Kinesins participate in flagellar assembly by transporting axonemal proteins to the distal tip of flagella. Nonmotile primary cilia participate in sensory processes.

7.19 Supplement: What if tubulin didn’t hydrolyze GTP?
If microtubules were equilibrium polymers they: would depolymerize very slowly would not easily reorganize Tubulin dimers hydrolyze GTP when they assemble. This makes the microtubule a nonequilibrium polymer that can depolymerize rapidly.

7.20 Supplement: Fluorescence recovery after photobleaching
The fluorescent tag on proteins or lipids can be locally destroyed using very bright light from a laser. Recovery of fluorescence into the photobleached area occurs as unbleached proteins or lipids move into the bleached area. They change places with the photobleached protein or lipid.

7.20 Supplement: Fluorescence recovery after photobleaching
Recovery of photobleached regions on fluorescently tagged microtubules requires: disassembly of the photobleached microtubule new polymerization incorporating unbleached, fluorescent tubulin dimers

7.21 Supplement: Tubulin synthesis and modification
Synthesis of new tubulin is regulated by the concentration of dimers in the cytoplasm. α- and β-tubulins require cytosolic chaperonins and additional cofactors to fold properly and assemble into a heterodimer. Tubulins are subject to a number of posttranslational modifications.

Some modifications only occur on tubulins in polymers.
7.21 Supplement: Tubulin synthesis and modification Some modifications only occur on tubulins in polymers. These modifications are associated with a stable subpopulation of microtubules. In some organisms, the presence of posttranslationally modified tubulins within a microtubule: enhances the binding of motor proteins provides an additional mechanism to regulate vesicle traffic in the cell

7.22 Supplement: Motility assays for microtubulebased motor proteins
Motors remain active in cell extracts, allowing their purification. Motor proteins stick to glass slides and power gliding of microtubules over their surface.

Beads coated with motor proteins are transported along microtubules.
7.22 Supplement: Motility assays for microtubulebased motor proteins Beads coated with motor proteins are transported along microtubules. Using polarity-marked microtubules, it is possible to determine which way a motor moves on a microtubule.

Actin By Enrique M. De La Cruz & E. Michael Ostap
Chapter 8 Actin By Enrique M. De La Cruz & E. Michael Ostap

8.1 Introduction Cell motility is a fundamental and essential process for all eukaryotic cells. Actin filaments form many different cellular structures. Proteins associated with the actin cytoskeleton produce forces required for cell motility.

The polymerization of actin can provide forces that drive the:
8.1 Introduction The actin cytoskeleton is dynamic and reorganizes in response to intracellular and extracellular signals. The polymerization of actin can provide forces that drive the: extension of cellular processes movement of some organelles

8.2 Actin is a ubiquitously expressed cytoskeletal protein
Actin is a ubiquitous and essential protein found in all eukaryotic cells. Actin exists as: a monomer called G-actin a filamentous polymer called F-actin

8.3 Actin monomers bind ATP and ADP
The actin monomer is a 43 kDa molecule that has four subdomains. A nucleotide and a divalent cation bind reversibly in the cleft of the actin monomer.

8.4 Actin filaments are structurally polarized polymers
In the presence of physiological concentrations of monovalent and divalent cations, actin monomers polymerize into filaments. The actin filament is structurally polarized and the two ends are not identical.

8.5 Actin polymerization is a multistep and dynamic process
De novo actin polymerization is a multistep process that includes nucleation and elongation steps. The rates of monomer incorporation at the two ends of an actin filament are not equal. The barbed end of an actin filament is the fast growing end.

8.6 Actin subunits hydrolyze ATP after polymerization
ATP hydrolysis by subunits in an actin filament is essentially irreversible. This makes actin polymerization a nonequilibrium process. The critical concentration for actin assembly depends on whether actin has bound ATP or ADP.

8.6 Actin subunits hydrolyze ATP after polymerization
The critical concentration of ATP-actin is lower than that of ADP-actin. In the presence of ATP, the two ends of the actin filament have different critical concentrations.

8.7 Actin-binding proteins regulate actin polymerization and organization
For the actin cytoskeleton to drive motility, the cell must be able to regulate actin polymerization and depolymerization. Actin-binding proteins: associate with monomers or filaments influence the organization of actin filaments in cells

8.8 Actin monomer-binding proteins influence polymerization
The two major actin monomer-binding proteins in many eukaryotic cells are: thymosin β4 profilin

In metazoan cells, thymosin β4:
8.8 Actin monomer-binding proteins influence polymerization In metazoan cells, thymosin β4: sequesters actin monomers maintains a cytosolic pool of ATP-actin that can be utilized for rapid filament elongation Profilin-actin monomer complexes contribute to filament elongation at barbed ends but not at pointed ends.

8.9 Nucleating proteins control cellular actin polymerization
Nucleating proteins allow the cell to control the time and place of de novo filament formation. The Arp2/3 complex and formins nucleate filaments in vivo.

Arp2/3 nucleation generates a branched filament network.
8.9 Nucleating proteins control cellular actin polymerization Arp2/3 nucleation generates a branched filament network. Formin proteins nucleate unbranched filaments. Arp2/3 is activated at cell membranes by proteins: Scar WASP WAVE

8.10 Capping proteins regulate the length of actin filaments
Capping proteins inhibit actin filament elongation. Capping proteins function at either the barbed or pointed ends of actin filaments.

Capping protein and gelsolin:
8.10 Capping proteins regulate the length of actin filaments Capping protein and gelsolin: inhibit elongation at barbed ends inhibited by phospholipids of the plasma membrane Tropomodulin is a protein that caps the pointed end of actin filaments.

8.11 Severing and depolymerizing proteins regulate actin filament dynamics
Actin filaments must disassemble to maintain a soluble pool of monomers. Members of the cofilin/ADF family of proteins sever and accelerate the depolymerization of actin filaments.

Actin filaments with bound ADP are targets for cofilin/ADF proteins.
8.11 Severing and depolymerizing proteins regulate actin filament dynamics Severing increases the number of filament ends available for assembly and disassembly. Cofilin/ADF binds cooperatively and changes the twist of actin filaments. Actin filaments with bound ADP are targets for cofilin/ADF proteins.

8.12 Crosslinking proteins organize actin filaments into bundles and orthogonal networks
Crosslinking proteins connect actin filaments to form: bundles orthogonal networks Actin bundles and networks are mechanically very strong.

Actin bundles help form:
8.12 Crosslinking proteins organize actin filaments into bundles and orthogonal networks Actin crosslinking proteins have two binding sites for actin filaments. Actin bundles help form: Stereocilia Filopodia Orthogonal actin networks form: sheets (lamellae) gels

8.13 Actin and actin-binding proteins work together to drive cell migration
Interactions among actin and proteins that bind actin monomers and filaments regulate the growth and organization of protrusive structures in cells. The addition of actin monomers to the barbed ends of actin filaments located at the cell’s plasma membrane pushes the membrane outward.

8.14 Small G proteins regulate actin polymerization
Members of the Rho family of small G proteins regulate actin polymerization and dynamics. Activation of Rho, Rac, and Cdc42 proteins induces formation of, respectively: Lamellipodia Filopodia Contractile filaments

8.15 Myosins are actin-based molecular motors with essential roles in many cellular processes
Myosin proteins are energy transducing machines that use ATP to: power motility generate force along actin filaments The myosin superfamily of actin-based molecular motors consists of at least eighteen classes Many classes have multiple isoforms.

Some myosins power muscle and cellular contractions.
8.15 Myosins are actin-based molecular motors with essential roles in many cellular processes Some myosins power muscle and cellular contractions. Others power membrane and vesicle transport. Myosins play key roles in regulating cell shape and polarity. Myosins participate in signal transduction and sensory perception pathways.

8.16 Myosins have three structural domains
Myosin family members have three structural domains termed the: head (or motor) domain regulatory domain tail domain The motor domain: contains the ATP- and actin-binding sites is responsible for converting the energy from ATP hydrolysis into mechanical work.

The tail domain of myosin:
8.16 Myosins have three structural domains In most myosins, the regulatory domain acts as a force transducing lever arm. The tail domain of myosin: interacts with cargo proteins or lipid determines its biological function

8.17 ATP hydrolysis by myosin is a multistep reaction
Members of the myosin superfamily share a conserved reaction pathway for the hydrolysis of ATP. Myosin’s affinity for actin depends on whether ATP, ADP-Pi, or ADP is bound to the nucleotide-binding site of myosin.

Myosins with bound ATP or ADP-Pi are in weak binding states.
8.17 ATP hydrolysis by myosin is a multistep reaction Myosins with bound ATP or ADP-Pi are in weak binding states. In its weak binding states, myosin rapidly associates and dissociates from actin. ATP hydrolysis: “activates” myosin occurs while myosin is detached from actin

8.17 ATP hydrolysis by myosin is a multistep reaction
Myosin’s force-generating powerstroke accompanies phosphate release after myosin-ADPPi rebinds actin. Myosins with either bound ADP or with no nucleotide bound are in strong binding states.

Myosins in the weak binding states do not bear force.
8.17 ATP hydrolysis by myosin is a multistep reaction Myosin in its strong binding states remains attached to actin for longer times. Myosins in the weak binding states do not bear force. Myosins in the strong binding states resist movement if external forces are applied.

8.18 Myosin motors have kinetic properties suited for their cellular roles
The ATPase cycle mechanism is conserved among all myosins. The ATPase cycle kinetics of different myosins are tuned for specific biological functions.

Low duty ratio myosins spend most of their time detached from actin.
8.18 Myosin motors have kinetic properties suited for their cellular roles Myosins with high duty ratios spend a large fraction of their cycle time attached to actin. Low duty ratio myosins spend most of their time detached from actin. Some high-duty ratio myosins are processive and “walk” along actin filaments for long distances.

8.19 Myosins take nanometer steps and generate piconewton forces
A single myosin motor generates enough force (several piconewtons) to transport biological molecules and vesicles. The stroke size of a myosin is proportional to the length of its “lever arm.”

8.20 Myosins are regulated by multiple mechanisms
The force-generating activity and cellular localization of myosins are regulated. Myosin function is regulated: by phosphorylation by interactions with actin- and myosinbinding proteins

8.21 Myosin-II functions in muscle contraction
Myosin-II is the motor that powers muscle contraction. Actin and myosin-II are the major components of the sarcomere. The sarcomere is the fundamental contractile unit of striated muscle.

Intermediate Filaments By E. Birgitte Lane
Chapter 9 Intermediate Filaments By E. Birgitte Lane

9.1 Introduction Intermediate filaments are major components of the nuclear and cytoplasmic cytoskeletons. Intermediate filaments are essential to maintain correct tissue structure and function.

Intermediate filaments:
9.1 Introduction Intermediate filaments: are between actin filaments and microtubules in diameter form robust networks Intermediate filaments are polymers of protein subunits.

Intermediate filament proteins:
9.1 Introduction Intermediate filament proteins: are heterogeneous re encoded by a large and complex gene superfamily Over 50 human diseases are associated with intermediate filament mutations.

9.2 The six intermediate filament protein groups have similar structure but different expression
Intermediate filament proteins all share a similar structure that is based on an extended central α-helical rod domain. The intermediate filament family is divided into six sequence homology classes.

9.2 The six intermediate filament protein groups have similar structure but different expression
Different kinds of intermediate filaments have different tissue expression patterns. Antibodies to individual intermediate filaments are important tools for monitoring cell differentiation and pathology.

9.3 The two largest intermediate filament groups are type I and type II keratins
Most of the intermediate filament proteins in mammals are keratins. Keratins are obligate heteropolymers of type I and type II proteins.

Simple keratins K8 and K18 are the least specialized keratins.
9.3 The two largest intermediate filament groups are type I and type II keratins Paired keratin expression is predictive of epithelial differentiation and proliferative status. Simple keratins K8 and K18 are the least specialized keratins.

Structural keratins of hard appendages:
9.3 The two largest intermediate filament groups are type I and type II keratins Barrier keratins have the most complex and varied expression of all intermediate filaments. Structural keratins of hard appendages: are distinct from other keratins may be the latest–evolving mammalian keratins

9.4 Mutations in keratins cause epithelial cell fragility
Mutations in K5 or K14 cause the skin blistering disorder epidermolysis bullosa simplex. Severe EBS mutations are associated with accumulated nonfilamentous keratin.

9.4 Mutations in keratins cause epithelial cell fragility
Many tissue fragility disorders with diverse clinical phenotypes are caused by structurally similar mutations in other keratin genes. Cell fragility disorders provide clear evidence of a tissue-reinforcing function for keratin intermediate filaments.

9.5 Intermediate filaments of nerve, muscle, and connective tissue often show overlapping expression
Some type III and type IV intermediate filament proteins have overlapping expression ranges. Many type III and type IV proteins can coassemble with each other.

Desmin is an essential muscle protein.
9.5 Intermediate filaments of nerve, muscle, and connective tissue often show overlapping expression Coexpression of multiple types of intermediate filament proteins may obscure the effect of a mutation in one type of protein. Desmin is an essential muscle protein. Vimentin is often expressed in solitary cells. Mutations in type III or type IV genes are usually associated with muscular or neurological degenerative disorders.

9.6 Lamin intermediate filaments reinforce the nuclear envelope
Lamins are intranuclear, forming the lamina that lines the nuclear envelope. Membrane anchorage sites are generated by posttranslational modifications of lamins.

Upon phosphorylation by Cdk1, lamin filaments depolymerize.
9.6 Lamin intermediate filaments reinforce the nuclear envelope Upon phosphorylation by Cdk1, lamin filaments depolymerize. This allows disassembly of the nuclear envelope during mitosis. Lamin genes undergo alternative splicing.

9.7 Even the divergent lens filament proteins are conserved in evolution
The eye lens contains two highly unusual intermediate filament proteins, CP49 and filensin. These constitute the type VI sequence homology group. These unusual intermediate filament proteins are conserved in evolution of vertebrates.

9.8 Intermediate filament subunits assemble with high affinity into strain-resistant structures
In vitro, intermediate filament assembly is rapid and requires no additional factors. The central portion of all intermediate filament proteins is a long α-helical rod domain that forms dimers.

Intermediate filament networks:
9.8 Intermediate filament subunits assemble with high affinity into strain-resistant structures Assembly from antiparallel tetramers determines the apolar nature of cytoplasmic intermediate filaments. Intermediate filament networks: are stronger than actin filaments or microtubules exhibit strain hardening under stress

9.9 Posttranslational modifications regulate the configuration of intermediate filament proteins
Intermediate filaments: are dynamic show periodic rapid remodeling Several posttranslational modifications affect the head and tail domains.

Proteolytic degradation:
9.9 Posttranslational modifications regulate the configuration of intermediate filament proteins Phosphorylation is the main mechanism for intermediate filament remodeling in cells. Proteolytic degradation: modulates protein quantity facilitates apoptosis

9.10 Proteins that associate with intermediate filaments are facultative rather than essential
Intermediate filament proteins do not need associated proteins for their assembly. Specific intermediate filament-associated proteins include: cell-cell and cell-matrix junction proteins terminal differentiation matrix proteins of keratinocytes

9.10 Proteins that associate with intermediate filaments are facultative rather than essential
Transiently associated proteins include the plakin family of diverse, multifunctional cytoskeletal linkers.

9.11 Intermediate filament genes are present throughout metazoan evolution
Intermediate filament genes are present in all metazoan genomes that have been analyzed. The intermediate filament gene family evolved by: duplication and translocation followed by further duplication events

Humans have 70 genes encoding intermediate filament proteins.
9.11 Intermediate filament genes are present throughout metazoan evolution Humans have 70 genes encoding intermediate filament proteins. Human keratin genes are clustered. But nonkeratin intermediate filament genes are dispersed.

Mitosis By Conly Rieder
Chapter 10 Mitosis By Conly Rieder

10.1 Introduction All cells are produced by the division of other cells through a process called mitosis. Mitosis occurs after a cell has replicated its chromosomes.

Errors in mitosis are catastrophic.
10.1 Introduction Mitosis separates the chromosomes into two equal groups and then divides the cell between them to form two new cells. Errors in mitosis are catastrophic. Mechanisms have evolved to ensure its accuracy.

10.2 Mitosis is divided into stages
Mitosis proceeds through a series of stages. The stages are characterized by the location and behavior of the chromosomes. Some of the conversions between stages: correspond to cell cycle events are irreversible transitions

10.3 Mitosis requires the formation of a new apparatus called the spindle
The chromosomes are separated by the mitotic spindle. The spindle is a symmetrical, bipolar structure composed of microtubules that extend between two poles. At each pole is a centrosome.

Chromosomes attach to the spindle via interactions between:
10.3 Mitosis requires the formation of a new apparatus called the spindle Chromosomes attach to the spindle via interactions between: their kinetochores the microtubules of the spindle

10.4 Spindle formation and function depend on the dynamic behavior of microtubules and their associated motor proteins The spindle is a complex assembly of microtubules and microtubule–dependent motor proteins. The microtubules are highly organized with respect to their polarity.

Spindle microtubules are very dynamic.
10.4 Spindle formation and function depend on the dynamic behavior of microtubules and their associated motor proteins Spindle microtubules are very dynamic. Some exhibit dynamic instability. Others experience subunit flux. Interactions between microtubules and motors generate forces that are required to assemble the spindle.

10.5 Centrosomes are microtubule organizing centers
define the poles of the spindle play a role in spindle formation nucleate microtubules often remain bound to microtubules’ minus ends afterward

10.6 Centrosomes reproduce about the time the DNA isreplicated
Centrosomes are composed of two centrioles surrounded by the pericentriolar material. The formation of a new centrosome requires duplication of the centrioles.

Centriole duplication is:
10.6 Centrosomes reproduce about the time the DNA isreplicated Centriole duplication is: controlled by the cell cycle coordinated with DNA replication Centrioles duplicate by the formation and growth of a new centriole immediately adjacent to each existing one.

10.7 Spindles begin to form as separating asters interact
As mitosis begins, changes in both the centrosomes and the cytoplasm cause a radial array of short, highly dynamic microtubules to form around each centrosome. Interactions between the asters formed by the two centrosomes initiate the formation of the mitotic spindle.

10.7 Spindles begin to form as separating asters interact
Separation of the centrosomes depends on microtubule–dependent motor proteins. The pathway of spindle formation depends on whether the centrosomes separate before or after the nuclear envelope breaks down.

10.8 Spindles require chromosomes for stabilization but can “self-organize” without centrosomes
In the absence of chromosomes, adjacent asters will: separate completely fail to form a spindle

Spindles can form in the absence of centrosomes, although they:
10.8 Spindles require chromosomes for stabilization but can “self-organize” without centrosomes By binding astral microtubules at their kinetochores, chromosomes stabilize both: the basic geometry of the spindle the microtubules in it Spindles can form in the absence of centrosomes, although they: form more slowly lack astral microtubules

10.9 The centromere is a specialized region on the chromosome that contains the kinetochores
Proper attachment of the chromosomes to the spindle is required for their accurate segregation.

10.9 The centromere is a specialized region on the chromosome that contains the kinetochores
Attachment occurs at the kinetochores, where the chromosomes interact with the spindle’s microtubules. The centromere is the site where the two kinetochores on each chromosome form.

Each chromosome has a single centromeric region.
10.9 The centromere is a specialized region on the chromosome that contains the kinetochores Each chromosome has a single centromeric region. Centromeres: lack genes are composed of highly specialized, repetitive DNA sequences that bind a unique set of proteins

10.10 Kinetochores form at the onset of prometaphase and contain microtubule motor proteins
Kinetochores change structure as mitosis begins, They form a flat plate or mat on the surface of the centromere.

The corona helps kinetochores capture microtubules.
10.10 Kinetochores form at the onset of prometaphase and contain microtubule motor proteins Unattached kinetochores have fibers extending out from them (the corona). The fibers contain many proteins that interact with microtubules. The corona helps kinetochores capture microtubules.

10.11 Kinetochores capture and stabilize their associated microtubules
Kinetochores and microtubules become connected by a search-and-capture mechanism. The mechanism is made possible by the dynamic instability of the microtubules. It gives spindle assembly great flexibility.

Capturing a microtubule causes a kinetochore to move poleward.
10.11 Kinetochores capture and stabilize their associated microtubules Capturing a microtubule causes a kinetochore to move poleward. This expedites the capture of additional microtubules This starts the formation of a kinetochore fiber. One sister kinetochore usually: captures microtubules develops a kinetochore fiber before the other does

10.11 Kinetochores capture and stabilize their associated microtubules
The ability of kinetochores to stabilize associated microtubules is essential for the formation of a kinetochore fiber. Kinetochores under tension are much more effective at stabilizing microtubules than kinetochores that are not under tension.

10.12 Mistakes in kinetochore attachment are corrected
Improper attachments often occur transiently as the chromosomes attach to the spindle.

Improper attachments are unstable.
10.12 Mistakes in kinetochore attachment are corrected Improper attachments are unstable. They do not allow kinetochores to stabilize attached microtubules. Only the correct, bipolar attachment of a chromosome produces a stable kinetochore attachment.

10.13 Kinetochore fibers must both shorten and elongate to allow chromosomes to move
Poleward forces are exerted on attached kinetochores during all stages of mitosis. Kinetochore fibers are anchored near the poles.

Anchorage may depend on the spindle matrix.
10.13 Kinetochore fibers must both shorten and elongate to allow chromosomes to move Anchorage may depend on the spindle matrix. The matrix is composed of the NuMA protein and a number of molecular motors. Kinetochore fibers change length by addition or loss of tubulin subunits at their ends. Both kinetochores and poles can remain attached to the ends of kinetochore fibers as the fibers change length.

10.14 The force to move a chromosome toward a pole is produced by two mechanisms
A kinetochore pulls the chromosome toward the pole. But it can move only as fast as the microtubules in the kinetochore fiber can shorten.

10.14 The force to move a chromosome toward a pole is produced by two mechanisms
Dynein at the kinetochore pulls a chromosome poleward on the ends of depolymerizing microtubules. Force generated along the sides of the kinetochore fiber also move the entire fiber poleward, pulling the chromosome behind it.

10.15 Congression involves pulling forces that act on the kinetochores
The balance of several forces aligns the chromosomes at metaphase. Forces at both the kinetochores and along the arms of a chromosome participate.

A plausible model suggests that:
10.15 Congression involves pulling forces that act on the kinetochores A plausible model suggests that: poleward forces proportional to the length of each kinetochore fiber position the chromosomes in the center of the spindle. This mechanism may align the chromosomes in some types of cells.

In many types of cells other forces must participate, including:
10.15 Congression involves pulling forces that act on the kinetochores In many types of cells other forces must participate, including: forces generated by the kinetochore another that pushes chromosomes away from poles

10.16 Congression is also regulated by the forces that act along the chromosome arms and the activity of sister kinetochores Forces that act on the arms of chromosomes push them away from a pole. These forces arise from interactions between: a chromosome’s arms spindle microtubules

Kinetochores can switch between active and passive states.
10.16 Congression is also regulated by the forces that act along the chromosome arms and the activity of sister kinetochores Kinetochores can switch between active and passive states. Switching of sister kinetochores between the two states is coordinated.

10.17 Kinetochores control the metaphase/anaphase transition
A checkpoint prevents anaphase from beginning until all the kinetochores are attached to the mitotic spindle. Unattached kinetochores produce a signal that prevents anaphase from beginning.

10.17 Kinetochores control the metaphase/anaphase transition
The checkpoint monitors the number of microtubules attached to a kinetochore. When all the kinetochores in a cell are properly attached the anaphase promoting complex (APC) is activated. Activation of the APC leads to the destruction of proteins that hold sister chromatids together.

10.18 Anaphase has two phases
Destroying the connections between sister chromatids allows them to begin moving toward opposite poles. Movement occurs because pulling forces that act on sister kinetochores throughout mitosis no longer oppose one another.

Spindle elongation is caused by both:
10.18 Anaphase has two phases Elongation of the mitotic spindle during anaphase increases the distance between the separating chromosomes. Spindle elongation is caused by both: pushing forces that act on midzone microtubules pulling forces that act on astral microtubules

10.19 Changes occur during telophase that lead the cell out of the mitotic state
The same cell cycle controls that initiate anaphase also: initiate events that lead to cytokinesis prepare the cell to return to interphase

10.19 Changes occur during telophase that lead the cell out of the mitotic state
Inactivation of CDK1 by destruction of cyclin B reverses the changes that drove the cell into mitosis. Destruction of cyclin B begins when the spindle assembly checkpoint is satisfied. A lag prevents telophase from beginning before the chromosomes have separated.

10.20 During cytokinesis, the cytoplasm is partitioned to form two new daughter cells
The two newly formed nuclei that are the products of karyokinesis are separated into individual cells. This process is called cytokinesis. Cytokinesis involves two new cytoskeletal structures: the midbody the contractile ring

Cytokinesis has three stages:
10.20 During cytokinesis, the cytoplasm is partitioned to form two new daughter cells The mitotic spindle, the midbody, and the contractile ring are all highly coordinated with one another. Cytokinesis has three stages: definition of the plane of cleavage ingression of the cleavage furrow separation of the two new cells

10.21 Formation of the contractile ring requires the spindle and stem bodies
The location of the mitotic spindle determines where the contractile ring forms. The mitotic spindle is positioned by interactions between: its astral microtubules the cortex of the cell

10.21 Formation of the contractile ring requires the spindle and stem bodies
Bundles of parallel microtubules called stem bodies form between the two separating groups of chromosomes in anaphase. As anaphase progresses the stem bodies coalesce into one large bundle called the midbody. Stem bodies signal to the cortex to cause the formation of the contractile ring.

10.22 The contractile ring cleaves the cell in two
Contraction of the contractile ring: causes it to constrict produces a furrow around the surface of a dividing cell The contractile ring is composed largely of actinand myosin. Its constriction is driven by their interaction.

Constriction by the contractile ring requires signals from:
10.22 The contractile ring cleaves the cell in two Constriction by the contractile ring requires signals from: the stem bodies or the midbody A significant amount of membrane fusion is required during cytokinesis.

10.23 The segregation of nonnuclear organelles during cytokinesis is based on chance
Many of the cell’s internal membranes: break down during mitosis are distributed between the two daughter cells as small vesicles These vesicles re-form the organelle after mitosis is finished.

Srinivas Venkatram, Kathleen L. Gould, & Susan L. Forsburg
Chapter 11 Cell Cycle Regulation By Srinivas Venkatram, Kathleen L. Gould, & Susan L. Forsburg

11.1 Introduction A cell contains all the information necessary for making a copy of itself during a cell division cycle. The eukaryotic cell division cycle (cell cycle) is composed of an ordered set of events. It results in the generation of two copies of a preexisting cell.

Two important phases of the cell cycle are:
11.1 Introduction The cell cycle is partitioned into distinct phases during which different events take place. Two important phases of the cell cycle are: Replication of a cell’s chromosomes Chromosome segregation

11.2 There are several experimental systems used in cell cycle analyses
Studies in a wide variety of organisms have contributed to our knowledge of cell cycle regulation. Each has advantages and disadvantages. Genetic analyses of the cell cycle in yeasts identified conserved cell cycle regulators.

11.2 There are several experimental systems used in cell cycle analyses
Biochemical analyses of protein complexes from multicellular organisms complemented the genetic studies of single-celled organisms. Synchronized populations of cells are important for analyzing cell cycle events.

11.3 The cell cycle requires coordination between events
Checkpoints act to: ensure error-free completion of DNA replication before entry into mitosis maintain the temporal coordination of S and M phases

11.4 The cell cycle as a cycle of CDK activities
CDKs: are the master regulators of the cell cycle are active only when complexed with cyclin proteins

11.4 The cell cycle as a cycle of CDK activities
Cyclins derive their name from the periodic oscillation of their protein levels during the cell cycle. A CDK can be partnered with different cyclins during different phases of the cell cycle.

11.5 CDK-cyclin complexes are regulated in several ways
CDK-cyclin complexes are regulated by: phosphorylation inhibitory proteins proteolysis subcellular localization

11.6 Cells may exit from and reenter the cell cycle
Cells may be maintained in a nondividing state called quiescence, or G0. Quiescent cells may be stimulated to return to the cell cycle by environmental cues.

Cells reenter the cell cycle primarily at G1.
11.6 Cells may exit from and reenter the cell cycle Cells reenter the cell cycle primarily at G1. Cells may also permanently leave the cell cycle by differentiating into a specialized cell type. Some cells are programmed to self-destruct by apoptosis.

11.7 Entry into cell cycle is tightly regulated
Cell divisions are not continuous. They are controlled by: external stimuli nutrient availability Cells detect the presence of chemical signals in their environment.

11.7 Entry into cell cycle is tightly regulated
Extracellular signals can elicit an intracellular biochemical response that results in either: entry into the cell cycle or cell cycle arrest in a G1/G0 phase

11.8 DNA replication requires the ordered assembly of protein complexes
Replication occurs after cells progress through the restriction point or START. Replication: is regulated in a stepwise fashion is coordinated with the completion of mitosis

Replication occurs at origins that may be defined by:
11.8 DNA replication requires the ordered assembly of protein complexes Replication occurs at origins that may be defined by: Sequence or Position or Spacing mechanisms Initiation occurs only at origins that are licensed to replicate. Once fired, origins cannot be reused until the next cell cycle.

11.9 Mitosis is orchestrated by several protein kinases
The transition from G2 to M is a major control point in many eukaryotic cells. Activation of several protein kinases is associated with the G2-M transition.

11.10 Many morphological changes occur during mitosis
The nuclear and cytoskeletal architectures change dramatically for mitosis. Mitotic kinases are required for the proper execution of mitotic events such as: nuclear envelope breakdown chromosome condensation and segregation spindle assembly cytokinesis

11.11 Mitotic chromosome condensation and segregation depend on condensin and cohesin
In preparation for separation, chromosomes: condense move to the center of the mitotic spindle Chromosomes become attached to microtubules emanating from opposite poles of the spindle through specialized regions called kinetochores.

Cohesion that binds sister chromatids together is released.
11.11 Mitotic chromosome condensation and segregation depend on condensin and cohesin Cohesion that binds sister chromatids together is released. This enables their separation. Independent sister chromatids are further separated in space before cytokinesis.

11.12 Exit from mitosis requires more than cyclin proteolysis
Exit from mitosis requires inactivation of Cdk1. Mitotic exit also involves the reversal of Cdk1 phosphorylation.

11.12 Exit from mitosis requires more than cyclin proteolysis
Inactivation of Cdk1 and reversal of Cdk1 phosphorylation are coordinated with: disassembly of the mitotic spindle cytokinesis

11.13 Checkpoint controls coordinate different cell cycle events
Cell cycle events are coordinated with one another. The coordination of cell cycle events is achieved by the action of specific biochemical pathways called checkpoints. Checkpoints delay cell cycle progression if a previous cell cycle event has not been completed.

Checkpoints may be essential only when cells are stressed or damaged.
11.13 Checkpoint controls coordinate different cell cycle events Checkpoints may be essential only when cells are stressed or damaged. They may also act during a normal cell cycle to ensure proper coordination of events.

11.14 DNA replication and DNA damage checkpoints monitor defects in DNA metabolism
Incomplete and/or defective DNA replication activates a cell cycle checkpoint.

11.14 DNA replication and DNA damage checkpoints monitor defects in DNA metabolism
Damaged DNA activates a different checkpoint that shares some components with the replication checkpoint. The DNA damage checkpoint halts the cell cycle at different stages depending on the stage during which the damage occurred.

11.15 The spindle assembly checkpoint monitors defects in chromosome-microtubule attachment
The mitotic spindle attaches to individual kinetochores of chromosomes during mitosis. Proper attachment of microtubules to kinetochores is a prerequisite for chromosome segregation.

11.15 The spindle assembly checkpoint monitors defects in chromosome-microtubule attachment
Defects in spindle-MT attachment are sensed by the “spindle assembly checkpoint.” This checkpoint subsequently halts the metaphase-anaphase transition to prevent errors in sister chromatid separation.

11.16 Cell cycle deregulation can lead to cancer
Proto-oncogenes encode proteins that drive cells into the cell cycle. Tumor suppressor genes encode proteins that restrain cell cycle events. Mutations in proto-oncogenes, tumor suppressor genes, or checkpoint genes may lead to cancer.

Apoptosis By Douglas R. Green
Chapter 12 Apoptosis By Douglas R. Green

12.1 Introduction Programmed cell death is a developmental process that usually proceeds by apoptosis. Apoptosis is also the mode of cell death occurring in a variety of other settings. It has roles in: normal homeostasis inhibition of cancer disease processes

12.1 Introduction Most animal cells possess the molecules comprising the pathways that can cause death by apoptosis. These pathways are activated by appropriate stimuli.

12.2 Caspases orchestrate apoptosis by cleaving specific substrates
Proteases called “caspases” fall into three types: Initiator Executioner Inflammatory The first two types function in apoptosis.

Many substrates for caspases have been identified.
12.2 Caspases orchestrate apoptosis by cleaving specific substrates The morphological and biochemical features of cells undergoing apoptosis are caused by the action of the executioner caspases on their substrates. Many substrates for caspases have been identified. In some cases the effects of their cleavage on the cell are known.

12.3 Executioner caspases are activated by cleavage, whereas initiator caspases are activated by dimerization Cleavage of executioner caspases at specific sites is necessary and sufficient for their activation.

This cleavage is usually mediated by the initiator caspases.
12.3 Executioner caspases are activated by cleavage, whereas initiator caspases are activated by dimerization This cleavage is usually mediated by the initiator caspases. Initiator caspases are activated by adaptor molecules that contain protein-protein interaction domains called death folds.

12.4 Some inhibitors of apoptosis proteins (IAPs) block caspases
The inhibitors of apoptosis proteins comprise a family of proteins with different functions. Some of these proteins: bind to and inhibit caspases induce their degradation by the proteasome

12.4 Some inhibitors of apoptosis proteins (IAPs) block caspases
Since executioner caspases are activated by cleavage, and since these caspases can cleave and activate each other… …any proteolytic activity of the caspases will be rapidly amplified in cells, resulting in their death by apoptosis. It is important that there be mechanisms present to limit potential “accidental” activation of caspases in cells that have not been signaled to die.

12.5 Some caspases have functions in inflammation
In addition to the initiator and executioner caspases, another set of proteases in this family acts to process cytokines rather than regulate apoptosis.

12.6 The death receptor pathway of apoptosis transmits external signals
Two well-characterized pathways of apoptosis are: the death receptor (extrinsic) pathway the mitochondrial (intrinsic) pathway Caspase activation and apoptosis are induced by the binding of specialized ligands in the TNF family to their receptors (death receptors).

12.7 Apoptosis signaling by TNFR1 is complex
Binding of TNF to one of its receptors, TNFR1, induces both apoptotic and antiapoptotic signals.

12.8 The mitochondrial pathway of apoptosis
Most apoptosis in mammalian cells proceeds via a pathway in which: the mitochondrial outer membranes are disrupted thus, releasing the contents of the mitochondrial intermembrane space into the cytosol Mitochondrial outer membrane permeabilization (MOMP) is a key feature of this pathway.

12.9 Bcl-2 family proteins mediate and regulate MOMP and apoptosis
The Bcl-2 family proteins are central to the mitochondrial pathway of apoptosis. There are 3 classes of Bcl-2 proteins that induce, directly cause, or inhibit MOMP.

12.10 The multidomain Bcl-2 proteins Bax and Bak are required for MOMP
are essential for the permeabilization of the mitochondrial outer membrane are required for the mitochondrial pathway of apoptosis Bax and Bak probably directly cause the membrane disruption associated with MOMP.

12.11 The activation of Bax and Bak are controlled by other Bcl-2 family proteins
The antiapoptotic members of the Bcl-2 family block the permeabilization of the mitochondrial outer membrane by Bax and Bak. The BH3-only proteins of the Bcl-2 family either: directly activate Bax and Bak or interfere with the antiapoptotic Bcl-2 protein functions

12.12 Cytochrome c, released upon MOMP, induces caspase activation
Holocytochrome c triggers the activation of cytosolic APAF-1. Cytosolic APAF-1 binds and activates caspase-9.

12.13 Some proteins released upon MOMP block IAPs
The mitochondrial intermembrane space proteins Smac and Omi antagonize the caspase-inhibitory activity of IAPs.

12.14 The death receptor pathway of apoptosis can engage MOMP through the cleavage of the BH3- only protein Bid Caspase-8, activated upon ligation of death receptors, cleaves the BH3-only protein Bid. This activates Bid.

Bid acts as a link between the two apoptotic pathways.
12.14 The death receptor pathway of apoptosis can engage MOMP through the cleavage of the BH3- only protein Bid Bid then triggers Bax and Bak to cause MOMP, thereby engaging the mitochondrial pathway of apoptosis. Bid acts as a link between the two apoptotic pathways.

12.15 MOMP can cause caspase-independent cell death
Once MOMP occurs, cells generally die even if caspase activation is blocked or disrupted. The precise mechanisms of this cell death are not fully known.

12.16 The mitochondrial permeability transition can cause MOMP
In some forms of cell death, the mitochondria are disrupted by a change in the mitochondrial inner membrane. This leads to swelling and rupture of the organelle.

12.17 Many discoveries about apoptosis were made in nematodes
Apoptosis in nematodes follows a simple pathway with similarities to the mitochondrial pathway of apoptosis in the vertebrates.

12.18 Apoptosis in insects has features distinct from mammals and nematodes
Apoptosis in insect cells follows a pathway with some similarities to the mitochondrial pathway of apoptosis in vertebrates.

12.19 The clearance of apoptotic cells requires cellular interaction
The removal of apoptotic cells from the body occurs by an active process.

12.20 Apoptosis plays a role in diseases such as viral infection and cancer
Viral infection and cancer are conditions in which apoptotic pathways may be blocked.

12.21 Apoptotic cells are gone but not forgotten
The uptake and clearance of apoptotic cells has lasting effects on the immune system.

Cancer—Principles and overview By Robert A. Weinberg
Chapter 13 Cancer—Principles and overview By Robert A. Weinberg

13.1 Tumors are masses of cells derived from a single cell
Cancers progress from: a single mutant cell to a tumor then to metastasis Tumors are clonal. Tumors are classified by cell type.

13.2 Cancer cells have a number of phenotypic characteristics
Cancer cells are characterized by several distinct properties. Unlike normal cells, cancer cells do not stop dividing when they contact a neighboring cell when such cells are propagated in a Petri dish.

Cancer cells have a greatly reduced requirement for growth factors to sustain growth and proliferation. Unlike normal cells, cancer cells in culture do not require attachment to a physical substrate in order to grow. The trait of anchorage independence

Unlike normal cells in culture, which halt division after a certain number of growth-and-division cycles: cancer cells are immortal they do not stop dividing after a predetermined number of generations Cancer cells often have chromosomal aberrations, including changes in chromosome number and structure.

13.3 Cancer cells arise after DNA damage
Agents that cause cancer may do so by damaging DNA. Mutations in certain genes cause a cell to grow abnormally.

Cancers usually arise in somatic cells.
13.3 Cancer cells arise after DNA damage Ames devised a test to determine the carcinogenicity of chemical agents. Cancers usually arise in somatic cells.

13.4 Cancer cells are created when certain genes are mutated
Oncogenes promote cell growth and division. Tumor suppressors inhibit cell growth and division.

Cellular genomes harbor multiple proto-oncogenes.
13.4 Cancer cells are created when certain genes are mutated Cellular genomes harbor multiple proto-oncogenes. Tumor viruses carry oncogenes. Genetic alterations can convert proto-oncogenes into potent oncogenes.

13.5 Cellular genomes harbor a number of protooncogenes
Gain-of-function mutations can activate protooncogenes. Overexpression of proto-oncogenes can cause tumors. Translocations can create hybrid proteins that are oncogenic.

13.6 Elimination of tumor suppressor activity requires two mutations
Both copies of a tumor suppressor gene must usually be inactivated to see a phenotype.

13.6 Elimination of tumor suppressor activity requires two mutations
Mechanisms that result in loss-of-heterozygosity are often responsible for the loss of the remaining normal copy of the tumor suppressor gene. Cancer susceptibility can be caused by the inheritance of a mutant copy of a tumor suppressor gene.

13.7 The genesis of tumors is a complex process
Cancer is a multistep process that requires four to six different mutations to reach the tumor state. Tumorigenesis progresses by clonal expansion, where increasingly abnormal clones of cells outgrow their less mutant neighbors.

13.8 Cell growth and proliferation are activated by growth factors
Cell signaling requires extracellular factors, receptors, and other proteins that transmit the signal to the nucleus.

Extracellular signals may be:
13.8 Cell growth and proliferation are activated by growth factors Extracellular signals may be: growth promoting or growth inhibiting Many genes encoding cell signaling molecules are proto-oncogenes and tumor suppressor genes.

13.9 Cells are subject to growth inhibition and may exit from the cell cycle
Cells that have differentiated have reached their final specialized form. Differentiated cells are usually postmitotic. Thus, differentiation reduces the pool of dividing cells.

Cells can commit suicide by apoptosis.
13.9 Cells are subject to growth inhibition and may exit from the cell cycle Cells can commit suicide by apoptosis. Apoptosis eliminates healthy cells during development and at other times in an organism’s lifetime.

13.9 Cells are subject to growth inhibition and may exit from the cell cycle
Apoptosis eliminates damaged cells that can pose a threat to the organism. Mutations that compromise a cell’s ability to carry out apoptosis can result in malignancy.

13.10 Tumor suppressors block inappropriate entry into the cell cycle
Cells decide whether or not to divide at the restriction point. pRb is a tumor suppressor that can prevent passage through the restriction point.

pRb can be inactivated by:
13.10 Tumor suppressors block inappropriate entry into the cell cycle pRb can be inactivated by: mutations sequestration by oncoproteins hyperactivity of the Ras pathway

13.11 Mutation of DNA repair and maintenance genes can increase the overall mutation rate
DNA repair proteins keep the spontaneous mutation rate low. Defects in DNA repair genes increase the basal rate of mutation in the cell. Mutations in checkpoint proteins compromise chromosome integrity.

13.12 Cancer cells may achieve immortality
Cancer cells avoid senescence by inactivating tumor suppressor genes. Cancer cells reach a crisis point at which many of them die off.

Cells that survive the crisis are immortalized.
13.12 Cancer cells may achieve immortality Cells that survive the crisis are immortalized. Telomeres become shorter each generation unless telomerase is activated.

13.12 Cancer cells may achieve immortality
When telomeres become too short to protect the chromosomes, the chromosomes fuse. This provokes crisis. Most cancer cells activate telomerase transcription, thereby escaping death.

13.13 Access to vital supplies is provided by angiogenesis
Tumor growth is limited by access to nutrients and waste removal mechanisms. Tumors can stimulate blood vessel growth (angiogenesis), which enables them to expand.

13.14 Cancer cells may invade new locations in the body
Some cells from a primary tumor can gain entrance to blood and lymphatic vessels (intravasation). The process of intravasation often requires breaking through barriers of neighboring tissue.

13.14 Cancer cells may invade new locations in the body
Cells that survive the trip through the blood vessels may colonize other organs. Metastasis, or colonization of other tissues, usually results in death of the individual.

Principles of Cell Signaling By Melanie H. Cobb & Elliott M. Ross
Chapter 14 Principles of Cell Signaling By Melanie H. Cobb & Elliott M. Ross

14.2 Cellular signaling is primarily chemical
Cells can detect both chemical and physical signals. Physical signals are generally converted to chemical signals at the level of the receptor.

14.3 Receptors sense diverse stimuli but initiate a limited repertoire of cellular signals
Receptors contain: a ligand-binding domain an effector domain Receptor modularity allows a wide variety of signals to use a limited number of regulatory mechanisms.

Cells may express different receptors for the same ligand.
14.3 Receptors sense diverse stimuli but initiate a limited repertoire of cellular signals Cells may express different receptors for the same ligand. The same ligand may have different effects on the cell depending on the effector domain of its receptor.

14.4 Receptors are catalysts and amplifiers
Receptors act by increasing the rates of key regulatory reactions. Receptors act as molecular amplifiers.

14.5 Ligand binding changes receptor conformation
Receptors can exist in active or inactive conformations. Ligand binding drives the receptor toward the active conformation.

14.6 Signals are sorted and integrated in signaling pathways and networks
Signaling pathways usually have multiple steps and can diverge and/or converge. Divergence allows multiple responses to a single signal. Convergence allows signal integration and coordination.

14.7 Cellular signaling pathways can be thought of as biochemical logic circuits
Signaling networks are composed of groups of biochemical reactions. The reactions function as mathematical logic functions to integrate information. Combinations of such logic functions combine as signaling networks to process information at more complex levels.

14.8 Scaffolds increase signaling efficiency and enhance spatial organization of signaling
organize groups of signaling proteins may create pathway specificity by sequestering components that have multiple partners

Scaffolds increase the local concentration of signaling proteins.
14.8 Scaffolds increase signaling efficiency and enhance spatial organization of signaling Scaffolds increase the local concentration of signaling proteins. Scaffolds localize signaling pathways to sites of action.

14.9 Independent, modular domains specify protein-protein interactions
Protein interactions may be mediated by small, conserved domains. Modular interaction domains are essential for signal transmission. Adaptors consist exclusively of binding domains or motifs.

14.10 Cellular signaling is remarkably adaptive
Sensitivity of signaling pathways is regulated to allow responses to change over a wide range of signal strengths. Feedback mechanisms execute this function in all signaling pathways.

14.10 Cellular signaling is remarkably adaptive
Most pathways contain multiple adaptive feedback loops to cope with signals of various strengths and durations.

14.11 Signaling proteins are frequently expressed as multiple species
Distinct species (isoforms) of similar signaling proteins expand the regulatory mechanisms possible in signaling pathways.

Isoforms may differ in:
14.11 Signaling proteins are frequently expressed as multiple species Isoforms may differ in: function susceptibility to regulation expression Cells may express one or several isoforms to fulfill their signaling needs.

14.12 Activating and deactivating reactions are separate and independently controlled
Activating and deactivating reactions are usually executed by different regulatory proteins. Separating activation and inactivation allows for fine-tuned regulation of amplitude and timing.

14.13 Cellular signaling uses both allostery and covalent modification
Allostery refers to the ability of a molecule to alter the conformation of a target protein when it binds noncovalently to that protein. Modification of a protein’s chemical structure is also frequently used to regulate its activity.

14.14 Second messengers provide readily diffusible pathways for information transfer
Second messengers can propagate signals between proteins that are at a distance. cAMP and Ca2+ are widely used second messengers.

14.15 Ca2+ signaling serves diverse purposes in all eukaryotic cells
Ca2+ serves as a second messenger and regulatory molecule in essentially all cells.

Ca2+ acts directly on many target proteins.
14.15 Ca2+ signaling serves diverse purposes in all eukaryotic cells Ca2+ acts directly on many target proteins. It also regulates the activity of a regulatory protein calmodulin. The cytosolic concentration of Ca2+ is controlled by organellar sequestration and release.

14.16 Lipids and lipid-derived compounds are signaling molecules
Multiple lipid-derived second messengers are produced in membranes. Phospholipase Cs release soluble and lipid second messengers in response to diverse inputs.

PI 3-kinase synthesizes PIP3 to modulate cell shape and motility.
14.16 Lipids and lipid-derived compounds are signaling molecules Channels and transporters are modulated by different lipids in addition to inputs from other sources. PI 3-kinase synthesizes PIP3 to modulate cell shape and motility. PLD and PLA2 create other lipid second messengers.

14.17 PI 3-kinase regulates both cell shape and the activation of essential growth and metabolic functions Phosphorylation of some lipid second messengers changes their activity. PIP3 is recognized by proteins with a pleckstrin homology domain.

14.18 Signaling through ion channel receptors is very fast
Ion channels allow the passage of ions through a pore. This results in rapid (microsecond) changes in membrane potential.

Channels are selective for particular ions or for cations or anions.
14.18 Signaling through ion channel receptors is very fast Channels are selective for particular ions or for cations or anions. Channels regulate intracellular concentrations of regulatory ions, such as Ca2+.

14.19 Nuclear receptors regulate transcription
Nuclear receptors modulate transcription by binding to distinct short sequences in chromosomal DNA known as response elements.

14.19 Nuclear receptors regulate transcription
Receptor binding to other receptors, inhibitors, or coactivators leads to complex transcriptional control circuits. Signaling through nuclear receptors is relatively slow, consistent with their roles in adaptive responses.

14.20 G protein signaling modules are widely used and highly adaptable
The basic module is: a receptor a G protein an effector protein

Cells express several varieties of each class of proteins.
14.20 G protein signaling modules are widely used and highly adaptable Cells express several varieties of each class of proteins. Effectors are heterogeneous and initiate diverse cellular functions.

14.21 Heterotrimeric G proteins regulate a wide variety of effectors
G proteins convey signals by regulating the activities of multiple intracellular signaling proteins known as effectors. Effectors are structurally and functionally diverse.

Effector proteins integrate signals from multiple G protein pathways.
14.21 Heterotrimeric G proteins regulate a wide variety of effectors A common G-protein binding domain has not been identified among effector proteins. Effector proteins integrate signals from multiple G protein pathways.

14.22 Heterotrimeric G proteins are controlled by a regulatory GTPase cycle
Heterotrimeric G proteins are activated when the Gα subunit binds GTP. GTP hydrolysis to GDP inactivates the G protein.

GTP hydrolysis is slow, but is accelerated by proteins called GAPs.
14.22 Heterotrimeric G proteins are controlled by a regulatory GTPase cycle GTP hydrolysis is slow, but is accelerated by proteins called GAPs. Receptors promote activation by allowing GDP dissociation and GTP association. Spontaneous exchange is very slow. RGS proteins and phospholipase C-βs are GAPs for G proteins.

14.23 Small, monomeric GTPbinding proteins are multiuse switches
Small GTP-binding proteins are: active when bound to GTP inactive when bound to GDP GDP/GTP exchange catalysts known as GEFs (guanine nucleotide exchange factors) promote activation.

GAPs accelerate hydrolysis and deactivation.
14.23 Small, monomeric GTPbinding proteins are multiuse switches GAPs accelerate hydrolysis and deactivation. GDP dissociation inhibitors (GDIs) slow spontaneous nucleotide exchange.

14.24 Protein phosphorylation/ dephosphorylation is a major regulatory mechanism in the cell
Protein kinases are a large protein family. Protein kinases phosphorylate: Ser and Thr or Tyr or all three

14.24 Protein phosphorylation/ dephosphorylation is a major regulatory mechanism in the cell
Protein kinases may recognize the primary sequence surrounding the phosphorylation site. Protein kinases may preferentially recognize phosphorylation sites within folded domains.

14.25 Two-component protein phosphorylation systems are signaling relays
Two-component signaling systems are composed of sensor and response regulator components.

14.25 Two-component protein phosphorylation systems are signaling relays
Upon receiving a stimulus, sensor components undergo autophosphorylation on a histidine (His) residue. Transfer of the phosphate to an aspartyl residue on the response regulator serves to activate the regulator.

14.26 Pharmacological inhibitors of protein kinases may be used to understand and treat disease
Protein kinase inhibitors are useful both: for signaling research as drugs Protein kinase inhibitors usually bind in the ATP binding site.

14.27 Phosphoprotein phosphatases reverse the actions of kinases and are independently regulated
Phosphoprotein phosphatases reverse the actions of protein kinases.

Phosphoprotein phosphatases may dephosphorylate:
14.27 Phosphoprotein phosphatases reverse the actions of kinases and are independently regulated Phosphoprotein phosphatases may dephosphorylate: phosphoserine/threonine phosphotyrosine or all three Phosphoprotein phosphatase specificity is often achieved through the formation of specific protein complexes.

14.18 Covalent modification by ubiquitin and ubiquitinlike proteins is another way of regulating protein function Ubiquitin and related small proteins may be covalently attached to other proteins as a targeting signal. Ubiquitin is recognized by diverse ubiquitin binding proteins.

Ubiquitination can cooperate with other covalent modifications.
14.18 Covalent modification by ubiquitin and ubiquitinlike proteins is another way of regulating protein function Ubiquitination can cooperate with other covalent modifications. Ubiquitination regulates signaling in addition to its role in protein degradation.

14.29 The Wnt pathway regulates cell fate during development and other processes in the adult
Seven transmembrane-spanning receptors may control complex differentiation programs. Wnts are lipid-modified ligands.

Wnts signal through multiple distinct receptors.
14.29 The Wnt pathway regulates cell fate during development and other processes in the adult Wnts signal through multiple distinct receptors. Wnts suppress degradation of β-catenin, a multifunctional transcription factor.

14.30 Diverse signaling mechanisms are regulated by protein tyrosine kinases
Many receptor protein tyrosine kinases are activated by growth factors. Mutations in receptor tyrosine kinases can be oncogenic.

Ligand binding promotes:
14.30 Diverse signaling mechanisms are regulated by protein tyrosine kinases Ligand binding promotes: receptor oligomerization autophosphorylation Signaling proteins bind to the phosphotyrosine residues of the activated receptor.

14.31 Src family protein kinases cooperate with receptor protein tyrosine kinases
Src is activated by release of intrasteric inhibition. Activation of Src involves liberation of modular binding domains for activation-dependent interactions. Src often associates with receptors, including receptor tyrosine kinases.

14.32 MAPKs are central to many signaling pathways
MAPKs are activated by Tyr and Thr phosphorylation. The requirement for two phosphorylations creates a signaling threshold. The ERK1/2 MAPK pathway is usually regulated through Ras.

14.33 Cyclin-dependent protein kinases control the cell cycle
The cell cycle is regulated by cyclin-dependent protein kinases (CDKs). Activation of CDKs involves: protein binding dephosphorylation phosphorylation

14.34 Diverse receptors recruit protein tyrosine kinases to the plasma membrane
Receptors that bind protein tyrosine kinases use combinations of effectors similar to those used by receptor tyrosine kinases. These receptors often bind directly to transcription factors.

The extracellular matrix and cell adhesion By George Plopper
Chapter 15 The extracellular matrix and cell adhesion By George Plopper

15.1 Introduction Cell-cell junctions are specialized protein complexes that allow neighboring cells to: adhere to one another communicate with one another The extracellular matrix is a dense network of proteins that: lies between cells is made by the cells within the network

Cells express receptors for extracellular matrix proteins.
15.1 Introduction Cells express receptors for extracellular matrix proteins. The proteins in the extracellular matrix and cell junctions control: the three-dimensional organization of cells in tissues the growth, movement, shape, and differentiation of these cells

15.2 A brief history of research on the extracellular matrix
The study of the extracellular matrix and cell junctions has occurred in four historical stages. Each is defined by the technological advances that allowed increasingly detailed examination of these structures. Current research in this field is focused on determining how the proteins in the extracellular matrix and cell junctions control cell behavior.

15.3 Collagen provides structural support to tissues
The principal function of collagens is to provide structural support to tissues. Collagens are a family of over 20 different extracellular matrix proteins. Together they are the most abundant proteins in the animal kingdom.

Collagen subunits are:
15.3 Collagen provides structural support to tissues All collagens are organized into triple helical, coiled-coil “collagen subunits.” They are composed of three separate collagen polypeptides. Collagen subunits are: secreted from cells then assembled into larger fibrils and fibers in the extracellular space

15.3 Collagen provides structural support to tissues
Mutations of collagen genes can lead to a wide range of diseases, from mild wrinkling to brittle bones to fatal blistering of the skin.

15.4 Fibronectins connect cells to collagenous matrices
The principal function of the extracellular matrix protein fibronectin is to connect cells to matrices that contain fibrillar collagen. At least 20 different forms of fibronectin have been identified. All of them arise from alternative splicing of a single fibronectin gene.

The soluble forms of fibronectin are found in tissue fluids.
15.4 Fibronectins connect cells to collagenous matrices The soluble forms of fibronectin are found in tissue fluids. The insoluble forms are organized into fibers in the extracellular matrix.

Fibronectin proteins contain six structural regions.
15.4 Fibronectins connect cells to collagenous matrices Fibronectin fibers consist of crosslinked polymers of fibronectin homodimers. Fibronectin proteins contain six structural regions. Each has a series of repeating units.

Fibrin, heparan sulfate proteoglycan, and collagen:
15.4 Fibronectins connect cells to collagenous matrices Fibrin, heparan sulfate proteoglycan, and collagen: bind to distinct regions in fibronectin integrate fibronectin fibers into the extracellular matrix network Some cells express integrin receptors that bind to the Arg-Gly-Asp (RGD) sequence of fibronectin.

15.5 Elastic fibers impart flexibility to tissues
The principal function of elastin is to impart elasticity to tissues. Elastin monomers (known as tropoelastin subunits) are organized into fibers. The fibers are so strong and stable they can last a lifetime.

15.5 Elastic fibers impart flexibility to tissues
The strength of elastic fibers arises from covalent crosslinks formed between lysine side chains in adjacent elastin monomers. The elasticity of elastic fibers arises from the hydrophobic regions, which: are stretched out by tensile forces spontaneously reaggregate when the force is released

Assembly of tropoelastin into fibers:
15.5 Elastic fibers impart flexibility to tissues Assembly of tropoelastin into fibers: occurs in the extracellular space is controlled by a threestep process Mutations in elastin give rise to a variety of disorders, ranging from mild skin wrinkling to death in early childhood.

15.6 Laminins provide an adhesive substrate for cells
Laminins are a family of extracellular matrix proteins. They are found in virtually all tissues of vertebrate and invertebrate animals. The principal functions of laminins are: to provide an adhesive substrate for cells to resist tensile forces in tissues

Laminin heterotrimers do not form fibers.
15.6 Laminins provide an adhesive substrate for cells Laminins are heterotrimers comprising three different subunits wrapped together in a coiled-coil configuration. Laminin heterotrimers do not form fibers. They bind to linker proteins that enable them to form complex webs in the extracellular matrix.

15.6 Laminins provide an adhesive substrate for cells
A large number of proteins bind to laminins, including more than 20 different cell surface receptors.

15.7 Vitronectin facilitates targeted cell adhesion during blood clotting
Vitronectin is an extracellular matrix protein. It circulates in blood plasma in its soluble form. Vitronectin can bind to many different types of proteins, such as: collagens integrins clotting factors cell lysis factors extracellular proteases

Vitronectin facilitates blood clot formation in damaged tissues.
15.7 Vitronectin facilitates targeted cell adhesion during blood clotting Vitronectin facilitates blood clot formation in damaged tissues. In order to target deposition of clotting factors in tissues, vitronectin must convert from the soluble form to the insoluble form, which binds clotting factors.

15.8 Proteoglycans provide hydration to tissues
Proteoglycans consist of a central protein “core” to which long, linear chains of disaccharides, called glycosaminoglycans (GAGs), are attached. GAG chains on proteoglycans are negatively charged. This gives the proteoglycans a rodlike, bristly shape due to charge repulsion.

Proteoglycans attract water to form gels that:
15.8 Proteoglycans provide hydration to tissues The GAG bristles act as filters to limit the diffusion of viruses and bacteria in tissues. Proteoglycans attract water to form gels that: keep cells hydrated cushion tissues against hydrostatic pressure

Expression of proteoglycans is:
15.8 Proteoglycans provide hydration to tissues Proteoglycans can bind to a variety of extracellular matrix components, including: growth factors structural proteins cell surface receptors Expression of proteoglycans is: cell type specific developmentally regulated

15.9 Hyaluronan is a glycosaminoglycan enriched in connective tissues
It forms enormous complexes with proteoglycans in the extracellular matrix. These complexes are especially abundant in cartilage. There, hyaluronan is associated with the proteoglycan aggrecan, via a linker protein.

Hyaluronan is highly negatively charged.
15.9 Hyaluronan is a glycosaminoglycan enriched in connective tissues Hyaluronan is highly negatively charged. It binds to cations and water in the extracellular space. This increases the stiffness of the extracellular matrix . This provides a water cushion between cells that absorbs compressive forces. Hyaluronan consists of repeating disaccharides linked into long chains.

Unlike other glycosaminoglycans, hyaluronans chains are:
15.9 Hyaluronan is a glycosaminoglycan enriched in connective tissues Unlike other glycosaminoglycans, hyaluronans chains are: synthesized on the cytosolic surface of the plasma membrane translocated out of the cell Cells bind to hyaluronan via a family of receptors known as hyladherins. Hyladherins initiate signaling pathways that control: cell migration assembly of the cytoskeleton

15.10 Heparan sulfate proteoglycans are cell surface coreceptors
Heparan sulfate proteoglycans are a subset of proteoglycans. They contain chains of the glycosaminoglycan heparan sulfate. Most heparan sulfate is found on two families of membrane-bound proteoglycans: the syndecans the glypicans

Cell surface heparan sulfate proteoglycans:
15.10 Heparan sulfate proteoglycans are cell surface coreceptors Heparan sulfates are composed of distinct combinations of more than 30 different sugar subunits. This allows for great variety in heparan sulfate proteoglycan structure and function. Cell surface heparan sulfate proteoglycans: are expressed on many types of cells bind to over 70 different proteins

Cell surface heparan sulfate proteoglycans
15.10 Heparan sulfate proteoglycans are cell surface coreceptors Cell surface heparan sulfate proteoglycans assist in the internalization of some proteins act as coreceptors for: soluble proteins such as growth factors insoluble proteins such as extracellular matrix proteins Genetic studies in fruit flies show that heparan sulfate proteoglycans function in: growth factor signaling development

15.11 The basal lamina is a specialized extracellular matrix
The basal lamina is a thin sheet of extracellular matrix is composed of at least two distinct layers is found at: the basal surface of epithelial sheets neuromuscular junctions

The basal lamina functions as:
15.11 The basal lamina is a specialized extracellular matrix The basement membrane consists of the basal lamina connected to a network of collagen fibers. The basal lamina functions as: a supportive network to maintain epithelial tissues a diffusion barrier a collection site for soluble proteins such as growth factors a guidance signal for migrating neurons

The components of the basal lamina vary in different tissue types.
15.11 The basal lamina is a specialized extracellular matrix The components of the basal lamina vary in different tissue types. But most share four principal extracellular matrix components: sheets of collagen IV and laminin are held together by: heparan sulfate proteoglycans the linker protein nidogen

15.12 Proteases degrade extracellular matrix components
Cells must routinely degrade and replace their extracellular matrix as a normal part of development wound healing

Extracellular matrix proteins are degraded by specific proteases, which cells secrete in an inactive form. These proteases are only activated in the tissues where they are needed. Activation usually occurs by proteolytic cleavage of a propeptide on the protease.

MMPs can activate one another by cleaving off their propeptides.
15.12 Proteases degrade extracellular matrix components The matrix metalloproteinase (MMP) family is one of the most abundant classes of these proteases. It can degrade all of the major classes of extracellular matrix proteins. MMPs can activate one another by cleaving off their propeptides. This results in a cascade-like effect of protease activation that can lead to rapid degradation of extracellular matrix proteins.

These proteases also bind to integrin extracellular matrix receptors.
15.12 Proteases degrade extracellular matrix components ADAMs are a second class of proteases that degrade the extracellular matrix. These proteases also bind to integrin extracellular matrix receptors. Thus, they help regulate extracellular matrix assembly and degradation.

Cells secrete inhibitors of these proteases to protect themselves from unnecessary degradation. Mutations in the matrix metalloproteinase-2 gene give rise to numerous skeletal abnormalities in humans. This reflects the importance of extracellular matrix remodeling during development.

15.13 Most integrins are receptors for extracellular matrix proteins
Virtually all animal cells express integrins. They are the most abundant and widely expressed class of extracellular matrix protein receptors. Some integrins associate with other transmembrane proteins.

The cytoplasmic portions bind to cytoskeletal and signaling proteins.
15.13 Most integrins are receptors for extracellular matrix proteins Integrins are composed of two distinct subunits, known as α and β chains. The extracellular portions of both chains bind to extracellular matrix proteins The cytoplasmic portions bind to cytoskeletal and signaling proteins.

In vertebrates, there are many α and β integrin subunits.
15.13 Most integrins are receptors for extracellular matrix proteins In vertebrates, there are many α and β integrin subunits. These combine to form at least 24 different αβ heterodimeric receptors. Most cells express more than one type of integrin receptor. The types of receptor expressed by a cell can change: over time or in response to different environmental conditions

All of the known sequences contain at least one acidic amino acid.
15.13 Most integrins are receptors for extracellular matrix proteins Integrin receptors bind to specific amino acid sequences in a variety of extracellular matrix proteins. All of the known sequences contain at least one acidic amino acid.

15.14 Integrin receptors participate in cell signaling
Integrins are signaling receptors that control both: cell binding to extracellular matrix proteins intracellular responses following adhesion Integrins have no enzymatic activity of their own. Instead, they interact with adaptor proteins that link them to signaling proteins.

Two processes regulate the strength of integrin binding to extracellular matrix proteins: affinity modulation varying the binding strength of individual receptors avidity modulation varying the clustering of receptors

They can result from changes:
15.14 Integrin receptors participate in cell signaling Changes in integrin receptor conformation are central to both types of modulation. They can result from changes: at the cytoplasmic tails of the receptor subunits or in the concentration of extracellular cations

In inside-out signaling, changes in receptor conformation result from intracellular signals that originate elsewhere in the cell. For example, at another receptor In outside-in signaling, signals initiated at a receptor are propagated to other parts of the cell. For example, upon ligand binding

The cytoplasmic proteins associated with integrin clusters vary greatly depending on: the types of integrins and extracellular matrix proteins engaged. The resulting cellular responses to integrin outside-in signaling vary accordingly. Many of the integrin signaling pathways overlap with growth factor receptor pathways.

15.15 Integrins and extracellular matrix molecules play key roles in development
Gene knockout by homologous recombination has been applied in mice to; over 40 different extracellular matrix proteins 21 integrin genes Some genetic knockouts are lethal, while others have mild phenotypes.

15.15 Integrins and extracellular matrix molecules play key roles in development
Targeted disruption of the β1 integrin gene has revealed that it plays a critical role in: the organization of the skin red blood cell development

15.16 Tight junctions form selectively permeable barriers between cells
Tight junctions are part of the junctional complex that forms between adjacent epithelial cells or endothelial cells. Tight junctions regulate transport of particles between epithelial cells.

15.16 Tight junctions form selectively permeable barriers between cells
Tight junctions also preserve epithelial cell polarity by serving as a “fence.” It prevents diffusion of plasma membrane proteins between the apical and basal regions.

15.17 Septate junctions in invertebrates are similar to tight junctions
The septate junction: is found only in invertebrates is similar to the vertebrate tight junction Septate junctions appear as a series of either straight or folded walls (septa) between the plasma membranes of adjacent epithelial cells.

15.17 Septate junctions in invertebrates are similar to tight junctions
Septate junctions function principally as barriers to paracellular diffusion. Septate junctions perform two functions not associated with tight junctions: they control cell growth and cell shape during development. A special set of proteins unique to septate junctions performs these functions.

15.18 Adherens junctions link adjacent cells
Adherens junctions are a family of related cell surface domains. They link neighboring cells together. Adherens junctions contain transmembrane cadherin receptors.

The best-known adherens junction is the zonula adherens.
15.18 Adherens junctions link adjacent cells The best-known adherens junction is the zonula adherens. It is located within the junctional complex that forms between neighboring epithelial cells in some tissues. Within the zonula adherens, adaptor proteins called catenins link cadherins to actin filaments.

15.19 Desmosomes are intermediate filamentbased cell adhesion complexes
The principal function of desmosomes is to: provide structural integrity to sheets of epithelial cells by linking the intermediate filament networks of cells.

Desmosomes are components of the junctional complex.
15.19 Desmosomes are intermediate filament-based cell adhesion complexes Desmosomes are components of the junctional complex. At least seven proteins have been identified in desmosomes. The molecular composition of desmosomes varies in different cell and tissue types.

Desmosomes function as both:
15.19 Desmosomes are intermediate filament-based cell adhesion complexes Desmosomes function as both: adhesive structures signal transducing complexes Mutations in desmosomal components result in fragile epithelial structures. These mutations can be lethal, especially if they affect the organization of the skin.

15.20 Hemidesmosomes attach epithelial cells to the basal lamina
Hemidesmosomes, like desmosomes, provide structural stability to epithelial sheets. Hemidesmosomes are found on the basal surface of epithelial cells. There, they link the extracellular matrix to the intermediate filament network via transmembrane receptors.

Hemidesmosomes are structurally distinct from desmosomes.
15.20 Hemidesmosomes attach epithelial cells to the basal lamina Hemidesmosomes are structurally distinct from desmosomes. They contain at least six unique proteins.

15.20 Hemidesmosomes attach epithelial cells to the basal lamina
Mutations in hemidesmosome genes give rise to diseases similar to those associated with desmosomal gene mutations. The signaling pathways responsible for regulating hemidesmosome assembly are not well understood.

15.21 Gap junctions allow direct transfer of molecules between adjacent cells
Gap junctions are protein structures that facilitate direct transfer of small molecules between adjacent cells. They are found in most animal cells.

Gap junctions consist of clusters of cylindrical gap junction channels, which: project outward from the plasma membrane span a 2-3 nm gap between adjacent cells The gap junction channels consist of two halves, called connexons or hemichannels. Each consists of six protein subunits called connexins.

Over 20 different connexin genes are found in humans.
15.21 Gap junctions allow direct transfer of molecules between adjacent cells Over 20 different connexin genes are found in humans. These combine to form a variety of connexon types. Gap junctions: allow for free diffusion of molecules 1200 daltons in size exclude passage of molecules 2000 daltons

Gating is controlled by changes in
15.21 Gap junctions allow direct transfer of molecules between adjacent cells Gap junction permeability is regulated by opening and closing of the gap junction channels, a process called “gating.” Gating is controlled by changes in intracellular pH calcium ion flux direct phosphorylation of connexin subunits

Two additional families of nonconnexin gap junction proteins have been discovered. This suggests that gap junctions evolved more than once in the animal kingdom.

15.22 Calcium-dependent cadherins mediate adhesion between cells
Cadherins constitute a family of cell surface transmembrane receptor proteins that are organized into eight groups. The best-known group of cadherins is called the “classical cadherins.” It plays a role in establishing and maintaining cell-cell adhesion complexes such as the adherens junctions.

Classical cadherins function as clusters of dimers.
15.22 Calcium-dependent cadherins mediate adhesion between cells Classical cadherins function as clusters of dimers. The strength of adhesion is regulated by varying both: the number of dimers expressed on the cell surface the degree of clustering

Classical cadherins bind to cytoplasmic adaptor proteins, called catenins. Catenins link cadherins to the actin cytoskeleton. Cadherin clusters regulate intracellular signaling by forming a cytoskeletal scaffold. This organizes signaling proteins and their substrates into a three-dimensional complex.

Classical cadherins are essential for tissue morphogenesis, primarily by controlling: specificity of cell-cell adhesion changes in cell shape and movement

15.23 Calcium-independent NCAMs mediate adhesion between neural cells
Neural cell adhesion molecules (NCAMs) are expressed only in neural cells. They function primarily as homotypic cell-cell adhesion and signaling receptors.

Nerve cells express three different types of NCAM proteins.
15.23 Calcium-independent NCAMs mediate adhesion between neural cells Nerve cells express three different types of NCAM proteins. They arise from alternative splicing of a single NCAM gene.

15.23 Calcium-independent NCAMs mediate adhesion between neural cells
Some NCAMs are covalently modified with long chains of polysialic acid (PSA). This reduces the strength of homotypic binding. This reduced adhesion may be important in developing neurons as they form and break contacts with other neurons.

15.24 Selectins control adhesion of circulating immune cells
Selectins are cell-cell adhesion receptors expressed exclusively on cells in the vascular system. Three forms of selectin have been identified: L-selectin P-selectin E-selectin

15.24 Selectins control adhesion of circulating immune cells
Selectins function to arrest circulating leukocytes in blood vessels so that they can crawl out into the surrounding tissue. In a process called discontinuous cell-cell adhesion, selectins on leukocytes bind weakly and transiently to glycoproteins on the endothelial cells. The leukocytes come to a “rolling stop” along the blood vessel wall.

Prokaryotic cell biology
Chapter 16 Prokaryotic cell biology By Jeff Errington, Matthew Chapman, Scott J. Hultgren, & Michael Caparon

16.1 Introduction The relative simplicity of the prokaryotic cell architecture compared with eukaryotic cells belies an economical but highly sophisticated organization.

A few prokaryotic species are well described in terms of cell biology.
16.1 Introduction A few prokaryotic species are well described in terms of cell biology. These represent only a tiny sample of the enormous diversity represented by the group as a whole. Many central features of prokaryotic cell organization are well conserved.

Prokaryotic genomes are highly flexible.
16.1 Introduction Diversity and adaptability have been facilitated by a wide range of optional structures and processes. These provide some prokaryotes with the ability to thrive in specialized and sometimes harsh environments. Prokaryotic genomes are highly flexible. A number of mechanisms enable prokaryotes to adapt and evolve rapidly.

16.2 Molecular phylogeny techniques are used to understand microbial evolution
Only a fraction of the prokaryotic species on Earth has been analyzed.

16.2 Molecular phylogeny techniques are used to understand microbial evolution
Unique taxonomic techniques have been developed for classifying prokaryotes. Ribosomal RNA (rRNA) comparison has been used to build a three-domain tree of life that consists of: Bacteria Archaea Eukarya

16.3 Prokaryotic lifestyles are diverse
The inability to culture many prokaryotic organisms in the laboratory has hindered our knowledge about the true diversity of prokaryotic lifestyles.

16.3 Prokaryotic lifestyles are diverse
DNA sampling has been used to better gauge the diversity of microbial life in different ecological niches. Prokaryotic species can be characterized by their ability to survive and replicate in environments that vary widely in: temperature pH osmotic pressure oxygen availability

16.4 Archaea are prokaryotes with similarities to eukaryotic cells
Archaea tend to: be adapted to life in extreme environments utilize “unusual” energy sources Archaea: have unique cell envelope components lack peptidoglycan cell walls

Archaea resemble bacteria in:
16.4 Archaea are prokaryotes with similarities to eukaryotic cells Archaea resemble bacteria in: their central metabolic processes certain structures, such as flagella Archaea resemble eukaryotes in terms of: DNA replication Transcription Translation However, gene regulation involves many Bacteria-like regulatory proteins

16.5 Most prokaryotes produce a polysaccharide-rich layer called the capsule
The outer surface of many prokaryotes consists of a polysaccharide-rich layer called the capsule or slime layer. The proposed functions of the capsule or slime layer are: to protect bacteria from desiccation to bind to host cell receptors during colonization to help bacteria evade the host immune system

16.5 Most prokaryotes produce a polysaccharide-rich layer called the capsule
E. coli capsule formation occurs by one of at least four different pathways. In addition to, or in place of the capsule, many prokaryotes have an S-layer. This is an outer proteinaceous coat with crystalline properties.

16.6 The bacterial cell wall contains a crosslinked meshwork of peptidoglycan
Most bacteria have peptidoglycan: a tough external cell wall made of a polymeric meshwork of glycan strands crosslinked with short peptides. The disaccharide pentapeptide precursors of peptidoglycan are: synthesized in the cytoplasm Exported assembled outside the cytoplasmic membrane

Many autolytic enzymes remodel, modify, and repair the cell wall.
16.6 The bacterial cell wall contains a crosslinked meshwork of peptidoglycan One model for cell wall synthesis is that a multiprotein complex carries out insertion of new wall material following a “make-before-break” strategy. Many autolytic enzymes remodel, modify, and repair the cell wall.

16.6 The bacterial cell wall contains a crosslinked meshwork of peptidoglycan
For some bacteria, the peptidoglycan cell wall is important for maintaining cell shape. A bacterial actin homolog, MreB, forms helical filaments in the cell cytoplasm. They direct the shape of the cell through control of peptidoglycan synthesis.

16.7 The cell envelope of Gram-positive bacteria has unique features
Gram-positive bacteria have a thick cell wall containing multiple layers of peptidoglycan. Teichoic acids are an essential part of the Grampositive cell wall. Their precise function is poorly understood.

Many Gram-positive cell surface proteins are covalently attached to:
16.7 The cell envelope of Gram-positive bacteria has unique features Many Gram-positive cell surface proteins are covalently attached to: membrane lipids or peptidoglycan Mycobacteria have specialized lipid-rich cell envelope components.

16.8 Gram-negative bacteria have an outer membrane and a periplasmic space
The periplasmic space is found between the cytoplasmic and outer membranes in Gram-negative bacteria.

Proteins destined for secretion across the outer membrane often interact with molecular chaperones in the periplasmic space. The outer membrane is a lipid bilayer that prevents the free dispersal of most molecules.

Lipopolysaccharide is a component of the outer leaflet of the outer membrane. During infection by Gram-negative bacteria, lipopolysaccharide activates inflammatory responses.

16.9 The cytoplasmic membrane is a selective barrier for secretion
Molecules can pass the cytoplasmic membrane by: passive diffusion active translocation

16.9 The cytoplasmic membrane is a selective barrier for secretion
Specialized transmembrane transport proteins mediate the movement of most solutes across membranes. The cytoplasmic membrane maintains a proton motive force between the cytoplasm and the extracellular milieu.

16.10 Prokaryotes have several secretion pathways
Gram-negative and Gram-positive species use the Sec and Tat pathways for transporting proteins across the cytoplasmic membrane.

16.10 Prokaryotes have several secretion pathways
Gram-negative bacteria also transport proteins across the outer membrane. Pathogens have specialized secretion systems for secreting virulence factors.

16.11 Pili and flagella are appendages on the cell surface of most prokaryotes
Pili are extracellular proteinaceous structures that mediate many diverse functions, including: DNA exchange adhesion biofilm formation by prokaryotes

16.11 Pili and flagella are appendages on the cell surface of most prokaryotes
Many adhesive pili are assembled by the chaperone/usher pathway, which features: an outer membrane usher proteins that form a pore through which subunits are secreted a periplasmic chaperone that: helps to fold pilus subunits guides pilus subunits to the usher

Flagella are extracellular apparati that are propellers for motility.
16.11 Pili and flagella are appendages on the cell surface of most prokaryotes Flagella are extracellular apparati that are propellers for motility. Prokaryotic flagella consist of multiple segments. Each is formed by a unique assembly of protein subunits.

16.12 Prokaryotic genomes contain chromosomes and mobile DNA elements
Most prokaryotes have a single circular chromosome. Genetic flexibility and adaptability is enhanced by: transmissible plasmids bacteriophages Transposons and other mobile elements promote the rapid evolution of prokaryotic genomes.

16.13 The bacterial nucleoid and cytoplasm are highly ordered
The bacterial nucleoid appears as a diffuse mass of DNA but is highly organized. Genes have nonrandom positions in the cell. Bacteria have no nucleosomes. A variety of abundant nucleoid-associated proteins may help to organize the DNA.

In bacteria, transcription takes place within the nucleoid mass.
16.13 The bacterial nucleoid and cytoplasm are highly ordered In bacteria, transcription takes place within the nucleoid mass. Translation takes place within the peripheral zone. Analogous to the nucleus and cytoplasm of eukaryotic cells RNA polymerase may make an important contribution to nucleoid organization.

16.14 Bacterial chromosomes are replicated in specialized replication factories
Initiation of DNA replication is a key control point in the bacterial cell cycle. Replication takes place bidirectionally from a fixed site called oriC.

Replication is organized in specialized “factories.”
16.14 Bacterial chromosomes are replicated in specialized replication factories Replication is organized in specialized “factories.” Replication restart proteins facilitate the progress of forks from origin to terminus. Circular chromosomes usually have a termination trap. This ensures that replication forks converge in the replication terminus region.

16.14 Bacterial chromosomes are replicated in specialized replication factories
Circular chromosomes require special mechanisms to coordinate termination with: decatenation dimer resolution segregation cell division The SpoIIIE (FtsK) protein completes the chromosome segregation process by transporting any trapped segments of DNA out of the closing division septum.

16.15 Prokaryotic chromosome segregation occurs in the absence of a mitotic spindle
Prokaryotic cells have no mitotic spindle, but they segregate their chromosomes accurately. Measurements of oriC positions on the chromosome show that they are actively separated toward opposite poles of the cell early in the DNA replication cycle.

The mechanisms of chromosome segregation are poorly understood.
16.15 Prokaryotic chromosome segregation occurs in the absence of a mitotic spindle The mechanisms of chromosome segregation are poorly understood. Probably because they are partially redundant The ParA-ParB system is probably involved in chromosome segregation in many bacteria and low-copy-number plasmids.

16.16 Prokaryotic cell division involves formation of a complex cytokinetic ring
At the last stage of cell division, the cell envelope undergoes either: constriction and scission, or septum synthesis followed by autolysis …to form two separate cells. A tubulin homolog, FtsZ, orchestrates the division process in bacteria, forming a ring structure at the division site.

16.16 Prokaryotic cell division involves formation of a complex cytokinetic ring
A set of about 8 other essential division proteins assemble at the division site with FtsZ. The cell division site is determined by two negative regulatory systems: nucleoid occlusion the Min system

16.17 Prokaryotes respond to stress with complex developmental changes
Prokaryotes respond to stress, such as starvation, with a wide range of adaptive changes.

The simplest adaptative responses to stress involve:
16.17 Prokaryotes respond to stress with complex developmental changes The simplest adaptative responses to stress involve: changes in gene expression and metabolism a general slowing of the cell cycle, preparing the cell for a period of starvation In some cases, starvation induces formation of highly differentiated specialized cell types. For example, the endospores of Bacillus subtilis.

16.17 Prokaryotes respond to stress with complex developmental changes
During starvation, mycelial organisms such as actinomycetes have complex colony morphology and produce: aerial hyphae spores secondary metabolites Myxococcus xanthus exemplifies multicellular cooperation and development of a bacterium.

16.18 Some prokaryotic life cycles include obligatory developmental changes
Many bacteria have been studied as simple and tractable examples of cellular development and differentiation. Caulobacter crescentus is an example of an organism that produces specialized cell types at every cell division.

16.19 Some prokaryotes and eukaryotes have endosymbiotic relationships
Mitochondria and chloroplasts arose by the integration of free-living prokaryotes into the cytoplasm of eukaryotic cells. There, they became permanent symbiotic residents.

Rhizobia species form nodules on legumes:
16.19 Some prokaryotes and eukaryotes have endosymbiotic relationships Rhizobia species form nodules on legumes: So that elemental nitrogen can be converted into the biologically active form of ammonia. The development and survival of pea aphids depends on an endosymbiotic event with Buchnera bacteria.

16.20 Prokaryotes can colonize and cause disease in higher organisms
Although many microbes make their homes in or on the human body, only a small fraction cause harm to us. Pathogens are often able to: colonize replicate survive within host tissues Many pathogens produce toxic substances to facilitate host cell damage.

16.21 Biofilms are highly organized communities of microbes
It has been estimated that most of the Earth’s prokaryotes live in organized communities called biofilms.

Biofilm formation involves several steps including:
16.21 Biofilms are highly organized communities of microbes Biofilm formation involves several steps including: surface binding growth and division polysaccharide production biofilm maturation dispersal Organisms within a biofilm communicate by quorum sensing systems.

Plant cell biology By Clive Lloyd
Chapter 17 Plant cell biology By Clive Lloyd

17.1 Introduction Plant and animal cells grow in fundamentally different ways. The tough cell wall prevents: cell movement uptake of large molecules as food Plant development depends upon how immobile cells manipulate the cell wall.

17.2 How plants grow Plants extend into the environment using apical growing points. Plant development continues beyond the embryonic stage. Plant growth is sensitive to the environment.

17.3 The meristem provides new growth modules in a repetitive manner
Apical meristems divide to produce new cells at the growing points. Growth occurs by repeated addition of new growth modules.

Cells divide, expand, then differentiate.
17.3 The meristem provides new growth modules in a repetitive manner Cells divide, expand, then differentiate. Massive expansion of cells behind the tips drives the growing points onward.

17.4 The plane in which a cell divides is important for tissue organization
In the absence of cell movement, orientation of the division plane helps determine shape. Formative divisions generate new cell types: proliferative divisions add more cells.

17.5 Cytoplasmic structures predict the plane of cell division before mitosis begins
The plane of cell division is predicted before mitosis by a ring of microtubules and actin filaments around the cortex. A sheet of cytoplasm also predicts the plane of division in vacuolated cells.

17.6 Plant mitosis occurs without centrosomes
The poles of plant mitotic spindles: do not contain centrioles can be much more diffuse than the poles of animal spindles

17.7 The cytokinetic apparatus builds a new wall in the plane anticipated by the preprophase band
The cytokinetic apparatus—the phragmoplast—is a ring of cytoskeletal filaments that expands outward.

The plane in which the cell plate grows conforms:
17.7 The cytokinetic apparatus builds a new wall in the plane anticipated by the preprophase band Vesicles directed to the midline of this double ring fuse to form the new cross-wall. The plane in which the cell plate grows conforms: to the preprophase band not to the spindle midzone

17.8 Secretion during cytokinesis forms the cell plate
The Golgi apparatus continues to make secretory vesicles throughout cytokinesis. These vesicles fuse to make a cell plate lined with new plasma membrane.

17.9 Plasmodesmata are intercellular channels that connect plant cells
Primary plasmodesmata are pores in the cell wall formed at cytokinesis. Plasmodesmata interconnect cells into multicellular units called symplasts, within which signaling occurs. Plasmodesmata can open and close Their pore size can be increased by viruses.

17.10 Cell expansion is driven by swelling of the vacuole
Uptake of water into the vacuole provides a unique, pressure-driven mechanism of cell expansion. There is more than one type of vacuole.

17.11 The large forces of turgor pressure are resisted by the strength of cellulose microfibrils in the cell wall The plant cell wall is based largely on carbohydrate. unlike the protein-rich extracellular matrix of animal cells

Proteins loosen the cell wall to allow cell expansion.
17.11 The large forces of turgor pressure are resisted by the strength of cellulose microfibrils in the cell wall The nonrandom arrangement of stiff cellulose microfibrils controls the swelling force of turgor pressure. Proteins loosen the cell wall to allow cell expansion. The orientation of cellulose microfibrils can change from layer to layer.

17.12 The cell wall must be loosened and reorganized to allow growth
Proteins loosen the cell wall to allow cell expansion. The orientation of cellulose microfibrils can change from layer to layer.

17.13 Cellulose is synthesized at the plasma membrane, not preassembled and secreted like other wall components Cellulose is polymerized by complexes embedded in the plasma membrane. The synthesizing complexes move along the face of the plasma membrane.

17.14 Cortical microtubules are thought to organize components in the cell wall
During interphase the microtubules in plant cells are primarily located immediately beneath the plasma membrane.

17.14 Cortical microtubules are thought to organize components in the cell wall
Cortical microtubules are often coaligned with the newest cellulose microfibrils. Cortical microtubules may organize the cell wall by providing tracks for the synthesis and assembly of cellulose microfibrils.

17.15 Cortical microtubules are highly dynamic and can change their orientation
Plant microtubules polymerize from multiple sites. Microtubules can move along the cortex after they have been nucleated.

The microtubule array can reorient in response to:
17.15 Cortical microtubules are highly dynamic and can change their orientation Microtubule-associated proteins organize microtubules into parallel groups. The microtubule array can reorient in response to: hormones gravity light

17.16 A dispersed Golgi system delivers vesicles to the cell surface for growth
The plasma membrane and cell wall materials needed for growth are provided by the ER/Golgi system. The Golgi apparatus is dispersed in plants. The actin system propels the dynamic Golgi apparatus over the ER network.

17.17 Actin filaments form a network for delivering materials around the cell
Organelles and vesicles move around the cell by cytoplasmic streaming, powered by actin-myosin interaction. Plants have two unique classes of myosin.

17.18 Differentiation of xylem cells requires extensive specialization
Files of xylem cells undergo programmed cell death to form water-conducting tubes.

17.18 Differentiation of xylem cells requires extensive specialization
The tubes are prevented from inward collapse by transverse patterns of secondary wall thickening. Cortical microtubules bunch-up to form patterns that anticipate the pattern of secondary thickening.

17.19 Tip growth allows plant cells to extend processes
Highly localized secretion of cell wall materials allows plant cells to extend long processes. In tip-growing cells, actin filaments and microtubules generally run parallel to the direction of outgrowth.

Bundles of actin filaments direct the movement of vesicles to the tip.
17.19 Tip growth allows plant cells to extend processes Bundles of actin filaments direct the movement of vesicles to the tip. There, they fuse with the plasma membrane, driving extension. Microtubules seem to control the number and location of cell tips. Symbiotic bacteria turn tip growth in on itself to gain access into the plant.

17.20 Plants contain unique organelles called plastids
Plastids are membrane-bounded organelles that are unique to plants. Several types of plastid exist, each with a different function.

All plastids differentiate from proplastids.
17.20 Plants contain unique organelles called plastids All plastids differentiate from proplastids. Plastids arose during evolution by an endosymbiotic event.

17.21 Chloroplasts manufacture food from atmospheric CO2
Photosynthesis occurs in specialized plastids called chloroplasts. Leaves maximize the amount of light for photosynthesis. Mesophyll cells are shaped for maximal gas exchange.

What is a Cell? By Benjamin Lewin

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