Unit I Flashcards

Question

Formation of lipid bilayers in aqueous solution is a spontaneous process, driven by the following forces.

Answer 1

- Hydrophobic effect (primary driving force) - van der Waals forces- favors close packing of hydrophobic tails. - Electrostatic and hydrogen bonding interactions between polar head groups and water molecules

Answer 2

(Flip flop) Occurs through the transfer of a phospholipid molecule from one leaflet of the bilayer to the other. This is very rare, unless mediated by proteins.

Answer 3

Occurs through the pairwise exchange of neighboring phospholipid molecules in the same leaflet.

Answer 4

1) Temperature 2) Length and Degree of Unsaturation of Fatty Acid Chains 3) Cholesterol Content

Answer 5

Fatty acyl chains can be in ordered rigid state (at very low temperature) or in a relatively disordered fluid state. At physiological temperatures, they generally exist in the disordered fluid state. In the ordered, rigid state, hydrocarbon chains of the the fatty acids "nest" together because there is little rotation around C-C single bonds. In the disordered, fluid state, the chains don't fit together as tightly because there is more rotation around C-C single bonds and thus more movement in the chains. The temperature where the transition between rigid and liquid states occurs is called the melting (or transition) temperature (Tm)

Answer 6

Long saturated hydrocarbon chains interact more strongly: fatty acid tails of lipids can consists of chains of 14-24 carbons. Adjacent long hydrocarbon chains can interact more strongly than short chains simply because there is more potential for van der Waals interactions between the longer chains. Unsaturation (cis double bonds) disrupts ordered packing of bilayer: Because the double bonds are in the "cis" conformation, the presence of a double bond introduces a stiff kink into the fatty acyl chain and prevents the tight packing of adjacent side chains. Therefore membranes with higher levels of unsaturated lipids will tend to be more fluid

Answer 7

- Tends to decrease fluidity in membranes by blocking large motions of saturated hydrocarbon chains. For this reason, it is found in "lipid rafts" which are regions of lower fluidity. - cholesterol prevents fatty acyl chains of nearby lipids from packing together tightly and therefore helps membranes from ever solidifying into a "gel phase" - the opposing effects of cholesterol help to ensure that biological membranes stay fluid over the range of physiological temperatures. This fluidity is important for maintaining biological function.

Answer 8

hydrophobic hydrocarbon core of the bilayer does not permit ions or other polar substances to pass through with the shell of water they would normally have in aqueous solutions. Polar molecules are poorly permeable. Increasing permeability: Na+ < K+ < Cl- < Glucose < Tryptophan < Urea, glycerol < Indole < H2O

Answer 9

All else being equal, smaller molecules will cross membranes more easily than larger molecules with the same chemical properties.

Answer 10

1) Passive diffusion 2) Hijacked transporters 3) Liposome delivery 4) Protein transduction

Answer 11

Peripheral Membrane Proteins: - bound to surface of membrane or to other integral membrane proteins - can be released without disrupting lipid bilayer Integral Membrane Proteins: - penetrate the lipid bilayer - require detergents to release them from the membrane bilayer

Answer 12

1) Integral membrane proteins are amphipathic | 2) Membrane Proteins Have a Defined Topology- they can't flip flop

Answer 13

Specific proteins can be recruited to rafts Rafts are implicated in many different processes: 1) Signal transduction 2) Protein sorting 3) Recogntion 4) Viral entry or exit from the cell

Answer 14

1) Certain lipids (sphingomyelin and cholesterol) help drive formation of lipid rafts 2) Lipids can be signalling molecules. 3) Abnormal lipid distribution is a signal that cells are dying 4) Different organelles have different phospholipid contents.

Answer 15

formed of microfilaments, intermediate filaments, and microtubules. These filament systems have different physical properties (stiffness, strength, and flexibility), different intracellular distributions, unique biochemical properties allow selective interaction of each filament type with other proteins and structures

Answer 16

- 42 kDa globular protein - six actin genes all encode very similar proteins but provide 6 unique promoters for tissue- and cell-specific regulation of expression

Answer 17

microfilaments are formed by the assembly of actin monomers into two-stranded, 5-7 nm diameter helical filaments of variable length. The uniform orientations of monomers results in structural polarity of filaments. One end of each filament is designated plus (barbed) while the other end is minus (pointed) Structural polarity can be determined by growth rate (plus end is fast growing) and by electron microscopic appearance after binding myosin S1 fragments. Hydrolysis of ATP to ADP on actin subunits of a filament results in different assembly equilibria at plus and minus ends and leads to treadmilling

Answer 18

In vivo actin assembly is regulated largely by two classes of actin monomer binding proteins, thymosins and profilins. Actin-binding proteins also affect the length, number, organization, and in vivo function of microfilaments. They can generate force (myosin), regulate motility (troponin), crosslink (filamin), bundle (alpha actinin and fimbrin), cap filaments (alpha/beta capping protein) and anchor filaments to other structures such as the plasma membrane (talin)

Answer 19

cell cortex is the combination of the plasma membrane and an underlying mesh of crosslinked actin filaments. Some of these structures are involved in contraction, extension of the plasma membrane to form filopodia and lamellipodia and in stabilization of a particular membrane shape 1) Microvilli- absorptive cells 2) Stress Fibers- terminate on the plasma membrane at focal contracts 3) Lamellipodia 4) Contractile ring

Answer 20

The Actin Related Protein (ARP) complex mediates assembly of a branched array of actin filaments at the leading edge of an extending cell membrane, as occurs when fibroblasts are migrating through the extracellular matrix in connective tissue. - Assembly near the membrane is essential for pushing out the thin lamellar edge of the cell - Capping proteins limit the length of growing filaments - Disassembly away from the edge regenerates actin monomers for new rounds of assembly

Answer 21

Phalloidin stabilizes actin filaments by binding along the sides of the filament; cytochalasins block actin filament assembly at the plus end. Both drugs disrupt cell motility and cytokinesis, showing the importance of having a dynamic actin cytoskeleton

Answer 22

Though interactions with myosin ATPase, microfilaments generate many varieties of motility such as muscle contraction, amoeboid movement, cytokinsesis, ruffling, and some forms of intracellular vesicle movement.. Myosins constitute a large family of motors, all plus-end directed, with similar sequences in their globular catalytic heads, but quite divergent sequences in their carboxyl-terminal tails. The C-terminal tails of myosin-II proteins mediate the assembly of two-headed dimers via a coiled-coil interaction. These dimers can then assemble in tail to tail configuration to give bipolar "thick" filaments. The C-terminal tails of myosin I proteins do not mediate self assembly but are specialized to interact with various "cargoes"

Answer 23

- single-headed (70 nm) - do not form filaments - individual myosin molecules bind to membranes and walk along filaments toward their plus ends

Answer 24

- assembles into bi-polar filaments with heads that face in to directions (150 nm) - to create movement, they interact with two overlapping sets of actin filaments polarized in opposite directions

Answer 25

- actin assembly extends the lamellipodium - attachment to the substrate and contraction of microfilament bundles pulls the center of the cell forward - detachment of the back end of the cell and further contraction brings the back bend of the cell forward

Answer 26

- Myosin II remains inactive as a monomer. - Phosphorylation of light chains is necessary for activation and assembly. - Protein kinases that phosphorylate myosin light chains are activated indirectly by increases in calcium ion concentration

Answer 27

-Multinucleated syncytial cell. -Contractile proteins bundled in myofibrils -Myofibrils surrounded by special endoplasmic reticulum (sarcoplasmic reticulum). -Each myofibril divided into contractile units (sarcomeres).

Answer 28

- sacromeres are anchored bundles of interdigitating actin and myosin filaments - plus ends of actin filaments (thin filaments) attach to Z discs - minus ends of actin filaments extend away from Z disc but do not overlap in the center of sacromeres (nebulin, a huge protein, associates with the actin filaments and determines the length of the microfilaments in the sacromere - bipolar myosin filaments (thick filaments) are held in the middle of each sacromere (titin, the largest protein yet described) extends from the Z-disc to thick myosin filaments and acts to center the myosin filaments in the sacaromere - myofilbrils are bound to each other by desmin intermediate fibers - the entire array is anchored to the plasma membrane by many proteins one of which is dystrophin (protein defective in muscular dystrophy) - each myofibril is separated from its neighbor by ER membrane compartments- sarcoplasmic reticulum

Answer 29

Rigor- the myosin head is tightly bound to the actin filament and nucleotide-free Release- ATP binding to the myosin head lowers the affinity of myosin for actin resulting in release Cocked- ATP hydrolysis causes a 5nm translocation of the head to cock it in preparation for the power stroke. This configuration has weak affinity for the actin filament Force-generating-dissociation of the inorganic phosphate increases the affinity of the myosin head for the actin filament and activates the power stroke Attached- dissociation of ADP is stimulated by translocation of the myosin head back to its original configuration

Answer 30

When all the myosins in a sarcomere are activated, heads facing opposite directions on each thick filaments toward the plus ends (Z discs) and the sacromere shortens. Simultaneous shortening of all the sacromeres in a muscle cell results in the shortening of the muscle, which pulls on tendons that attach to bones

Answer 31

Ca++ regulation of skeletal muscle contraction is mediated by the troponin-tropomyosin complex. Troponin consists of 3 polypeptides: troponin T binds to tropomyosin thereby positioning the complex on the actin filament, troponin I binds to the actin filaments and affects tropomyosin positioning on the actin filament and troponin C binds Ca++ ions. This is called actin- or thin filament=based regulation Tropomyosin associates with actin filaments in two configurations: one configuration blocks the myosin binding site (absence of Ca++) the other allows myosin binding (presence of Ca++) Binding of Ca++ ions to troponin C causes troponin I to release its hold on actin thus allowing tropomyosin to move away from the myosin binding site

Answer 32

- an action potential originating from a nerve cell is transmitted down the plasma membrane to the transverse tubules - this action potential is relayed to the sarcoplasmic reticulum, a membranous network that surrounds the myofibril and contains large stores of Ca++ ions - a voltage gated Ca++ channel imbedded in the transverse tubule senses the action potential and in response sacroplasmic reticulm membrane Ca++ release channels open to spill Ca++ ions into the cytosol surrounding the myofibrils - when the nerve impulse stops, CaATPase pumps in the sarcoplasmic reticulum membrane pump the Ca++ back out of the cytosol, and myosin is prevented from interacting with actin. Contraction stops and the muscle relaxes.

Answer 33

- 10 nm diameter filaments assembled from homo- or heterodimers - no apparent polarity and are ill-suited for a role im motility

Answer 34

-have rod-like regions which form alpha-helical coiled-coils and hetereogeneous globular ends Keratins- epithelial cells, hair, nails; provide strength, certain keratins can be useful in treatment of epithelial cancers Vimentin,Desmin, and Glial Fibrullary Acidic protein- vimentin is widespread in cells of mesodermal origin, desmin which hold together adjacent myofibrils, GFA in astrocytes and glial cells Neurofilaments- extend along the length of axons Nuclear Lamins- meshwork on inner surface of all the nuclear membrane of all cells, mutation could cause premature aging syndrome progeria

Answer 35

- 25 nm diameter hollow tubes assembled from dimers of alphaa and beta tubulin - both alpha and beta tubulin are 55 kd globular proteins that contain GTP binding sites - only beta tubulin can hydrolyze its bound GTP to GDP when it is assembled into a microtubule. formation of the tubulin dimer protects the GTP on alpha tubulin

Answer 36

- in cells, assembly requires GTP, Mg++, and a critical subunit concentration - beta tubulin in a microtubule acts as a slow GTPase, and GDP must be exchanged for GTP again before a subunit is re-used for assembling another microtubules - end to end binding in head to tail orientation results in structural polarity of microtubules, which have plus (fast growing) and minus (slow growing) ends - microtubule-associated proteins and drugs can regulate assembly in vitro and in vivo

Answer 37

colchicine: binds to free tubulin and blocks its assembly into microtubules. Originally extracted from meadow saffron; it has been used to treat gout. This drug and its close chemical relative colcemid are also anti-mitotic agents that disrupt the mitotic spindle of dividing cells vinblastine/vincristine: block MT assembly. These anti-mitotic as well and preferentially kill dividing cells. Used in chemotherapy taxol: binds to and stablizes MTs and arrests dividing cells in mitosis. Powerful anticancer drugs especially ovarian cancer

Answer 38

•Most microtubules alternate between phases of slow growth and rapid disassembly (dynamic instability) •Most microtubule assembly and disassembly in cells happens at (+) ends. •Most microtubules are nucleated from organizing centers (MTOCs) such as centrosomes, and have their (–) ends associated with the organizing center. •Therefore, microtubules growing from a centrosomeform a polarized array.

Answer 39

-The nucleating sites on centrosomes are rings of gamma tubulin -Centrosomes in most mammalian cells form around a pair of centrioles and associate with the nucleus. -Centrioles are short bundles of special triplet microtubules - Centrioles usually occur in pairs and are needed for centrosome formation - Microtubules assembled from centrioles probe the cell. - Most interphase cells have a single MTOC. - Centrosomes duplicate before cell division. - Centrioles act as nucleating sites for cilia assembly.

Answer 40

- not all microtubule arrays are dynamic - ones without dynamic instability have undergone maturation - post translational modification of alpha tubulin by acetylation and detyrosination contributes to the stability of these stable MT arrays

Answer 41

- associated proteins serve to create specialized microtibule arrays in different places within cells and tissues, and change the surface of the microtubule for interaction with other cellular proteins - MAPs

Answer 42

Both motors use ATP hydrolysis to do mechanical work. •Dyneins move toward microtubule – ends. •Kinesins move toward microtubule + ends. •Each motor may carry many different cargoes.

Answer 43

* “outward” transport (e.g., neurotransmitters) uses kinesins. * “inward” transport (e.g., recycled membrane) relies on dyneins. * neurotropic viruses use dynein as a transport carrier. * Kinesin stretches the ER from the nucleus out toward microtubule (+) ends. * Dynein keeps the Golgi near the nucleus (microtubule (–) ends).

Answer 44

•Most microtubules alternate between phases of slow growth and rapid disassembly (dynamic instability) •Most microtubule assembly and disassembly in cells happens at (+) ends. •Most microtubules are nucleated from organizing centers (MTOCs) such as centrosomes, and have their (–) ends associated with the organizing center. •Therefore, microtubules growing from a centrosomeform a polarized array.

Answer 45

-The nucleating sites on centrosomes are rings of gamma tubulin -Centrosomes in most mammalian cells form around a pair of centrioles and associate with the nucleus. -Centrioles are short bundles of special triplet microtubules - Centrioles usually occur in pairs and are needed for centrosome formation - Microtubules assembled from centrioles probe the cell. - Most interphase cells have a single MTOC. - Centrosomes duplicate before cell division. - Centrioles act as nucleating sites for cilia assembly.

Answer 46

- not all microtubule arrays are dynamic - ones without dynamic instability have undergone maturation - post translational modification of alpha tubulin by acetylation and detyrosination contributes to the stability of these stable MT arrays

Answer 47

- associated proteins serve to create specialized microtibule arrays in different places within cells and tissues, and change the surface of the microtubule for interaction with other cellular proteins - MAPs

Answer 48

Both motors use ATP hydrolysis to do mechanical work. •Dyneins move toward microtubule – ends. •Kinesins move toward microtubule + ends. •Each motor may carry many different cargoes.

Answer 49

* “outward” transport (e.g., neurotransmitters) uses kinesins. * “inward” transport (e.g., recycled membrane) relies on dyneins. * neurotropic viruses use dynein as a transport carrier.

Answer 50

- cylinders of nine doublet microtubules that project from the cell surface and are surrounded by the plasma membrane - 9+2 - doublet microtubules and all of their associated proteins are called the axoneme - basal body Flagella (symmetrical wave form): •single-celled eukaryotes -spermatozoa Cilia (asymmetric wave form): •widespread among eukaryotes •ciliated epithelia

Answer 51

- sperm - cilia can be found in airways, fallopian tubes and in the brain ventricles - embryonic cilia generate body plan asymmetry seen in adult organs such as heart, kidneys and liver (Kartagener's Syndrome)

Answer 52

Most common ciliopathy is Polycystic Kidney Disease (PKD), caused by lack of receptors in membranes of non-motile cilia. Non-motile cilia are needed for many sensory systems (including vision and smell) and during limb development, so loss of these cilia results in a wide range of symptoms.

Answer 53

* Cilia and flagella are cylinders of microtubules that bend. * The cylinder wall of cilia is made from doublet microtubules. * Bending is powered by dyneins * Spokes and central pair regulate dynein activity patterns tocontrol bend shape and beat frequency -Dynein-powered microtubule sliding is converted to a bend ``` Dynein regulation: •beat is usually planar •regions of activity propagate, base-to-tip •radial spokes regulate dyneins to change bend shape, beat frequency ```

Answer 54

1) transport with nuclear pores- cytosol to nucleus 2) transport via protein translocators- within organelle membrane directly transport proteins from cytosol into the organelle. Occurs co-translationally for the ER and post-translationally for mitochondria and peroxisomes 3) transport via vesicles- moving proteins from one organelle to another

Answer 55

- sorting signals that direct proteins to the correct organelles - continuous stretch of amino acids (3-60 residues long) - may be removed by signal peptidase after transport - different type=different destination

Answer 56

powerplants of the cell (90%) of energy, ATP - ATP is made by electron transport and oxidative phosphorylation - cells with high energy needs have a large number of mitochondria - can move freely along microtubules - two distinct membranes separating two distinct internal components

Answer 57

- large internal space with high concentration of enzymes that break down fatty acids via beta-oxidation and those involved with the citric acid - location of mitochondrial DNA genome and the transcription and translational machinery required for the expression of mitochondrial genes

Answer 58

- encloses the matrix space - highly convoluted forming infoldings known as cristae which greatly increase the surface area of membrane - contains proteins of the electron transport chain and ATP synthase which are both essential for oxidative phosphorylation (synthesis of ATP) - contains transport proteins regulating the passage of metabolities into and out of the matrix - electrochemical gradient that drives ATP synthesis is established across this membrane by the electron transport chain

Answer 59

- separates the mitochondrion from the cytosol - contains porin molecules which form large aqueous channels through the lipid bilayer making the membrane permeable to small molecules

Answer 60

- small space located between the inner and outer membranes - contains cytochrome c, a component of the electron transport chain, which is released into the cytosol during apoptosis

Answer 61

- when a cell needs energy, fats and glycogen, the cell's fuel reservoirs, are converted to fatty acids and pyruvate in the cytosol. - pyruvate and fatty acids are then selectively transported into the mitochondrial matrix where they are converted to acetyl coenzyme A (acetyl CoA) - acetyl CoA enters the citric acid cycle and is converted to CO2 and high energy electrons which are transiently held by NADH and FADH2 - high energy electrons are transported down the electron transport chain located in the inner membrane, releasing energy which is used to pump protons out of the matrix creating an electrochemical proton gradient across the inner membrane. At the end of the chain, the electrons are transfered to O2 to produce H2O - protons flow down the electrochemical gradient into the matrix through the ATP synthase complex which catalyzes the conversion of ADP + Pi to ATP, thus complete oxidative phosphorylation - newly formed ATP is transported from the matrix to the cytosol, and ADP and Pi generated by hydrolysis of ATP in the cytosol are pumped back into the matrix for recharging

Answer 62

- apoptosis is programmed cell death - mitochondria release cytochrome c from the intermembrane space into the cytosol which activates the caspace cascade and intracellular proteolytic cascade responsible for cleaving key cellular proteins

Answer 63

- proteins destined for the mitochondria are typically synthesized with an N-terminal signal sequence and transported soon after their release from polyribosomes in the cytosol (post-translational) - transport is mediated by protein translocators TOM and TIM complexes located in the outer and inner membranes respectively - the precursor protein binds to a receptor compnent of TOM via the signal sequence - the precursor protein/TOM complex diffuse laterally to a contact site where the inner and outer membranes meet - the precursor protein is translocated across both membranes, signal sequence first, via TOM and TIM in an unfolded state, chaperone proteins help fold - signal sequence cleaved by mitochondrial signal peptidase and folded into final conformation * Requires both ATP hydrolosis and electrochemical gradient across the inner membrane

Answer 64

- very small (-16,500 bp) circular double stranded DNA - encodes 2 rRNAs, 22 tRNAs, and 13 mRANS; most of the original bacterial genes have moved to nuclear genome - very little regulatory sequence and no introns - the genetic code is slightly different, 4 of the 64 codons have different meanings than those same codons in nuclear genome - each mitochondrion contains 10-20 copies of the mitochondria genome found in clusters in the mitochondrial matrix

Answer 65

- mitochondria carry out their own DNA replication, transcription and protein synthesis in the matrix using mitochondria specific proteins encoded by the nuclear genome (~900) - Replication: - throughout the cell cycle, not limited to S phase - the total number of mitochondrial DNA molecules doubles in every cell cycle as the organelles grow and divide prior to each cell division Transcription: - both strands of mitochondrial DNA are transcribed from a single promoter region on each strand (HSP, heavy strand promoter and LSP, light strand promoter - produces two giant RNA molecules - each giant RNA molecule is cleaved into 2 rRNAs, 22 tRNAs, annd 13 mRNAs Translation: - occurs in matrix using tRNAs and rRNAs encoded by mDNA - produces only 13 polypeptides all of which are subunits of complexes involved in electron transport and oxidative phosphorylation.

Answer 66

- small multi-functional organelles - one of the major sites of oxygen utilization in the cell - contain high concentrations of oxidative enzymes used in reactions that break down lipids and destroy toxic molecules - their size, number and enzymatic content vary depending upon the cell type and metabolic needs of the organism - typical human cell has several hundred peroxisomes

Answer 67

-peroxisomes contain enzymes that remove hydrogen atoms from organic substrates (R) in an oxidative reaction that produces hydrogran peroxide RH2 + O2 -> R + H2O2 Catalase uses hydrogen peroxide to oxidize a variety of substrates such as phenols, formic acid, formaldehyde, and alcohol in the peroixidation reaction: H2O2 + R'H2 -> R' +2H2O This reaction is important in kidney and liver cells where peroxisomes detoxify toxic molecules in the bloodstream. One quarter of consumed alcohol is oxidized to acetaldehyde by catalase. Catalase can also eliminate excess hydrogen peroxide by converting it to water

Answer 68

-in peroxisomes shortens very long chain fatty acids sequentially in blocks of two carbon atoms producing acetyl CoA

Answer 69

``` peroxisomes are essential for catalyzing the initial reactions required to make plasmalogens, which are the most abundent class of phospholipids in myelin, the membrane sheath wrapped around neuronal axons. -plasmalogen deficiency results in serious abnormalities in the myelination of nerve cells, which is why many peroxisomal disorders lead to neurological disease ```

Answer 70

-peroxisome matrix and membrane proteins are synthesized in the cytosol and imported into perixisomes post-translationally via specific protein translocators

Answer 71

1) defective peroxisomal protein import (peroxisomal biogenesis disorders) - dramatic loss of peroxisome function - partially or complete empty peroxisomes (i.e. lacking peroxisomal enzymes) or a complete lack of peroxisomes In Zellweger syndrome, peroxisomal enzymes are synthesized normally in the cytosol, but a defect in their import leads to "empty" peroxisomes. These patients suffer severe abnormalities in the brain, liver, kidneys, and die soon after birth 2) single-protein defects - less severe phenotype - defect in synthesis, important or function of one specific peroxisomal enzyme - results in partially functional peroxisomes In X-linked adrenoleukodystrophy (ALD), peroxisomes lack a membrane protein required for degradation of very long chain fatty acids. Build up of these fatty acids leads to the demyelination of neurons and dysfunction of the nervous system.

Answer 72

1) Allogenic hematopoietic stem cell transplantation (HCT)- high morbidity due to complications; compatible donor cells not always available; must be performed at an early stage of brain lesions 2) Gene therapy- recent success in two boys Hematopoietic stem cells collected from two 7 year old ALD patients with no compatible donor -HSCs corrected ex vivo using HIV-derived leniviral vector expressing wildtype ALD protein -chemotherapy used to eraticate bone marrow, then patients' own corrected HSCs were infused -progeny of HSCs distributed throughout the body including brain microglia responsible for maintaining myelin Follow up: 10-11% of hematopoietic cell lineages

Answer 73

``` protein synthesis protein modification protein quality control lipid synthesis synthesis of steroid hormones Detoxification of lipid soluble drugs Ca2+ storage ```

Answer 74

- by definition, the rough ER has bound ribosomes that are actively involved in protein synthesis - serves as entry point for proteins destined for other organelles or the plasma membrane as well as the ER itself Protein synthesis in the ER is responsible for producing: - proteins destined for the lumens or membranes of ER, Golgi, lysosomes, or endosomes - proteins destined for secretion to the cell exterior Once inside the ER or embedded in the ER membrane, individual proteins do not return to the cytosol. They may go to the ER or other organelles In contrast, proteins synthesized in the cytosol as cytosolic proteins or may be transported to mitochondria or peroxisomes if they contain the appropriate signal

Answer 75

-import of proteins in ER occurs co-translationally, the driving force for this transport is provided by the protein synthesis process itself - begins in the cytosol when the ribosomal subunits bind to the mRNA - as newly synthesized polypeptide emerges from the ribosome and ER targeting signal sequence within the polypeptide directs the ribosome to the ER membrane where protein synthesis continues with growing polypeptide entering the ER membrane or lumen - a single mRNA molecule can have many ribosomes bound forming a polyribosome; the growing polypeptide chains link the polyribosome to the ER membrane - if no ER targeting signal sequence is present, synthesis continues in the cytosol on free polyribosomes. Membrane-bound and free ribosomes are structurally and functionally identical and differ only in the protein they are making at a given time

Answer 76

- two components guide the ER signal sequence to the ER membrane: a signal-recognition particle (SRP) in the cytosol that binds to the ER signal sequence and an SRP receptor or docking protein embedded in the ER membrane - SRP binds to the ER signal sequence as it emerges from the ribsome thereby slowing protein synthesis - the ribosome-SRP complex binds to the ER membrane with the SRP binding to the SRP receptor and the ribosome binding to the translocation channel - binding of the SRP to its receptor causes the SRP to release the signal sequence thereby allowing protein synthesis to resume with the polypeptide being threaded through the translocation channel - SRP is recycled back to the cytosol

Answer 77

- for soluble proteins, ER signal sequences are almost always at the N-terminus - once the ribosome-SRP complex has bound the the ER membrane, the N-terminal signal sequence opens the translocation channel and remains bound to it - as protein synthesis continues the rest of the protein is threaded through the chennel as a large loop - during translocation, the signal sequence is cleaved off by signal peptidase on the luminal side of the ER membrane, releasing the newly synthesized protein into the ER lumen and the signal peptide is degraded Soluble proteins transported into the ER lumen include ER resident proteins- BiP-chaperone protein, nucleases, proteases, horomones, fibronectin, laminin

Answer 78

- integral membrane proteins have membrane spanning domains that may cross the lipid bilayer one or more times - the ER targeting signal sequence for these types of proteins may be located at the N-terminal or internally - when integral membrane proteins are imported into the ER, some parts of the polypeptide chain are transported across the membrane, while the membrane spanning domains are released laterally from the translocation channel to become embedded in the ER membrane. The amino acid sequence of the membrane spanning domains directs their lateral release from the translocation channel while protein synthesis is proceeding -integral membrane proteins imported into the ER will always be inserted into the ER membrane in only one orientation (topology) as dictated by their sequence, to ensure that the appropriate domains will always be localized to the correct side of the membrane

Answer 79

- most proteins imported into the ER lumen or ER membrane are converted to glycoproteins by the covalent addition of sugars - N-linked glycosylation is the most common type, 90%: - a preformed oligosaccharide of 14 sugars is covalently attached to asparagine residues during translocation (co-translationally) - oligosaccharyl transferase located in the ER lumen, transfers the oligosaccharide block from dolichol, a specialized lipid in the ER membrane, to the polypeptide as it emerges from the ribosome - called "N-linked" because they are attached to the NH2 group of asparagines that are found within a specific amino acid sequence - initial N-linked oligosaccharides are modified by sugar removals and additions carried out by additional enzymes in both the ER and the Golgi apparatus as the protein moves through these organelles

Answer 80

-collagen molecules are hydroxylated on prolines and lysines to allow interchain hydrogen bonds to help stabilize the triple stranded heliz of collagen molecules

Answer 81

- after translocation into the ER, newly synthesized polypeptides must be folded correctly; chaperone proteins, located in the ER, help with this process. - Disulfide bonds between cysteine side chains are formed in the ER by the enzyme protein disulfide isomerase, which resides in ER lumen - the disulfide bonds help stablize the proteins and contribute to their proper folding - disulfide bonds do not form in the cytosol because of its reducing environment

Answer 82

- multi-subunit proteins must be assembled with partner polypeptides to form the mature protein within the ER.. - the acetylcholine receptor consists of 5 separate polypeptides which must be assembled in the ER prior to transport to the cell surface

Answer 83

- a few proteins that enter the ER contain an ER retention signal of four amino acids (KDEL) at their C-termini that "retains" them in the ER (or returns them to the ER when they leave for the Golgi); these are known as ER resident proteins - i.e. protein disulfide isomerase, signal peptidase

Answer 84

- exit from the ER is highly selective in that proteins that fold incorrecttly or fail to assembly properly are actively retained in the ER by binding to chaperone proteins that reside in the ER - this holds the proteins in the ER until proper holding and assembly occur - proteins that remain misfolded or unassembled will eventually be degraded via proteasomes

Answer 85

- membrane factory of the cell; it produces nearly all of the lipids required for making new cell membranes including phospholipids and cholesterol. - it makes all of the lipids for organelles of the secretory pathway and plasma membrane and most of the lipids for the mitochondria and peroxisomes - the cytosolic half of the ER bilayer contains enzyms necessary for phospholipid synthesis, so new phospholipids are added only to the cytosolic half of the bilayer - some newly synthesized phospholipids are transferred to the luminal side of the membrane bilayer to maintain symmetric growth of the membrane; this reaction is catalyzed by phospholipid-specific flippases - newly synthesized lipids are delivered to Golgi, lysosomes, endosomes, and plasma membrane via vesicles during vesicular transport - transfer of newly synthesized lipids to peroxisomes and mitochondria, which do not participate in vesicular transport, requires cytosolic lipid carrier proteins

Answer 86

- because the smooth ER is continuous with the rough ER, most smooth ER functions are not exclusive to the smooth ER - the amount of smooth ER is very small in most cell types - however, certain specialized cells have large amounts of smooth ER to carry out specific functions

Answer 87

steroid hormone synthesizing cells such as testosterone secreting Leydig cells in the testes contain lots of smooth ER to carry out steroid hormone synthesis

Answer 88

- liver cells (hepatocytes) have more smooth ER than most cells because of their involvement in lipid metabolism - liver cells also detoxify lipid soluble drugs and other harmful components, such as ingested alcohol. Large quantities of some drugs can induce synthesis of detoxification enzymes (cytochrome P450) in the liver causing the surface area of the smooth ER to double in just a few days. Once the drug is removed from the system, the smooth ER will reduce back to its original size

Answer 89

- release of Ca2+ into the cytosol from the ER, and its subsequent reuptake, mediate many rapid responses to extracellular signals - in muscle cells the specialized smooth ER called the sarcoplasmic reticulum releases Ca2+ into the cytosol to induce muscle contraction

Answer 90

- most proteins that enter the ER will be transported to the Golgi apparatus and from there to other organelles via transport vesicles - these vesicles transport proteins and lipids outward from the ER to the plasma membrane as well as inward from the plasma membrane to lysosomes

Answer 91

secretory pathway (outward)- proteins synthesized in the ER are delivered to the cell surface or lysosomes via the Golgi apparatus endocytic pathway (inward)- responsible for the ingestion and degradation of extracellular molecules; proteins are taken up at the plasma membrane and delivered to lysosomes via endosomes - Cells contain many distinct membrane bounded compartments that continually exchange components through the budding and fusion of transport vesicles. - proteins associated with transport vesicle membrane guide vesicle budding, targeting and fusion, and thereby control the specificity of vesicular transport. Each transport vesicle that buds off from an organelle takes with it only those proteins that are appropriate for its target organelle.. And the vesicles fuses only with the appropriate target organelle

Answer 92

- most transport vesicles have a specific protein coat on their cytosolic surface - vesicles bud from protein coated regions of membranes to form coated vesicles. The protein coats are discarded from the vesicles prior to fusion with the target membrane - the coat shapes the membrane into a bud and helps to capture molecules for transport - the best characterized vesicles are the clathrin coated vesicles which bud from the Golgi apparatus in the outward secretory pathway and from the plasma membrane in the inward endocytic pathway

Answer 93

- clathrin is the major coat protein of clathrin-coated vesicles - it assembles on the cytosolic surface of the trans Golgi membrane or the plasma membrane forming a basketlike network consisting of hexagons and pentagons. The assembly of such a basket is thought to drive the formation of a clathrin-coated bud by introducing curvature into the membrane - adaptins are the second major coat protein in clathrin-coated vesicles. They bind the clathrin coat to the vesicle membrane and help select cargo molecules for transport via its interaction with both clathrin and various transmembrane cargo receptors. Although clathrin is the same in all clathrin-coated vesicles, the adaptins vary depending on the nature of the cargo receptors to which they must bind. - dynamin- a small monomeric GTP binding protein, assembles as a ring around the neck of each bud. Hydrolysis of the bound GTP causes the ring to constrict, pinching off the vesicle from the membrane. After the vesicle pinches off, the clathrin coat is quickly removed by disassembly

Answer 94

- after budding from a membrane, vesicles are actively transported to their their membranes by motor proteins that move along microtubules - transport vesicles must be selective in the target membrane with which they fuse. Transport vesicles display surface markers that identify its origin and cargo, and these markers must be recognized by receptors on the target membranes The recognition step is controllwd by Rabs, tethering proteins and SNAREs - Rabs are a very large subfamily of monomeric GTPases that serve as the molecular markers identifying each membrane type; they are recognized by tethering proteins on target membranes - tethering proteins capture vesicles via their interaction Rabs - complementary SNAREs (vSNAREs on vesicles and t-SNAREs on target membranes) interact to dock vesicles

Answer 95

once a transport vesicle has recognized its target membrane and docked, it must fuse with the membrane to release its cargo, which includes the vesicle membrane which becomes part of the target membrane - docking and fusion do not always occur concurrently - docking involves interactions between proteins in the vesicle and target membranes - fusion requires a much closer approach between the lipid bilayers which is energetically unfavorable because water must be displaced

Answer 96

-exocytosis is the process by which newly made proteins and lipids are delivered from the ER, via the Golgi apparatus, to the cell surface and the cell exterior by transport vesicles that fuse with the plasma membrane

Answer 97

- sorting and dispatching station for proteins and lipids made in ER - modification of N-linked oligosaccharide chains on glycoproteins made in ER - synthesis of O-linked oligosaccharides on proteins and lipids made in the ER - synthesis of glycosaminoglycan chains on core proteins of proteoglycans

Answer 98

-flattened membrane-bounded cisternae stacked together -two distinct faces in each golgi stack cis face (entry face), adjacent to the ER trans face (exit face), pointing toward the plasma membrane -network of interconnected tubular and cisternal structures form the cis and trans Golgi networks at either end of the stack -usually located near the cell nucleus -number of Golgi stacks per cell varies from one to many depending on cell type

Answer 99

transport vesicles containing proteins and lipids enter the cis Golgi network from the ER and exit from the trans Golgi network to the cell surface or other organelle. Protein sorting occurs on both sides of the Golgi appartus: -cis Golgi network sorts proteins that need to be returned to the ER from those that will continue through the Golgi; proteins with an ER retension signal may exit the ER, but they are returned to the ER when the signal binds to a specific receptor in cis Golgi network transport vesicles that return to the ER- bidirectional traffic between ER and Golgi -trans Golgi network sorts proteins destined for lysosomes or regulated secretion from those that will continue to the plasma membrane via the default pathway

Answer 100

golgi are involved in the synthesis and modification of oligosaccharides on glycoproteins - this processing occurs in an organized sequence in the Golgi stack with each cisterna (cis, medial, trans) containing its own set of processing enzymes. - processing therefore occurs in a spatial as well as biochemical sequence: enzymes catalyzing early processing events are localized toward the cis side of the stack, while enzymes catalyzing late processing events are located toward the trans side

Answer 101

=the modification of N-linked oligosaccharides that began in the ER is continued in the Golgi apparatus - an ordered series of sugar removals and additions is carried out by specific glycosidases and glycosyl transferases as the protein moves through the golgi stack. - each step in the processing pathway is dependent on completion of the previous step - each enzyme will only recognize the product of the previous reaction as substrate - the degree of modification can vary to produce diverse N-linked oligosaccharides which have been divided into 3 major classes: high mannose, complex, and hybrid

Answer 102

- O-linked glycosylation is the covalent attachment of oligosaccharides to the OH groups of serine of threonine residues in proteins, hence the name "O-linked". - Synthesis of O-linked oligosaccharides in the Golgi differes from that of N-linked oligosaccharides in the ER in a couple of ways: - sugars are added to proteins one at a time - sugars are added post-translationally, rather than co-translationally, via the serial action of specific glycosyltransferases located in the Golgi membrane

Answer 103

- more than 95% carbohydrate with a small core protein - always consists of glycosaminoglycan chains, linear polymers of a repeating disaccharide unit - contain a high density of negative charges = attract water and form gels - 6 classes that differ in specific functions and locations - proteoglycans come in a variety of size with varying numbers and types of glycosaminoglycans attached- attached to a core protein via a standard linkage to a serine residue - function as lubricants and gels that spring back when compressed, like synovial fluid in joints and vitreous humor in eye

Answer 104

- the core protein is synthesized in the ER and then transported to the Golgi - in the Golgi, a series of different glycosyltransferases act sequentially to build the 4 sugar linker region on a serine of the core protein - then repeated action of two specific glycosyltransferases adds the sugars of the repeating disaccharide unit one at a time to build the glycosaminoglycan - additional enzymes modify the sugars (ex. sulfation) as the chain is enlongeing Three types of glycosylation on proteoglycans: 1) N-linked oligosaccharides 2) O-linked oligosaccharides 3) O-linked glycosaminoglycans

Answer 105

- called the default pathway because all proteins passing through the Golgi will enter this pathway unless directed elsewhere by a specific signal - vesicles bud from the trans Golgi network and fuse with plasma membrane - operates continually in all cells and supplies the plasma membrane with newly synthesized lipids and proteins - responsible for constitutive secretion of proteins to the cell exterior

Answer 106

- found in specialized secretory cells such as those that secrete large quantities of hormones or digestive enzymes - proteins are diverted into secretory vesicles which bud off from the trans Golgi network and accumulate near the plasma membrane - vesicle fuse with the plasma membrane to release their contents only in response to an extracellular signal

Answer 107

-cells take up fluid, macromolecules and particulates at the cell surface and route them to lysosomes via endosomes, the ingested material is digested in the lysosomes pinocytosis- ingested of fluid and small molecules via small vesicles, continues continually Phagocytosis-ingestion of large particles via large vesicles called phagosomes; require receptor activation at the cell surface

Answer 108

- macrophages and neutrophils act as phagocytes - requires activated receptors send signals to the cell interior to trigger process - once induced the phagocytic cell extends projections of its plasma membrane to engulf the microorganism and form a phagosome - phagosomes then fuse with lysosomes and the ingested material is degraded - they also get rid of senescent and damaged cells and debris

Answer 109

- carried out by clathrin-coated pits and vesicles - clathrin coated pits quickly invaginate into the cell and pinch off to form clathrin-coated vesicles - within seconds of forming, these vesicles shed their coat and fuse with early endosomes - the extracellular fluid trapped in the clathrin-coated puts is also internalized and delived to early endodomes

Answer 110

- pinocytosis provides the cell with an efficient pathway for taking up specific macromolecules from the extracellular fluid in a process called receptor-mediated endocytosis - the macromolecule binds to a specific cell receptor in the plasma membrane which then accumulates in coated pits and is internalized in clathrin coated vesicles - this processes increases the effciency of internalization more than 1000-fold compared to ordinary pinocytosis, so even minor components of the extracellular fluid can be taken up efficiently

Answer 111

- most blood cholesterol is transported as low density lipoprotein particles - when cholesterol is needed for membrane synthesis, cells made LDL receptors and insert them in the plasma membrane - LDL receptors associate with newly forming clathrin-coated pits and are internalized, along with any bound LDL particles, in clathrin coated vesicles - vesicles shed their clathrin coats and fuse with early endosomes whose acidic environment causes the dissociation of LDL from its receptor - LDL is transported to lysosomes and hydrolyzed to free cholesterol which is then released into the cytosol for membrane synthesis - LDL receptor is recycled back to the plasma membrane from the early endosome

Answer 112

- familial hypercholesterolemia, LDL receptors are defective, so cholesterol uptake is blocked and it accumulates in the blood - this leads to the formation of plaques in blood vessel walls that can block blood flow and lead to heart attacks - iron is also taken into cells in this way - viruses such as influenza and HIV use this pathway of entry

Answer 113

Early endosomes are located near the plasma membrane - act as the main sorting station in the endocytic pathway - endocytosed materials appear here within a minute of uptake - acidic environment (ph~6) allows some receptors to release their ligands; released ligands are usually transported to lysosomes for degredation Late endosomes are located near the nucleus - endocytosed materials arrive here from early endosomes 5 to 15 minutes after uptake - materials are ultimately transported to lysosomes via either transport vesicles or the gradual conversion of the late endosome into a lysosome by import of lysosomal proteins

Answer 114

1) recycling- return to the plasma membrane (LDL receptor) 2) degradation- from early endosome to lysosome, leads to receptor down-regulation 3) transcytosis- return to a different plasma membrane domain in polarized cells: transportation of antibodies from the bloodstream to mothers milk, receptor antibody complexes endocytosed at the basolateral membrane are delivered to the apical membrane

Answer 115

- principle sites of intracellular digestion found in all eukaryotic cells - contain ~40 acid hydrolases which participate in the controlled intracellular digestion of extracellular materials and worn out organelles - membranes contain an ATP-driven proton pump that maintains the lumen at an acidic pH of 5.0 which is optimal for lysosomal hydrolases; acid dependence of hydrolases protects the contents of the cytosol from degredation if the enzymes leaked - membranes contain transport proteins that transport digestion products such as amino acids, sugars and nucleotides to cytosol - membrane proteins are heavily glycosylated to help protect them from lysosomal proteases

Answer 116

- lysosomal enzymes and membrane proteins are synthesized in the ER and transported through the Golgi apparatus to the trans Golgi network. Transport vesicles budding from the trans Golgi network deliver lysosomal proteins to lysosomes via endosomes - while in the ER and cis Golgi network, lysosomal hydrolases are tagged with mannose 6-phosphate (M6P) marker that is recognized by the M6P receptor in the trans Golgi network. This tagging allows the hydrolases to be recognized and packaged into specific transport vesicles in the trans Golgi network that will deliver their contents to lysosomes via endosomes

Answer 117

endocytosis-endocytic vesicles which deliver their contents to lysosomes via early and late endosomes. phagosomes-uptake of extracellular particles in phagosomes which fuse with late endosomes/lysosomes autophagy- digestion of obsolete cell parts; a double membrane surrounds an organelle forming an autophagosome which then fuses with a late endosome/lysosome (removal of expanded smooth ER in liver)

Answer 118

Mucopolysaccharidoses- genetic diseases caused by defects in the enzyme required for degradation of glycosaminoglycans, so they build up in the blood, cell death. Patients normal at birth, but show progressive decline in physical and/or mental function Oligosaccharides- genetic diseases with defects in lyssosomal hydrolases required for degradation of oligosaccharides Inclusion-cell disease- rare lysosomal storage disease in which almost all of the hydrolytic enzymes are missing from lysosomes - the defect is missing the M6P marker - the hydrolases cannot be sorted and are secreted instead

Answer 119

Cell cycle: G1- gap before DNA synthesis (2N DNA/cell) S- DNA synthesis (gradually increasing DNA/cell) G2- gap after DNA synthesis (4N DNA/cell) M- mitosis (4N DNA/cell until cytokinesis)

Answer 120

- checkpoints are times when the cell carefully moniters specific activities before proceeding to the next cell cycle stage - G1/S border (Enter S or start)- trigger DNA replication machinery and replicate DNA - G2/M border (Enter M)-trigger mitosis machinery, assemble mitotic spindle Metaphase/Anaphase transition in M (Exit M)- trigger anaphase and proceed to cytokinesis leads to complete cell division

Answer 121

catalytic subunt + regulatory subunit (cyclin) = complete CDK - different combinations are needed at different points of the cycle - some specific proteins like p21 can bind to them and inhibit them so the cell cycle is blocked

Answer 122

- typical resting phase - general biosynthesis (growth/maintenance) - external signals and internal state combine to make decision to remain in G1 (G0) or divide (proceed to S): external signals: receptor activation internal signals: size, DNA integrity

Answer 123

- histone synthesis - synthesis of enzymes required for DNA replication - replication of DNA from multiple Replication Origins - removal of replication licensing factors from origin recognition complex, prevents re-replication because you only want one copy of each - also duplication of centrioles (but no centrosomes until M phase)

Answer 124

- continued synthesis of proteins required for mitosis and cytokinesis, including the cyclin for the cdk that regulates entry into M phase - DNA repair checkpoint activity via p53 - addition of cohesins link sister chromatids

Answer 125

- still have the nuclear membrane - chromosomes condense in parallel with phosphylation of histone H1 and addition of condensin protein - spindle forms (duplicated centrosomes separate)- kinesin motors aid in elongation - kinetochores assemble

Answer 126

- nuclear envelop breaks down (lamin intermediate filament by mitotic cdk) - spindle invades nucleus - kinetochores capture microtubules - leads to bipolar attachment of chromosomes equal tension from both spindle poles and alignment of chromosomes on the metaphase plate - unattached kinetochores cause a checkpoint and prevent transition to anaphase

Answer 127

- balanced forces prevent collapse of the spindle - tension on kinetochore fibers pull inward, balanced by an outward force from overlapping polar microtubules - unattached microtubules are astral microtubules

Answer 128

-checkpoint controlled by kinase activity: tension on kinetochores inhibits a kinase, which allows the activitiy of a phosphatase to dephosphorylate the mitotic cdk, which shuts off kinase activity - phosphatase also activates the anaphase promoting complex (APC) which triggers destruction of the cyclin subunit and cohesins. - Chromatids separate and move to opposite poles (Anaphase) - tension on the kinetochores activates the APC - APC activity and cohesin degradation trigger anaphase

Answer 129

Anaphase A-Chromosome to pole:chromosomes are pulled poleward, shortening of the kinetochore microtubules which forces generated at kinetochores to move daughter chromosomes toward their spindle pole Anaphase B Pole-pole separation: the poles themselves move apart a sliding force is generated between polar microtubules from opposite poles to push them apart, a pulling force acts directly on the poles to move them apart -there is microtubules growth at plus end of polar microtubules

Answer 130

- reformation of the nucleus - phosphatase activity reverses the effects of cdk during anaphase and telophase - spindle begins to disassemble, nucleus reassembles - preparation for cytokinesis (usually) - assembly of actin and myosin II at right angle to the spindle

Answer 131

- a contractile ring of antiparallel microfilaments associated with the cell membrane and non-muscle myosin II, similar to a belt junction constricts the cell - the orientation of the mitotic apparatus determines the position of the contractile ring - perpendicular to the spindle, in the same plane as the metaphase plate

Answer 132

Not always linked - cells lose adhesion and round up during mitosis and cytokinesis - cells that fail to complete cytokinesis may become binucleate - cells that fail to complete mitosis may become polyploid - many cells blocked in mitosis undergo apoptosis

Answer 133

- drugs that disrupt microtubule dynamic instability (such as vincristine and taxol) block progression through mitosis - a prolonged block to mitosis in animal cells leads to cell death (apoptosis), so these drugs work as relatively non-selective anti-cancer agents

Answer 134

- signaling requires activation of a receptor, usually through interaction with another molecule called a ligand - ligands may take many forms; receptors are proteins - ligand-receptor interactions are non-covalent (*reversible binding) - ligand binding induces a change in receptor conformation or induces dimerization of the receptor protein - they can be big or small, ie, nucleotide, a.a., dissolved gas, or big like a protein

Answer 135

- receptor may be either a cell surface protein or an intracellular protein - ligand binding changes conformation of receptor and alters its function by changing its enzyme activitiy (if it is an enzymatic receptor) or binding affinity for something else (if it is non-enzymatic) - activated receptor may change the cell after non-covalent bonding - there can also be second messengers

Answer 136

- amplification usually involves second messenger molecules - activation of one receptor by one signaling molecule can make many second messengers and get a response - response occurs faster than without amplification - some second messengers can diffuse through the cytoplasm

Answer 137

- depends on the balance between how fast the molecule is synthesized or released and how fast it is degraded or removed - in most cases the rate of removal is constant and the concentrations are changed by altering the rate of production/secretion - fast degredation = short half-life - show degradation rate = long half life of signaling molecule - long half life = slow changes in concentration

Answer 138

-changing the number of receptors per cell can change the responsiveness of the cell at all ligand concentration cellular responses to a particular signal depend on: - the signaling molecule concentration - the number of available receptors - receptor affinity for the signaling molecule - expression of tissue- or cell-type specific second messenger systems

Answer 139

- changing the response to a constant concentration of ligand 1) prolonged receptor activation may cause changes that desensitize receptors (reduce their response to ligand binding) 2) endocytosis can remove receptors from the cell surface, sometimes receptors are recycled sometimes they are degraded into lysosomes 3) second messengers may change the rate of transcription of the receptor gene, leading to changes in the number of receptors available on the cell surface

Answer 140

1) cellular responses are dependent upon the specific receptor type expressed by that cell and by a balance among many signals reaching the cell 2) cells receive many different signals at the same time. Different ligands may compete for binding to the same receptor, others may bind to different receptors that stimulate the same pathway 3) Some cellular responses are all-or-none responses, such as differentiation from an undifferentiated stem cell into a particular cell type. Others are graded responses that increase with signal strength 4) A steep activation curve can give a threshold effect where little or no response is seen until a certain ligand concentration is reached, and a small change in concentration gives a large change in response, similar to all-or- none

Answer 141

- each cell integrates information from many signals - one signal can bind to different receptors in different cells - the same type of receptor can activate different second messengers in different cells - two signaling molecules may act through the same second messenger, so that a boost in the concentration of one signal makes the cell more sensitive to the other one

Answer 142

- endocrine signals are carried through the blood stream and so have very low concentrations and so must have high affinity receptors - paracrine are within tissue and so have intermediate affinity. - neuronal cells have neurotransmitters which are provided at high concentrations at the synaptic cleft and have low-affinity - it is unknown about contact-dependent

Answer 143

- small diffusible molecules, CO, NO - hydrophobic molecules (steroids and eicosinoids, bind to two recepot types) - hydrophilic molecules (peptides, amino acid derivatives such as glutamate) - sensory signals (taste, smell)

Answer 144

- Nitroglycerine prevents heart attacks because it is metabolized to nitric oxide (NO) which dilates blood vessels by activating guanylate cyclase, increasing cGMP concentration, and relaxing the smooth muscle in arteriole walls - Viagra works in the same pathway by inhibiting cGMP breakdown

Answer 145

- steroids, retinoids, thyroid hormones - usually carried by binding proteins in the blood and have relatively long half lives (hours to days) - they pass directly through cell membranes to bind to cytoplasmic or nuclear receptos of the steroid hormone or nuclear receptor family

Answer 146

- bind surface receptors - inflammatory response and blood clotthing - short half life, usually autocrine signals - synthesis of eicosinoids is inhibited by cortisone and aspirin

Answer 147

- peptides, nucleotide, amino acid - bind to cell surface receptos - short half lives

Answer 148

- electromagnetic radiation (light), mechanical vibration (sound), and a wide range of chemicals (smells and tastes) - cell surface receptors - not actually cell-cell signaling process

Answer 149

- receptors are intracellular, binding to their ligands in the cytoplasm and then transducing signals in the nucleus - modulate the rates of transcription of target genes by binding to their promoters - when the ligand (hormone) binds to the receptor, the DNA binding part of the receptor is exposed and the receptor can bind to all genes with matching promoter sequences - activation of some genes may require another transcription factor

Answer 150

- ion-chanel linked receptor - G protein linked receptor - enzyme linked receptors

Answer 151

- voltage gated - ligand-gated (extracellular ligand) - ligand-gated (intracellular ligand) - stress-gated - some are highly selective- just Ca++, others are broad specificity for either anions or cations - often used for synaptic transmission

Answer 152

- composed mostly of cells - integrity/properties derived from cell-cell and cell-extracellular matrix (ECM) interactions - i,e. cell junctions

Answer 153

- tissue primarily composed of extracellular matrix with few cells - the cells synthesize/remodel and bind the ECM - the properties of the tissue e.g. strength/elasticity is derived from the composition of the ECM

Answer 154

1) tight junction 2) adherens junction 3) desmosome junction 4) gap junction 5) hemidesmosome 6) focal adhesions

Answer 155

- maintain tissue integrity when subjected to mechanical stress (like epithelia and skin epidermis) - achieved by interactions with the actin (microfilament) cytoskeleton or intermediate filament cytoskeleton - either cell-cell or cell-ECM Has 3 basic components: 1) transmembrane glycoprotein 2) complex of linker proteins on cytoplasmic face stablizes link to 3rd component & regulate assembly 3) cytoskeleton without the attachment to the cytoskeleton it would just be pulled straight out of the lipid bilayer

Answer 156

- cadherins (Ca2+)- homophilic interaction - linker proteins - actin micro filaments type of actin-based junction -this provides stability and function of ZA's in development- oriented contractions of the actin filaments to initiate invagination of an epithelial sheet, which can pinch off to form a separate tube of epithelial cells- i.e. formation of neural tube

Answer 157

-type of actin-based junction has - integrins (Ca2+ sensitive), two subunits- alpha/beta heterodimers - linker protines - actin cytoskeleton (stress fibers) Cell-ECM interaction is heterophilic - found in vascular endothelium in areas of turbulent flow and in migrating cells - cancer cell migration and metastasis, immune surveillance and tissue repair

Answer 158

- intermediate filament associated adhering junction - cell-cell - cadherins (Ca2+) (homophilic) - linker proteins - intermediate filaments e.g. Keratin

Answer 159

- intermediate filament associated adhering junction - cell- ECM - integrin alpha6/beta4- attaches to ECM of basal lamina (heterophilic) This is the only integrin associated with intermediate filament network - linker proteins - intermediate filaments

Answer 160

Pemphigus- auto-immune- generate antibodies to cadherins disrupt cell-cell junctions Epidermolysis bullosa simplex-defect in keratin (intermediate filament) assembly (1 in 50,000) Result of either- loss of tissue integrity/blistering

Answer 161

- provide a permeability barrier across epithelial sheets (small intestine, bladder) - allows for regulated transport of nutrients e.g. Glucose through the cells- transcellular transport - Na2+ dependent uptake at the apical membranes and facilitated diffusion at baso-lateral membranes 1) barrier function-can be demonstrated using electron dense tracers 2) tight junctions also maintain cell polarity apical membrane vs basolateral membrane Major proteins of tight junctions: claudin and occludin- strings of transmembrane proteins interact with each other on adjacent cells via homophilic interactions

Answer 162

- provide communication between neighboring cells - most apparent in tissues comprised of electrically excitable cells like cardiac muscle - protein component is transmembrane protein caleld connexin - six connexin molecules associate in the plasma membrane to form a pore called a connexon - connexons on adjacent cells associate to form a gap function

Answer 163

High intracellular Ca2+ or low pH gap junction is CLOSED Low intracellular Ca2+ or high pH gap junction is OPEN

Answer 164

-synthesized by a small number of cells dispersed within the matrix -secreted locally and then assembled -ECM is the major component of connective tissues eg Cartilage/bone/tendons -ECM provides major characteristics of tissue e.g. Tensile strength/elasticity/permeability -ECM is mostly produced by fibroblasts -Some tissues use specialized cells chrondroblasts-cartilage osteoblasts- matrix- calcified- bone

Answer 165

1) Fibrous proteins - collagens and elastin 2) bulky-space filling proteins - proteoglycans 3) cross-linking proteins - fibronectin/laminin

Answer 166

The fibrillar collagens (Type I = 90% of all collagens) Collagen- most abundant protein - 25% of total body protein - many tissues require both tensile strength and elasticity - e.g. blood vessels, skin, lungs - Collagen provides tensile strength and resists stretching -Ehlers-Danlos Syndrome- hyperextensible skin and joints

Answer 167

- synthesized as pro-alpha chain molecule in ER - post translational modifications (hydroxylation/glycosylation of proline and lysines) occur in the Golgi and three pro-alpha chains associate into a triple helix (pro-collagen molecule) - secreted from cell - in extracellular space collagenases slip of the pro-peptides allowing triple helical collage molecules to self-associate into higher order structures, forming fibrils and fibers (e.g. tendons which are very resistant to stretching) - cells may further remodel/order the matrix by attaching to it via integrins on the cell surface and tugging on it

Answer 168

Type IV Collagen cannot form fibrils - pro-peptide is not cleaved- blocks cross-linking and thus fibril formation - forms a mesh and is a major component of basal lamina

Answer 169

- provides the elastic component of skin, lungs and blood vessels - 750 AA extensive cross-linking following secretion via covalent linking of lysine residues - elastic features due primarily to molecule containing a large amount of random coil and turns due to a high proline content-very flexible

Answer 170

- stability of elastic (elastin) fibers requires association with microfibrils of fibrillin - a glycoprotein, which forms a sheath around the elastin fibers (resists stretching) - fibrillin mutations = Marfans Syndrome = Aorta prone to rupture

Answer 171

- space filling - resist compression forces (e.g. cartilage in joints) - permit rapid diffusion-soluble molecules e.g. growth factors - permit cell migration (e.g. during embryogenesis immune cell response to infection

Answer 172

-major component of cartilage/loose connective tissue Glycosaminoglycans (GAG's)-unbranched polysaccharide chains of repeating disaccharides Core protein backbone- covalent link to GAGs via serine residues Can complex further with hyaluronic acid using linker proteins Can range in size: decorin MW 40, 000; aggrecan MW 3,000,000 Numerous sulfate and carboxyl groups (negative charge on GAGs) - > hydrophilic- binds large # H2O molecules - > Hydrated Gel (10% is the proteoglycan) - > Resists compression forces e.g. cartilage in joints

Answer 173

- cross-linker protein - multi-domain glycoprotein - homo-dimer (each chain -225 kDa) - can self-associate into bundles and fibrils - alternative-splice variants (modify function) Contains multiple binding sites: - integrins (Cell adhesions/ focal adhesions) via RGDS sequence in fibronectin - heparin (a GAG) - Type I, II, III collagen (not Type IV) - fibrin (platelet clotting) Important in: loose connective tissue/ blood clotting/ wound repair/ cell migration/ development

Answer 174

- cross-linker protein - three chain polypeptide - binds integrins on cell surface (focal adhesions and hemidesomosomes) - binds Type IV collagen - binds heparin - component of basal lamina (along with type IV collagen and proteoglycans)

Answer 175

-a specialized ECM forming a dense meshwork Composition: 1) Type IV collagen (binds integrins on cells- focal adhesions and hemi-desmosomes) 2) Laminin (also bind integrins on cell surface & cross-links other ECM components 3) Proteoglycans Functions: 1) surrounds and supports muscle cells (Role in DMD) ALso links muscle to tendon 2) Support for epithelial sheets (controls proliferation) 3) Kidney- molecular filter- blocks loss of protein from blood into kidney tubule 4) Guidance pathways- development e.g. neural crest cells -> peripheral nervous system

Answer 176

-Any protein with one or more covalently bound carbohydrate units that do NOT contain a serial repeat (i.e. the carbohydrate is not a glycosaminoglycan) . Typically, but not always, they are mostly protein with a little carbohydrate attached. •mass of carbohydrate varies from 2 to 80% •number of covalently linked carbohydrates varies from 1 to 100s •number of sugar residues in each carbohydrate varies from 1 to 15 •carbohydrate may be covalently bound to t he amino group of Asn (N-linked) or the hydroxyl group of Ser or Thr (O-linked) •structure of the carbohydrates on a single protein can be very different from each other creating extensive microheterogeneity

Answer 177

Any protein with one or more covalently bound glycosaminoglycan chains. Typically, but not always, they are mostly carbohydrate with a very small core protein. * mass of carbohydrate usually ≥95% * core protein is very small

Answer 178

Linear polymer of a repeating disaccharide unit (uronic acid (or galactose)–hexosamine)n. -These chains are typically 100s of sugars long and carry many negative charges on the carboxyl groups of the uronic acids and on sulfate groups which are added to many of the sugars. (Example: heparin)

Answer 179

Monosaccharide A single sugar residue (ex: glucose).\ Disaccharide Two sugars covalently bound together (ex: sucrose, lactose) Oligosaccharide 3-15 sugars covalently bound in a linear or branched chain (ex: ABO blood group antigens) Polysaccharide Long linear or branched polymer of sugars (ex:glycosaminoglycans, glycogen, starch)

Answer 180

Enzymes that cleave glycosidic bonds.

Answer 181

Enzymes that form glycosidic bonds; they transfer a monosaccharide from a nucleotide sugar (i.e. UDP-glucose) to a growing oligosaccharide or polysaccharide.

Answer 182

Enzyme that transfers a pre-formed oligosaccharide from its lipid anchor (dolichol) to an appropriate Asn residue in a polypeptide during N-linked glycosylation in the ER

Answer 183

Most soluble and membrane proteins synthesized in the ER,including those bound for other locations, are glycoproteins. The enzymes that add carbohydrates to proteins are located within the ER and Golgi, so the carbohydrates are only added to portions of proteins that are exposed to the lumens of these organelles. This means that membrane proteins will have carbohydrates on their lumenal sides, which is the same side that will face the extracellular space if the membrane protein is destined for the plasma membrane. This also means that most soluble proteins destined for secretion from the cell will be glycosylated. In fact, most cells have a thick layer of carbohydrate on their surface (MBC5 Fig 10-28aandb), and are surrounded by an extracellular matrix full of glycosylated proteins.

Answer 184

Glycoproteins carry out a wide array of biological functions including: •Structure and support in the extracellular matrix (ex: collagen, fibrin) •Hormones (ex: follicle stimulating hormone, chorionic gonadotropin) •Lubrication and protection (ex: mucins, mucus secretions) •Enzymes (ex: lysosomal hydrolases, proteases) •Immunologic molecules (ex: immunoglobulins, complement) •Cell surface antigens (ex: ABO blood group antigens) •Plasma proteins (ex: blood clotting proteins)

Answer 185

Epithelial surfaces throughout the body are covered with a layer of mucus which provides lubrication to minimize shear forces and provides a protective physical barrier to noxious substances such as gastric acid and bacteria. Mucus is particularly prominent in the respiratory tract, gastrointestinal tract, and genital tract. The most abundant macromolecules in mucus are mucins, which are typically synthesized and secreted by specialized cells within the epithelium. Mucins are viscous glycoproteins composed of ~80% carbohydrate by mass.Note that these are atypical glycoproteins in that they contain much more carbohydrate than protein. The vast majority of this carbohydrate consists of O- linked oligosaccharides of varying structure, although some N-linkedoligosaccharides are also present (see Fig below from J Clin Invest 1991 88:1012). Mucins are rod shaped proteins with a central region enriched in Ser and Thr to allow for the high degree of O-glycosylation. Other regions are enriched in Cys which allows polymerization of the molecules via disulfide bonds. The polymerization and high density of carbohydrate allowthese glycoproteins to generate a hydrated gel and makes them resistant to proteases

Answer 186

The ABO blood group antigens, which consist of spec ific oligosaccharide structures, are very important in transfusion medicine. A blood transfusion with an incompatible blood type can cause death because these blood group antigens are extremely immunogenic. In an incompatible transfusion, the recipient’s antibodies will recognize the red blood cells as foreign and cause rapid intravascular hemolysis, resultingin coagulation, shock, acute renal failure, and death.The A, B and O antigens are oligosaccharide components of O-linked glycoproteins and glycolipidsfound on the suface of red blood cells. They are determined by a single genetic locus, the ABO locus, that encodes a glycosyltransferase responsible for transfering a terminal sugar to a galactose in the O antigen (also called the H antigen; see Fig11.17 below): A allele- encodes a transferase that transfers an N-acetyl galactosamine (GalNAc); codominant withB allele B allele- encodes a transferase that transfers a galactose (Gal); differs from the A allele by only 4 amino acids; codominant with A allele O allele– encodes a non-functional protein due to a single nucleotide deletion that causes a frameshift; recessive The product of the ABO gene locus determines if a sugar will be added to the O antigen and if so, whether it will be GalNAc or Gal.

Answer 187

``` The degradation of glycoproteins and proteoglycans occurs in lysosomes by the sequential action of lysosomal hydrolases (proteases and glycosidases): ``` -endoglycosidases first remove the carbohydrates from the proteins -proteases cleave the protein component into amino acids which can be reused by the cell. -specific glycosidases act on each glycosidic bond in a serial fashion but in reverse order to that in which they were added (last on, first off); this dismantles the oligosaccharides and glycosaminoglycans into their component monosaccharides which can be reused by the cell. -additional enzymes are required to remove other chemical groups from the sugars such as sulfates and acetyl groups. Defects in the lysosomal hydrolases involved in the breakdown of proteoglycans and glycoproteins lead to lysosomal storage diseases. The mucopolysaccharidoses are caused by defects in enzymes required for the degradation of glycosaminoglycans, while the oligosaccharidoses are caused by defects in enzymes required for the degradation of oligosaccharides.

Answer 188

- protein kinases add phosphates to regulate target proteins - phosphates may be added to serine, threonine, or tyrosine residues in proteins - phosphorylation can change conformation, activity or binding affinity of the protein - protein phosphatases remove phosphates to reverse the regulation

Answer 189

- G proteins non-cavently bind GTP - G-proteins are slow GTPases that work as molecular ON/OFF switches - protein confirmation changes when GTP is hydrolyzed - the GTP-bound conformation is the ON position - hydrolysis of GTP turns the switch OFF - in the ON position, G-proteins bind to other enzymes and modify their activity

Answer 190

- trimeric G proteins have alpha, beta, and gamma subunits - all known trimeric G proteins are associated with cell surface receptor signaling - some monomeric or small G-proteins are receptor-linked (Ras family), others are important in other types of cellular processes such as vesicle sorting and fusion (Rab family) and control of the actin cytoskeleton (Rac and Rho families)

Answer 191

1) Receptors are seven pass transmembrane proteins that bind extracellular ligands 2) Ligand binding stimulates interaction with trimeric G-protein and exchange of GTP for GDP on alpha subunit 3) GTP binding causes dissociation of trimeric complex into two active complexes, both of which modulate the function of other proteins 4) Activated subunits are linked to membrane, but can diffuse laterally and bind to targets 5) Binding activates the target. Targets include enzymes and channels. Beta/gamma or alpha 6) Beta/gamma subunits dissociate from target and rebind with alpha, and GTP is hydrolyzed to GDP on alpha to stop the signal

Answer 192

1) The Gs alpha subunit activates adenylate cyclase 2) The activated cyclae makes cAMP faster, cAMP concentrations increase 3) cAMP diffuses through the cytoplasm and activates PKA, which phosphoylates a specific target amino acid (a serine or threonine) on its substrate protein. PKA is an abbreviation for Protein Kinase A 4) Virtually all cells have PKA, some cells have cAMP gated ion channels as well

Answer 193

1) PKA is inactive when regulatory subunits are bound 2) Each regulatory subunit has two cAMP binding sites 3) When cAMP is bound to the regulatory subunit, the catalytic subunits are released in an active form Example, adrenalin stimulates glycogen breakdown in a muscle cell, kinase cascades, or used in gene regulation phosphorylation of TF CREB

Answer 194

- inhibition of adenylate cyclase leads to reductions of in cAMP concentration - activation of a Gi receptor can reverse the effects of activation of a Gs receptor

Answer 195

1) Activation of phosphololipase C generates IP3 and DAG. DAG diffuses along the membrane and activates PKC 2) IP3 binds to gated channels in the ER and releases Ca2+ 3) Ca2+ stimulates the activated PKC (as well as CAM kinases)

Answer 196

- calmodulin is a protein that changes conformation drametically when Ca2+ ions bind to its four calcium binding sites - in the presence of Ca2+ calmodulin activates serine/ threonine-specific CAM kinases such as myosin light chain kinase

Answer 197

1) Activation of phospholipase C generates IP3 and DAG. DAG diffuses along the membrane and activates PKC 2) IP3 binds to gated channels in the ER and releases Ca2+ 3) Ca2+ stimulates the activated PKC as well as CAM kinases

Answer 198

- binding of a ligand (usually a growth factor) to a receptor tyrosine kinase induced receptor dimerization. Receptor dimerization results in transphoporylation - when other proteins in the cell bind to the phoshotyrosines, their conformation changes and they pass the signal on. Protein domains that bind phosphotyrosines are called SH2 domains

Answer 199

- binding stimulates phospholipase C-gamma, activating IP3 and DAG pathways - SH2 domains of SH2-SH3 adaptor proteins bind and activate the Ras monomeric G protein pathway - monomeric G proteins are activated by GTP Exchange Factors and turned off the GTPase Activating Proteins (GAPs)

Answer 200

-Ras with GTP bound activates the MAP kinase cascaade- MAP kinase kinase kinase phosphorlyates MAP kinase kinase phosphorylates MAP kinase, causes changes in protein activity and in gene expression

Answer 201

1) Receptor lacks kinase activity but ligand binding causes receptor dimerization and activates a separate protein tyrosine kinase associated with the receptor protein. Activation causes kinase trans-phosphorylation and receptor phosphorylation. Other proteins with SH2 groups bind the phosphotyrosines 2) The family of cytoplasmic, non-receptor tyrosine kinases is large, and mutated forms of nearly all of these have been linked with tumor formation in humans JAK-STAT signaling activates gene transcription