BIOL 3450 Exam 4

class II MHC pathway present antigens delivered to endocytic pathway

1. acquisition of antigen- antigen is acquired by phagocytosis or receptor mediated endocytosis [B cells which arent phagocytic can also acquire antigen by receptor mediated endocytosis using antigen specific B cell receptors] [also autophagy] 2. targeting antigen for destruction- combined action of low pH and reducing environment that brings about protein folding in endocytic pathway preps antigens for proteolysis 3. proteolysis- lysosomal proteases (cathepsins) 4. encounter of peptides w/ class II molecules- peptides generated by proteolysis reside in same space as class II molecules themselves so no delivery 5. binding of peptide to class II molecules- CLIP segment is firmly lodged in class II peptide binding cleft so its resistant to proteolytic attacks [CLIP is removed through interaction w/ chaperone DM so now it can bind peptides that are abundantly present in endocytic pathway] 6. display of class II MHC peptide complexes at cell surface- complexes are localized in late endosome compartments [tubulation along tracks of microtubules allows these compartments to elongate and deliver complexes to surface by membrane fusion]

class I MHC pathway presents cytosolic antigens

1. acquisition of antigen- mistakes in protein synthesis affect both host cells own proteins and viral proteins [such error containing proteins have to be rapidly removed] [rate of cytosolic proteolysis must be matched to rate at which mistakes in protein synthesis and folding occur] [these proteins are source of antigen peptides destined for presentation by class I MHC molecules] 2. targeting antigen for destruction- ubiquitin conjugation system 3. proteolysis- ubiquitinated proteins are destroyed by proteasomal proteolysis [3 catalytically active subunits of proteasome can be replaced by immune specific subunits to generate immunoproteasome (the output of which is matched to requirements for peptide binding by class I MHC molecules)] 4. delivery of peptides to class I molecules- class I MHC molecules are in lumen of ER so peptides must cross ER membrane to bind [TAP complex binds to cytoplasmic face and in cycle that includes ATP binding and hydrolysis peptides are translocated to ER] 5. binding of peptides to class I molecules- peptide loading complex has 2 chaperones which interacts w/ TAP and class I MHC molecule [once peptide loading occurs conformational change releases loaded MHC from peptide loading complex] [this ensures only peptide loaded molecules are displayed at cell surface] 6. display of class I MHC peptide complexes at cell surface- released from peptide loading complex and transfer from Golgi to cell surface

CD4 T cells are divided into 3 major classes based on their cytokine production and expression of surface markers

~(1) provide assistance to B cells and guide differentiation into plasma cells that secrete high affinity antibodies (2) secreting cytokines that contribute to establishment of inflammatory environment [can produce IFN-γ, TNF, IL-4 and IL-10] [inflammatory T cells can activate macrophages and stimulate inflammatory response] (3) regulatory T cells that attenuate immune response by exerting suppressive effect on cytokine production by other T cells [restrain activity of self reactive T cells and important to maintaining tolerance] ~chemokines tell leukocytes where to go (when tissue damage occurs fibroblasts produce chemokine IL-8 that attracts neutrophils to site of damage) [chemokine binding allows navigation of leukocytes from where they are generated in bone marrow into bloodstream for transport to target destination] [homeostatic chemokines direct lymphocytes to leave circulation and take up residence in lymph nodes whereas inflammatory chemokines recruit lymphocytes to sites of inflammation]

recombination and meiosis-specific cohesion subunit are necessary for specialized chromosome segregation in meiosis I

~2 physical links b/w homologous chromosomes resist pulling force of spindle until anaphase- (1) crossing over b/w chromatids one from each pair of homologous chromosomes (2) cohesions distal to crossover point ~at onset of anaphase I cohesions b/w chromosome arms are cleaved by separase [cohesin subunit Rec8 is necessary for stepwise loss of cohesins] [cohesin removal differs for meiosis I b/c when Rec8 replaces Scc1 in cohesin complex the complex doesnt dissociate in prophase when its phosphorylated- it can only be removed from chromatin via action of separase] ~in mitosis and meiosis II sister kinetochores attach to spindle microtubules emanating from opposite spindle poles (bi oriented) [but in meiosis I they are co oriented] ~monopolin complex associates w/ kinetochores during meiosis I and links sister kinetochores to favor attachment to microtubules from same spindle poles [Rec8 cohesions impose rigid kinetochore structure restricting movement of sister kinetochores and favoring attachment to microtubules from same spindle pole] [correct attachment in meiosis I is also mediated by tension- chiasmata generated by recombination prevent them from being pulled to poles] ~DNA replication is prevented b/w the 2 meiotic divisions b/c of partial drop in CDK activity- sufficient to promote disassembly of meoisis I spindle but insufficient to promote MCM helicase loading

production of high affinity antibodies requires collaboration b/w B and T cells

~B cells that require antigen via B cell receptors internalize immune complex and process it for presentation via class II MHC pathway [convert BCR acquired antigen into call for T cell help in form of class II MHC-peptide complex] ~T cell identifies via TCR an antigen experienced B cell by means of class II MHC-peptide complexes displayed [B cell also displays co stimulatory molecules and receptors for cytokines produced by activated T cells] [B cells then proliferate and differentiate into plasma cells or memory B cells] [first wave of antibodies produced is alway IgM but class switching and somatic hypermutation can cause other antibodies to be produced (but requires persistence of antigen or repeated exposure to antigen)]

during adaptive response B cells switch from making membrane bound Ig to making secreted Ig

~BCR is membrane bound Ig but neutralization of antigen requires that these products be released from B cell [domain in heavy chain locus has 2 polyadenylation sites- if downstream site is chosen then processing yields mRNA that encodes membrane bound form of BCR] [if upstream site is chosen then secreted form of heavy chain is processed] ~terminally differentiated B cells (called plasma cells) are devoted almost exclusively to synthesis of secreted antibodies ~upstream of each cluster of exons (for the different isotypes) are repetitive sequences (switch sites) that are recombination prone so B cells can class swithc from IgM to one of the other isotypes located downstream and the intervening DNA is deleted [class switch generates antibodies w/ different constant regions but identical antigenic specificity]

mitochondria play central role in regulation of apoptosis in vertebrate cells

~Bcl-2 (which resides in outer mitochondrial membrane) functions to maintain low permeability of that membrane preventing cytochrome c and other proteins localized in intermembrane space from diffusing to cytosol and activating apoptotic caspases ~each Bcl-2 protein has either a pro-survival or pro-apoptotic function ~Bax/Bak is required for mitochondrial damage and induction of apoptosis [Bax/Bak reside in outer mitochondrial membrane and are normally tightly bound to Bcl-2] [when released from Bcl-2 Bax/Bak form oligomers that generate pores in outer mitochondrial membrane and this allows release into cytosol of mitochondrial proteins which activates caspase-9] [overproduction of Bcl-2 blocks release of cytochrome c and blocks apoptosis while overproduction of Bak promotes release of cytochrome c and promotes apoptosis]

evolutionarily conserved proteins participate in apoptotic pathway

~Bcl-2 keeps cells alive when otherwise they would be programmed to die [act as regulator that suppresses apoptotic pathway and serves as sensor that controls apoptotic pathway in response to external stimuli] ~caspase-9 is required to destroy cell components during apoptosis, Apaf-1 is protease activating factor that causes autocleavage of CED-3 precursor protein creating active caspase-9 that initiates cell death ~caspases- contain key cysteine residue in catalytic site and works as homodimers w/ one domain stabilizing the active site of the other [initially made as procaspases that must be cleaved to become active] [initiator caspases are activated by dimerization induced by binding to other types of proteins which help initiators to aggregate] [activated initiator capases cleave effector caspases to activate them] [procaspases exist in large enough numbers to accomplish digestion of much of cellular protein when activated by small number of molecules that constitute activation signal] [intracellular targets include proteins of nuclear lamina and cytoskeleton]

regulation of CDK activity

~CDKs are only active when bound to regulatory cyclin subunit [diff types of cyclin-CDK complexes initiate diff events- G1 CDKs and G1/S CDKs promote entry into cell cycle while S CDKs trigger S phase and M CDKs initiate mitosis] [multiple mechanisms are in place to ensure that diff CDKs are only active in stages of cell cycle they trigger] ~CDKs are family of small serine/threonine kinases [require activating subunit to be active as protein kinase] [CDK4 and CDK6 are G1 CDKs and promote entry into cell cycle, CDK2 is G1/S and S CDK and CDK1 is mitotic CDK] ~not only regulated by cyclin binding but also by activating and inhibitory phosphorylation [unphosphorylated inactive CDKs have flexible region called T loop that blocks access of protein substrates to active site where ATP is bound so this is why there is no protein kinase activity] [interactions b/w cyclin and T loop cause shift in position of T loop exposing CDK active site] [kinase activity of phosphorylated complex is 100x greater than that of unphosphorylated]

CDK inhibitors control cyclin-CDK activity

~CKIs directly bind to cyclin-CDK complex and inhibit activity [essential to prevent premature activation of S phase and M phase CDKs] [inhibitors of G1 CDKs play essential role in mediating G1 arrest in response to proliferation inhibitory signals] ~class of CKIs called INK4s include several small closely related proteins that interact only w/ G1 CDKs and blocks their protein kinase activity ~CKIs regulating G1 CDKs play critical role in preventing tumor formation ~CDKs initiate different cell cycle phases by phosphorylating specific proteins [phosphorylate myriad of substrates directly initiating all aspects of given cell cycle phase]

inner cell mass is source of embryonic stem (ES) cells

~ES cells are pluripotent and can differentiate into wide range of cell types of the 3 primary germ layers either in vitro or after reinsertion into host embryo [when placed in suspension culture ES cells from aggregates called embryoid bodies which resemble early embryos in variety of tissues they form] ~DNA methylation, transcription factors, chromatin regulators and micro-RNAs all affect which genes become active and give early embryo cells their plasticity

E2F transcription factor and its regulator Rb control G1-S phase transition in metazoans

~G1 cyclins are present throughout G1 but expressed at increased levels in response to growth factors [G1 CDKs activate E2Fs] [during G1 E2Fs are held inactive by association w/ Rb and G1 CDKs activate E2Fs by phosphorylating and inactivating Rb] [E2Fs then activate genes encoding proteins involved in DNA synthesis and stimulate transcription of genes encoding G1/S cyclins and S cyclins] ~when E2F are bound to Rb they function as transcriptional repressors [this is b/c Rb recruits chromatin modifying enzymes that promote condensation of chromatin to transcriptionally inactive form] ~Rb protein regulation by G1 CDKs in mammalian cells is analogous to that of Cln3-CDK regulation of Whi5 ~phosphorylation on multiple sites by G1 CDKs prevents Rb association w/ E2Fs so they can activate transcription of genes required for S phase entry [as they accumulate S and M CDKs maintain Rb in phosphorylated state throughout S, G2 and early M phases but after cells complete anaphase and enter G1 or G0 fall in cyclin-CDK activities leads to dephosphorylation of Rb so Rb is now available to inhibit E2F activity during early G1 of next cycle]

degradation of S phase CDK inhibitor triggers DNA replication

~G1/S CDKs turn of degradation machinery that degrades S phase cyclins during exit from mitosis and G1 and induce degradation of CKI that inhibits S CDKs ~Cdh1- part of G1/S cyclin-CDK complex and targets APC/C to ubiquitinylate S and M cyclins marketing them for proteolysis [this remain activate throughout G1 prveneting premature accumulation of S and M cyclins] [phosphorylation of Cdh1 cause it to dissociate from APC/C complex inhibiting further ubiquitinylation so this allows S cyclins to accumulate as G1/S cyclin-CDK levels rise] [S and M CDKs maintain Cdh1 in inactive state and only when M CDKs decline that Cdc14 is activated and reactivates Cdh1] ~Sic1- expressed late in mitosis and in early G1 [inactivates S and M CDK complexes but has no effect on G1 and G1/S CDKs so functions as S phase inhibitor] [initiation of DNA replication occurs when Sic1 inhibitor is degraded by ubiquitination] [degradation of Sic1 is induced by phosphorylation by G1/S CDKs] [Sic1 has 6 phosphorylation sites so at low levels of G1/S CDK activity only a few sites are phosphorylated and Sic1 isnt destroyed but when G1/S CDK levels are high Sic1 is sufficiently phosphorylated at multiple sites and targeted for degradation] [once Sic1 is degraded S cyclin-CDKs induce DNA replication by phosphorylating several proteins involved in activating replicative helicases] ~p27- prevents premature activation of S CDKs during G1 [2 pathways contribute to degradation- (1) stimulation with mitogens where mitogen activated protein kinases phosphorylate p27 promoting its export from nucleus where KPC is found (2) targets p27 for degradation at G1-S transition [as G1/S CDKs reach high levels during late G1 they phosphorylate p27 targeting for ubiquitination by SCF] [degradation of p27 causes activation of S CDKs which initiate S phase by phosphorylating proteins important for initiation of DNA replication]

voltage sensing S4 ∂ helices move in response to membrane depolarization

~K+ channel protein has pore whose walls are formed by helices S5 and S6 [outside the core there is four arms each containing helices S1-S4] [opening of voltage gated Na+ or K+ channel is accompanied by movement of 12 to 14 protein bound positive charges from cytosolic to exoplasmic surface of membrane] ~in resting state positive charges on arms are attracted to negative charges on cytosolic face while in depolarized membrane these same charges become attracted to negative charges on expolasmic surface causing arms to move across membrane and opens channel ~in open channel conformation the position of S4-S5 linker forces S6 helix to form kink near cytosolic surface and the pore inside is open [pores diameter is sufficient to accommodate hydrated K+ ions] ~when cell membrane is repolarized and voltage sensor moves toward cytosolic membrane surface the S4-S5 linkers are twisted down towards inside of cell [S6 helices are straightened squeezing channel closed]

rearrangement of heavy chain locus involves V, D and J segments

~RSSs are such that D segments can join J segments and V segments to already arranged DJ segments [during DJ and VDJ rearrangements TdT may add nucleotides to free 3' end of DNA onto the N region (creating additional sequence diversity at the junctions) [if rearrangement yields sequence encoding functional protein its called productive] ~somatic hypermutation- enzyme deaminates C to U so when B cell that carries this lesion replicates it may cause G to A transition [mutations thus accumulate w/ every successive round of B cell division] [net result is generation of B cell population whose antibodies show higher affinity for antigen] ~affinity maturation- in course of immune response antibody exhibits increase in average affinity of antibodies for antigen as result of somatic hypermutation

Toll like receptors perceive variety of pathogen derived macromolecular patterns

~Toll like receptors can be activated by various microbial products and these receptors are expressed by variety of cell types (function is crucial for activation of dendritic cells and macrophages) ~microbial products recognized by Toll like receptors are macromolecules found in cell envelop of bacteria like LPS, flagellins, bacterial lipoproteins, pathogen derived nucleic acids, viral RNA ~several of these receptors participate in assembly of inflammasome whose major function is to convert procaspase-1 to caspase-1 [core components of inflammasomes are leucine rich repeats, members of neuronal inhibitors of apoptosis (NALP) family, NOD proteins] [Ipaf-1 allows recruitment of ASC to mediate complex formation w/ procaspase-1 which converts it to caspase-1] [many substances can induce assembly of inflammasome like silica, uric acid and asbestos] ~TLR signaling cascade- target genes are those encoding IL-1ß and IL-6 which contribute to inflammation and genes for TNF and IL-2 [expression of interfeurons is also turned on in response to TLR signaling] [cell response to TLR signaling- up regulation of co stimulatory molecules, production of cytokines, allows dendritic cells to migrate from where they encounter pathogen to lymph nodes] ~combination of surface proteins and cytokine profile induced by TLR engagement creates unique phenotype for dendritic cell [identity of microbe encountered sets pattern of TLRs that will be activates] [these in turn shape differentiation pathways of dendritic cells in terms of cytokines produced, surface molecules displayed and chemotactic cues to which cells respond]

opening of acetylcholine gated cation channels leads to muscle contraction

~acetylcholine causes opening of cation channel but since resting potential of muscle plasma membrane is near Ek opening of acetylcholine receptor channels causes little increase in efflux of K+ ions but Na+ ions flow into muscle cell driven by Na+ electrochemical gradient [simultaneous increase in permeability to Na+ and K+ ions produces net depolarization and this triggers opening of voltage gated Na+ channels leading to conduction of action potential in muscle cell membrane] [when membrane depolarization reaches special tubules in membrane it acts on Ca2+ channels and this releases Ca2+ from sarcoplasm reticulum into cytosol (enough to induce muscle contraction)]

fertilization unifies the genome

~acrosome- is membrane bound compartment at sperms leading tip for interaction w/ oocyte [inside are soluble enzymes including hydrolases and proteases] [during fertilization acrosome undergoes exocytosis releasing its contents onto surface of oocyte so enzymes digest egg surface layers to begin process of sperm entry] ~first sperm to reach triggers response by oocyte that prevents polyspermy [once it reaches egg sperm must penetrate layer of cumulus cells and the zona pellucida (ECM composed of ZP1, ZP2 and ZP glycoproteins)] [after sperm fuses w/ oocyte a flux of calcium starts from site of sperm entry and causes cortical granules to release contents to outside of plasma membrane and form shielding fertilization membrane that blocks other sperm from entering]

gain of function mutations convert proto-oncogenes into oncogenes

~activation of proto-oncogene into oncogene generally involves a gain of function mutation [4 mechanisms can produce oncogenes- (1) point mutation [change in single base pair that results in hyperactive protein product] (2) chromosomal translocation that fuses 2 genes together to produce hybrid whose protein activity is hyperactive (3) chromosomal translocation that brings growth regulatory gene under control of different promoter that causes inappropriate expression of gene (4) amplification of DNA segment so that numerous copies exist leading to overproduction] [gain of function mutations that convert to oncogenes are genetically dominant so only 1 of 2 alleles is sufficient for induction of cancer]

mitotic CDK inactivation triggers exit from mitosis

~anaphase spindle elongation and exit from mitosis are brought about by dephosphorylation of CDK substrates [inactivation of M CDK by APC/C mediated degradation of mitotic cyclins] [Cdc14 brings about second step of M CDK inhibition- complete inactivation requires destruction of mitotic cyclins by APC/C (Cdh1) and accumulation of CDK inhibitor Sic1] ~Cdc14 is kept inactive during cell cycle but activated during anaphase by GTPase pathway known as mitotic exit network (MEN) [this pathway is responsive to spindle position so only becomes activated during anaphase when spindles are properly positioned] [once activated Cdc14 dephosphorylates APC/C and Sic1 to promote mitotic cyclin degradation and M CDK inactivation which leads to exit from mitosis] ~reversely of M CDK phosphorylation changes activities of many proteins back to their interphase state [dephosphorylated inner nuclear membrane proteins bind to chromatin again so projections of ER membrane associate w/ surface of decondensing chromosomes and then fuse w/ one another to form continuous double membrane around each chromosome] [Ran-GTP stimulates fusion of ER projections to form daughter nuclear envelopes]

engagement of Toll-like receptors leads to activation of antigen presenting cells

~antigen presenting cells engage in continuous endocytosis and even in absence of pathogens display class I and class II MHC molecules loaded w/ self peptides at surface ~in presence of pathogens TLRs on cells are activated making antigen presenting cells motile (start migrating in direction of lymph node based on cues provided by chemokines) ~activated antigen presenting cells up regulate expression of co stimulatory molecules which allows them to activate T cells more effectively [initial contact of antigen presenting cell w/ pathogen results in migration to lymph node where is activates naive T cell (antigen is displayed in peptide-MHC complex, co stimulatory molecules are present and cytokines are produced that assist proper differentiation program for T cells)] ~antigen dendritic cells engage antigen specific T cells which respond by proliferating and differentiating [cytokines produced determine whether CD4 T cell will polarize toward inflammatory or helper cell phenotype] [if engagement occurs via class I MHC molecules CD8 T cell may develop from precursor to become killer T cell] ~activated T cells are motile and move through lymph node in preparation to encounter B cells or to enter circulation and execute effector functions elsewhere in body

antigen presentation is process by which fragments are complexed w/ MHC products and posted to cell surface

~antigen processing- when dendritic cells/macrophages/B cells acquire antigen and then display it in form that can be recognized by T cells ~antigen processing for both class I and II pathways is 6 steps- (1) acquisition of antigen (2) tagging antigen for destruction (3) proteolysis (4) delivery of peptides to MHC molecules (5) binding of peptide to MHC molecule (6) display of peptide loaded MHC molecule on cell surface

neurotrophins promote survival of neurons

~apoptosis is regulated by intracellular signals generated from many secreted and cell surface protein hormones and also environmental stressors like UV radiation and DNA damage ~when neurons grow to make connections more neurons grow then will survive [those that make connections survive and those that fail die] [number of neurons innervating peripheral cells depends on size of tissue to which they would connect (target field)] [incremental increases in target field size are accompanied by incremental increases in number of neurons innervating target field] ~NGF belongs to family of trophic factors called neurotrophins (BDNF and NT-3 are members) [bind to and activate receptor tyrosine kinases Trks and these bindings provide survival signal for different classes of neurons] [as neurons grow neurotrophins produced by target tissues bind to Trk receptors on growth cones of extending axons promoting survival of neurons that successfully reach targets]

communication at synapses

~arrival of action potential at axon terminus in presynaptic cell leads to opening of voltage sensitive Ca2+ channels and influx of Ca2+ [rise in Ca2+ triggers fusion of synaptic vesicles w/ plasma membrane releasing neurotransmitters into synaptic cleft] ~neurotransmitters bind to receptors and induce localized changes in potential across plasma membrane [if potential becomes depolarized an action potential will tend to be induced in postsynaptic cell (these synapses are excitatory and involve opening of Na+ channels in postsynaptic membrane)] [in inhibitory synapses binding of neurotransmitter to receptor causes hyperpolarization which results in opening of Cl- channels that hinders generation of action potential] ~neurotransmitter receptor classes- (1) ligand gated ion channels [open immediately upon neurotransmitter binding] (2) G protein coupled receptors ~duration of neurotransmitter signal depends on amount of transmitter released by presynaptic cell which in turn depends on amount of transmitter that had been stored as well as freq of action potentials arriving at synapse [duration also depends on how rapidly any unbound neurotransmitter is degraded or transported back]

multiple factors control pluripotency of ES cells

~as fertilized egg divides both paternal and maternal DNA becomes demethylated [pattern of methylation is reset during first few cell divisions erasing earlier epigenetic marking of DNA and creating condition where cells have greater potential for diverse pathways of development] ~Oct4, Sox2 and Nanog have essential roles and are required for specification of ICM cells in embryo as well as for ES cells in culture [these transcription factors also bind to promoter/enhancer regions of many genes encoding proteins and micro-RNAs important for proliferation and self renewal of ES cells] ~chromatin regulators that control gene transcription are also important in ES cells- Polycomb group proteins form complexes to maintain gene repression states that have been previously established by DNA binding transcription factors [PRC1 and PRC2- adding methyl groups to lysine of Histone 3 altering chromatin structure to repress genes] [both silence genes whose miRNAs would otherwise induce differentiation and maintains them in preactivation state so they are ready to become activated later]

stem cells, asymmetry and cell death

~asymmetric cell division- differences among cells arise when 2 daughter cells diverge after receiving distinct developmental/environmental signals [may differ in shape, size, protein composition or genes may be in diff states of activity] ~stem cells- unspecialized cells that can reproduce themselves as well as generate specific types of more specialized cells [zygote is ultimate totipotent stem cell b/c it has capability to generate every cell type in body as well as supportive placental cells that are required for embryonic development] ~group of cells called inner cell mass (ICM) will give rise to tissues of embryo and another set of cells will form placenta [cells that can generate all embryonic tissues but not extra embryonic tissues are called pluripotent] ~small number of factors can convert some somatic cells into induced pluripotent stem cells (iPS) that have properties indistinguishable from embryonic stem cells ~cell lineage- series of cell divisions like family tree [traces birth order of cells as they progressively become more restricted in their developmental potential and differentiate into specialized cells] ~stem cells are important during both development and for replacement of outworn cells in adults [stem cells in adults are multipotent- can give rise to some types of different cells found in organism but not all of them] ~diversity of cells requires asymmetric cell division so mother cell must become polarized before cell division so contents are unequally distributed b/w the 2 daughters

information flows b/w neurons via synapses

~axon terminus of presynaptic cell contains many small synaptic vesicles that are filled w/ neurotransmitters [arrival of action potential at terminus triggers exocytosis of synaptic vesicles releasing neurotransmitters] ~neurotransmitters diffuse across synapse and bind to receptors on dendrite of adjacent neuron [binding triggers opening or closing of specific ion channels in post synaptic cells leading to changes in membrane potential] [these changes depolarize the membrane and triggers action potential] ~in some synapses the effect of neurotransmitters is to hyperpolarize and lower likelihood of action potential ~afferent neurons- sensory or receptor neurons that carry nerve impulses from receptors towards central nervous system [report an event that has happened] ~efferent neurons- carry nerve impulses away from central nervous system to generate a response ~interneurons- relay signals from afferent to efferent neurons and to other interneurons as part of neural pathway [reflex arc- circuit where interneurons connect multiple sensory and motor neurons allowing one sensory neuron to affect multiple motor neurons and one motor neuron to be affected by multiple sensory neurons to integrate and enhance reflexes] ~output of nervous system depends on its circuit properties- amount of wiring, interconnections b/w neurons and the strength of these connections

formation of synapses requires assembly of presynaptic and postsynaptic structures

~axons extend from cell body during development guided by signals from other cells along the way so that axon termini reach correct location [astrocytes and Schwann cells send protein signals to neurons to stimulate the formation of synapses and help preserve them- one signal is thrombospondin (TSP)] ~release of neurotransmitter into synaptic cleft occurs in active zone (specialized region of plasma membrane containing proteins who modify the properties of synaptic vesicles and bring them into position for docking w/ plasma membrane] [similar region is in postsynaptic cell called postsynaptic density (PSD)] ~neuromuscular junction- at these synapses acetylcholine is neurotransmitter and its receptor is AChR [formation of synapse is process requiring signaling interactions b/w motor neurons and muscle fibers] [MuSK is a kinase localized in AChR-rich patches of plasma membrane that induces clustering of AChRs and attract termini of growing neuron axons] [Agrin is a glycoprotein transported in vesicles along axon microtubules and binds LRP4 which increase MuSK kinase activity]

Par proteins direct cell asymmetry

~before first cell division zygote is visibly asymmetric - cytoplasmic complexes called P granules are concentrated at posterior end of cell [P granules always concentrate in cells that will eventually become the germ line] ~Par proteins localize either at cortex of anterior half of cell or at cortex of posterior half [Par3 localizes anteriorly while Par2 and Par1 localize posteriorly] [antagonistic interactions exist b/w these protein complexes so if Par2 is localized to one region it excludes Par3 and vice versa] ~asymmetry is defined by sperm entry site which becomes posterior end [prior to sperm entry egg cortex is under tension by actin meshwork- Rho is maintained in active state in unfertilized egg which activates myosin] [sperm entry defines posterior region by depleting Rho and lowering active myosin so actin-myosin network contracts toward anterior and as it does it drags the anterior complex containing Par3 to that end] [w/ removal of anterior complex Par2 can now occupy posterior complex and cell asymmetry is established]

cyclins determine activity of CDKs

~bind and activate CDKs, only present during cell cycle stage that they trigger and absent in other cell cycle stages, regulate particular cell cycle stage and also set in motion events in preparation for next cell cycle stage (propel cell cycle forward) ~all cyclins have conserved 100 amino acid region known as cyclin box and possess similar 3D structures [G1 cyclins activity is subject to regulation by signal transduction pathways that sense presence of growth factors or cell proliferation inhibitory signals] ~G1/S cyclins trigger G1-S phase transition known as START (this is the point where cells are irreversibly committed to cell division and can no longer return to G1 stage] [mitotic cyclin is only protein that is limiting the cell to enter mitosis or not]

hematopoietic stem cells form all blood cells

~blood stem cells are located in embryonic liver and in bone marrow in adults [various types of blood cells derive from single type of multipotent hematopoietic stem cell (HSC) which gives rise to myeloid and lymphoid progenitor stem cells that are capable of limited self renewal] ~each branch of cell lineage has different cytokine regulators [if all blood cells are needed multiple cytokines are produced but if only one type is needed its more specific (just erythropoietin or G-CSF or M-CSF)] ~one major type of cell in bone marrow niche is osteoblasts (bone forming cells that are localized to bone surface) [Delta and SCF produced by niche cells signal to Notch on surface of HSCs that stimulate HSCs and other types of cells participating in forming HSC niche]

MHC molecules bind peptide antigens and interact w/ T cell receptor

~both class I and II MHC molecules are polymorphic so many allelic variants exist among individuals of same species [over 2000 distinct allelic products identified in humans] ~polymorphic residues that distinguish one allelic MHC molecule from another are located around peptide binding cleft so these residues therefore determine the architecture of peptide binding pocket and hence specificity of peptide bonding [residues also affect surface of MHC molecule so points of contact w/ T cell receptor- T cell receptor designed to interact w/ one particular class I MHC allele will not interact w/ unrelated MHC molecules b/c of diff surface architectures] ~class II MHC molecules evolved to present peptides generated in endosomes and lysosomes [interactions b/w peptide and class II MHC molecules takes place in these organelles and class II MHC molecules are targeted specifically to those locations after their synthesis in ER]

somatic cells can generate induced pluripotent stem (iPS) cells

~both human and mouse somatic cells could be reprogrammed to the induced pluripotent stem cell state w/ retroviruses encoding just 4 factors- KLF4, SOX2, OCT4 and c-MYC ~single iPS cells can be experimentally introduced into blastocyst and form all tissues of mouse including germ cells showing that somatic cells can be reprogrammed into embryonic state

tumor cells and the onset of cancer

~cancer cells acquire drive to proliferate that doesnt require external inducing signal, fail to sense signals that restrict cell division and continue to live when they should die, change attachment to cell wall or ECM and break loose to move away, hypoxic (oxygen starved) so obtain blood supply by signaling the growth of blood vessels into the tumor ~carcinomas are tumors that derive from epithelia (endoderm or ectoderm) and sarcomas derive from mesoderm [most tumors are solid masses but leukemias (sarcomas) grow as individual cells in blood] [lymphomas (sarcomas) are solid tumors of lymphocytes and plasma cells] [glioblastomas are tumors of glial cells in brain]

carcinogens and caretaker genes in cancer

~carcinogens cause mutations that reduce function of tumor suppressor genes, create oncogenes from proto-oncogenes or damage DNA repair systems [damage to caretaker genes leads to increased mutation rate that affect cell cycle regulators and the cells bearing these can become cancerous] ~form of protection against mutation for stem cells is their relatively low rate of division which reduces the possibility of DNA damage incured during DNA replication and mitosis [progeny of stem cells also dont have ability to divide indefinitely] ~when cells w/ stem cell like growth properties are mutagenized by environmental poisons and unable to efficiently repair the damage cancer can occur ~direct acting carcinogens- compounds modify bases in DNA so to distort normal pattern of base pairing [if modified nucleotides arent repaired they allow incorrect nucleotide to be incorporated during replication] ~indirect acting carcinogens- cytochrome P-450 enzymes add electrophilic centers to nonpolar foreign molecules [most chemical carcinogens have little mutagenic effect until they have been modified by cellular enzymes]

cell cycle is ordered series of events leading to cell replication

~cell cycle is divided into 4 main phases- M, G1, S and G2 [replicating mammalian somatic cells grow in size and synthesize RNAs and proteins required for DNA synthesis during G1] [when cells have reached appropriate size and have synthesized the proteins they enter cell cycle by traversing point in G1 called START and once this point has been crossed cells are committed to cell division] ~entry into S phase where cells actively replicate their chromosomes and after going through G2 cells begin mitosis (prophase, metaphase, anaphase, telophase and cytokinesis) ~each chromosome is composed of 2 identical DNA molecules resulting from DNA replication plus associated histones and proteins [2 identical DNA molecules that form one chromosome are called sister chromatids and these are attached to each other by protein cross links] ~during interphase (cell cycle b/w end of one M phase and beginning of next) outer nuclear membrane is continuous w/ ER [during prophase the envelope retracts and Golgi membranes break down into vesicles] [after nuclear envelope break down kinetochores of sister chromatids associate w/ microtubules coming from opposite spindle poles and this aligns chromosomes for metaphase] ~during anaphase sister chromatids separate as they are pulled by microtubules toward spindle poles [mitotic spindle then disassembles and chromosomes decondense during telophase] ~most differentiated cells exit the cell cycle and service for days/lifetime if organism w/o dividing again [these postmitotic cells exit during G1 entering phase called G0- some G0 cells can return to cell cycle and resume replicating]

eukaryotic cell cycle

~cell cycle is ordered series of events that lead to cell division and production of 2 daughter cells each containing chromosomes identical to those of parent cell [2 main molecular processes take place w/ resting intervals in between- in S phase each parental chromosome is duplicated to form 2 identical sister chromatids while in M phase resulting chromatids are distributed to each daughter cell] ~high accuracy is required so cell division is controlled by checkpoint pathways that prevent initiation of each step in cell division until earlier steps on which it depends have been completed and mistakes that occurred during process have been corrected ~controllers of cell cycle are small number of heterodimeric protein kinases that contain regulatory subunit (cyclin) and catalytic subunit (CDK) [regulate proteins involved in entry into cell cycle, DNA replication and mitosis] [regulated degradation is also important since protein degradation is irreversible this ensures that processes move in only one direction through cell cycle]

mechanisms of cell polarity and asymmetric cell division

~cell polarity- ability of cells to organize their internal structure resulting in changes of cell shape and regions of plasma membrane w/ diff protein and lipid compositions [if polarized cell divides it undergoes asymmetric cell division] ~cell polarity requires determinants including mRNAs, proteins and lipids to be asymmetrically localized in cell [if mitotic spindle is positioned so that these determinants are segregated during cell division then the daughter cells will have different fate] [(1) need to have receptors to sense cue (2) after sensing cue signal transduction pathways regulate cytoskeleton to reorganize in appropriate polarized manner (3) polarized cytoskeleton provides framework for transport of membrane trafficking organelles and polarity determinant (4) polarity is reinforced by returning polarity determinants that have moved from polarization site]

growth checkpoint pathway ensures that cells only enter cell cycle after sufficient macromolecule biosynthesis

~cell proliferation requires that cells multiply through cell division and individual cells grow through macromolecule biosynthesis ~growth rate and hence cell cycle control by growth is determined by protein synthesis [G1 cyclin Cln3 is subject to translational control making levels of cyclin especially sensitive to protein synthesis rate] [length of G1 and critical cell size change w/ nutrient availability] ~when cells are small Pom1 inhibits Cdr2 so Wee1 is active and prevents entry into mitosis [as cells grow Pom1 concentration declines and Cdr2 becomes active and inhibits Wee1 so cells can now enter mitosis] ~nutrients are not limiting in multicellular organisms and cell growth is controlled by growth factor signaling pathways like Ras, AMPK and TOR pathways

DNA damage response halts cell cycle progression when DNA is compromised

~cells that DNA damage response system that senses many different types of DNA damage and responds by activating repair pathways and halting cell cycle progression until damage has been repaired [cell arrest can occur in either G1, S or G2 depending on whether DNA damage occurred before cell cycle entry or during DNA replication] [in multicellular organisms severe DNA damage is dealt w/ by programmed cell death (apoptosis)] ~types of DNA damage- double stranded break, single stranded break, structural changes in nucleotides, DNA mismatches [different sensors for different types of damage that scan genome and when detect lesion assemble signaling and repair factors on site of lesion] ~ATM and ATR are kinases that get recruited to sites of DNA damage and initiate recruitment of adapter proteins and other kinases Chk1 and Chk2 [these activate repair mechanisms that cause cell cycle arrest or apoptosis] ~ATM only recognizes double stranded breaks while ATR can recognize stalled replication forks, damaged nucleotides, etc [Chk1/2 halt cell cycle by phosphorylating Cdc25] [ATR continues to inhibit Cdc25 until there is complete DNA replication so this makes initiation of mitosis dependent on completion of chromosome replication] ~ATM gets directly recruited to DNA ends by MRN complex which binds to broken ends and holds them together [ATM then phosphorylates Chk2 and recruits repair proteins which initiate homologous recombination] [ATM can also initiate nonhomologous end joining] [ATM activation also halts cell cycle progression by inhibiting Cdc25 and preventing activation of CDKs] ~p53- highly unstable tumor suppressor that is rapidly degradated [degradation is inhibited by ATM and ATR which phosphorylate p53- this greatly increases p53's ability to activate transcription of specific genes that help cell cope w/ DNA damage] [when DNA damage is extensive p53 activates expression of genes that lead to apoptosis] [most cancer cells have mutations in both alleles of p53 gene or in pathways that stabilize p53 in response to DNA damage]

cell death and its regulation

~cellular interactions regulate cell death in 2 ways- (1) all cells require specific protein hormone signals to stay alive and in absence of such signals (trophic factors) cells activate suicide program (2) other specific hormone signals induce murder program that kills cells [whether cells commit suicide or are murdered death is mediated by common molecular pathway] ~dying cells shrink, condense and then fragment releasing small membrane bound apoptotic bodies which are engulfed by other cells [in dying cells nuclei condense and DNA is fragmented] [intracellular constituents arent released into ECM b/c they could have deleterious effects on neighboring cells] ~genes involved in cell death encode proteins w/ 3 distinct functions- (1) killer proteins required for cell to begin apoptotic process (2) destruction proteins that do things like digest DNA (3) engulfment proteins required for phagocytosis of dying cell by another cell [engulfment involves assembly of halo of actin in engulfing cell around dying cell triggered by proteins that activate Rac] ~in contrast to apoptosis cells that die in response to tissue damage have different morphological changes (necrosis) [cells that undergo this will swell and burst releasing intracellular contents which can cause damage to surrounding cells and inflammation]

surveillance mechanisms in cell cycle regulation

~checkpoint pathways ensure that next cell cycle is not initiated until previous one has been completed [consists of sensors that monitor a particular cellular event, signaling cascade that initiates response and effector that halts cell cycle progression and activates repair pathways] ~cell cycle events monitored by checkpoint pathways include growth, DNA replication, DNA damage, kinetochore attachment to mitotic spindle and position of spindle within cell ~pathways function by controlling kinase activity of cyclin-CDKs through regulation of synthesis and degradation of cyclins, phosphorylation of CDKs at inhibitory sites, regulation of synthesis and stability of CKIs that inactivate cyclin-CDK complexes and regulation of APC/C ubiquitin ligase ~checkpoint pathway- cdc13 mutants have damaged DNA that signals cells to arrest cell cycle progression and induce repair of damage b/c mitosis of cells w/ damaged DNA would almost certainly lead to cell death [in cells lacking RAD9 the signal that halts cell cycle progression doesnt work and cells undergo mitosis despite incompletely replicated DNA which kills the cell] ~each checkpoint is similar- sensor detects defect in particular process and in response to this defect activates signal transduction pathway [effectors activated by signaling pathway initiate repair of defect and halt cell cycle until defect is corrected]

chromosome condensation facilitates chromosome segregation

~chromosome segregation requires that DNA is compacted into travel ready structures [cells compact chromosome during prophase and this results in dramatic reduction in chromosome length] ~other part of compaction process is untangling of intertwined sister chromatids (sister chromatid resolution) and this is mediated w/ topoisomerase II ~condensin complex- when condension function is lost chromosomes dont condense and sister chromatid tangles arent resolved [chromosome condensation is triggered by M CDKs] ~dissociation of cohesions from chromosomes also acts in parallel to condensins to contribute to chromosome compaction [cohesions are removed from chromosomes by phosphorylation from aurora B and polo kinases] [cohesions around centromeres are protected from phosphorylation/removal by PP2A]

each B cell produces unique immunoglobulin

~clonal selection theory- each lymphocyte carries antigen binding receptor of unique specificity [when lymphocyte encounters antigen for which its specific then clonal expansion (rapid cell division) occurs and allows amplification of response leading to clearing of antigen [b/c each lymphocyte is endowed w/ unique receptor and clonally expands in response to antigen the response is called polyclonal] ~(1) no 2 tumors produced light chains of identical biochemical properties so they were all unique in sequence (2) differences in sequence were not randomly distributed but clustered in domain called variable region of light chain (VL) which is about 110 amino acids [remainder of sequence is identical and called constant region CL] (3) residues that distinguish one heavy chain from another were also concentrated in domain called variable region of heavy chain VH ~three hypervariable regions in heavy and light chains (HV1, HV2 and HV3) which are sandwiched b/w framework regions [in properly folded immunoglobulins these regions are close in proximity and make contact w/ antigen (so also called complementarity determining regions (CDRs))

duplicated DNA strands become linked during replication

~cohesins- protein complexes that establish cohesion/linkages b/w sister chromatids [composed of Smc1, Smc3, Scc1 and Scc3] ~cohesins associate w/ chromosomes during G1 and during DNA replication they are loaded onto chromosomes to hold sister chromatids together [essential for attaching replicated sister chromatids onto mitotic spindle and for their segregation during mitosis]

model organisms and methods to study cell cycle

~complex molecular processes such as initiation of DNA replication and entry into mitosis are all regulated and coordinated by small number of master cell cycle regulatory proteins [these proteins and regulators are high conserved so cell cycle is identical in all eukaryotes] ~yeast- yeast w/ temperature sensitive mutations cause defects in proteins required to progress through cell cycle (cdc mutants) [transformed cdc mutant can grow into colony in non permissive temps if it also contains plasmid that carries wild type allele that complements recessive mutation- plasmids bearing wild type allele can then be recovered from those cells allowing identification of complementing gene] [human cDNAs cloned into yeast expression vectors can often complement yeast cell cycle mutants leading to isolation of human genes encoding cell cycle control proteins] ~fruit flies- nuclear divisions and rapid cycles of DNA replication and mitosis (w/ no gap phases) fueled by key cell cycle regulators that are stock piled in egg cytoplasm [as stock pile runs out gap phases are introduced and most cells cease to divide at this point and utilize special cell cycle called endocycle where cells replicate DNA but dont undergo mitosis (grow by increase in cell size but not through cell multiplication)] ~replicative senescence- normal human cells divide 15-20 times but then proliferation slows and eventually stops [cells can escape this fate and become immortalized and establish cell lines]

cyclin dependent kinases control the eukaryotic cell cycle

~concentrations of CDKs are constant throughout cell cycle except they have no kinase activity unless they are associated w/ cyclin subunit [each cyclin is only present and active during cell cycle stage is promotes and so restricts kinase activity of CDKs it binds to just that cell cycle ~oscillations in CDK activity is fundamental and generated by positive feedback mechanisms where specific CDKs promoter their own activation [coupled to negative feedback loop where CDKs promote their own inactivation]

sequential opening and closing of voltage gated Na+ and K+ channels generate action potentials

~cyclical changes in membrane potential result from opening and closing of number of voltage gated Na+ channels in segment of axon plasma membrane and then opening and closing voltage gated K+ channels ~voltage gated Na+ channels- small depolarization of membrane increases likelihood that any one channel will open (the greater the depolarization the greater probability that channel will open) [depolarization causes channel proteins to open gate permitting Na+ to pass through] [as Na+ flows in excess charges on face of membrane diffuse short distance away from site of depolarization and this passive spread depolarizes adjacent segments of plasma membrane and opening of more voltage gated Na+ channels] [as cell becomes more depolarized opening more channels and causing explosive entry of Na+] ~as membrane potential reaches Ena the net inward movement of Na+ ceases (b/c of now inside positive membrane potential) [action potential at its peak is close to value of Ena] ~as long as membrane remains depolarized the channel inactivating segment remains in channel open and this channel is inactivated and cant be reopened (refractory period) [after inside negative potential has been reestablished the channel returns to closed resting state and is able to be opened again by depolarization] ~voltage gated K+ channels- repolarization of membrane that occurs during refractory period is due to opening of K+ channels [increased efflux of K+ from cytosol removes excess positive charges restoring negative inside potential and for a brief instant becomes hyperpolarized (potential approaches Ek)] [open slightly after initialy depolarization at height of action potential]

release of cytochrome c and SMAC/DIABLO proteins from mitochondria leads to formation of apoptosome and caspase activation

~cytochrome c activates apoptosis by binding Apaf-1 [in absence of cytochrome c Apaf-1 is bound to dATP and after binding it cleaves dATP to dADP and undergoes assembly into apoptosome] ~apoptosome serves as activation machine for initiator caspase-9 [becomes activated by dimerization following binding to apoptosome and then caspase-9 cleaves multiple effector caspases leading to destruction of cell proteins] ~inhibitor apoptosis proteins (IAPs) provide another way to restrain both initiator and effector caspases [have zinc binding domains that bind directly to caspases and inhibit their protease activity] [IAPs create problem when cells do need to undergo apoptosis so SMAC/DIABLO mitochondrial proteins inhibit IAPs] [assembly of Bax/Bak leads to release of SMAC/DIABLOs which then binds IAPs in cytosol blocking IAPs from binding to caspases so promote caspase activity and cell death]

cytokinesis creates two daughter cells

~cytokinesis- cytoplasm and organelles are distributed b/w 2 future daughter cells [brought about by contractile ring made of actin and myosin] [during cytokinesis ring contracts pulling membrane inward and closing connection b/w 2 daughter cells] ~contractile ring forms during anaphase and is placed in middle of anaphase spindle to ensure that each daughter cell gets half genetic material [microtubules of spindle interct w/ cell cortex positioning cleavage furrow w/ respect to spindle pole position] ~surveillance mechanisms ensure site of cytokinesis is coordinated w/ spindle position [this is especially important during asymmetric cell division] ~major signal for cytokinesis is inactivation of M CDKs [cells w/ stabilized version of mitotic cyclins go through anaphase but dont undergo cytokinesis]

signaling via antigen specific receptors triggers proliferation and differentiation of T and B cells

~cytosolic portions of antigen specific receptors are short so dont protrude much beyond cytosolic leaflet of plasma membrane and are incapable of recruitment of downstream signaling molecules [associate w/ ITAMs which recruit kinases and other adapter molecules to initiate transcription programs that determine fate of activated lymphocyte (proliferation and differentiation)] ~following antigen stimulation of T cell first gene turned on is IL-2 which makes T cells make more IL-2 (autocrine stimulation and positive feedback loop) ~T cells born w/ receptors that cant engage self MHC are useless [will fail to perceive survival signals via newly generated T cell receptors and die] ~T cells endowed w/ perfect fit receptors for self MHC complex would cause autoimmunity [if number of self peptide MHC combinations passes threshold sufficient to allow triggering of T cell receptor than these T cells are instructed to apoptosis (negative selection)] [this serves to purge T cell repertoire of overly self reactive T cells] ~avidity model of T cell selection- heterogeneous peptide MHC complexes displayed on surface of T cell make it probable that T cell receptor interprets signal in qualitative (strength/duration) manner but also in additive fashion (summation of binding energies of diff MHC self peptide combinations helps determine outcome of selection)

meiosis

~decision to enter meiotic divisions is made in G1 [depletion of nitrogen and carbon induces diploid cells to undergo meiosis instead of mitosis yielding haploid cells] ~DNA replication relies on Ime2 which takes over the role of G1/S CDKs in promoting DNA replication- (1) phosphorylation of Cdh1 inactivating it so S and M cyclins can accumulate (2) phosphorylation of transcription factors to induce genes required for S phase (3) phosphorylation of S CDK inhibitor Sic1 leading to release of active S CDKs and onset of pre-meiotic DNA replication ~kinetochores of sister chromatids attach to spindle fibers emanating rom same pole rather than from opposite poles like in mitosis (co oriented) [however kinetochores of maternal and paternal chromosomes of each bivalent attach to spindle microtubules from opposite spindle poles (bi oriented)] ~to facilitate 2 consecutive chromosome segregation phases cohesions have to be lost from chromosomes in step wise manner [cohesions are lost from chromosome arms by end of meiosis I but pool of cohesions around kinetochores is protected from removal and this is removed at anaphase II]

mitotic CDKs promote nuclear envelope breakdown

~during interphase chromosomes are surrounded by nuclear envelope and for chromosomes to interact w/ microtubules from mitotic spindles the nuclear envelope needs to be dismantled ~nuclear envelope is extension of ER and the lipid bilayer of inner membrane is associated w/ nuclear lamina (meshwork of lamin filaments adjacent to inside of nuclear envelope) [the 3 lamins (A, B and C) are intermediate filaments] [lamin B is modified by addition of isoprenyl group and then this fatty acid is embedded in inner nuclear membrane anchoring the two together] ~once M CDKs are activated at end of G2 they phosphorylate specific serine residues in all 3 lamins and this causes depolymerization of the lamin intermediate filaments which leads to disintegration of nuclear lamina meshwork and disassembly of nuclear envelope ~phosphorylation of integral membrane proteins of inner nuclear membrane by M CDK decreases their affinity for chromatin and further contributes to disassembly of nuclear envelope

each olfactory receptor neuron expresses a single type of odorant receptor

~each ORN only produces a single type of odorant receptor [some receptors can bind more than one kind of molecule but the molecules detected are usually close in structure] [some odorants can bind to multiple receptors] ~initial odorant sensing info is carried directly to higher parts of brain w/o processing so its just a simple report of what odorant has been detected ~ORNs can send either excitatory or inhibitory signals from axon termini in order to distinguish attractive vs repulsive odors ~glomeruli located near each other respond to odorants w/ related chemical structures [this arrangement reflects subdivision of olfactory part of brain] ~each cell has only one receptor and this makes difficulties- (1) each receptor must be able to distinguish a type of odorant or set of molecules w/ specificity adequate to needs of organism [not useful is stimulated too easily or frequently] (2) each cell must express one and only one receptor gene product so all other receptor genes must be turned off (3) neuronal writing of olfactory system must make discrimination among odorants possible so that brain can determine which odorants are present [this is solved b/c all cells that respond to same odorant send processes to same destination]

neural stem cells form nerve and glial cells in central nervous system

~earliest stages of neural development involve rolling up of tube of ectoderm that extends length of embryo from head to tail [this neural tube will form brain and spinal cord] [thickness of tube is originally single layer of cells (embryonic neural stem cells) that will give rise to entire central nervous system] ~inside of neural tube forms fluid filled compartments called ventricles and lining of tube where most cell division takes place is subventricular zone (this has stem cell niche properties) ~stem cells can divide symmetrically or asymmetrically producing one cell that migrate outward called transient amplifying (TA) cells b/c they divide rapidly to form neural precursors neuroblasts [newly formed cells traverse layers of preexisting cells before taking up residence on outside] ~neuroblast can produce 2 daughters- one a neuron and the other a glial cell [some cells near hippocampus continue to act as stem cells to generate new neurons and can differentiate into neural lineages including neurons, astrocytes, oligodendrocytes] ~neural stem cell niche is created by signals from ependyma cells that form layer just inside neural tube and by endothelial cells that form blood vessels in vicinity

Par proteins and other polarity complexes are involved in epithelial-cell polarity

~epithelial cell polarization- (1) interaction b/w adjacent cells through nectin (cell adhesion molecule) and junctional protein JAM-A [these interactions signal cells to recruit Par complex] (2) Crumbs complex is recruited apically and Scribble complex defines basolateral surface (3) arrangement of polarity proteins recognizes cytoskeletion w/ distinct organizations of microfilaments making up apical and basolateral membranes (4) new membrane proteins destined for apical and basolateral membranes are packaged in transport vesicles at trans Golgi network and then transported to appropriate surface

intestinal stem cells continuously generate all of the cells of the intestinal epithelium

~epithelium of small intestine is composed of 3 types of differentiated cells- most important is absorptive enterocytes transport nutrients from intestinal lumen into body [intestinal epithelium continuously regernerate from stem cell population located in crypts] [stem cells produce precursor cells that proliferate and differentiate as they ascend sides of crypts to form surface layer of villi] ~overproduction of ß-catenin (activated by Wnt signals) in intestinal cells leads to excess proliferation of epithelium [blocking function of ß-catenin by interfering w/ Wnt activated TCF abolishes stem cells in intestine] ~Lgr5 binds class of secreted hormones termed R-spondins and activates intracellular signaling pathways that activate Wnt signaling [descendants of these Lgr cells gave rise to all intestinal epithelial cells] [marker of intestinal stem cells] ~Paneth cells constitute major part of niche for intestinal stem cells- produce Wnt as well as EGF and Delta protein that are essential for intestinal stem cell maintenance [constitute much if not all of the niche for intestinal stem cell maintenance]

loss of DNA-repair systems can lead to cancer

~even w/o external mutagen normal processes generate large amount of DNA damage [due to depurination reactions, alkylation reactions and to generation of ROS all of which alter DNA] [normal role of caretaker genes is to prevent of repair DNA damage] ~all DNA repair mechanisms utilize family of DNA polymerases to correct DNA damage [DNA polymerase ß is capable of using templates that contain DNA adducts and other chemical modifications (even missing bases) (these are called lesion bypass DNA polymerases)] [DNA pol ß doesnt proofread and is overexpressed in certain tumors b/c its needed at high levels for cells to be able to divide at all in face of growing burden of mutations] [mutations in DNA pol ß are associated w/ tumors] ~double strand breaks are sever lesions b/c incorrect rejoining of them can lead to chromosomal rearrangements and translocations that produce hybrid gene or bring growth regulatory gene under control of different promoter [B and T cells are particularly susceptible to DNA rearrangements caused by double strand breaks created during rearrangement of their immunoglobulin or T cell receptor genes]

magnitude of action potential is close to Ena and is caused by Na+ influx through open Na+ channels

~exit of Na+ ions from cell into cytosol is thermo favored driven by both the Na+ concentration gradient and the inside negative membrane potential [however most Na+ channels in plasma membrane are closed so resting cells have little inward movement of Na+] ~during action potential some Na+ channels open allowing inward movement which depolarizes the membrane [voltage gated channels- action potentials are propagated down axon b/c change in voltage in one part opens channels in next section of axon] ~during action potential there is net inward movement of cations so plasma membrane becomes depolarized to such extent that inside face becomes positive w/ respect to external face ~there is a relationship b/w magnitude of action potential and concentration of Na+ ions inside and outside cell [if concentration of Na+ ions in solution is reduced then magnitude of depolarization is reduced]

influx of Ca2+ triggers release of neurotransmitters

~features critical to synapse function- (1) secretion is tightly coupled to arrival of action potential at axon terminus (2) synaptic vesicles are recycled locally to axon terminus after fusion w/ plasma membrane ~depolarization of plasma membrane cant cause synaptic vesicles to fuse on its own- depolarization opens Ca2+ channels permitting influx of Ca2+ ~2 pools of neurotransmitter filled synaptic vesicles are present in axon termini- those docked at plasma membrane (ready to be exocytosed) and thise in reserve in active zone [each rise in Ca2+ generated by arrival of single action potential triggers exocytosis of 10% of docked vesicles]

cleavage of mammalian embryo leads to first differentiation events

~fertilization is quickly followed by cleavage (series of cell divisions that take about one day each) [each cell at 8-cell stage is totipotent but in the 16-cell morula form the cell affinites increase substantially and embryo undergoes compaction (driven by increased cell cell adhesion that results in more solid mass of cells the compacted morula)] [in next step fluid flows into internal cavity called blastocoel and divisions produce blastocyst stage (64-cell) that has separated into 2 cell types- trophectoderm which will form extra embryonic tissues and ICM which gives rise to embryo] ~ICM cells are in loose mass (mesenchyme) during blastocyst phase [fate of cell in early embryo is determined by cells location- cells on outside tend to form extra embryonic tissues while cells on inside tend to form embryo tissues]

M CDKs promote mitotic spindle formation

~function of mitotic spindle is to segregate chromosomes so that sister chromatids separate from each other and are moved to opposite sides of mitotic spindle [to do this chromosomes have to attach to mitotic spindles so that one kinetochore of each sister chromatid pair attaches to microtubules emanating from opposite poles (this is called bi-oriented)] ~during G1 cells contain single chromosome that functions as major microtubule nucleating center of cell [mitotic spindle formation occurs at G1-S transition when centrioles duplicate] [the 2 centrioles split apart and each begins to grow daughter centriole so each centriole pair assembles and by G2 2 centrosomes have formed] ~key initiating step of mitotic spindle formation is severing of ties that link duplicated chromosomes [this centrosome disjunction occurs in G2 and is triggered by M CDKs] [as soon as the separation occurs microtubules are nucleated from both centrosomes and are pulled away from each other by dynein] ~ultimate goal of chromosome attachment to mitotic spindle is that every chromosome is attached in bi oriented manner (amphitelic attachment) [many chromosomes can attach to mitotic spindle in faulty ways- (1) merotelic attachment [kinetochore attaches to microtubules emanating from both poles] (2) syntelic attachment [kinetochores of pair attach to microtubules from same pole] (3) monotelic attachment [only one kinetochore attaches to microtubules]] ~sensing mechanism to detect incorrect attachments is based on tension- when sister chromatids are correctly attached their kinetochores are under tension [microtubules attached to kinetochores pull them and cohesion molecules withstand these forces creating tension] ~Aurora B sense kinetochores that arent under tension and sever these attachments giving cells second chance to get attachment right [when microtubules are incorrectly attached Aurora B can phosphorylate them and destabilize the attachment] [when microtubules are attached correctly to kinetochores microtubule forces pull kinetochores away from Aurora B and the kinase cant reach the target kinetochore to phosphorylate it] ~once all chromosomes are attached to microtubules in correct manner that only thing holding them back from segregating are cohesion complexes [severing cohesion molecules initiates anaphase]

calcium binding protein regulates fusion of synaptic vesicles within plasma membrane

~fusion of synaptic vesicles depends on SNAREs [v-SNARE tightly binds t-SNAREs in plasma membrane to form complexes] [after fusion SNAP and NSF promote dissociation of t-SNAREs] ~speed w/ which synaptic vesicles fuse w/ presynaptic membrane after rise in cytosolic Ca2+ indicates that fusion machinery is entirely assembled in resting state and can undergo conformational change leading to exocytosis of neurotransmitter [binding of Ca2+ to synaptotagmin relieves inhibition releasing complexin and allowing fusion event to occur] ~synaptic vesicles are formed by endocytic budding from plasma membrane of axon termini [endocytosis involves clathrin coated pits and several unique membrane proteins (neurotransmitter transporters) are specifically incorporated into the endocytosed vesicles] [synaptic vesicle membrane proteins can be reused and recycled vesicles refilled w/ neurotransmitter] [pinching off of endocytosed synaptic vesicles requires dynamin]

functional light chain gene requires assembly of V and J gene segments

~genes encoding intact immunoglobulins dont exist and instead required gene segments are brought together and assembled during B cell development ~immunoglobulin light chains are encoded by clusters of V gene segments followed downstream by single C element [during B cell development there is commitment to particular V segment (a random process) that results in juxtaposition w/ one J segment (also random) forming exon encoding entire light chain variable region] [recombination signal sequence (RSS)- conserved sequence element at 3' end of each V gene segment] ~deletional joining- recombination method where RSS ends are joined creating deletion circle (containing intervening DNA) which is lost altogether [occurs when V gene segment involved has same transcriptional orientation as other gene segments] [inversional joining- when V gene segments have opposite transcriptional orientation are intervening DNA and RSSs arent lost] ~if opening of hairpin is asymmetric short single stranded palindrome sequence is created (filling in of this overhang results in addition of P-nucleotides that werent part of original coding region) [alternatively the overhang can be removed exonucleolytically resulting in removal of nucleotide from original coding region] [symmetric opening retains all original coding info] ~junctional imprecision- addition and loss of nucleotides at coding joints so when segments combine the reading frame of the product cant be predicted

glial cells form myelin sheaths and support neurons

~glial cells- play role in brain but dont themselves conduct electrical impulses and outnumber neurons 10 to 1 [2 types of glia produce myelin sheaths- (1) oligodendrocytes which make sheaths for central nervous system (2) Schwann cells which make them for the peripheral nervous system] [astrocytes- provide growth factors and other signals to neurons, receive signals from neurons and induce synapse formation b/w neurons] ~astrocytes- surround synapses and influence free concentration of ions in extracellular space so affecting membrane potentials of neurons [produce ECM proteins which are used as guidance cues by migrating neurons and also produce growth factors that carry info to neurons] [astrocytes are joined to each other by gap junctions so changes in composition of one astrocyte is communicated to adjacent astrocytes]

MHC determines ability of 2 unrelated individuals of same species to accept or reject grafts

~helper T cells- T cells that help B cells and are antigen specific [both killer and helper T cells make use of antigen specific receptors whose genes are generated same way as B cell immunoglobulin genes] [antigen specific receptors on T cells recognize short snippets of protein antigens presented to receptors by membrane glycoproteins encoded by major histocompatibility complex (MHC)] ~various antigen presenting cells digest pathogen proteins and then post these snippets to cell surface in physical complex w/ MHC protein [T cells inspect these complexes and if they detect pathogen derived protein the T cells take action] ~human fetus is considered graft b/c it only shares half of the genetic material as mother [if fetal cells end up in maternal circulation it can stimulate maternal immune response against paternal antigens]

nerve cells

~human brain contains 10^11 neurons and these neurons are connected by 10^14 synapses [glial cells occupy the spaces b/w neurons and modulate their functions] ~neuron communicates information by (1) electrical signals [process and conduct info within neurons and the electrical pulses that travel along neurons are called action potentials and info is encoded as freq at which action potentials are fired] (2) chemical signals [transmit info b/w cells utilizing processes similar to those employed by other types of cell signaling] ~sensory neurons- have specialized receptors that convert diverse types of stimuli from environment into electrical signals [electrical signals are then converted into chemical that are passed on to interneurons which convert info back into electrical signals] [info is transmitted to muscle stimulating motor neurons or to other neurons that stimulate other types of cells] ~receiving neuron measures both total amount of incoming signal and whether signals are synchronous [input from one neuron to another can be either excitatory (combining signals to trigger electrical transduction) or inhibitory (signals cancel each other out and discourages transmission)]

immunology

~immune system capable of dealing w/ massively diverse collection of rapidly evolving pathogens may mount attack on host organisms own cells and tissues (autoimmunity) ~2 features that characterize immune system are ability to distinguish b/w closely related substances (specificity) and ability to recall previously experienced exposure to foreign substance (memory) [this is accomplished through antigen specific receptors (diversity) trained on self molecules and purged of self reactive components (tolerance)] ~host defense comprises 3 layers- mechanical/chemical defenses, innate immunity and adaptive immunity [mechanical/chemical defenses are always present, innate responses involve molecules present at all times that are rapidly activated but ability to distinguish pathogens is limited, adaptive responses take days to develop but are highly specific] ~receptors on B cells can interact w/ intact antigens directly while T cells recognize processed (cleaved) forms of antigen presented on surface of target cells by glycoproteins encoded by MHC

immunoglobulin domains have characteristic fold composed of two ß sheets stabilized by disulfide bond

~immunoglobulin fold- domain contains 2 β sheets held together by disulfide bond where hydrophobic residues point inward and stabilize structure [spacing of cysteine residues that make up disulfide bond and small number of strongly conserved residues characterize this structural motif] ~region on antigen where it makes contact w/ corresponding antibody is called epitope [antigen usually has multiple epitopes which are exposed loops and so accessible to antibodies] [each antibody derived from clonal population of B cells recognizes single epitope on corresponding antigen] ~antibodies recognize antigen via variable regions but constant regions determine functional properties like the neutralizing capacity [by binding to epitopes antibodies may block productive interaction b/w pathogen and receptors on host cells thereby neutralizing infection] ~Fc-receptors (FcRs)- antibodies attached to pathogens can be recognized directly by cells that express FcRs specific for immunoglobulins [by means of FcRs phagocytic cells can engage antibody decorated particles and destory them] ~antibody-dependent cell-mediated cytotoxicity- when FcRs allow immune system cells to directly engage target cells where antibodies are attached and this release toxic small molecules of cytotoxic granules (perforins and granzymes) that attach themselves to surface of cell and kill it

adaptive immunity

~immunoglobulins- serum proteins that carry out pathogen destruction [can neutralize bacterial toxins and viruses by binding directly to them in manner that prevents virus from attaching itself to host cells] [produced by B cells] ~passive immunization- antibodies administered that keep toxin/pathogen from binding to its targets in hosts so neutralizes it ~immunoglobulins have 2 identical heavy (H) chains covalently attached to 2 identical light (L) chains [based on biochemical properties they are divided into different classes or isotypes] [there are 2 light chain isotypes λ and κ and heavy chain isotypes are µ, δ, γ, α and ε] ~avidity is defined as sum total of strength of interactions (affinity) of available individual binding sites and number of such binding sites ~transocytosis (when fragment is released from apical side to basolateral side of epithelial cell) if IgG antibodies from maternal circulation across the placenta delivers maternal antibodies to fetus

cell polarization and asymmetry before cell division follow common hierarchy

~in order to know which direction to polarize cells must have specific cues that provide it w/ spatial information [these cues can be localized soluble facrots or signals from other cells or the ECM] ~cell responds to cues by processing incoming signal into spatial info to define orientation of polarity ~local reorganization of cytoskeletal elements and then molecular motors direct trafficking of polarity factors to their appropriate locations ~polarity can be reinforced or maintained through concentration of polarity determinants by moving them from sites of lower concentration back to polarized site

killing activity of killer T cells is antigen specific and MHC restricted

~in virus infected cells MHC molecules interact w/ protein fragments derived from pathogens and display these on cell surface where killer T cells can recognize them [T cells w/ receptors of appropriate specificity destroy target cell membrane and also cell] [MHC restriction- killer T cells for one strain of virus will kill that virus infected target cells from another strain only if 2 strains match at MCH for relevant MHC molecules] ~MHC encodes class I and class II MHC molecules [both involved in presenting antigens to T cells but class I serve to alert killer T cells to presence of intracellular invaders and allows T cells to destroy infected cell while class II are found on antigen presenting cells and when present antigen this means that it requires B cell involvement, cytokine production and assistance from killer T cells] ~B cells dont undergo final differentiation into antibody secreting plasma cells w/o assistance from helper T cells [killer T cells have CD8 marker and are class I MHC restricted while helper T cells have CD4 marker and are class II MHC restricted]

action potentials are propagated unidirectionally w/o diminution

~inability of Na+ channels to reopen during refractory period ensures that action potentials are propagated in only one direction from initial axon segment where they originate to axon terminus ~depolarization of membrane during action potential results from movement of just small number of Na+ ions into neuron and doesnt affect intracellular Na+ concentration [b/c relatively few Na+ and K+ ions move across plasma membrane during each action potential the ATP driven Na+/K+ pump plays no direct role in impulse conduction] [since ion movements during action potential involve so few ions nerve cells can fire hundreds or thousands of times even in absence of ATP]

inflammation is complex response to injury that encompasses both innate and adaptive immunity

~inflammatory response is characterized by 4 classical signs- redness, swelling, heat, pain [caused by increased leakiness of blood vessels (vasodilation), attraction of cells to site of damage and production of mediators responsible for heat and pain] ~chemokines- dendritic cells that sense presence of pathogens via TLRs and respond to them by releasing cytokines [neutrophils- leave circulation and migrate to wherever tissue injury or infection has occurred in response to cytokines and chemokines produced during tissue damage] [activated neutrophils can release bacteria destroying enzymes as well as defensins (also activate enzymes that generate superoxide and ROS which can kill microbes at short range)] ~mast cells- when activated by stimuli they release histamine which increases vascular permeability and facilitates access to plasma proteins (complement) that can act against pathogen ~when pathogen burden at site of damage is high it may exceed capacity of innate defenses to deal w/ them (or pathogens have acquired tools to bypass innate defenses) so adaptive immune response is required to control infection

innate immunity provides a second line of defense

~innate immune system includes macrophages, neutrophils and dendritic cells [all of these are phagocytic and have Toll like receptors (TLRs)] [detect broad patterns of pathogen specific markers and sense presence of invaders] [dendritic cells and macrophages whose TLRs have detected pathogens also function as antigen presenting cells (APCs) by displaying processed foreign materials to antigen specific T cells] ~complement- collection of serum proteins that can bind directly to microbial or fungal surfaces [this binding activates proteolytic cascade that forms pore creating proteins (membrane attack complex) capable of permeabilizing the pathogens protective membrane] [3 distinct pathways can activate complement- (1) classical pathway [requires presence of antibodies produced in adaptive response and bound to surface of microbe] (2) alternative pathway [microbial surfaces w/ physico-chemical properties] (3) mannose binding lectin pathway [pathogens that contain mannose rich cell walls]] [the 3 pathways converge at activation of complement protein C3] ~C3 has strained thioester linkage which becomes highly reactive upon proteolytic activation of C3 [this activated thioester can react w/ molecules in close proximity yielding covalent bond linking C3 w/ nearby protein or carbohydrate [this limits effects of complement to nearby surfaces avoiding inappropriate attack on cells that dont display antigens targeted] ~regardless of activation pathway activated C3 unleashes complement cascade C5 through C9 leading to formation of membrane attack complex which inserts itself into biological membranes making them permeable ~all pathways also generate C3a and C5a which bind to G protein coupled receptors and function as chemoattractants for neutrophils and other cells involved in inflammation [opsonization- phagocytic cells make use of C3a to recognize, ingest and destroy the decorated particles] ~virus infected cells produce interferons which activate natural killer (NK) cells which direct protection by eliminating factory of new virus particles and also secrete IFN-γ which helps antiviral defenses [interferons are classified as cytokines or small secreted proteins that help regulate immune responses]

many oncogenes encode constitutively active signal transduction proteins

~large number of oncogenes are derived from proto-oncogenes whose encoded proteins aid in transducing signals from activated receptor to cellular target ~Ras pathway- any number of changes in Ras protein can leads to its uncontrolled dominant activity [this mutation maintains Ras in active GTP bound state] [Ras transduces signals from activated receptors to cascade of protein kinases that synthesize cell cycle and differentiation specific proteins] ~Src protein kinase- Src oncoproteins have constitutive kinase activity and dont require activation by phosphatase ~Abl protein kinase- oncogene Abl can phosphorylate and activate many intracellular signal transduction proteins (many of which arent normal)

tools to study the cell cycle

~light microscopy shows estimate of cell cycle progression [whether cells are in interphase (G1, S or G2) or in mitosis] [cells are flat and adhere to dish during interphase but round up and form spherical structures as they undergo mitosis] ~fluorescence microscopy shows proteins that are only present in certain cell cycle stages and allows for more accurate determination of cell cycle stage ~use flow cytometry to determine DNA content of cell population [cells are sorted by DNA content and this can determine % of cells in G1, S, G2 or M] [cells in G1 will have half as much DNA as cells in G2 or mitosis] [cells in S will have intermediate amount of DNA] ~to characterize diff cell cycle events must examine cell pops that progress through cell cycle in unison [reversibly arresting cells by restricting nutrients or adding anti growth factors which cause cells to arrest in G1]

mechanical and chemical boundaries form first layer of defense against pathogens

~mechanical defenses include skin, epithelium, arthropod exoskeleton [can only be breached by mechanical damage or through chemo enzymatic attack] ~chemical defenses include low pH in gastric secretions and enzymes like lysozyme ~enveloped viruses possess membrane proteins endowed w/ fusogenic properties [following adhesion of virion to surface of cell to be infected direct fusion of viral envelope w/ host cells membrane results in delivery of viral genetic material into host cytoplasm where its now available for transcription, translation and replication] ~certain pathogenic bacteria secrete collagenases that compromise integrity of connective tissue and so facilitate entry of bacteria

mechanoreceptors are gated cation channels

~mechanosensors embedded in various tissues make us aware of touch, position of limbs/head, pain and temp [these receptors are Na+ or Na+/Ca2+ channels that are gated and open in response to specific stimuli] [activation of these receptors causes influx of Na+ or Ca2+ leading to membrane depolarization] ~MEC4/6/10 are genes for channels that open directly in response to mechanical stimulation ~nociceptors (pain receptors)- respond to mechanical change, heat and toxic chemicals [TRPV1 is a Na+/Ca2+ channel that is activated by heat greater then 43 °C, acidic pH and capsaicin and this activation leads to burning sensation]

mutations that promote unregulated passage from G1 to S phase are oncogenic

~most tumors contain oncogenic mutation that causes overproduction or loss of one of the components of the pathway that controls entry into S phase such that cells are propelled into S phase in absence of proper extracellular growth signals [cyclin D1 is translocated so its transcription is under control of antibody gene enhancer so there is elevated cyclin production throughout cell cycle regardless of extracellular signals] ~it is thought that most if not all human tumors either have mutations in p53 itself or proteins that regulate p53 activity [cells w/ functional p53 become arrested in G1 when exposed to DNA damage] [in normal cells amount of p53 protein is heightened only in stressful situations and then activates ATM/ATR to these sites of damage] [p53 also stimulates production of pro-apoptotic proteins and DNA repair enzymes] ~activity of p53 is normally kept low by Mdm2 which when its bound inhibits transcription activity ability of p53 and catalyzes ubiquitination of p53 marking it for proteasomal degradation [even if functional p53 is produced by tumor cells elevated Mdm2 levels reduce p53 concentration enough to abolish p53 induced G1 arrest] [when p53 G1 checkpoint control doesnt operate properly damaged DNA can replicate perpetuating mutations and DNA rearrangements that are passed on to daughter cells and apoptosis is inhibited leading to evolution of transformed cells]

multi hit model of cancer

~mutation in one cell (perhaps stem cell) gives it slight growth advantage [one of progeny cells would then undergo second mutation that allows its descendants to grow more uncontrollably and form small benign tumor] [third mutation in cell within this tumor would allow it to outgrow the others and overcome constraints imposed by tumor microenvironment and its progeny would form mass of cells each of which would have these 3 mutations] [additional mutation in one of these cells would allows its progeny to escape into bloodstream and establish daughter colonies at other sites] ~colon cancer- both alleles of APC gene (tumor suppressor) carry inactivating mutation and polyps form, one of the cells in polyp undergoes another mutation (activating mutation of ras gene) then it forms larger adenoma, inactivation of p53 (tumor suppressor) follows and results in formation of malignant carcinoma ~Warburg effect- cancer cells utilize glycolysis to produce energy even in presence of oxygen instead of oxidative phosphorylation [glycolysis yields 2 ATP per molecule of glucose instead of 36] ~tumor cells normally are aneuploidy (presence of aberrant number of chromosomes- usually too many)

cancer

~mutations in 3 types of genes have been implicated in onset of cancer- (1) proto-oncogenes [normally promote cell growth and mutations change them into oncogenes whose products are excessively active in growth promotion so result in increased gene expression or production of hyperactive product] (2) tumor suppressor genes [normally restrain growth so mutations that inactivate them allow inappropriate cell division] (3) caretaker genes [normally protect integrity of genome so when inactivated cells acquire additional mutations at increased rate] ~most cancer cells have lost one or more genome maintenance and repair systems due to mutation which may explain the large number of additional mutations they accumulate ~cancer forming process (oncogenesis)- most cancers arise after genes are altered by carcinogens or by errors in copying and repair of genes [series of mutations in multiple genes creates rapidly proliferating cell type that escapes normal growth restraints creating opportunity for additional mutations] [also acquire ability to escape from normal epithelia and stimulate growth of vacsulature to obtain oxygen] ~clone of cells grows into tumor and if primary tumor migrates to new sites where it forms secondary tumors then this called metastasis ~normally occurs later in life b/c it takes many years to accumulate the multiple mutations required to form tumor [common b/c of lack of evolutionary selection against the disease since it normally happens after reproduction age]

neurotransmitters are transported into synaptic vesicles by H+ linked antiport proteins

~neurotransmitters can be acetlycholine, amino acids or derivatives of amino acids or nucleotides like ATP [each neuron generally produces just one type of neurotransmitter] [all signaling by neurotransmitters either results in transmission of electrical signal or its inhibition] ~synthesized in cytosol and imported into synaptic vesicles within axon termini where they are stored [vesicles have low pH generated by proton pumps and this proton concentration gradient powers neurotransmitter import by ligand specific H+ linked neurotransmitter antiporters] [antiporters move neurotransmitter into synaptic vesicles while protons are moved in other direction] ~cytoskeletal fibers in axon terminus help localize synaptic vesicles in active zone [vesicles are linked together by synapsin and filaments of synapsin also radiate from plasma membrane and bind to vesicle associated synapsin to keep vesicles close to part of plasma membrane facing synapse]

trophic factors induce inactivation of Bad a pro-apoptotic BH3 only protein

~neurotrophins protect neurons from cell death and this mediated by protein Bad [in absence of trophic factors Bad is unphosphorylated and binds to Bcl-2 in mitochondrial membrane] [this inhibits ability of Bcl-2 to bind Bax/Bak thereby allowing Bak channels to form and promoting cell death] [phosphorylated Bad cant bind Bcl-2 and is found in cytosol complexed to protein 14-3-3] ~trophic factors (NGF) lead to activation of protein kinase B which phosphorylates Bad and inhibits its pro apoptotic activity ~Bad pro apototic actvity is regulated by diverse transcriptional and post transcriptional mechanisms [Puma and Noxa are transcriptionally induced by p53 and this is part of checkpoint where unrepaired damage to DNA can induce apoptosis] [detachment of cells from microtubule cytoskeleton disrupts integrin signaling and leads to release of Bim] [Bim binds to Bak/Bax releasing them from Bcl-2 and allowing formation of pores and apoptosis] ~cell death can arise from absence of survival factors or can be stimulated by positively acting death signals [both TNF-∂ and Fas are proteins present on surface of cell that binds to death receptors on adjacent cell] [Fas then binds FADD to cell membrane which serves as recruiter to activate initiator caspase and starts amplification cascade]

replication at each origin is initiated only once during cell cycle

~no eukaryotic DNA replication origin initiates more than once per S phase [S phase continues until replication from multiple origins along length of each chromosome results in complete replication of entire chromosome] ~S CDKs initiate DNA replication only at G1-S phase transition and prevent reinitiation from origins that have already fired ~protein complex origin recognition complex (ORC) is associated w/ all DNA replication origins [chromatin associated factors target ORCs to the DNA where ORC and 2 replication initiation factors Cdc6 and Cdt1 associate w/ DNA at origins during G1 to load replicative helicases known as MCM helicase complex onto DNA] [MCM helicases unwind DNA during initiation of DNA replication] ~MCM helicases can only load onto DNA in state of low CDK activity that occurs when CDKs are inactivated during exit from mitosis (and when they are phosphorylated) [activation of MCM helicases and recruitment of DNA polymerases are triggered by S phase CDKs that only become active when CKIs of S CDKs are destroyed] [phosphorylation by S CDK and DDK that activates MCM helicase] ~(1) ORC, Cdc6 and Cdt1 recruit MCM to sires of replication initiation when CDK activity is low (2) DDK and S CDKs are activated in late G1 and phosphorylate MCM and Sld2 and Sld3 [this promotes MCM activators to sites of replication] (3) Cdc45-Sld3 complex and GINS complex recruit polymerase to DNA to synthesize leading and lagging strands ~geminin contributes to inhibition of reinitiation at origins until cells complete full cycle [expressed in late G1 and binds/inhibits MCM loading factors as they are released from origins once DNA replication is initiated [has destruction box that causes it to be degraded in late anaphase so this frees MCM loading factors which are dephosphorylated as CDK activity declines to bind to ORC on replication origins and load MCMs during following G1 phase]

information flows through neurons from dendrites to axons

~nucleus of neuron is found in rounded part of cell called cell body [dendrites are at one end and are main structures where signals are received from other neurons via synapses] [end of cell opposite dendrites forms axon which is the transmission wire] ~axons are covered w/ myelin sheath which is made up of glia cells that provides electrical insulation [insulation speeds electrical transmission and prevents short circuits] [branched ends at end of axon are axon terminus and this is where signals are passed along to next neuron or cell] ~excitable cells- have inside negative voltage (membrane potential) so the potential can suddenly become 0 or be reversed (where inside is positive w/ respect to outside) [membrane voltage in typical neuron (resting potential) is established by Na+/K+ pumps in plasma membrane] [these pumps use ATP to move Na+ ions out of cell and K+ ions inward followed by movement of K+ out of cells through resting K+ channels results in net negative charge inside cell (- 60 mV)] ~depolarization- signals that cause brief voltage changes from inside negative to inside positive [surge of depolarizing change moving from one end of neuron to another is called action potential] ~after action potential passes a sector of neuron channel proteins and pumps restore the inside negative resting potential (repolarization) and this chases action potential down axon to terminus leaving neuron ready to signal again ~action potentials are all or nothing- once threshold to start is reached a full firing occurs [signal info is carried not by intensity but by timing and frequency of them]

plethora of receptors detect odors

~odor molecules have diverse chemical structures so olfactory receptors face the challenge that they need to bind and distinguish many variants of relatively small molecules ~olfactory receptors are produced by cells called olfactory receptor neurons (ORNs) that transduce chemical signal into action potentials ~ORNs extend single dendrite to surface of epithelium so cilia bind to inhaled odorants from air [ORNs also project axons to next higher level of nervous system (so olfactory bulb of brains)] [ORN axons synapse w/ dendrites from mitral neurons and these synapses occur in clusters of synaptic structures called glomeruli] ~despite vast number of olfactory receptors all generate same intracellular signals through activation of same trimeric G proteins (Gαolf) [this leads to production of cAMP which binds to site on cytosolic face of Na+/Ca2+ channel opening the channel and leading to depolarization]

two types of glia produce myelin sheaths

~oligodendrocytes- major protein constituents are MBP (myelin basic protein) and PLP (proteolipid protein) [form spiral myelin sheaths around axons of central nervous system] ~multiple sclerosis is caused by production of auto-antibodies that react w/ MBP or secretion of proteases that destroy myelin proteins ~Shcwann cells- form myelin sheaths around peripheral nerves [each Schwann cell myelinates only one axon and the sheaths are composed of 70% fats and 30% proteins] [MBP and P0 are proteins constituents]

activation of M CDKs initiates mitosis

~once S phase is complete and entire genome has been duplicated the sister chromatids are segregated to future daughter cells [chromosomes condense and attach to mitotic spindle, nuclear envelope is disassembled, organelles are rebuilt or modified which is all triggered by M CDKs] ~M cyclins grdually accumulate during S phase [phosphorylation of tyrosine and threonine maintains M cyclin CDK complexes in inactive state which is controlled by protein kinase Wee1 and phosphatase Cdc25] [activation of M CDKs is consequence of rapid inactivation of Wee1 and activation of Cdc25] [phosphorylation of Cdc25 by M CDKs stimulates its phosphatase activity and phosphorylation of Wee1 by CDKs inhibits its kinase activity] ~M CDKs initially associate w/ centrosomes where they facilitate centrosome maturation and then they enter the nucleus where they bring about chromosome condensation and nuclear envelope breakdown [Polo kinase family is critical for formation of mitotic spindle and Aurora kinases ensure chromosomes attach to mitotic spindle in correct way]

oncogenic receptors can promote proliferation in absence of external growth factors

~oncogene addition- continuous activity of oncogenes is required for survival of many different tumors [dependence of tumor on continuous production of oncogene can provide new opportunities for treatment] ~oncogenes encoding cell surface receptors that transduce growth promoting signals have been associated w/ several types of cancer [these receptors have intrinsic kinase activity] [ligand binding to receptor kinases (RTKs) leads to activation of kinase activity initiating intracellular signaling pathway that leads to proliferation] [point mutation changes normal RTK into one that dimerizes and is constitutively active even in absence of ligand] [deletion of extracellular ligand binding domain also produces constitutively active oncogenic receptor]

generation of antibody diversity and B cell development

~pathogens have short replication times, diverse in genetics and evolve quickly so adequate defense must be able to produce equally diverse response ~B cells use mechanism where genetic info required for synthesis of immunoglobulin heavy and light chains is stitched together from separate DNA sequence element (Ig gene segments) to create functional transcription unit [this is known as somatic gene rearrangement] [this unusual recombination method only in antigen receptors of B and T cells makes it possible to specify enormously diverse set of receptors w/ minimal expenditure of DNA coding space]

CDKs are regulated by activating and inhibitory phosphorylation

~phosphorylation of threonine near active site of enzyme is required for CDK activity [this phosphorylation is mediated by CDK-activating kinase (CAK)] [CAK activity is constant throughout cell cycle and phosphorylates CDK as soon as cyclin-CDK complex is formed] ~highly conserved tyrosine and adjacent threonine are subject to regulated phosphorylation that inhibits CDK activity [both residues are in ATP binding pocket of CDK so phosphorylation interferes w/ positioning of ATP] [kinase Wee1 brings about inhibitory phosphorylation and phosphatase Cdc25 mediates dephosphorylation]

planar cell polarity pathway orients cells within epithelium

~planar cell polarity- cells are polarized in at least 2 dimensions (top to bottom and front to back) ~overall planar polarity of epithelium is determined by gradient of ligand [this gradient polarizes all cells in epithelium in same manner w/ one class of proteins (Frizzled and Disheveled) on one side of the cell and another group (Flamingo and Strabismus) on the other ~mechanisms that set up asymmetric cell divisions- (1) cell fate determinants are segregated to one end of cell before cell division in response to external cues (2) stem cell divides w/ reproducible orientation so that it remains associated w/ stem cell niche whereas daughter is placed away from niche and can then differentiate ~neuroblast stem cell- (1) neuroblast cell enlarges and moves basally into interior of embryo but remains in contact w/ ectoderm epithelium (2) divides asymmetrically (3) gives rise to new neuroblast stem cell and ganglion mother cell [ganglion mother can only divide once giving rise to 2 cells either nerve and/or glial] (4) neuroblast (being stem cell by maintaining association w/ neurogenic ectoderm niche) can divide repeatedly giving rise to many ganglion mother cells and hence neurons and glial cells (5) populates central nervous system

myelination increases velocity of impulse conduction

~presence of myelin sheath around axon increase velocity of impulse conduction to 10-100 meters per second [in nonmyelinated neurons the conduction velocity of action potential is roughly proportional to diameter of axon b/c thicker axon will gave greater number of ions that can diffuse] ~myelin sheath is formed from many glial cells and each region of myelin formed by individual glial cell is separated from next region by unmyelinated area called node of Ranvier [all voltage gated channels and Na+/K+ pumps which maintain ionic gradients in axon are located in nodes] ~saltatory conduction- excess ions generated at node during depolarization spread passively through axonal cytosol to next node w/ no loss of attenuation since they cant cross myelinated axonal membrane [this causes depolarization at one node to spread rapidly to next node and induce action potential there]

B cell development requires input from pre-B-cell receptor

~productive rearrangement generates complete µ heavy chain and production of this indicates to B cell that no further rearrangements are required (B cells in this state are called pre-B cells b/c dont have light chain yet so cant engage in antigen activation) [pre-B cells form complex w/ surrogate light chains but engagement of pre-BCR results in recruitment of kinase which recruits molecules essential for signal transduction] [allelic exclusion- ensures only one of 2 available copies of heavy chain locus will be rearranged and expressed as complete chain] [signals that emanate from pre-BCR initiate pre-B cell proliferation to expand number of B cells that have undergone recombination] ~progressive dilution of surrogate light chains w/ every successive cell division allows real light chains to start recombination [after rearrangement the B cell can make both heavy chains and light chains so assembles into functional B cell receptor (BCR) which can recognize antigen]

separase mediated cleavage of cohesions initiates chromosome segregation

~protease called separase cleaves subunit of cohesion called Scc1 or Rad21 breaking the protein circles linking sister chromatids [once this link is broken anaphase begins as the force exerted on kinetochores now moves split sister chromatids towards spindle poles ~prior to anaphase securin binds and inhibits separase [once all kinetochores have attached to spindle microtubules in correct way the APC/C ubiquitin ligase directed by Cdc20 ubiquitinates securin which is degraded by proteasomes thereby releasing separase] ~APC/C (Cdc20) is activated in prophase by M CDK phosphorylation of several APC/C subunits [however this APC/C isnt active until all chromosomes have bi oriented on mitotic spindle] ~Cdc20 is inhibited until every kinetochore has attached to microtubules and tension is applied to kinetochores of all sister chromatids pulling them towards opposite spindle poles ~M CDK activity inhibits separase during prophase and metaphase [only when M CDK activity declines at meta-ana transition through APC/C mediated protein degradation can separase become active and trigger chromosome segregation

T cells require 2 types of signal for full activation

~require signal via antigen specific receptor (TCR) for activation but also need co stimulatory signals (CD28 and CTLA4) [co stimulatory molecules can either be stimulatory or inhibiting and provide means of controlling activation status and duration of T cell response] ~killer T cells carry CD8 protein marker and are restricted in recognition by class I molecules [kill target cells that display even single appropriate MHC-peptide combination] [killing involves perforins and granzymes that act synergisitically] [performins- form pores in membranes to which they attach and leads to loss of small solutes which kills cell] [granzymes- enter target cell via pores created by perforin and activate effector caspases to propel target on path of apoptosis] [open binding of T cell receptor to antigen cytotoxic granules (containing perforin and granzyme) are released into cleft formed b/w T cell and target cell] ~cytokines bind to receptors on lymphocyte surface and initiate transcriptional program that allows lymphocyte to either proliferate or differentiate into cell ready to exert cytotoxic activity (CD8 T cells), helper activity (CD4 T cells) or antibody secreting activity (B cells) [cytokines produced by or that act on leukocytes are called interleukins] ~IL-2 acts as autocrine growth factor and drives clonal expansion of activated T cells, IL-4 helps B cells to proliferate and undergo class switch recombination and somatic hypermutation, IL-7 is essential for development of B and T cells from committed precursors, IL-7 and IL-15 play role in maintenance of T cells in form of memory cells

aberrations in signaling pathways that control development are associated with many cancers

~secreted signals like Hh, Wnt and TNF-ß are used to direct cells to particular developmental fates [effects of such signals must be regulated so that growth is limited to right place and time] [mechanisms available for stopping developmental signals are inducible intracellular antagonists, receptor blockers and competing signals] [mutations that prevent restraining mechanisms from operating are likely to be oncogenic causing cancerous growth] ~tumor suppressor gene mutations wont cause cancer in tissues where primary role of developmental regulator is to control cell fate but not cell division [mutations in developmental proto-oncogenes may induce tumor formation in tissues where affected gene normally promotes cell proliferation or in another tissue where gene has become aberrantly active]

signaling at synapses is terminated by degradation or reuptake of neurotransmitters

~signaling can be terminated by diffusion of transmitter away from synaptic cleft but this is slow process ~acetylcholine is terminated when its hydrolyzed to acetate and choline by acetylcholinesterase [choline is transported back into presynaptic axon by Na+/choline symporter and used in synthesis of more acetylcholine] ~all other neurotransmitters are removed by transport back into axon by being recycled intact [movement of Na+ into cell down its electrochemical gradient provides energy for uptake of neurotransmitter] [to maintain electroneutrality Cl- is often transported via ion channel along w/ Na+]

nerve cells make all or nothing decision to generate action potential

~single neuron can be affected simultaneously by signals received at multiple excitatory and inhibitory synapses [neuron integrates these signals and decides whether or not to generate action potential] ~various small depolarizations and hyperpolarizations generated at synapses move along membrane from dendrites to cell body to axon where they are summed together [action potential is generated if sum at axon causes depolarized to certain voltage (threshold potential)] ~action potential will always have same magnitude in any particular neuron [its the frequency w/ which action potentials are generated in particular neuron thats the important parameter in its ability to signal other cells] ~electrical synapses- sometimes signals go from cell to cell electrically w/o intervention of chemical synapses [this depends on gap junction channels that link 2 cells together] [electrical synapse is bi directional so either neuron can excite the other] [differences- transmission is instantaneous, presynaptic cell doesnt have to reach threshold at which it can cause action potential (any electrical current continues to next cell and causes depolarization in proportion to current)]

spindle position checkpoint pathway ensures that nucleus is accurately partitioned b/w 2 daughter cells

~site of cytokinesis is determined during G1 so axis of division is defined before mitosis and mitotic spindle must be aligned along this axis during every cell division [when this process fails spindle position checkpoint prevents M CDK inactivation giving cell opportunity to reposition spindle prior to cytokinesis] [if spindle checkpoint fails cells misposition spindles and give rise to mitotic products w/ too many or too few nuclei] ~Tem1 associates w/ spindle pole bodies as soon as they form [inhibitor of Tem1 called Kin4 localizes to mother cell but is absent from daughter cell and an inhibitor of Kin4 called Lte1 localizes to daughter cell but is absent from mother and inhibits any residual Kin4 that leaks into daughter] ~when spindle microtubule elongation has correctly positioned segregating daughter chromosomes Tem1 inhibition by Kin4 is relieved so Tem1 activates kinase signaling cascade which inhibits Cdc14 releasing Cdc14 phosphatase into cytoplasm and nucleus in both mother and daughter cell [once active Cdc14 is available M CDKs are inactivated and cells exit mitosis] ~when spindle fails to position correctly Tem1 cant activate mitotic exit network so cells arrest in anaphase

spindle assembly checkpoint pathway prevents chromosome segregation until chromosomes are accurately attached to mitotic spindle

~spindle assembly checkpoint pathway prevents entry into anaphase until every kinetochore of every chromatid is properly attached to spindle microtubules [recognize and bind to unoccupied microtubule binding sites at kinetochores and create anaphase inhibitory signal] [kinetochore bound Mad2 rapidly exchanges w/ soluble form of Mad2 that inhibits all Cdc20 in cell] [when microtubules attach to kinetochores they release bound Mad2 and cease process] ~entry into anaphase is also inhibited when attachments of microtubules to kinetochores are faulty [faulty interactions are destabilized by Aurora B phosphorylation and this leads to generation of unattached kinetochores which are recognized by spindle assembly checkpoint] ~nondisjunction- when anaphase is initiated before both kinetochores of replicated chromosome become attached to microtubules from opposite spindles the dauughter cells that are produced having missing or extra chromosomes

stem cells give rise to both stem cells and differentiating cells

~stem cells have 3 key properties- (1) can give rise to multiple types of differentiated cells (multipotent) [different from progenitor cells which give rise to single type of differentiated cell] (2) stem cells are undifferentiated so dont express proteins characteristic of differentiated cell types formed by their descendants (3) number of stem cells of particular type remains constant over lifetime ~can divide symmetrically to yield 2 daughter cells identical to itself or divide asymmetrically to generate one copy of itself and one daughter stem cell that has more restricted capabilities ~stem cells have ability to reproduce themselves indefinitely so they must divide asymmetrically to form one daughter stem cell identical to itself [many stem cell divisions are symmetrical but at some point progeny need to differentiate] ~mitotic division of stem cells can either enlarge population of stem cells or maintain stem cell population while steadily producing stream of differentiating cells

stem cells for different tissues occupy sustaining niches

~stem cells need intrinsic regulatory signals (presence of certain regulatory proteins) and extrinsic hormonal and regulatory signals from surrounding cells to maintain status as stem cells [location where stem cell fate is maintained is called stem cell niche (right combination of intrinsic and extrinsic regulation that supports existence and competitive advantage of particular population of stem cells)] ~2 or 3 germ cell lines in location (germarium of oocyte) next to cap cells which create niche by secreting TGF-ß and Hedgehog proteins [TGF-ß signals repress transcription of differentiation factor Bam protein in neighboring germ line stem cells] [stem cells are held in niche by transmembrane cell surface protein E-cadherin] [Arm connects cytoplasmic tails of E-cadherin to actin cytoskeleton and maintains stem cell niche] ~when germ line stem cell divides one of daughters remains adjacent to cap cells and is maintained as stem cell while other daughter is displaced and becomes cystoblast (Bam expression turns on causing germ cell to differentiate0] ~each seminiferous tubule contains small number of germ line stem cells that divide asymmetrically to recreate themselves and to produce spermatogonial cells which proliferate and progeny become spermatocytes (eventually become sperm) [niche is created by specialized region of Sertoli cell along w/ myoid cell]

cyclin levels are primarily regulated by protein degradation

~timely activation of CDKs depends on presence of appropriate cyclins in cell cycle stage where they are needed [transcriptional control of cyclin is one mechanism that ensures proper temporal expression of cyclins] [waves of transcription factor activities help establish waves of cyclin activity] ~transcription of G1/S cyclins is promoted by E2F transcription factor complex (transcribes transcriptions factors that promote synthesis of mitotic cyclins) ~imp regulatory control that restricts cyclins to appropriate cell cycle stage is ubiquitin mediated proteasome dependent protein degradation [since irreversible it ensures cell cycle engine is drive forward and cells cant go backward in cell cycle] [cyclins are degraded through action of ligases SCF and anaphase promoting complex or cyclosome (APC/C)] [SCF controls G1-S transition by degrading G1/S cyclins and CDK inhibitory proteins] [APC/C degrades S and mitotic cyclins promoting exit from mitosis] ~SCF recognizes substrates only when they are phosphorylated and SCF is continuously active throughout cell cycle [APC/C is activated by phosphorylation at metaphase-anaphase transition so its then active throughout rest of mitosis and during G1 to promote degradation of cyclins] ~during anaphase APC/C bound to Cdc20 ubiquitinylates proteins that lead to chromosome segregation while during telophase and G1 APC/C Cdh1 targets diff substrates for degradation [substrates of APC/C contain recognition motifs including destruction box which is found in most S and mitotic cyclins]

T cell development

~to generate antigen specific receptors T cells rearrange genes encoding T cell receptor subunits by somatic recombination identical to B cells rearranging immunoglobulin genes ~T cells recognize antigens only together w/ polymorphic MHC molecules that happen to be present in host [T cells must learn identity of self MHC molecules and which MHC peptide complexes to ignore] ~T cells that have been activated through engagement of antigen specific T cell receptors proliferate and acquire capacity to kill target cells or to secrete cytokines that assist B cells in their differentiation [RAG deficiency prevents both B and T cell development] ~TCR genes are just like immunoglobulin genes except they dont undergo somatic hypermutation [dont have affinity maturation of antibodies during course of response and cant class switch recombination or use alternative polyadenylation sites to create membrane bound versions of antigen specific receptors]

cancer causing viruses contain oncogenes or activate cellular proto-oncogenes

~transducing retrovirus- oncogenes in these viruses arose from transducing normal cellular proto-oncogene into their genome where it was mutated and converted into oncogene which can induce cell transformation even in presence of normal proto-oncogene ~slow acting retroviruses- dont have oncogene but cause cancer by integrating into host cell DNA near proto-oncogene and activating its expression [act slowly b/c integration near proto-oncogene is rare event and additional mutations have to occur before full fledged tumor appears] ~tumor suppressor genes encode proteins that inhibit cell proliferation so loss of function in mutations in these genes leads to development of cancer [proteins encoded by tumor suppressor genes are (1) intracellular proteins that inhibit entry into cell cycle [p16 and Rb] (2) receptors for secreted hormones that inhibit cell proliferation [TGF-ß and Patched] (3) checkpoint control proteins that arrest cell cycle if DNA is damaged or is chromosome segregation is abnormal [p53] (4) proteins that promote apoptosis (5) enzymes that participate in DNA repair] [recessive so both alleles of gene must be inactivated to promote tumor development]

leukocytes circulate throughout the body and take up residence in tissues and lymph nodes

~transport function of circulation ensures delivery of lymphocytes from sites where they are generated (bone marrow, thymus, fetal liver) to sites where they can be activated (lymph nodes, spleen) and then to site of infection ~primary lymphoid organs- sites at which lymphocytes are generated and acquire their properties include thymus (where T cells are generated) and bone marrow (where B cells are generated) ~secondary lymphoid organs- adaptive immune responses are initiated in lymph nodes and spleen (require functionally competent lymphocytes) ~vertebrate blood vessels allow escape of fluid from circulation driven by positive pressure exerted by heart [fluid contains proteins that carry out defensive functions] [fluid that leaves circulation ultimately returns in the form of lymph via lymphatic vessels] ~blood carries B and T cells to lymph nodes and lymph carries cells that have encountered antigens (as well as some antigens) from tissue to lymph nodes [in lymph nodes cells required for adaptive response interact and execute necessary function to rid body of pathogen] ~cells that have received instruction from lymph node drain into circulation and move into tissues where they destroy pathogens

cancers usually originate in proliferating cells

~tumor promoting mutations have ability to transform nondividing terminally differentiated cell into proliferating cell w/ precursor like properties [in some cancers return of cell to precursor like state could be tumor initiating event] [whether tumors originate from differentiated cells that have regained ability to proliferate or through mutated stem cells there are only certain cells w/ ability to divide uncontrollably and generate new tumors (cancer stem cells)] ~inflammatory response can promote tumorigenesis (immune cells produce growth factors to promote healing) and tumor formation can trigger inflammatory response (oncogenes induce transcription that leads to recruitment of macrophages which produce cytokines w/ additional growth factors and promote blood vessel growth) ~angiogenesis- tumors induce formation of new bloods vessels that invade tumor and nourish it [requires degradation of basement membrane that surrounds nearby capillary, migration of endothelial cells lining capillary into tumor, division of these endothelial cells, formation of new basement membrane around newly elongated capillary] [b-FGF, TGF∂ and VEGF are secreted by tumors and have angiogenic properties]

metastatic tumor cells are invasive and can spread

~tumors arise w/ great freq but if they are localized and small then they are benign [cell adhesion molecules keep benign tumor cells localized to tissues where they originate] [only become problem if they are large and interfere w/ normal functions or if they secrete excess amounts of hormones] ~malignant cells can invade nearby tissues (spreading and seeding additional tumors while cells continue to proliferate) ~normal cells are restricted to place in tissue by cell-cell adhesion and by physical barriers like the basement membrane [cancer cells have ability to penetrate basement membrane using cell protrusion call invadopodium] ~during metastasis EMT regulatory pathways (epithelial to mesenchymal transition where there is a change in pattern of gene expression and results in changes in cell morphology like loss of cell-cell adhesion, loss of cell polarity and acquisition of migratory and invasive properties) are activated at invasive front of tumor producing single migratory cells [Snail and Twist are 2 transcription factors involved in EMT and cause down regulation of cell adhesion factors] ~as basement membrane disintegrates some tumor cells enter bloodstream but few survive (circulating tumor cells) to colonize another tissue and form secondary metastatic tumor [after escaping original tumor and entering blood cells will seed new tumors must then adhere to endothelial cell lining capillary and migrate across it into underlying tissue (this is called extravasation)]

five primary tastes are sensed by subsets of cells in each taste bud

~we taste many chemicals that are hydrophilic and nonvolatile molecules floating in saliva [many toxic substances taste bitter or acidic and nourishing foods taste sweet] [taste is less demanding of nervous system then smell b/c fewer types of molecules are monitored] ~there are receptors for salty, sweet, sour, umami and bitter and these receptors can either be channel proteins (for salty and sour) or seven transmembrane domain proteins (for sweetness, umami and bitterness) ~taste buds are located in bumps in tongue called papillae and the microvilli on taste cells apical tips bear taste receptors directly contacting external environment in oral cavity [reception of taste signal causes cell depolarization that triggers action potential] ~bitter taste- detected by family of G protein coupled receptors known as T2Rs [different bitter taste molecules are quite distinct in structure so this accounts for the diverse family of T2Rs] [multiple T2Rs are often expressed in same taste cell and about 15% of all taste cells express T2Rs] ~sweet/umami taste- detected by T1Rs [T1R3 is receptor for both sweet and umami and thats b/c it detects sweets when combined w/ T1R2 and umami when combined w/ T1R1] [taste cells express either T1R1 or T1R2 not both b/c this would send ambiguous message to brain] ~salty taste- sensed by family of Na+ channels called ENaC channels ~sour taste- due to detection of H+ ions [many sour molecules are weak organic acids which in their protonated forms diffuse through membrane and acidifies the cytosol] [protons block sensitive K+ channel and thus depolarize membrane]

cells are irreversibly committed to cell division at a cell cycle point called START

~when cells in G1 have grown sufficiently in size they begin gene expression that leads to entry in cell cycle [if G1 cells are shifted from rich medium to medium low in nutrients before they reach critical size they remain in G1 however once they reach critical size they become committed to completing cell cycle even if they are shifted to medium low in nutrients] ~CDK activity is essential for entry into S phase [G1 CDKs stimulate formation of G1/S CDKs which then initiate bud formation, centrosome duplication and DNA replication] [G1 cyclin gene is CLN3 and its mRNA is produced at constant level throughout cell cycle but its translation is regulated in response to nutrient levels] ~once sufficient Cln3 is synthesized from mRNA Cln3-CDK complexes phosphorylate and inactivate transcriptional repressor Whi5 (this promotes its export out of nucleus and SBF induces transcription of G1/S cyclin genes as well as other important genes for DNA replication)

extracellular signals govern cell cycle entry

~whether or not cells enter cell cycle is influenced by extracellular as well as intracellular signals [critical cell size is controlled by nutrients available in environment] ~G1 cyclin synthesis is responsive to protein synthesis rate which is in turn controlled by pathways that are regulated by nutrients in environment [in multicellular organisms cells are surrounded by nutrients and so this isnt rate limiting for proliferation [controlled by presence of growth promoting factors (mitogens) and growth inhibitory factors (anti mitogens) in cells surroundings] ~mitogens activate transcription of multiple genes- early response or delayed response genes [transcription of early response genes induced within few minutes after addition of growth factors] [many of these early response genes encode transcription factors that stimulate transcription of delayed response genes] ~anti mitogens prevent accumulation of G1 CDKs and antagonize production of G1 cyclins and induce production of CKIs [TGF-ß is anti mitogen hormone that induces signaling cascade that brings about G1 arrest]