Block 1 Review Study Slides PDF

Block 1 Review: Study Slides BMS 532 MOLECULAR BIOLOGY AND GENETICS BLOCK 1 REVIEW SLIDES FOR STUDY ASSISTANCE Overall Study Aids: An Example of Functional Summaries Molecule or Activity/Area of Impact If upregulated or activated If downregulated or inactivated Structure MAD2...

Block 1 Review: Study Slides BMS 532 MOLECULAR BIOLOGY AND GENETICS BLOCK 1 REVIEW SLIDES FOR STUDY ASSISTANCE Overall Study Aids: An Example of Functional Summaries Molecule or Activity/Area of Impact If upregulated or activated If downregulated or inactivated Structure MAD2 Signal that indicates an MAD2 present = Kinetochore is unattached Attached Kinetochores = GO for unattached kinetochore The cell should NOT progress THUS if anaphase (soluble version = upregulated or activated: mitosis will STOP Loss of MAD2 = loss of regulation unattached) NO MAD2 = mitosis will GO CDC20 Rate-limiting for APC If available and able to bind APC, cell is GO If unavailable (i.e. bound to MAD2, activity for anaphase cell will STOP (no anaphase) THUS more CDC20 or activated CDC20 THUS loss of CDC20 will stall the cell should make the cell GO EXCEPTION: Functional MAD2 that can bind will BLOCK DREAM Suppress E2F DREAM forms and blocks E2F transcription = No DREAM = potential for E2F- transcription no G1 to S progression; if more = cell stuck mediated transcription in G1 Loss of DREAM = potential for S phase Arp2/3 Actin nucleation and More Arp2/3 = more potential for actin No or less Arp2/3 = less branching polymerization and branching polymerization and branching = reduced motility BCL-2 Suppress apoptosis More BCL-2 = less apoptosis Less BCL-2 = more apoptosis Review of Cell Structures Cell Structure Function Additional Considerations Rough Endoplasmic Reticulum Synthesis and processing of Close association with ribosomes; proteins needed at plasma important for synthesis of membrane and for export excreted proteins Smooth Endoplasmic Reticulum Metabolism and detoxification of Expanded in cells responsible for exogenous proteins detox or processing of toxins Golgi Apparatus Processing (sorting and exporting) Impairment or loss would impact vesicular trafficking Mitochondrion Energy Required for cellular replication and maintenance of cell energy Lysosomes Degradation of material Required for autophagy and recycling Vesicles Transport of material Required for movement to and from plasma membrane and between organelles Vesicular Trafficking Definitions ◦ Anterograde: rER to Golgi to plasma membrane ◦ Retrograde: backward (plasma membrane back toward organelles or to lysosome; Golgi to rER) Compare and Contrast Anterograde Retrograde Kinesin Dynein COPI, COPII, Clathrin COPI **the only coating that would enable movement in both directions would be COPI Microtubules Microtubules  Minimal Threshold Model G1 to S During S G2 to M During M Cyclin E/CDK2 Cyclin E/CDK2 Cyclin A/CDK1 or Cyclin B/CDK1 CDK2 Hochegger et al 2008, Nature Reviews Overview of Regulation Players that PROMOTE division/proliferation ◦ CDK activity regulated by cyclin availability ◦ E2F transcription ◦ Hyperphosphorylation (Rb and others) Players that SUPPRESS division/STOP division ◦ p21 ◦ DREAM ◦ Hypophosphorylation ◦ Lack of CDK activity due to lack of cyclins 7 Mitosis Summary Stage Details Additional information Prophase Chromosome condensation and spindle General stage at which cytoskeletal issues formation would stall the cell; stage of chromosome condensation Prometaphase Chromosomes begin to associate with Variable and frequently not included in the list spindle fibers of stages; associated with the movement of centrosomes and nuclear envelope breakdown Metaphase Alignment of chromosomes at Checkpoint prior to chromosome segregation; metaphase plate (equator) role of Anaphase promoting complex Anaphase Separation of chromosomes Breakdown of cohesion precipitates sister chromatid separation Telophase Chromosome arrival at the poles Nuclear envelope reforms and chromosomes decondense; failures in cytokinesis would stall the cell here Cytokinesis Division of cytoplasm Requires actin, myosin, and microtubules Meiosis Summary Stage Details Prophase I Chromosome condensation, nuclear envelope breakdown; beginning of chromosome association with spindle fibers; Crossing-over Metaphase I Alignment of chromosomes on metaphase plate; entirely random but enables segregation of homologous chromosomes Anaphase I Separation/segregation of homologous chromosomes in duplicated form Telophase I Chromosomes arrive at poles; breakdown of spindles; (variable decondensation and nuclear envelope reformation); daughter cells include 1 copy of each duplicated chrom. Interkinesis Space between division phases; spectrum of consequences with some cells entirely decondensing chromosomes and reforming the nucleus and others skipping this entirely Prophase II Resembles prophase and prophase I; new spindles are required Metaphase II Chromosome alignment on metaphase plate randomly Anaphase II Sister chromatid separation Telophase II Chromosomes arrive at poles; reform nuclear envelope and decondense Cytokinesis Identical to mitosis except daughter cells are haploid with 1 copy of each chromosome Contractile Ring Formation The players in focal adhesion formation are responsible for creating contractile forces and the contractile ring is a type of contractile force Positioning of the ring is determined by signals or activity of microtubules ◦ Concentration of signals and responses determining location of contractile ring ◦ Past divisions can influence positioning  Division of Cytoplasm: Cytokinesis In typical somatic mitosis, the division is nearly perfectly in half with each daughter cell receiving half the cytoplasmic contents In embryogenesis, asymmetrical cell divisions are possible enabling concentration of materials into one of the two daughter cells generating concentration gradients Polarity in cells can be generated via asymmetrical cell division This enables the development of cells that are unique in materials and gene expression ◦ Part of morphogenesis and specialization of cell types Berricka et al 2014 Rose and Gonczy 2014 Oogenesis Oogenesis is a complex process with much remaining poorly defined or understood During oogenesis of humans prenatally there is a large loss of cells ◦ Selection methods are unknown and remain of significant interest in fertility studies Overall, during oogenesis, there are 2 distinct pauses in meiosis ◦ 1. pre-puberty the process arrests at prophase I of meiosis ◦ 2. after-puberty but before fertilization the cell arrests at metaphase II Ovulation leads to release of the arrest oocyte where meiosis can continue in conjunction with fertilization Linking this block to human disease and the next block… Variation at the genetic level that impacts cellular behavior and function is the basis of human disease Proteins exhibit their effects and consequences of their activities are observed at the cellular level Changes in signaling, growth, differentiation, or apoptosis: ◦ Pathogenic if the variation increases growth or reduces differentiation or apoptosis ◦ Benign if changes do not alter overall cellular activity or tissue behavior ◦ Unclear/Uncertain if the link has not yet been established or the consequence not yet fully understood LO1, LO2 Necrosis vs. Apoptosis NECROSIS Apoptosis Harmful to NOT harmful neighboring to neighboring cells due to cells due to leakage of controlled cellular management contents Activity of Changes in DNA nucleases ions, destroys DNA osmolarity, in an and pH organized Can begin with fashion signaling and Can be mitochondria triggered and but ends will involve differently mitochondria to carefully deal with cell contents LO1, LO2 More on Autophagy Macroautophagy General Stages Upstream Signal Membrane Nucleation Elongation and closure of autophagosome Fusion with lysosome Degradation and Release of Contents  Actin vs Microtubules ACTIN MICROTUBULES 1. Polymerization of actin monomers requires 1. Polymerization of alpha-beta tubulin ATP hydrolysis dimers via GTP hydrolysis 2. Initiation and nucleation via Arp2/3 (also 2. Requires APC to associate with focal needed for branching); APC helps with adhesions and ACF-7 for crosslinking with polymerization of actin filaments actin; extend TOWARD periphery in movement 3. Generates protrusive forces and resists compressive forces 3. Generates contractile forces and plays a key role in defining polarity 4. Helps generate and maintain cell geometry ◦ Role in structural integrity 4. Also plays a role in cell geometry (organization matches geometry) **Alterations of actin and especially actin associated **Alterations in tubulin impact migration and structural proteins most profoundly impact motility and migration development LO5 The 4 Pillars of Cellular Migration in Embryogenesis Polarization ◦ Gives directionality to the movement ◦ Defines front from back (**Microtubules play a role here) Protrusion ◦ Actual start of movement/migration ◦ Involves leading edge and polymerization of actin (**Actin will typically be BRANCHED as a network in mesenchymal migration and lamellipodia; PROTRUSIVE FORCES HERE) Adhesion ◦ Attachment to surrounding matrix via integrins and formation of focal adhesions ◦ Gives cell pushing off force (**APC attachment of microtubules at focal adhesions plays a role here; CONTRACTILE FORCES HERE) Retraction ◦ Release of adhesions at the rear to enable forward movement (Movement/Forward Momentum due to release of CONTRACTILE force) LO1, LO2 Signaling Pathway Basics Post-translational modifications of proteins are critical to the function and activity of signaling pathways Termination Initiation Propagation and Reset Receptor dimerization Signal Mediators Recycle receptor and Degrade proteins autophosphorylation Build new proteins for next activity Each step in a pathway can serve as a point for regulation of the pathway ◦ Enzymes represent a key means of controlling the rate and progression of the reactions 19 Cell Signaling OVERVIEW Pathway leads to growth (mitogenic) Pathway leads to death (apoptotic) Pathway leads to movement (migration or motility) Pathway leads to specialization (role in development or differentiation) Pathway triggers more than 1 activity (typical for growth stimulatory in development or embryogenesis) All of the activities discussed in the block are linked to the activity of cell signaling! General MAP Kinase Signaling Kinase signaling involves changes in phosphorylation along a pathway Multiple kinases are involved with specificity for the next kinase in the pathway Often exhibit overlap and cross-talk with other MAP = mitogen pathways activated protein Growth factor signaling is a form of MAP kinase signaling ALL MITOGENIC SIGNALING IS GROWTH STIMULATORY!! 21 The pathways… Using your general knowledge of signaling and given a pathway, you should be able to: ◦ Explain what “upstream effectors” are and how they initiate a signal ◦ Determine what component would generate the described change to a signaling pathway ◦ Identify mediators and regulators ◦ Explain effects if a change to a mediator or regulator occurs ◦ Explain what changes could counteract a specific change ◦ Determine/define how “downstream effects” are generated (role of transcription factors) ◦ Explain the role of domains in signaling and the consequence of losing domains