Biology Module 2: Cell Biology Reminder of the tenets of cell theory:- Cells are the fundamental units of life- All living things are made of cells- All cells come from pre-existing cellsCompare and Contrast: Prokaryotes and EukaryotesBoth eukaryotic cells and prokaryotic cells have DNA, ribosomes and cytoplasm. Eukaryotic cells have a nucleus and organelles while prokaryotic cells do not. Organelles are membrane-bound structures within cells that are important for compartmentalizing and regulating trafficStudying cells Light Microscopy- Limit of resolution 200nm- Used to see general size and shape of cells and large organelles- Specifically binds a particular portion of a specific protein; polysaccharide- DAPI is used to see the nucleus and binds to the minor groove of DNA and fluorescesFluorescence microscopy- Limit of resolution 200nm- Used to see specific cell components- Epifluoresence: blurry- D2.1- Confocal fluorescence: clearer- D2.2Electron microscopy- Used to see subcellular structures and surfaces in more detail- Practical limit of resolution 2-3 nm- Can be used to see protein polymers- D2.3- Transmission microscopy up to 250,000x- Used to closely see one unit- D2.4- Scanning electron microscopy up to 50,000x- Used to see several units- D2.5Crystallography- Used to solve 3-D structures of proteins and nucleic acids- D2.6Differential centrifugation- Used to separate cell components- D2.7Density gradient centrifugation- D2.8Subcellular Structure-The actin cytoskeleton“A cell is kinda like a pool with a floating octopus”Filamentous proteins- Microfilaments: small diameter; polymer made of actin- Intermediate filaments: intermediate diameter; comprised of various proteins- Microtubules: large diameter made of alpha and beta proteinsCytoskeletal filaments are long chains made up of repeating protein subints- Protein monomer (D2.9)- Protein heterodimer(D2.10)Microfilament subunits are called actin monomers- Globular and filamentous actin- Globular individual subunits form filamentous actinActin filaments are asymmetric/have polarityActin forms different types of bundles that help to shape the cell- Contractile bundle (stress fiber)- D2.11- Cell cortex (gel-like network)- D2.12- Filopodium (tight parallel bundle)- D2.13Dynamic actin filaments extend and retract Filopodia as they polymerize and depolymerizeActin filaments support relatively stable microvilli that help to increase surface area of a cell (and also look like Top Thrill Dragster and Kingda Ka)D2.14 and D2.15Dynamic actin filaments extend lamellipodia (protrusion; gel-like network/bundle) to facilitate cell crawlingMyosins are motor proteins that use the energy from ATP hydrolysis to travel along actinD2.16Allows direction movement and coordinated contractionSome myosins can carry “cargo”Allows directional transport of substances across the cell- Myosin can move organelles and cytoplasm in plants: cytoplasmic streaming- Actin filaments can form antiparallel bundles that allow contraction similarly to myosin- Filamentous myosin (myosin II) effects contraction of antiparallel actin filaments- Muscle cells- Electron microscopy- Cytokinesis in all animal cells- D2.17Intermediate filaments provide the cell with tensile strength- Long chains- Rope-like structure- Many bonds forming, such as hydrogen bonds, which are weak but the sum is strong2 proteins= dimerIntermediate filaments are less dynamic than actin which grows and shrinks very quicklyImmunofluorescence is used to study IfsIfs are vital for cell-cell interactionsDesmosomes:- Hold shit together in areas where the tissues are exposed to high mechanical forces such as the skin and the heart- D2.18Hemidesmosomes- Cell-striatum interactions- D2.19- StructureNuclear Lamins- Located in the nucleus- Gives the nucleus shape and anchors chromosomes- Progeria is a mutation in the nuclear laminsIf subunits are antiparallel heterotetramer then there is no directionality and the ends are identical to one anotherMicrotubules- Alpha and beta tubulin heterodimers- Chain of 13 forms hollow rigid, unbranched tubes (unlike actin)- D2.20- Microtubules give cells shape, resist particularly compression force, and form a structural framework for organelles (organization)- They form a radial network- similar to roads into/out of a city- Originate at the Microtubule Organizing Center (MTOC)- D2.21- Unlike Intermediate Filaments, microtubules are asymmetric and have polarity- Alpha end is positive- Beta end is negative- Contain motor proteins which are important for directional transport- Kinesin is positive- Dynein is negative- D2.22Motors “walk” along the microtubule where every step hydrolyzes ATP into ADP and Phosphate for energy- D2.23Kinesin and Dynein control the coloration in fish and amphibians by carrying pigment granules- D2.24Microtubules form the mitotic spindle where the chromosomes align- Not static, will gain and lose subunitsCancer cells can be targeted using microtubulesMicrotubules form the core of cilia (located in fallopian tubes for example) and eukaryotic flagella (only sperm cells)“9 and 2” arrangement of microtubules in cilia and flagella-known as the axonemCilia and flagella movement is powered by motor proteins- Dynein- hydrolyses ATPSteps in protein synthesis- Transcribe info encoded by DNA into mRNA- Translate info encoded by mRNA into protein- Fold and modify protein- Deliver protein to its proper place within or outside of the cellThe nucleusFunctions:- DNA Replication- Transcription- mRNA processing- Ribosome assemblyThe nuclear envelope has a double membrane and is selectively permeableRole:- Protection- Nucleotides- mRNA and ribosomesAll incoming and outgoing traffic goes through nuclear pores (aqueous)Large proteins only get in if they have a series of amino acidsNLSSmall molecules can diffuse through pores- Ribosomes are assembled in the nucleolus and are machines for protein synthesis- Cytosolic, Mitochondrial, nuclear proteins are translated by free ribosomes- Endomembrane and secreted proteins are translated by ribosomes bound to the Rough ERThe Endomembrane System- The ER is contiguous with the nuclear envelope- An RER signal sequence steers ribosomes translating endomembrane system and secreted proteins to the ER- Proteins are folded and glycosylated in the RER lumen- Chaperone proteins monitor folding- Adding sugars to protein is call glycosylation- The RER is in charge of quality control- Proteosome- degrades missed folded