Prokaryotic vs Eukaryotic Cells Organelles PROKARYOTES EUKARYOTES Cell

Prokaryotic vs. Eukaryotic Cells

Organelles PROKARYOTES EUKARYOTES Cell (plasma) membrane Cell wall Cytoplasm Nucleus Cell (plasma) membrane Cell wall (plant cells only) Cytoplasm Nucleus Rough Endoplasmic reticulum Smooth Endoplasmic reticulum Golgi complex Lysosome (animal cells only) Vacuole (plant cells only) Chloroplast (plant cells only) Mitochondria Cytoskeleton Peroxisome Ribosomes Flagella (animal cells only) Ribosomes Flagella Pili

Prokaryotic (bacterial) Cell

Eukaryotic Cell Animal cell Plant cell

Nuclear material Prokaryotes - circular DNA:

Nuclear material Eukaryotes - linear DNA:

Eukaryotic Cell Most cells (somatic cells) have 2 copies of each chromosome (diploid) Gametes, germline cells (egg and sperm) have only 1 copy of each chromosome (haploid)

Eukaryotic Cell We have 2 meters of DNA in all our somatic cells HOW DOES IT ALL FIT? ? Condensation of DNA by proteins!!

The nucleosome • 8 histones form a complex • 140 -150 bp DNA wound twice around it. 50 -70 bp DNA between each nucleosome • + Linker histones

DNA - acidic, negatively charged Histones proteins contain many basic amino acids (Lys, Arg), positively charged

Beads on a String (in Colorado)

The Histone Code Methylation - yellow hexagon Acetylation - green flag Phosphorylation - grey circle Other modifications? ?

The Histone Code Methylation - yellow hexagon Acetylation - green flag Phosphorylation - grey circle Other modifications? ?

Chromatin types • Euchromatin: open chromatin - associated with gene activity • Heterochromatin: densely packed chromatin - indicates little or no gene activity

Chromatin types • Euchromatin: open chromatin - associated with gene activity • Heterochromatin: densely packed chromatin - indicates little or no gene activity Euchromatin Heterochromatin

The Histone Code Methylation - yellow hexagon Acetylation - green flag Phosphorylation - grey circle Other modifications? ?

Packing and the cell cycle • Between cell divisions (interphase) - euchromatin dominates, so open chromatin & gene activity • When the cell is about to divide (metaphase) the chromsome is densely packed

In mitosis, the chromosomes appear as the thick rod-shaped bodies which can be stained and visualized under light microscopy. The modern way to visualize condensed chromosomes is by FISH -- fluorescence in situ hybridization. In this method, fluorescent antibodytagged DNA probes hybridize to their complementary sequences in the chromosomes. By using FISH probes with different colored fluorophores, one can color each human chromosome independently, and thus identify all 23 chromosomes. This is called chromosome painting.

M-FISH/SKY (multifluor-FISH/spectral karyotyping)

Isolate cell nuclei

Red blood cells Skeletal muscle cell Secretory cells of pancreas Sperm cells Human embryo at 2 -cell stage

Cell breakage AKA cell disruption, cell disintegration, lysis Goal - destroy outer cell membrane without destroying organelle membranes Cells broken open (plasma membrane dissolved) by: Mechanical • freeze-thaw • grinding • shearing (homogenizer) • shearing (french press) Chemical • solubilize with detergents • organic solvents • alkali treatment • enzymatic digestion

Cell breakage Mechanical • freeze-thaw ice crystals form and disrupt cell after slow freezing and thawing • grinding (mortar & pestle or blender) use force to grind and smash cells • shearing (homogenizer) use pressure to induce a shear force on cell wall pump cell slurry through a restricted orifice valve • shearing (french press) use pressure to induce a shear force on cell wall uses HIGH pressure & rapid decompression to disrupt cell

Cell breakage Chemical • solubilize with detergents mostly used to disrupt animal cells detergents destroy cell lipid membrane • organic solvents dissolves cell membrane • alkali treatment uses Na. OH/SDS (sodium hydroxide/sodium dodecyl sulfate) to solubilize the phospholipid and protein components of cell membrane, fast & reliable, most commonly used for plasmid DNA isolation out of prokaryotic cells • enzymatic digestion dissolves cell membrane, “gentle” technique since enzyme attack specific components of cell membrane EX: lysozyme digests peptidoglycan layer of bacterial cell wall

Cell fractionation If done correctly, disruption reduces cells to EXTRACT (homogenate) with soluble components, intact organelles and plasma membrane fragments DIFFERENTIAL CENTRIFUGATION Tissue homogenization Low speed Supe to medium speed Supe to high speed Tissue homogenate Supe to very high speed Pellet of whole cells, nuclei, cytoskeleton, plasma membrane Pellet of mitochondria, lysosomes, peroxisomes Pellet of micorsomes (fragments of ER), small vesicles Pellet of ribosomes, large macromolecules Supernatant contains soluble proteins

Cell fractionation Centrifugation Separate proteins by size or density Differential centrifugation - separates large from small particles Isopycnic (sucrose-density) centrifugation - separates particles of different densities DIFFERENTIAL CENTRIFUGATION ISOPYCNIC (SUCROSE-DENSITY) CENTRIFUGATION Tissue homogenization centrifugation Low speed Supe to medium speed Supe to high speed Tissue homogenate Sample Supe to very high speed Pellet of whole cells, nuclei, cytoskeleton, plasma membrane Sucrose gradient Less dense Pellet of mitochondria, lysosomes, peroxisomes Pellet of micorsomes (fragments of ER), small vesicles Pellet of ribosomes, large macromolecules More dense Supernatant contains soluble proteins Fractionation

Object of lab: Isolate DNA from nuclei of eukaryotic cell (calf thymus) 1. Isolate nuclei (centrifugation after cell disruption) thymus tissue + buffer cell membrane breakage using Waring blender filter homogenate through cheese cloth centrifuge homogenate resuspend pellet (contains nuclei) w/ buffer filter through cheese cloth NUCLEAR SUSPENSION 2. Compare isolated nuclei to intact nuclei use microscope 3. Isolate DNA from nuclei (nuclear membrane disruption, dissociation of protein (histones) from DNA, alcohol-insoluble DNA isolated) add SDS to dissolve nuclear membrane and dissociate protein from DNA add alcohol to top of solution use glass rod to pull DNA fibers into alcohol layer on top