Cells Model Systems and Proteins I Modern Cell Theory organisms a Cell fundamental unit of structure and function in all living b Activity of organism total activity of independent cells c All cells come from pre existing cells by cell division d All cells basically same in chemical composition e Evolutionary tree i Prokaryotes eu bacteria and archaebacteria ii Eukaryotes iii Common ancestor b w archaebacteria and eukaryotes after split from eubacteria No viruses on cell tree II Cell Organization a Prokaryotic cell i Single compartment w PM ii Single cells may be colonial b Eukaryotic cell i Enclosed by PM w multiple internal membrane enclosed compartments organelles ii Single celled e g yeast or multicellular III Viruses Influenza HIV AIDS small pox plague a NOT cells b c Have genetic info DNA or RNA d CANNOT replicate autonomously i No cell machinery to make own component parts ii Must infect cells and commandeer cellular machinery to IV Model Experimental Systems reproduce plants a E g viruses bacteria yeast roundworm fruit fly zebrafish mice and V Proteins a Primary structure Linear polymers of AA attached end end through i Peptide bond b w carboxyl group AAn and amino group of peptide bonds AAn 1 b 20 different R groups i 5 classes of R groups 1 3 classes of hydrophilic AA a Basic charge b Acidic charge c Polar 0 charge 2 1 class of hydrophobic AA 3 1 class of special AA c Secondary structure strings of AA form 3D structures i Alpha helix and B sheet ii Depends on freely rotatable alpha carbon bonds in peptide chain iii Alpha helix 1 Stabilized by H bonds b w C O of AAn and N H of AAn 4 2 3 6 residues per turn 3 R groups stick out from helix bottlebrush a Determine nature of helix surface 4 Amphipathic helix nature of R groups projecting from 1 side of helix differs from other side iv Beta sheet a Coiled coil dimerization hydrophobic AA on position 1 and 4 of heptad repeats generate stripe of hydrophobicity and interacts with hydrophobic face on second helix 1 Interaction of pleated planar backbones stabilized by H bonds b w C O of one AA in one strange and N H of AA on other strand 2 R groups alternate sticking up and down from sheet a Similar properties in every 2nd position determine nature of protein sheet face b R groups from sides of helixes facing pocket contribute to what can bind into pocket d Motifs e Domains i Combination of secondary structures with characteristic 3D structure that has specific function ii Contains invariant or highly conserved AA in certain positions i Structural and functional domains f Quaternary structure i Organization of several polypeptide chains to make multimeric protein protein ii Number and relative positions of polypeptides in multimeric iii Polypeptide subunits held together by noncovalent bonds and or disulfide bonds VI Protein Families a Globin family i Bind heme groups carry oxygen ii Myoglobin monomer iii Hemoglobin tetramer each subunit similar in structure to myoglobin iv Common ancestral protein Membrane Composition Structure and Proteins I Eukaryotic cells a Surrounded by PM b Membrane bound organelles c Cells w different shapes for specific functions i PM w different shapes as well II Biological Membrane a Barrier that defines aqueous compartments i Internal aqueous environment has properties different from external aqueous environment b Membrane properties dependent on properties of component parts c Major structural components lipids especially phospholipids i Membrane structural components ii Most prevalent membrane lipids have fatty acid tails esterified to glycerol backbone III Phospholipids a Glycerol backbone 3 carbon chain b Two fatty acid tails hydrophobic c Polar charged head group hydrophilic d Head and tail attached by phosphate group e Amphipathic one end differs in solubility from the other hydrophilic vs hydrophobic f 4 common PLs in mammalian cell membranes vary by head group 1 Hydrophilic head groups maximize water contact 2 Hydrophobic tails minimize contact and attract each other thus maximizing contact w each other ii Fusible self healing 1 No covalent bonds holding PLs to each other i Choline 0 ii Ethanolamine 0 iii Serine iv Inositol 0 sugar head group can be further phosphorylated g On water surface i Monolayer coherent slick h Submerged in water i PLs form bilayer to minimize tail and maximize head contact with water 1 Form liposome internal and external aqueous compartments 2 Presence of two tails and length of tails prevents formation of micelle i Mobility i No covalent bonds anchoring PL position ii Exchange position with neighbors often but do not flip from leaflet to leaflet very often j Lipid Composition i Asymmetrically distributed between inner and outer membrane leaflets ii Composition affects thickness and curvature k Membrane Hydrophobic Core and Saturation i Fatty acid tails form hydrophobic core ii Degree of C C bond saturation determines fluidity of core 1 Saturation has to do with H s bonded to C iii Unsaturated double bond forms inflexible kink in tail 1 Kinked tails pack more loosely in membrane core less van der Waals interactions 2 Less bonds more fluidity iv More saturated less fluidity 1 More C C saturated bonds less fluidity 2 More C C unsaturated bonds more fluidity v Heating up increases fluidity vi Membrane PLs may contain unsaturated FA tails 1 Common FA tails 16 20 C C bonds long with 1 4 double bonds vii Laser tweezers use forces of laser radiation pressure to trap small particles and move them 1 Can be used to see fluidity of membrane IV Cholesterol a Amphipathic molecular i Polar OH head group b Compromises significant of molecules in eukaryotic cell PM c Integrates in membrane structure and associated with PL tails d Regions with cholesterol can be thicker AKA lipid rafts i Cholesterol concentrated in lipid rafts islands of associated lipids cholesterol in leaflet of membrane V Fluid Mosaic Model a 1972 Nicolson and Singer b Phospholipids provide structure c Proteins float in sea of lipids i Little structural role but crucial for function d Peripheral extrinsic membrane proteins do not interact e w hydrophobic core of bilayer but may bind to integral membrane protein Integral intrinsic membrane proteins interact with hydrophobic core of PL bilayer i Span membrane one or more alpha helices or multiple beta sheets or anchored by fatty acid ii Membrane spanning proteins have distinct structural functional domains on each side of membrane VI Glycophorin single alpha