UNIT 1 EXAM REVIEW1) Introduction to the Cella) Cell Theoryi) Cells are the functional units of lifeii) All living organisms are composed of cellsiii) 8 Common Features of All Cellsb) Cell Structures and Organellesc) Features of Cellsi) Cells are highly complex and organizedii) Cells posses a genetic programiii) Cells are capable of producing more of themselvesiv) Cells are biochemical factories constantly acquiring and assimilating energyv) Cells engage in mechanical activitiesd) Two Classes of cellsi) Eukaryotesii) Prokaryotese) Prokarytotes: Evolutionarily optimized for rapid and efficient reproductioni) Organotrophs: obtain energy by feeding on living things or organic materialii) Phototrophs: obtain energy by using sunlight to convert inorganic substances into organic materialiii) Lithotrophs: obtain energy by converting inorganic chemicals into organic materialsf) Genetic Innovation can occur viai) Intragenic mutationii) Gene duplicationiii) Dna segment shufflingiv) Horizontal transfer2) Visualization Techniquesa) Scaleb) Light Microscope: used to image large-scale cellular structure but resolution is limited(1) Resolution: ability to distinguish 2 objects that are close to each otherc) Fluorescence Microscopy: chemical dyes selectively absorb specific wavelengths of light; fluorescent molecules absorb light at one wavelength and emit light of a lower wavelengthi) Limited by fluorescence from out-of-focus parts of cellsd) Confocal microscopy: uses a scanning laser and pinhole apertures to limit detection to thefocal plane; out of focus light is excludede) Vital microscopy: 2-photon microscopy uses two separate long-wave photons of light instead of one short-wave photonf) Electron Microscopy: focused beam of electrons replaces light to image cellsi) Allows much higher resolution that light microscopy but requires special cellular preservation and staining techniques flow cytometryii) Scanning electron microscopy: images the outside surface of a sampleiii) Transmission electron microscopy: images internal structuresg) Flow cytometry: live cells are analyzed in real-time in an aqueous stream as they pass though a laser3) Cell Chemistrya) Hierarchy of Cellular Chemical Bondsb) Carbohydrates: energy source, structural support, binding surfacei) Highly polarii) Monomer linked together via a condensation reactioniii) Describing sugar linkagesc) Lipids: hydrophobic membranes barriers, energy sourcei) Hydrocarbon chains with polar COOH, amphipathicd) Amino acids: building block of proteins, can be metabolized for energyi) Uniform chemical structure with directionality and side group variabilityii) Amino acid monomers are linked together to form polymers via condensation rxnse) Nucleotides: building blocks of nucleic acids, short term energy carriersi) Uniform chemical structure with some side group variability, polar, chargedii) Nucleotide monomers are linked via condensation reactionf) ATP synthesisg) Metabolism: myriad of chemical reactions that cells obtain and use energy throughh) Step-wise oxidation of organic moleculesi) Cells and Thermodynamicsi) 1st Law of Thermodynamics: amount of energy in a system is constant(i.e. energy are neither created or destroyed)ii) 2nd Law of Thermodynamics: all processes in the universe are driven in the direction that increases disorderj) ∆Goverall = ∆G° + .616 ln[products]/[reactants]k) NADP vs NADPHl) Glycolysism) Fermentationn) Fats vs Carbohydrates as energy sourcesi) Oxidation of one gram of fat yields twice as much energy as oxidation of one gram ofalcohol4) Protein Structure and Functiona) Factors that determine protein structurei) Factor #1: peptide backbone flexibility (1) Flexibility: how freely a chemical bond can rotate about the atoms it joins together(2) Three covalent bonds:(a) N - Cα flexible(b) Cα – C flexible(c) C – N (peptide bond) – inflexibleii) Factor #2: noncovalent attractions within polypeptide backboneiii) Factor #3: noncovalent attraction among side chains(1) Proline disrupts secondary structures(2) Covalent disulfide bonds can form between cysteine residues to cross-link parts ofthe polypeptide backbone(3) Hydrophobic interaction among R group drive protein foldingb) Chaperonins: provide isolated chemical environment in which they can foldc) Higher order structuresi) Protein arrays: repeating copies of one of more proteins to form a regular polyhedron,often of structural proteinsii) Multi-protein complexes: collection of interacting but otherwise independent, proteins that bind non-covalently to function more efficientlyd) Protein Mutationi) Silent: nucleiotide change does not alter amino acidii) Conservative: substitution of an amino acid with similar propertiesiii) Non-conservative: substitution with a very different amino acide) Site-directed mutagenesisi) cDNA coding for a protein is amplified by cloning it in bacterial cells and mutated in vitroii) amplified cDNA is then altered – “mutated”iii) mutated cDNA is expressed in a cell line or a genetically-modified organism5) Protein Structure and Function Pt. 2a) Phosphorylationi) Carried out by protein kinaseii) Reversed by protein phosphataseiii) Each phosphate adds two negative charges to the protein which can participate in newionic bonds with neighboring positively charged amino acid R groups or with ions in solution; can be strong enough to drive major structural changes; may create new recognition site that allows other proteins to bind to the phosphorylated proteinb) Glycosylationi) Carbohydrate chains can be joined to OH group of serine or NH2 group of asparagines forming a glycoproteinc) Addition of lipidsi) Addition of phospholipids or fatty acids to cysteine or N-terminal glycine residue forming a lipoproteinii) Fatty acid chain can insert into the hydrophobic core of biological membranes anchoring a protein to the membraned) Ubiquitylationi) Addition of ubiquitinii) Mark proteins for degradation or direct proteins to specific locations in the celliii) Catalyzed by ubiquitin ligase(1) Form a multisubunit protein complex with other proteins that enables them to bind the target protein and bind ubiquitine) Ligands: molecules to which proteins bind tooi) Binding strength achieved through”(1) 3D complementarity of binding(2) Formation of several noncovalent bondsf) GTPasesg) Molecular Integration6) Protein Structure and Function Pt. 3a) Enzymes: catalytic proteins, speeding up cellular reactions to allow lifei) Do not alter ∆Gii) Do
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