UNIT 1 EXAM REVIEW 1 Introduction to the Cell a Cell Theory i Cells are the functional units of life ii All living organisms are composed of cells iii 8 Common Features of All Cells b Cell Structures and Organelles c Features of Cells i Cells are highly complex and organized ii Cells posses a genetic program iii Cells are capable of producing more of themselves iv Cells are biochemical factories constantly acquiring and assimilating energy v Cells engage in mechanical activities d Two Classes of cells i Eukaryotes ii Prokaryotes e Prokarytotes Evolutionarily optimized for rapid and efficient reproduction i Organotrophs obtain energy by feeding on living things or organic material ii Phototrophs obtain energy by using sunlight to convert inorganic substances into iii Lithotrophs obtain energy by converting inorganic chemicals into organic materials organic material f Genetic Innovation can occur via Intragenic mutation i ii Gene duplication iii Dna segment shuffling iv Horizontal transfer 2 Visualization Techniques a Scale b 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 other c Fluorescence Microscopy chemical dyes selectively absorb specific wavelengths of light fluorescent molecules absorb light at one wavelength and emit light of a lower wavelength i Limited by fluorescence from out of focus parts of cells d Confocal microscopy uses a scanning laser and pinhole apertures to limit detection to the focal plane out of focus light is excluded e Vital microscopy 2 photon microscopy uses two separate long wave photons of light instead of one short wave photon f Electron Microscopy focused beam of electrons replaces light to image cells i Allows much higher resolution that light microscopy but requires special cellular preservation and staining techniques flow cytometry ii Scanning electron microscopy images the outside surface of a sample iii Transmission electron microscopy images internal structures g Flow cytometry live cells are analyzed in real time in an aqueous stream as they pass though a laser 3 Cell Chemistry a Hierarchy of Cellular Chemical Bonds b Carbohydrates energy source structural support binding surface i Highly polar ii Monomer linked together via a condensation reaction iii Describing sugar linkages c Lipids hydrophobic membranes barriers energy source i Hydrocarbon chains with polar COOH amphipathic d Amino acids building block of proteins can be metabolized for energy i Uniform chemical structure with directionality and side group variability ii Amino acid monomers are linked together to form polymers via condensation rxns e Nucleotides building blocks of nucleic acids short term energy carriers i Uniform chemical structure with some side group variability polar charged ii Nucleotide monomers are linked via condensation reaction f ATP synthesis g Metabolism myriad of chemical reactions that cells obtain and use energy through h Step wise oxidation of organic molecules i Cells and Thermodynamics neither created or destroyed i 1st Law of Thermodynamics amount of energy in a system is constant i e energy are ii 2nd Law of Thermodynamics all processes in the universe are driven in the direction that increases disorder j Goverall G 616 ln products reactants k NADP vs NADPH l Glycolysis m Fermentation n Fats vs Carbohydrates as energy sources i Oxidation of one gram of fat yields twice as much energy as oxidation of one gram of alcohol 4 Protein Structure and Function a Factors that determine protein structure i 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 C flexible b C C flexible c C N peptide bond inflexible ii Factor 2 noncovalent attractions within polypeptide backbone iii 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 of the polypeptide backbone 3 Hydrophobic interaction among R group drive protein folding b Chaperonins provide isolated chemical environment in which they can fold c Higher order structures i Protein arrays repeating copies of one of more proteins to form a regular polyhedron often of structural proteins ii Multi protein complexes collection of interacting but otherwise independent proteins that bind non covalently to function more efficiently d Protein Mutation i Silent nucleiotide change does not alter amino acid ii Conservative substitution of an amino acid with similar properties iii Non conservative substitution with a very different amino acid e Site directed mutagenesis i cDNA coding for a protein is amplified by cloning it in bacterial cells and mutated in vitro ii amplified cDNA is then altered mutated iii mutated cDNA is expressed in a cell line or a genetically modified organism 5 Protein Structure and Function Pt 2 a Phosphorylation i Carried out by protein kinase ii Reversed by protein phosphatase iii Each phosphate adds two negative charges to the protein which can participate in new ionic 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 protein i Carbohydrate chains can be joined to OH group of serine or NH2 group of b Glycosylation asparagines forming a glycoprotein c Addition of lipids forming a lipoprotein i Addition of phospholipids or fatty acids to cysteine or N terminal glycine residue ii Fatty acid chain can insert into the hydrophobic core of biological membranes anchoring a protein to the membrane d Ubiquitylation i Addition of ubiquitin ii Mark proteins for degradation or direct proteins to specific locations in the cell iii Catalyzed by ubiquitin ligase 1 Form a multisubunit protein complex with other proteins that enables them to bind the target protein and bind ubiquitin e Ligands molecules to which proteins bind too i Binding strength achieved through 1 3D complementarity of binding 2 Formation of several noncovalent bonds f GTPases g Molecular Integration 6 Protein Structure and Function Pt 3 a Enzymes catalytic proteins speeding up cellular reactions to allow life i Do not alter G ii Do not change concentrations iii Can increase rate of reaction 108 1012 fold b Enzymes Classified by the type of
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