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Biology 314, Week 2 notes

by: Danielle Garrison

Biology 314, Week 2 notes Bio 314

Marketplace > Iowa State University > Biology > Bio 314 > Biology 314 Week 2 notes
Danielle Garrison

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These notes cover week 2 of the course.
Principles of Molecular Cellular Biology
Class Notes
Biology, 314
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This 5 page Class Notes was uploaded by Danielle Garrison on Thursday September 1, 2016. The Class Notes belongs to Bio 314 at Iowa State University taught by Nilsen-Hamilton in Fall 2016. Since its upload, it has received 60 views. For similar materials see Principles of Molecular Cellular Biology in Biology at Iowa State University.


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Date Created: 09/01/16
Chapter 2 – Macromolecules and macromolecular structures  Macromolecules (functional unit of cell) o Monomers that are linked via covalent bonds  Sugar – polysaccharide  AA – protein  Nucleotide – nucleic acid o Assemblies  Gathered in “stable” grouping  Linked via noncovalent bonds  Structure related to function  Together they (assembly) perform a function  Subunit (AAs) (covalent bonds)  macromolecules (noncovalent bonds)  macromolecular assembly o Polymers  Protein, nucleic acids, carbohydrates  Location – in and out of cells o Macromolecular assemblies – in cell (plasma membrane)  Protein – protein complexes  Proteins assemble in membranes  Protein – nucleic acid complexes o Macromolecular assembly – out of plasma membrane  Carbohydrates and protein predominate  Not many nucleic acids here  Environment in vs out of cell o Inside  Protected environment – stable pH, degradative enzymes separated by cytosolic proteins  Reducing environment – high concentration of glutathione; antioxidative  Few disulfide bonds o Outside  Non-reducing, pH varies  Many proteins contain disulfide bonds – tighter structure  Many proteins glycosylated – prevents other proteins from coming close  Meaning of inside and outside of cell o Inside – reducing environment; cytoplasm; nucleus, mitochondria, chloroplasts, peroxisomes o Outside – non-reducing; plant - cell wall; animal – extracellular matrix o Partly outside – ER, golgi apparatus, lysosomes  Macromolecular structure – defined by inter-atomic bonds in polymer o Atoms – number of bonds, bond angle, bond distance o Type of bond – single vs double o Position of atoms relative to each other – defined by polymer sequence  Chemical groups (macromolecules) hold structures together – common groups o Methyl (-CH 3 o Hydroxyl (-OH) o Phenyl (-C6H5) o Carboxyl (-COOH) o Carbonyl (-C=O) o Thiol (-SH) 2- o Phosphoryl (-PO 3 o Amino (-NH 2 o Disulfide (-S-S-)  Carbohydrates o Glucose – monosaccharide o Sucrose – disaccharide o Amylose – polysaccharide/starch o Glycogen – storage of glucose o Cellulose – plants o Chitin – plants o Hydroxyl (-OH) o Carboxyl (-COOH) o Amino (-NH 2 o Acetyl (-Ac)  Cell surfaces – allow certain things to attach here (lipids)  Glycogen granules o Liver – blood sugar o Muscle – energy source o Cells – energy source  Starch (plant) o Amylopectin and amylose  Plant cell wall (outside cell) (macromolecular complex) o Carbohydrates mostly (formed) o “Disordered” (all over the place) (tangled) o Some proteins and lipids within o Stiff structure – function of cell wall  Animal extracellular matrix o Protein mostly – attached polysaccharides o “Disordered” – entangled o Fibrous – large (long) proteins o Flexible structure (due to being made by protein)  Nucleic acids o DNA – chromosomes, genetic, double stranded helix o RNA – many functions within cell, single stranded, adopt structures, carry protein code from nucleus, regulate gene expression, regulate RNA levels, catalyze chemical reactions  World hypothesis – in early evolution thought that this formed function of cell (RNA)  Weak forces stabilize double helix o Hydrophobic effects – buried within double helix (purine and pyrimidine rings) o Stacking interactions – stacked base pairs form van der Waals contacts o H-bonds – H bonding between base pairs  DNA wrapped around proteins to from nucleosomes  Ribosomes o Macromolecular assembly o RNA and protein o Catalytic (synthesize/make protein)  RNA provides this o Protein components – provide structure and exert control  Membranes – composed of lipids, form bilayers in aqueous environment o Macromolecular assembly o Lipids and proteins  Control movement of small and large molecules in and out of cell  Control movement of molecules between organelles  Protein – polymer of AAs o AAs – have different side chains with different properties (polar and nonpolar AAs) o Held together via weak bonds  Interactions between side chains sum to large force  Electrostatic (ionic)  Van der Waals  Hydrogen bonds  Involved in forming macromolecular assemblies  Macromolecular surfaces NEED – sufficient “complementarity” to survive thermal jolting o Macromolecular assembly held together by many weak noncovalent bonds  When together are strong Chapter 3 – Energy, Catalysis, and Biosynthesis 1 law of Thermodynamics o Total energy of closed system remains constant o Universe – closed system o Life – component of system o Energy neither created or destroyed  Can be converted between different forms nd 2 law of Thermodynamics o State of entropy of entire universe, isolated system, will increase over time o Changes in entropy, never negative o Machines, closed systems, shift from 1 state of equilibrium to another o Living organisms, open systems, never in equilibrium  Quasi-equilibrium  Cycle with time  Plants: take in sun’s energy, CO2 and water – metabolize – release heat, O2, and breakdown products  Animals: take in food, water, and O2 – metabolize – release heat, CO2, and breakdown products  Eventually die and rot Order within cell increase disorder in environment (net entropy increased) Oxidation (e- loss) and reduction (e- gain) o E- transfer could be partial or complete loss o Oxidation and reduction of organic molecules – important in cells o Energy harvested by oxidation of organic molecules  Enzymes make it possible o Series of enzyme-catalyzed reactions forms metabolic pathway  Catabolic – breakdown  Anabolic – building up Respiration involves enzymes of central metabolism o Happens within cytoplasm and mitochondria Plants – photosynthesis (chloroplasts) - energy of sunlight Most living organisms – uses chemical bond energy Chemical reactions o Follow 1 and 2 ndlaws of thermodynamics  Total energy of system is the same  Entropy increases with reaction  Energy lost during reaction o Gibbs Free Energy (∆G)  ∆G = ∆H - T∆S o Stable molecules  Average energy decreases energy requirement for spontaneous reaction  Energy provided by collisions – jiggling, vibrations, spinning  Enzyme catalysts o Increase number of molecules in population that can undergo chemical reaction o Fig. 3.13  Enzymes lower energy barriers (Fig. 3.12)  Catalyst remains unchanged after reaction is completed o Can repeat reaction many times o Can be changed during process of reaction  Enzymes present in cell determine which metabolic pathways o Cell differentiation  Different sets of genes activated  Encode different enzymes  Different metabolism  Energetically unfavorable reactions, also catalyzed by enzymes o Fig. 3.17  Energetically favorable: YX, increase in entrophy, ∆G less than (<) 0  Coupled reaction o Enzyme doesn’t change equilibrium point for reaction (Fig. 3.18)  Activated carriers o Provide means of coupling an energetically favorable reaction to an unfavorable one o Fig. 3.30 o Can help promote energetically unfavorable reactions  Cleavage of phosphoanhydride bonds in ATP o Highly energetically favorable  Synthesis of biological polymers o Involves condensation, required energy  Energy from ATP hydrolysis  NADH and NADPH o Couple+oxidation/reduction reactions o NADP - oxidized form o NADPH – reduced form  Value of K – reflects energy binding interactions o Fig. 3.20 o Dissociation and association o Equilibrium: association = dissociation  K on) (B) = K off(AB) o K is equilibrium constant o Equilibrium constant (association)  K or Ka o Dissociation constant  Convenient – units of Kd concentration units (molar)  Equal to Km  Enzyme’s performance depends on how rapidly it can process substrate o Fig. 3.25  Enzyme inhibitors regulate enzyme activities o Natural inhibitors, drugs, insecticides, herbicides o Competitive inhibitor – directly blocks substrate binding


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