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UCSD BILD 1 - Lecture 2

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The Chemistry of Life: Atoms, Molecules and Water Cholesterol DNA Reading: Ch. 2, Ch. 3The$structure$of$Glycine,$the$smallest$amino$acid$ - C, carbon - H, hydrogen - O, oxygen - N, nitrogenWhat$elements$is$Glycine$composed$of?$ELEMENT: Cannot be broken down into other substances.Atoms and Bonds 25 / 92 Natural elements are essential for life Element % of Human Body Weight O 65% C 19% H 10% N 3% Elements combine to form chemical bonds and compounds These 4 elements make up 96% of living matterClicker$ques;on$Q2>1$$What$type$of$bonds$connects$between$the$different$elements$of$Glycine?$A. Covalent B. Ionic C. Hydrogen D. Van der Waals interactions Two or more elements connected via a covalent bond form a moleculeClicker$Q2>3$What$type$of$bonds$connects$between$the$different$elements$of$Glycine?$Indicate the number of covalent bonds each of the elements of Glycine is forming: C – H – N – O –• Covalent)bond)anima.on)Figure$2.12$Two$types$of$Covalent$bonds$Electron- shell diagram Structural formula Space- filling model H H O O O H H H H H O H O O Non-polar (equal sharing of electrons) Polar (unequal sharing of electrons)Figure)2.13)Polar)covalent)bonds)in)a)water)molecule)This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens. H2O δ– O H H δ+ δ+ Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.In addition to covalent bonds, the following bonds play great importance in life processes - Ionic bonds (interactions between DNA and proteins) - Hydrogen bonds (formation of protein structure) - Van der Waals interactions (interactions between phospholipids in a membrane)Figure$2.14$Electron$transfer$and$ionic$bonding$Cl– Chloride ion (an anion) – Na Na Cl Cl + Na Sodium atom (an uncharged atom) Cl Chlorine atom (an uncharged atom) Na+ Sodium on (a cation) Sodium chloride (NaCl) IONIC BOND: Transfer of electrons between atomsFigure)2.15)Ionic)Compounds)Na+ Cl– sodium chloride crystalFigure)p.)41,)Van)der)Waals)interac.ons)VAN DER WAALS: slight interactions between nonpolar covalent moleculesFigure)2.16)A)hydrogen)bond)Water (H2O) Ammonia (NH3) δ– δ+ O H H δ+ δ– N H H H δ+ δ+ δ+ HYDROGEN BOND: H shared between polar moleculesFigure)3.2)Hydrogen)bonds)between)water)molecules)Hydrogen bonds δ + δ+ H H δ+ δ+ δ– δ– δ– δ–Figure)3.7)Water)is)an)excellent)solvent)(dissolving)agent))+ + + + Cl – – – – – Na+ ++ + + – – – – – – Na+ Cl– A crystal of table salt dissolving in waterFigure)3.8)A)waterLsoluble)protein)This oxygen is attracted to a slight positive charge on the lysozyme molecule. This hydrogen is attracted to a slight negative charge on the lysozyme molecule. (a) Lysozyme molecule in a nonaqueous environment (b) Lysozyme molecule (purple) in an aqueous environment such as tears or saliva (c) Ionic and polar regions on the protein’s Surface attract water molecules. δ+ δ–Hydrophobic and hydrophilic substances Hydrophilic substances – soluble in water: polar or charged (ionic). NH3 – covalent polar NaCl – ionic Polar or charged parts of proteins Hydrophobic substances – Non-soluble in water: uncharged, non-polar Lipids: dominant bonds are C-C and C-H, with equal sharing of electronsHydrophilic or hydrophobic? Substance 1 Substance 2 Clicker Q2-2 A. Hydrophobic B. Hydrophilic There is a C atom bound to 1 or 2 atoms of H in each of the points of these hexagons and the pentagon (Carbon always forms 4 bonds in a lolecule)IV. Acids & Bases • Dissociation of water results in ions. H2O H+ + OH- Hydrogen ion Hydroxide ion • Pure water has equal concentrations: [H+] = [OH-]. • Pure water is NEUTRAL, or pH 7.pH Scale H+ Measures level of acidity H+ pH = -log [H+] • ACID: Increases [H+], or reduces pH • BASE: Reduces [H+], or increases pHTextbook reading • Today: Read Chapters 2-3. • Friday: Read Chapter 4-5. Reminders •No TA Sections this week. No Office Hours this


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UCSD BILD 1 - Lecture 2

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