Biology- Chemical fundamentals:o Elements and atomso Compounds and moleculeso Chemical reactionso Chemistry in water- Element: substance that cannot be broken down to other substances by chemical reactionso 92 natural elements (25 required for life)o Most common in living organisms: oxygen, carbon, hydrogen, nitrogen(95% of mass in human body)- Atomso Make up elementso Fundamental form of mattero Chemical reactions and structures are determined by atomso Mass of atoms expressed in Daltons 1 Dalton = mass of one neutron or proton Electrons = mass-lesso Atomic mass = total number of protons and neutrons in an atom- Atomic number : number of protons in each unique element- Isotopes : atoms of an element that differ in the number of neutrons- Radioisotopes are heavy and release excess neutrons as they decay- Basis of chemistry = behavior and distribution of electrons in atoms- Electronso Occupy layers or shells around nucleus of atomo Each shell can hold fixed number of electronso Exist in orbitals within each shell Each orbital holds 2 electronso Reactivity determined by electrons in outer shell (Valence electrons)- Most common elements of life occur in first 18 places in periodic tableo Periodic table is organized shell filling in neutral atoms- Compoundso Made up of 2 or more interacting atomso Interactions between atoms are through valence electrons and form bonds All different types of bonds that determine structure and functiono Shape is determined by arrangement of interacting electrons in their orbitalso Different ways to represent compounds: Name and molecular formula Electron-distribution diagram Lewis Dot structure and Structural Formula Space-filling model- Molecular Bonds:o Covalent bondso Ionic bondso Hydrogen bondso Van der Waals interactions (b/c of charge in nucleus)- Covalent Bondso Strong, electron sharing interactions b/w atoms in a moleculeo Atoms may be joined by single, double, or even higher bondso Take considerable energy to make or breako Electron sharing allows both atoms to fill electron orbitals togethero Atoms differ in Electronegativity: power to attract and hold electrons in their orbitals If bonded atoms differ in electronegativity, shared electrons associate more with 1 atom than the other creates asymmetry or Polarity to the compound- Ionic Bondso Weak, electron stripping interactions between atoms in a moleculeo Extreme differences in electronegativity = no sharing One atom strips electron from the other Atoms remain together in a compound through charge interactionso Salts = compounds formed by ionic bonds + tend to form crystalso Ions = charged atoms in an ionic compoundo Anions = negatively charged (extra electron)o Cations = positively charged (missing electron)- Hydrogen Bondso Occur between covalent compounds having hydrogen atoms in highly polar configurations- Reaction chemistry: chemical reaction occurs when bonds are broken or formed, either using or liberating energyo A + B (Reactants) (Reaction) C + D (Products)o Reactions are reversibleo Depending on energy requirements, reversible reactions form Equilibrium concentrations of reactants and products - Chemistry in watero Chemistry of life on Earth evolved in water (aqueous)o Properties of water = fundamental to chemistry of life- Properties of water1. Polarity of water moleculeso Hydrogen bondingo Cohesion/adhesion (stick to itself and other things using hydrogen bonds) Surface tension2. Moderation of temperatureo Water has high Specific Heat Water molecules don’t move easily, absorbs a lot of heat, storesand releases heato Water has high Heat of Vaporization Evaporative cooling; cool you, cools the oceans3. Ice Floatso Does not crush everything in the watero Insulates the watero Ice = less dense as solid than liquid4. Water as Universal Solvento Highly polar solvento High capacity to dissolve ionic compounds into solutiono Dissolves even large polar molecules (Hydration shell)o Hydrophilic substances like water (are polar)o Hydrophobic substances are non-polar molecules and will not form a solution in water- Aqueous Solutionso Solutions are described by the amount of molecules (solutes) dissolved in water (solvent)o In chemistry, 1 Mole = 6.02 x 10^23 molecules 1 Mole of solute in water = 1 Molar solution- pHo Water forms certain amounts of H+ and OH- ions dynamicallyo Amount of H+ ions is measured as pH, or concentration of hydrogen ions on a log scaleo Goes from 0-14. 1 = acid, 7 = neutral, 14 = basic- Buffers: form equilibrium reactions that resist changes in pHMolecules of Life: Organic Chem + Biological Macromolecules 9/8/10- Molecular challenges of a cell: o Make/break molecules, build/take apart structures, use/store energy,move/change shape, interact with other cells, organize cell- Single most important element for all organic molecules: Carbon- Carbon = backbone of lifeo Has 4 unpaired valence electrons Maximum potential diversityo Orbital behavior of electrons causes carbon compounds to have tetrahedral shapes Creates geometric variation- Organic Chemistryo Organic molecules made from carbon fixed from atmospheric CO2 or other sources (ex. Methane gas)o Organic molecules based on chains of carbon atoms (carbon backbone)o Large diversity of organic molecules can be created by variations in carbon backbone- Ane is single bonds; ene is double- # of possible variants of carbon backbone is increased by existence of isomerso Isomers have same chemical formula, but components atoms have diff. arrangemento Structural isomers – molecules differ in covalent arrangements of component atoms and positions of double bondso Geometric isomers - molecules have same covalent organization, but differ in spatial arrangements of elements around carbon backbone Stable geometric isomers result from inflexibility of double bondso Enantomers – “mirror image” isomers resulting from arrangement of groups around an asymmetric carbon Asymmetric carbons have 4 different side groups Enantomers form “left handed” and “right handed” versions of molecules- Diversity of organic molecules is increased by addition of side groups (functional groups) to carbon backboneo Hydrogen = least likely to be important as a functional side group on an organic moleculeo Functional groups alter reactivity and chemical properties of organic molecules; makes polaro ** learn figure 4-10! (table)- Macromoleculeso Cells use
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