Biology● Chemical fundamentals:○ Elements and atoms○ Compounds and molecules○ Chemical reactions○ Chemistry in water● Element: substance that cannot be broken down to other substances by chemical reactions○ 92 natural elements (25 required for life)○ Most common in living organisms: oxygen, carbon, hydrogen, nitrogen (95% of mass in human body)● Atoms○ Make up elements○ Fundamental form of matter○ Chemical reactions and structures are determined by atoms○ Mass of atoms expressed in Daltons■ 1 Dalton = mass of one neutron or proton■ Electrons = mass-less○ 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● Electrons○ Occupy layers or shells around nucleus of atom○ Each shell can hold fixed number of electrons○ Exist in orbitals within each shell■ Each orbital holds 2 electrons○ Reactivity determined by electrons in outer shell (Valence electrons)● Most common elements of life occur in first 18 places in periodic table○ Periodic table is organized shell filling in neutral atoms● Compounds○ Made up of 2 or more interacting atoms○ Interactions between atoms are through valence electrons and form bonds■ All different types of bonds that determine structure and function○ Shape is determined by arrangement of interacting electrons in their orbitals○ Different ways to represent compounds:■ Name and molecular formula■ Electron-distribution diagram■ Lewis Dot structure and Structural Formula■ Space-filling model● Molecular Bonds:○ Covalent bonds○ Ionic bonds○ Hydrogen bonds○ Van der Waals interactions (b/c of charge in nucleus)● Covalent Bonds○ Strong, electron sharing interactions b/w atoms in a molecule○ Atoms may be joined by single, double, or even higher bonds○ Take considerable energy to make or break○ Electron sharing allows both atoms to fill electron orbitals together○ 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 Bonds○ Weak, electron stripping interactions between atoms in a molecule○ Extreme differences in electronegativity = no sharing■ One atom strips electron from the other■ Atoms remain together in a compound through charge interactions○ Salts = compounds formed by ionic bonds + tend to form crystals○ Ions = charged atoms in an ionic compound○ Anions = negatively charged (extra electron)○ Cations = positively charged (missing electron)● Hydrogen Bonds○ 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 energy○ A + B (Reactants) (Reaction) C + D (Products)○ Reactions are reversible○ Depending on energy requirements, reversible reactions form Equilibrium concentrations of reactants and products ● Chemistry in water○ Chemistry of life on Earth evolved in water (aqueous)○ Properties of water = fundamental to chemistry of life● Properties of water1. Polarity of water molecules○ Hydrogen bonding○ Cohesion/adhesion (stick to itself and other things using hydrogen bonds)■ Surface tension2. Moderation of temperature○ Water has high Specific Heat■ Water molecules don’t move easily, absorbs a lot of heat, stores and releases heat○ Water has high Heat of Vaporization■ Evaporative cooling; cool you, cools the oceans3. Ice Floats○ Does not crush everything in the water○ Insulates the water○ Ice = less dense as solid than liquid4. Water as Universal Solvent○ Highly polar solvent○ High capacity to dissolve ionic compounds into solution○ Dissolves even large polar molecules (Hydration shell)○ Hydrophilic substances like water (are polar)○ Hydrophobic substances are non-polar molecules and will not form a solution in water● Aqueous Solutions○ Solutions are described by the amount of molecules (solutes) dissolved in water (solvent)○ In chemistry, 1 Mole = 6.02 x 10^23 molecules■ 1 Mole of solute in water = 1 Molar solution● pH○ Water forms certain amounts of H+ and OH- ions dynamically○ Amount of H+ ions is measured as pH, or concentration of hydrogen ions on a log scale○ 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: ○ 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 life○ Has 4 unpaired valence electrons■ Maximum potential diversity○ Orbital behavior of electrons causes carbon compounds to have tetrahedralshapes■ Creates geometric variation● Organic Chemistry○ Organic molecules made from carbon fixed from atmospheric CO2 or other sources (ex. Methane gas)○ Organic molecules based on chains of carbon atoms (carbon backbone)○ 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 isomers○ Isomers have same chemical formula, but components atoms have diff. arrangement○ Structural isomers – molecules differ in covalent arrangements of component atoms and positions of double bonds○ 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 bonds○ 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 backbone○ Hydrogen = least likely to be important as a
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