Unit OneBasic Chemistry of Life Part I- Electro negativity- how tightly an atom holds on to its outer electrons- In a covalent bond where two one atom is more electronegative, the more electronegative atom with have the electrons for a larger percentage of time and will have a partial negative charge, whereas the other will have a partial positive charge.- O>N>C=H- All biological reactions occur within water. Polar, nonpolar, and ionic bonds interact differently with water.- Nonpolar don’t interact with water, but do with each other (fats, carbohydrates) They also tend to contain more energy (fats and oils have most stored energy)- Polar bonds interact with water, ions, and other polar bondso More polar bonds=more soluble, less likely to cross membrane unaided, give molecule 3D shape- Reading molecular diagrams: Bioskills- Carbon bonds can form lines, rings, and other intricate shapeso Double and single bonds change the shape- Functional groupso H-N-H Amino attracts protons and acts as a base (take sin proton fromsolution)o H-C=O Carbonyl Polaro OH-C=O Carboxyl Polar, acts as an acid (loses proton in solution)o OH- Hydroxyl Polar, hydrogen bonds with water, acts as a weak acido O3-P=O – Phosphate Highly polar, contain a lot of energy in bondso SH- Sulfhydryl Can form disulfide bridges is proteinsBasic Chemistry of Life Part II- Hydrocarbons are molecules that consist of only Carbon and Hydrogen.- Water is a polar molecule and therefore interacts with itself, ions (which dissolve in it) and other polar molecules- Hydrophilic means a molecule interacts with water (polar), hydrophobic means the molecule does not interact with water (hydrophobic)- Hydrogen bonding can pull H+ off of other water molecules (act as an acid in solution), and also off of molecules in solution- Homeostasis: keeps cells at a “normal” state where hydrogen bonding can occur- Structure-Function: Altering hydrogen bonding alters the shape of moleculesBasic Chemistry of Life Part III- Life follows all the regular laws of physics- All reactions are reversibleo One direction is spontaneous, the other requires extra energyo In any reaction, some energy becomes unusableo Building complex macromolecules always requires extra energy- Abiogenesis: Building complex molecules form less complex moleculeso Simple Molecules (CO, CN, etc.) + energy  Simple organic compounds (HCN, H2CO) + energy  Complex organic compounds (Amino acids, sugars, nitrogenous bases)- Urey Miller Experiment: Showed evidence that complex organic molecules can, under the right conditions, self assemble from similar compounds- Proteins had both the building blocks present and were able to be polymerized under early earth conditions- DNA & RNA: All of the building blocks were there, only some can be polymerized- Early lipids had all building blocks present, and can polymerize (assemble into layers) under early earth conditions- In order to self-replicate, early-life molecules must:o Catalyze chemical reactionso Store and contain rudimentary informationo Reproduce that information faithfully- Most likely that RNA was the first self-replicating molecule- Protocells: Lipid bilayer spontaneously assembles in water  Self-replicatingmolecules in a protected environment- Life began 3.5 billion years agoBiological Polymers Part 1: Proteins- Most large biological molecules (proteins, carbohydrates, nucleic acids) are polymerso Biological polymers are all built from the same mechanism: Dehydration synthesis, which is endergonico Polymers are broken down through hydrolysis, which is exergonic- Common properties of all proteins:o Each unit of a protein is a string, which is a polymero Each polymer is made up of monomers, which are amino acidso Monomers are joined by peptide bonds, built from the N-terminus to C-terminus direction- Protein properties are dependent upon their R-groupsReview what makes an R-group acidic or basic- Amino acids determine properties, and interactionso Mutations alter which amino acids are present, and therefore their shape and functiono Some mutations are worse than others- Primary structure: Order of amino acids, held together by very strong covalent bonds.- Secondary and Tertiary structure: determine 3D shape- Quaternary structure: How multiple strings stick together- A single change in the primary sequence can have huge effectsBiological Polymers Part 2: Proteins- Secondary, tertiary, and quaternary structure all:o Depends on primary structureo Are held together by weak bondso Give a protein 3D shapeo Are damaged by anything that disrupts weak bondso The damage is often reversible- Primary Structure:o Can only be broken down by enzymeso Is directly encoded by DNAo When damaged, is irreversible- Secondary structure consists of hydrogen bonding between like portions of amino acids (Not R-groups)o Can create alpha helices (spirals) or beta pleated sheets (ribbed and make a U)- Tertiary structureo Consist of interactions between R-groupso Are mostly weak interactions (except for disulfide bridges)o Create highly diverse shapeso Dependent upon previous structures- Quaternary Structureo Multiple strings form a larger functional unito Proteins that only have one string have no quaternary structure- Functions of proteinso Modify properties of the cell membrane (transporters, pumps etc.)o Provide defense (Antibodies)o Promote movement (intracellular transport, movement and division)o Provide structure support (Within and outside of a cell)o Regulate gene expression (Turn genes on/off, make RNA, fix/replicateDNA)o Send messengers to other cells (intracellular messengers, receivers)o Control all chemical reactions in a cell (Enzymes)Metabolism, Part 1- Factors that effect likelihood and rate of all chemical reactions:o Temperatureo Concentration of reactantso Pressureo Free energy of reactants vs. free energy of productso Presence of a catalysto Conditions in water (pH, salinity)- Bolded aspects cells can control- Chemical reactions are spontaneous (net decrease in energy) or nonspontaneous (net increase in energy)- Entropy: amount of disordero Increases with every transformation- A chemical reaction is a transformation of energy (energy is never created or destroyed)- Free energy is the ability to do worko G (Gibb’s Free energy) = energy and entropy possessed by themolecules involved in a chemical reactiono ∆G – difference of G between products and reactantso ∆G=∆H-T∆S , H= Enthalpy, S=