Basic Chemistry of Life Part I Unit One 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 bonds o 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 shapes o Double and single bonds change the shape Functional groups solution o H N H Amino attracts protons and acts as a base take sin proton from o H C O Carbonyl Polar o 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 acid o O3 P O Phosphate Highly polar contain a lot of energy in bonds o SH Sulfhydryl Can form disulfide bridges is proteins Basic 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 molecules Basic Chemistry of Life Part III Life follows all the regular laws of physics All reactions are reversible o One direction is spontaneous the other requires extra energy o In any reaction some energy becomes unusable o Building complex macromolecules always requires extra energy Abiogenesis Building complex molecules form less complex molecules o 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 reactions o Store and contain rudimentary information o Reproduce that information faithfully Most likely that RNA was the first self replicating molecule Protocells Lipid bilayer spontaneously assembles in water Self replicating molecules in a protected environment Life began 3 5 billion years ago Biological Polymers Part 1 Proteins Most large biological molecules proteins carbohydrates nucleic acids are polymers o Biological polymers are all built from the same mechanism Dehydration synthesis which is endergonic o 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 polymer o Each polymer is made up of monomers which are amino acids o Monomers are joined by peptide bonds built from the N terminus to C terminus direction Protein properties are dependent upon their R groups Review what makes an R group acidic or basic Amino acids determine properties and interactions o Mutations alter which amino acids are present and therefore their shape and function o 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 effects Biological Polymers Part 2 Proteins Secondary tertiary and quaternary structure all o Depends on primary structure o Are held together by weak bonds o Give a protein 3D shape o Are damaged by anything that disrupts weak bonds o The damage is often reversible Primary Structure o Can only be broken down by enzymes o Is directly encoded by DNA o 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 structure o Consist of interactions between R groups o Are mostly weak interactions except for disulfide bridges o Create highly diverse shapes o Dependent upon previous structures Quaternary Structure Functions of proteins o Multiple strings form a larger functional unit o Proteins that only have one string have no quaternary structure o 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 replicate DNA 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 Temperature o Concentration of reactants o Pressure o Free energy of reactants vs free energy of products o Presence of a catalyst o 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 disorder o Increases with every transformation destroyed Free energy is the ability to do work A chemical reaction is a transformation of energy energy is never created or o G Gibb s Free energy energy and entropy possessed by the molecules involved in a chemical reaction o G difference of G between products and reactants o G H T S H Enthalpy S entropy dependent on T Enthalpy is the total energy within a thermodynamic system o G is spontaneous and Exergonic G is nonspontaneous and endergonic Both reactions may need additional energy input but