BIO10& ch2‐3& Chemistry&of&Life/&Organic&Molecules&&7&7&&&The Chemistry of Life • Organisms are chemical machines • Any substance in the universe that has mass and occupies space is comprised of matter • all matter is made up of atoms Atoms All atoms have the same structure • at the core is a dense nucleus comprised of two subatomic particles • protons (positively charged) • neutrons (no associated charge) • orbiting the nucleus is a cloud of another subatomic particles electrons (negatively charged) Atoms are characterized by # of protons it has or by its overall mass • atomic number : # of protons in the nucleus atoms w/ same atomic # exhibit the same chemical properties and are considered to belong to same element • mass number (atomic mass): # of protons + # of neutrons in nucleus. electrons have negligible mass. Defines the isotopeBIO10& ch2‐3& Chemistry&of&Life/&Organic&Molecules&&8&8&Electrons determine the chemical behavior of atoms these subatomic components are the parts of the atom that come close enough to each other in nature to interact • Electrons are associated with energy • electrons have energy of position, called potential energy • the field of energy around an atom is arranged as levels called electron shells • within this volume of space, orbitals are where electrons are most likely to be found Electron shells have specific numbers of orbitals that may be filled with electrons • atoms that have incomplete electron orbitals tend to be more reactive • atoms will lose, gain, or share electrons in order to fill completely their outermost electron shell • these actions are the basis of chemical bonding • as electrons move to a lower energy level, closer to the nucleus, energy is released • moving electrons to energy levels farther out from the nucleus requires energy Ions and Isotopes Ions – atoms that have gained or lost one or more electrons Isotopes – atoms that have the same # of protons but different # of neutrons. most elements in nature exist as mixtures of different isotopes • Some isotopes are unstable • break up into particles w/ lower atomic numbers • this process is known as radioactive decay Radioactive isotopes have multiple uses 1. nuclear medicine: Can be used as tracers to study how the body functions. Short-lived isotopes decay rapidly and do not harm the body 2. dating fossils: rate of decay of a radioactive element is constant. By measuring the fraction of radioactive elements that have decayed, scientists can date fossils the older the fossil, the greater the fraction of its radioactive atoms that have decayedBIO10& ch2‐3& Chemistry&of&Life/&Organic&Molecules&&9&9& Molecule: A group of atoms held together by energy called a chemical bond 3 principal types of chemical bonds 1.ionic 2.covalent 3.hydrogenBIO10& ch2‐3& Chemistry&of&Life/&Organic&Molecules&&10&10& Hydrogen bonds • form in association with polar molecules • each atom with a partial charge acts like a magnet to bond weakly to another polar atom with an opposite charge • H bonds have cumulative strength • Hydrogen Bonds Give Water Unique Properties Water is essential for life. The chemistry of life is water chemistry. Water is a polar molecule water can form hydrogen bonds This hydrogen bonding confers on water many different special properties 5 Unique Properties of Water 1. Heat Storage: water temperature changes slowly and holds temperature well 2. Ice Formation: few hydrogen bonds break at low temperatures water becomes less dense as it freezes because hydrogen bonds stabilize and hold water molecules farther apart 3. High Heat of Vaporization: at high temperatures, hydrogen bonds can be broken. Water requires tremendous energy to vaporize because of all the hydrogen bonds that must be broken 4. Water molecules are sticky • cohesion – when one water molecule is attracted to another water molecule • adhesion – when polar molecules other than water stick to a water molecule 5. The last unique property of water is that it is highly polar • in solution, water molecules tend to form the maximum number of hydrogen bonds •hydrophilic molecules are attracted to water and dissolve easily in it –these molecules are also polar and can form hydrogen bonds •hydrophobic molecules are repelled by water and do not dissolve –these molecules are non-polar and do not form hydrogen bondsBIO10& ch2‐3& Chemistry&of&Life/&Organic&Molecules&&11&11& Water Ionizes • The covalent bond within a water molecule breaks spontaneously • This produces two ions in a process called ionization • because of the great strength of covalent bonds, this does not occur too often The amount of ionized hydrogen from water in a solution can be measured as pH pH Scale • The pH scale is logarithmic, which means that a pH scale difference of 1 unit actually represents a 10-fold change in hydrogen ion concentration • Pure water has a pH of 7 (there are equal amounts of [H+] relative to [OH-] • Acid – any substance that dissociates in water and increases the hydrogen ion concentration • acidic solutions have pH values below 7 • Base – any substance that combines with [H+] when dissolved in water • basic solutions have pH values above 7 • The pH in most living cells and their environments is fairly close to 7 • proteins involved in metabolism are sensitive to any pH changes • metabolic activities & dietary intake and processing creates acids and bases • Organisms use buffers to minimize pH disturbances Buffer – a chemical substance that takes up or releases hydrogen ions • buffers don’t remove the acid or the base affecting pH but minimize their effect on it • most buffers are pairs of substances, one an acid and one a baseBIO10& ch2‐3& Chemistry&of&Life/&Organic&Molecules&&12&12& 4 types of Macromolecules (polymers) Proteins Nucleic Acids Carbohydrates Lipids Monomers: single unit that repeats to make up a polymer. Organic Molecule: any molecule that has a carbon based core with special groups attached. • These special groups give the molecule it’s identity. How are Macromolecules Made & Destroyed? Enzymes are required. Making a Macromoledule Dehydration Synthesis Remove a H2O (H from one and OH from another) Destroying a Macromolecule (polymer) Hydrolysis