General Biology/Getting Started/Matter

Matter Matter is defined as anything that has mass (an amount of matter in an object) and occupies space (which is measured as volume). Particles, from smallest to largest and amal is the greatest Subatomic particles Electrons Protons Neutrons Atoms Molecules Macromolecules Origin of matter Big Bang, about 13.7 billion years ago Hydrogen, helium Heavier elements formed in suns, super nova Earth's matter predates formation of sun, 4.5 billion years ago All matter consists of atoms, which are composed of : electrons, protons, neutrons The atom Example: Hydrogen The simplest element One proton (+) One electron in orbit (-) Built by adding one proton (and one electron) at a time Number of protons determines atomic number and number of electrons Neutrons Neutral charge Contribute mass May decay Oxygen 8 protons (mass) 8 electrons 8 neutrons (mass) Mass and isotopes Atomic mass Sum of masses of protons and neutrons Measured in daltons or AMU (Atomic Mass Unit) An AMU is 1/12 the mass of Carbon-12 proton ~1 AMU or dalton 6.024 x 1023 daltons/gram Atoms with same atomic number belong to same element Isotopes Same atomic number but different atomic mass Some are radioactive Uses of isotopes Radioactive: 3H, 14C, 32P, 35S Tracers in biochemical reactions Detection of molecules in recombinant DNA technology (genetic engineering) Half-life: dating of rocks, fossils Non-radioactive (N, C, O) Diet of organisms (including fossils) Biochemical tracers Electrons Negative charge Held in orbit about nucleus by attraction to positively charged nucleus Atom may gain or lose electron, altering charge Cation: loses electron, positive charge Na+ Anion: gains electron, negative charge Cl- Determine chemical properties of atoms Number Energy level Chemical bonds Form molecules Enzymes: make, break, rearrange chemical bonds in living systems Ionic Covalent Sharing of one or more pairs of electrons Called single, double, or triple No net charge (as in ionic bonds) No free electrons Give rise to discrete molecules Hydrogen Chemical reactions Formation and breaking of chemical bonds Shifting arrangement of atoms Reactants -> products Reactions are influenced by: Temperature Concentration of reactants, products Presence of catalysts (enzymes) Oxidation:reduction Water Essential for life ~75% earth's surface is water Life evolved in water Solvent for many types of solutes High specific heat High polarity Creates a slightly negative Oxygen and a Slightly positive hydrogen allows formation of Hydrogen Bonds Hydrogen bonding A type of polar interaction Critical for: Protein structure Enzymatic reactions Movement of water in plant stems Weak and transient Powerful cumulative effect Solubility of many compounds Cohesion (capillary action) Lower density of ice Formed between molecules other than water Protein structure DNA, RNA structure Water organizes nonpolar molecules Nonpolar molecules: no polarity (+/-) charges Hydrophobic: exclude water because they don't form hydrogen bonds with it Consequences: Membranes Protein structure Hydrophilic: polar substances associate with water Ionization of water: H2O -> H+ + OH- Forms a Hydrogen ion (H+), hydroxide ion (OH-) Due to spontaneous breakage of covalent bond At 25 °C, 1 liter of water contains 10-7 moles of H+ ions: 10-7 moles/liter pH A convenient way of indicating H+ concentration pH = -log[H+] For water, pH = -log[10-7] = 7 Since for each H+ in pure water, there is one OH-, pH of 7 indicates neutrality Logarithmic scale Buffer Reservoir for H+ Maintains relatively constant pH over buffering range References This text is based on notes very generously donated by Dr. Paul Doerder, Ph.D., of the Cleveland State University.