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
Water organizes nonpolar molecules Ionization of water: H2O -> H+ + OH- pH
 * 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
 * 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
 * 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
 * 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