Chapter 2-Basic Chemistry

2.1 Chemical Elements

• matter-anything that takes up space and has mass
• matter can exist as a solid, liquid, or gas
• elements-basic substances that cannot be broken down to substances with different properties (a property is a physical or chemical characteristic, such as density, solubility, melting point, and reactivity)
• only 92 naturally occurring elements
• 6 elements: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur make up the body weight of most organisms (CHNOPS)
• atoms-tiny particles
• early 1800s, John Dalton proposed elements contain one type of atom individually
• atomic symbol-one or two letters that stand for the element's name (H for hydrogen, Na for natrium/sodium in Latin)
• most stable subatomic particles: proton, neutron, electron
  
• proton-positive subatomic particle, located in the nucleus and having a weight of approximately one atomic mass unit
• neutron-neutral subatomic particle, located in the nucleus and having a weight of approximately one atomic mass unit
• electron-negative subatomic particle, moving about in an energy level around the atom
• most of an atom is empty space
• atomic mass-sum of protons and neutrons
• mass is constant while weight changes according to gravitational force
• atomic number-number of protons
• the atomic number is written as a subscript while the atomic mass is written as a superscript
• isotopes-atoms of the same element that have the same number of protons and differ only in the number of neutrons
• radioactive isotopes-an isotope that emits radiation in the form of radioactive particles or radiant energy when decaying
• radioactive isotopes are used in medicine since they are absorbed by metabolically active tissues and can be tracked (PET, positron emission tomography)
• 1913, Niels Bohr proposed that electrons orbit in concentric energy levels about the nucleus; although electrons have the same mass and charge, they vary in energy content
• electron shells-energy levels
• electrons differ in amount of potential energy, and the shells indicate the relative amounts of stored energy electrons have: electrons with the least amount of potential energy are located in the K shell, closest to the nucleus, then L and M
• it takes energy to keep an electron farther away from the nucleus as opposed to closer to the nucleus
• octet rule-outer shell is most stable when it has eight electrons
• atoms with eight electrons normally do not react and are inert
• orbital-volume of space where a rapidly moving electron is statistically predicted to be found
• electrons occupy an orbital rather than orbit
• an orbital has a characteristic energy state and a characteristic shape
• at the first energy level, at most two electrons are found about the nucleus in a single spherical orbital because the most likely location for each electron is a fixed distance in all directions from the nucleus
• at the second energy level, there are four orbitals and a maximum of eight electrons; one is spherical but the other three are dumbbell shaped, which allows electrons to be the most distant from one another
  
• when bonding occurs, the orbitals of the L shell sometimes hybridize, forming teardrop-shaped orbitals that point to the corners of a triangular pyramid called a tetrahedron
• photosynthesis: 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂
• equation is balanced

2.2 Compounds and Molecules

• molecules can form when two or more atoms of the same element react with one another
• compound-when two or more different elements react or bond together (O₂, H₂O is a compound that contains the elements hydrogen and oxygen)
• molecule-the smallest part of a compound that still has the properties of that compound
• ionic bonds form when electrons are transferred from one atom to another
• electron transfers may cause a charge imbalance in each atom
• ions-charged particles
• ionic bond-attraction between charged ions
• covalent bond-when two atoms share electrons in such a way that each atom has an octet of electrons in the outer shell
• molecules have a three-dimensional shape that determines their biological function
• hormones have shapes that allow them to be recognized by the cells in the body
• one form of diabetes occurs when the receptors of cells fail to recognize the hormone insulin
• AIDs occurs when blood cells have receptors that bind to the HIV virus, allowing it to enter, multiple, and destroy the cell
• nonpolar covalent bond-when the sharing of electrons between two atoms is fairly equal
• polar covalent bond-the unequal sharing of electrons in a covalent bond
• in the case of water, the sharing of electrons between oxygen and each hydrogen is not completely equal; the larger O atom has a greater number of protons and thus dominates the association, as it is more electronegative than the hydrogen atom and can attract the electron pair to a greater extent, assuming a negative charge (δ^-) and caushing the hydrogen atoms to assume a slightly positive charge (δ⁺)
  
• electronegativity-the attraction of an atom for the electrons of a covalent bond
• hydrogen bond-an attractive force creating a weak bond
• in water
• a hydrogen bond is more easily broken than a covalent bond, but many hydrogen bonds together are quite strong and help maintain proper sutrcture and function of cellular molecules

2.3 Chemistry of Water

• the first cells evolved in water, and all living things are 70-90% water
• water is a polar molecule and water molecules are hydrogen bonded together
• taken together, hydrogen molecules cause water molecules to cling together
• because of hydrogen bonding, water boils at 100°C and freezes at 0°C
• the temperature of water rises and falls more slowly than other liquids under the same conditions
• a calorie is the amount of heat energy needed to raise the temperature of one gram of water 1C
• the many hydrogen bonds that link water molecules help water absorb heat without a great change in temperature
• water has a high heat of vaporization and thus a high boiling point
• hydrogen bonds must be broken to change water to steam
• water facilitates chemical reactions bother outside of and within living systems
• water dissolves a lot of things because it is polar
• when a salt, such as NaCl, is put into water the negative ends of the water molecules are attracted to the sodium ions and the positive ends of the water are attracted to the sodium ions, and the positive ends of the water molecules are attracted to the chloride ions, causing the sodium ions and the chloride ions to separate and to dissociate in water
• water is also a solvent for larger molecules that contain ionized atoms or are polar molecules
• when ions and molecules disperse in water, they move about and collide, allowing reactions to occur
• hydrophilic-(molecules) attracting water
• hydrophobic-(nonionized and nonpolar molecules that) cannot attract water
• water molecules are cohesive and adhesive
• water molecules flow freely, but do not separate from each other; they cling to each other because of hydrogen bonding, and because they have poles, they adhere to surfaces and particularly polar surfaces
• water can fill a tubular vessel and still flow, dissolved and suspended molecules are evenly distributed throughout a system
• water is an excellent transport system both outside of and within living organisms
• one-celled organisms rely on external water to transport nutrient and waste molecules
• multicellular organisms often contain internal vessels in which water serves to transport nutrients and wastes
• the liquid portion of our blood is 90% water that contains dissolved and suspended substances
• contributes to the transport of water in plants
• plants have roots anchored in soil where they absorb water, but the leaves are uplifted and exposed to solar energy. A plant contains a sytem of vessels that reaches from the roots to the leaves, so water evaporating from the leaves is immediately replaced with water molecules from the vessels. Because water molecules are cohesive, a tension is created that pulls water up from the roots. Adhesion of water to the walls of the vessels also helps prevent the water column from breaking apart
  
• unlike most substances, frozen water is less dense than liquid water
• as water cools, the molecules come closer together (densest at 4°C)
• at temperatures below 4°C there is only vibrational movement, and hydrogen bonding becomes more rigid but also more open, so water expands as it freezes and is less dense)
• bodies of water freeze from the top, acting as an insulator to protect water underneath and making life possible instead of accumulating at the bottom of lakes and oceans
• hydrogen ions (H⁺)
• hydroxide ions (OH^-)
• H-O-H ↔ H⁺ + OH^-
• only a few water molecules at a time are dissociated, and the actual number of these ions is very small (10^-7 moles/liter)
• acids-molecules that dissociate in water, releasing hydrogen ions (H⁺)/higher concentration
  
• strong acids dissociate almost completely, strong bases dissociate almost completely
• bases-molecules that either take up hydrogen ions (H⁺) or release hydroxide ions (OH^-)/higher concentration
  
• pH scale-indicates acidity and basicity (alkalinity) of a solution
  
• ranges from 0 to 14
• logarithmic as opposed to exponential
• devised to simplify discussion of the hydrogen ion concentration [H⁺] and hyroxide ion concentration [OH^-] by eliminating th use of cumbersome numbers
• each pH has 10 times the amount of hydrogen ions as the next higher unit
• 7 is neutral pH, pure water has an equal number of hydrogen and hydroxide ions
• source: one mole of pure water contains only 10^-7 moles/liter of hydrogen ions
• in living things pH needs to be maintained within a narrow range or there are health consequences
• pH of our blood is always about 7.4, slightly basic
• buffers-most important of mechanisms to prevent pH changes; keep pH within normal limits because they are chemicals or combinations of chemicals that take up excess hydrogen or hydroxide ions
• blood always contains a combination of some carobic acid and some bicarbonate ions, so in case:
  H⁺ + HCO₃^- → H₂CO₃, then
  OH^- + H₂CO₃ → HCO₃^- + H₂O
• these reactions prevent any significant change in blood pH