Bio Chapter 2

==Chemical connection to biology: == * Biology:: is the study of life * Organisms & the environment is subject to the laws of physics and chemistry * %%Matter::%% is made up of chemical elements and combinations (compounds) * Organisms are made up of matter * Takes up space and has mass * Chemical compounds can be broken down by chemical reactions & are arranged in a fixed ratio.
==Elements of Life: == * 20-25% of 92 elements are required for life (oxygen, nitrogen - ammonia, carbon, hydrogen) * They make up 96% of living matter (carbon + hydrogen = organic molecules) * Most of the remaining 4% are calcium, phosphorus (in ATP → ADP + P inorganic, DNA), postassium, and sulfur. * %%TRACE ELEMENTS::%% Elements required in very little amounts/minute quantities (ex. iron, magnesium, sodium, chlorine).
==Element’s Properties depend on structure of its atoms:== * Atom:: composed of subatomic molecules (ie. neutrons, protons, electrons) * Electrons form negatively charged “cloud” around nucleus * %%Mass #:%%: mass of neutrons + protons (approx. by atomic mass) * %%Atomic #::%% number of protons * Neutron mass:: ~ proton mass * @@Isotopes::@@ 2 atoms of the same element with different number of neutrons * $Radioactive isotopes::$ decay spontaneously, giving off particles and energy * It loses its protons, transforming the atom into a different element * @@Radioactive tracers::@@ * Diagnostic tool in medicine * Tracers used to track atoms through the body’s metabolism * Used with imaging instruments * Ex. Bromium drink * @@Radioactive Dating::@@ * Parent isotope decays into the daughter isotope (@ a fixed rate = half-life) * We can measure the ratio of isotopes and calculate how many half-lives have passed
==Energy Levels of Electrons:: == * Energy causes change * %%Potential energy::%% energy that electrons possess because of their location and structure * Electrons are located in electron clouds and their state of energy is determined by their electron shell
==Electron distribution and chemical properties::== * The chemical behavior of an atom is based on the distribution of electrons in the electron shells * Atoms with full valence shells are chemically inert/unreactive * @@Electron orbitals:@@ * Each electron shell consists of a specific number of orbitals * Orbitals are a space where electrons spend 90% of their time * 1s^2, 2s^2, 2p^6, 3s^2… * Electrons can move/jump between orbitals depending on the energy absorbed or released as light * @@Formation + Function depends on the chemical bonds between atoms@@ * Atoms with incomplete valence shells can give away or receive electrons * These form attractions between atoms * Bonding capacity is based on an atom’s valence
==Covalent Bonds == * Bonds that hold atoms together by 2 shared pairs of electrons * 1 bond = 1 shared pair (2 bonds = 2 shared pairs) * Molecule = 2+ atoms held together by covalent bonds
==Ionic Compounds & Polarity== * Dissociate in water because its ions are attracted to the charge on water molecules (negative or positive dipoles) * Attracted to the polar/non-polar atoms in a water molecule * Polar dissolves in polar, non-polar dissolves in non-polar * Ex. Cellulose (non-polar), when bonded with glucose, makes the molecule symmetrical * Cellulose looks polar because of its asymmetry, but it is non-polar because its long chains become symmetrical. * Polar molecules are NON-SYMMETRICAL (99% of the time) * %%ASYMMETRICAL%% molecules are polar if at least 1 bond is polar and non-polar if all bonds are non-polar * %%Symmetrical%% molecules are ALWAYS non-polar * H2O = O has a slight negative charge, H has a positive charge (electronegativity differences) * The water molecule is bent 104.5 (electron repulsion) degrees to perform its functions
@@Application: Ponds & lakes are colder when more oxygen is dissolved@@ * Biological oxygen demand = the amount of oxygen consumed by microorganisms when they’re decomposing organic matter under aerobic conditions.
==Electronegativity==: * Atoms’ attraction for electrons in a covalent bond * High electronegativity = an atom’s strong pull of electrons towards itself * In non-polar covalent bonds, the electrons are shared almost completely equally * In polar covalent bonds, one atom is more electronegative than the other, causing there to be a slight negative charge on the atom with a higher electronegativity and a slight pos charge on the atom having its shared electrons pulled away
==Ionic Bonds: ==
The attraction between a cation (positive charge) and an anion (negative charge) (after one atom strips off its electron and gives it to another atom to form 2 ions)
Compounds formed by ionic bonds = ionic compounds/salts
Dissociate in water
Water always follows a salt (why mouth tastes salty when dehydrated - to stimulate water)
==Weak Chemical Interactions:== * Most of the strong bonds in organisms are covalent bonds that form a cell’s molecule * Larger molecules are held together by weak bonds that allow them to perform their function * Reversibility of weak bonds is an advantage (ie. homeostasis)
^^Hydrogen Bonds:^^ Intermolecular force * Forms, when a hydrogen atom bonded to an electronegative atom, is also attracted to another electronegative atom * Commonly between H and O, F, or N atoms (O or N in living organisms) * Can break with a little bit of energy (individually), but very strong collectively * The strongest of all weak bonds
^^Vaan der Waals Interactions/London Dispersion Force: Intermolecular force^^ * In every interaction * Occurs when electrons accumulate on one side of the molecule due to uneven distribution * The charge on these molecules create attractions between atoms or molecules that are instantaneous and cause an instant net dipole that disappears once electrons rearrange * Weak individually but can be strong collectively (ex. gecko hand hairs and the wall) * Cloud of electrons around one compound attracted to the nucleus of another compound * Positive on one side
^^Dipole-Dipole ^^ * Hydrogen bonds with any other molecule (ex. HCl) * Stronger than LDF but weaker than Hydrogen bonds * Occurs between 2 polar molecules (when the positive end of one polar molecule is attracted to the negative end of another polar molecule)
==Molecular Shape and Function == * Form (determined by the atom’s orbitals) fits the function * In covalent bonds, s and p orbitals may hybridize to create a tetrahedron shape * Elements have no shape, shape is only relevant when forming compounds * Molecular shapes determine how molecules interact and recognize one another * Opiate and naturally produced endorphins have similar effects because of their similarities in shape and the fact that they both bind to the same receptors in the brain. * Morphine prevents people from feeling pain (but people can grow immune to its effects and even stop producing endorphins naturally)
==Chemical reactions make and break chemical bonds:== * Photosynthesis → sunlight powers the production of 6CO2 and 6H2O into C6H12O6 + 6O2 * All biological chemical reactions are reversible because of maintaining homeostasis * Once homeostasis is achieved, the body dies (and can be restimulated from stress that is applied to it) * Chemical equilibrium occur when reactions and its reverse reaction occur at the same rate (an increased amount of reactants = an increased chance at reactions occurring) * At equilibrium, the concentrations of reactants and products do not change (remain fixed in a set ratio)