LZ

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)