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)

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