==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)