2. biochemistry

polymers vs. macromolecules

• polymers need a chain of molecules with the same base (eg. DNA, amino acids, starch)
• macromolecules are large molecules (eg. carbohydrates, protein, lipids)
• all polymers are macromolecules but not all macromolecules are polymers

The elements of life

• about 20-25% of the 92 elements are required for life
• carbon and hydrogen are required to make organic compounds
• carbon hydrogen oxygen and nitrogen make up 96% of living matter
  • nitrogen - ammonia which is found in amino acids
• the remaining 4% consists of calcium, phosphorus, potassium and sulphur
  • phosphorus - ATP, and DNA
• trace elements are required in very small amounts

isotopes

• all atoms of an element have the same number of protons but may differ in neutrons. these are isotopes
• radioactive isotopes decay spontaneously, giving off particles of energy
  • can be used as diagnostic tools in medicine eg. iodine - thyroid
• radioactive tracing - used to track atoms through metabolism
• radioactive dating - measure dating using time

energy levels of electrons

• energy is the capacity to cause change

• potential energy is the energy that matter has because of its location or structure

• electrons in an atom differ in their amounts of PE

• an electron’s state of PE is called its energy level or electron shell

• form equals function

  • when something is not the right shape, they won’t work

• electrons live in orbitals 1s2, 2s2, 2p6

• electrons can move between orbitals

  • when electrons jump, they emit light
  • in photosynthesis, light is used to make electrons jump between orbitals

• atoms with incomplete valence shells like to combine

  

covalent bonds

• the sharing of a pair of valence electrons by 2 atoms

• a molecule consists of 2 or more atoms held together by covalent bonds

• single bonds are the sharing of one pair of electrons

• double bonds are the sharing of two pairs of electrons

• form equals function

• the shape of a molecule determines how it is recognized and responded to

  • opiates such as morphine works similarly to endorphins since they have similar shapes and bond to the same receptors in your brain to make you feel good

  

polarity

• water is polar

• polar = unsymmetrical, non polar = symmetrical

• ionic compounds dissolve in water and only polar molecules

• when a compound dissolves in water, the water surrounds the positive atom creating a hydration

• cellulose is non-polar despite it being unsymmetrical. this is because when a chain of molecules come together, they become symmetrical which is why water does not dissolve plants

• in the covalent bond H2O, oxygen pulls hydrogen’s electron towards it giving oxygen a very small 𝛿- charge and hydrogen a 𝛿+ charge. (delta charge)

• H2O has an angular or bent shape because the electrons repel each other

  • the angle between the hydrogens is 104.5

• methane is non-polar, however, it can dissolve in water under extremely high pressure

• electronegativity is an atom’s attraction for the electrons in a covalent bond

  • when a covalent bond is formed between 2 identical atoms (H2 or Cl2), the electrons are shared equally since the 2 atoms have the same attraction to the electrons. However, between 2 different elements, one atom will have a larger nucleus and a greater attraction to the electrons.

  arrow points toward the negatively charged atom, 𝛿+ had lower electronegativity and 𝛿- has greater EN

• electronegativity: 0 - 0.39 = non polar, 0.4 - 1.7 = polar, 1.8 < = ionic

• nonpolar bonds share the electrons evenly

• in polar bonds, one atom is more electronegative and they do not share the electrons evenly

ionic bonds

• cations are positively charged ions
• anions are negatively charged ions
• ionic compounds are called salts

weak chemical interactions

• large biological molecules are held together by weak bonds

• intramolecular forces - within a molecule

  • covalent, polar covalent and ionic

• intermolecular forces - between 2 molecules ↓

• hydrogen bonds - when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom (same as dipole-dipole but much stronger)

  • hydrogen bonding is why water is referred to as the universal solvent
  • Oxygen, fluorine, nitrogen

  

• Van der Waals interactions - attractions between molecules that are close together as a result of unevenly distributed electrons in a molecule

  • electrons are not always evenly distributed and may accumulate in one part of a molecule
  • relatively weak attractive forces that act on neutral atoms and molecules and arise because of the electric polarization induced in each of the particles by the presence of other particles.
  • london dispersion forces - a temporary force that results when the electrons of 2 atoms occupy positions where there is a temporary dipole force (as the atoms move around). results from a very short separation of charge or dipole that occurs due to temporary electron density fluctuations around atoms or molecules.
  • LDF forces are the weakest intermolecular forces and occur between all molecules
  • it is the only force acting between non-polar molecules
  • the larger the molecules, the stronger the forces
  • dipole-dipole forces - when hydrogen bonds with anything other than O, F, N (attractive forces between the positive end of one polar molecule and the negative end of another polar molecule)
  • because polar molecules have a net dipole (a positive end and a negative end), the force between oppositely charged ends of polar molecules is a dipole-dipole force
  • only exists in polar molecules

  

chemical reactions

• the making and breaking of chemical bonds
• eg. photosynthesis: 6 CO2 + 6 H2O → C6H12O6 + 6 O2
• all chemical reactions are reversible
• chemical equilibrium is reached when the forward and reverse reactions occur at the same rate