Key Terms

Atoms:

• electrons: both energy and substance particles
• neutrons
• protons

Molecules:

• Formed by atoms
• Joined by chemical bonds
• molecular formula and structure formula

Organic Molecules/macromolecules:

• amino acids --> proteins
• monosacchrides --> polysaccharides
• fatty acids --> lipids
• nucleotides --> nucleic acids

Isotope: atoms have same proton numbers but may differ in neutron numbers
Energy shell: Electrons occupy orbital around nucleus, these are called energy shell.  The most inner shell (K) contains 2 electron maximun, the L and M shell contain 8 maximum each.
Organic chemicals: chemicals are made from living organisms and contain carbon backbones.
Isomers: Chemicals that have same molecular formula but different structure formula.
Buffers: solutions which resist change in pH upon addition of small amounts of acid or base.
Electrolytes: chemicals that can release ions into solutions
pH: pH represents the concentration of hydrogen ions [H+] in solution.
pH = -log [H+]
Enzymes: proteins that serve as catalysts for biochemical reactions.
Enthropy: a measure for a system's degree of disorder. It increases with increasing disorder.  
Law of thermodynamics:

• The first Law: The total energy of the universe is always conserved. Energy can neither be created nor destroyed.
• The second Law: The universe tends towards maximum disorder, or, in other words: the direction of all spontaneous processes is such as to increase the entropy of a system plus its surroundings 

ΔG: Change of free energy of a system. 

• ΔG negative reaction: spontaneous
• ΔG positive reaction: non-spontaneous

Chemical Bonds

Chemical bonds store energy.  For covalent bonds, the more electrons a bond share, the more energy it stores.

Ion bond: ion bond forms when atoms lose or gain electrons.
Covalent bond: Covalent bonds form when atoms share electrons, very strong bonds.  The major one in organic chemicals.
Hydrogen bond: Weak electrical attraction between the positive end of one molecule and the negative end of another

Organic Chemicals

Important Biochemical Molecules

Organic Molecules/macromolecules:

• Polysaccharides
  • Monomer unit: monosaccharide
  • store energy, provide building unit
• Lipids
  • Monomer unit: fatty acids, glycerol
  • Store energy, membrane construction, hormones
• Proteins:
  • Monomer unit: amino acids
  • Structure protein, enzymes
• Nucleic Acids:
  • Monomer unit: nucleotides
  • Genetic material

Chemical Reactions

Coupled reactions: many biosynthesis reactions are coupled to ATP hydrolysis which can provide energy and therefore the overall reaction can be delta G negative.  

• ΔG negative reaction: spontaneous
• ΔG positive reaction: non-spontaneous

Enzyme catalyzed reactions: lower the activation free energy but do not change the ΔG. 

Biochemical Reaction Types and Enzymes

• Oxidation-reduction reactions: oxidoreductase
• Intramolecular or intermolecular functional group-transfer reactions: Transfease
• Hydrolysis of esters, ethers, and amides: hydrolase
• Elimination or addition reactions: Lyase.
• Isomerization reactions: isomerase
• Formation of ester, thiol ester, and amide linkages: Ligase