CH.

2 CHEMSITRY OF LIFE

 CHON - most of matter

 Electrons
o PE directly related to distance from nucleus
o Lowest state of PE
 Strong bonds
o Covalent - EN
o Dry ionic - complete transfer of electrons
 Weak bonds - reversible, 3D protein shape
o H-bond - b/t partially positive H and negative EN atom
o Van der Waals - changing regions of +/-
 Unequal sharing of electrons in H2O leads to polar bonds, which leads to H bonds between water
and other molecules
 Properties of water - due to H bonds
o Cohesion/Adhesion - capillary action, surface tension
o Specific heat - resists temp changes; allows life to exist
o Evaporative cooling - due to high heat of vaporization - prevents overheating
o Expansion upon freezing - crystalline lattice with more space; life underneath floating ice
o Versality as solvent - hydration shells around ions, H-bonds around polar molecules
 Acids
o Add H+
o Combine H+ with OH- to form water
 Bases
o Add OH-
o Accept H+
o Combine H+ with OH- to form water
 Acidification
o
CO2 + H2O = Excess H+ combines with
H2CO3 CO32- (carbonate) to form
(carbonic bicarbonate. Carbonate is
acid) = H+ required for calcification
HCO3- (calcium carbonate) by
(bicarbonate) marine animals. Loss of
calcium carbonate leads to
loss of coral reef and loss
of biodiversity.

Definitions:

 Bonding capacity/valence: # of e- needed to complete octet

 Covalent molecule: definite size and # of atoms
 Ionic compound: ratio of elements
 Evaporative cooling: surface of liquid cools due to molecules with greatest KE evaporating, so avg
KE decreases; molecules must extract heat of vaporization from liquid, so it cools
 Buffer: accepts excess H+, donates them where needed
  Temperature: average KE, regardless of volume
 Thermal energy: total KE, depends on volume
 Spring turn: ice melts in spring and sinks; O2 returns to bottom and nutrients carried to top

CH. 4 CARBON

 Variation of carbon skeleton

o Length
o Branching
o Double-bond position
o Presence of rings
 Isomers
o structural (covalent arrangement)
o cis/trans isomer (spatial arrangement)
o enantiomers (mirror)
 Functional groups - directly involved in reactions
o Hydroxyl - dissolve
o Carbonyl - ketone/aldehyde
o Carboxyl - acid
o Amino - base
o Sulfhydryl - cross link
o Phosphate - gives negative charge, ability to react with water; releasing energy
o Methyl - tag
 Monosaccharide classification:
o Aldose, ketose
o # of C in skeleton
o Arrangement around asymmetric carbon
 Polysaccharides
o Storage - starch and glycogen
o Structural - cellulose and chitin
 Protein - diverse structures = diverse functions
o Storage
o Enzymes
o Hormones
o Motor and contractile molecules
o Defense
o Transport
o Receptor
o Structure
 Levels of protein structure
o Primary - amino acids
o Secondary - alpha helix/beta-pleated sheet due to H-bonds between polypeptide backbone
o Tertiary - hydrophobicity, disulfide bridges, H-bonds, ionic bonds, Van der Waals between R
groups
o Quaternary - aggregation of polypeptides
 Nucleotide sequence - amino sequence - protein structure and function
 RNA - base pairs with DNA or with itself (tRNA); variable in shape
 Carbs - CH2O
  Protein: CHON,S
 Fats: CHO,P
 Nucleic acids: CHON,P

Definitions:

 Asymmetric carbon: C attached to 4 different elements

 Glyosidic linkage: between two monosaccharide
 Ester linkage: 1 glycerol bonded to 3 fatty acids
 Unsaturated fats: double bonds, less H atoms
 Hydrogenated fats: unsaturated fats converted to saturated by adding H
 Steroids/cholesterol: 4 fused rings with chemical groups attached
 Polypeptide backbone: contains N terminus and C terminus; R group extends out
 Sickle cell: abnormal hemoglobin aggregates in chains, deforming RBCs into sickle shape
 Denaturation: protein loses shape and becomes inactive due to disruption of weak bonds (heat,
pH, salinity)
 X-ray crystallography: diffracts x-ray through crystal to find structure of proteins
 Intrinsically disordered proteins: must binds with another molecule to see shape
 Nucleotide: pentose, nitrogenous base, phosphate
 Phosphodiester linkage: forms polynucleotides
o 5' end: phosphate group
o 3' end: OH group
 Chaperone proteins: help protein-folding