1.

1 Properties of Water
- Chemical bond = new substance is created
- Properties of water that benefit life
- Freezing from top down
- High heat capacity
- High heat of vaporization
- Dissolves many substances
- Cohesion and adhesion (capillary action)
- Surface tension

1.2 Organic Chemistry and Functional Groups

- Hydrocarbons = carbon + hydrogen
- Bonds between hydrocarbons store energy released when
these molecules are burnt
- Hydrocarbon rings can be 5-6 carbon rings
- Benzene: important hydrocarbon ring found in amino acids,
cholesterol

- Isomers: differ in arrangement of atoms or types of bonds

between atoms
- Structural: different covalent arrangement of atoms
- Geometric: different arrangement of atoms around a double
bond
- Enantiomers: differ in 3d arrangement and are mirror
images (non-superimposable)

- Functional groups
- Hydroxyl: OH
- Polar
- Carbonyl: C=O
- Very reactive (important in building molecules and
energy releasing reactions)
 - polar
- Aldehyde: end of a chain and only bonded to 1 alkyl
- Keto: middle of a chain and bonded to 2 alkyls
- Carboxylic acid: COOH
- Acidic
- polar
- Amino: NH2
- Basic
- polar
- Phosphate
- Negatively charged
- Sulfhydryl: SH
- Little polar
- Give up H to form S-S (disulfide bridge)

1.3-1.4 Reactions and Metabolism

- Dehydration Synthesis (condensation reaction)
- Form molecules
- Anabolic
- Endergonic (requires energy)
- Decrease entropy
- Gibbs free energy is gained

- Hydrolysis
- Break down molecules
- Catabolic
- Exergonic (releases energy)
- Increase entropy
- Gibbs free energy is lost

- Anabolism + catabolism = metabolism

 - First law of thermodynamics
- Energy is neither created nor destroyed
- The amount of energy before transformation equals total
energy after transformation
- Second law of thermodynamics
- Entropy always increases
- After transformation: Usable energy (free energy) +
unusable energy
- Life requires a constant input of energy to maintain order

Carbohydrates
- Number carbons: carbon outside the molecule is the last one
- The carbon to the right of the one outside is always 1

- Energy, structure, recognition, signaling

- Hexos
- 6 carbon sugars, C6H12O6
- Ring or linear (ring in aqueous solutions)
- Glucose
- Galactose - part of lactose/milk
- Fructose - part of sucrose/fruit

- Glycosidic linkage: condensation reaction to form disaccharide

- Covalent bond
- Maltose (grain sugar)
- Glucose, glucose
- Lactose (milk sugar)
- Glucose, galactose
- Sucrose (table sugar)
- Glucose, fructose

- Oligosaccharides
 - Contains several monosaccharides
- Recognition and signaling: bonded to proteins and lipids on
cell surfaces

- Polysaccharide
- Branched / unbranched
- Starch: energy in plants (branched)
- Glycogen: energy in animals/humans (highly branched)
- Cellulose: structure in plants cell wall (unbranched, linear)
- Chitin: structure in animals (arthropod exoskeleton) and in
fungi cell wall (contains nitrogen)

Lipids
- Non-polar, hydrophobic
- Energy storage (2x that of carbons)
- Insulation, cushioning, protection, building blocks of hormones,
component of cell membrane)
- Fats, oils, waxes, phospholipids, steroids

- Triglyceride
- 3 fatty acids
- Hydrocarbon chain + COOH
- 1 glycerol
- Alcohol with 3 OH groups
- Ester bonds: 3 condensation reactions to form 3 covalent
bonds

- Saturated fatty acid

- Fats
- Bad health
- Unsaturated fatty acid
- Double bonds
 - Liquid - oils
- healthiest
- Monounsaturated - 1 double bond
- Polyunsaturated - more than 1 double bond
- Cis - hydrogen of double bond on same side of chain
- Trans - hydrogen on opposite sides of chain
- Does not cause kink (most unhealthy)
- Can increase cholesterol (bad for heart)

- Essential: body cannot produce, must intake

- Omega 3,6 fatty acids (good for heart)

- Wax: long fatty chains esterified with alcohol

- Modifiers like charge of polar groups can be added to the

position labeled “R”
- Amphipathic: have both hydrophilic and hydrophobic regions

- Steroids
- Four carbon rings
- Short tail
 - Less oxygen compared to carbs
- Cholesterol
- Synthesized in liver
- Precursor to testosterone estradiol, vitamin D, bile
salts

Amino acids
- Amino group, central carbon, carboxyl group
- 20 types
- Peptide bonds hold amino acids together (dehydration synthesis)
- Carboxyl links to amino
- Polypeptide - a chain of amino acids
- Protein - a functional polypeptide or multiple polypeptides

Proteins
- Most abundant organic molecule
- Functions of proteins
- Enzymes, defensive proteins (antibodies), hormonal and
regulatory proteins, receptor proteins, storage proteins,
structural proteins, transport proteins, genetic regulatory
proteins
- Primary - the sequence of amino acids determined by the DNA
sequence
- Secondary -alpha helix or beta pleated sheet structure resulting
from hydrogen bonding of C=O and NH groups
- Tertiary - bent and folded resulting in 3-d shape
- Interactions between R groups determine tertiary structure
- Disulfide bridges (S-S)
- Hydrogen bonding
- Hydrophobic interactions
- Van der Waals interactions
 - Ionic interactions (salt bridges)
- Quaternary - hydrophobic, ionic interactions and hydrogen bonds
- Aid the proteins function
- Denaturing
- Temperature, ph
- Change in solvent (ie. egg placed into nonpolar substance
instead of polar)

- Additional stuff for proteins to function

- Cofactors - inorganic ions
- Coenzymes - intermediate carriers of chemical groups that
can add or remove them from substrate
- Prosthetic groups (non-amino acid) permanently bound to
enzyme

Enzymes
- Catalytic - affects the rate of reaction
- Catalyzed and uncatalyzed reactions have the same amount of
free energy
- Enzymes and substrates are held together by hydrogen bonding,
electrical attraction, or temporary covalent bonding

Nucleic Acid
- Store and transmit genetic information, regulatory functions
- Pyrimidines: cytosine, thymine (uracil)
- 1 ring
- Purines: adenine, guanine

- A to T
- 2 bonds
- C to G
 - 3 bonds

- Phosphodiester bonds
- 3’ carbon of the chain bonds to top of phosphate group of
new base
- Condensation reaction
- Phosphate group sticks out on 5’ end (bonded to 5’ carbon
of its nucleotide)

- RNA usually single stranded

- Can fold into 3-d structures through hydrogen bonding of
complementary base pairings, so structure determined by order
of bases

- Transcription can happen in reverse but not translation