1. Chemical Principles

2. Atoms and Molecules: - A cell is more than a bag of chemicals
- Important knowing how molecules interact
Elements defined:
Atoms defined:
Molecule defined:
Only ~16 of 92 naturally occurring elements are essential to most plants

3. Four major elements make up more than 95% of mass
Hydrogen [H]
Oxygen [O]
Carbon [C]
Nitrogen [N]
Organic Compounds defined:
Inorganic Compounds defined:
Biochemicals defined: organic and inorganic molecules that occur in living things

4. Living things: 80% water, 20% organics Four Major Categories of Molecules: - Carbohydrates - Protein - Lipids - Nucleic Acids
- Most of the mass is primarily these
- Some other, lesser compounds:
phenolics, alkaloids, terpenoids, and flavonoids
Large Molecules: The Polymers
Monomers:
Polymers: (ex. Protein, DNA, lignin, tannin)

5. Carbohydrates: Sugars and starches: (ex. Glucose)(formula)
Isomers: different compounds with the same formulas.
Rarely found as monomers
Sizes: monosaccharides
disaccharides
polysaccharides

6. Structural polysaccharides: hold cells and organisms together. (ex
Structural polysaccharides: hold cells and organisms together. (ex. Cellulose fibers)
Each cellulose fiber is composed of dozens of microfibrils
Microfibril: 1000 or more cellulose polymers twisted together.
Pectins: gluey polysaccharides that hold cellulose fibers together.
Gums: complex, branched polysacs made of many kinds of monomers

7. 2 important commercial polysacs
agar and carrageenan
Storage polysaccharides: store food
Two most common in plants:
Amylose and Amylopectin (starch)
Ex. Monosaccharides: glucose and fructose
Ex. Disaccharides: sucrose, lactose, maltose
Ex. Polysaccharides: starch, glycogen

8. Proteins: 2nd in mass in plants after cellulose
One or more polypeptides, sugars, or lipids
Polypeptides – chain of amino acids (20 different ones to choose from)
Used for: cell structure, storage, enzymes
Protein Structure:
Primary structure
Secondary structure
Tertiary structure
Quaternary structure

9. Protein Denaturation
Storage proteins:
- nutrition source
- seeds Ex. zein, gliadin
Toxins: Ex. ricin D, abrin

10. Proteins in cell walls:
- proteins are a major part of cell membranes and cell walls
- 2-10% of cell wall protein
Ex. Expansins and extensins (glycoproteins)
Enzymes: catalysts
- most of the proteins
- proteases Ex. Alpha - amylase

11. Nucleic Acids: - most complex, polymer of nucleotides
- two kinds: DNA and RNA
- nucleotides: the monomers, 4 different kinds
- DNA structure: the double helix
- self-replicate
- store information

12. Lipids: Are not polymers, water repellent 3 major plant lipids:
Phospholipids
Oils
Waxes
Very diverse
Gives rise to more specialized cells
Functions: storage, basic metabolism

13. Oils: Fats and Fatty Acids
- liquid at room temperature (for plants)
- triglycerides
- structure:
Saturated (bad fats) vs. Unsaturated (better)
- most abundant in seeds

14. Phospholipids - hydrophilic and hydrophobic
- major component of membranes
- structure:

15. Waxes Mixtures of fatty acids and long chain alcohols.
Epicuticular Layer: comprise the outermost layer (cuticle) of leaves, fruits, and stems
Cuticular wax: embedded in the cuticle, primary layer of wax, 2 types
Cutin: makes up most of cuticle
Suberin: underground plant parts
Waxes: more water repellent & harder than other lipids

16. Secondary Metabolites
- Less made chemicals, scarce
- Occur irregularly or rarely in plants
- Byproducts of cell metabolism
- No known role in cells for metabolism (?)
Ex. Morphine, caffeine, nicotine, menthol
- Most can be classified based on:
1. Kind of plant
2. Structure
3. Biosynthetic pathway

17. 3 major groups of secondary metabolites
1. Alkaloids
2. Terpenoids
3. Phenolics
Glycosides: secondary metabolites combined with one or more sugars for transport.
Minor Secondary Metabolites
- Nitrogen-sulfur compounds
- Non-protein amino acids
- Cyanogenics

18. Alkaloids - contain nitrogen in a ring structure
- alkaline (basic) substances
- bitter tasting
- generally poisonous
Ex. Coniine, strychnine, tomatine

19. Terpenoids Polymers, monomer called a isoprene
Smallest called monoterpenes, 2 isoprene units (dimer), ex. Geraniol and Menthol
Also diterpenes (pines) and triterpenes
Sterols: kind of triterpene, similar to steroid hormones, ex. Digitalin
Carotenoids: class of yellow to red pigments formed of 8 isoprene units
Rubber: largest terpenoids there are
(up to 6,000 or more monomers long)

20. Phenolics:
- fully unsaturated carbon ring (phenol) linked to an oxygen
Ex. Salicylic acid (aspirin)
- subclass called phenylpropanoids involved in flavor
Ex. Nutmeg flavor
Others include:
complex flavonoids, anthocyanins, tannin, lignin