BIOL 103 - Microbes and You

Lecture 3 Outline

Chemistry Primer


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Chemistry Basics
atoms are composed of electrons, protons, and neutrons
electrons are important in forming chemical bonds that hold atoms together in molecules
the atoms in salts are bond through ionic bonds
the atoms in ionic bonds do not share electrons, electrons are passed from one to the other
thus, one atom becomes negatively charged and the other positively charged ions
atoms in covalent bonds share electrons
water is a solvent in which other molecules dissolve
water is polar, having partial positive and negative charges
polar molecules can form H-bonds (hydrogen bonds) that do not involve eletrons directly

Organic Chemistry Basics
organic molecules contain carbon with at least one hydrogen atom
CH4, methane, is an organic molecule
CO2, carbon dioxide is an inorganic molecule
simple hydrocarbons only contain C and H, like propane
the hydrocarbon chains can be straight or branched

Functional groups on organic molecules
functional groups are used to perform chemical reactions
often have charges or extra electrons for making chemical bonds
A. Alcohol - OH is a hydroxyl group
B. Aldehyde - C double bonded to O is a carbonyl. if terminal, then an aldehyde
C. Ketone - an internal carbonyl group
D. Acid - C double bonded to O with another OH bound to the same carbon atom is called a carboxyl group. The carboxyl group can be ionized to give a negatively charged carboxylic acid and a proton (H+).
E. Amine - NH2 is an amine group.
(amino acids contain a carboxyl group and an amine group on the same molecule)
F. Sulfhydryl - also called 'thio' contains a sulfur as SH
G. Phosphate - PO4 is a phosphate group. When a phosphate group is included in an organic molecule it forms a special phosphoester linkage that contains a lot of energy.

Biological Molecules
"macromolecules" are polymers
each monomer acts as a building block to be strung together to make a polymer
simple sugars are linked to form polysaccharides
fatty acids are linked to form lipids (fats and oils)
nucleotides are linked to form nucleic acids
amino acids are linked to form proteins

Carbohydrates
glucose and fructose are simple sugars or monosaccharides
these are linked through a dehydration reaction to form complex carbohydrates or polysaccharides
carbohydrates have the formula CH2O
complex carbohydrates include starch, glycogen, cellulose, and pectin
carbohydrates are used in cells as structural components such as the cell wall, as nutrients for growth, and as storage compounds

Lipids
lipids are fats and oils and contain C, H, and O
simple lipids are formed when two or three fatty acids are linked with glycerol
lipids have long greasy (hydrophobic) hydrocarbon chains and polar (water-loving, hydrophilic) head groups

Nucleic acids
composed of C, H, O, P, N are polymers of nucleotides
nucleotides contain a nitrogenous base, a 5-carbon sugar, and phosphate
the sugars and phosphates form the backbone of the chain and the bases hang off
DNA uses four bases - AGCT
RNA uses four bases - AGCU

Proteins
composed of C, H, O, N, S are polymers of amino acids
20 amino acids are generally used for proteins
usually proteins are 100 amino acids long or longer
often several protein chains work together
many proteins are enzymes that catalyze (speed up) chemical reactions
enzymes do the work of the cell
proteins can also be structural components of the cell
proteins are good nutrients, containing N and S
proteins are made on ribosomes
ribosomes are complex machines of 100 proteins with special RNA molecules


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