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Organic Chemistry
Why carbon?
Shortcuts
a. Condensed structures (omit most bonds and add parentheses)
b. Skeletal structures
each vertex = a C atom Add H atoms to get 4 bonds per C atom
Functional Groups
Thiol RSH SH
sulfhydryl group
Phosphoryl Group
Functional groups make organic compounds polar
Polar or ionic compounds are more soluble in water
All polar functional groups can from hydrogen bonds
All charged functional groups can form ionic bonds with oppositely
charged groups
Different classes of biological molecules contain different types of
functional groups
Hydrocarbons
pH
Weak acids reach equilibrium, so some molecules are HA, some are A-
In biological system, the strongest acid is H3O+, and the strongest base
-
is OH
Why?
b. Meaning of pH
Carboxyl groups act as acids (we usually see them after they have
given up a proton)
d. Buffering
Cells and biological fluids contain multiple weak acids/bases that react
with (or buffer) excess H+ or OH- to maintain constant pH
Monosaccharides
1. Intro to Carbohydrates
2. Monosaccharide Structures
3. Cyclic Forms
4. Monosaccharide reactions
Reducing group
Monosaccharides
have 3-6 carbons with a carbonyl group at either the terminal carbon
Monosaccharides with a carbonyl group at C1 are aldehydes called aldoses
Monosaccharides with a carbonyl group at C2 are ketones called ketoses
Structure of Monosaccharides
aldose or ketose
tri-,tetr-,pent,-hexose
lots of constitutional isomers (same formula, different arrangements of
atoms)
Chirality
Biological polymers
Condensation:
2 amino acids condense to form a peptide bond. The bond linking the
amino acid residues is a peptide bond.
Hydrolysis:
The alpha anomer has the OH group drawn down, below the fint
The beta anomer has the OH group drans up, above the ring
2. Dissacharides
6. Polysaccharides
Peptidoglycan
Oligosaccharides
Oligo = few
shorter chains of different monosaccharides residues
Function as markers on cell surface
7. Glycosaminoglycans
Biofilm
Amino Acids
1. Structures
Amino acids with an additional COOH group are called acidic amino
acids
Those with an additional basic N atom in the side chain are called
basic amino acids
All others are neutral amino acids
Epinephrine (adrenalin)
Serotonin:
Histamine:
Local signal released by mast cells (type of WBC in skin, resp. tract,
GI tract)
Triggers bronchoconstriction, mucus production, vasodilation and
increased vascular permeability
Part of immune response to bacteria and parasites (and allergens)
4. Peptide Bonds
Proteins
Configuration = depends on covalent bonding (cannot be changed unless
bonds are broken)
1. Structure
Primary Structure
Secondary Structure
Alpha helix:
Tertiary Structure
Disulfide bonds
Quaternary Structure
Collagen
Keratin
3. Globular Proteins
5 carbon sugar
ribose in RNA
2-deoxyribose in DNA
Naming Nucleosides: