Chapter 3
The Chemistry of Organic
Molecules
Figure 4.3 Valences for the major elements of organic molecules
Why Carbon?
• Most versatile building blocks of molecules
– Tetravalence
– Can link together
– Covalent compatibility with variety of elements
• Variation in carbon skeletons contributes to
the diversity of organic molecules
– Hydrocarbons
– Isomers – shape can dramatically alter activity
Figure 4.4 Variations in carbon skeletons
Figure 4.2 The shapes of three simple organic molecules
Figure 4.6 Three types of isomers
Figure 4.6ax Structural isomers
Figure 4.7 The pharmacological importance of enantiomers
Functional Groups
• A specific configuration of atoms
commonly attached to C-skeletons, usually
involved in chemical reactions
• Behave consistently from one organic
molecule to the next
• Contribute to distinctive properties of
organic molecules
• Most molecules have two or more
Table 4.1 Functional Groups of Organic Compounds
Functional Groups cont.
• Hydroxyl
– Alcohols
– Polar
– Increase solubility
• Carbonyl
Functional Groups cont.
• Carboxyl
– Carboxylic acids
– Very polar
• Amino
– Amines
– Basic
Functional Groups Cont.
• Sulfhydryl
– Thiols
– Can interact to help
stabilize structures
• Phosphate
– One fxn includes
energy transfer
Recap
• Emergent properties of organic compounds
due to:
– Arrangement of carbon skeleton
– Functional groups added to skeleton
• Variation at molecular level underlies
biological diversity
Macromolecules
• Large biological molecules formed from
small organic molecules
• Polymers…made up of monomers
• Synthesized by cells…how?
Figure 5.2 The synthesis and breakdown of polymers
Carbohydrates
•
•
•
•
Sugars
End in -ose
CH2O
Carbonyl group and
multiple hydroxyl
groups
• Monosaccharides and
disaccharides = fuel
and carbon sources
Figure 5.3 The structure and classification of some monosaccharides
Figure 5.3x Hexose sugars
Glucose
Galactose
Figure 5.4 Linear and ring forms of glucose
Figure 5.5 Examples of disaccharide synthesis
Figure 5.5x Glucose monomer and disaccharides
Glucose monomer
Sucrose
Maltose
Polysaccharides
• thousands of monosaccharides
• Storage and structural roles
• Glycogen, starch, cellulose, peptidoglycan
(sugars + amino acids), and chitin (contains
nitrogen)
Figure 5.7a Starch and cellulose structures
Figure 5.7b,c Starch and cellulose structures
Figure 5.7x Starch and cellulose molecular models
 Glucose
 Glucose
Cellulose
Starch
Figure 5.6 Storage polysaccharides
Figure 5.8 The arrangement of cellulose in plant cell walls
Figure 5.x1 Cellulose digestion: termite and Trichonympha
Figure 5.x2 Cellulose digestion: cow
Chitin
Figure 5.9 Chitin, a structural polysaccharide: exoskeleton and surgical thread
Peptidoglycan
Lipids
•
•
•
•
Diverse group of nonpolymers
Share one trait: hydrophobic
Consist mainly of hydrocarbons
Fats, phospholipids, waxes, steroids
Fats
• Glycerol + fatty acids
• Fatty acids: carbon
chain with carboxyl
group at end
• Triglycerols
• Saturated vs
unsaturated
Figure 5.11 Examples of saturated and unsaturated fats and fatty acids
Fats cont.
• Functions:
– Energy (2x a
polysaccharide)
– Storage – adipose
tissue – swells and
shrinks
– Cushions
– Warmth
Artherosclerosis
Phospholipids
• Glycerol + 2 fatty acids + phosphate group
• Amphipathic
• Major components of cell membranes
Figure 5.12 The structure of a phospholipid
Figure 5.13 Two structures formed by self-assembly of phospholipids in aqueous
environments
Steroids
• Carbon skeletons
consisting of four
fused rings
• Hormones (many
produced from
cholesterol)
• Vary in their
functional groups
Figure 4.8 A comparison of functional groups of female (estradiol) and male
(testosterone) sex hormones
Waxes
• Protectant
• Water-proofing
• Corrosion prevention
Proteins
•
•
•
•
Greek: “first place”
50% + of dry weight of most cells
Instrumental in activities
Structural support, storage, transport,
signaling within organism, movement of
organism, defense against foreign
substances, enzymes (help regulate
metabolism)
Proteins cont.
• Vary extensively in structure
• Unique 3d shape
• Polymers of amino acids: polypeptides
Figure 5.15 The 20 amino acids of proteins: nonpolar
Figure 5.15 The 20 amino acids of proteins: polar and electrically charged
Peptide Bonds
Proteins cont.
• A functional protein consists of 1+
polypeptides precisely twisted, folded, and
coiled into a precise 3d conformation
• Globular vs fibrous
• Function depends on ability to recognize
and bind to some other molecule
• Determined by amino acid sequence
Figure 5.18 The primary structure of a protein
Figure 5.20 The secondary structure of a protein
Figure 5.22 Examples of interactions contributing to the tertiary structure of a protein
Figure 5.23 The quaternary structure of proteins
Figure 5.24 Review: the four levels of protein structure
Figure 5.17 Conformation of a protein, the enzyme lysozyme
Figure 5.19 A single amino acid substitution in a protein causes sickle-cell disease
Fibrous vs globular
Figure 5.21 Spider silk: a structural protein
What determines protein
conformation?
•
•
•
•
•
Amino acid sequence
pH
Salt concentration
Temperature
Chaperonins – protein
molecules that assist
the proper folding
other proteins; keep it
away from “bad
influences”
• If environment is
changed or altered
from “native”
conditions = denatured
Figure 5.25 Denaturation and renaturation of a protein
Figure 5.27 X-ray crystallography
Table 5.1 An Overview of Protein Functions
Nucleic Acids
• DNA and RNA
• Genetic material
• DNA directs the synthesis of RNA, which
then directs the ribosomes to make proteins
• Polymers of nucleotides
Figure 5.29 The components of nucleic acids
Figure 5.x3 James Watson and Francis Crick
Figure 5.x4 Rosalind Franklin
Erwin Chargaff
3’ and 5’ ends
Genetic Material
Figure 5.30 The DNA double helix and its replication
DNA and proteins as tape
measures of evolution
• Two species that are
more closely related
share a greater
proportion of their
DNA and protein
sequences than do
distantly related
species
ATP
• RNA nucleotide +
• 2 more P groups
• Energy transfer!