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

Starch

Cellulose

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!