1. Chapter 24 The Chemistry of Life: Organic and Biological Chemistry
Lecture Presentation
Chapter 24 The Chemistry of Life: Organic and Biological Chemistry
James F. Kirby
Quinnipiac University
Hamden, CT

2. Organic Chemistry and Biochemistry
Chapter focus on the molecules that bridge chemistry and biology.
Most common elements: C, H, O, N
Organic chemistry: Study of compounds containing carbon.
Biochemistry: study of chemistry of living systems.

3. 24.1 General Characteristics of Organic Molecules
Carbon can have a maximum of 4 bonds.
4 single bonds: tetrahedral, sp3 hybridized.
1 double bond: trigonal planar, sp2 hybridized.
1 triple bond: linear, sp hybridized.
C—H are most common in organic molecules.
C forms stable (strong) bonds with many elements, including C, H, O, N, and the halogens.
Groups of atoms that determine how an organic molecule reacts are called functional groups.

4. Remember: Carbon can have a maximum of 4 bonds.
Hydrocarbons
Alkanes (CnH2n+2) – only C−C single bonds
CH3–CH2–CH2–CH3
Alkenes (CnH2n) – one or more C−C double bonds
CH3–CH2–CH=CH2
Alkynes (CnH2n-2) – one or more C−C triple bonds
CH3–CH2–CΞCH
Remember: Carbon can have a maximum of 4 bonds.

5. 24.2-24.3 Hydrocarbons C3H6 C4H8 C6H12 Cyclic Alkanes (CnH2n)
– ring, only C−C single bonds
cyclopropane
cyclobutane
cyclohexane
Isomerism: Same formula but different bonds
C4H10
C4H10
n-butane
2-methylpropane
isobutane

6. Hydrocarbons
Aromatic hydrocarbons – ring, alternating double/triple and single bonds
The simplest aromatic hydrocarbon is benzene (C6H6).

7. 24.2-24.3 Hydrocarbon Nomenclature
IUPAC Rules of Naming Alkanes
1. For alkanes, add –ane to the Greek root for the number of carbons.
CH3–CH2–CH2–CH2–CH2–CH3 hexane
2. Alkyl substituents: drop the –ane and add –yl.
C2H6 ethane
C2H5 ethyl

8. 24.2-24.3 Hydrocarbons increasing molar mass increasing mp
increasing bp

9. 24.2-24.3 Hydrocarbons: Nomenclature
Alkyl Substituents
Used when the alkyl part is not in the longest hydrocarbon chain.

10. 24.2-24.3 Hydrocarbons: Nomenclature
IUPAC Rules of Naming Alkanes
Prefix−Parent−Suffix
What substituents?
How many carbons?
What family?
1. Find the parent (longest) hydrocarbon.
2. Number the atoms in the chain sequentially as such substituents are at lowest possible number along the chain.
3. Substituents are named in alphabetical order and use di–, tri–, etc.
CH3–CH2–CH–CH2–CH2–CH3
CH3
3-methyl
hex
ane
CH3–CH2–CH–CH2–CH2–CH3
CH3
3,4-dimethyl
hex
ane

11. Name the following compounds:
EXERCISE #1
Name the following compounds: a) b)
2,2,4,5-tetramethyl
hex
ane
3,6-diethyl-3-methyl
oct
ane

12. 24.2-24.3 Hydrocarbons: Nomenclature
Prefix−Parent−Suffix
IUPAC Rules of Naming Alkenes
1. For alkenes, add –ene to the Greek root for the number of carbons.
C2H4 ethene
2. With more than 3 carbons, double bond is indicated by the lowest–numbered carbon atom in the bond.
CH3–CH=CH–CH2–CH3
2–pentene

13. 24.2-24.3 Hydrocarbons: Nomenclature
Prefix−Parent−Suffix
IUPAC Rules of Naming Alkynes
Same as for alkenes except use –yne as suffix.
C2H2 ethyne
CH3–CH2–CΞC–CH2–CH2–CH2–CH3
3–octyne

14. Name the following compounds:
EXERCISE #2
Name the following compounds: a) b)
2,3,5-trimethyl-2-hexene
6-ethyl-3-methyl-3-octene

15. 24.4 Organic Functional Groups
An atom or a group of atoms attached to a hydrocarbon.

16. EXERCISE #3
Identify the functional group in the following hydrocarbon. a) b) c)
alcohol, ROH
ether, ROR’
ester, RCOOR’

17. 24.6 Introduction to Biochemistry
Biomolecules
Biopolymers (large biological molecules built from small molecules.
Proteins
Polysaccharides (carbohydrates)
Nucleic acids
Lipids are large molecules, but are not polymers.

18. 24.7 Proteins Proteins (polypeptides) H C R COOH H2N
C = α-carbon
R = side chains
Biopolymers made up of monomers called amino acids.
Biomolecules with molar masses ~ 6000 to > 1,000,000 g/mol.
There are 20 amino acids commonly found in proteins.
Peptide bond

19. 20 natural a-amino acids that make up proteins

20. 24.7 Proteins Protein structure
Primary structure: the sequence of amino acids in a polypeptide strand.
Secondary structure:
a-helix formed from C＝O and N—H interactions between side-chains in a strand.
b-sheets formed from interactions between amide H of one strand and carbonyl O of another strand.

21. 24.7 Proteins Protein structure
Tertiary structure: gives the 3D structure of proteins. Tertiary structure is formed from interactions between side-chains of multiple strands.
Quaternary structure: arrangement of multiple tertiary structures and/or incorporation of non-amino acid portions of proteins.

22. Starch (energy source)
24.8 Carbohydrates
Carbohydrates
glucose
Sucrose (table sugar)
Biopolymers made up of monomers e.g. glucose, fructose, and/or galactose.
The name comes from an empirical formula for sugars: Cx(H2O)y—for the simplest sugars, x = y.
Glycoside bond
Cellulose (cell wall)
Starch (energy source)

23. 24.9 Lipids Lipids Nonpolar, water insoluble biomolecules.
Our energy storage (fats, oils) and building blocks in biological structures (phospholipids in cell membranes).
Fats and oils are made from glycerol and long-chain carboxylic acids.
Fats have only saturated carboxylic acids.
Oils have at least one unsaturated carboxylic acid.
Phospholipids are made from glycerol with ester linkage to two fatty acids, and phosphate ester linkage to one polar or charged group, such as choline.

24. 24.9 Lipids
Comparing Fats to Phospholipids

25. 24.10 Nucleic Acids Nucleic acids
Biopolymers made up of monomers nucleotides.
DNA (deoxyribonucleic acid) stores and transmits genetic information, responsible for protein synthesis.
Molar masses of several billion g/mol.
deoxyribose
RNA (ribonucleic acid) helps in protein synthesis. OH
Molar masses 20,000 – 40,000 g/mol.
ribose

26. 22.6 – Natural Polymers
Organic bases in DNA and RNA
DNA OH
RNA

27. End of Chapter 24