1. Lecture 5 Organic Compounds
September 19, 2012

2. Carbon-based molecules
Although most of a living cell is composed of water, the rest of the cell is composed of mainly carbon-based molecules.
Organic chemistry is the
study of carbon-based
molecules
Biochemistry is the study
of chemical substances
and processes occurring in
living cells.

3. We do we need Organic Chemistry and Biochemistry?
Understand the structure and function of biological macromolecules
Understand cellular metabolism
Understand molecular genetics – how life is replicated

4. Increasing Complexity
Levels of Biological
Organization
Fig. 1.1
Biosphere
Ecosystem
Community
Population
Individual
Organ Systems
Increasing Complexity
Organs
Tissues
Cells
Cell Organelles
Molecules

5. Increasing Complexity
Levels of Biological
Organization
Fig. 1.1
Biosphere
Ecosystem
Community
Simple organic compounds
(monomers)
Macromolecules
(polymers)
Supramolecular structures
Population
Individual
Organ Systems
Increasing Complexity
Organs
Tissues
Cells
Cell Organelles
Molecules

6. Carbon is a versatile atom
Carbon atoms can form diverse molecules by bonding to up to four other atoms Carbon compounds range from simple molecules to complex ones

7. C2 is formed through a quadruple bond

8. Hydrocarbons
The simplest carbon molecules contain only carbon and hydrogen atoms.
Structural formula
Ball-and-stick model
Space-filling model
The four single bonds of carbon point to the corners of a tetrahedron.

9. (b) Mammalian adipose cells
Hydrocarbons
Hydrocarbons are found in many cellular molecules
(a) A fat molecule
(b) Mammalian adipose cells
100 µm
Fat droplets (stained red)

10. Carbon compounds are diverse
Carbon skeletons vary in length
Ethane
Propane
Butane
Isobutane
Skeletons are branched or unbranched
Skeletons may have double bonds
1-Butene
2-butene
Skeletons may be arranged in rings
Cyclohexane
Benzene
Carbon compounds are diverse
Carbon atoms form
covalent bonds
between other carbons
to form an endless
variety of carbon
skeletons.

11. Shape of Organic Molecules
Each organic molecule has a unique
3-dimensional shape dictated by the covalent
bonds between atoms.
Molecular shape and size
give rise to molecular
function

12. Isomers H
CO2H
CH3
NH2 C X
Structural
Molecules with the same molecular formula but different structures and properties.
Geometric
Structural isomers have different covalent arrangements of their atoms
Cis-trans isomers have the same covalent bonds but differ in spatial arrangements
Enantiomers are isomers that are mirror images of each other
Enantiomers

13. Enantiomers are important in the pharmaceutical industry
Effective
Enantiomer
Ineffective
Enantiomer
Drug
Condition
Pain; inflammation
Ibuprofen
S-Ibuprofen
R-Ibuprofen
Albuterol
Asthma
R-Albuterol
S-Albuterol

14. Molecular size, shape and Functional Groups give rise to molecular function
A functional group is a chemical groups that imparts properties to the compound to which it is bound
Hydroxyl group
Distinctive properties of organic molecules depend on the carbon skeleton and on the molecular components attached to it
Functional groups are the components of organic molecules that are most commonly involved in chemical reactions
The number and arrangement of functional groups give each molecule its unique properties
Methane
Ethane

15. Molecular size, shape and Functional Groups give rise to molecular function
A functional group is a chemical group that imparts properties to the compound to which it is bound
Hydroxyl group OH
Methane
Ethane
Methanol
Ethanol

16. Common functional groups

17. Polar functional groups
Many functional groups are polar making regions of the molecules they are bound to more hydrophilic. (Greek: hydros – water; philia – love) ‘water loving’

18. Polymers: Giant Molecules
Polymers are large molecules or macromolecules
Polymers are built from smaller molecules called monomers

19. Monomers are bonded together into a polymer through a common mechanism
monomers are diverse (amino acids, nucleic acids,
sugars, fatty acids) but polymers are formed through
dehydration reactions (condensation reaction).
Each monomer
contributes a
hydroxyl (-OH)
or hydrogen (-H).

20. Breaking polymers
Polymers are disassembled to monomers through hydrolysis reactions.
(Greek: hydros - water; lysis – to break)
Bonds between
monomers are
broken by the
addition of H2O.

21. Examples of Polymers
Proteins
Lipids
Carbohydrates
Nucleic Acids

22. Macromolecules
There are four different types of large molecules in cells: Carbohydrates Lipids Proteins Nucleic Acids

23. Carbohydrates Carbohydrates are composed of single
sugars in combinations or alone.
Sugars are composed of carbon,
oxygen and hydrogen molecules.
Carbohydrates include small
sugars found in soft-drinks.
AND long polymers of sugar
molecules like starch.

24. Types of Carbohydrates
Sugar and their polymers
monosaccharides, single sugars, simple sugars
C6H12O6
galactose
fructose
glucose

25. Monosaccharides combine to form polysaccharides
glucose
fructose
sucrose
raffinose

26. Polysaccharides are long chains of sugar monomers
Starch granules in potato tuber cells
Starch
Glucose monomer
Glycogen granules in muscle tissue
Glycogen
Cellulose microfibrils in a plant cell wall
Cellulose
Hydrogen bonds
Cellulose molecules