Lecture 5 Organic Compounds September 19, 2012

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.

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

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

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

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

C2 is formed through a quadruple bond

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.

(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)

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.

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

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

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

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

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

Common functional groups

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’

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

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).

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.

Examples of Polymers Proteins Lipids Carbohydrates Nucleic Acids

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

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.

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

Monosaccharides combine to form polysaccharides glucose fructose sucrose raffinose

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