Lec 10-12 basic chem of macromoleules .docx

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Basic Organic Chemistry of Important Macromolecules
Lecture 10-12
Structure
1. What are the organic molecules?
2. Polymer Principles
3. Carbohydrates- Fuel and Building Material
4. Lipids- Diverse Hydrophobic Molecules
5. Proteins- The Molecular Tools of the Cell
6. Nucleic Acids- informational Polymers
1. Organic Molecules
- Organic molecules are those that:
o Formed by the actions of living things; and/or
o Have a carbon backbone
- Carbon has four electrons in outer shell, and can bond with up to four other atoms (usually H, O,
N, and C)
- Since carbon can make covalent bonds with another carbon atom, carbon chains and rings that
serve as the backbones of organic molecules are possible
- Chemical bonds store energy.
- The C-C covalent bonds has 83.1 Kcal per mole while the C=C double covalent bond has
147kcal/mole
- Energy is in two forms:
o Ek or energy in use/motion
o Ep or energy at rest or in storage (chemical bonds)
- Chemical bonds are potential energy until they are converted into another form of energy
(according to law of thermodynamics)
- Methane (CH4) is an example of this
o If we remove the H from one of the methane units and begin linking them up, while
removing other H units, we begin to form an organic molecule
o NOTE: Not all methane is organically derived; methane is a major component of the
atmosphere of Jupiter, which we think of as devoid life.
o When the two methane’s are combined the resultant molecule is Ethane, C2H6
- Molecules made of H and C are known as hydrocarbons
The shapes of three simple organic molecules
- Whenever a carbon atom has four single bonds, the bonds angle toward the corners of an
imaginary tetrahedron.
- When two carbons are joined by a double bond, all bonds around those atoms are in the same
plane.
Variations in carbon skeletons
- Carbon skeletons can vary in length
- Skeletons may be branched or un-branched
- The skeleton may have double bonds which can vary in location
- Some carbon skeletons are arranged in rings (The abbreviated structural formulas omit the
corner carbons and the hydrogen’s attached to them.)
Three types of isomers
- Compounds with the same molecular formula but different structures
- Isomers are a source of diversity in organic molecules.
o Structural isomers: variation in covalent partners
o Geometric isomers: variation in arrangement about a double bond
o Enantiomers: variation in spatial arrangement around an asymmetric carbon, resulting
in molecules that are mirror images (like right and left hands). Enantiomers cannot be
superimposed on each other.
The pharmacological importance of enantiomers
- L-dopa is a drug used for Parkinson’s disease
- The drug’s enantiomer mirror image molecule is designated d-dopa has no effect on patients.
Functional groups in organic molecules
- Small groups of atoms that are frequently bonded to the carbon skeleton of organic molecules
o Have specific chemical and physical properties
o Are the regions of organic molecules which are commonly chemically reactive
o Behave consistently from one organic molecule to another
o Depending upon their unique number and arrangement, determine unique chemical
properties of organic molecules in which they occur.
- Hydroxyl group:
o Polar water soluble
- Carbonyl group
o Polar water soluble, Found in sugars.
- Carboxyl group:
o Polar, water soluble
o Donates protons
o Has acidic properties
- Amino group
o Polar, water soluble
o Act as a weak base
o The unshared pair of electrons on the N can accept a proton, giving the amino group +1
charge
- Phosphate group
o Dissociated form of phosphoric acid
o Polar, water soluble
o Negatively charged
o Acid properties
- Sulfhydryl group
o Stabilizes the protein structure
o Organic compounds with this croup are called thiols
2. Polymer Principles
- A polymer is a long molecule consisting of many identical or similar parts linked by covalent
bonds.
- The repeating units are called monomers
- Macromolecules: Large organic molecules formed from smaller building block molecules