Foundations of Biochemistry Doba Jackson, Ph.D. Dept. of Chemistry & Biochemistry Huntingdon College

Biological organisms have extroordinary properties that distinguish them from other forms of matter High degree of chemical complexity and organization (muscle tissue) System for extracting energy from the environment (bird) The ability to self-replicate (zebra) Ability to sense changes in the surroundings and respond Defined functions of each component and regulated interactions The ability to adapt with time (evolution)

Three stages of Life’s development Chemical Evolution- Simple chemicals reacted early in life’s existence to form biological polymers (DNA, RNA, Proteins, complex Carbohydrates). Biochemical Evolution- Self-organization of biological polymers to form a living system. Biological Evolution- Changes within living systems to form the complex degree of differences in modern life forms.

Chemical Foundations “What are the common chemical principals important to all cells”

Only 30 of the 90 naturally occuring elements are found in biological systems

Components of macromolecules: the ABC’s of Biochemistry Proteins Nucleic AcidsLipids Carbohydrates

You must remember all of these functional groups!!!!! Biomolecules are hydrocarbons with attached functional groups

What do these have in common? Hydrocarbons

What do these have in common? All have carbon-oxygen bonds

What do these have in common? All have carbon-nitrogen bonds

What do these have in common? All have carbon-sulfur bonds

What do these have in common? All have carbon-phosphate bonds

Some Definitions Chiral center- a carbon atom with four different a substituents (ie.- asymmetric carbon) Enantiomers- pairs of stereoisomers that are mirror images of each other. Diastereomers- pairs of stereoisomers that are not mirror images of each other.

4 substituents 3 substituents EnantiomersSame molecule

Example: 2,3 disubstituted butanes

Stereoisomers distinguisable by taste Aspartate Phenylalanine

Summary of chemical foundations Only 30 of the 90 naturally occuring elements are found in biological systems 99.9% of biomolecules are considered organic compounds Most biomolecules have more than one functional group Conformation, configuration, and constitution are all important factors for determination of biological activity

Hierarchy in the molecular organization

Atoms are held together by covalent interactions Atoms, macromolecules and supramolecular complexes are held in place by non-covalent interactions

Why do biological reactions occur so fast? Enzymes provide a easier path for a chemical or a pair of chemicals to reach their transition state by selective binding and stabilization

- DNA exist as a double helix - Each strand is separated and replicated independently - DNA strands are long and very thin (some DNA strands may approach a meter in length however all DNA has a with of 10 Ǻ.

Evolutionary Foundations

Three stages of Life’s development Chemical Evolution- Simple chemicals reacted early in life’s existence to form biological polymers (DNA, RNA, Proteins, complex Carbohydrates). Biochemical Evolution- Self-organization of biological polymers to form a living system. Biological Evolution- Changes within living systems to form the complex degree of differences in modern life forms.

Mutation & Evolution

Stanley Miller’s 1953 experiment Small Organic & Biological molecules

Some Organic molecules from Stanley Miller’s Experiment Small Organic Molecules Acetate Acetonitrile Small Biological Molecules

RNA world: Why must RNA had to exist before DNA RNA is less stable than DNA- More susceptible to hydrolysis RNA can adopt more unique structures RNA can serve as a template for RNA synthesis RNA can serve as an enzyme (catalyst)