Biochemical Reactions that Make and Break Molecules

Carbon—The Backbone of Biological Molecules Although cells are 70–95% water, the rest consists mostly of carbon-based compounds. Carbon is unparalleled in its ability to form large, complex, and diverse molecules. Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds.

Organic Molecules All organic molecules contain carbon. Carbon has four valence electrons and forms four covalent bonds. Functional groups are the parts of organic molecules usually involved in chemical reactions and give molecules unique properties.

Macromolecules These are large organic molecules The four main types of macromolecules are Carbohydrates – sugars and starches Lipids – fats and waxes Proteins Nucleic acids – DNA and RNA Most macromolecules are also polymers

Polymers and Monomers “poly” means “many”, “mono” means “one” “mer” means “unit” Each single unit is a monomer So a polymer is a large molecule made of many monomers For example: sugar + sugar  starch amino acid + amino acid  protein

Five Major Biochemical Reactions Condensation Hydrolysis Neutralization Redox Phosphorylation

1. Condensation Reactions A condensation reaction builds polymers by joining monomers When a bond is formed between two monomers a water molecule is also produced This is also called a dehydration synthesis Example: Condensation of Sucrose + + H20

2. Hydrolysis Reactions A hydrolysis reaction breaks a polymer into monomers Water is added to a molecule which causes a bond to break The H+ is added to one monomer and the OH- to the other monomer Example: Hydrolysis of Sucrose

LE 5-2 Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond Longer polymer Dehydration reaction in the synthesis of a polymer Review: making large molecules involves dehydration synthesis whereas breaking large molecules requires the use of water. Why are we thirsty after eating a lot of spaghetti? Hydrolysis adds a water molecule, breaking a bond Hydrolysis of a polymer

3. Neutralization Reactions A neutralization reaction occurs when acids (-COOH or H+) and bases (-OH) react to produce a salt and water. Buffers are molecules or reactions that minimize changes in pH in a cell. Buffers absorb excess H+ (acids) or OH- (bases)

4. Redox Reactions Short form for reduction – oxidation reactions “LEO goes GER” Loss of Electrons is Oxidation Gain of Electrons is Reduction Common in metabolic reactions Example in photosynthesis and respiration

5a. Substrate-level Phosphorylation ATP, adenosine triphosphate is the energy molecule of an organism. Substrate-level phosphorylation is a type of chemical reaction that results in the formation and creation of ATP by the direct transfer and donation of a phosphate group to ADP from a reactive molecule.

5b. Oxidative phosphorylation Oxidative phosphorylation is a metabolic pathway that uses energy released by the oxidation of nutrients to produce ATP.

5c. Photophosphorylation Photophosphorylation is the production of ATP using the energy of sunlight.

ISOMERS Just because a molecule has the same chemical formula is no reason to assume that it has the same shape or similar properties. Isomers are compounds that have the same molecular formula but have different arrangements of atoms. Two types of isomers: Structural Isomers Stereoisomers or geometric isomers

1. Structural isomers – differ in connection of the atoms LE 4-7a 1. Structural isomers – differ in connection of the atoms

LE 4-7b 2. Geometric isomers – a stereoisomer in which there is restricted rotation about a bond, usually a C=C bond

LE 4-7c L-isomer D-isomer Stereoisomers

Two stereoisomers of a drug may have different effects. LE 4-8 L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically Inactive) Two stereoisomers of a drug may have different effects.