Organic Chemistry

Organic Chemistry

Carbon: The Backbone of Life • Organic chemistry is the study of carbon compounds • Life is carbon-based due to carbon’s ability to form large, complex molecules • Carbon usually bonds in conjunction with hydrogen, oxygen, nitrogen, phosphorus, and sulfur in living things (CHONPS). • These compounds can be simple or massive.

Carbon has 4 valence electrons, thus makes 4 bonds • With four valence electrons, carbon can form four covalent bonds with a variety of atoms • This ability makes large, complex molecules possible

Those four bonds can vary…

Carbon Skeletons Vary • Carbon chainsform the skeletons of most organic molecules and can vary in length and shape

Functional Groups A few chemical groups are key to the function of biomolecules • The carbon skeleton often has accessory chains (functional groups) that determine what the compound can do

Functional Groups • FGs are most commonly involved in chemical reactions • The number and arrangement of functional groups give each molecule its unique properties • Let’s meet the FGs

Hydroxyl STRUCTURE Alcohols (Their specific names usually end in -ol.) NAME OF COMPOUND (may be written HO—) • Is polar as a result of the electrons spending more time near the electronegative oxygen atom. EXAMPLE FUNCTIONALPROPERTIES Ethanol • Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars.

Carbonyl STRUCTURE Ketones if the carbonyl group is within a carbon skeleton NAME OF COMPOUND Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE • A ketone and an • aldehyde may be • structural isomers • with different properties, • as is the case for • acetone and propanal. FUNCTIONALPROPERTIES • Ketone and aldehyde • groups are also found • in sugars, giving rise • to two major groups • of sugars: ketoses • (containing ketone • groups) and aldoses • (containing aldehyde • groups). Acetone Propanal

Carboxyl STRUCTURE Carboxylic acids, or organic acids NAME OF COMPOUND • Acts as an acid; can donate an H+ because the covalent bond between oxygen and hydrogen is so polar: EXAMPLE FUNCTIONALPROPERTIES Acetic acid Nonionized Ionized • Found in cells in the ionized form with a charge of 1– and called a carboxylate ion.

Amino Amines STRUCTURE NAME OF COMPOUND •Acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms): EXAMPLE FUNCTIONALPROPERTIES Glycine Ionized Nonionized •Found in cells in the ionized form with a charge of 1.

Sulfhydryl Thiols STRUCTURE NAME OF COMPOUND (may be written HS—) •Two sulfhydryl groups can react, forming a covalent bond. This “cross-linking” helps stabilize protein structure. EXAMPLE FUNCTIONALPROPERTIES •Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be “permanently” curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds. Cysteine

Phosphate Organic phosphates STRUCTURE NAME OF COMPOUND EXAMPLE •Contributes negative charge to the molecule of which it is a part (2– when at the end of a molecule, as at left; 1– when located internally in a chain of phosphates). FUNCTIONALPROPERTIES Glycerol phosphate •Molecules containing phosphate groups have the potential to react with water, releasing energy.

Example of FG in action- ATP: Chemical Energy for Cells • Adenosine triphosphate(ATP), is made of adenosine bonded to three phosphate groups. Adding or removing phosphate groups stores and releases energy. • Draw

Organic Macromolecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids

The FOUR Classes of Large Biomolecules • All life is made of four classes of biomolecules: • Carbohydrates • Lipids • Protein • Nucleic Acids • Macromolecules are large molecules composed of thousands of covalently bonded atoms • Their structure determines their function!!!

The FOUR Classes of Large Biomolecules • Most Macromolecules are polymers, built from monomers • A polymer = molecule made of repeating smaller monomers • Three of the four classes of life’s organic molecules are polymers • Carbohydrates • Proteins • Nucleic acids

Building polymers • A dehydration synthesis links monomers by removing a water molecule

Digesting polymers • Hydrolysis is the reverse, and disassembles polymers by adding a water • Why is water important for food digestion?

Carbohydrates • Monosaccharide sugars (monomer) and polysaccharide starches (polymer). • Both used for chemical energy (sugar = fast, starch = long) and sometimes structure (e.g. wood, common in plants) • The simplest carbohydrates (sugars) are monosaccharides, or single sugars with formula ratios of 1C:2H:1O used for quick energy (draw one) • Carbohydrate macromolecules (starches) are polysaccharides, or chains of sugars; used to build cell parts or store energy (draw one)

Sugars: Monosaccharides • Glucose (C6H12O6) is the most common monosaccharide • Monosaccharides are classified by • The location of the carbonyl group • The number of carbons in the carbon skeleton

Sugars: Disaccharides • A disaccharide is formed when dehydration synthesis joins two monosaccharides; still a sugar

Synthesizing Maltose & Sucrose

Special Polysaccharides • Starch is a storage polysaccharide of plants that consists entirely of glucose monomers • Plants store surplus starch as granules within chloroplasts and other plastids • The simplest form of starch is amylose

Special Polysaccharides • Glycogen is a storage polysaccharide in animals (“animal starch”); branched structure as compared to amylose starch • Humans and other vertebrates store glycogen mainly in liver and muscle cells as a tier 2 energy option

Types of Polysaccharides • Celluloseis a polysaccharide used to build plant cell walls • Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ; very difficult to digest!

Cellulose Structure - Such Elegance!

Polysaccharide Random Acts of Biology • Cellulose in human food passes through the digestive tract as insoluble fiber • Some microbes use enzymes to digest cellulose • Many herbivores, from cows to termites, have symbiotic relationships with these microbes • Chitin is the structural polysaccharide in animal exoskeletons (crunch!) and fungal cell walls (surprise!)

Lipids Lipids are a diverse group of hydrophobic molecules • Lipidsare the one class of large biological molecules that do not form polymers • The unifying feature of lipids is having little or no affinity for water (water fearing) • Lipids are non-polare and hydrophobic • The most biologically important lipids are fats/oils/wax, phospholipids, and steroids

Fats: Start with a Simple Little Glycerol Molecule • Triglyceride Fats are constructed from two types of smaller molecules: glycerol and fatty acids • Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon • A fatty acid consists of a carboxyl group attached to a long carbon skeleton

Dehydration Rxn 1: Add a Fatty Acid • Next, add a “fatty acid” through a dehydration synthesis reaction • What makes it an acid? The C double bond O, single bond OH!

Dehydration Rxn 2!! • Next, add a SECOND “fatty acid” through a dehydration synthesis reaction

Dehydration Reaction THREE!!! • How many water molecules will it take to disassemble this molecule?

Saturated or Unsaturated? • Some fats called saturated fats are solid at room temperature • Most animal fats are saturated (lard) • Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds, so they are straight (dense/solid at room temp)

Saturated or Unsaturated? • Fats that are liquid are unsaturated. • Plant fats and fish fats are usually unsaturated • Unsaturated fatty acids have one or more double bonds cause them to bend

Fats: Major function is storage! • Fats mostly function for long term energy storage, but also waterproof/insulate, protect and/or communicate • Humans and other mammals store their fat in adipose cells

Phospholipids • Phospholipids are the major component of all cell membranes; b/c the phosphate head is hydrophilic and the lipid tail is hydrophobic, they self assemble into a bi-layer in water

A Single Phospholipid Molecule Choline Hydrophilic head Phosphate Glycerol Fatty acids Hydrophobic tails Hydrophilichead Hydrophobictails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol

Steroids • Steroids are lipids with a carbon skeleton consisting of four fused rings used for communication • Ex: The steroid Cholesterol is a component in animal cell membranes • Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease • Ex: Many hormones are steroids

Proteins • Proteins are very diverse. • Cells are mostly made of and run by Proteins, as they account for more than 50% of the dry mass of most cells • Protein functions include structure, storage, transport, communication, movement, defense… (basically everything that keeps you alive…) • Let’s take a look at a few we’ll learn this year!

Enzymatic Enzymatic proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysisof bonds in food molecules. Enzyme

Storage Storage proteins Function: Storage of amino acids Examples: Casein, the protein of milk, is the majorsource of amino acids for baby mammals. Plants havestorage proteins in their seeds. Ovalbumin is theprotein of egg white, used as an amino acid sourcefor the developing embryo. Amino acidsfor embryo Ovalbumin

Hormonal Hormonal proteins Function: Coordination of an organism’s activities Example: Insulin, a hormone secreted by thepancreas, causes other tissues to take up glucose,thus regulating blood sugar concentration Insulinsecreted Normalblood sugar Highblood sugar

Defensive Defensive proteins Function: Protection against disease Example: Antibodies inactivate and help destroyviruses and bacteria. Antibodies Virus Bacterium

Transport Transport proteins Function: Transport of substances Examples: Hemoglobin, the iron-containing protein ofvertebrate blood, transports oxygen from the lungs toother parts of the body. Other proteins transportmolecules across cell membranes. Transportprotein Cell membrane

Receptor Receptor proteins Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of anerve cell detect signaling molecules released byother nerve cells. Receptorprotein Signalingmolecules

Structural Structural proteins Function: Support Examples: Keratin is the protein of hair, horns,feathers, and other skin appendages. Insects andspiders use silk fibers to make their cocoons and webs,respectively. Collagen and elastin proteins provide afibrous framework in animal connective tissues. Collagen Connectivetissue 60 m

Enzymes • SPECIAL PROTEIN: Enzymes are protein catalysts that control chemical reactions; they are reusable and specific to one function (based on their shape); ex: digestive enzymes, buffers, etc

Protein Monomer Side chain (R group) • Amino acids are the monomers of all proteins. • Only 20 amino acids exist. They differ in their properties due to differing side chains, called R groups  carbon Aminogroup Carboxylgroup

Polypeptides • Polypeptide chains (protein polymers) are made of chained arrangements of the 20 available amino acids, then folded into proteins. • A protein consists of one or more polypeptides

Organic Chemistry