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CHAPTER 3 THE CHEMICAL BASIS OF LIFE II: ORGANIC MOLECULES Learning Outcomes 1. Explain the properties of carbon that make it the chemical basis of all life. 2. Describe the variety and chemical characteristics of common functional groups of organic compounds. 3. Distinguish among...

CHAPTER 3 THE CHEMICAL BASIS OF LIFE II: ORGANIC MOLECULES Learning Outcomes 1. Explain the properties of carbon that make it the chemical basis of all life. 2. Describe the variety and chemical characteristics of common functional groups of organic compounds. 3. Distinguish among different types of carbohydrate molecules 4. List the different classes of lipid molecules important in living organisms. 5. Give examples of the general functions that are carried out by different proteins. 6. Describe how amino acids are joined to form a polypeptide. 7. Explain the four levels of protein structure. 8. Outline the factors that determine protein shape and function. 9. Describe the three components of a nucleotide. 10. Distinguish between the structures of DNA and RNA. 2  Organic Chemistry. Organic molecules contain Carbon (C) and Hydrogen (H). Organic molecules are mainly abundant in living organisms. Macromolecules are large, complex organic molecules. Four categories of Macromolecules: - Carbohydrates - Lipids - Proteins - Nucleic Acids Bacterial cell contains about 5000 different organic molecules and Plant or animal cell contains twice that number 3  Inorganic Molecules Organic Molecules Usually contains positive and negative ions Always contains carbon and hydrogen Usually ionic bonding Always covalent bonding Always contains small number of atoms Often quite large, with many atoms Often associated with non living matter Usually associated with living organisms 4  The four class of organic molecules and macromolecules Carbohydrates, lipids, proteins, and nucleic acids are referred to as macromolecules because of their large size. Polymers are made up of monomers. Protein (polymer) can contain hundreds of amino acids (monomers) and nucleic acid can contain hundreds of nucleotides. How can polymers get so large? 5 Polymer formation: Dehydration - Removal of water molecule. Polymer degradation: Hydrolysis - Addition of water molecule. 6  Stearic acid (fatty acid) Glycerol Triglyceride hydrolysis  Carbohydrates An immediate energy source in living organisms Large molecule Composed of C, H, and O atoms General formula: Cn(H2O)n Most of the C atoms in a carbohydrate are linked to a H atom and a OH group Plays structural roles in a variety of organisms The term carbohydrates include single sugar molecules and also chains of sugars 9  Carbohydrates: Monosaccharides Simplest sugars. Monosaccharides (monos, single and sacchar, sugar). Ready energy Molecular formula for a single sugar is a multiple of CH2O. Sugars have many hydroxyl groups, and this polar functional group makes them soluble in water. Most common are 5 or 6 carbons Pentoses: 5C (component of RNA and DNA molecules) ribose (C5H10O5); found in RNA deoxyribose (C5H10O4); found in DNA Hexose: 6C glucose (C6H12O6); water soluble Different ways to depict structures Ring or linear 10  Glucose isomers Structural isomers: different arrangement of same elements Glucose and galactose Stereoisomers: Geometric isomers:above or below ring α- and β-glucose Enantiomers: mirror image D- and L-glucose 11  Carbohydrates: Disaccharides Composed of 2 monosaccharides Joined by dehydration/condensation reaction Broken apart by hydrolysis Examples:. Sucrose = Glucose (6C) + Fructose (5C), -Sucrose is the form in which sugar is transported in plants; -Sugar we use to sweeten our food. Maltose = Glucose + Glucose [malt sugar]. Lactose = Glucose + Galactose) [milk sugar] 12  Carbohydrates: Polysaccharides Many monosaccharides linked together to form long polymers Short term energy storage Large molecules can’t pass through plasma membrane (not soluble in water, and much larger than sugar) when an organism requires energy, polysaccharides are broken down to release sugar molecules Glucose molecules can be stored by organisms as different macromolecules. Energy storage molecules: Starch in plants, (energy storage) Glycogen in animals, (energy storage) Structural role : Cellulose (plants), chitin (insects and fungi), glycosaminoglycans (animals) 13  Carbohydrates: Polysaccharides (Energy Storage Molecules) Starch: is a mixture of two complex carbohydrates: amylose and amylopectin, both of which are polymers of glucose. It is used by plants as a way to store excess glucose. Glycogen: Animals store glucose as Glycogen (granules in liver). polysaccharide of glucose which functions as the primary short term energy storage in animal cells. Hormones control release and storage of glucose: Insulin released from the pancreas promotes the storage of the glucose as glycogen. Glucagon, another hormone released from the pancreas stimulates glycogen breakdown into glucose. 14  Carbohydrates: Polysaccharides (Structural Molecules) Cellulose:. Most abundante of all the carbohydrates. Cellulose. Polymer of -glucose. Cell walls in plants contain Cellulose.. Parallel glucose chains → cellulose Chitin:. Form the external skeleton of many insects and the cell wall of fungi.. The sugar monomer of chitin have nitrogen-containing groups attached to them. Glycosaminoglycans:. Found in animals.. Abundantly found in cartilage.. Tend to have sugar monomers with carboxyl and sulfate groups. 15  Lipids Organic molecules Composed predominantly of H and C atoms (hydrocarbon chains). Defining feature of lipids is that they are nonpolar (Hydrogen bonded only to carbon have no tendency to form hydrogenated bonds with water molecules) and therefore very insoluble in water. Lipids (fats) used for both insulation and long-term energy storage by animals. Plants use oil instead of fat for a long-term energy storage Phospholipids and steroids: other important lipids found in living things. 16  Lipids: Fats Mixture of triglycerides (Also known triacylglycerols), Long-term Energy storage Formed by bonding glycerol to three fatty acids; joined by dehydration or condensation reaction Broken apart by hydrolysis Glycerol: compound with three OH groups (OH is polar group- glycerol soluble in water). Fatty acid consists of long hydrocarbon (R) chain with a carboxyl (-COOH) group at one end. Chemical formula: R-COOH Fat and oils formation: Acid portions of the three fatty acids react with the OH group of glycerol during a dehydration reaction.  Lipids: Fats (contd) The three fatty acids can be all different, all the same, or only two the same. 18  Lipids: Fats (contd) Fatty acids are either saturated or unsaturated. Saturated fatty acids:. Have no double bonds between the carbon atoms. All carbons are linked by single covalent bonds.. Tend to be solid at room temperature Unsaturated fatty acids:. contain one or more double bonds in the carbon chain - 1 double bond: monounsaturated - 2 or more: polyunsaturated. Tend to be liquids at room temperature (plant oils) Fats are important for energy storage: 1g of fat stores twice as much energy as 1g of glycogen or starch Fats can also be structural in providing cushioning and insulation Saturated and unsaturated fatty acids 20 Lipids: Phospholipids Phospholipids: membrane components, contains phosphate group. Instead of third fatty acid attached to glycerol as in fat, there is a polar phosphate group. Amphipathic molecule Hydrophilic heads (phosphate region) hydrophobic tails ( Fatty acid chains) Arrange themselves so polar heads are adjacent to water. Bulk of cell plasma membrane consists of phospholipid bilayer. 21  Lipids: Steroids Have skeletons of 4 interconnected carbon rings Usually not very water soluble Cholesterol, estrogen and testosterone Cholesterol is the precursor of several other steroids, such as testosterone and estrogen. Testosterone and estrogen differ only by the functional group attached to the same carbon skeleton, and yet have a profound effect on the body and the sexuality of an animal. 22  Waxes Long-chain fatty acid bonds with a long-chain alcohol, secreted onto plant leaves and insect cuticles Very nonpolar and exclude water: provide a barrier to water loss High melting point: Solid at normal temperature. Waterproof Resistant to degradation Structural elements in colonies (bee hives) 23  Proteins Diverse functions: - Support: keratin (hair, nail, ligaments..) - Enzymes: bring reactants together - Transport: channel and carrier protein (plasma membrane) allow substance to enter and exit cells. Hemoglobin: transport of oxygen. - Defense: antibodies (combine with foreign subjects and prevent them from destroying cells) - Hormones: eg. insulin regulates blood glucose - Motion: eg. actin and myosin allow parts of cells to move and cause muscles to contract Composed of C, H, O, N, and small amounts of other elements, notably S Amino acids are the monomers of proteins. Common structure with variable R-group. 20 amino acids. Side-chain determines structure and function. Bond to a hydrogen atom, an amino group -NH2, an acidic group -COOH, and an R (remainder) group. 24 Proteins: Amino Acids Structure Amino acids are usually classified by properties of the side chain into four groups: acidic, basic, hydrophilic (polar), and hydrophobic (nonpolar). 25 26  Proteins: Peptide bond formation Image:Peptidformationball.svg. Amino acids are joined by dehydration or condensation reaction through a covalent bond called “peptide bond”.. Peptide: Two or more amino acids bonded together.. Polypeptide : Chain of many amino acids joined by peptide bonds.. Proteins are made up of 1 or more polypeptides. Peptide bonds are broken apart by hydrolysis 27 28 Protein Structure Primary: Sequence of amino acids. Secondary: Polypeptide coils or folds in a particular fashion. Hydrogen bonding often holds the secondary structure Tertiary: Folding and twisting that results in final three dimensional shape of a polypeptide. Quaternary: Consists of more than one polypeptide. 29  Protein structure Primary structure:. Amino acid sequence. Determined by genes Secondary structure:. Chemical and physical interactions cause folding. Irregular or repeating. α helices and β pleated sheets - Key determinants of a protein’s characteristics. “Random coiled regions” - Not α helix or β pleated sheet - Shape is specific and important to function 30  The five factors promoting protein folding and stability 1. H bonds: promotes protein folding and stability 2. Ionic bonds: ionic and polar interactions promote folding and stability 3. Hydrophobic effects: avoid water contact 4. Van der Waals forces: atoms that have weak attarctions 5. Disulfide bridges: covalent bonds that link 2 cysteine aminoi acids that contain sulfthydryl group 31  Protein-protein interactions Many cellular processes involve steps in which two or more different proteins interact with each other Very specific binding at surface Use first 4 factors 32  Proteins Contain Functional Domains Within Their Structures Module or domains in proteins have distinct structures and function Signal transducer and activator of transcription (STAT) protein example Each domain of this protein is involved in a distinct biological function Proteins that share one of these domains also share that function  Nucleic Acids Responsible for the storage, expression, and transmission of genetic information Two classes. Deoxyribonucleic acid (DNA) ◼ Store genetic information coded in the sequence of their monomer building blocks. Ribonucleic acid (RNA) ◼ Involved in decoding this information into instructions for linking together a specific sequence of amino acids to form a polypeptide chain Monomer is a nucleotide Made up of phosphate group, a 5C sugar (either ribose or deoxyribose), and a single or double ring of C and N atoms known as a base Sugar-phosphate backbone 34 Structure of a DNA strand The double-stranded structure of DNA 35  DNA vs. RNA DNA RNA Deoxyribonucleic acid Ribonucleic acid Deoxyribose Ribose Thymine (T) Uracil (U) Adenine (A), guanine (G), cytosine (C) used in both 2 strands- double helix Single strand 1 form Several forms 36