Basic Biology Chapter 3: Organic Molecules PDF

Basic Biology Chapter 3 The Chemical Basis of Life II: Organic Molecules Prof. Ranjit Vijayan Department of Biology [email protected] 03 713 6302 Organic Chemistry. Organic molecules contain Carbon (C) and Hydrogen...

Basic Biology Chapter 3 The Chemical Basis of Life II: Organic Molecules Prof. Ranjit Vijayan Department of Biology [email protected] 03 713 6302 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 Inorganic and Organic molecules 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 The four class of organic molecules Carbohydrates, lipids, proteins, and nucleic acids are referred to as macromolecules because of their large size. Carbohydrates Lipids Proteins Nucleic acids 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? Polymer formation: Condensation or Dehydration - Removal of water molecule. Polymer degradation: Hydrolysis Addition of water molecule. Carbohydrates An immediate energy source in living organisms 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 (hydroxyl) group Plays structural roles in a variety of organisms The term carbohydrates include single sugar molecules and also chains of sugars 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 Glucose isomers Structural isomers: different arrangement of same elements Glucose and fructose Stereoisomers: Geometric isomers:above or below ring α- and β-glucose Enantiomers: mirror image D- and L-glucose Carbohydrates: Disaccharides Composed of 2 monosaccharides Joined by dehydration/condensation reaction. Forms a glycosidic bond. Broken apart by hydrolysis Examples:. Sucrose = Glucose (6C – 6 member ring) + Fructose (6C – 5 member ring), -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] Carbohydrates: Polysaccharides Many monosaccharides linked together to form long polymers Short term energy storage 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, released from the pancreas stimulates glycogen breakdown into glucose. Carbohydrates: Polysaccharides Structural molecules Cellulose: - Most abundant of all the carbohydrates. - Polymer of b-glucose - Cell walls in plants contain cellulose. - Parallel glucose chains. Chitin: - Form the external skeleton of many insects and the cell wall of fungi. - The sugar monomer of chitin have nitrogen-containing groups attached. Glycosaminoglycans: - Found in animals. - Abundantly found in cartilage. - Tend to have sugar monomers with carboxyl and sulfate groups. Lipids Composed predominantly of hydrogen and carbon atoms (hydrocarbon chains) Defining feature of lipids is that they are nonpolar (Hydrogen bonded only to carbon have no tendency to form hydrogen bonds with water molecules) and therefore very insoluble in water. Include fats, phospholipids, steroids, waxes Lipids comprise about 40% of the organic matter in the average human body 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; 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. Fat and oils formation: Acid portions of the three fatty acids react with the OH group of glycerol during a dehydration reaction. H O H O H C OH HO C CH2 (CH2)15 CH3 H C O C CH2 (CH2)15 CH3 O O + Dehydration H C OH HO C CH2 (CH2)15 CH3 H C O C CH2 (CH2)15 CH3 O O H C OH HO C CH2 (CH2)15 CH3 3 H2O H C O C CH2 (CH2)15 CH3 H H Glycerol 3 Fatty acids Triglyceride (fat) Lipids: Fats The three fatty acids can be all different, all the same, or only two the same. Lipids: Fats 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 (known as 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 Lipids: Phospholipids Formed from glycerol, two fatty acids and a 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. Lipids: Steroids Have skeletons of 4 interconnected carbon rings Usually insoluble in water Examples: 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. Waxes Mixture of hydrocarbons and long-chain fatty acid bonded to long-chain alcohols. 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. Water-resistant Resistant to degradation Structural elements in colonies (bee hives) Proteins Diverse functions: - Support: keratin (hair, nail, ligaments..) - Enzymes: bring reactants together (e.g. hydrolases, ligases) - 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. Proteins: Structure of Amino Acids Amino acids are usually classified by properties of the side chain into four groups: acidic, basic, hydrophilic (polar), and hydrophobic (nonpolar). Proteins: Peptide bond formation 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 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. 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 sheets - Key determinants of a protein’s characteristics. “Random coiled regions” - Not α helix or β sheet - Shape is specific and important to function Protein structure Tertiary structure: Quaternary structure: Made up of 2 or more polypeptides Folding gives complex 3-D shape Individual chains are protein subunits Sometimes final level of structure Multimeric proteins made of different polypeptides Protein structure: Hemoglobin Protein folding and stability 1. Hydrogen bonds: promotes protein folding and stability 2. Ionic/polar bonds: ionic and polar interactions promote folding and stability 3. Hydrophobic effects: avoid water contact 4. Van der Waals forces: atoms that have weak attractions 5. Disulfide bridges: covalent bonds that link 2 cysteine amino acids that contain sulfhydryl group Protein-protein interactions Many cellular processes involve steps in which two or more different proteins interact with each other Also important for building cellular structures Very specific binding at surface Use first 4 factors to bind Hydrogen bonds Ionic/polar interactions Hydrophobic effects Van der Waals forces  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) n Stores genetic information encoded in the sequence of nucleotide monomers. Ribonucleic acid (RNA) n Decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain Monomer is a nucleotide. Consists of a 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 forms the backbone Single and double strand of a DNA Structure of a DNA strand The double-stranded structure of DNA DNA vs. RNA DNA RNA Deoxyribonucleic acid Ribonucleic acid Deoxyribose Ribose Adenine (A), Guanine (G), Cytosine (C) used in both Thymine (T) Uracil (U) 2 strands- double helix Single strand 1 form Several forms