Organic Molecules PDF

Chemistry is the Basis of Life: Organic Molecules Dr. Cravaritis  The Carbon Atom and Organic Molecules Organic molecules contain carbon Organic molecules are abundant in living organisms Macromolecules are large, complex organic molecules 2  CAR...

Chemistry is the Basis of Life: Organic Molecules Dr. Cravaritis  The Carbon Atom and Organic Molecules Organic molecules contain carbon Organic molecules are abundant in living organisms Macromolecules are large, complex organic molecules 2  CARBON Carbon has 4 electrons in its outer shell Needs 4 more electrons to fill the shell It can make up to four bonds  Usually single or double bonds Carbon can form nonpolar or polar bonds  Molecules with polar bonds are water soluble  Molecules with nonpolar bonds (like hydrocarbons) are not very water soluble 3 ATOMIC STRUCTURE OF CARBON 4  H H O H C C C OH H H Oxygen is more C—C and C— electronegati H bonds ve than are carbon; thus, electrically C—O neutral and C–O and bonds nonpolar. Propionic acid are polar. 5 FUNCTIONAL GROUPS Groups of atoms with special chemical features that are functionally important Each type of functional group exhibits the same properties in all molecules in which it occurs 6 FUNCTIONAL GROUPS Copyright © McGraw-Hill Education. All rights reserved. No reproduction or distribution without the prior written consent of McGraw-Hill Education. 7  Formation of Organic Molecules and Macromolecules Dehydration reaction Links monomers to form polymers HO H + HO H HO H Hydrolysis Polymers broken down into monomers HO H HO H + HO H 8 Polymer formation by dehydration reactions Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H2O H2O H2O Monomers HO H + HO H HO H HO H HO H HO H HO H A molecule of water is removed each time a new monomer is added, thus a “dehydration” reaction The process repeats to form long polymers A polymer can consist of thousands of monomers 9 Dehydration is catalyzed by enzymes Breakdown of a polymer by hydrolysis reactions Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. HO H HO H HO H HO H HO H HO H + HO H H2O H2O H2O A molecule of water is added back each time a monomer is released The process repeats to break down long polymer Hydrolysis is catalyzed by enzymes 10 FOUR MAJOR TYPES OF ORGANIC MOLECULES AND MACROMOLECULES CH2OH H O H H OH H HO OH H OH Carbohydrates Lipids Nucleic Acids Proteins 11  Carbohydrates Composed of carbon, hydrogen, and oxygen atoms Cn(H2O)n Most of the carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group Is a polymer composed of monomer units = monosaccharides  Beads on a string 12  MONOSACCHARIDES Monomer unit for carbohydrates Simplest sugars Most common are 5 or 6 carbons Pentoses  Ribose (C5H10O5)  Deoxyribose (C5H10O4) Hexose  Glucose (C6H12O6) Different ways to depict structures Ring Linear 13  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. (a) Linear and ring structures of D-glucose 14  CH2OH CH2OH OH O H O DISACCHARIDES H H OH H H HO + H CH2OH HO OH H OH OH H Glucose Fructose Composed of two monosaccharides dehydration reaction Joined by dehydration CH2OH or condensation H H O H Glycosidic reaction OH H bond  Glycosidic bond HO H OH Broken apart by O + H2O hydrolysis CH2OH O Examples: sucrose, H H HO CH2OH maltose, lactose OH H 15 Sucrose POLYSACCHARIDES Many monosaccharides linked together to form long polymers Examples: Energy storage – starch, glycogen Structural – cellulose, chitin, glycosaminoglycans 16  Lipids Composed predominantly of hydrogen and carbon atoms Defining feature of lipids is that they are nonpolar and therefore very insoluble in water Include fats, phospholipids, steroids, waxes Lipids comprise about 40% of the organic matter in the average human body Composed of units – but not uniformly repeated as in a traditional polymer 18  FATS Also known as triglycerides or triacylglycerols Formed by bonding glycerol to 3 fatty acids Joined by dehydration; broken apart by hydrolysis The hydrogens from The hydroxyl groups from The new bond created each hydroxyl group is called an ester in glycerol are each carboxyl group of the bond. removed. 3 fatty acids are removed. Fatty Acids Saturated – all carbons linked by single bonds Tend to be solid at room temperature Unsaturated – contain one or more double bonds Tend to be liquid at room temperature (known as oils) Cis forms naturally; trans formed artificially Trans fats are linked to disease 20  Animal fats are usually saturated fats Plant fats are usually unsaturated fats High temperature converts After cooling, saturated Unsaturated fats have solid, saturated fasts to fats return to their solid low melting points and liquid. form. are liquid at room temperature. a)Animal fats at high and low temperatures b) Vegetable fats at low temperature a (left, right): ©Tom Pantages; b: ©Felicia Martinez Photography/PhotoEdit 21  Fats Fats are important for energy storage 1 gram of fat stores more energy than 1 gram of glycogen or starch Fats can also be structural, providing cushioning and insulation 22  PHOSPHOLIPIDS Formed from glycerol, two fatty acids and a phosphate group Phospholipids are amphipathic molecules  Phosphate head – polar / hydrophilic  Fatty acid tail – nonpolar / hydrophobic 23 PHOSPHOLIPIDS AND WHERE THEY ARE FOUND a) Structure and model of a phospholipid b) Arrangement of phospholipids in a bilayer 24  STEROIDS Four interconnected rings of carbon atoms Usually insoluble in water ex: Cholesterol Tiny differences in structure can lead to profoundly different, specific biological properties  Estrogen vs. testosterone 25 TESTOSTERONE VERSUS ESTROGEN 26  Proteins Composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements, notably sulfur Monomer units of proteins are amino acids 20 different amino acids Common structure with variable sidechain that determines structure and function 27 AMINO ACID STRUCTURE General designation for an amino acid side chain Amino group - Carboxyl group - positively negatively charged at neutral pH charged at neutral pH 28 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 30 olypeptide formation Amino acids joined by dehydration reaction  Carboxyl + amino forms peptide bond  Polymers of amino acids known as polypeptides  Proteins may be formed from one or several polypeptides Polypeptides are broken down by hydrolysis 31 a) Formation of a peptide bond between 2 amino acids 32 a)Formation of a peptide bond between 2 amino acids b) Polypeptide – a linear chain of amino acids c) Numbering system of amino acids in a polypeptide Access the text alternative for slide i mages. 33 PROTEIN STRUCTURE 34  PRIMARY  STRUCTURE Amino acid sequence Encoded directly by genes  SECONDARY STRUCTURE Chemical and physical interactions cause protein folding 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 36 TERTIARY STRUCTURE Folding gives protein complex 3D shape This is the final level of structure for a single polypeptide chain 37  QUATERNARY STRUCTURE Made up of two or more polypeptides  Individual polypeptide chains are protein subunits  Protein can be formed from several copies of the same polypeptide Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.  Or may be multimeric – composed from different polypeptides 38  FIVE FACTORS THAT PROMOTE PROTEIN FOLDING AND STABILITY 1. Hydrogen bonds 2. Ionic bonds and other polar interactions 3. Hydrophobic effects 4. Van der Waals forces 5. Disulfide bridges 39 PROTEIN STRUCTURE 40 PROTEIN-PROTEIN INTERACTIONS Many cellular processes involve steps in which two or more different proteins interact Specific binding at surface Use first four factors to bind 1. Hydrogen bonds 2. Ionic bonds and other polar interactions 3. Hydrophobic effects 4. Van der Waals forces 41 DENATURING A PROTEIN If a protein is heated, the secondary and tertiary structure is broken down; the protein is said to be denatured.  High temperature  pH changes  High concentrations of polar molecules  Nonpolar substances When cooled, some proteins return to normal tertiary structure, demonstrating that the information to specify protein shape is contained in its primary structure.  Nucleic Acids Responsible for the storage, expression, and transmission of genetic information Two classes  Deoxyribonucleic acid (DNA)  Stores genetic information encoded in the sequence of nucleotide monomers  Ribonucleic acid (RNA)  Decodes DNA into instructions for linking together a specific sequence of amino acids to form a polypeptide chain 44 Nucleic Acid monomer is a nucleotide  Made up of phosphate group, a five-carbon sugar (either ribose or deoxyribose), and a single or double ring of carbon and nitrogen atoms known as a base  Nucleotides are linked into polymer by a sugar-phosphate backbone 45 NUCLEOTIDE STRAND 46  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 47 48