Chapter 3 The Chemical Basis of Life II: Organic Molecules PDF

Because learning changes everything. ® Chapter 3 The Chemical Basis of Life II: Organic Molecules Lecture Outline BIOLOGY Sixth Edition Robert J. Brooker, Eric P. Widmaier, Linda E. Graham, Peter D. Stiling © 2023 McGraw Hill, LLC. All rights reserved. Authorized only for...

Because learning changes everything. ® Chapter 3 The Chemical Basis of Life II: Organic Molecules Lecture Outline BIOLOGY Sixth Edition Robert J. Brooker, Eric P. Widmaier, Linda E. Graham, Peter D. Stiling © 2023 McGraw Hill, LLC. All rights reserved. Authorized only for instructor use in the classroom. No reproduction or further distribution permitted without the prior written consent of McGraw Hill, LLC.  Key Concepts The Carbon Atom Synthesis and Breakdown of Organic Molecules and Macromolecules Overview of the Four Major Classes of Organic Molecules Found in Living Cells Carbohydrates Lipids Proteins Nucleic Acids © McGraw Hill, LLC 2  The Carbon Atom Organic molecules contain carbon Organic molecules are abundant in living organisms Macromolecules are large, complex organic molecules © McGraw Hill, LLC 3  Organic Chemistry Science of carbon-containing molecules Vitalism - 19th century concept that organic molecules were created by and imparted with a vital life force within a plant or animal’s body Believed organic compounds could not be synthesized Later disproven – organic compounds can be synthesized © McGraw Hill, LLC 4  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 © McGraw Hill, LLC 5  Figure 3.1 © McGraw Hill, LLC 6  Figure 3.2 © McGraw Hill, LLC 7  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 © McGraw Hill, LLC 8  Table 3.1 top half Table 3.1 Some Biologically Important Functional Groups That Bond to carbon Functional group* (with Formula† Examples of where Properties shorthand notation) the group is found Amino (–NH2) Amino (N H 2): A nitrogen atom is Amino acids Weakly basic (can accept H+); bonded to an R group and 2 hydrogen atoms. (proteins) polar; forms part of peptide bonds Carbonyl (–CO)‡ Ketone Carbonyl, ketone (C O): A carbon Steroids, waxes, Polar; highly chemically reactive; atom is single-bonded to an R, R prime and double-bonded to oxygen. proteins forms hydrogen bonds Aldehyde (–CHO) Aldehyde (C H O): A carbon atom is Linear forms of Acidic (gives up H+ in water); single-bonded to an R, hydrogen atom, and double-bonded to an sugars and some forms part of peptide bonds oxygen atom. odor molecules Carboxyl (–COOH) Carboxyl (C O O H): A carbon atom Amino acids, fatty Polar; forms hydrogen bonds with is single-bonded to an R, hydroxyl group, and double-bonded to an acids water oxygen atom. Hydroxyl (–OH) Steroids, alcohol, Nonpolar Hydroxyl group (O H): An R group is carbohydrates, some bonded to a hydroxyl group. amino acids It is polar! And can hydrogen bond. *This list contains many of the functional groups that are important in biology. However, many more functional groups have been identified by biochemists. †R and R′ represent the remainder of the molecule. ‡A carbonyl group is C=O. In a ketone, the carbon of this group forms covalent bonds with two other carbon atoms. In an aldehyde, the carbon is bonded to a hydrogen atom. © McGraw Hill, LLC 9  Table 3.1 bottom half Table 3.1 Some Biologically Important Functional Groups That Bond to carbon Functional group* (with Formula† Examples of where Properties shorthand notation) the group is found Methyl (–CH3) May be attached to Nonpolar DNA, proteins, and carbohydrates Methyl (C H 3): A central carbon atom is bonded to an R group and three hydrogen atoms. Phosphate ( — PO2 ) Nucleic acids, ATP, Polar; weakly acidic and 4 phospholipids negatively charged at typical pH of living organisms Phosphate (P O 4 2 negatives): A central P group is double-bonded to an O atom and single-bonded to two O anions and an O atom that is bonded to an R group. Sulfate ( — SO4 ) May be attached to Polar; negatively charged at carbohydrates, typical pH of living organisms proteins, and lipids Sulfate (S O 4 negative): A central S group is double bonded to two O atoms and single bonded to an O anion and an O atom that is bonded to an R group. -SH Sulfhydryl (–COOH) Proteins that contain Polar; forms disulfide bridges in the amino acid many proteins Also known as thiol cysteine Sulfhydryl (S H): An R group is bonded to an S atom bonded to a hydrogen atom. *This list contains many of the functional groups that are important in biology. However, many more functional groups have been identified by biochemists. †R and R′ represent the remainder of the molecule. ‡A carbonyl group is C=O. In a ketone, the carbon of this group forms covalent bonds with two other carbon atoms. In an aldehyde, the carbon is bonded to a hydrogen atom. © McGraw Hill, LLC 10  Isomers Two molecules with an identical molecular formula but different structures and characteristics Structural isomers - contain the same atoms but in different bonding relationships Stereoisomers - identical bonding relationships, but the spatial positioning of the atoms differs in the two isomers Cis-trans isomers - positioning around double bond Enantiomers - mirror image molecules Difference in orientation leads to different binding abilities Enzymes that recognize one enantiomer usually do not recognize the other © McGraw Hill, LLC 11  Figure 3.3 © McGraw Hill, LLC 12  Synthesis and Breakdown of Organic Molecules and Macromolecules Some organic molecules are large macromolecules composed of thousands or millions of atoms Formed by linking monomers (one part) and polymers (many parts) When a polymer is formed, two smaller molecules combine through a condensation reaction – produces a larger organic molecule plus a water molecule © McGraw Hill, LLC 13  Polymer formation by dehydration (condensation) reactions 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 Dehydration is catalyzed by enzymes © McGraw Hill, LLC 14  Breakdown of a polymer by hydrolysis reactions 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 © McGraw Hill, LLC 15  Four Major Classes of Organic Molecules Found in Living Cells Carbohydrates Lipids Proteins Nucleic acids © McGraw Hill, LLC 16  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 © McGraw Hill, LLC 17  Monosaccharides Simplest sugars Most common are 5 or 6 carbons Pentoses Ribose C5H10O5 Deoxyribose (C5H10O4) Hexose Glucose (C6H12O6) Different ways to depict structures Ring Linear © McGraw Hill, LLC 18  Figure 3.5a © McGraw Hill, LLC 19  Glucose isomers Stereoisomers of glucose α- and β-glucose Hydroxyl group of carbon 1 is above or below ring D- and L-glucose Enantiomers with mirror image structure D-glucose commonly found in living cells L-glucose rarely found in living cells Galactose Hydroxyl group on carbon 4 of glucose is above the plane of the ring instead of below it © McGraw Hill, LLC 20  Figure 3.5 © McGraw Hill, LLC 21  Disaccharides Composed of two monosaccharides Joined by dehydration or condensation reaction Glycosidic bond Examples: sucrose, maltose, lactose © McGraw Hill, LLC 22  Figure 3.6 © McGraw Hill, LLC 23  Polysaccharides Many monosaccharides linked together to form long polymers Examples: Energy storage – starch, glycogen Structural – cellulose, chitin, glycosaminoglycans, peptidoglycan © McGraw Hill, LLC 24  Figure 3.7 © McGraw Hill, LLC 25  Lipids Composed predominantly of hydrogen and carbon atoms, and some oxygen 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 © McGraw Hill, LLC 26  Fats 1 Also known as triglycerides Formed by bonding glycerol to 3 fatty acids Joined by dehydration; resulting bond is an ester bond © McGraw Hill, LLC 27  Fatty acids Saturated – all carbons have the maximal amount of hydrogens 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 © McGraw Hill, LLC 28  Figure 3.10 Animal fats are usually saturated fats Plant fats are usually unsaturated fats a (left, right): Tom Pantages; b: Felicia Martinez Photography/PhotoEdit © McGraw Hill, LLC 29  Fats 2 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 © McGraw Hill, LLC 30  Phospholipids Formed from glycerol, two fatty acids and a phosphate group Phospholipids are amphipathic molecules Phosphate head – polar/hydrophilic Fatty acid tail – nonpolar/hydrophobic © McGraw Hill, LLC 31  Figure 3.11 © McGraw Hill, LLC 32  Steroids Four interconnected rings of carbon atoms Usually insoluble in water Example: Cholesterol Tiny differences in structure can lead to profoundly different, specific biological properties Estrogen versus testosterone © McGraw Hill, LLC 33  Figure 3.12 Adam Jones/Science Source © McGraw Hill, LLC 34  Waxes Many plants and animals produce lipids called waxes that are secreted onto their surface May contain hundreds of different compounds but all contain one or more hydrocarbons and long structures that resemble a fatty acid attached by its carboxyl group to another long hydrocarbon chain Very nonpolar; barrier to water loss © McGraw Hill, LLC 35  Proteins Composed of carbon, hydrogen, oxygen, nitrogen, and small amounts of other elements, notably sulfur Building blocks of proteins are amino acids 20 different amino acids Common structure with variable sidechain that determines structure and function © McGraw Hill, LLC 36  Table 3.3 Table 3.3 Major Categories and Functions of Proteins Category Functions Examples Proteins involved in Make mRNA from a DNA template; RNA polymerase catalyzes the gene expression and synthesize polypeptides from mRNA; synthesis of RNA using DNA as a regulation regulate genes template. Motor proteins Initiate movement Myosin provides the contractile force of muscles. Defense proteins Protect organisms against disease Antibodies help destroy bacteria or viruses. Metabolic enzymes Increase rates of chemical reactions Hexokinase is an enzyme involved in sugar metabolism. Cell-signaling proteins Enable cells to communicate with Taste receptors in the tongue allow each other and with the environment animals to taste molecules in food. Structural proteins Support and strengthen structures Actin provides shape to the cytoplasm of plant and animal cells. Collagen gives strength to tendons. Transporters Promote movement of solutes across Glucose transporters move glucose membranes from outside cells to inside cells, where it can be used for energy. © McGraw Hill, LLC 37  Amino acid structure © McGraw Hill, LLC 38  Figure 3.14 © McGraw Hill, LLC 39  Figure 3.14: Nonpolar Amino Acids only © McGraw Hill, LLC 40  Figure 3.14 Polar Amino Acids – Uncharged and Charged © McGraw Hill, LLC 41  Polypeptide formation Amino acids joined by dehydration reaction Carboxy + amino forms peptide bond Polymers of amino acids known as polypeptides The free amino group of a polypeptide is the N-terminus The free carboxyl end is the C-terminus Proteins may be formed from one or several polypeptides © McGraw Hill, LLC 42  Figure 3.15a: Reactants only © McGraw Hill, LLC 43  Formation of a peptide bond © McGraw Hill, LLC 44  Figure 3.15 © McGraw Hill, LLC 45  Proteins have a Hierarchy of Structure Four progressive levels: Primary Secondary Tertiary Quaternary © McGraw Hill, LLC 46  Figure 3.16 © McGraw Hill, LLC 47  Primary structure Amino acid sequence Determined by genes Ribonuclease – 124 amino acids © McGraw Hill, LLC 48  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 and β pleated sheet Shape is specific and important to function © McGraw Hill, LLC 49  Tertiary structure Folding gives protein complex 3D shape This is the final level of structure for a single polypeptide chain © McGraw Hill, LLC 50  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 © McGraw Hill, LLC 51  Five factors that promote protein folding and stability Hydrogen bonds Ionic bonds and other polar interactions Hydrophobic effects Van der Waals forces Disulfide bridges – link the –SH groups in two cysteine side chains together © McGraw Hill, LLC 52  Figure 3.18 © McGraw Hill, LLC 53  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 Hydrogen bonds Ionic bonds and other polar interactions Hydrophobic effects Van der Waals forces © McGraw Hill, LLC 54  Figure 3.19 © McGraw Hill, LLC 55  Anfinsen Showed That the Primary Structure of Ribonuclease Determines Its Three-Dimensional Structure Prior to 1960s, the mechanisms by which proteins assume their 3D structures were not understood. Christian Anfinsen postulated that proteins contain all the information necessary to fold into their proper conformation without needing organelles or factors He hypothesized that proteins spontaneously assume their most stable conformation based on the laws of chemistry and physics © McGraw Hill, LLC 56  Anfinsen’s Ribonuclease experiment 1 Won him the Nobel Prize in 1972 Performed in vitro - no other cellular components present Chemicals that disrupt bonds caused the enzyme to lose function; removal of those chemicals restored function Conclusion: Even in the complete absence of any cellular factors or organelles, an unfolded protein can refold into its functional structure Since then, we have learned that some proteins do require assistance in folding © McGraw Hill, LLC 57  Anfinsen’s Ribonuclease experiment 2 © McGraw Hill, LLC 58  Anfinsen’s Ribonuclease experiment 3 © McGraw Hill, LLC 59  Proteins Contain Functional Domains Within Their Structures Modules or domains in proteins have distinct structures and function Example: Nuclear receptors Each domain of this protein is involved in a distinct biological function Ligand binding DNA binding Nuclear localization domain Activation domain Proteins that share a particular domain also share the associated function © McGraw Hill, LLC 60  Figure 3.21 © McGraw Hill, LLC 61  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 © McGraw Hill, LLC 62  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 Purines: adenine (A) & guanine (G) Pyrimidines: cytosine (C) & thymine (T) Nucleotides are linked into polymer by a sugar-phosphate backbone © McGraw Hill, LLC 63  Figure 3.23 © McGraw Hill, LLC 64  DNA is Composed of Two Strands of Nucleotides DNA molecule consists of two strands of nucleotides coiled around each other in a double helix Held together by hydrogen bonds between a purine base in one strand and a pyrimidine base in the opposite strand A pairs with T; C pairs with G © McGraw Hill, LLC 65  DNA versus RNA DNA RNA Deoxyribonucleic acid Ribonucleic acid Deoxyribose Ribose Thymine (T) Uracil (U) Adenine (A), guanine (G), Adenine (A), guanine (G), cytosine (C) used in both cytosine (C) used in both 2 strands, double helix Single strand 1 form Several forms © McGraw Hill, LLC 66  Figure 3.24 © McGraw Hill, LLC 67