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INTRODUCTION TO ORGANIC COMPOUNDS Copyright © 2009 Pearson Education, Inc. Organic Compounds – Carbon-based molecules are called organic compounds – By sharing electrons, carbon can bond to four other atoms – By doing so, it can branch in up to four directions Copyright © 2009 Pearson Education, Inc. Structural formula Ball-and-stick model Space-filling model Methane The four single bonds of carbon point to the corners of a tetrahedron. • Methane and other compounds composed of only carbon and hydrogen are called hydrocarbons – Carbon, with attached hydrogen, can bond together in chains of various lengths Ethane Propane Length. Carbon skeletons vary in length. Copyright © 2009 Pearson Education, Inc. Butane Isobutane Branching. Skeletons may be unbranched or branched. 1-Butene Double bonds. 2-Butene Skeletons may have double bonds, which can vary in location. Cyclohexane Rings. Benzene Skeletons may be arranged in rings. • An organic compound has unique properties that depend upon – The size and shape of the molecule – The groups of atoms (functional groups) attached to it • A functional group affects a biological molecule’s function in a characteristic way Copyright © 2009 Pearson Education, Inc. • Compounds containing functional groups are hydrophilic (water-loving) –This means that they are soluble in water, which is a necessary prerequisite for their roles in water-based life Copyright © 2009 Pearson Education, Inc. Functional Groups • Hydroxyl group— consists of a hydrogen bonded to an oxygen • Carbonyl group—a carbon linked by a double bond to an oxygen atom • Carboxyl group— consists of a carbon doublebonded to both an oxygen and a hydroxyl group Functional Groups (Cont’d) • Amino group—composed of a nitrogen bonded to two hydrogen atoms and the carbon skeleton • Phosphate group—consists of a phosphorus atom bonded to four oxygen atoms • Methyl group- consists of a carbon bonded to three hydrogen Estradiol Female lion Testosterone Male lion • Four classes of biological molecules: –Carbohydrates –Proteins –Lipids –Nucleic acids Copyright © 2009 Pearson Education, Inc. • The four classes of biological molecules contain very large molecules – macromolecules – Polymers -made from identical building blocks(monomers) strung together – monomers -building blocks Copyright © 2009 Pearson Education, Inc. • A cell makes a large number of polymers from a small group of monomers – Proteins are made from only 20 different amino acids, and DNA is built from just four kinds of nucleotides • The monomers used to make polymers are universal Copyright © 2009 Pearson Education, Inc. • dehydration reactions- remove water and link monomers to form polymers • hydrolysis- addition of water, breaks apart polymers • All biological reactions of this sort are mediated by enzymes, which speed up chemical reactions in cells Copyright © 2009 Pearson Education, Inc. Short polymer Unlinked monomer Short polymer Dehydration reaction Longer polymer Unlinked monomer Hydrolysis CARBOHYDRATES Monosaccharides, disaccharides and polysaccharides 1:2:1 ratio of C:H:O Copyright © 2009 Pearson Education, Inc. Monosaccharides – Monosaccharides-Sugar monomers – -such as glucose, galactose and fructose - bond together to form the polysaccharides Copyright © 2009 Pearson Education, Inc. Monosaccharides • carbon skeletons - three to seven carbon atoms – Glucose and fructose are six carbons long – main fuels for cellular work – used as raw materials to manufacture other organic molecules Copyright © 2009 Pearson Education, Inc. Glucose (an aldose) Fructose (a ketose) Structural formula Abbreviated structure Simplified structure • Disaccharide-Two monosaccharides (monomers) bonded in a dehydration synthesis reaction – An example is a glucose monomer bonding to a fructose monomer to form sucrose, a common disaccharide Copyright © 2009 Pearson Education, Inc. • Disaccharide-Two monosaccharides bonded in a dehydration synthesis reaction – Glucose + fructose sucrose + water – Glucose + galactose lactose + water Copyright © 2009 Pearson Education, Inc. Glucose Glucose Glucose Glucose Maltose • Polysaccharides are polymers of monosaccharides – They can function in the cell as a storage molecule or as a structural compound Copyright © 2009 Pearson Education, Inc. Polysaccharides • Starch is a storage polysaccharide composed of glucose monomers and found in plants • Glycogen is a storage polysaccharide composed of glucose, which is hydrolyzed by animals when glucose is needed • Cellulose is a polymer of glucose that forms plant cell walls • Chitin is a polysaccharide used by insects and crustaceans to build an exoskeleton and used in fungi cell walls Copyright © 2009 Pearson Education, Inc. Starch granules in potato tuber cells Glycogen granules in muscle tissue STARCH Glucose monomer GLYCOGEN CELLULOSE Cellulose fibrils in a plant cell wall Hydrogen bonds Cellulose molecules Starch granules in potato tuber cells STARCH Glucose monomer Glycogen granules in muscle tissue GLYCOGEN CELLULOSE Cellulose fibrils in a plant cell wall Hydrogen bonds Cellulose molecules LIPIDS Copyright © 2009 Pearson Education, Inc. • Lipids-water insoluble (hydrophobic) compounds energy storage Copyright © 2009 Pearson Education, Inc. - Triglycerides • Fatty acids link to glycerol by a dehydration reaction • Glycerol-alcohol with 3 carbons, each with hydroxyl group • Fatty Acid- carboxyl group and hydrocarbon chain of 16-18 carbons in length Copyright © 2009 Pearson Education, Inc. Glycerol Fatty acid Figure 2.15a • Some fatty acids contain double bonds – This causes kinks or bends in the carbon chain because the maximum number of hydrogen atoms cannot bond to the carbons at the double bond – unsaturated fats -have fewer than the maximum number of hydrogens – saturated fats- Fats with the maximum number of hydrogens Copyright © 2009 Pearson Education, Inc. • Phospholipids • - structurally similar to triglycerides • -important component of all cells Copyright © 2009 Pearson Education, Inc. Chemical Nature of Phospholipids head tails Hydrophilic heads Water Hydrophobic tails Water • Steroids are lipids composed of fused ring structures Copyright © 2009 Pearson Education, Inc. Four Ring Structure of Steroids PROTEINS Copyright © 2009 Pearson Education, Inc. Proteins • A protein is a polymer built from various combinations of 20 amino acid monomers – Structures directly related to functions – Enzymes-proteins that serve as metabolic catalysts, regulate the chemical reactions within cells – “-ase” Copyright © 2009 Pearson Education, Inc. Proteins • Structural • • • • • contractile Defensive Signal Receptor transport Copyright © 2009 Pearson Education, Inc. Proteins • Amino acids-building blocks of proteins • Central carbon • have an amino group and a carboxyl group – Also bonded to the central carbon is a hydrogen atom and some other chemical group symbolized by R Copyright © 2009 Pearson Education, Inc. Amino group Carboxyl group • Amino acids are classified as hydrophobic or hydrophilic nonpolar R group and are hydrophobic polar R group and are hydrophilic Copyright © 2009 Pearson Education, Inc. Leucine (Leu) Hydrophobic Serine (Ser) Aspartic acid (Asp) Hydrophilic Carboxyl group Amino acid Amino group Amino acid Carboxyl group Amino acid Amino group Amino acid Peptide bond Dehydration reaction Dipeptide • A polypeptide chain – 100’s or 1000’s of amino acids linked by peptide bonds – The shape of a protein determines its specific function Copyright © 2009 Pearson Education, Inc. • If for some reason a protein’s shape is altered, it can no longer function – Denaturation – changes in salt concentration and pH, temperature Copyright © 2009 Pearson Education, Inc. • A protein can have four levels of structure – – – – Primary structure Secondary structure Tertiary structure Quaternary structure Copyright © 2009 Pearson Education, Inc. • The primary structure- unique amino acid sequence – The correct amino acid sequence is determined by the cell’s genetic information – The slightest change in this sequence affects the protein’s ability to function Copyright © 2009 Pearson Education, Inc. Amino acids Primary structure Four Levels of Protein Structure Primary structure Amino acids • secondary structure-coiling or folding of the polypeptide – Coiling results in a helical structure called an alpha helix – Folding may lead to a structure called a pleated sheet – Hydrogen bonds Copyright © 2009 Pearson Education, Inc. Amino acids Hydrogen bond Alpha helix Secondary structure Pleated sheet Four Levels of Protein Structure Primary structure Amino acids Hydrogen bond Secondary structure Alpha helix Pleated sheet • tertiary structure-three-dimensional shape of a protein – results from interactions between the R groups of the various amino acids – Disulfide bridges are covalent bonds that further strengthen the protein’s shape Copyright © 2009 Pearson Education, Inc. Four Levels of Protein Structure Primary structure Amino acids Hydrogen bond Secondary structure Alpha helix Tertiary structure Polypeptide (single subunit of transthyretin) Pleated sheet Polypeptide (single subunit of transthyretin) Tertiary structure • quaternary structure-two or more polypeptide chains (subunits) associate Copyright © 2009 Pearson Education, Inc. Transthyretin, with four identical polypeptide subunits Quaternary structure Four Levels of Protein Structure Primary structure Amino acids Hydrogen bond Secondary structure Alpha helix Tertiary structure Quaternary structure Pleated sheet Polypeptide (single subunit of transthyretin) Transthyretin, with four identical polypeptide subunits HOW ENZYMES FUNCTION Copyright © 2009 Pearson Education, Inc. • Energy is the capacity to do work and cause change Copyright © 2009 Pearson Education, Inc. – There are two kinds of energy – Kinetic energy is the energy of motion – Potential energy is energy that an object possesses as a result of its location, stored energy Energy is converted from one form to another. • Chemical energy -potential energy • it is the energy stored in chemical bonds, energy available for release in a chemical reaction Copyright © 2009 Pearson Education, Inc. Chemical Reactions • Release or store energy • Exergonic reaction- releases energy – reaction releases the energy in covalent bonds of the reactants Copyright © 2009 Pearson Education, Inc. Potential energy of molecules Reactants Amount of energy released Energy released Products Chemical Reactions • Endergonic reaction-requires an input of energy • yields products rich in potential energy – energy is absorbed and stored in covalent bonds of the products – Building macromolecules Copyright © 2009 Pearson Education, Inc. Potential energy of molecules Products Energy required Reactants Amount of energy required – Metabolism- all of the exergonic and endergonic reactions that occur in an organism Copyright © 2009 Pearson Education, Inc. Activation Energy – The start up energy – Energy that must be absorbed by the reactants in any chemical reaction in order to be break bonds – Energy must be available to break bonds and form new ones – This energy is called energy of activation Copyright © 2009 Pearson Education, Inc. Catalysts A Catalyst is a substance that can change the rate of a chemical reaction. It does this by decreasing the activation energy that is needed to start a chemical reaction. A Catalyst is NOT reactant or product. It is not changed or used up during a reaction. Enzymes are catalysts for chemical reactions in living things. Copyright © 2009 Pearson Education, Inc. Reaction without enzyme EA without enzyme EA with enzyme Reactants Net change in energy (the same) Reaction with enzyme Products Progress of the reaction Enzymes • Proteins- have unique three-dimensional shapes – Shape critical for function – Substrates- the specific reactants that an enzyme acts on -- the enzyme has an active site where the enzyme interacts with the enzyme’s substrate Copyright © 2009 Pearson Education, Inc. 1 Enzyme available with empty active site Active site Enzyme (sucrase) 1 Enzyme available with empty active site Active site Enzyme (sucrase) Substrate (sucrose) 2 Substrate binds to enzyme with induced fit 1 Enzyme available with empty active site Active site Substrate (sucrose) 2 Substrate binds to enzyme with induced fit Enzyme (sucrase) 3 Substrate is converted to products 1 Enzyme available with empty active site Active site Glucose Substrate (sucrose) 2 Substrate binds to enzyme with induced fit Enzyme (sucrase) Fructose 4 Products are released 3 Substrate is converted to products • Some enzymes require nonprotein helpers – Cofactors are inorganic, such as zinc, iron, or copper – Coenzymes are organic molecules and are often vitamins Copyright © 2009 Pearson Education, Inc. • Inhibitors are chemicals that inhibit an enzyme’s activity – One group inhibits because they compete for the enzyme’s active site and thus block substrates from entering the active site – These are called competitive inhibitors Copyright © 2009 Pearson Education, Inc. Substrate Active site Enzyme Normal binding of substrate Competitive inhibitor Noncompetitive inhibitor Enzyme inhibition • Other inhibitors do not act directly with the active site – These bind somewhere else and change the shape of the enzyme so that the substrate will no longer fit the active site – These are called noncompetitive inhibitors Copyright © 2009 Pearson Education, Inc. • Enzyme inhibitors are important in regulating cell metabolism – Often the product of a metabolic pathway can serve as an inhibitor of one enzyme in the pathway, a mechanism called feedback inhibition – The more product formed, the greater the inhibition, and in this way, regulation of the pathway is accomplished Copyright © 2009 Pearson Education, Inc. NUCLEIC ACIDS Copyright © 2009 Pearson Education, Inc. • DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • composed of monomers called nucleotides – Nucleotides have three parts – A five-carbon sugar – called ribose in RNA and deoxyribose in DNA – A phosphate group – A nitrogenous base Copyright © 2009 Pearson Education, Inc. Nitrogenous base (adenine) Phosphate group Sugar • DNA nitrogenous bases- adenine (A), thymine (T), cytosine (C), and guanine (G) – RNA - A, C, and G, but instead of T, it has uracil (U) Copyright © 2009 Pearson Education, Inc. • A nucleic acid polymer, a polynucleotide, forms from the nucleotide monomers when the phosphate of one nucleotide bonds to the sugar of the next nucleotide – The result is a repeating sugar-phosphate backbone with protruding nitrogenous bases Copyright © 2009 Pearson Education, Inc. Nucleotide Sugar-phosphate backbone • DNA • double helix- 2 polynucleotide strands • Bases of each strand hydrogen bond to each other • A pairs with T, and C pairs with G, producing base pairs • RNA is usually a single polynucleotide strand Copyright © 2009 Pearson Education, Inc. Base pair • A particular nucleotide sequence that can instruct the formation of a polypeptide is called a gene – Most DNA molecules consist of millions of base pairs and, consequently, many genes – These genes, many of which are unique to the species, determine the structure of proteins and, thus, life’s structures and functions Copyright © 2009 Pearson Education, Inc. Adenosine Triphosphate (ATP) • Temporary molecular storage of energy • Consists of 3 phosphate groups attached to adenine & 5-carbon sugar (ribose) Figure 2.23