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Introductory Chemistry: Concepts & Connections 4th Edition by Charles H. Corwin Chapter 20 Biochemistry Christopher G. Hamaker, Illinois State University, Normal IL © 2005, Prentice Hall Introduction to Biochemistry • There are 30 elements which are essential for life. • The study of the chemistry of living things is biochemistry. • Biological compounds are often large and complex with molar masses greater than 1,000,000 g/mol. • These large molecules are polymers of smaller molecules. Chapter 20 2 Biological Compounds Chapter 20 3 Proteins • Proteins are naturally occurring polymers composed of many amino acids. • An amino acid has both an amine and a carboxylic acid functional group. • Amino acids are linked together by amide bonds which are referred to as peptide linkages. Chapter 20 4 Carbohydrates • A carbohydrate is either a simple sugar or a polymer composed of many simple sugars. • A carbohydrate usually contains either an aldehyde or ketone functional group and several alcohol groups. • Starch is a carbohydrate polymer composed of glucose units linked together by glycoside linkages. Chapter 20 5 Lipids • A lipid is a water-insoluble compound usually composed of an alcohol and one or more carboxylic acid molecules. • Fats and oils are esters of glycerol, an alcohol that has three –OH groups. • As a result, each molecule of a fat or an oil contains three ester groups from three carboxylic acid molecules joined to one glycerol molecule. Chapter 20 6 Nucleic Acids • A nucleic acid is a biochemical polymer composed of a very large number of individual units. • Each unit in the nucleic acid contains a sugar molecule attached to an organic nitrogen-containing molecule and an attached phosphate group. • The units are attached together by phosphate linkages. Chapter 20 7 Amino Acids • Proteins are composed of amino acids. • An amino acid has an amine (-NH2) and a carboxy group (-COOH) attached to a carbon atom with side chain (R) attached to the a-carbon. • There are twenty naturally occurring amino acids in human proteins. Each one has a different side chain. Chapter 20 8 The 20 Natural Amino Acids Neutral Amino Acids Acidic Amino Acids Basic Amino Acids 9 Polypeptides • In proteins, amino acids are linked together with peptide linkages or a peptide bond. • In a dipeptide, two amino acid units are joined together by a peptide bond. • In a polypeptide, up to 50 amino acids are linked together. • Human insulin is composed of 48 amino acids. Chapter 20 10 Primary Structure of Proteins • Proteins are polypeptides composed of hundreds or thousands of amino acid units. • The primary structure of a protein is the sequence of amino acids. Individual amino acids are represented by the colored ovals in the figure below. • The replacement of one amino acid by another in the primary structure of a protein can completely alter its biological activity. Chapter 20 11 Secondary Structure of Proteins • When the peptide chain twists and bends, proteins acquire a secondary structure. • There are two primary types of secondary structures, a-helix and pleated sheet. • An a-helix is analogous to that in a coiled telephone cord. Chapter 20 12 Pleated Sheet • In a pleated sheet, the chains run antiparallel to each other. It looks like a sheet of paper folded in an accordion shape. • Secondary structure in proteins is a result of hydrogen bonds. Chapter 20 13 Tertiary Structure of Proteins • The overall three-dimensional structure of a protein is referred to as its tertiary structure. • The tertiary structure of a protein may be long and extended or compact and folded. • The tertiary structure of a protein is held together by intermolecular forces. Chapter 20 14 Enzymes • An enzyme is a protein that acts as a biological catalyst. • Enzymes are incredibly selective for specific molecules. • An enzyme can speed up a biochemical reaction so that the rate is a million times faster than it would be in the absence of the enzyme. • Many reactions catalyzed by enzymes would be too slow without the enzyme to sustain life. Chapter 20 15 Enzyme Mechanisms • The location where the reaction occurs on the enzyme is the active site. • The molecule that reacts is the substrate. • We can use the lock-and-key model to describe enzyme mechanisms. • In the model, the key is the enzyme and the lock it the substrate. Chapter 20 16 Enzyme Reactions • An enzyme reaction takes place in two steps. • First, the substrate (S) binds to the active site on the enzyme (E). Step 1: E + S → ES • Second, the enzyme releases two or more products (P1 and P2). Step 2: ES → E + P1 + P2 Chapter 20 17 Enzyme Reactions • The active site of an enzyme has a shape designed to specifically bind its substrate. • Once the reaction has occurred, the active site is free to bind another substrate molecule and repeat the reaction. Chapter 20 18 The Enzyme Ptyalin • The enzyme ptyalin is in human saliva and catalyzes the breaking down of starch molecules into sugar units. • The reaction would take about a two years to occur without the enzyme. Chapter 20 19 Carbohydrates • The word carbohydrate means “hydrates of carbon” and many have the empirical formula CH2O. • Carbohydrate names usually end in the suffix -ose. • Carbohydrates have an aldehyde or ketone functional group and several hydroxyl groups. Chapter 20 20 Simple Sugars • A simple sugar molecule typically has three to six carbons, and aldehyde or ketone group, and a few hydroxyl groups. • A simple sugar is referred to as a monosaccharide. • A monosaccharide with an aldehyde group is an aldose and one with a ketone group is a ketose. Chapter 20 21 Aqueous Structures of Sugars • In aqueous solution, sugar molecules usually exist in ring structures. • Glucose forms a cyclic structure by joining a hydroxyl group to an aldehyde group. • The resulting ring structure has 5 carbon atoms and 1 oxygen atom. Chapter 20 22 Disaccharides • A disaccharide is two monosaccharide molecules joined together. • In the formation of a disaccharide, two simple sugars split out water and are joined together by a special –O– bond called a glycoside linkage. Chapter 20 23 Polysaccharides • A polysaccharide is a polymer of many monosaccharide linkages joined by glycoside linkages. • Starch and cellulose are both polysaccharides composed only of glucose units but with slightly different 3-dimentional structures. Starch Cellulose Chapter 20 24 Lipids • Unlike most other biological compounds, lipids are not water soluble. • Lipids include – Fats and oils – Waxes – Steroids – The water insoluble vitamins A, D, E, and K Chapter 20 25 Fatty Acids • A fatty acid is a carboxylic acid with a long hydrocarbon chain. • Fatty acids can be saturated or unsaturated. Chapter 20 26 Triglycerides • A triglyceride is a lipid formed from glycerol, a trihydroxy alcohol, and three fatty acids. • When three fatty acids react with glycerol, a triglyceride is formed with three ether linkages. Chapter 20 27 Fats • In triglycerides obtained from animals, the fatty acids are mostly saturated and have few double bonds. • A semisolid lipid obtained from an animal source is a fat. • The following structure is and example of a saturated triglyceride from animal fat. Chapter 20 28 Oils • A liquid lipid obtained from a plant source is an oil. • Triglycerides obtained from plants have mostly unsaturated fatty acid chains. • The following structure is and example of an unsaturated triglyceride from a vegetable oil. Chapter 20 29 Nucleic Acids • Nucleic acids are biochemical compounds found in every living cell. • Nucleic acids contain the genetic information responsible for the reproduction of a species. • There are two basic types of nucleic acids: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). • A nucleic acid is a polymer composed of many repeating units, each of which is called a nucleotide. Chapter 20 30 Nucleotides • Each nucleotide consists of three similar component molecules: a five-carbon sugar, a nitrogen-containing base, and a molecule of phosphoric acid. • The five-carbon sugars are similar in RNA and DNA. The two sugars are identical except for a hydroxyl group. The structures are shown here: Chapter 20 31 Nitrogen Bases • There are five nitrogen bases. • Three are found in both DNA and RNA, one is found only in DNA and one is found only in RNA. • Their structures are shown below: Chapter 20 32 Nucleotide Structures • Nucleotides for DNA and RNA are the sugar with a phosphoric acid and the nitrogen base attached. • Shown here are structures of a DNA and RNA nucleotide. Chapter 20 33 DNA and RNA • DNA and RNA are polymers of individual nucleotides. A segment is shown here. • A DNA molecule is actually two strands of DNA wound together in a spiral structure called a double helix. • The double strand is held together by hydrogen bonds between nitrogen pairs. Chapter 20 34 DNA Double Helix • An adenine (A) on one strand always hydrogen bonds to a thymine (T) on the other strand. • Also, a cytosine (C) on one strand always hydrogen bonds to a guanine (G) on the other strand. • These interactions give DNA its characteristic structure. Chapter 20 35 Conclusions • There are 4 major types of biological molecules: – Proteins are composed of amino acids. – Carbohydrates are composed of simple sugar molecules. – A lipid is a water insoluble biological molecule. – A nucleic acid is a polymer composed of a sugar molecule, a nitrogen base, and phosphoric acid. Chapter 20 36 Conclusions Continued • An enzyme is a catalyst for biological reactions. • Enzymes work by a lock-and-key mechanism where only a specific substrate fits into the enzyme to react. • Reactions catalyzed by enzymes can be completed in a matter of seconds where the reaction would normally take many years. Chapter 20 37 Conclusions Continued • A triglyceride is an ester of glycerol and three different fatty acids. • A fat is a triglyceride from an animal source. An oil is a triglyceride from a plant source. • A nucleic acid is a molecule that carries genetic information. • DNA and RNA are the two basic types of nucleic acids. Chapter 20 38