Biochemistry: The Molecules of Life • Within cells, small organic molecules are joined together to form larger molecules • Macromolecules are large molecules composed of thousands of covalently connected atoms – – – – Carbohydrates Lipids Proteins Nucleic acids Macromolecules - Polymers • A polymer is a long molecule consisting of many similar building blocks called monomers • Most macromolecules are polymers, built from monomers • An immense variety of polymers can be built from a small set of monomers • Three of the four classes of life’s organic molecules are polymers: – Carbohydrates – Proteins – Nucleic acids Polymers • Monomers form larger molecules by condensation reactions called dehydration reactions • Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond Longer polymer Dehydration reaction in the synthesis of a polymer Hydrolysis adds a water molecule, breaking a bond Hydrolysis of a polymer Carbohydrates • Carbohydrates serve as fuel and building material • They include sugars and the polymers of sugars • The simplest carbohydrates are monosaccharides, or single (simple) sugars • Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks Sugars • Monosaccharides have molecular formulas that contain C, H, and O in an approximate ratio of 1:2:1 • Monosaccharides are used for short term energy storage, and serve as structural components of larger organic molecules • Glucose is the most common monosaccharide Monosaccharides • Monosaccharides are classified by location of the carbonyl group and by number of carbons in the carbon skeleton • 3 C = triose e.g. glyceraldehyde • 4 C = tetrose • 5 C = pentose e.g. ribose, deoxyribose • 6 C = hexose e.g. glucose, fructose, galactose • Monosaccharides in living organisms generally have 3C, 5C, or 6C: Triose sugars (C3H6O3) Pentose sugars (C5H10O5) Hexose sugars (C5H12O6) Glyceraldehyde Ribose Galactose Glucose Dihydroxyacetone Ribulose Fructose Monosaccharides • Monosaccharides serve as a major fuel for cells and as raw material for building molecules • The monosaccharides glucose and fructose are isomers – They have the same chemical formula – Their atoms are arranged differently • Though often drawn as a linear skeleton, in aqueous solutions they form rings Glucose Fructose Monosaccharides • In aqueous solutions, monosaccharides form rings Linear and ring forms Abbreviated ring structure Monosaccharides: Hexoses Monosaccharides: Pentsoses Pentoses (5-carbon sugars) 5 CH2OH O OH 1 4 H H H H 3 2 OH OH Ribose 5 CH2OH O OH 4 1 H H H H 2 3 H OH Deoxyribose Disaccharides • A disaccharide is formed when a dehydration reaction joins two monosaccharides • Disaccharides are joined by the process of dehydration synthesis • This covalent bond is called a glycosidic linkage Dehydration reaction in the synthesis of maltose 1–4 glycosidic linkage Glucose Glucose Dehydration reaction in the synthesis of sucrose Maltose 1–2 glycosidic linkage Glucose Fructose Sucrose Disaccharides • • • • Lactose = Glucose + Galactose Maltose = Glucose + Glucose Sucrose = Glucose + Fructose The most common disaccharide is sucrose, common table sugar • Sucrose is extracted from sugar cane and the roots of sugar beets Polysaccharides • Complex carbohydrates are called polysaccharides • They are polymers of monosaccharides - long chains of simple sugar units • Polysaccharides have storage and structural roles • The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages (a) Starch (b) Glycogen (c) Cellulose Storage Polysaccharides - Starch Chloroplast • Starch, a storage polysaccharide of plants, consists entirely of glucose monomers • Plants store surplus starch as granules within chloroplasts and other plastids Starch 1 µm Amylose Amylopectin Starch: a plant polysaccharide Storage Polysaccharides - Glycogen • Glycogen is a storage polysaccharide in animals • Humans and other vertebrates store glycogen mainly in liver and muscle cells Mitochondria Glycogen granules 0.5 µm Glycogen Glycogen: an animal polysaccharide Structural Polysaccharides • Cellulose is a major component of the tough wall of plant cells • Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ • The difference is based on two ring forms for glucose: alpha () and beta () a Glucose b Glucose a and b glucose ring structures Starch: 1–4 linkage of a glucose monomers. – Polymers with alpha glucose are helical – Polymers with beta glucose are straight Cellulose: 1–4 linkage of b glucose monomers. Cellulose • Enzymes that digest starch by hydrolyzing alpha linkages can’t hydrolyze beta linkages in cellulose • Cellulose in human food passes through the digestive tract as insoluble fiber • Some microbes use enzymes to digest cellulose • Many herbivores, from cows to termites, have symbiotic relationships with these microbes Cellulose microfibrils in a plant cell wall Cell walls Microfibril 0.5 µm Plant cells Cellulose molecules Glucose monomer Lipids • Lipids are the one class of large biological molecules that do not form polymers • Utilized for energy storage, membranes, insulation, protection • Greasy or oily substances • The unifying feature of lipids is having little or no affinity for water - insoluble in water • Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds Fats • The most biologically important lipids are fats, phospholipids, and steroids • Fats are constructed from two types of smaller molecules: glycerol and fatty acids • Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon • A fatty acid consists of a carboxyl group attached to a long carbon skeleton Fatty acid (palmitic acid) Glycerol Dehydration reaction in the synthesis of a fat Fatty Acids • A fatty acid has a long hydrocarbon chain with a carboxyl group at one end. • Fatty acids vary in length (number of carbons) and in the number and locations of double bonds • Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds • Unsaturated fatty acids have one or more double bonds, – Monounsaturated (one double bond) – Polyunsaturated (more than one double bond) • H can be added to unsaturated fatty acids using a process called hydrogenation • The major function of fats is energy storage Stearate Oleate Fats • Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats • In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride Glycerides • Glycerol + 1 fatty acid = monoglyceride • Glycerol + 2 fatty acids = diglyceride • Glycerol + 3 fatty acids = triglyceride (also called triacylglycerol or “fat”.) Ester linkage Fat molecule (triacylglycerol) Saturated Fats • Fats made from saturated fatty acids are called saturated fats • Most animal fats are saturated • Saturated fats are solid at room temperature • A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits Stearic acid Saturated fat and fatty acid. Unsaturated Fats • Fats made from unsaturated fatty acids are called unsaturated fats • Plant fats and fish fats are usually unsaturated • Plant fats and fish fats are liquid at room temperature and are called oils Oleic acid Unsaturated fat and fatty acid. cis double bond causes bending Fat Sources • Most animal fats contain saturated fatty acids and tend to be solid at room temperature • Most plant fats contain unsaturated fatty acids. They tend to be liquid at room temperature, and are called oils. Phospholipids • In phospholipids, two of the –OH groups on glycerol are joined to fatty acids. The third –OH joins to a phosphate group which joins, in turn, to another polar group of atoms. • The phosphate and polar groups are hydrophilic (polar head) while the hydrocarbon chains of the 2 fatty acids are hydrophobic (nonpolar tails). Choline Phosphate Glycerol Fatty acids Hydrophilic head Hydrophobic tails Structural formula Space-filling model Phospholipid symbol Phospholipids Phospholipids • When phospholipids are added to water, they orient so that the nonpolar tails are shielded from contact with the polar H2O may form micelles • Phosopholipids also may self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior • The structure of phospholipids results in a bilayer arrangement found in cell membranes Water Lipid head (hydrophilic) Lipid tail (hydrophobic) Micelle Water Phospholipid bilayer Water Steroids • Steroids are lipids characterized by a carbon skeleton consisting of four fused rings • Cholesterol, an important steroid, is a component in animal cell membranes • Testosterone and estrogen function as sex hormones Proteins • Proteins have many structures, resulting in a wide range of functions • They account for more than 50% of the dry mass of most cells • Protein functions – – – – – Structural support / storage / movement - fibers Catalysis - Enzymes Defense against foreign substances– Immunoglobulins Transport – globins, membrane transporters Messengers for cellular communications - hormones Proteins • A protein is composed of one or more polypeptides that performs a function • A polypeptide is a polymer of amino acids joined by peptide bonds to form a long chain • Polypeptides range in length from a few monomers to more than a thousand • Each polypeptide has a unique linear sequence of amino acids • A protein consists of one or more polypeptides which are coiled and folded into a specific 3-D shape. • The shape of a protein determines its function. Amino Acids • Amino acids are monomers of polypetides • They composed of a carboxyl group, amino group, and an “R”Group • Amino acids differ in their properties due to differing side chains, called R groups • Cells use 20 amino acids to make thousands of proteins carbon Amino group Carboxyl group Amino Acids CH3 CH3 H H3N+ C CH3 O H3N+ C O– H Glycine (Gly) C H H3N+ C CH CH3 CH3 O C H3N+ C C O– Alanine (Ala) CH2 CH2 O O– CH3 CH3 O H3C H3N+ C H Valine (Val) Leucine (Leu) C O C O– O– H CH H Isoleucine (Ile) Nonpolar CH3 CH2 S NH CH2 CH2 H3N+ C H3N+ C O– H Methionine (Met) Figure 5.17 CH2 O C CH2 O H3 N+ C C O– H Phenylalanine (Phe) O H2C CH2 H2N C O C O– H C O– H Tryptophan (Trp) Proline (Pro) Amino Acids OH NH2 O C NH2 O OH Polar CH2 H3N+ C CH O H3N+ C O– H Serine (Ser) C C SH CH3 OH CH2 O H3N+ C O– H C CH2 O C H O– H3N+ CH2 O H3N+ C C Electrically charged CH2 H3N+ C O O– H H3N+ NH3+ O C O C O– H C CH2 CH2 CH2 CH2 CH2 C O CH2 C O– H3N+ C H NH2+ C H3N+ H3N+ C Lysine (Lys) C H CH2 O– NH CH2 CH2 O H Glutamic acid (Glu) NH+ NH2 CH2 H Aspartic acid (Asp) O– H C CH2 C H3N+ C Basic O– O CH2 O Asparagine Glutamine (Gln) (Asn) Tyrosine (Tyr) Acidic –O C O– H Cysteine (Cys) Threonine (Thr) C CH2 O C O– O C O– Arginine (Arg) Histidine (His) Amino Acids and Peptide Bonds • Two amino acids can join by condensation to form a dipeptide plus H2O. • The bond between 2 amino acids is called a peptide bond. Protein Conformation and Function • A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape • The sequence of amino acids determines a protein’s threedimensional conformation • A protein’s conformation determines its function • Ribbon models and spacefilling models can depict a protein’s conformation Groove A ribbon model Groove A space-filling model Four Levels of Protein Structure • The primary structure of a protein is its unique sequence of amino acids • Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain • Tertiary structure is determined by interactions among various side chains (R groups) • Quaternary structure results when a protein consists of multiple polypeptide chains pleated sheet Amino acid subunits helix Levels of Protein Structure Interactions that Contribute to a Protein’s Shape 42 43 Enzymes as Catalysts • To increase reaction rates: – Add Energy (Heat) - molecules move faster so they collide more frequently and with greater force. – Add a catalyst – a catalyst reduces the energy needed to reach the activation state, without being changed itself. Proteins that function as catalysts are called enzymes. Energy released Energy supplied Activation Energy and Catalysis Activation energy Activation energy Reactant Reactant Product Uncatalyzed Product Catalyzed Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Enzymes Are Biological Catalysts • Enzymes are proteins that carry out most catalysis in living organisms. • Unlike heat, enzymes are highly specific. Each enzyme typically speeds up only one or a few chemical reactions. • Unique three-dimensional shape enables an enzyme to stabilize a temporary association between substrates. • Because the enzyme itself is not changed or consumed in the reaction, only a small amount is needed, and can then be reused. • Therefore, by controlling which enzymes are made, a cell can control which reactions take place in the cell. Substrate Specificity of Enzymes • • • • • • Almost all enzymes are globular proteins with one or more active sites on their surface. The substrate is the reactant an enzyme acts on Reactants bind to the active site to form an enzyme-substrate complex. The 3-D shape of the active site and the substrates must match, like a lock and key Binding of the substrates causes the enzyme to adjust its shape slightly, leading to a better induced fit. When this happens, the substrates are brought close together and existing bonds are stressed. This reduces the amount of energy needed to reach the transition state. Substate Active site Enzyme Enzyme- substrate complex The Catalytic Cycle Of An Enzyme 1 The substrate, sucrose, consists of glucose and fructose bonded together. Glucose Fructose 2 The substrate binds to the enzyme, forming an enzyme-substrate complex. Bond H2O Active site Enzyme 3 The binding of the substrate and enzyme places stress on the glucose-fructose bond, and the bond breaks. 4 Products are released, and the enzyme is free to bind other substrates. Conformational Change and Enzyme Activity • In addition to primary structure, physical and chemical conditions can affect conformation • Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel • This loss of a protein’s native conformation is called denaturation • A denatured protein is biologically inactive Denaturation Normal protein Denatured protein Renaturation Effects of Temperature and pH • Each enzyme has an optimal temperature in which it can function Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic Rate of reaction (heat-tolerant) bacteria 0 20 40 Temperature (Cº) (a) Optimal temperature for two enzymes 80 100 Effects of Temperature and pH – Each enzyme has an optimal pH in which it can function Optimal pH for pepsin (stomach enzyme) Rate of reaction Optimal pH for trypsin (intestinal enzyme) 3 4 0 2 1 (b) Optimal pH for two enzymes Figure 8.18 5 6 7 8 9 Nucleic Acids • Nucleic acids store and transmit hereditary information • The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene • Genes are made of DNA, a nucleic acid The Roles of Nucleic Acids • There are two types of nucleic acids: – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) • DNA provides directions for its own replication • DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis • Protein synthesis occurs in ribosomes DNA Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA Movement of mRNA into cytoplasm via nuclear pore Ribosome Synthesis of protein Polypeptide Amino acids The Structure of Nucleic Acids • Nucleic acids are polymers called polynucleotides • Each polynucleotide is made of monomers called nucleotides • Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group • The portion of a nucleotide without the phosphate group is called a nucleoside 5 end Nucleoside Nitrogenous base Phosphate group Nucleotide 3 end Pentose sugar Nucleotide Monomers • Nucleotide monomers are made up of nucleosides and phosphate groups • Nucleoside = nitrogenous base + sugar • There are two families of nitrogenous bases: – Pyrimidines have a single sixmembered ring – Purines have a six-membered ring fused to a five-membered ring • In DNA, the sugar is deoxyribose • In RNA, the sugar is ribose Nitrogenous bases Pyrimidines Cytosine C Thymine (in DNA) Uracil (in RNA) U T Purines Adenine A Guanine G Pentose sugars Deoxyribose (in DNA) Nucleoside components Ribose (in RNA) Nucleotide Polymers • Nucleotide polymers are linked together, building a polynucleotide • Adjacent nucleotides are joined by covalent bonds that form between the –OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next • These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages • The sequence of bases along a DNA or mRNA polymer is unique for each gene The DNA Double Helix • A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix • In the DNA double helix, the two backbones run in opposite 5´ to 3´ directions from each other, an arrangement referred to as antiparallel • One DNA molecule includes many genes • The nitrogenous bases in DNA form hydrogen bonds in a complementary fashion: A always with T, and G always with C 5 end 3 end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand 5 end New strands 5 end 3 end 5 end 3 end ATP • Adenosine triphosphate (ATP), is the primary energytransferring molecule in the cell • ATP is the “energy currency” of the cell • ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups • The energy stored in the bond that connects the third phosphate to the rest of the molecule supplies the energy needed for most cell activities