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Chapter 5 The Structure and Function of Large Biological Molecules What do you know about… • Carbohydrates? • Lipids? • Proteins? • Nucleic Acids? Concept 5.2: Carbohydrates serve as fuel and building material • Carbohydrates include sugars and the polymers of sugars • The simplest carbohydrates are monosaccharides, or single sugars • Carbohydrate macromolecules are polysaccharides, polymers composed of many repeating single sugars (monomers) Trioses (C3H6O3) Pentoses (C5H10O5) Hexoses (C6H12O6) Glyceraldehyde Ribose Glucose Galactose Dihydroxyacetone Ribulose Fructose Sugars • Monosaccharides – empiracle formula (simplest form) = • Monosaccharides are classified by – The location of the carbonyl group (as aldose or ketose) – The number of carbons in the carbon skeleton • Though often drawn as linear skeletons, in aqueous solutions many sugars form rings • Monosaccharides serve as a major fuel for cells and as raw material for building molecules (a) Linear and ring forms (b) Abbreviated ring structure • Monosaccharides join to form disaccharides and polysaccharides – RXN = – Requires enzymes – glycosidic linkage 1–4 glycosidic linkage Glucose Glucose (a) Dehydration reaction in the synthesis of maltose Maltose Polysaccharides can be broken down, or digested in the opposite reaction… • Digestion – use H2O to breakdown polymers • reverse of dehydration synthesis • cleave off one monomer at a time • H2O is split into H+ and OH– HO – H+ & OH– attach to ends HO – requires enzymes – releases energy H2O enzyme H H HO H Polysaccharides Polymers of sugars costs little energy to build easily reversible = release energy differ in position of glycosidic linkages Function: energy storage starch (plants) glycogen (animals) in liver & muscles structure cellulose (plants) chitin (arthropods & fungi) Why does the structure matter? How does it work? slow release starch (plant) fast release glycogen (animal Structural Polysaccharides • The polysaccharide 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 Glucose (b) Starch: 1–4 linkage of glucose monomers Glucose (b) Cellulose: 1–4 linkage of glucose monomers The key – different enzymes do the job! Specific to the alpha & beta linkage forms • Cellulose – undigestable roughage Most abundant organic compound on Earth herbivores have evolved a mechanism to digest cellulose most carnivores have not what do they eat? How is this related to corn fuels?? How can herbivores digest cellulose so well? BACTERIA live in their digestive systems & help digest cellulose-rich (grass) meals Caprophage Concept 5.3: Lipids are a diverse group of hydrophobic molecules • Lipids are the one class of large biological molecules that do not form polymers • The unifying feature of lipids is having little or no affinity for water – Hydro …? • The most biologically important lipids are fats, phospholipids, and steroids Fats - Fats are constructed from two types of smaller molecules: glycerol and fatty acids - Glycerol - Fatty acids Fatty acid (palmitic acid) Glycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage (b) Fat molecule (triacylglycerol) • Fatty acids vary in length and number and locations of double bonds • Saturated fats vs. Unsaturated fats Properties of saturated vs. unsaturated fats? Fats can be hydrogenated to make them saturated • A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits atheriosclerosis Adding hydrogens • Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds • These trans fats may contribute more than saturated fats to cardiovascular disease Why fat? • Energy • Storage – plants and animals • Adipose tissue also cushions vital organs and insulates the body No fat? • two fatty acids and a phosphate group are attached to glycerol Hydrophobic tails • Component of cell membrane Hydrophilic head Phospholipids Choline Phosphate Glycerol Hydrophilic head Fatty acids Hydrophobic tails • When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior 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 Proteins have many structures, resulting in a wide range of functions • Proteins account for more than 50% of the dry mass of most cells • Protein functions include: – structural support, storage, transport, cellular communications, movement, and defense against foreign substances Polypeptides = proteins • Amino acids are the monomers Amino group Carboxyl group Amino Acid Polymers Peptide bond • Polypeptides range in length from a few to more than a thousand monomers (a) • Each polypeptide has a unique linear sequence of amino acids Side chains Peptide bond Backbone (b) Amino end (N-terminus) Carboxyl end (C-terminus) Fig. 5-17 Nonpolar Glycine (Gly or G) Structure = function Valine (Val or V) Alanine (Ala or A) Methionine (Met or M) Leucine (Leu or L) Trypotphan (Trp or W) Phenylalanine (Phe or F) Isoleucine (Ile or I) Proline (Pro or P) Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine Glutamine (Asn or N) (Gln or Q) Electrically charged Acidic Aspartic acid Glutamic acid (Glu or E) (Asp or D) Basic Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Protein Structure 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 three-dimensional structure • A protein’s structure determines its function • Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word Primary Structure 1 5 +H 3N Amino end 10 Amino acid subunits 15 • Primary structure is determined by inherited genetic information of DNA 20 25 Protein Folding in the Cell • It is hard to predict a protein’s structure from its primary structure • Chaperonins are protein molecules that assist the proper folding of other proteins Polypeptide Correctly folded protein Cap Hollow cylinder Chaperonin (fully assembled) Steps of Chaperonin 2 Action: 1 An unfolded polypeptide enters the cylinder from one end. The cap attaches, causing the 3 The cap comes cylinder to change shape in off, and the properly such a way that it creates a folded protein is hydrophilic environment for released. the folding of the polypeptide. • The coils and folds of secondary structure result from hydrogen bonds between the polypeptide backbone • Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet pleated sheet Examples of amino acid subunits helix Secondary Structure • Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents • These interactions include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions • Strong covalent bonds called disulfide bridges may reinforce the protein’s structure Hydrophobic interactions & van der Waals interactions Hydrogen bond Disulfide bridge Ionic bond Polypeptide backbone • Quaternary structure results when two or more polypeptide chains form one macromolecule Polypeptide chain Chains • Collagen is a fibrous protein consisting of three polypeptides coiled like a rope • Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains Iron Heme Chains Hemoglobin Collagen Denaturation • Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel – lose its PRIMARY structure • A denatured protein is biologically inactive • Enzymes act as a catalyst to speed up chemical reactions • Enzymes can perform their functions repeatedly Substrate (sucrose) Glucose OH Fructose HO Enzyme (sucrase) H2O Concept 5.5: Nucleic acids store and transmit hereditary information • The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene • DNA codes for RNA, which makes proteins 5' end 5'C Nucleotide = nucleoside + PO4 3'C Nucleoside Nitrogenous base 5'C Phosphate group 5'C 3'C (b) Nucleotide 3' end (a) Polynucleotide, or nucleic acid 3'C Sugar (pentose) Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Adenine (A) Guanine (G) (c) Nucleoside components: nitrogenous bases 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 → 3 directions from each other, an arrangement referred to as antiparallel • One DNA molecule includes many genes • The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Joining nucleotides Covalent phosphodiestser bonds form between the sugar-phosphate units (-OH of 3’ carbon and PO4 of 5’) Weak hydrogen bonds form between the Nitrogenous bases Fig. 5-28 5' end 3' end Sugar-phosphate backbones Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand 3' end 5' end New strands 5' end 3' end 5' end 3' end DNA and Proteins as Tape Measures of Evolution • The linear sequences of nucleotides in DNA molecules are passed from parents to offspring • Two closely related species are more similar in DNA than are more distantly related species • Molecular biology can be used to assess evolutionary kinship