Chapter 5 The Structure and Function of Large

Chapter 5: The Structure and Function of Large Biological Molecules

Overview: The Molecules of Life All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids Macromolecules are large molecules composed of thousands of covalently connected atoms Structure and function are related!!!! Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Concept 5. 1: Macromolecules are polymers, built from monomers A polymer is a long molecule consisting of many similar building blocks These small building-block molecules are called monomers Three of the four classes of life’s organic molecules are polymers: ◦ Carbohydrates ◦ Proteins ◦ Nucleic acids Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 5 -2 HO 1 2 3 H HO H Short polymer Unlinked monomer Condensation/ Dehydration removes a water dehydration molecule, forming a new bond H 2 O reaction=two monomers bond together HO 2 H 4 1 3 through the loss of a water Longer polymer molecule (a) Dehydration reaction in the synthesis of a polymer Hydrolysis= addition of water to separate a polymer HO H 3 4 2 1 (reverse of Enzymes= dehydration proteins that reaction) speed up the Hydrolysis adds a water H 2 O molecule, breaking a bond reaction without being consumed in the reaction HO 1 2 3 (b) Hydrolysis of a polymer H HO H

Concept 5. 2: Carbohydrates serve as fuel and building material Carbohydrates include sugars and the polymers of sugars ◦ Ratios: 1 carbon: 2 hydrogen: 1 oxygen Monosaccharides=single sugars (glucose (C 6 H 12 O 6) , fructose, galactose) Polysaccharides=polymers composed of many single (monomer) sugar building blocks (starch, glycogen, cellulose) ◦ Have storage and structural roles Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 5 -3 Aldoses Trioses (C 3 H 6 O 3) Pentoses (C 5 H 10 O 5) Hexoses (C 6 H 12 O 6) Glyceraldehyde Ribose Ketoses Glucose Galactose Dihydroxyacetone Ribulose Fructose

Fig. 5 -4 (a) Linear and ring forms (b) Abbreviated ring structure Figure 5. 4 Linear and ring forms of glucose

Fig. 5 -5 A disaccharide is formed when a dehydration reaction joins two monosaccharides. This bond is called a glycosidic linkage 1– 4 glycosidic linkage Glucose Maltose (a) Dehydration reaction in the synthesis of maltose 1– 2 glycosidic linkage Glucose Fructose (b) Dehydration reaction in the synthesis of sucrose Sucrose

Fig. 5 -6 Energy storage polysaccharides of plants and animals Chloroplast Mitochondria Glycogen granules Starch 0. 5 µm 1 µm Glycogen Amylose Amylopectin (a) Starch: a plant polysaccharide made of glucose monomers- stored In chloroplasts and plastids (b) Glycogen: an animal polysaccharide. Stored in the liver and muscle cells in humans

Fig. 5 -7 The polysaccharide cellulose is a major component of the tough wall of plant cells (a) �and �glucose ring structures �Glucose (b) Starch: 1– 4 linkage of �glucose monomers �Glucose (b) Cellulose: 1– 4 linkage of �glucose monomers 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 ( )

Fig. 5 -8 Cell walls Cellulose microfibrils in a plant cell wall Microfibril 10 µm 0. 5 µm Cellulose molecules b Glucose monomer

Enzymes that digest starch by hydrolyzing linkages can’t hydrolyze linkages in cellulose Cellulose in human food passes through the digestive tract as insoluble fiber Some microbes use enzymes to digest cellulose. Herbivores, from cows to termites, have symbiotic relationships with these microbes Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 5 -10 • Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods and cell walls of fungi (a) The structure of the chitin monomer. (b) Chitin forms the exoskeleton of arthropods. (c) Chitin is used to make a strong and flexible surgical thread.

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 Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds The most biologically important lipids are fats, phospholipids, and steroids Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fats are constructed from two types of smaller molecules: 1 glycerol and 3 fatty acids (triacylglycerol or triglyceride) ◦ Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats A fatty acid consists of a carboxyl group attached to a long hydrocarbon chain. These are nonpolar and hydrophobic Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 5 -11 Fatty acid (palmitic acid) Glycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage (b) Fat molecule (triacylglycerol)

Fig. 5 -12 Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds. Animal fats/solid at room temperature Structural formula of a saturated fat molecule Unsaturated fatty acids have one or more double bonds. Plant/fish fats/liquid at room temperature Structural formula of an unsaturated fat molecule Stearic acid, a saturated fatty acid (a) Saturated fat Oleic acid, an unsaturated fatty acid (b) Unsaturated fat cis double bond causes bending

A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds These trans fats may contribute more than saturated fats to cardiovascular disease Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

The major function of fats is energy ◦ Store 2 x’s as many calories/gram as carbohydrates storage Fats also function in protection of vital organs and insulation ◦ Humans and other mammals store their fat in adipose cells Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Hydrophobic tails Hydrophilic head Fig. 5 -13 (a) Structural formula Choline Phosphate Glycerol In a phospholipid, two fatty acids and a phosphate group are attached to glycerol The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head Fatty acids Hydrophilic head Hydrophobic tails (b) Space-filling model (c) Phospholipid symbol

Fig. 5 -14 Figure 5. 14 Bilayer structure formed by self-assembly of phospholipids in an aqueous environment Hydrophilic head Hydrophobic tail WATER Phospholipids are the major component of all cell membranes

Steroids are lipids characterized by a carbon skeleton consisting of four fused rings Cholesterol, an important steroid, is a component in animal cell membranes Estrogen and testosterone are steroid hormones Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Table 5 -1 Concept 5. 4: Proteins have many structures, resulting in a wide range of functions Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances

Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 5 -16 Figure 5. 16 The catalytic cycle of an enzyme Glucose OH Fructose HO Enzyme (sucrase) Substrate (sucrose) H 2 O

Fig. 5 -UN 1 �carbon Amino group Carboxyl group Amino acids are organic molecules with carboxyl and amino groups. Amino acids differ in their properties due to differing R groups

Fig. 5 -17 Nonpolar Glycine (Gly or G) 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)

Fig. 5 -18 Amino acids are linked by peptide bonds A polypeptide is a polymer of amino acids Peptide bond (a) Side chains Peptide bond Backbone (b) Amino end (N-terminus) Carboxyl end (C-terminus)

Fig. 5 -19 A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape Groove (a) A ribbon model of lysozyme (b) A space-filling model of lysozyme

The sequence of amino acids determines a protein’s three-dimensional structure A protein’s structure determines its function Antibody protein Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings Protein from flu virus

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 Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 5 -21 Primary Structure Secondary Structure �pleated sheet +H N 3 Amino end Examples of amino acid subunits �helix Tertiary Structure Quaternary Structure

Fig. 5 -21 a Primary Structure 1 +H 5 3 N Amino end 10 Amino acid subunits 15 Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word Primary structure is determined by inherited genetic information 20 25

Fig. 5 -21 c Secondary Structure �pleated sheet Examples of amino acid subunits �alpha helix The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone (amino & COOH groups) Typical secondary structures are: helix and pleated sheet

Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions Strong covalent bonds called disulfide bridges may reinforce the protein’s structure Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 5 -21 e Tertiary Structure Tertiary structure is determined by interactions between R groups. , (including: hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions). Strong covalent bonds called disulfide bridges may reinforce the protein’s structure Quaternary Structure Quaternary structure -two or more polypeptide chains form one macromolecule Examples: Collagen has three polypeptides coiled like a rope Hemoglobin has four polypeptides

Fig. 5 -21 f Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Ionic bond Figure 5. 21 Levels of protein structure—tertiary and quaternary structures

Fig. 5 -21 g Polypeptide chain �Chains Iron Heme �Chains Hemoglobin Collagen Figure 5. 21 Levels of protein structure— tertiary and quaternary structures

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Sickle-Cell Disease: A Change in Primary Structure A slight change in primary structure can affect a protein’s structure and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 5 -22 Normal hemoglobin Primary structure 1 2 3 4 5 6 7 Secondary and tertiary structures �subunit Normal hemoglobin (top view) Val His Leu Thr Pro Val Glu 1 2 3 Normal red blood cells are full of individual hemoglobin moledules, each carrying oxygen. 6 7 �subunit � Sickle-cell hemoglobin � Function � Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced. 10 µm Red blood cell shape 5 Exposed hydrophobic region � Molecules do not associate with one another; each carries oxygen. 4 � Quaternary structure � Function Secondary and tertiary structures Sickle-cell hemoglobin � � Quaternary structure Primary structure Val His Leu Thr Pro Glu 10 µm Red blood cell shape Fibers of abnormal hemoglobin deform red blood cell into sickle shape.

Fig. 5 -23 A denatured protein is biologically inactive Denaturation Normal protein Renaturation Denatured protein The loss of a protein’s native structure is called denaturation Alterations in p. H, salt concentration, temperature, or other environmental factors can cause a protein to unravel

Fig. 5 -24 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.

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 Genes are made of DNA, a nucleic acid Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

The Roles of Nucleic Acids There are two types of nucleic ◦ Deoxyribonucleic acid (DNA) ◦ Ribonucleic acid (RNA) Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings acids:

The Structure of Nucleic Acids Nucleic acids are polymers Polymer= polynucleotides Monomer= nucleotides Each nucleotide consists of: 1. nitrogenous base 2. pentose sugar 3. phosphate group Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

Fig. 5 -27 In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose 5�end Nitrogenous bases Pyrimidines 5� C 3� C Nucleoside Nitrogenous base Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Phosphate group 5� C Sugar (pentose) (b) Nucleotide 3� C Adenine (A) Guanine (G) Sugars 3�end (a) Polynucleotide, or nucleic acid Pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring Purines (adenine and guanine) have a six-membered ring fused to a fivemembered ring Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components: sugars

Nucleotide Polymers 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 sugarphosphate units with nitrogenous bases as appendages Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

The DNA and RNA A DNA molecule has two polynucleotides spiraling around an imaginary axis, forming a double helix 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) RNA is single-stranded ◦ The nitrogenous bases in RNA pair up and form hydrogen bonds: adenine (A) always with uracil (U), and guanine (G) always with cytosine (C) Copyright © 2008 Pearson Education, Inc. , publishing as Pearson Benjamin Cummings

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

Fig. 5 -UN 2