The Structure and Function of Macromolecules Chapter 5 The Structure and Function of Macromolecules

Figure 5.1 Scientists working with computer models of proteins

Figure 5.2 The synthesis and breakdown of polymers (a) Dehydration reaction in the synthesis of a polymer (b) Hydrolysis of a polymer HO H 1 2 3 4 H2O Short polymer Unlinked monomer Longer polymer Hydrolysis adds a water molecule, breaking a bond Dehydration removes a water molecule, forming a new bond

Figure 5.3 The structure and classification of some monosaccharides Triose sugars (C3H6O3) Pentose sugars (C5H10O5) Hexose sugars (C6H12O6) H C OH H C OH HO C H H C OH C O HO C H H C O Aldoses Ketoses Glyceraldehyde Ribose Glucose Galactose Dihydroxyacetone Ribulose Fructose

Figure 5.4 Linear and ring forms of glucose H H C OH HO C H H C O C 1 2 3 4 5 6 OH 4 C 6 CH2OH 5 C H OH 2 C 1C 3 C 2C 1 C CH2OH HO 3 2 (a) Linear and ring forms. Chemical equilibrium between the linear and ring structures greatly favors the formation of rings. To form the glucose ring, carbon 1 bonds to the oxygen attached to carbon 5. (b) Abbreviated ring structure. Each corner represents a carbon. The ring’s thicker edge indicates that you are looking at the ring edge-on; the components attached to the ring lie above or below the plane of the ring.

Figure 5.5 Examples of disaccharide synthesis Dehydration reaction in the synthesis of maltose. The bonding of two glucose units forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. Dehydration reaction in the synthesis of sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. (a) (b) H HO H OH OH O CH2OH H2O 1 2 4 1– 4 glycosidic linkage 1–2 glycosidic linkage Glucose Fructose Maltose Sucrose

Figure 5.6 Storage polysaccharides of plants and animals Chloroplast Starch Amylose Amylopectin 1 m 0.5 m (a) Starch: a plant polysaccharide (b) Glycogen: an animal polysaccharide Glycogen Mitochondria Giycogen granules

Figure 5.7 Starch and cellulose structures (c) Cellulose: 1– 4 linkage of  glucose monomers H O CH2OH OH HO 4 C 1 (a)  and  glucose ring structures (b) Starch: 1– 4 linkage of  glucose monomers  glucose  glucose

Figure 5.8 The arrangement of cellulose in plant cell walls Plant cells 0.5 m Cell walls Cellulose microfibrils in a plant cell wall  Microfibril CH2OH OH O Glucose monomer Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. A cellulose molecule is an unbranched  glucose polymer. Cellulose molecules

Figure 5.9 Cellulose-digesting bacteria are found in grazing animals such as this cow

Figure 5.10 Chitin, a structural polysaccharide (a) The structure of the chitin monomer. O CH2OH OH H NH C CH3 (b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.

Figure 5.11 The synthesis and structure of a fat, or triacylglycerol (b) Fat molecule (triacylglycerol) H O H C OH Glycerol Fatty acid (palmitic acid) HO O (a) Dehydration reaction in the synthesis of a fat Ester linkage

Figure 5.12 Examples of saturated and unsaturated fats and fatty acids (a) Saturated fat and fatty acid Stearic acid (b) Unsaturated fat and fatty acid cis double bond causes bending Oleic acid

Figure 5.13 The structure of a phospholipid Hydrophilic head CH2 N(CH3)3 O P CH C Choline Phosphate Glycerol (a) Structural formula (b) Space-filling model Fatty acids (c) Phospholipid symbol Hydrophobic tails Hydrophilic head Hydrophobic tails + –

Figure 5.14 Bilayer structure formed by self-assembly of phospholipids in an aqueous environment Hydrophilic head WATER Hydrophobic tail

Figure 5.15 Cholesterol, a steroid H3C

Table 5.1 An Overview of Protein Functions

Unnumbered Figure p. 78 H N C R O OH Amino group Carboxyl  carbon

Figure 5.16 The catalytic cycle of an enzyme Substrate (sucrose) Enzyme (sucrase) Glucose OH H O H2O Fructose 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. 2 Substrate binds to enzyme. 4 Products are released. 3 Substrate is converted to products.

Figure 5.17 The 20 amino acids of proteins H3N+ C CH3 CH CH2 NH H2C H2N Nonpolar Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro) H3C O O–

Polar Electrically charged OH CH2 C H H3N+ O CH3 CH SH NH2 Polar Electrically charged –O NH3+ NH2+ NH+ NH Serine (Ser) Threonine (Thr) Cysteine (Cys) Tyrosine (Tyr) Asparagine (Asn) Glutamine (Gln) Acidic Basic Aspartic acid (Asp) Glutamic acid (Glu) Lysine (Lys) Arginine (Arg) Histidine (His)

Figure 5.18 Making a polypeptide chain DESMOSOMES OH CH2 C N H O Peptide bond SH Side chains H2O Amino end (N-terminus) Backbone (a) Carboxyl end (C-terminus) (b)

Figure 5.19 Conformation of a protein, the enzyme lysozyme Groove (a) A ribbon model Groove (b) A space-filling model

Unnumbered Figure page 82 Spider silk: a structural protein containing  pleated sheets Abdominal glands of the spider secrete silk fibers that form the web The radiating strands, made of dry silk fibers maintained the shape of the web The spiral strands (capture strands) are elastic, stretching in response to wind, rain, and the touch of insects

Figure 5.20 Levels of protein structure H O R Gly Thr Glu Seu Lya Cya Pro Leu Met Val Asp Ala Arg Ser Amino acid subunits pleated sheet a helix +H3N Amino end 1 5 10 15 20 25

Figure 5.20 Exploring Levels of Protein Structure: Primary structure – Amino acid subunits +H3N Amino end o Carboxyl end c Gly Pro Thr Glu Seu Lys Cys Leu Met Val Asp Ala Arg Ser lle Phe His Asn Tyr Trp Lle

Figure 5.20 Exploring Levels of Protein Structure: Secondary structure  pleated sheet O C  helix O H C O H C R C O H C R C O H C R H N H H N H Amino acid subunits H R C R C H R C H C C N N N N H C O N H N H C C C O C O R C H O H R C R C H R C H R C H C O C O C O C O N H N H N H N H N H H C R H C R H C R C O N H C O N H C O N H C O C C R H R C H C N H O C N H O C N H N H O C H C R H C H C R H C R R N H O C N H O C O C N H O C N H C C R H R H

Figure 5.20 Exploring Levels of Protein Structure: Tertiary structure CH2 O H O C OH NH3+ -O S CH CH3 H3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Ionic bond Disulfide bridge

Figure 5.20 Exploring Levels of Protein Structure: Quaternary Structure Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme

Sickle-cell hemoglobin Figure 5.21 A single amino acid substitution in a protein causes sickle-cell disease Primary structure Secondary and tertiary structures Quaternary structure Function Red blood cell shape Hemoglobin A Molecules do not associate with one another; each carries oxygen Normal cells are full of individual hemoglobin molecules, each carrying oxygen   10 m Hemoglobin S Molecules interact with one another to crystallize into a fiber, capacity to carry oxygen is greatly reduced Fibers of abnormal hemoglobin deform cell into sickle shape  subunit 1 2 3 4 5 6 7 Normal hemoglobin Sickle-cell hemoglobin . . . Val His Leu Thr Pro Glu Glu Val His Leu Thr Pro Val Glu Exposed hydrophobic region

Figure 5.22 Denaturation and renaturation of a protein Normal protein Denatured protein Renaturation

Figure 5.23 A chaperonin in action Hollow cylinder Cap Chaperonin (fully assembled) Steps of Chaperonin Action: An unfolded poly- peptide enters the cylinder from one end. The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. Correctly folded protein Polypeptide 2 1 3

Figure 5.24 Research Method x-ray crystallography X-ray diffraction pattern Photographic film Diffracted X-rays X-ray source X-ray beam Crystal Nucleic acid Protein (a) X-ray diffraction pattern (b) 3D computer model

Synthesis of mRNA in the nucleus Figure 5.25 DNA  RNA  protein: a diagrammatic overview of information flow in a cell 1 2 3 Synthesis of mRNA in the nucleus Movement of mRNA into cytoplasm via nuclear pore Synthesis of protein NUCLEUS CYTOPLASM DNA mRNA Ribosome Amino acids Polypeptide

Figure 5.26 The components of nucleic acids CH Uracil (in RNA) U 5’ end 5’C O 3’ end OH Nitrogenous base Nucleoside O O P CH2 Phosphate group Pentose sugar (b) Nucleotide C N H NH2 HN CH3 Cytosine Thymine (in DNA) T HC NH Adenine A Guanine G Purines HOCH2 5’ 4 3’ 2’ 1’ 3’ 2’ Pentose sugars Deoxyribose (in DNA) Ribose (in RNA) Nitrogenous bases Pyrimidines (c) Nucleoside components (a) Polynucleotide, or nucleic acid

Figure 5.27 The DNA double helix and its replication 3¢ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand A 5¢ end New strands C G T