Chapter 5 Macromolecules

The Molecules of Life Another level in the hierarchy of biological organization is reached when small organic molecules are joined together

Macromolecules Large molecules composed of smaller molecules Complex structure Figure 5.1

Most macromolecules are polymers, built from monomers 3 classes are polymers Carbohydrates Proteins Nucleic acids

Polymer Lg. molecule consisting of many similar building blocks (monomers)

The Synthesis and Breakdown of Polymers Condensation reactions (dehydration reactions) (a) Dehydration reaction in the synthesis of a polymer HO H 1 2 3 4 H2O Short polymer Unlinked monomer Longer polymer Dehydration removes a water molecule, forming a new bond Figure 5.2A

(b) Hydrolysis of a polymer HO 1 2 3 H 4 H2O Hydrolysis adds a water molecule, breaking a bond Figure 5.2B

Carbohydrates: fuel and building material Sugars and their polymers

Sugars Monosaccharides Simplest sugars Fuel Converted into other organic molecules Combined into polymers

Examples of 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 Glyceraldehyde Ribose Glucose Galactose Dihydroxyacetone Ribulose Ketoses Fructose Figure 5.3

Monosaccharides Linear, or Rings 4C 3 2 OH Figure 5.4 H C OH HO C H H C O C 1 2 3 4 5 6 OH 4C 6CH2OH 5C 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. Figure 5.4

Disaccharides 2 monosaccharides Joined by a glycosidic linkage

Examples of disaccharides 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 5.5

Polysaccharides Polymers of sugars

Storage Polysaccharides Starch - glucose monomers Major storage form of glucose in plants Chloroplast Starch Amylose Amylopectin 1 m (a) Starch: a plant polysaccharide Figure 5.6

(b) Glycogen: an animal polysaccharide Glucose monomers Storage form of glucose in animals Mitochondria Giycogen granules 0.5 m (b) Glycogen: an animal polysaccharide Glycogen Figure 5.6

Structural Polysaccharides Cellulose - Polymer of glucose Different glycosidic linkages than starch (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 5.7 A–C

Major component of the 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 5.8

Cellulose, difficult to digest Microbes in cow stomach Figure 5.9

Chitin Exoskeleton of arthropods Surgical thread (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 5.10 A–C

Lipids Hydrophobic Not polymers

(a) Dehydration reaction in the synthesis of a fat Fats Single glycerol and three fatty acids H O H H H H H H H H H H H H H H H H O H C OH Glycerol Fatty acid (palmitic acid) HO O (a) Dehydration reaction in the synthesis of a fat Ester linkage Figure 5.11 (b) Fat molecule (triacylglycerol)

(a) Saturated fat and fatty acid Saturated fatty acids Max # of hydrogen atoms possible No double bonds (a) Saturated fat and fatty acid Stearic acid Figure 5.12

(b) Unsaturated fat and fatty acid Unsaturated fatty acids 1 or more double bonds (b) Unsaturated fat and fatty acid cis double bond causes bending Oleic acid Figure 5.12

(a) Structural formula (b) Space-filling model Phospholipids 2 fatty acids, plus phosphate group Hydrophilic “head” and hydrophobic “tails” CH2 O P CH C Phosphate Glycerol (a) Structural formula (b) Space-filling model Fatty acids (c) Phospholipid symbol Hydrophobic tails Hydrophilic head Hydrophobic tails – Hydrophilic head Choline + Figure 5.13 N(CH3)3

The structure of phospholipids Bilayer arrangement found in cell membranes Hydrophilic head WATER Hydrophobic tail Figure 5.14

One steroid, cholesterol Found in cell membranes Precursor for some hormones HO CH3 H3C Figure 5.15

Proteins Table 5.1

Protein catalyst, speeds up chemical reactions Enzymes Protein catalyst, speeds up chemical reactions Substrate (sucrose) Enzyme (sucrase) Glucose OH H O H2O Fructose 3 Substrate is converted to products. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate binds to enzyme. 2 4 Products are released. Figure 5.16

Polypeptides Polymers of amino acids A protein 1 or more polypeptides Amino acids - carboxyl & amino groups Properties due to side chains, (R groups)

20 different amino acids make up proteins H 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 Figure 5.17 S

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)

Amino Acid (AA) Polymers Linked by peptide bonds DESMOSOMES OH CH2 C N H O Peptide bond SH Side chains H2O Amino end (N-terminus) Backbone (a) Figure 5.18 (b) Carboxyl end (C-terminus) OH

Protein Conformation and Function (a) ribbon model (b) space-filling model Groove Figure 5.19

Four Levels of Protein Structure Primary structure Unique sequence of AAs Figure 5.20 – 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

Secondary structure Folding or coiling of the polypeptide  helix and the  pleated sheet O C  helix  pleated sheet Amino acid subunits N H R H Figure 5.20

3-D shape of a polypeptide Tertiary structure 3-D shape of a polypeptide Results from interactions between AAs and R groups CH2 CH O H O C HO NH3+ -O S CH3 H3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hyrdogen bond Ionic bond Disulfide bridge

Quaternary structure 2 or more polypeptide subunits Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme

4 levels of protein structure +H3N Amino end Amino acid subunits helix

Sickle-cell hemoglobin Hemoglobin structure and 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.  subunit 1 2 3 4 5 6 7 Normal hemoglobin Sickle-cell hemoglobin . . . Figure 5.21 Exposed hydrophobic region Val Thr His Leu Pro Glul Glu Fibers of abnormal hemoglobin deform cell into sickle shape.

Denaturation Protein unravels and loses its native conformation Renaturation Denatured protein Normal protein Figure 5.22

Chaperonins Proteins that assist in folding of other proteins 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 5.23

X-ray crystallography Determines molecule’s 3-D structure 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 Figure 5.24

Nucleic acids store and transmit hereditary information Genes Units of inheritance Program AA sequence Made of nucleic acids

The Roles of Nucleic Acids There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)

DNA Stores information for the synthesis of proteins

Synthesis of mRNA in the nucleus Directs RNA synthesis Directs protein synthesis through RNA 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 5.25

The Structure of Nucleic Acids Polymers called polynucleotides 3’C 5’ end 5’C 3’ end OH Figure 5.26 O (a) Polynucleotide, or nucleic acid

Consists of monomers called nucleotides Nitrogenous base Nucleoside O O O P CH2 5’C 3’C Phosphate group Pentose sugar (b) Nucleotide Figure 5.26

(c) Nucleoside components Nucleotide Monomers Made up of nucleosides and phosphate groups CH Uracil (in RNA) U Ribose (in RNA) Nitrogenous bases Pyrimidines C N O H NH2 HN CH3 Cytosine Thymine (in DNA) T HC NH Adenine A Guanine G HOCH2 OH Pentose sugars Deoxyribose (in DNA) 4’ 5” 3’ 2’ 1’ Figure 5.26 (c) Nucleoside components

The sequence of bases(A, T, C, G) along a nucleotide polymer Unique for each gene

DNA double helix 2 antiparallel nucleotide strands Figure 5.27 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 Figure 5.27

Nitrogenous bases in DNA Form hydrogen bonds in a complementary fashion (A with T only, and C with G only)

DNA and Proteins as Tape Measures of Evolution Molecular comparisons among species