Chapter 5 The Structure and Function of Macromolecules

Chapter 5 The Structure and Function of Macromolecules Power. Point Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Concept 5. 1: Most macromolecules are polymers, built from monomers • Three of the classes of life’s organic molecules are polymers – Carbohydrates – Proteins – Nucleic acids Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• A polymer – Is a long molecule consisting of many similar building blocks called monomers Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Synthesis and Breakdown of Polymers • Monomers form larger molecules by condensation reactions called dehydration reactions HO 1 3 2 H Unlinked monomer Short polymer Dehydration removes a water molecule, forming a new bond HO Figure 5. 2 A 1 2 H HO 3 H 2 O 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Polymers can disassemble by – Hydrolysis HO 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond HO 1 2 3 H Figure 5. 2 B (b) Hydrolysis of a polymer Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings H H 2 O HO H

• Concept 5. 2: Carbohydrates serve as fuel and building material • Carbohydrates – Include both sugars and their polymers Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Sugars • Monosaccharides – Are the simplest sugars – Can be used for fuel – Can be converted into other organic molecules – Can be combined into polymers Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Examples of monosaccharides Triose sugars Pentose sugars (C 3 H 6 O 3) (C 5 H 10 O 5) H O H Aldoses C O Hexose sugars (C 6 H 12 O 6) H C H O C H C OH H C OH HO C H C OH H Glyceraldehyde H Ribose H C OH H HO C H C OH HO C H H C OH H H Glucose H H C Ketoses H C OH H C O Galactose H C OH C O O C OH HO H H C OH Dihydroxyacetone H C OH H Figure 5. 3 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ribulose O C C H H Fructose

• Monosaccharides – May be linear – Can form rings O H 1 C H HO H 2 3 C C 4 C H 5 H 6 C C 6 CH OH 2 OH H OH OH OH 5 C H H OH 4 C OH 3 C H 6 CH OH 2 O H H H 2 C OH H 4 C 1 C O OH 5 C H OH 3 C H CH 2 OH O H H H 1 C 2 C OH OH 6 5 4 HO H OH 3 H O 1 2 OH OH H Figure 5. 4 (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. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings H

• Disaccharides – Consist of two monosaccharides – Are joined by a glycosidic linkage Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Examples of disaccharides (a) Dehydration reaction in the synthesis of maltose. The bonding of two glucose units H forms maltose. The glycosidic link joins the number 1 carbon of one glucose to the HO number 4 carbon of the second glucose. Joining the glucose monomers in a different way would result in a different disaccharide. CH 2 OH O H OH HO (b) Dehydration reaction in the synthesis of HO sucrose. Sucrose is a disaccharide formed from glucose and fructose. Notice that fructose, though a hexose like glucose, forms a five-sided ring. H OH H H OHOH H HO O H OH H H 1– 4 1 glycosidic linkage H 4 O H H OH O H OH CH 2 OH H OH OH H 2 O Glucose CH 2 OH H O CH 2 OH O H OH H H CH 2 OH HO CH 2 OH O H HO CH 2 OH OH OH Maltose H HO H OH H O H 1– 2 glycosidic 1 linkage H O OH Fructose Figure 5. 5 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 2 H Sucrose H HO CH 2 OH OH H 2 O Glucose CH 2 OH O H

Polysaccharides • Polysaccharides – Are polymers of sugars – Serve many roles in organisms Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Storage Polysaccharides • Starch – Is a polymer consisting entirely of glucose monomers Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

– Is the major storage form of glucose in plants Chloroplast Starch 1 m Amylose Amylopectin Figure 5. 6 (a) Starch: a plant polysaccharide Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Glycogen – Consists of glucose monomers – Is the major storage form of glucose in animals Mitochondria Giycogen granules 0. 5 m Glycogen Figure 5. 6 (b) Glycogen: an animal polysaccharide Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Structural Polysaccharides • Cellulose – Is a polymer of glucose Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

– Has different glycosidic linkages than starch H H 4 CH 2 O H OH HO H O CH 2 O H H O OH H 4 1 OH H HO H C OH glucose H C OH HO C H H C OH H OH glucose (a) and glucose ring structures CH 2 O H O HO 4 1 OH OH OH CH 2 O H O O 4 1 OH OH (b) Starch: 1– 4 linkage of glucose monomers CH 2 O H O HO Figure 5. 7 A–C OH CH 2 O H O OH 1 O 4 OH O O CH 2 O OH OH H H (c) Cellulose: 1– 4 linkage of glucose monomers Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings OH

– Is a major component of the tough walls that enclose plant cells Microfibril Cell walls Cellulose microfibrils in a plant cell wall About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 0. 5 m Plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. Figure 5. 8 OH CH 2 OH O O OH OH O O O CH OH OH CH 2 OH 2 H CH 2 OH OH OH CH 2 OH O O OH OH OH O O O O CH OH OH CH 2 OH 2 H Glucose monomer Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Cellulose molecules A cellulose molecule is an unbranched glucose polymer.

• Cellulose is difficult to digest – Cows have microbes in their stomachs to facilitate this process Figure 5. 9 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Chitin, another important structural polysaccharide – Is found in the exoskeleton of arthropods – Can be used as surgical thread CH 2 O H O OH H H NH C O CH 3 (a) The structure of the (b) Chitin forms the exoskeleton of arthropods. This cicada chitin monomer. is molting, shedding its old exoskeleton and emerging Figure 5. 10 A–C in adult form. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.

• Concept 5. 3: Lipids are a diverse group of hydrophobic molecules • Lipids – Are the one class of large biological molecules that do not consist of polymers – Share the common trait of being hydrophobic Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Fats • Fats – Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids H H C O OH H C OH HO C H H C H H C H H C H H C H Fatty acid (palmitic acid) H Glycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage O H H C O C H O H C H Figure 5. 11 O C H C H H H C H H C H H C H H C H (b) Fat molecule (triacylglycerol) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings H C H H C H H C H H C H H C H H C H H H C H H

• Fatty acids – Vary in the length and number and locations of double bonds they contain Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Saturated fatty acids – Have the maximum number of hydrogen atoms possible – Have no double bonds Stearic acid Figure 5. 12 (a) Saturated fat and fatty acid Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Unsaturated fatty acids – Have one or more double bonds Oleic acid Figure 5. 12 (b) Unsaturated fat and fatty acid Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings cis double bond causes bending

Phospholipids • Phospholipids – Have only two fatty acids – Have a phosphate group instead of a third fatty acid Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Phospholipid structure CH 2 + N(CH ) Choline 3 3 CH 2 O O P O– Phosphate O CH 2 CH O O C CH 2 Figure 5. 13 Glycerol O Hydrophobic tails Hydrophilic head – Consists of a hydrophilic “head” and hydrophobic “tails” (a) Structural formula Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Fatty acids Hydrophilic head Hydrophobic tails (b) Space-filling model (c) Phospholipid symbol

• The structure of phospholipids – Results in a bilayer arrangement found in cell membranes WATER Hydrophilic head WATER Hydrophobic tail Figure 5. 14 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Steroids • Steroids – Are lipids characterized by a carbon skeleton consisting of four fused rings Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• One steroid, cholesterol – Is found in cell membranes – Is a precursor for some hormones H 3 C CH 3 Figure 5. 15 HO Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings CH 3

• Concept 5. 4: Proteins have many structures, resulting in a wide range of functions – Proteins • Have many roles inside the cell Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• An overview of protein functions Table 5. 1 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Enzymes – Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate (sucrose) 2 Substrate binds to enzyme. Glucose OH Enzyme (sucrase) H 2 O Fructose H O 4 Products are released. Figure 5. 16 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 3 Substrate is converted to products.

Polypeptides • Polypeptides – Are polymers of amino acids • A protein – Consists of one or more polypeptides Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Amino Acid Monomers • Amino acids – Are organic molecules possessing both carboxyl and amino groups – Differ in their properties due to differing side chains, called R groups Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• 20 different amino acids make up proteins CH 3 H H 3 N+ C CH 3 O H 3 N+ C H Glycine (Gly) O– C H 3 N+ C H Alanine (Ala) O– CH CH 3 O C CH 2 O H 3 N+ C H Valine (Val) CH 3 O– C O C H Leucine (Leu) H 3 C H 3 N+ O– CH C O C H Isoleucine (Ile) O– Nonpolar CH 3 CH 2 S NH CH 2 H 3 N+ C H CH 2 O H 3 N+ C O– Methionine (Met) C H 3 N+ O– Phenylalanine (Phe) Figure 5. 17 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings CH 2 O C H O H 2 C CH 2 H 2 N C O C H C O– Tryptophan (Trp) Proline (Pro) O–

OH OH Polar CH 2 H 3 N+ C CH O H 3 N+ C O– H Serine (Ser) C CH 2 O H 3 N+ C O– H C CH 2 O C H O– C H 3 N+ O H 3 N+ C O– H Electrically charged H 3 N+ CH 2 C H 3 N+ O– C NH 3+ O C CH 2 CH 2 O CH 2 C O– H H 3 N+ C O CH 2 C H O– H 3 N+ C H Aspartic acid (Asp) O C O– H Glutamine (Gln) NH 2 C C C Basic O– O O Asparagine (Asn) Acidic –O CH 2 H Tyrosine (Tyr) Cysteine (Cys) Threonine (Thr) C NH 2 O C SH CH 3 OH NH 2 O Glutamic acid (Glu) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings C Lysine (Lys) NH 2+ H 3 N+ CH 2 O O– NH+ CH 2 H 3 N+ C H NH CH 2 O C C O– H O C O– Arginine (Arg) Histidine (His)

Amino Acid Polymers • Amino acids – Are linked by peptide bonds Peptide bond OH OH SH CH 2 H N H CH 2 H C C H N C C OH H N C H O H (a) C OH O DESMOSOMES H 2 O OH DESMOSOMES SH OH Peptide CH 2 bond CH 2 H H N C C H O Figure 5. 18 (b) Amino end (N-terminus) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings H H N C C H O N C C OH H O Carboxyl end (C-terminus) Side chains Backbone

Determining the Amino Acid Sequence of a Polypeptide • The amino acid sequences of polypeptides – Were first determined using chemical means – Can now be determined by automated machines Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Protein Conformation and Function • A protein’s specific conformation – Determines how it functions Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Two models of protein conformation Groove (a) A ribbon model Groove Figure 5. 19 (b) A space-filling model Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Four Levels of Protein Structure • Primary structure – Is the unique sequence of amino acids in a polypeptide HN Amino acid + Gly Pro. Thr Gly Thr 3 Amino end Gly subunits Glu Cys. Lys. Seu Leu. Pro Met Val Lys Val Leu Asp Ala. Val Arg Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Lys Trp Tyr Leu Ala Gly lle Ser Pro. Phe. His Glu Ala Thr Phe. Val Asn His Ala Glu Val Asp Tyr Arg Ser Arg Gly Pro Thr Ser Tyr Thr lle Ala Leu Ser Pro Ser. Tyr Thr Ala Val Lys. Glu Thr Asn. Pro Figure 5. 20 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings o c – o Carboxyl end

• Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the helix and the pleated sheet O H H C C N Amino acid subunits C N H R R O H H C C N O H H R C C N OH H R O R C H R O C N H N H O C H C R N H O C O C H C O N H N C C H R R H C C H H helix Figure 5. 20 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings R O H H C C N OH H R O C H H H C N HC C C N HC N N H H C O C C O R R O N O H H C C N R R H R O C H H NH C N C H O C R R C C O R H C N H O C

• Tertiary structure – Is the overall three-dimensional shape of a polypeptide – Results from interactions between amino acids and R groups Hydrophobic Hyrdogen bond CH 2 O H 3 C CH CH 3 H 3 C CH 3 CH interactions and van der Waals interactions Polypeptide backbone HO C CH 2 S S CH 2 Disulfide bridge O CH 2 NH 3+ -O C CH 2 Ionic bond Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Quaternary structure – Is the overall protein structure that results from the aggregation of two or more polypeptide subunits Polypeptide chain Collagen Chains Iron Heme Chains Hemoglobin Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• The four levels of protein structure +H N 3 Amino end Amino acid subunits helix Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Sickle-Cell Disease: A Simple Change in Primary Structure • Sickle-cell disease – Results from a single amino acid substitution in the protein hemoglobin Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Hemoglobin structure and sickle-cell disease Primary structure Normal hemoglobin Val His Leu Thr 1 2 3 4 5 6 7 Secondary and tertiary structures Red blood cell shape Figure 5. 21 Val His Leu Thr Molecules do not associate with one another, each carries oxygen. Quaternary structure Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Val Glu . . . 10 m Red blood cell shape Exposed hydrophobic region subunit Function 10 m Normal cells are full of individual hemoglobin molecules, each carrying oxygen Pro structure 1 2 3 4 5 6 7 Secondary subunit and tertiary structures Quaternary Hemoglobin A structure Function Pro Glul Glu Sickle-cell hemoglobin . . . Primary 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.

What Determines Protein Conformation? • Protein conformation – Depends on the physical and chemical conditions of the protein’s environment Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Denaturation – Is when a protein unravels and loses its native conformation Denaturation Normal protein Figure 5. 22 Denatured protein Renaturation Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Protein-Folding Problem • Most proteins – Probably go through several intermediate states on their way to a stable conformation Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Chaperonins – Are protein molecules that assist in the proper folding of other proteins Polypeptide Cap Correctly folded protein Hollow cylinder Chaperonin (fully assembled) Figure 5. 23 2 The cap attaches, causing 3 The cap comes Steps of Chaperonin the cylinder to change shape in off, and the properly Action: such a way that it creates a folded protein is 1 An unfolded polyhydrophilic environment for the released. peptide enters the cylinder from one end. folding of the polypeptide. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• X-ray crystallography – Is used to determine a protein’s three. X-ray dimensional structure diffraction pattern Photographic film Diffracted X-rays X-ray beam source Crystal Nucleic acid Protein Figure 5. 24 (a) X-ray diffraction pattern Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings (b) 3 D computer model

• Concept 5. 5: Nucleic acids store and transmit hereditary information • Genes – Are the units of inheritance – Program the amino acid sequence of polypeptides – Are made of nucleic acids Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Roles of Nucleic Acids • There are two types of nucleic acids – Deoxyribonucleic acid (DNA) – Ribonucleic acid (RNA) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• DNA – Stores information for the synthesis of specific proteins Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

– Directs RNA synthesis – Directs protein synthesis through RNA DNA 1 Synthesis of m. RNA in the nucleus m. RNA NUCLEUS CYTOPLASM m. RNA 2 Movement of m. RNA into cytoplasm via nuclear pore Ribosome 3 Synthesis of protein Figure 5. 25 Polypeptide Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Amino acids

The Structure of Nucleic Acids • Nucleic acids – Exist as polymers called polynucleotides 5’ end 5’C O 3’C O O 5’C O 3’C OH Figure 5. 26 3’ end (a) Polynucleotide, or nucleic acid Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• Each polynucleotide – Consists of monomers called nucleotides Nucleoside Nitrogenous base O O P 5’C O CH 2 O O Phosphate group Figure 5. 26 (b) Nucleotide Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 3’C Pentose sugar

Nucleotide Monomers • Nucleotide monomers – Are made up of nucleosides and phosphate groups Nitrogenous bases Pyrimidines NH 2 O O C C CH 3 C N CH C CH HN HN CH C C CH N N O O H H H Cytosine Thymine (in DNA) Uracil (in RNA) Uracil (in U C U T Purines O NH 2 C N CC NH N HC HC C CH N C N NH 2 N N H H Adenine Guanine Pyrimidines A G 5” Pentose sugars HOCH 2 O OH 4’ H H 1’ 5” HOCH 2 O OH 4’ H H 1’ H H H 3’ 2’ OH H OH OH Deoxyribose (in DNA) Ribose (in RNA) H Figure 5. 26 (c) Nucleoside components Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

Nucleotide Polymers • Nucleotide polymers – Are made up of nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• The sequence of bases along a nucleotide polymer – Is unique for each gene Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The DNA Double Helix • Cellular DNA molecules – Have two polynucleotides that spiral around an imaginary axis – Form a double helix Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

• The DNA double helix – Consists of two antiparallel nucleotide strands 5’ end 3’ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands A 3’ end Nucleotide about to be added to a new strand 5’ end 3’ end Figure 5. 27 5’ end Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings New strands 3’ end

• The nitrogenous bases in DNA – Form hydrogen bonds in a complementary fashion (A with T only, and C with G only) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

DNA and Proteins as Tape Measures of Evolution • Molecular comparisons – Help biologists sort out the evolutionary connections among species Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings

The Theme of Emergent Properties in the Chemistry of Life: A Review • Higher levels of organization – Result in the emergence of new properties • Organization – Is the key to the chemistry of life Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings