Chapter 5: The Structure and Function of Macromolecules (PDF)

Chapter 5 The Structure and Function of Macromolecules PowerPoint Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Overview: The Molecules of Life – Another leve...

Chapter 5 The Structure and Function of Macromolecules PowerPoint Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece Lectures by Chris Romero Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Overview: The Molecules of Life – Another level in the hierarchy of biological organization is reached when small organic molecules are joined together Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Macromolecules – Are large molecules composed of smaller molecules – Are complex in their structures Figure 5.1 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 2 3 H HO H Short polymer Unlinked monomer Dehydration removes a water H2O molecule, forming a new bond HO 1 2 3 4 H Longer polymer Figure 5.2A (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 H Hydrolysis adds a water H2O molecule, breaking a bond HO 1 2 3 H HO H Figure 5.2B (b) Hydrolysis of a polymer Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  The Diversity of Polymers Each class of polymer – Is formed from a specific set of monomers 1 2 3 H HO Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Although organisms share the same limited number of monomer types, each organism is unique based on the arrangement of monomers into polymers An immense variety of polymers can be built from a small set of monomers Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 Hexose sugars (C3H6O3) (C5H10O5) (C6H12O6) H O H O H O H O C C C C H C OH H C OH H C OH H C OH Aldoses H C OH H C OH HO C H HO C H H H C OH H C OH HO C H H C OH H C OH H C OH Glyceraldehyde H H C OH H C OH Ribose H H Glucose Galactose H H H H C OH H C OH H C OH C O C O C O Ketoses H C OH H C OH HO C H H H C OH H C OH Dihydroxyacetone H C OH H C OH H H C OH Ribulose H Figure 5.3 Fructose Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Monosaccharides – May be linear – Can form rings H O 1C 6CH OH 2 6CH OH 2 2 CH2OH H C OH 5C O H 5C O 6 H H H H H O HO 3 C H 5 H 4C H 1C 4C H 1C H 4 4 1 OH H OH H OH H C OH O HO 3 2 OH OH 2C OH 3C 2C OH H 5 C OH 3 C H OH 6 H OH H OH H C 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  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 CH2OH CH2OH CH2OH CH2OH of two glucose units O O O O forms maltose. The H H H H H H 1–4 H H H H H 1 glycosidic 4 H glycosidic link joins OH H OH H OH H linkage OH H OHOH the number 1 carbon OH HO of one glucose to the HO HO O OH number 4 carbon of the second glucose. H OH H OH H OH H OH Joining the glucose H2O monomers in a Glucose Maltose Glucose different way would result in a different disaccharide. CH2OH CH2OH CH2OH CH2OH H O O H O H 1–2 O H H H H H 1 glycosidic 2 (b) Dehydration reaction OH H H HO OH H linkage H HO OH HO in the synthesis of HO CH2OH HO O CH2OH sucrose. Sucrose is a disaccharide formed H OH OH H H OH OH H from glucose and fructose. Notice that fructose, H2O though a hexose like Glucose Fructose Sucrose glucose, forms a five-sided ring. Figure 5.5 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 O CH2O C CH2O H H O H C OH H O OH H H H H 4 OH H HO C H 4 1 OH H HO OH HO H H C OH H OH C H OH H OH  glucose H C OH  glucose (a)  and  glucose ring structures CH2O CH2O CH2O CH2O H H H H O O O O 1 4 1 4 1 4 1 OH OH O OH O OH O HO O OH OH OH OH (b) Starch: 1– 4 linkage of  glucose monomers CH2O CH2O OH OH H H O O O OH O OH OH 1 4 O OH HO OH O O CH2O CH2O OH OH H H (c) Cellulose: 1– 4 linkage of  glucose monomers Figure 5.7 A–C Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  – Is a major component of the tough walls that enclose plant cells About 80 cellulose Cellulose microfibrils molecules associate in a plant cell wall Microfibril to form a microfibril, the Cell walls main architectural unit of the plant cell wall. 0.5 m Plant cells CH2OH OH CH2OH OH O O O O OH OH OH OH O O O O O O CH OH OH CH2OH H 2 Cellulose CH2OH OH CH2OH OH molecules O O O O OH OH OH OH Parallel cellulose molecules are O O O O O O CH OH OH CH2OH held together by hydrogen H 2 bonds between hydroxyl CH2OH OH CH2OH OH O O O O groups attached to carbon OH OH O OH O O OH O atoms 3 and 6. O CH OH O A cellulose molecule OH CH2OH H 2 is an unbranched  Figure 5.8  Glucose glucose polymer. monomer Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 CH2O H H O OH H OH H OH H H NH C O CH3 (a) The structure of the (b) Chitin forms the exoskeleton (c) Chitin is used to make a chitin monomer. of arthropods. This cicada strong and flexible surgical is molting, shedding its old thread that decomposes after exoskeleton and emerging the wound or incision heals. Figure 5.10 A–C in adult form. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 – Most important lipids to biology: fats, phospholipids and steroids 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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Unsaturated fatty acids – Have one or more double bonds Oleic acid cis double bond Figure 5.12 (b) Unsaturated fat and fatty acid causes bending Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 – Consists of a hydrophilic “head” and hydrophobic “tails” CH2 + N(CH ) 3 3 Choline CH2 O O P O– Phosphate O CH2 CH CH2 Glycerol O O C O C O Fatty acids Hydrophilic head Hydrophobic tails (c) Phospholipid (a) Structural formula (b) Space-filling model Figure 5.13 symbol Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 H3C CH3 CH3 CH3 CH3 Figure 5.15 HO Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 2 Substrate binds to a molecule of substrate, the enzyme. Substrate reactant on which the enzyme acts. (sucrose) Glucose Enzyme OH (sucrase) H2O Fructose H O 4 Products are released. 3 Substrate is converted Figure 5.16 to products. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 CH3 CH3 CH3 CH3 CH3 CH CH2 H CH3 CH3 CH2 H3C CH O O O O O H3N+ C C H3N+ C C H3N+ C C H3N+ C C H3N+ C C O– O– O– O– O– H H H H H Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile) Nonpolar CH3 CH2 S H2C CH2 NH O CH2 H2N C C CH2 O CH2 CH2 O– O O H H3N+ C C H3N+ C C H3 N+ C C O– O– O– H H H Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro) Figure 5.17 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  OH NH2 O NH2 O C OH SH C CH2 Polar OH CH3 CH2 CH CH2 CH2 CH2 O CH2 O O O O O H3N+ C C H3N+ C C H3N+ C C H3N+ C C H3N+ C C H3N+ C C O– O– O– O– O– O– H H H H H H Cysteine Tyrosine Asparagine Glutamine Serine (Ser) Threonine (Thr) (Gln) (Cys) (Tyr) (Asn) Acidic Basic NH3+ NH2 NH+ –O O O– O C C CH2 C NH2+ NH Electrically CH2 CH2 O CH2 CH2 CH2 charged O H3N+ C C CH2 CH2 CH2 H3N+ C C O O– CH2 O– H3N+ C C O CH2 H H O– H H3N+ C C CH2 O O– H H3N+ C C O– H Aspartic acid Glutamic acid Lysine (Lys) Arginine (Arg) Histidine (His) (Asp) (Glu) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Amino Acid Polymers Amino acids – Are linked by peptide bonds OH Peptide bond OH SH CH2 CH2 CH2 H H H N H C C N C C OH H N C C OH H O H O H O DESMOSOMES (a) H2O OH DESMOSOMES DESMOSOMES Side OH SH Peptide chains CH2 CH2 bond CH2 H H H H N C C N C C N C C OH Backbone H O H O H O Amino end Carboxyl end Figure 5.18 (b) (N-terminus) (C-terminus) Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 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 + 3 Gly ProThr Gly Thr Gly Amino LeuPro Cys LysSeu Glu subunits end Met Val Lys Val Leu Asp AlaVal Arg Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Lys Trp Tyr Leu Ala Gly lle Ser ProPhe His Glu His Ala Glu Val Ala Thr PheVal Asn lle Thr Asp Tyr Ala Arg Ser Arg Ala Gly Pro Leu Leu Ser Pro SerTyr Tyr Thr Ser Thr Ala Val o Val LysGlu c Thr AsnPro o– Figure 5.20 Carboxyl end Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Secondary structure – Is the folding or coiling of the polypeptide into a repeating configuration – Includes the  helix and the  pleated sheet  pleated sheet O H H O H H O H H O H H R R R Amino acid C C N C C N C C N C C N C N C C N C C N C C N C C subunits R R R R H O H H OH H OH H O R R R R O C O O C O H C H H H C H C N HC H H C N HC N N C NH C N C N HC N H H C H O C H C O C O O C R R R R H R H C C N H O C N H O C N H O C O C N H  helix 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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Tertiary structure – Is the overall three-dimensional shape of a polypeptide – Results from interactions between amino acids and R groups Hydrophobic interactions and CH van der Waals CH22 CH H3C CH3 interactions O Hyrdogen H H3C CH3 Polypeptide bond O CH backbone HO C CH2 CH2 S S CH2 Disulfide bridge O CH2 NH3+ -O C CH2 Ionic bond Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  The four levels of protein structure +H 3N 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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 Denatured protein Figure 5.22 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 Correctly folded Polypeptide protein Cap Hollow cylinder Chaperonin Steps of Chaperonin 2 The cap attaches, causing 3 The cap comes (fully assembled) Action: the cylinder to change shape in off, and the properly 1 An unfolded poly- such a way that it creates a folded protein is peptide enters the hydrophilic environment for the released. Figure 5.23 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- dimensional structure X-ray diffraction pattern Photographic film Diffracted X-rays X-ray X-ray source beam Crystal Nucleic acid Protein Figure 5.24 (a) X-ray diffraction pattern (b) 3D computer model Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm Ribosome via nuclear pore 3 Synthesis of protein Amino Figure 5.25 Polypeptide acids Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  The Structure of Nucleic Acids Nucleic acids – Exist as polymers called polynucleotides Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Each polynucleotide – Consists of monomers called nucleotides Nucleoside Nitrogenous base O 5’C − O P O CH2 O O− Phosphate 3’C group Pentose sugar Figure 5.26 (b) Nucleotide Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  Nucleotide Monomers Nucleotide monomers – Are made up of nucleosides and phosphate groups Nitrogenous bases Pyrimidines NH2 O O C C CH 3 C N CH HN C HN CH C CH C CH C CH O N O N O N H H H Cytosine Thymine (in DNA) Uracil (in RNA) Uracil (in RNA) C T UU Purines NH2 O N CC N C C N NH HC HC N C CH N C N N NH2 H H Adenine Guanine A G Pentose sugars 5” 5” HOCH2 O OH HOCH2 O OH 4’ H H 1’ 4’ H H 1’ H 3’ 2’ H H H 3’ 2’ OH H OH OH Deoxyribose (in DNA) Ribose (in RNA) 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 Nucleotide about to be added to a new strand A 3’ end 5’ end 3’ end New strands Figure 5.27 5’ end 3’ end Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings  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 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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