3 Carbon and the Molecular Diversity of Life

Transcription

1 CAMPBELL BIOLOGY IN FOCUS Urry Cain Wasserman Minorsky Jackson Reece 3 Carbon and the Molecular Diversity of Life Lecture Presentations by Kathleen Fitzpatrick and Nicole Tunbridge

2 Overview: Carbon Compounds and Life Aside from water, living organisms consist mostly of carbon-based compounds Carbon is unparalleled in its ability to form large, complex, and diverse molecules A compound containing carbon is said to be an organic compound

3 Critically important molecules of all living things fall into four main classes Carbohydrates Lipids Proteins Nucleic acids The first three of these can form huge molecules called macromolecules

4 Figure 3.1

5 Concept 3.1: Carbon atoms can form diverse molecules by bonding to four other atoms An atom s electron configuration determines the kinds and number of bonds the atom will form with other atoms This is the source of carbon s versatility

6 The Formation of Bonds with Carbon With four valence electrons, carbon can form four covalent bonds with a variety of atoms This ability makes large, complex molecules possible In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape However, when two carbon atoms are joined by a double bond, the atoms joined to the carbons are in the same plane as the carbons

7 When a carbon atom forms four single covalent bonds, the bonds angle toward the corners of an imaginary tetrahedron When two carbon atoms are joined by a double bond, the atoms joined to those carbons are in the same plane as the carbons

8 Figure 3.2 Name Methane Ethane Ethene (ethylene) Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model

9 The electron configuration of carbon gives it covalent compatibility with many different elements The valences of carbon and its most frequent partners (hydrogen, oxygen, and nitrogen) are the building code that governs the architecture of living molecules

10 Figure 3.3 Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4)

11 Carbon atoms can partner with atoms other than hydrogen; for example: Carbon dioxide: CO2 Urea: CO(NH2)2

12 Figure 3.UN01 Estradiol Testosterone

13 Molecular Diversity Arising from Variation in Carbon Skeletons Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape Animation: Carbon Skeletons

14 Figure 3.4 (a) Length Ethane (c) Double bond position Propane (b) Branching Butane 1-Butene 2-Butene (d) Presence of rings 2-Methylpropane (isobutane) Cyclohexane Benzene

15 Figure 3.4a (a) Length Ethane Propane

16 Figure 3.4b (b) Branching Butane 2-Methylpropane (isobutane)

17 Figure 3.4c (c) Double bond position 1-Butene 2-Butene

18 Figure 3.4d (d) Presence of rings Cyclohexane Benzene

19 Hydrocarbons are organic molecules consisting of only carbon and hydrogen Many organic molecules, such as fats, have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy

20 The Chemical Groups Most Important to Life Functional groups are the components of organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups give each molecule its unique properties

21 The seven functional groups that are most important in the chemistry of life: Hydroxyl group Carbonyl group Carboxyl group Amino group Sulfhydryl group Phosphate group Methyl group

22 Figure 3.5 Chemical Group Hydroxyl group ( Compound Name OH) Carbonyl group ( C Examples Alcohol O) Ethanol Ketone Aldehyde Acetone Carboxyl group ( Propanal COOH) Carboxylic acid, or organic acid Acetic acid Amino group ( NH2) Amine Glycine Sulfhydryl group ( SH) Thiol Phosphate group ( OPO32 ) Organic phosphate Methyl group ( Glycerol phosphate CH3) Methylated compound Cysteine 5-Methyl cytosine

23 Figure 3.5a Chemical Group Hydroxyl group ( OH) Carbonyl group ( C O) Compound Name Examples Alcohol Ethanol Ketone Aldehyde Acetone Carboxyl group ( COOH) Carboxylic acid, or organic acid Acetic acid Amino group ( NH2) Amine Glycine Propanal

24 Figure 3.5aa Hydroxyl group ( OH) (may be written HO ) Alcohol (The specific name usually ends in -ol.) Ethanol, the alcohol present in alcoholic beverages

25 Figure 3.5ab Carbonyl group ( C O) Ketone if the carbonyl group is within a carbon skeleton Aldehyde if the carbonyl group is at the end of a carbon skeleton Acetone, the simplest ketone Propanal, an aldehyde

26 Figure 3.5ac Carboxyl group ( COOH) Carboxylic acid, or organic acid Acetic acid, which gives vinegar its sour taste Ionized form of COOH (carboxylate ion), found in cells

27 Figure 3.5ad Amino group ( NH2) Amine Glycine, an amino acid (note its carboxyl group) Ionized form of found in cells NH2

28 Figure 3.5b Chemical Group Sulfhydryl group ( Compound Name SH) Thiol Phosphate group ( Glycerol phosphate CH3) Methylated compound Cysteine OPO32 ) Organic phosphate Methyl group ( Examples 5-Methyl cytosine

29 Figure 3.5ba Sulfhydryl group ( SH) Thiol (may be written HS ) Cysteine, a sulfurcontaining amino acid

30 Figure 3.5bb Phosphate group ( OPO32 ) Organic phosphate Glycerol phosphate, which takes part in many important chemical reactions in cells

31 Figure 3.5bc Methyl group ( CH3) Methylated compound 5-Methyl cytosine, a component of DNA that has been modified by addition of a methyl group

32 ATP: An Important Source of Energy for Cellular Processes One organic phosphate molecule, adenosine triphosphate (ATP), is the primary energytransferring molecule in the cell ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups

33 Figure 3.UN02 Adenosine

34 Figure 3.UN03 Reacts with H2O Adenosine Adenosine ATP Inorganic phosphate ADP Energy

35 Concept 3.2: 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 Some molecules that serve as monomers also have other functions of their own

36 The Synthesis and Breakdown of Polymers Cells make and break down polymers by the same process A dehydration reaction occurs when two monomers bond together through the loss of a water molecule Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction These processes are facilitated by enzymes, which speed up chemical reactions Animation: Polymers

37 Figure 3.6 (a) Dehydration reaction: synthesizing a polymer Short polymer Longer polymer (b) Hydrolysis: breaking down a polymer Unlinked monomer

38 Figure 3.6a (a) Dehydration reaction: synthesizing a polymer Short polymer Dehydration removes a water molecule, forming a new bond. Longer polymer Unlinked monomer

39 Figure 3.6b (b) Hydrolysis: breaking down a polymer Hydrolysis adds a water molecule, breaking a bond.

40 The Diversity of Polymers Each cell has thousands of different macromolecules HO Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species An immense variety of polymers can be built from a small set of monomers

41 Concept 3.3: Carbohydrates serve as fuel and building material Carbohydrates include sugars and the polymers of sugars The simplest carbohydrates are monosaccharides, or simple sugars Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks

42 Sugars Monosaccharides have molecular formulas that are usually multiples of CH2O Glucose (C6H12O6) is the most common monosaccharide Monosaccharides are classified by the number of carbons in the carbon skeleton and the placement of the carbonyl group

43 Figure 3.7 Triose: 3-carbon sugar (C3H6O3) Pentose: 5-carbon sugar (C5H10O5) Glyceraldehyde An initial breakdown product of glucose in cells Ribose A component of RNA Hexoses: 6-carbon sugars (C6H12O6) Glucose Fructose Energy sources for organisms

44 Figure 3.7a Triose: 3-carbon sugar (C3H6O3) Glyceraldehyde An initial breakdown product of glucose in cells

45 Figure 3.7b Pentose: 5-carbon sugar (C5H10O5) Ribose A component of RNA

46 Figure 3.7c Hexoses: 6-carbon sugars (C6H12O6) Glucose Fructose Energy sources for organisms

47 Though often drawn as linear skeletons, in aqueous solutions many sugars form rings Monosaccharides serve as a major fuel for cells and as raw material for building molecules

48 Figure 3.8 (a) Linear and ring forms (b) Abbreviated ring structure

49 A disaccharide is formed when a dehydration reaction joins two monosaccharides This covalent bond is called a glycosidic linkage Animation: Disaccharides

50 Figure Glucose Fructose

51 Figure Glucose Fructose 1 2 glycosidic linkage Sucrose

52 Polysaccharides Polysaccharides, the polymers of sugars, have storage and structural roles The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages

53 Storage Polysaccharides Starch, a storage polysaccharide of plants, consists entirely of glucose monomers Plants store surplus starch as granules The simplest form of starch is amylose

54 Glycogen is a storage polysaccharide in animals Humans and other vertebrates store glycogen mainly in liver and muscle cells Animation: Polysaccharides

55 Figure 3.10 Starch granules in a potato tuber cell Starch (amylose) Glucose monomer Glycogen granules in muscle tissue Cellulose microfibrils in a plant cell wall Cellulose molecules Glycogen Cellulose Hydrogen bonds between OH groups (not shown) attached to carbons 3 and 6

56 Figure 3.10a Starch granules in a potato tuber cell Starch (amylose) Glucose monomer

57 Figure 3.10aa Starch granules in a potato tuber cell

58 Figure 3.10b Glycogen granules in muscle tissue Glycogen

59 Figure 3.10ba Glycogen granules in muscle tissue

60 Figure 3.10c Cellulose microfibrils in a plant cell wall Cellulose molecules Cellulose Hydrogen bonds between OH groups on carbons 3 and 6

61 Figure 3.10ca Cellulose microfibrils in a plant cell wall

62 Structural Polysaccharides The polysaccharide cellulose is a major component of the tough wall of plant cells Like starch and glycogen, cellulose is a polymer of glucose, but the glycosidic linkages in cellulose differ The difference is based on two ring forms for glucose

63 Figure 3.11 (a) α and β glucose ring structures α Glucose β Glucose (b) Starch: 1 4 linkage of α glucose monomers (c) Cellulose: 1 4 linkage of β glucose monomers

64 Figure 3.11a a) α and β glucose ring structures α Glucose β Glucose

65 In starch, the glucose monomers are arranged in the alpha (α) conformation Starch (and glycogen) are largely helical In cellulose, the monomers are arranged in the beta (β) conformation Cellulose molecules are relatively straight

66 Figure 3.11b (b) Starch: 1 4 linkage of α glucose monomers

67 Figure 3.11c (c) Cellulose: 1 4 linkage of β glucose monomers

68 In straight structures (cellulose), H atoms on one strand can form hydrogen bonds with OH groups on other strands Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants

69 Enzymes that digest starch by hydrolyzing α linkages can t hydrolyze β linkages in cellulose Cellulose in human food passes through the digestive tract as insoluble fiber Some microbes use enzymes to digest cellulose Many herbivores, from cows to termites, have symbiotic relationships with these microbes

70 Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods Chitin also provides structural support for the cell walls of many fungi

71 Concept 3.4: Lipids are a diverse group of hydrophobic molecules Lipids do not form true polymers The unifying feature of lipids is having little or no affinity for water Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds The most biologically important lipids are fats, phospholipids, and steroids

72 Fats Fats are constructed from two types of smaller molecules: glycerol and fatty acids Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon A fatty acid consists of a carboxyl group attached to a long carbon skeleton Animation: Fats

73 Figure 3.12 Fatty acid (in this case, palmitic acid) Glycerol (a) One of three dehydration reactions in the synthesis of a fat Ester linkage (b) Fat molecule (triacylglycerol)

74 Figure 3.12a Fatty acid (in this case, palmitic acid) Glycerol (a) One of three dehydration reactions in the synthesis of a fat

75 Fats separate from water because water molecules hydrogen-bond to each other and exclude the fats In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride

76 Figure 3.12b Ester linkage (b) Fat molecule (triacylglycerol)

77 Fatty acids vary in length (number of carbons) and in the number and locations of double bonds Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds Unsaturated fatty acids have one or more double bonds

78 Figure 3.13 (a) Saturated fat Structural formula of a saturated fat molecule Space-filling model of stearic acid, a saturated fatty acid (b) Unsaturated fat Structural formula of an unsaturated fat molecule Space-filling model of oleic acid, an unsaturated fatty acid Double bond causes bending.

79 Figure 3.13a (a) Saturated fat Structural formula of a saturated fat molecule Space-filling model of stearic acid, a saturated fatty acid

80 Figure 3.13aa

81 Figure 3.13b (b) Unsaturated fat Structural formula of an unsaturated fat molecule Space-filling model of oleic acid, an unsaturated fatty acid Double bond causes bending.

82 Figure 3.13ba

83 Fats made from saturated fatty acids are called saturated fats and are solid at room temperature Most animal fats are saturated Fats made from unsaturated fatty acids, called unsaturated fats or oils, are liquid at room temperature Plant fats and fish fats are usually unsaturated

84 The major function of fats is energy storage Fat is a compact way for animals to carry their energy stores with them

85 Phospholipids 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 Phospholipids are major constituents of cell membranes

86 Figure 3.14 Hydrophobic tails Hydrophilic head Choline Phosphate Glycerol Fatty acids (a) Structural formula Hydrophilic head Hydrophobic tails (b) Space-filling model (c) Phospholipid symbol (d) Phospholipid bilayer

87 Figure 3.14ab Hydrophobic tails Hydrophilic head Choline Phosphate Glycerol Fatty acids (a) Structural formula (b) Space-filling model

88 When phospholipids are added to water, they selfassemble into a bilayer, with the hydrophobic tails pointing toward the interior This feature of phospholipids results in the bilayer arrangement found in cell membranes

89 Figure 3.14cd Hydrophilic head Hydrophobic tails (c) Phospholipid symbol (d) Phospholipid bilayer

90 Steroids Steroids are lipids characterized by a carbon skeleton consisting of four fused rings Cholesterol, an important steroid, is a component in animal cell membranes Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease Video: Cholesterol Space Model Video: Cholesterol Stick Model

91 Figure 3.15

92 Concept 3.5: Proteins include a diversity of structures, resulting in a wide range of functions Proteins account for more than 50% of the dry mass of most cells Protein functions include defense, storage, transport, cellular communication, movement, and structural support Animation: Contractile Proteins Animation: Defensive Proteins Animation: Enzymes

93 Animation: Gene Regulatory Proteins Animation: Hormonal Proteins Animation: Receptor Proteins Animation: Sensory Proteins Animation: Storage Proteins Animation: Structural Proteins Animation: Transport Proteins

94 Figure 3.16 Enzymatic proteins Defensive proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Example: Antibodies inactivate and help destroy viruses and bacteria. Enzyme Function: Protection against disease Antibodies Bacterium Virus Storage proteins Transport proteins Function: Storage of amino acids Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Ovalbumin Transport protein Amino acids for embryo Cell membrane Receptor proteins Hormonal proteins Function: Coordination of an organism s activities Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration. High blood sugar Function: Transport of substances Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. Insulin secreted Receptor protein Normal blood sugar Signaling molecules Structural proteins Contractile and motor proteins Function: Movement Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles. Actin Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. Function: Support Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Myosin Collagen Muscle tissue 30 µm Connective tissue 60 µm

95 Figure 3.16a Enzymatic proteins Defensive proteins Function: Selective acceleration of chemical reactions Function: Protection against disease Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Example: Antibodies inactivate and help destroy viruses and bacteria. Antibodies Enzyme Virus Bacterium Storage proteins Transport proteins Function: Storage of amino acids Function: Transport of substances Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. Transport protein Ovalbumin Amino acids for embryo Cell membrane

96 Figure 3.16aa Enzymatic proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Enzyme

97 Figure 3.16ab Defensive proteins Function: Protection against disease Example: Antibodies inactivate and help destroy viruses and bacteria. Antibodies Virus Bacterium

98 Figure 3.16ac Storage proteins Function: Storage of amino acids Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Ovalbumin Amino acids for embryo

99 Figure 3.16aca

100 Figure 3.16ad Transport proteins Function: Transport of substances Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. Transport protein Cell membrane

101 Figure 3.16b Hormonal proteins Receptor proteins Function: Coordination of an organism s activities Function: Response of cell to chemical stimuli Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration. Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. Receptor protein High blood sugar Insulin secreted Signaling molecules Normal blood sugar Structural proteins Contractile and motor proteins Function: Support Function: Movement Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles. Actin Myosin Collagen Muscle tissue 30 µm Connective tissue 60 µm

102 Figure 3.16ba Hormonal proteins Function: Coordination of an organism s activities Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration. High blood sugar Insulin secreted Normal blood sugar

103 Figure 3.16bb Receptor proteins Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. Receptor protein Signaling molecules

104 Figure 3.16bc Contractile and motor proteins Function: Movement Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles. Actin Muscle tissue 30 µm Myosin

105 Figure 3.16bca Muscle tissue 30 µm

106 Figure 3.16bd Structural proteins Function: Support Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Collagen Connective tissue 60 µm

107 Figure 3.16bda Connective tissue 60 µm

108 Life would not be possible without enzymes Enzymatic proteins act as catalysts, to speed up chemical reactions without being consumed by the reaction

109 Polypeptides are unbranched polymers built from the same set of 20 amino acids A protein is a biologically functional molecule that consists of one or more polypeptides

110 Amino Acids Amino acids are organic molecules with carboxyl and amino groups Amino acids differ in their properties due to differing side chains, called R groups

111 Figure 3.UN04 Side chain (R group) α carbon Amino group Carboxyl group

112 Figure 3.17 Nonpolar side chains; hydrophobic Side chain (R group) Glycine (Gly or G) Alanine (Ala or A) Phenylalanine (Phe or F) Methionine (Met or M) Leucine (Leu or L) Valine (Val or V) Isoleucine (Ιle or Ι) Tryptophan (Trp or W) Proline (Pro or P) Polar side chains; hydrophilic Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Electrically charged side chains; hydrophilic Basic (positively charged) Acidic (negatively charged) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

113 Figure 3.17a Nonpolar side chains; hydrophobic Side chain (R group) Glycine (Gly or G) Methionine (Met or M) Alanine (Ala or A) Valine (Val or V) Phenylalanine (Phe or F) Leucine (Leu or L) Tryptophan (Trp or W) Isoleucine (Ιle or Ι) Proline (Pro or P)

114 Figure 3.17b Polar side chains; hydrophilic Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q)

115 Figure 3.17c Electrically charged side chains; hydrophilic Basic (positively charged) Acidic (negatively charged) Aspartic acid Glutamic acid (Asp or D) (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

116 Polypeptides Amino acids are linked by peptide bonds A polypeptide is a polymer of amino acids Polypeptides range in length from a few to more than a thousand monomers Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)

117 Figure 3.18 Peptide bond New peptide bond forming Side chains Backbone Amino end (N-terminus) Peptide Carboxyl end bond (C-terminus)

118 Figure 3.18a Peptide bond

119 Figure 3.18b Side chains Backbone Amino end (N-terminus) Peptide bond Carboxyl end (C-terminus)

120 Protein Structure and Function A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape

121 Figure 3.19 Groove Groove (a) A ribbon model (b) A space-filling model

122 Figure 3.19a Groove (a) A ribbon model

123 Figure 3.19b Groove (b) A space-filling model

124 The sequence of amino acids, determined genetically, leads to a protein s three-dimensional structure A protein s structure determines its function

125 Figure 3.20 Antibody protein Protein from flu virus

126 Four Levels of Protein Structure Proteins are very diverse, but share three superimposed levels of structure called primary, secondary, and tertiary structure A fourth level, quaternary structure, arises when a protein consists of more than one polypeptide chain

127 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 from interactions between multiple polypeptide chains

128 Video: Alpha Helix with No Side Chain Video: Alpha Helix with Side Chain Video: Beta Pleated Sheet Video: Beta Pleated Stick Animation: Introduction to Protein Structure Animation: Primary Structure Animation: Secondary Structure Animation: Tertiary Structure Animation: Quaternary Structure

129 Figure 3.21a Primary structure Amino acids Amino end Primary structure of transthyretin Carboxyl end

130 Figure 3.21aa Primary structure Amino acids Amino end 30 25

131 Figure 3.21b Secondary structure Tertiary structure Quaternary structure Transthyretin polypeptide Transthyretin protein α helix β pleated sheet

132 Figure 3.21ba Secondary structure α helix β pleated sheet Hydrogen bond β strand Hydrogen bond

133 Figure 3.21bb Tertiary structure Transthyretin polypeptide

134 Figure 3.21bc Quaternary structure Transthyretin protein

135 Figure 3.21c

136 Figure 3.21d Hydrogen bond Hydrophobic interactions and van der Waals interactions Disulfide bridge Ionic bond Polypeptide backbone

137 Figure 3.21e Collagen

138 Figure 3.21f Heme Iron β subunit α subunit α subunit β subunit Hemoglobin

139 Sickle-Cell Disease: A Change in Primary Structure Primary structure is the sequence of amino acids on the polypeptide chain 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

140 Figure 3.22 Secondary and Tertiary Structures Sickle-cell Normal Primary Structure Quaternary Structure Function Red Blood Cell Shape Normal Molecules do not hemoglobin associate with one another; each carries oxygen. β subunit α β α β Exposed hydrophobic region Sickle-cell Molecules crystallized hemoglobin into a fiber; capacity to carry oxygen is reduced. α β subunit 5 µm β β α 5 µm

141 Figure 3.22a Normal Primary Structure Secondary and Tertiary Structures Quaternary Structure Function Normal Molecules do not hemoglobin associate with one another; each carries oxygen. β subunit α β α β

142 Figure 3.22aa 5 µm

143 Figure 3.22b Sickle-cell Primary Structure Secondary and Tertiary Structures Quaternary Structure Function Sickle-cell Molecules crystallized hemoglobin into a fiber; capacity to carry oxygen is reduced. Exposed hydrophobic region α β subunit β β α

144 Figure 3.22ba 5 µm

145 What Determines Protein Structure? In addition to primary structure, physical and chemical conditions can affect structure Alterations in ph, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a protein s native structure is called denaturation A denatured protein is biologically inactive

146 Figure Normal protein

147 Figure Normal protein Denatured protein

148 Figure Normal protein Denatured protein

149 Protein Folding in the Cell It is hard to predict a protein s structure from its primary structure Most proteins probably go through several intermediate structures on their way to their final, stable shape Scientists use X-ray crystallography to determine 3-D protein structure based on diffractions of an X-ray beam by atoms of the crystalized molecule

150 Figure 3.24 Experiment Diffracted X-rays X-ray source X-ray beam Crystal Digital detector X-ray diffraction pattern Results RNA DNA RNA polymerase ΙΙ

151 Figure 3.24a Experiment Diffracted X-rays X-ray source X-ray beam Crystal Digital detector X-ray diffraction pattern

152 Figure 3.24b Results RNA DNA RNA polymerase ΙΙ

153 Concept 3.6: Nucleic acids store, transmit, and help express 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 made of monomers called nucleotides

154 The Roles of Nucleic Acids There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA provides directions for its own replication DNA directs synthesis of messenger RNA (mrna) and, through mrna, controls protein synthesis

155 Figure DNA 1 Synthesis of mrna mrna NUCLEUS CYTOPLASM

156 Figure DNA 1 Synthesis of mrna mrna NUCLEUS CYTOPLASM mrna 2 Movement of mrna into cytoplasm

157 Figure DNA 1 Synthesis of mrna mrna NUCLEUS CYTOPLASM mrna 2 Movement of mrna into cytoplasm Ribosome 3 Synthesis of protein Polypeptide Amino acids

158 The Components of Nucleic Acids Nucleic acids are polymers called polynucleotides Each polynucleotide is made of monomers called nucleotides Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups The portion of a nucleotide without the phosphate group is called a nucleoside Animation: DNA and RNA Structure

159 Figure end Sugar-phosphate backbone (on blue background) Nitrogenous bases Pyrimidines 5 C 3 C Nucleoside Nitrogenous base Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines 5 C 3 C Phosphate group Sugar (pentose) Adenine (A) Guanine (G) (b) Nucleotide 3 end Sugars (a) Polynucleotide, or nucleic acid Deoxyribose (in DNA) (c) Nucleoside components Ribose (in RNA)

160 Figure 3.26a 5 end Sugar-phosphate backbone (on blue background) 5 C 3 C Nucleoside Nitrogenous base 5 C 3 C Phosphate group (b) Nucleotide 3 end (a) Polynucleotide, or nucleic acid Sugar (pentose)

161 Figure 3.26b Nucleoside Nitrogenous base Phosphate group (b) Nucleotide Sugar (pentose)

162 Figure 3.26c Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Adenine (A) Guanine (G)

163 Figure 3.26d Sugars Deoxyribose (in DNA) Ribose (in RNA)

164 Each nitrogenous base has one or two rings that include nitrogen atoms The nitrogenous bases in nucleic acids are called cytosine (C), thymine (T), uracil (U), adenine (A), and guanine (G) Thymine is found only in DNA, and uracil only in RNA; the rest are found in both DNA and RNA

165 The sugar in DNA is deoxyribose; in RNA it is ribose A prime ( ) is used to identify the carbon atoms in the ribose, such as the 2 carbon or 5 carbon A nucleoside with at least one phosphate attached is a nucleotide

166 Nucleotide Polymers Adjacent 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 of the next These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages The sequence of bases along a DNA or mrna polymer is unique for each gene

167 The Structures of DNA and RNA Molecules RNA molecules usually exist as single polypeptide chains DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix In the DNA double helix, the two backbones run in opposite 5 3 directions from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes

168 The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C) This is called complementary base pairing Complementary pairing can also occur between two RNA molecules or between parts of the same molecule In RNA, thymine is replaced by uracil (U), so A and U pair

169 Animation: DNA Double Helix Video: DNA Stick Model Video: DNA Surface Model

170 Figure Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding 3 5 (a) DNA Base pair joined by hydrogen bonding (b) Transfer RNA

171 Figure 3.27a (a) DNA Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding

172 Figure 3.27b Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding (b) Transfer RNA

173 DNA and Proteins as Tape Measures of Evolution The linear sequences of nucleotides in DNA molecules are passed from parents to offspring Two closely related species are more similar in DNA than are more distantly related species Molecular biology can be used to assess evolutionary kinship

174 Figure 3.UN05

175 Figure 3.UN06

176 Figure 3.UN06a

177 Figure 3.UN06b

178 Figure 3.UN07