Becker's World of the Cell Chapter 3 Study Guide PDF

Becker’s World of the Cell Tenth Edition Chapter 3 The Macromolecules of the Cell Lectures by Anna Hegsted, Simon Fraser University Modified by Taras Nazarko, G...

Becker’s World of the Cell Tenth Edition Chapter 3 The Macromolecules of the Cell Lectures by Anna Hegsted, Simon Fraser University Modified by Taras Nazarko, Georgia State University Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Macromolecules of the Cell Polymers are synthesized by condensation reactions in which activated monomers are linked together by the removal of water. Most biological macromolecules in cells are synthesized from about 30 common small molecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 3.1 Proteins Proteins are extremely important macromolecules in all organisms, occurring nearly everywhere in the cell. Proteins fall into nine major classes. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Classes of Proteins (1 of 2) Enzymes serve as catalysts, increasing the rates of chemical reactions. Structural proteins—physical support and shape Motility proteins—contraction and movement Regulatory proteins—control and coordinate cell function Transport proteins—move substances into and out of cells Copyright © 2022 Pearson Education, Inc. All Rights Reserved Classes of Proteins (2 of 2) Signaling proteins—communication between cells Receptor proteins—enable cells to respond to chemical stimuli from the environment Defensive proteins—protect against disease Storage proteins—reservoirs of amino acids Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Monomers Are Amino Acids Only 20 kinds of amino acids are used in protein synthesis. Some contain additional amino acids, usually the result of modification. No two different proteins have the same amino acid sequence. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Common Small Molecules in Cells Table 3.1 Common Small Molecules in Cells Kind of Number Figure Number Names of Molecules Role in Cell Molecules Present for Structures Monomeric units of all Amino acids 20 See list in Table 3-2 3-2 proteins Aromatic Components of nucleic 5 Adenine 3-15 bases acids Cytosine 3-15 Guanine 3-15 Thymine 3-15 Uracil 3-15 Sugars Varies Ribose Component of RNA 3-15 Deoxyribose Component of DNA 3-15 Energy metabolism; Glucose component of starch and 3-21 glycogen Energy metabolism; Lipids Varies Fatty acids Components of 3-27a phospholipids and membranes Cholesterol 3-27e Copyright © 2022 Pearson Education, Inc. All Rights Reserved Amino Acids Every amino acid has the same basic structure. Each has a unique side chain, called an R group. All amino acids except glycine have an asymmetric α carbon atom. The specific properties of amino acids depend on the nature of their R groups. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure and Stereochemistry of an Amino Acid Figure 3.1 The Structure and Stereochemistry of an Amino Acid. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Classes of R Groups Nine amino acids have nonpolar, hydrophobic R groups. The remaining 11 amino acids are hydrophilic, with R groups that are either polar or charged at cellular pH. Acidic amino acids are negatively charged, whereas basic amino acids are positively charged. Polar amino acids tend to be found on the surfaces of proteins. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structures of the 20 Amino Acids Found in Proteins Figure 3.2 The Structures of the 20 Amino Acids Found in Proteins. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Table 3.2 Abbreviations for Amino Acids Amino Acid Three-Letter Abbreviation One-Letter Abbreviation Alanine Ala A Arginine Arg R Asparagine Asn N Aspartate Asp D Cysteine Cys C Glutamate Glu E Glutamine Gln Q Glycine Gly G Histidine His H Isoleucine Ile I Leucine Leu L Lysine Lys K Methionine Met M Phenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr T Tryptophan Trp W Tyrosine Tyr Y Valine Val V Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Polymers Are Polypeptides and Proteins Amino acids are linked together stepwise into a linear polymer by dehydration (or condensation) reactions. As the three atoms comprising the H2O are removed, a covalent C—N bond (a peptide bond) is formed. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Directionality of Polypeptides Because of the way peptide bonds are formed, polypeptides have directionality. The end with the amino group is called the N- (or amino) terminus. The end with the carboxyl group is called the C- (or carboxyl) terminus. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Peptide Bond Formation Figure 3.3 Peptide Bond Formation. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Proteins and Polypeptides The process of elongating a chain of amino acids is called protein synthesis. However, the immediate product of amino acid polymerization is a polypeptide. A polypeptide does not become a protein until it has assumed a unique, stable, three-dimensional shape and is biologically active. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Monomeric and Multimeric Proteins Proteins that consist of a single polypeptide are monomeric proteins, whereas multimeric proteins consist of two or more polypeptides. Proteins consisting of two or three polypeptides are called dimers or trimers, respectively. Hemoglobin is a tetramer, consisting of two α subunits and two β subunits. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure of Hemoglobin Figure 3.4 The Structure of Hemoglobin. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Several Kinds of Bonds and Interactions Are Important in Protein Folding and Stability Both covalent bonds and noncovalent interactions are needed for a protein to adopt its proper shape, or conformation. These same bonds and interactions are required for polypeptides to form multimeric proteins. The interactions involve carboxyl, amino, and R groups of the amino acids, called amino acid residues once incorporated into a polypeptide. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Bonds and Interactions Involved in Protein Folding and Stability Figure 3.5 Bonds and Interactions Involved in Protein Folding and Stability. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Disulfide Bonds Covalent disulfide bonds form between the sulfur atoms of two cysteine residues. They form through the removal of two hydrogen ions (oxidation) and can be broken only by the addition of two hydrogens (reduction). Once formed, disulfide bonds confer considerable stability to the protein conformation. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Categories of Disulfide Bonds Intramolecular disulfide bonds form between cysteines in the same polypeptide. Intermolecular disulfide bonds form between cysteines in two different polypeptides. They link the two polypeptides together. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Noncovalent Bonds and Interactions Noncovalent bonds and interactions include hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic interactions. These are individually weaker than covalent bonds but collectively can strongly influence protein structure and stability. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Hydrogen Bonds Hydrogen bonds form in water and between amino acids in a polypeptide chain via their R groups. Hydrogen bond donors (e.g., hydroxyl or amino groups) have hydrogen atoms covalently linked to more electronegative atoms. Hydrogen bond acceptors (e.g., carbonyl or sulfhydryl groups) have an electronegative atom that attracts the donor hydrogen. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Ionic Bonds Ionic bonds, or electrostatic interactions, form between positively and negatively charged R groups. They exert attractive forces over longer distances than some of the other noncovalent interactions. Because they depend on the charge on the R groups, changes in pH can disrupt ionic bonds. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Van Der Waals Interactions Molecules with nonpolar covalent bonds may have transient positively and negatively charged regions. These are called dipoles, and two molecules with dipoles will be attracted to one another if they are close enough. This transient interaction is called a van der Waals interaction or van der Waals force. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Hydrophobic Interactions A hydrophobic interaction is the tendency of hydrophobic molecules or parts of molecules to be excluded from interactions with water. Amino acids with hydrophobic side chains tend to be found within proteins. Protein folding is a balance between the tendency of hydrophilic groups to interact with water and of hydrophobic groups to avoid interaction with water. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Chaperone Interactions Molecular chaperones are proteins that aid in the proper and accurate folding of other proteins. They act during protein synthesis or facilitate refolding. The general mechanism involves shielding parts of the protein from the interactions discussed until more of the protein can be made. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Protein Structure Depends on Amino Acid Sequence and Interactions The overall shape and structure of a protein are described in terms of four levels of organization – Primary structure—amino acid sequence – Secondary structure—local folding of polypeptide – Tertiary structure—three-dimensional conformation – Quaternary structure—interactions between monomeric proteins to form a multimeric unit Copyright © 2022 Pearson Education, Inc. All Rights Reserved Levels of Organization of Protein Structure Table 3.3 Levels of Organization of Protein Structure Kinds of Bonds and Level of Structure Basis of Structure Interactions Involved Primary Amino acid sequence Covalent peptide bonds Hydrogen bonds between NH Folding into α helix, β sheet, or Secondary and CO groups of peptide bonds random coil in the backbone Disulfide bonds, hydrogen Three-dimensional folding of a bonds, ionic bonds, van der Tertiary single polypeptide chain Waals interactions, hydrophobic interactions Association of multiple Quaternary polypeptides to form a Same as for tertiary structure multimeric protein Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Four Levels of Organization of Protein Figure 3.6 The Four Levels of Organization of Protein Structure. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Primary Structure Primary structure refers to the amino acid sequence. By convention, amino acid sequences are written from the N-terminus to the C-terminus, the direction in which the polypeptide was synthesized. The first protein to have its amino acid sequence determined was the hormone insulin. Insulin consists of one A and one B subunit with 21 and 30 amino acids, respectively. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure of Insulin Figure 3.7 The Structure of Insulin. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Determining Amino Acid Sequence Sanger obtained the Nobel Prize for his work on the insulin protein sequence. He cleaved the protein into smaller fragments and analyzed the amino acid order within individual overlapping fragments. Sanger’s work paved the way for the sequencing of hundreds of other proteins and for advancements in the methods used for sequencing proteins. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Importance of Primary Structure Primary structure is important genetically because the sequence is specified by the order of nucleotides in the corresponding messenger RNA. It is important structurally because the order and identity of amino acids directs the formation of the higher-order (secondary and tertiary) structures. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Secondary Structure The secondary structure of a protein describes local regions of structure that result from hydrogen bonding between NH and CO groups along the polypeptide backbone. These result in two major patterns, the α helix and the β sheet. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The α Helix (1 of 2) The α helix is spiral in shape, consisting of the peptide backbone, with R groups jutting out from the spiral. There are 3.6 amino acids per turn of the helix. A hydrogen bond forms between the NH group of one amino acid and the CO group of another amino acid that is one turn away from the first. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The α Helix (2 of 2) Figure 3.8 The α Helix and β Sheet. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The β Sheet (1 of 3) The β sheet is an extended sheetlike conformation with successive atoms of the polypeptide chain located at “peaks” or “troughs.” The R groups jut out on alternating sides of the sheet. Because of the formation of peaks and troughs, it is sometimes referred to as a β-pleated sheet. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The β Sheet (2 of 3) The β sheet is characterized by a maximum of hydrogen bonding, but β sheet formation may involve different polypeptides or different regions of a single polypeptide. If the parts of polypeptides forming the β sheet have the same polarity (relative to the N- and C- termini), they are called parallel. If the parts of polypeptides forming the β sheet have opposite polarity, they are called antiparallel. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The β Sheet (3 of 3) Figure 3.8 The Helix and Sheet. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Amino Acid Sequence and Secondary Structure Certain amino acids (e.g., leucine, methionine, glutamate) tend to form α helices, whereas others (e.g., isoleucine, valine, phenylalanine) tend to form β sheets. Proline cannot form hydrogen bonds and tends to disrupt α helix structures by introducing a bend in the helix. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Motifs Certain combinations of α helices and β sheets have been identified in many proteins. These units of secondary structure consist of short stretches of α helices and β sheets and are called motifs. Examples include the β–α–β, the hairpin loop, and the helix-turn-helix motifs. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Common Structural Motifs Figure 3.9 Common Structural Motifs. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Tertiary Structure The tertiary structure reflects the unique aspect of the amino acid sequence because it depends on interactions of the R groups. Tertiary structure is neither repetitive nor easy to predict. It results from the sum of hydrophobic residues avoiding water, hydrophilic residues interacting with water, the repulsion of similarly charged residues, and attraction between oppositely charged residues. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Native Conformation The most stable possible three-dimensional structure of a particular polypeptide is called the native conformation. Proteins can be divided into two broad categories – Fibrous proteins – Globular proteins Copyright © 2022 Pearson Education, Inc. All Rights Reserved Fibrous Proteins Fibrous proteins have extensive regions of secondary structure, giving them a highly ordered, repetitive structure. Some examples include: – Fibroin proteins of silk – Keratin proteins of hair and wool – Collagen found in tendons and skin – Elastin found in ligaments and blood vessels Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Fibroin Structure Figure 3.10 Fibroin Structure. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure of Hair Figure 3.11 The Structure of Hair. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Globular Proteins Most proteins are globular proteins that are folded into compact structures. Each type of globular protein has its own unique tertiary structure. Most enzymes are globular proteins. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Three-Dimensional Structure of Ribonuclease Figure 3.12 The Three- Dimensional Structure of Ribonuclease. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Structures of Globular Proteins Globular proteins can be mainly α helical, mainly β sheet, or a mixture of both structures. Many globular proteins consist of a number of segments called domains. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structures of Several Globular Proteins Figure 3.13 Structures of Several Globular Proteins. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Protein Domains A domain is a discrete, locally folded unit of tertiary structure, usually with a specific function. A domain is typically 50–350 amino acids long, with regions of α helices and β sheets packed together. Proteins with similar functions often share a common domain. Proteins with multiple functions usually have a separate domain for each function, like modular units from which globular proteins are constructed. Copyright © 2022 Pearson Education, Inc. All Rights Reserved An Example of Protein Containing Two Functional Domains Figure 3.14 An Example of a Protein Containing Two Functional Domains. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Prediction of Tertiary Structure It is known that primary structure determines the final folded shape of a protein. However, we are still not able to predict exactly how a given protein will fold, especially for larger proteins. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Quaternary Structure The quaternary structure of a protein is the level of organization concerned with subunit interactions and assembly. The term applies specifically to multimeric proteins. Some proteins consist of multiple identical subunits; others, such as hemoglobin, contain two or more types of polypeptides. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Maintenance of Quaternary Structure The bonds and forces maintaining quaternary structure are the same as those responsible for tertiary structure. The process of subunit assembly is usually spontaneous. Sometimes, molecular chaperones are required to assist the process. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Higher Levels of Assembly A higher level of assembly is possible in the case of proteins (often enzymes) that are organized into multiprotein complexes. Each protein in the complex may be involved sequentially in a common multistep process. An example is the pyruvate dehydrogenase complex, in which three enzymes and five other proteins form a multienzyme complex. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 3.2 Nucleic Acids Nucleic acids are of paramount importance to the cells because they store, transmit, and express genetic information. They are linear polymers of nucleotides. DNA is deoxyribonucleic acid, and RNA is ribonucleic acid. Copyright © 2022 Pearson Education, Inc. All Rights Reserved D N A and R N A Differ DNA and RNA differ chemically and in their role in the cell – RNA contains the five-carbon sugar ribose, and DNA contains the related sugar deoxyribose. – DNA serves as the repository of genetic information, whereas RN A plays several roles in expressing that information. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Monomers Are Nucleotides RNA and DNA each consist of only four different types of nucleotides, the monomeric units. Each nucleotide consists of a five-carbon sugar to which a phosphate group and N-containing aromatic base are attached. Each base is either a purine or a pyrimidine. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure of a Nucleotide Figure 3.15 The Structure of a Nucleotide. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Types of Nucleotides Purines are adenine (A) and guanine (G). Pyrimidines are thymine (T) and cytosine (C), and in RNA, uracil (U). The sugar-base portion without the phosphate group is called a nucleoside. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Nomenclature Nucleosides with one phosphate group can be thought of as nucleoside monophosphates (example: adenosine monophosphate, AMP). Adenosine diphosphate (ADP) has two phosphate groups, and adenosine triphosphate (ATP) has three. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Bases, Nucleosides, and Nucleotides of RNA and DNA Table 3.4 The Bases, Nucleosides, and Nucleotides of RNA and DNA Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Phosphorylated Forms of Adenosine Figure 3.16 The Phosphorylated Forms of Adenosine. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Polymers Are DNA and RNA Nucleic acids are linear polymers of nucleotides linked by a 3′, 5′ phosphodiester bridge, a phosphate group linked to two adjacent nucleotides via two phosphodiester bonds. The polynucleotide formed by this process has a directionality with a 5′ phosphate group at one end and a 3′ hydroxyl group at the other. Nucleotide sequences are conventionally written in the 5′ to 3′ direction. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure of Nucleic Acids Figure 3.17 The Structure of Nucleic Acids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Nucleic Acid Synthesis A preexisting molecule is used to ensure that new nucleotides (NTPs for RNA, dNTPs for DNA) are added in the correct order. This molecule is called a template, and correct base pairing between the template and the incoming nucleotide is required to specify correct order. A complementary relationship exists between certain purines and pyrimidines. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Complementary Base Pairing Complementary base pairing allows A to form two hydrogen bonds with T and G to form three hydrogen bonds with C. This base pairing is a fundamental property of nucleic acids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Hydrogen Bonding in DNA Nucleic Acid Structure Figure 3.18 Hydrogen Bonding in DNA Nucleic Acid Structure. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The DNA Molecule Is a Double- Stranded Helix Francis Crick and James Watson postulated the double helix structure of DNA in 1953. The structure accounted for the known physical and chemical properties of DNA. It also suggested a mechanism for DNA replication. Two antiparallel and complementary strands of DNA twist around a common axis to form a right-handed spiral structure. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure of Double-Stranded DNA Figure 3.19 The Structure of Double- Stranded DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Base Pairing and RNA RNA is normally single stranded. RNA structure also depends on base pairing. However, the pairing is usually between bases in different areas of the same molecule and is less extensive than that of DNA. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 3.3 Polysaccharides Polysaccharides are long chain polymers of sugars and sugar derivatives. They serve primarily in structure and storage. They usually consist of a single kind of repeating unit or sometimes an alternating pattern of two kinds. Short polymers, oligosaccharides, are sometimes attached to cell surface proteins. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Monomers Are Monosaccharides Repeating units of polysaccharides are monosaccharides. A sugar may be an aldehyde, aldosugars with a terminal carbonyl group; or ketone, ketosugars with an internal carbonyl group. Sugars within these groups are named generically based on how many carbon atoms they contain. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Structures of Monosaccharides Figure 3.20 Structures of Monosaccharides. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Classification of Sugars Most sugars have between three and seven carbons and are classified as – Trioses (three carbons) – Tetroses (four carbons) – Pentoses (five carbons) – Hexoses (six carbons) – Heptoses (seven carbons) Copyright © 2022 Pearson Education, Inc. All Rights Reserved Glucose The single most common monosaccharide is the aldohexose D-glucose (C6H12O6). The formula CnH2nOn is common for sugars and led to the general term carbohydrate. For every molecule of CO2 incorporated into a sugar, one water molecule is consumed. The carbons of glucose (and other organic molecules) are numbered from the more oxidized, carbonyl end. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure of Glucose D-glucose is the most stable form of glucose though many other stereoisomers are possible. D-glucose is often depicted as a linear molecule, as in the Fischer projection, in which the H and OH groups are intended to project out of the plane of the diagram. In the cell, D-glucose exists in a dynamic equilibrium between the linear and ring form. The Haworth projection shows the ring form of the molecule. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure of D-Glucose Figure 3.21 The Structure of D-Glucose. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Two Ring Forms of D-Glucose The formation of a ring by D-glucose can result in two alternative forms. These depend on the spatial orientation of the hydroxyl group on carbon number 1. These forms are designated α (hydroxyl group downward) and β (hydroxyl group upward). Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Ring Forms of D-Glucose Figure 3.22 The Ring Forms of D-Glucose. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Glucose Also Exists in Disaccharides Glucose exists in disaccharides, in which two monosaccharide units are covalently linked. Common disaccharides include – Maltose, two glucose units – Lactose, one glucose linked to one galactose – Sucrose, one glucose linked to one fructose Copyright © 2022 Pearson Education, Inc. All Rights Reserved Disaccharides The linkage of disaccharides is a glycosidic bond, formed between two monosaccharides by the elimination of water. Glycosidic bonds involving the α form of glucose are called α glycosidic bonds (e.g., maltose); those involving the β form are called β glycosidic bonds (e.g., lactose). Copyright © 2022 Pearson Education, Inc. All Rights Reserved Some Common Disaccharides Figure 3.23 Some Common Disaccharides. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Polymers Are Storage and Structural Polysaccharides The most familiar storage polysaccharides are starch in plant cells and glycogen in animal cells and bacteria. Both consist of α-D-glucose units linked by α glycosidic bonds, involving carbons 1 and 4 (1→4). Occasionally α(1→6) bonds may form, allowing for the formation of side chains (branching). Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure of Starch and Glycogen Figure 3.24 The Structure of Starch and Glycogen. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Glycogen Glycogen is highly branched, the branches occurring every 8–10 glucose units along the backbone. Glycogen is stored mainly in the liver (as a source of glucose) and muscle tissues (as a fuel source for muscle contraction) of animals. Bacteria also store glycogen as a glucose reserve. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Starch (1 of 2) Starch is the glucose reserve commonly found in plant tissue. It occurs both as unbranched amylose (10–30%) and branched amylopectin (70–90%). Amylopectin has α(1→6) branches once every 12–25 glucose units and has longer side chains than glycogen. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Starch (2 of 2) Starch is stored as starch grains within the plastids: – Chloroplasts, the sites of carbon fixation and sugar synthesis in photosynthesis – Amyloplasts, which are specialized for starch storage Copyright © 2022 Pearson Education, Inc. All Rights Reserved Structural Polysaccharides The best-known structural polysaccharide is the cellulose found in plant cell walls. Cellulose, composed of repeating monomers of β-D-glucose, is very abundant in plants. Mammals cannot digest cellulose (though some have microorganisms in their digestive systems that can). Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Structure of Cellulose Figure 3.25 The Structure of Cellulose. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Other Structural Polysaccharides The cellulose of fungal cell walls differs from that of plants and may contain either β(1→4) or β(1→3) linkages. Bacterial cell walls contain two kinds of sugars: GlcNAc (N-acetylglucosamine) and MurNAc (N-acetylmuramic acid). Both are derivatives of β-glucosamine and are linked alternately in cell walls. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Chitin The polysaccharide chitin consists of GlcNAc units only, joined by β(1→4) bonds. Chitin is found in insect exoskeletons, crustacean shells, and fungal cell walls. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Polysaccharides of Bacterial Cell Walls and Insect Exoskeletons Figure 3.26 Polysaccharides of Bacterial Cell Walls and Insect Exoskeletons. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Polysaccharide Structure Depends on the Type of Glycosidic Bonds Involved α and β glycosidic bonds are associated with marked structural differences. Starch and glycogen (α polysaccharides) form loose helices that are not highly ordered because of the side chains. Cellulose (that forms β linkages) exists as rigid linear rods that aggregate into microfibrils, about 5–20 nm in diameter. Plant and fungal cells walls contain these rigid microfibrils in a noncellulose matrix containing other polymers (hemicellulose, pectin) and a protein called extensin. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 3.4 Lipids Lipids are not formed by the same type of linear polymerization that forms proteins, nucleic acids, and polysaccharides. However, they are regarded as macromolecules because of their high molecular weight and their importance in cellular structures, particularly membranes. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Features of Lipids Although heterogeneous, all have a hydrophobic nature and thus little affinity for water; they are readily soluble in nonpolar solvents such as chloroform or ether. They have relatively few polar groups, but some are amphipathic, having polar and nonpolar regions. Functions include energy storage, membrane structure, or specific biological functions such as signal transmission. Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Main Classes of Lipids (1 of 2) The lipids can be divided into six classes based on their structure: – Fatty acids – Triacylglycerols – Phospholipids – Glycolipids – Steroids – Terpines Copyright © 2022 Pearson Education, Inc. All Rights Reserved The Main Classes of Lipids (2 of 2) Figure 3.27 The Main Classes of Lipids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Fatty Acids Figure 3.27 The Main Classes of Lipids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Fatty Acids Are the Building Blocks of Several Classes of Lipids Fatty acids are components of several other kinds of lipids. A fatty acid is a long amphipathic, unbranched hydrocarbon chain with a carboxyl group at one end. The polar carboxyl group is the “head,” and the nonpolar hydrocarbon chain is the “tail.” Copyright © 2022 Pearson Education, Inc. All Rights Reserved Fatty Acid Structure (1 of 2) The hydrocarbon tails are variable in length but usually 12 to 20 carbons long. Even numbers of carbons are favored because fatty acid synthesis occurs via the stepwise addition of two-carbon units to the growing chain. Fatty acids are highly reduced and so yield a large amount of energy upon oxidation. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Some Common Fatty Acids in Cells Table 3.5 Some Common Fatty Acids in Cells Number of Carbons Number of Double Bonds Common Name* 12 0 Laurate 14 0 Myristate 16 0 Palmitate 18 0 Stearate 20 0 Arachidate 16 1 Palmitoleate 18 1 Oleate 18 2 Linoleate 18 3 Linolenate 20 4 Arachidonate *Shown are the names for the ionized forms of the fatty acids as they exist at the near neutral pH of most cells. For the names of the free fatty acids, simply replace the –ate ending with –ic acid. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Fatty Acid Structure (2 of 2) In saturated fatty acids, each carbon atom in the chain is bonded to the maximum number of hydrogens. These have long straight chains that pack together well. Unsaturated fatty acids have one or more double bonds, so they have bends in the chains and are less tightly packed. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Structures of Saturated and Unsaturated Fatty Acids Figure 3.28 Structures of Saturated and Unsaturated Fatty Acids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Trans Fats Trans fats are a type of unsaturated fatty acid with a particular type of double bond that causes less of a bend in the chain. They are relatively rare in nature and are produced artificially in shortening and margarine. They have been linked to increased risk of heart disease and elevated cholesterol levels. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Triacylglycerols and Their Synthesis Figure 3.27 The Main Classes of Lipids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Triacylglycerols Are Storage Lipids Triacylglycerols, also known as triglycerides, consist of a glycerol molecule with three fatty acids attached to it. Glycerol is a three-carbon alcohol with a hydroxyl group on each carbon. Fatty acids are linked to glycerol, one at a time, by ester bonds formed by the removal of water. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Triacylglycerol Structure Monoacylglycerols contain a single fatty acid. Diacylglycerols have two fatty acids. The three fatty acids on a triacylglycerol may vary in length and degree of saturation. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Triacylglycerol Function The main function of triacylglycerols is energy storage. Triacylglycerols containing mostly saturated fats are usually solid or semisolid at room temperature and are called fats. Triacylglycerols in plants are liquid at room temperature (e.g., vegetable oil) and are predominantly unsaturated. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Phospholipids Figure 3.27 The Main Classes of Lipids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Phospholipids Are Important in Membrane Structure Phospholipids are important to membrane structure because of their amphipathic nature. Phospholipids can be divided into phosphoglycerides or sphingolipids, depending on their chemistry. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Phosphoglycerides (1 of 2) Phosphoglycerides are the predominant phospholipids in most membranes. The basic components of phosphoglycerides is phosphatidic acid, which has two fatty acids and a phosphate group attached to a glycerol. Membrane phosphoglycerides invariably have a small hydrophilic alcohol linked to the phosphate by an ester bond. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Structures of Common Phosphoglycerides Figure 3.29 Structures of Common Phosphoglycerides. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Phosphoglycerides (2 of 2) The alcohol is usually serine, ethanolamine, choline, or inositol, which contributes to the polar nature of the phospholipid head group. Typical phosphoglycerides often have one saturated and one unsaturated fatty acid. The length and degree of saturation of the fatty acids have profound effects on membrane fluidity. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Sphingolipids (1 of 2) Sphingolipids are based on the amine sphingosine, which has a long hydrocarbon chain with a single site of unsaturation near the polar end. Sphingosine can form an amide bond to a long-chain fatty acid, resulting in a molecule called a ceramide. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Sphingolipids (2 of 2) A whole family of sphingolipids exists, with different polar groups attached to the hydroxyl group of the ceramide. Sphingolipids are predominantly found in the outer leaflet of the plasma membrane bilayer, often in lipid rafts, localized domains within a membrane. Lipid rafts are important in communication between a cell and its external environment. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Glycolipids Figure 3.27 The Main Classes of Lipids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Glycolipids Are Specialized Membrane Components Glycolipids are lipids containing a carbohydrate instead of a phospholipid and are often derivatives of sphingosine and glycerol (glycosphingolipids). Carbohydrate groups attached to a glycolipid may be one to six sugar units (D-glucose, D-galactose, or N-acetyl-D- galactosamine). Glycolipids occur largely on the outer monolayer of the plasma membrane. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Steroids Figure 3.27 The Main Classes of Lipids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Steroids Are Lipids with a Variety of Functions Steroids are derivatives of a four-ringed hydrocarbon skeleton, which distinguishes them from other lipids. They are relatively nonpolar and therefore hydrophobic. Steroids differ from one another in the positions of double bonds and functional groups. The most common steroid in animal cells is cholesterol. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Structures of Several Common Steroid Hormones Figure 3.30 Structures of Several Common Steroid Hormones. Copyright © 2022 Pearson Education, Inc. All Rights Reserved A Variety of Sterols Cholesterol is insoluble and found primarily in plasma membranes of animal cells and most membranes of organelles. Similar molecules are found in plant cells (stigmasterol and sitosterol) and fungal cells (ergosterol). Copyright © 2022 Pearson Education, Inc. All Rights Reserved Steroid Hormones (1 of 2) Cholesterol is the starting material for synthesis of steroid hormones, including male and female sex hormones, the glucocorticoids, and the mineralocorticoids. Sex hormones include estrogens produced by the ovaries of females (e.g., estradiol) and androgens produced by male testes (e.g., testosterone). Copyright © 2022 Pearson Education, Inc. All Rights Reserved Steroid Hormones (2 of 2) The glucocorticoids (e.g., cortisol) are a family of hormones that promote synthesis of glucose and suppress inflammation. Mineralocorticoids (e.g., aldosterone) regulate ion balance by promoting reabsorption of sodium, chloride, and bicarbonate ions by the kidney. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Terpenes Figure 3.27 The Main Classes of Lipids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Terpenes Are Formed from Isoprene Terpenes are synthesized from the five-carbon compound isoprene and are sometimes called isoprenoids. Isoprene and its derivatives are joined in various combinations to produce substances such as vitamin A and carotenoid pigments. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Other Isoprene-Based Compounds The isoprene-based compounds, dolichols, are involved in activating sugar compounds. Electron carriers such as coenzyme Q and plastoquinone are also isoprene derivatives. Polyisoprenoids, polymers of isoprene, are found in cell membranes of the Archaea. Copyright © 2022 Pearson Education, Inc. All Rights Reserved Copyright This work is protected by United States copyright laws and is provided solely for the use of instructors in teaching their courses and assessing student learning. Dissemination or sale of any part of this work (including on the World Wide Web) will destroy the integrity of the work and is not permitted. The work and materials from it should never be made available to students except by instructors using the accompanying text in their classes. All recipients of this work are expected to abide by these restrictions and to honor the intended pedagogical purposes and the needs of other instructors who rely on these materials. Copyright © 2022 Pearson Education, Inc. All Rights Reserved