Chapter2_3710_10th.pdf

8/27/23 Becker’s World of the Cell Tenth Edition Chapter 2 The Chemistry of the Cell Lectur...

8/27/23 Becker’s World of the Cell Tenth Edition Chapter 2 The Chemistry of the Cell Lectures by Anna Hegsted, Simon Fraser University Copyright © 2022 Pearson Education, Inc. All Rights Reserved 1 The Chemistry of the Cell Five principles important to cell biology – Characteristics of carbon – Characteristics of water – Selectively permeable membranes – Synthesis by polymerization of small molecules – Self-assembly Copyright © 2022 Pearson Education, Inc. All Rights Reserved 2 2.1 The Importance of Carbon Organic chemistry is the study of carbon- containing compounds. Biological chemistry (biochemistry) is the study of the chemistry of living systems. The carbon atom (C) is the most important atom in biological molecules. Specific bonding properties of carbon account for the characteristics of carbon-containing compounds (diversity and stability). Copyright © 2022 Pearson Education, Inc. All Rights Reserved 3 1  8/27/23 Bonding Properties of the Carbon Atom The carbon atom has a valence of 4 (outermost electron shell lacks 4 of 8 electrons needed to fill it), so it can form four chemical bonds with other atoms. Low atomic weight. Carbon atoms are most likely to form covalent bonds with other carbon atoms and with oxygen (O), hydrogen (H), nitrogen (N), and sulfur (S). Covalent bonds—the sharing of a pair of electrons between two atoms Copyright © 2022 Pearson Education, Inc. All Rights Reserved 4 Some Biologically Important Atoms and Their Valences Figure 2.1 Electron Configurations of Some Biologically Important Atoms and Molecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 5 Covalent Bonding of Carbon Atoms Sharing one pair of electrons between two atoms forms a single bond Double bonds and triple bonds involve two atoms sharing two and three pairs of electrons, respectively. Whether carbon atoms form single, double, or triple bonds with other atoms, the total number of covalent bonds per carbon atom is four. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 6 2  8/27/23 Some Simple Organic Molecules with Single Bonds Figure 2.1 Electron Configurations of Some Biologically Important Atoms and Molecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 7 Some Simple Molecules with Double Bonds Figure 2.1 Electron Configurations of Some Biologically Important Atoms and Molecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 8 Some Simple Molecules with Triple Bonds Figure 2.1 Electron Configurations of Some Biologically Important Atoms and Molecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 9 3  8/27/23 Carbon-Containing Molecules Are Stable Stability is expressed as bond energy—the amount of energy required to break 1 mole (~6 × 1023) of such bonds. Bond energy is expressed as calories per mole (cal/mol). A calorie is the amount of energy needed to raise the temperature of 1 g of water by 1°C. A kcal (kilocalorie) is equal to 1000 calories. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 10 Bond Energies of Covalent Bonds A lot of energy is needed to break covalent bonds – C—C, 83 kcal/mol – C—N, 70 kcal/mol – C—O, 84 kcal/mol – C—H, 99 kcal/mol Double and triple bonds are even harder to break – C ═ C, 146 kcal/mol – C ═ C, 212 kcal/mol Copyright © 2022 Pearson Education, Inc. All Rights Reserved 11 Energies of Biologically Important Bonds Figure 2.2 Energies of Biologically Important Bonds. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 12 4  8/27/23 Strong Covalent Bonds Necessary for Life Solar radiation has an Figure 2.3 The Relationship Between Energy (E) and Wavelength (λ) for inverse relationship between Electromagnetic Radiation. wavelength and bond energy. The visible portion of sunlight is lower in energy than C—C bonds. So, visible light cannot break the bonds of organic molecules. Higher-energy ultraviolet light is more hazardous. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 13 Carbon-Containing Molecules Are Diverse A large variety of compounds can be formed by relatively few kinds of atoms. Rings or chains of carbon atoms can form. Chains may branch and may have single or double bonds between the carbons. Variety of structures possible is due to the tetravalent nature of the carbon atom. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 14 Hydrocarbons Hydrocarbons are chains or rings composed only of carbon and hydrogen. They are economically important; for example, petroleum products, including gasoline and natural gas, are hydrocarbons. In biology, they are of limited importance because they are not soluble in water, except as a component of biological membranes. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 15 5  8/27/23 Some Simple Hydrocarbon Compounds Figure 2.4 Some Simple Hydrocarbon Compounds. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 16 Biological Compounds These normally contain carbon, hydrogen, and one or more atoms of oxygen, as well as nitrogen, phosphorus, or sulfur. These (O, N, P, S) are usually part of functional groups, common arrangements of atoms that confer specific chemical properties on a molecule. – Confer water solubility – Chemical reactivity Copyright © 2022 Pearson Education, Inc. All Rights Reserved 17 Functional Groups Important functional groups include – Carboxyl and phosphate groups (negatively charged) – Amino groups (positively charged) – Hydroxyl, sulfhydroxyl, carbonyl, and aldehyde groups (uncharged, but polar) Figure 2.5 Some Common Functional Groups Found in Biological Molecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 18 6  8/27/23 Bond Polarity In polar bonds, electrons are not shared equally between two atoms. Polar bonds result from a high electronegativity (affinity for electrons) of oxygen and sulfur compared to carbon and hydrogen. Polar bonds have high water solubility compared to C—C or C—H bonds, in which electrons are shared equally. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 19 Carbon-Containing Molecules Can Form Stereoisomers The carbon atom is a tetrahedral structure. An asymmetric carbon atom has four different substituents Two stereoisomers (non-superimposable configurations like mirror images) are possible for each asymmetric carbon atom A compound with n asymmetric carbons will have 2n possible stereoisomers Copyright © 2022 Pearson Education, Inc. All Rights Reserved 20 Stereoisomers Figure 2.6 Stereoisomers. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 21 7  8/27/23 Stereoisomers of Biological Molecules Figure 2.7 Stereoisomers of Biological Molecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 22 2.2 The Importance of Water Water has an indispensable role as the universal solvent in biological systems. It is the single most abundant component of cells and organisms. About 75–85% of a cell by weight is water. Many cells also depend on an aqueous extracellular environment. Its chemical characteristics make water indispensable for life. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 23 Water Molecules Are Polar Unequal distribution of electrons gives water its polarity. The water molecule is bent rather than linear. The oxygen atom at one end of the molecule is highly electronegative, drawing the electrons toward it. This results in a partial negative charge at this end of the molecule, and a partial positive charge around the hydrogen atoms. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 24 8  8/27/23 Polarity of Water The most critical attribute of water is its polarity, which accounts for water’s: –Cohesiveness –Temperature- stabilizing capacity Figure 2.8 Hydrogen Bonding Among Water Molecules. –Solvent properties Copyright © 2022 Pearson Education, Inc. All Rights Reserved 25 Water Molecules Are Cohesive Figure 2.8 Hydrogen Bonding Among Water Molecules. Because of their polarity, water molecules are attracted to each other. The electronegative oxygen of one molecule is associated with the electropositive hydrogens of nearby molecules. Such associations, called hydrogen bonds, are about 1/10 as strong as covalent bonds. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 26 Hydrogen Bonds and Cohesiveness Water is characterized by an extensive network of hydrogen-bonded molecules, which make it cohesive. The combined effect of many hydrogen bonds accounts for water’s high – Surface tension – Boiling point – Specific heat – Heat of vaporization Copyright © 2022 Pearson Education, Inc. All Rights Reserved 27 9  8/27/23 Surface Tension of Water Is the result of the collective strength of vast numbers of hydrogen bonds Allows insects to walk along the surface of water without breaking the surface Allows water to move upward through conducting tissues of some plants Copyright © 2022 Pearson Education, Inc. All Rights Reserved 28 Walking on Water Figure 2.9 Walking on Water. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 29 Water Has a High Temperature- Stabilizing Capacity High specific heat gives water its temperature-stabilizing capacity. Specific heat—the amount of heat a substance must absorb to raise its temperature 1ºC The specific heat of water is 1.0 calorie per gram, which is much higher than most liquids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 30 10  8/27/23 Temperature-Stabilizing Capacity Heat that would raise the temperature of other liquids is first used to break numerous hydrogen bonds in water. Water therefore changes temperature relatively slowly, protecting living systems from extreme temperature changes. Without this characteristic of water, energy released in cell metabolism would cause overheating and death. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 31 Heat of Vaporization Heat of vaporization is the amount of energy required to convert 1 gram of liquid into vapor. This value is high for water because of the many hydrogen bonds that must be broken. The high heat of vaporization makes water an excellent coolant. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 32 Water Is an Excellent Solvent A solvent is a fluid in which another substance, the solute, can dissolve. Because of its polarity, water is able to dissolve a large variety of substances. Many of the molecules in cells are also polar and so can form hydrogen bonds or ionic bonds with water. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 33 11  8/27/23 Solutes Solutes that have an affinity for water and dissolve in it easily are called hydrophilic (“water-loving”). Many small molecules—sugars, organic acids, some amino acids—are hydrophilic. Molecules not easily soluble in water—such as lipids and proteins in membranes—are called hydrophobic (“water-fearing”). Copyright © 2022 Pearson Education, Inc. All Rights Reserved 34 NaCl in Water A salt, such as NaCl, exists as a lattice of Na+ cations (positively charged) and Cl− anions (negatively charged). For a salt to dissolve in a liquid, the attraction of anions and cations in the salt must be overcome. In water, anions and cations take part in electrostatic interactions with the water molecules, causing the ions to separate. The polar water molecules form spheres of hydration around the ions, decreasing their chances of reassociation. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 35 The Solubilization of Sodium Chloride Figure 2.10 The Solubilization of Sodium Chloride. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 36 12  8/27/23 Solubility of Molecules with No Net Charge Some molecules have no net charge at neutral pH. Some of these are still hydrophilic because they have some regions that are positively charged and some that are negatively charged. Water molecules will cluster around such regions and prevent the solute molecules from interacting with each other. Hydrophobic molecules, such as hydrocarbons, tend to disrupt the hydrogen bonding of water and are therefore repelled by water molecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 37 2.3 The Importance of Selectively Permeable Membranes Cells need a physical barrier between their contents and the outside environment. Such a barrier should be: – Impermeable to much of the cell contents – Not completely impermeable, allowing some materials into and out of the cell – Insoluble in water to maintain the integrity of the barrier – Permeable to water to allow flow of water in and out of the cell Copyright © 2022 Pearson Education, Inc. All Rights Reserved 38 Membranes Surround Cells The cellular membrane is a hydrophobic permeability barrier. It consists of phospholipids, glycolipids, and membrane proteins. The membranes of most organisms also contain sterols —cholesterol (animals), ergosterols (fungi), or phytosterols (plants). Copyright © 2022 Pearson Education, Inc. All Rights Reserved 39 13  8/27/23 Membrane Lipids Are Amphipathic Membrane lipids are amphipathic; they have both hydrophobic and hydrophilic regions. Amphipathic phospholipids have a polar head; the polarity is due to a negatively charged phosphate group linked to a positively charged group. They also have two nonpolar hydrocarbon tails. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 40 The Amphipathic Nature of Membrane Phospholipids Figure 2.11 The Amphipathic Nature of Membrane Phospholipids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 41 A Membrane Is a Lipid Bilayer with Proteins Embedded in It In water, amphipathic molecules undergo hydrophobic interactions. The polar heads of membrane phospholipids face outward toward the aqueous environment. The hydrophobic tails are oriented inward. The resulting structure is the lipid bilayer. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 42 14  8/27/23 The Lipid Bilayer as the Basis of Membrane Figure 2.12 The Lipid Bilayer as the Basis of Membrane Structure. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 43 Lipid Bilayers Are Selectively Permeable Because of the hydrophobic interior, a lipid bilayer is readily permeable to nonpolar molecules. However, it is quite impermeable to most polar molecules and highly impermeable to all ions. Cellular constituents are mostly polar or charged and are prevented from entering or leaving the cell. However, very small molecules diffuse. Biological membranes are best described as selectively permeable Copyright © 2022 Pearson Education, Inc. All Rights Reserved 44 Permeability of Membranes of Various Classes of Solutes Figure 2.13 Permeability of Membranes to Various Classes of Solutes. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 45 15  8/27/23 Ions Must Be Transported Even the smallest ions are unable to diffuse across a membrane. This is due to both the charge on the ion and the surrounding hydration shell. Ions must be transported across a membrane by specialized transport proteins. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 46 Transport Proteins Transport proteins act as either hydrophilic channels or carriers. Transport proteins of either type are specific for a particular ion or molecule or class of closely related molecules or ions. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 47 2.4 The Importance of Synthesis by Polymerization Most cellular structures are made of ordered arrays of linear polymers called macromolecules. Important macromolecules in the cell include proteins, nucleic acids, and polysaccharides. Lipids share some features of macromolecules but are synthesized somewhat differently. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 48 16  8/27/23 Macromolecules Are Critical for Cellular Form and Function Cellular hierarchy: biological molecules and structures are organized into a series of levels, each building on the preceding one. Most cellular structures are composed of small water-soluble organic molecules obtained from other cells or synthesized from nonbiological molecules (C O2 , N H4 , P O4 , etc.). Copyright © 2022 Pearson Education, Inc. All Rights Reserved 49 Hierarchical Assembly Figure 2.14 The Hierarchical Nature of Cellular Structures and Their Assembly. The small organic molecules then polymerize to form biological macromolecules. Biological macromolecules may function on their own or assemble into a variety of supramolecular structures. The supramolecular structures are components of organelles and other subcellular structures that make up the cell. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 50 General Principle of Biological Chemistry The macromolecules that are responsible for most of the form and order of living systems are generated by the polymerization of small organic molecules. The repeating units are called monomers; examples include the glucose present in sugar or starch, amino acids in proteins, and nucleotides in nucleic acids. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 51 17  8/27/23 The Synthesis of Biological Macromolecules Figure 2.15 The Synthesis of Biological Macromolecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 52 Cells Contain Three Different Kinds of Macromolecular Polymers The major macromolecular polymers in the cell are proteins, nucleic acids, and polysaccharides. Nucleic acids and proteins have a variety of monomers that may be arranged in nearly limitless ways; the order and type of monomer are critical for function. Polysaccharides, composed of one or two monomers, have relatively few types. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 53 Informational Macromolecules Nucleic acids are called informational macromolecules because the order of the four kinds of nucleotide monomers in each is nonrandom and carries important information. – D N A and R N A serve a coding function, containing the information needed to specify the precise amino acid sequences of proteins. Proteins are informational macromolecules because the amino acid sequence determines the three-dimensional structure, thus the function, of a protein Copyright © 2022 Pearson Education, Inc. All Rights Reserved 54 18  8/27/23 Polysaccharides Polysaccharides typically consist of single repeating subunits or two alternating subunits. The order of monomers carries no information and is not essential for function. Most polysaccharides are structural macromolecules (e.g., cellulose or chitin) or storage macromolecules (e.g., starch or glycogen). Copyright © 2022 Pearson Education, Inc. All Rights Reserved 55 Figure 2-16A Figure 2-16B Copyright © 2022 Pearson Education, Inc. All Rights Reserved 56 Macromolecules Are Synthesized by Stepwise Polymerization of Monomers (1 of 2) Despite some differences, the production of most polymers follows the basic principles: 1. Macromolecules are always synthesized by the stepwise polymerization of monomers. 2. The addition of each monomer occurs by the removal of a water molecule (condensation reaction). Copyright © 2022 Pearson Education, Inc. All Rights Reserved 57 19  8/27/23 Macromolecules Are Synthesized by Stepwise Polymerization of Monomers (2 of 2) 3. The monomers must be present as activated monomers before condensation can occur. 4. To become activated, a monomer must be coupled to a carrier molecule. 5. The energy to couple a monomer to a carrier molecule is provided by adenosine triphosphate (A T P) or a related high-energy compound. 6. Macromolecules have directionality; the chemistry differs at each end of the polymer. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 58 Macromolecule Biosynthesis Figure 2.16 Macromolecule Biosynthesis. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 59 Carrier Molecules A different kind of carrier molecule is used for each kind of polymer. – For protein synthesis, amino acids are linked to carriers called transfer R N A (t R N A). – Sugars (often glucose) that form polysaccharides are activated by linking them to A D P (adenosine diphosphate), or U D P (uridine diphosphate). – For nucleic acids, the nucleotides themselves are high-energy molecules (A T P, GT P). Copyright © 2022 Pearson Education, Inc. All Rights Reserved 60 20  8/27/23 Condensation and Hydrolysis Activated monomers react with one another in a condensation reaction and then release the carrier molecule. The continued elongation of the polymer is a sequential, stepwise process. Degradation of polymers occurs via hydrolysis, breaking the bond between monomers through addition of one H+ and one OH− (a water molecule). Copyright © 2022 Pearson Education, Inc. All Rights Reserved 61 2.5 The Importance of Self-Assembly The principle of self-assembly states that information needed to specify the folding of macromolecules and their interactions to form complex structures is inherent in the polymers themselves. Proteins called molecular chaperones are sometimes needed to prevent incorrect folding. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 62 Noncovalent Bonds and Interactions Are Important in the Folding of Macromolecules Many cellular structures are held together by noncovalent bonds and interactions. – Hydrogen bonds (previously discussed) – Ionic bonds – Van der Waals interactions – Hydrophobic interactions Copyright © 2022 Pearson Education, Inc. All Rights Reserved 63 21  8/27/23 Ionic Bonds Ionic bonds are strong noncovalent electrostatic interactions between two oppositely charged ions. They form between negatively charged and positively charged functional groups. Ionic bonds between functional groups on the same protein play an important role in the structure of the protein. Ionic bonds may also influence the binding between macromolecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 64 Van der Waals Interactions Van der Waals interactions (or forces) are weak attractions between two atoms that occur only if the atoms are very close to one another and oriented appropriately. Atoms that are too close together will repel one another. The van der Waals radius of an atom defines how close other atoms can come to it, and it is the basis for space-filling models of molecules. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 65 © 2016 Pearson Education, Inc. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 66 22  8/27/23 Hydrophobic Interactions Hydrophobic interactions describe the tendency of nonpolar groups within a macromolecule to associate with each other and minimize their contact with water. These interactions commonly cause nonpolar groups to be found in the interior of a protein or embedded in the nonpolar interior of a membrane. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 67 Many Proteins Spontaneously Fold into Their Biologically Functional State The immediate product of amino acid polymerization is a polypeptide. Once the polypeptide has assumed its correct three-dimensional structure, or conformation, it is called a protein. The native (natural) conformation of a protein can be altered by changing conditions, such as the pH or temperature, or by treating with certain chemical agents. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 68 Denaturation and Renaturation The unfolding of polypeptides, denaturation, leads to loss of biological activity (function). When denatured proteins are returned to conditions in which the native conformation is stable, they may undergo renaturation, a refolding into the correct conformation. In some cases, renaturation is associated with the return of the protein function (e.g., ribonuclease). Copyright © 2022 Pearson Education, Inc. All Rights Reserved 69 23  8/27/23 The Spontaneity of Protein Folding Figure 2.17 The Spontaneity of Polypeptide Folding. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 70 Molecular Chaperones Assist the Assembly of Some Proteins Some proteins require molecular chaperones, which assist the assembly process. Molecular chaperones are not components of the completed structures and they convey no information. They bind to exposed regions in the early stages of assembly to inhibit unproductive assembly pathways that would lead to incorrect structures. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 71 Types of self-assembly and chaperones Strict self-assembly - no factors other than the polypeptide sequence itself are needed Assisted self-assembly - requires a specific molecular chaperone to ensure that the correct conformation predominates over incorrect forms Chaperone proteins are abundant, and even more so under stresses such as high temperature Many chaperones fall into one of two categories of heat shock proteins Copyright © 2022 Pearson Education, Inc. All Rights Reserved 72 24  8/27/23 Hierarchical Assembly Provides Advantages for the Cell Hierarchical assembly is the dependence on subassemblies that act as intermediates of the process of assembly of increasingly complex structures. Biological structures are almost always assembled hierarchically. Copyright © 2022 Pearson Education, Inc. All Rights Reserved 73 Advantages of Hierarchical Assembly Chemical simplicity—relatively few subunits are used for a wide variety of structures Efficiency of assembly—a small number of kinds of condensation reactions is needed Quality control—defective components can be discarded prior to incorporation into higher-level structure, reducing the waste of energy and materials Copyright © 2022 Pearson Education, Inc. All Rights Reserved 74 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 75 25