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Chapter 2 The Chemistry of the Cell Modified by Dr. Jordan Lectures by Kathleen Fitzpatrick Simon Fraser University © 2012 Pearson Education, Inc. 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 © 2012 Pearson Education, Inc. Importance of Carbon • To study cellular molecules means to study carbon. • Proteins, lipids, carbohydrates, nuclei acids are various combinations of carbon © 2012 Pearson Education, Inc. The Importance of Carbon • Study of all classes of carbon-containing compounds is organic chemistry • Biological chemistry (biochemistry) is the study of the chemistry of living systems (functions) • 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 © 2012 Pearson Education, Inc. 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 can form 4 chemical bonds with other atoms • Carbon atoms are most likely to form covalent bonds with one another and with oxygen (O), hydrogen (H), nitrogen (N), and sulfur (S) • Covalent bonds - the sharing of a pair of electrons between two atoms © 2012 Pearson Education, Inc. Figure 2-1A © 2012 Pearson Education, Inc. Covalent bonding of carbon atoms • Sharing one pair of electrons between two atoms forms a single bond • Double 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 is four © 2012 Pearson Education, Inc. Figure 2-1B-D © 2012 Pearson Education, Inc. Carbon-Containing Molecules Are Stable • Stability is expressed as bond energy - the amount of energy required to break 1 mole (~6x 1023) of bonds • Bond energy is expressed as calories per mole (cal/mol) • A calorie is the amount of energy needed to raise the temperature of 1g of water by 1oC • A kcal (kilocalorie) is equal to 1000 calories © 2012 Pearson Education, Inc. 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 © 2012 Pearson Education, Inc. Strong covalent bonds necessary for life • Solar radiation has an inverse relationship between wavelength and energy content • 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 © 2012 Pearson Education, Inc. Figure 2-3 Pollutants that destroy ozone Layer that normally filter out the UV light that would reach Earth And break covalent bonds © 2012 Pearson Education, Inc. 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 © 2012 Pearson Education, Inc. Hydrocarbons • Hydrocarbons are chains or rings composed only of carbon and hydrogen • They are economically important, because petroleum products, including gasoline and natural gas, are hydrocarbons • In biology, they are of limited importance because they are not soluble in water © 2012 Pearson Education, Inc. Figure 2-4 © 2012 Pearson Education, Inc. Biological compounds • Hydrocarbons are important in membranes • 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 © 2012 Pearson Education, Inc. Functional groups • Important functional groups include – Carboxyl and phosphate groups (negatively charged) – Amino groups (positively charged) – Hydroxyl, sulfhydroxyl, carbonyl, aldehyde (uncharged; but polar) © 2012 Pearson Education, Inc. Figure 2-5A,B © 2012 Pearson Education, Inc. Bond polarity • In polar covalent 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 © 2012 Pearson Education, Inc. Figure 2-5C © 2012 Pearson Education, Inc. Activity: Functional Groups © 2012 Pearson Education, Inc. Carbon-Containing Molecules Can Form Stereoisomers • The carbon atom is a tetrahedral structure • When four atoms are bonded to the four corners of the tetrahedron, two spatial configurations are possible • These non-superimposable configurations are mirror images, called stereoisomers © 2012 Pearson Education, Inc. Figure 2-6 © 2012 Pearson Education, Inc. Activity: Isomers – Part 1 Activity: Isomers – Part 2 Activity: Isomers – Part 3 © 2012 Pearson Education, Inc. Figure 2-7A © 2012 Pearson Education, Inc. Figure 2-7B © 2012 Pearson Education, Inc. The Importance of Water • Water has an indispensable role as the universal solvent in biological systems-exist as solid, liquid, and gas • It is the single most abundant component of cells and organisms • About 75-85% of a cell by weight is water • Its chemical characteristics make water indispensable for life © 2012 Pearson Education, Inc. 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 © 2012 Pearson Education, Inc. Water Molecules Are Cohesive • Because of their polarity, water molecules are attracted to each other and orient so 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 © 2012 Pearson Education, Inc. © 2012 Pearson Education, Inc. Hydrogen bonds and cohesiveness • Water is characterized by an extensive network of hydrogen-bonded molecules, which make it cohesive • Water move from soil up the plants • The combined effect of many hydrogen bonds accounts for water’s high – – – – Surface tension Boiling point Specific heat Heat of vaporization © 2012 Pearson Education, Inc. 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 © 2012 Pearson Education, Inc. Water Has a High TemperatureStabilizing Capacity • High specific heat gives water its temperaturestabilizing 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, much higher than most liquids © 2012 Pearson Education, Inc. Temperature-stabilizing capacity • Water therefore changes temperature relatively slowly, protecting living systems from extreme temperature changes • Pools, rivers, arctic • Without this characteristic of water, energy released in cell metabolism would cause overheating and death © 2012 Pearson Education, Inc. Heat of vaporization • Heat of vaporization is the amount of energy required to convert one 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 of water makes it an excellent coolant © 2012 Pearson Education, Inc. Water Is an Excellent Solvent • A solvent is a fluid in which another substance, the solute, can dissolve • Water is able to dissolve a large variety of substances, due to its polarity • Most of the molecules in cells are also polar and so can form hydrogen bonds, or ionic bonds with water © 2012 Pearson Education, Inc. Solutes • Solutes that have an affinity for water and dissolve in it easily are called hydrophilic (generally polar molecules or ions) • 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 (generally nonpolar molecules) © 2012 Pearson Education, Inc. NaCl in water • A salt, such as NaCl, exists as a lattice of Na+ cations (positively charged) and Cl- anions (negatively charged). What type of bond for salt? • 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 © 2012 Pearson Education, Inc. Figure 2-10A © 2012 Pearson Education, Inc. Figure 2-10B © 2012 Pearson Education, Inc. 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 – permeable to water to allow flow of water in and out of the cell © 2012 Pearson Education, Inc. Membranes surround cells • The cellular membrane is a hydrophobic permeability barrier • Consists of phospholipids, glycolipids, and membrane proteins • Membranes of most organisms also contain sterols - cholesterol (animals), ergosterols (fungi), or phytosterols (plants) © 2012 Pearson Education, Inc. Membrane lipids are amphipathic • Membrane lipids are amphipathic; they have both hydrophobic and hydrophilic regions • Amphipathic phospholipids have a polar head, due to a negatively charged phosphate group linked to a positively charged group • They also have two nonpolar hydrocarbon tails © 2012 Pearson Education, Inc. Figure 2-11 © 2012 Pearson Education, Inc. Video: Dynamics of a Lipid Bilayer © 2012 Pearson Education, Inc. 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 © 2012 Pearson Education, Inc. Figure 2-12 © 2012 Pearson Education, Inc. Figure 2-13A © 2012 Pearson Education, Inc. Figure 2-13B © 2012 Pearson Education, Inc. Membrane proteins • Membrane proteins may play a variety of roles – Transport proteins, for moving specific substances across an otherwise impermeable membrane – Enzymes, that catalyze reactions associated with the membrane – Receptors on the cell’s surface, and other proteins in mitochondrial or chloroplast membranes © 2012 Pearson Education, Inc. Membranes Are Selectively Permeable • Because of the hydrophobic interior, membranes are readily permeable to nonpolar molecules • However, they are quite impermeable to most polar molecules and very impermeable to ions • Cellular constituents are mostly polar or charged and are prevented from entering or leaving the cell • However, very small molecules diffuse © 2012 Pearson Education, Inc. 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 © 2012 Pearson Education, Inc. Transporter 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 © 2012 Pearson Education, Inc. 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, carbohydrates • Lipids share some features of macromolecules, but are synthesized somewhat differently © 2012 Pearson Education, Inc. Figure 2-14 © 2012 Pearson Education, Inc. Fundamental 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 © 2012 Pearson Education, Inc. Figure 2-15 © 2012 Pearson Education, Inc. Informational macromolecules • DNA and RNA serve a coding function, containing the information needed to specify the precise amino acid sequences of proteins © 2012 Pearson Education, Inc. Proteins • Proteins are composed of a nonrandom series of amino acids • Amino acid sequence determines the threedimensional structure, thus the function, of a protein • With 20 different amino acids, a nearly infinite variety of protein sequences is possible © 2012 Pearson Education, Inc. Polysaccharides • Polysaccharides typically consist of single repeating subunits or two altering 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) © 2012 Pearson Education, Inc. Figure 2-16A © 2012 Pearson Education, Inc. Figure 2-16B © 2012 Pearson Education, Inc. Macromolecules Are Synthesized by Stepwise Polymerization of Monomers • Despite some differences, the production of most polymers follows 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) © 2012 Pearson Education, Inc. Basic principles (continued) – 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 (ATP) or a related high-energy compound – 6. Macromolecules have directionality; the chemistry differs at each end of the polymer © 2012 Pearson Education, Inc. Figure 2-17 © 2012 Pearson Education, Inc. Condensation and hydrolysis • Activated monomers react with one another in a condensation reaction, 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) © 2012 Pearson Education, Inc. 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) © 2012 Pearson Education, Inc. Figure 2-18A © 2012 Pearson Education, Inc. Figure 2-18B © 2012 Pearson Education, Inc. Molecular Chaperones Assist the Assembly of Some Proteins • Some proteins require molecular chaperones, which assist the assembly process by inhibiting interactions that would produce incorrect structures • Under lab conditions, such proteins do not regain their native conformation after the conditions of denaturation are reversed • Molecular chaperones are not components of the completed structures and they convey no information © 2012 Pearson Education, Inc. 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 moreso under stresses such as high temperature • Many chaperones fall into one of two categories of heat shock proteins © 2012 Pearson Education, Inc. Ionic bonds • Ionic bonds are 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 © 2012 Pearson Education, Inc. Van der Waals interactions • Van der Waals interactions (or forces) are weak attractions between two atoms that only occur 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 is the basis for space-filling models of molecules © 2012 Pearson Education, Inc. Hydrophobic interactions • Hydrophobic interactions describes 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 © 2012 Pearson Education, Inc. The Tobacco Mosaic Virus Is a Case Study in Self-Assembly • A virus is a complex of nucleic acids and proteins that uses living cells to produce more copies of itself via self-assembly • A good example is the tobacco mosaic virus (TMV) • It is a rodlike particle, with a single RNA strand and about 2130 copies of a coat protein that form a cylindrical covering for the RNA © 2012 Pearson Education, Inc. Figure 2-20 © 2012 Pearson Education, Inc. Self-assembly of TMV is quite complex • The unit of assembly is a two-layered disc of coat protein that changes conformation (from cylinder to helix) as it interacts with the central RNA molecule • This conformational change allows another disc to bind and to interact with the RNA, and thus change its conformation as well • The process repeats until the end of the RNA molecule is reached © 2012 Pearson Education, Inc. Figure 2-21A,B © 2012 Pearson Education, Inc. Figure 2-21C,D © 2012 Pearson Education, Inc.