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Published byRoland Baldwin Modified over 9 years ago
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The Chemistry of the Cell Modified by Dr. Jordan
Chapter 2 The Chemistry of the Cell Modified by Dr. Jordan
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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
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Importance of Carbon To study cellular molecules means to study carbon. Proteins, lipids, carbohydrates, nuclei acids are various combinations of carbon
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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
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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
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Figure 2-1A Atoms and valences
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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
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Figure 2-1B-D
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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
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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
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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
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Pollutants that destroy ozone Layer that normally filter out the
Figure 2-3 Pollutants that destroy ozone Layer that normally filter out the UV light that would reach Earth And break covalent bonds
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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
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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
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Figure 2-4
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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
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Functional groups Important functional groups include
Carboxyl and phosphate groups (negatively charged) Amino groups (positively charged) Hydroxyl, sulfhydroxyl, carbonyl, aldehyde (uncharged; but polar)
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Figure 2-5A,B
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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
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Figure 2-5C
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Activity: Functional Groups
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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
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Figure 2-6
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Activity: Isomers – Part 1
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Figure 2-7A
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Figure 2-7B May not need to separate a and b
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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
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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
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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
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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
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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
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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, much higher than most liquids
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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
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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
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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
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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)
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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
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Figure 2-10A
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Figure 2-10B
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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
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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)
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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
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Figure 2-11
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Video: Dynamics of a Lipid Bilayer
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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
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Figure 2-12
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Figure 2-13A
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Figure 2-13B
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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
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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
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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
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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
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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
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Figure 2-14
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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
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Figure 2-15
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Informational macromolecules
DNA and RNA serve a coding function, containing the information needed to specify the precise amino acid sequences of proteins
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Proteins Proteins are composed of a nonrandom series of amino acids
Amino acid sequence determines the three-dimensional structure, thus the function, of a protein With 20 different amino acids, a nearly infinite variety of protein sequences is possible
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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)
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Figure 2-16A
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Figure 2-16B
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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)
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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
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Figure 2-17
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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)
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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)
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Figure 2-18A
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Figure 2-18B
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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
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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
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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
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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
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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
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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
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Figure 2-20
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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
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Figure 2-21A,B
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Figure 2-21C,D
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