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Lecture 3

Lecture 3 Textbook Readings Notes Detailed and concise notes on the required readings for Lecture 3 with diagrams and panels.

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University of Toronto St. George
Kenneth Yip

Chapter 2 Cell Chemistry and Biosynthesis THE CHEMICAL COMPONENTS OF A CELL An atom often behaves as if it has a fixed radiusSpacefilling models give us a more accurate representation of molecular structure A solid envelope represents the radium of the electron cloud at which strong repulsive forces prevent a closer approach of any second nonbonded atomthe socalled van der Waals radius for an atomAt slightly greater distances any two atoms will experience a weak attractive force known as a van der Waals attractionThere is a distance at which repulsive and attractive forces precisely balance to produce an energy min in each atoms interaction with an atom of a second nonbonded element Water is the most abundant substance in cellsWater accounts for 70 of a cells weightHydrogen bond the electrical attraction when acharged region of one water approaches acharged region of a second water weaker than covalent bonds and are easily broken by the random thermal motion due to the heat energy of the molecules so each bond lasts only a short timeExplains why water is a liquid at room temp with a high bp and high surface tensionMolecules that contain polar bonds can form H bonds with water dissolve readily in water Ions likewise interact favourably with waterSuch molecules are hydrophilic water lovingHydrophobic water hating are uncharged and form few or no H bonds and so go not dissolve in water Some polar molecular are acids and bases Proton a molecule that had largely given up its electron to the companion atomWhen water molecules surround the polar molecule the proton is attracted to the partial negative charge on the O atom of an adjacent water molecule and can dissociate from its original partner to associate instead withthe oxygen atoms of the water to generate a hydronium ion Acids substances that release protons to formwhen they dissolve in waterBase accepts protons to lower the concentration ofions and thereby raise the concentration ofThe concentration of is expressed using a log scale called the pH scaleThe interior of a cell is kept close to neutrality and it is buffered by the presence of many chemical groups that can take up and release protons near pH 7Four types of noncovalent attractions help bring molecules together in cells In aqueous solutions covalent bonds are 10100x stronger than the other attractive forces between atoms Much of biology depends on the specific binding which is mediated by a group of noncovalent attractions that are individually quite weak but whose energies can sum to create an effective force between two separate molecules1 Electrostatic attractions a Result from the attractive forces between oppositely charged atoms b Quite strong in the absence of water c Readily form between permanent dipoles but are greatest when the 2 atoms involves are fully charged d Water cluster around both full charged ions and polar molecules greatly reducing the attractiveness of these charged species for each other in most biological settings 2 Hydrogen bonds a Represents a special form of polar interaction in which an electropositive H atom is partially shared by 2 electronegative atoms b H can be viewed as a proton that has partially dissociated from a donor atom allowing it to be shared by a second acceptor atom c Highly directionalbeing strongest when a straight line can be drawn between all 3 of the involved atoms d Water weakens these bonds by forming competing Hbond interactions 3 Van der Waals attraction a Electron cloud around any nonpolar atom will fluctuate producing a flickering dipole which will transiently induce an oppositely polarize flickering dipole in a nearby atom b Generates a very weak attraction c Water does not weaken these attractionsFourth effect is not a bond at all strictly speakingA very important hydrophobic force is caused by a pushing of nonpolar surfaces out of the Hbonded water networkBrining any 2 nonpolar surfaces together reduces their contact with water the force is nonspecific A cell is formed from carbon compoundsBecause C is small and 4 e and 4 vacancies nearly all the molecules in a cell are based on CHigh stable covalent CC bonds form chains and rings and hence generate large and complex moleculesCertain combination of atoms occur repeatedly in organic molecules these chemical groups have distinct physical and chemical properties that influence the behaviour of the molecule in which the group occurs Cells contain 4 major families of small organic moleculesSome organic molecules are used as monomer subunits to construct macromoleculesproteins nucleic acids and large polysaccharidesof the cellSmall organic molecules are much less abundant that the organic macromolecules3 major families sugars fatty acids the amino acids and the nucleotides Sugars provide an energy source for cells and are the subunits of polysaccharides The simplest sugarsmonosaccharidesare compounds with the general formula where n is usually 3 4 5 6 7 or 8
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