Chapter 2Chemical Foundations

The Chemicals of Life

The Chemicals of Life(b) Macromolecules (23%)

neutronprotonelectron Carbon atom

atomic number (protons) = 6atomic mass (protons + neutrons) = 12

Hydrogen atom

atomic number = 1atomic mass = 1ECB Fig. 2-2Atoms

ECB, Fig. 2-5Energy levels, Energy Shells, Orbitals

Covalent bondsFormed when two different atoms share electrons in the outer atomic orbitalsEach atom can make a characteristic number of bonds (e.g., carbon is able to form 4 covalent bonds)Covalent bonds in biological systems are typically single (one shared electron pair) or double (two shared electron pairs) bonds

ECB, Fig. 2-6Covalent Bonds

The making or breaking of covalent bonds involves large energy changesIn comparison, thermal energy at 25C is < 1 kcal/mol

Covalent bonds have characteristic geometriesFigure 2-2

Covalent double bonds cause all atoms to lie in the same plane

A water molecule has a net dipole moment caused by unequal sharing of electronsFigure 2-3

Asymmetric carbon atoms are present in most biological moleculesCarbon atoms that are bound to four different atoms or groups are said to be asymmetric The bonds formed by an asymmetric carbon can be arranged in two different mirror images (stereoisomers) of each otherStereoisomers are either right-handed or left-handed and typically have completely different biological activitiesAsymmetric carbons are key features of amino acids and carbohydrates

Stereoisomers of the amino acid alanineFigure 2-12

Different monosaccharides have different arrangements around asymmetric carbonsFigure 2-8

and glycosidic bonds link monosaccharidesFigure 2-17

Noncovalent bondsSeveral types: hydrogen bonds, ionic bonds, van der Waals interactions, hydrophobic bondsNoncovalent bonds require less energy to break than covalent bondsThe energy required to break noncovalent bonds is only slightly greater than the average kinetic energy of molecules at room temperatureNoncovalent bonds are required for maintaining the three-dimensional structure of many macromolecules and for stabilizing specific associations between macromolecules

The hydrogen bond underlies waters chemical and biological propertiesFigure 2-6Molecules with polar bonds that form hydrogen bonds with water can dissolve in water and are termed hydrophilic

Hydrogen bonds within proteins

Ionic bondsIonic bonds result from the attraction of a positively charged ion (cation) for a negatively charged ion (anion)In ionic bonds, electrons are not shared. The electron is completely transferred from one atom to another atom.Ions in aqueous solutions are surrounded by water molecules, which interact via the end of the water dipole carrying the opposite charge of the ion

Ionic bonds

Ions in aqueous solutions are surrounded by water moleculesFigure 2-5

van der Waals interactions are caused by transient dipolesWhen any two atoms approach each other closely, a weak nonspecific attractive force (the van der Waals force) is created due to momentary random fluctuations that produce a transient electric dipoleFigure 2-8

Multiple weak bonds stabilize large molecule interactionsFigure 2-10

Chemical equilibriumThe extent to which a reaction can proceed and the rate at which the reaction takes place determines which reactions occur in a cellReactions in which the rates of the forward and backward reactions are equal, so that the concentrations of reactants and products stop changing, are said to be in chemical equilibriumAt equilibrium, the ratio of products to reactants is a fixed value termed the equilibrium constant (Keq) and is independent of reaction rateA + B X + YKeq = [X][Y] [A][B]

Equilibrium constants reflect the extent of a chemical reactionThe Keq is always the same for a reaction, whether a catalyst is present or not.Many reactions involve non-covalent binding of one molecule to another. For these reactions we usually refer to KD, dissociation constant, which is the inverse of the Keq.For example, KD is the term we use to describe the affinity of a ligand for a receptor.The lower the KD, the higher the affinity for the receptor.

Biological fluids have characteristic pH valuesAll aqueous solutions, including those in and around cells, contain some concentration of H+ and OH- ions, the dissociation products of waterIn pure water, [H+] = [OH-] = 10-7 MThe concentration of H+ in a solution is expressed as pHpH = -log [H+] So for pure water, pH = 7.0On the pH scale, 7.0 is neutral, pH < 7.0 is acidic, and pH > 7.0 is basicThe cytosol of most cells has a pH of 7.2

Hydrogen ions are released by acids and taken up by basesWhen acid is added to a solution, [H+] increases and [OH-] decreasesWhen base is added to a solution, [H+] decreases and [OH-] increasesThe degree to which an acid releases H+ or a base takes up H+ depends on the pH

Biochemical energeticsLiving systems use a variety of interconvertible energy formsEnergy may be kinetic (the energy of movement) or potential (energy stored in chemical bonds or ion gradients)

The change in free energy determines the direction of a chemical reactionLiving systems are usually held at constant temperature and pressure, so one may predict the direction of a chemical reaction by using a measure of potential energy termed free energy (G)The free-energy change (G) of a reaction is given byG = Gproducts - GreactantsIf G < 0, the forward reaction will tend to occur spontaneouslyIf G > 0, the reverse reaction will tend to occurIf G = 0, both reactions will occur at equal rates

Many cellular processes involve oxidation-reduction reactionsThe loss of electrons from an atom or molecule is termed oxidation and the gain of electrons is termed reductionIf one atom or molecule is oxidized during a chemical reaction then another molecule must be reducedThe readiness with which an atom or molecule gains electrons is its redox potential E. Molecules with -E make good electron donors. Molecules with +E make good electron acceptors.

The oxidation of succinate to fumarateFigure 2-25

An unfavorable chemical reaction can proceed if it is coupled to an energetically favorable reactionMany chemical reactions are energetically unfavorable (G > 0) and will not proceed spontaneously Cells can carry out such a reaction by coupling it to a reaction that has a negative G of larger magnitudeEnergetically unfavorable reactions in cells are often coupled to the hydrolysis of adenosine triphosphate (ATP), which has a G = -7.3 kcal/molThe useful free energy in an ATP molecule is contained is phosphoanhydride bonds

The phosphoanhydride bonds of ATPFigure 2-24

ATP is used to fuel many cell processes

Figure 1-14The ATP cycle

Activation energy and reaction rateMany chemical reactions that exhibit a negative G do not proceed unaided at a measurable rateChemical reactions proceed through high energy transition states. The free energy of these intermediates is greater than either the reactants or products

Example changes in the conversion of a reactant to a product in the presence and absence of a catalystEnzymes accelerate biochemical reactions by reducing transition-state free energy

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