Chapter 2

Chemical Foundations

The Chemicals of Life

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

neutron

proton

electron

Carbon atom

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

Hydrogen atom

atomic number = 1atomic mass = 1

ECB Fig. 2-2

Atoms

ECB, Fig. 2-5

Energy levels, Energy Shells, Orbitals

Covalent bonds

Formed when two different atoms share electrons in the outer atomic orbitals

Each 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. 2-6

Covalent Bonds

The making or breaking of covalent bonds involves large energy changes

In comparison, thermal energy at 25ºC is < 1 kcal/mol

Covalent bonds have characteristic geometries

Figure 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 electrons

Figure 2-3

Asymmetric carbon atoms are present in most biological molecules

Carbon 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 other

Stereoisomers are either right-handed or left-handed and typically have completely different biological activities

Asymmetric carbons are key features of amino acids and carbohydrates

Stereoisomers of the amino acid alanine

Figure 2-12

Different monosaccharides have different arrangements around asymmetric carbons

Figure 2-8

and glycosidic bonds link monosaccharides

Figure 2-17

Noncovalent bonds

Several types: hydrogen bonds, ionic bonds, van der Waals interactions, hydrophobic bonds

Noncovalent bonds require less energy to break than covalent bonds

The energy required to break noncovalent bonds is only slightly greater than the average kinetic energy of molecules at room temperature

Noncovalent bonds are required for maintaining the three-dimensional structure of many macromolecules and for stabilizing specific associations between macromolecules

The hydrogen bond underlies water’s chemical and biological properties

Figure 2-6

Molecules with polar bonds that form hydrogen bonds with water can dissolve in water and are termed hydrophilic

Hydrogen bonds within proteins

Ionic bonds

Ionic 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 molecules

Figure 2-5

van der Waals interactions are caused by transient dipoles

When 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 dipole

Figure 2-8

Multiple weak bonds stabilize large molecule interactions

Figure 2-10

Chemical equilibrium

The extent to which a reaction can proceed and the rate at which the reaction takes place determines which reactions occur in a cell

Reactions 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 equilibrium

At equilibrium, the ratio of products to reactants is a fixed value termed the equilibrium constant (Keq) and is independent of reaction rate

A + B X + Y Keq = [X][Y] [A][B]

Equilibrium constants reflect the extent of a chemical reaction

The 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 values

All aqueous solutions, including those in and around cells, contain some concentration of H+ and OH- ions, the dissociation products of water

In pure water, [H+] = [OH-] = 10-7 M The concentration of H+ in a solution is expressed as pH

pH = -log [H+] So for pure water, pH = 7.0 On the pH scale, 7.0 is neutral, pH < 7.0 is acidic, and pH >

7.0 is basic The cytosol of most cells has a pH of 7.2

Hydrogen ions are released by acids and taken up by bases

When acid is added to a solution, [H+] increases and [OH-] decreases

When base is added to a solution, [H+] decreases and [OH-] increases

The degree to which an acid releases H+ or a base takes up H+ depends on the pH

Biochemical energetics

Living systems use a variety of interconvertible energy forms Energy 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 reaction

Living 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 by

G = Gproducts - Greactants

If G < 0, the forward reaction will tend to occur spontaneously If G > 0, the reverse reaction will tend to occur If G = 0, both reactions will occur at equal rates

Many cellular processes involve oxidation-reduction reactions

The loss of electrons from an atom or molecule is termed oxidation and the gain of electrons is termed reduction

If one atom or molecule is oxidized during a chemical reaction then another molecule must be reduced

The 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 fumarate

Figure 2-25

An unfavorable chemical reaction can proceed if it is coupled to an energetically favorable reaction

Many 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 magnitude

Energetically unfavorable reactions in cells are often coupled to the hydrolysis of adenosine triphosphate (ATP), which has a Gº = -7.3 kcal/mol

The useful free energy in an ATP molecule is contained is phosphoanhydride bonds

The phosphoanhydride bonds of ATP

Figure 2-24

ATP is used to fuel many cell processes

Figure 1-14

The ATP cycle

Activation energy and reaction rate

Many chemical reactions that exhibit a negative G°´ do not proceed unaided at a measurable rate

Chemical 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 catalyst

Enzymes accelerate biochemical reactions by reducing transition-state free energy