By: Debbie SchwagermanBy: Debbie Schwagerman

January 31, 2005January 31, 2005

Atomic Bonds and Molecular Atomic Bonds and Molecular InteractionsInteractions

Each atom has a Each atom has a defined number defined number and geometry of and geometry of covalent bonds.covalent bonds.

Atomic Bonds and Molecular Atomic Bonds and Molecular InteractionsInteractions

Electrons are shared Electrons are shared unequally in polar unequally in polar covalent bonds. covalent bonds.

Atoms with higher Atoms with higher electronegativity electronegativity

values have a values have a greater attraction greater attraction

for electrons.for electrons.

Atomic Bonds and Molecular Atomic Bonds and Molecular InteractionsInteractions

Covalent bonds are Covalent bonds are much stronger and much stronger and more stable than more stable than

noncovalent bonds.noncovalent bonds.

Atomic Bonds and Molecular Atomic Bonds and Molecular InteractionsInteractions

Ionic bonds result from the attraction of a Ionic bonds result from the attraction of a positively charged ion (cation) for a positively charged ion (cation) for a negatively charged ion (anion).negatively charged ion (anion).

The atoms that form the bond have very The atoms that form the bond have very different electronegativity values and the different electronegativity values and the electron is completely transferred to the electron is completely transferred to the more electronegative atom.more electronegative atom.

Ions in aqueous solutions are surrounded Ions in aqueous solutions are surrounded by water molecules, which interact via the by water molecules, which interact via the end of the water dipole carrying the end of the water dipole carrying the opposite charge of the ion.opposite charge of the ion.

Atomic Bonds and Molecular Atomic Bonds and Molecular InteractionsInteractions

Van der waals interactions are Van der waals interactions are caused by transient dipoles.caused by transient dipoles.

Atomic Bonds and Molecular Atomic Bonds and Molecular InteractionsInteractions

The hydrophobic The hydrophobic effect causes nonpolar effect causes nonpolar molecules to adhere molecules to adhere

to one another.to one another.

Atomic Bonds and Molecular Atomic Bonds and Molecular InteractionsInteractions

Molecular Molecular complementarity complementarity

permits tight, highly permits tight, highly specific binding of specific binding of

biomolecules.biomolecules.

Chemical Building Blocks of Chemical Building Blocks of CellsCells

ProteinsProteins Amino AcidsAmino Acids

Nucleic AcidsNucleic Acids NucleotidesNucleotides

PolysaccharidesPolysaccharides MonosaccharideMonosaccharide

ss

Chemical Building Blocks of Chemical Building Blocks of CellsCells

Common structure Common structure of amino acids.of amino acids.

Chemical Building Blocks of Chemical Building Blocks of CellsCells

20 amino acids.20 amino acids. All amino acids in nature are L form.All amino acids in nature are L form. Structure consists of CStructure consists of Caa, to which an , to which an

amino group, a carboxyl group, a amino group, a carboxyl group, a hydrogen atom, and a variable hydrogen atom, and a variable group.group.

Amino acids are classed according to their R group.

Chemical Building Blocks of Chemical Building Blocks of CellsCells

Common Common structure structure

ofof

nucleotidenucleotides.s.

Chemical Building Blocks of Chemical Building Blocks of CellsCells

Common structure: Common structure: phosphate group, base, phosphate group, base, and a five-carbon sugar.and a five-carbon sugar.

Sugar is either DNA or Sugar is either DNA or RNA.RNA.

Bases are adenine, Bases are adenine, guanine, cytosine, guanine, cytosine, thymine (DNA), and thymine (DNA), and uracil (RNA).uracil (RNA).

Nucleotides link Nucleotides link together to build together to build nucleic acids.nucleic acids.

Chemical Building Blocks of Chemical Building Blocks of CellsCells

Monosaccharides are Monosaccharides are carbohydrates of carbohydrates of combinations of combinations of carbon and water in a carbon and water in a one-to-one ratio.one-to-one ratio.

Except for fructose, all Except for fructose, all sugars are in nature sugars are in nature are D form.are D form.

D-Glucose (CD-Glucose (C66HH1212OO66) is ) is primary energy primary energy source.source.

Chemical Building Blocks of Chemical Building Blocks of CellsCells

Polysaccharides:Polysaccharides: Disaccharides are

simplest polysaccharides.

Anomeric carbon of one sugar molecule is linked to hydroxyl oxygen of another sugar molecule.

Polysaccharides can contain dozens to hundreds of monosaccharides.

Chemical EquilibriumChemical Equilibrium

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

Reactions in which the rates of the forward Reactions in which the rates of the forward and backward reactions are equal, so that the and backward reactions are equal, so that the concentrations of reactants and products stop concentrations of reactants and products stop changing, are said to be in chemical changing, are said to be in chemical equilibrium.equilibrium.

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

Chemical EquilibriumChemical Equilibrium

KKeqeq depends on the nature of the reactants depends on the nature of the reactants and products, the temperature, and the and products, the temperature, and the pressure.pressure.

The The KKeqeq is always the same for a reaction, is always the same for a reaction, whether a catalyst is present or not.whether a catalyst is present or not.

KKeqeq equals the ratio of the forward and equals the ratio of the forward and reverse rate constants (reverse rate constants (KKeqeq = k = kff/k/krr).).

The concentrations of complexes can be The concentrations of complexes can be estimated from equilibrium constants for estimated from equilibrium constants for binding reactions.binding reactions.

Biochemical EnergeticsBiochemical Energetics

The change in free energy The change in free energy ∆G∆G is the most useful is the most useful measure for predicting the direction of chemical measure for predicting the direction of chemical reactions in biological systems. Chemical reactions in biological systems. Chemical reactions tend to proceed in the direction for reactions tend to proceed in the direction for which which ∆G is negative.∆G is negative.

A chemical reaction having a positive ∆G can A chemical reaction having a positive ∆G can proceed if it is coupled with a reaction having a proceed if it is coupled with a reaction having a negative ∆G of larger magnitude.negative ∆G of larger magnitude.

The chemical free energy change ∆G equals -The chemical free energy change ∆G equals -2.3RT log keq. Thus the value of ∆G can be 2.3RT log keq. Thus the value of ∆G can be calculated from the experimentally determined calculated from the experimentally determined concentrations of reactants and products at concentrations of reactants and products at equilibrium.equilibrium.