27 August, 2004 Chapters 2-3 Nucleic Acid Structure and Weak Bonds

Overview DNA replicates semiconservatively, indicating that strands separate during replication. DNA specifies an RNA transcript, which specifies protein sequence. Translation uses non-specific ribosomes to read mRNA sequence. tRNA is the adaptor that allows nucleic acids to specify protein sequence, and is the basis for the genetic code. Weak chemical interactions are critically important in mediating the transient interactions between biological molecules. K eq is Exponentially related to  G. Weak bonds have energies of 1-7 kcal / mol. Vander Waals forces, Hydrophobic interactions, and Hydrogen Bonds are the most biologically important weak bonds.

Pulse-Chase experiments support semiconservative DNA replication.

Information Flow in Biological Systems: DNA > RNA > Protein TranscriptionTranslation RNA is chemically similar to DNA, so transcription can proceed like a single-stranded replication.

Translation Protein is not chemically similar to nucleic acids, so an adaptor molecule must take part in translation. Ribosomes are non-specific, and bind mRNA, tRNA and other factors to catalyze peptide bond formation. The codon-anticodon interaction specifies the genetic code.

The Genetic Code

Protein Synthesis proceeds from N- to C-Terminal. Codons are three letter words without delimiters. Special codons signal start and stop. The code is redundant but not ambiguous. The code minimizes the effects of mutation on protein function.

Covalent bonds are strong, stable bonds. Van der Waals forces, hydrophobic interactions, and hydrogen bonds are weak interactions that determine the transient binding interactions between biological molecules. Bond Characteristics: bond length, bond angle, valence, and rotational freedom. Chemical Bonds

Chemical bond formation involved a change in the form of energy. A + B -----> A-B + Energy. The stronger the bond, the more energy is released when it is formed. Energy changes are quantified in units of kcal per mole of bonds. Breaking a bond requires kinetic energy: A-B + energy ----> A + B The amount of energy required to make and to break the bond is the same.

The Equilibrium Constant The equilibrium constant K eq determined by the concentrations of A, B, and A-B at equilibrium: For A + B ---> A-B, K eq = [A-B] / [A][B] Note that the existence of an equilibrium constant does not imply equal concentrations of bonded and unbonded A and B. Neither does this expression indicate that biological systems operate at equilibrium. The K eq is related to the free energy of a reaction: A decrease in free energy is associated with spontaneous reactions, and with a K eq greater than 1 (where [A-B] > [A][B] at equilibrium).

K eq is related to  G. K eq = e -  G/RT So, K eq less than one give positive  G, while K eq greater than one give negative  G. Covalent bonds have  G of -50 to -110 kcal / mol. Weak bonds have  G of -1 to -7 kcal / mol. This means that these bonds can be broken and reformed with relative ease at physiological temperatures.

Weak interactions, charge, and polarity Weak interactions all involve partial charge. Hydrogen bonds occur because of charge that is permanently asymmetrically distributed. This occurs in polar molecules like water, where the oxygen is more electronegative than the hydrogens, and maintains a partial negative charge. Nonpolar molecules do not form hydrogen bonds because their atoms have similar electronegativity, and therefore no partial charge.

Van der Waals Forces Van der Waals Forces arise from induced dipoles of fluctuating charge synchronized with a nearby molecule:

Van der Waals Forces Van der Waals Forces have energies in the 1 kcal / mole range, and are therefore only biologically significant in large numbers. These bonds, though, are prefect for specifying interactions based on molecular shape, like antigen-antibody interactions, where multiple Van der Waals contacts can generate binding energies of kcal / mole.

Hydrogen Bonds and Hydrophobic Interactions Hydrogen bonds usually involve hydrogen atoms covalently bound to O or N. Most have bond energies of about 3 -7 kcal / mole. These bonds are highly directional, and are useful for specifying orientation of donor and acceptor groups. In water, most molecules participate in hydrogen bonds. Molecules that can participate in this network are water-soluble. Non-polar molecules cannot form hydrogen bonds, and are not water-soluble. Hydrophobic molecules are excluded from water. This is sometimes called a hydrophobic bond.