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Lecture 1. Foundations
Introduction to the course. Inventory of concepts from prior courses that are
important for biochemistry.
Reading: Voet, Voet and Pratt, 4th ed. (VVP4e); Chapters 1 and 2.
Summary
Chemical foundations
Among the important chemical concepts for biochemistry, we have the following:
Aqueous solutions
Properties of water as a solvent
Aqueous chemistry: acid-base reactions
Definitions of pH, pKa, etc.
Buffers and the Henderson-Hasselbalch equation
Functional groups
It is important to know the common functional groups from organic chemistry,
their properties and reactivities (for a list, see Table 1.2, p.4 in the text).
Examples of ionizable functional groups (carboxyl/carboxylate and protonated
amine/amine conjugate pairs) with pH-dependent charge states. We will not
memorize pK values, but it is important to have a "ballpark" idea of the values and
know the order of acid strength of the various acidic functional groups.
Nomenclature
Redox reactions
Oxidation-reduction, or "redox", reactions figure prominently in metabolism. An
example is provided by the electron transport protein cytochrome c.
Chemical kinetics: The velocity of chemical reactions
Enzyme kinetics: Enzymes are biological catalysts that greatly speed up the rates
of specific spontaneous chemical reactions.
Thermodynamics
Living organisms obey the laws of thermodynamics!
A spontaneous process is one that is thermodynamically favored; however, the
thermodynamic favorability of a process does not imply anything about its rate
(kinetics).
For processes occurring in a system at constant temperature, the Gibbs free
energy function (G) is used to assess spontaneity:
ΔG < 0 for the process ⇔ process is spontaneous
Covalent (bonding) interactions and noncovalent interactions
It is quite important to understand the distinction between covalent or ionic
bonding and noncovalent forces.
Noncovalent forces determine the conformations (shapes) of biological
macromolecules and the interactions between molecules (see below for a summary
of noncovalent forces)
Among the topics where there is a large intersection between cell biology and
biochemistry are
The major classes of biological molecules are proteins, nucleic acids, carbohydrates,
and lipids. These molecules are characteristically very large - much larger than the
"small" molecules we are used to dealing with in introductory chemistry courses. Thus,
we often refer to these as biological macromolecules, which commonly have molecular
masses in the range several thousand on up to millions of atomic mass units (amu). In
biochemistry, instead of the amu, the equivalent unit dalton (D or Da) is used. The
molecular weights of biological macromolecules are most conveniently expressed in
kilodaltons (kD). Our initial goal is to learn the basic covalent structures of these
classes of molecules, and relate them to some of their properties or functions. For
example, proteins are polymers of amino acids covalently linked together in a specific
sequence by amide bonds. These linkages are given the special name peptide bonds,
and the chains of amino acids that make up proteins are referred to as polypeptide
chains or polypeptides.
Learning objectives
Discuss the major chemical and biological concepts relevant to biochemistry and
explain their relevance.
Name the major classes of biological molecules, and describe their biological roles.
Identify the major types of noncovalent interactions that are important in determining
biomolecular structures.
Describe the characteristics of hydrogen bonds, electrostatic and van der Waals
interactions.
Page updated 9-3-2016
References
1. Asimov, I. Life and Energy (1962, Doubleday). This is a classic by my lights, worth
reading if you can find it. Reading this book in high school convinced me to become a
biochemist!
2. Creighton, TE. Proteins: Structure and Molecular Properties (2nd ed, 1993. Freeman).
3. Atkins, PW, de Paula, J. Physical Chemistry for the Life Sciences (2006,
Freeman/Oxford Univ. Press)
4. Chang, R. Physical Chemistry for the Biosciences (2005, University Science Books)