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CHEM 440

Biochemistry I J. D. Cronk Syllabus Previous lecture | Next lecture

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

We begin our semester-long journey exploring the chemistry of life by taking an


inventory of the concepts and principles developed in the biology and chemistry courses
you've taken up to this point. The list of courses we developed includes General
Chemistry [CHEM 101], Organic Chemistry I & II [CHEM 230, 331], Bioanalytical Chem
[CHEM 240], Quantitative Analysis [CHEM 310], Information Flow in Biological Systems
[BIOL 105], Energy flow in Biological Systems [BIOL 106], Genetics [BIOL 207]. Note
that many of the concepts we'll find relevant are reviewed in the reading assignment
(Chs. 1 & 2 of Voet, Voet, and Pratt).

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)

Noncovalent forces that determine macromolecular structure

One of the major themes of biochemistry is how biomolecular structure determines


function. Of course we must know the covalent structure of the molecules of life, but the
functional implications depend on a detailed picture of the conformations adopted by
these molecules. Because of the sheer size of biological macromolecules, an
astronomical number of conformations are possible in principle. That molecules such as
proteins and nucleic acids in fact assume a unique structure, or a very restricted range
of conformations, has something to do with the relationship between a particular
conformation and the energy associated with it. A knowledge of noncovalent forces is
essential to an understanding of biomolecular structure, since these determine the
energetics of conformations and the interactions between molecules in defined
conformational states. There are several kinds of forces that play predominant roles in
defining the energetic landscape that specifies biomolecular structure: electrostatic
interactions, van der Waals forces, and hydrogen bonds. These can be thought of
as contributing to enthalpy in processes such as protien folding and formation of
complementary double-stranded DNA from the separated single strands. In addition, we
discuss the hydrophobic effect, which arises as a result of entropic contributions of
water solvation of nonpolar surface area.

The cellular nature of life

Cells are spatially defined as membrane-bounded microsystems of great functional and


compositional complexity. They are thermodynamically open systems that are able to
sustain a dynamic, non-equilibrium steady-state. Furthermore, cells have the ability to
self-replicate, by mitosis, and form higher order associations as multicellular organisms.
The internal environment of cells is regulated, and levels of ions, metabolites, chemical
energy, reducing potential, and transmembrane electrochemical potential, are
maintained within typically narrow ranges. This characteristic of cells, referred to as
cellular homeostasis is apparently for their continued survival. One of the central
tasks that concerns biochemistry is a complete molecular-level description of the
mechanisms underlying homeostasis and self-replication.

Among the topics where there is a large intersection between cell biology and
biochemistry are

Compartmentation, catalysts, precursors, energy sources


The distinction between prokaryotes and eukaryotes; eukaryotic organelles
Prokaryotes lack a nucleus or other membrane-bound organelles
Eukaryotes have specialized membrane-bound organelles: e.g. mitochondria,
chloroplasts
Mechanical properties of cells and their ability to generate kinetic energy
Cytoskeletal structure
Motility: bacterial flagella
Muscle contraction: myofibrils

The major classes of biological molecules

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)

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