This document explores the field of industrial chemistry, focusing on the chemical processes and engineering principles applied in industrial settings. It covers a broad range of topics, including the manufacturing of chemicals on a large scale, the design and optimization of chemical processes, an...
Review: Read the Chap. 1 Appendix section & sections concerning cell biology in the textbook. Also
review the supplemental chemistry information at the end of this part of the notes.
I. The science of biochemistry.
The ultimate goal of biochemistry is to explain all life processes in molecular detail.
Because life processes are performed by organic molecules the discipline of biochemistry relies
heavily on fundamental principles of organic chemistry and other basic sciences. It is of no
surprise that the first "biochemists" actually were organic chemists who specialized in the
chemistry of compounds derived from living organisms. The text provides an historical
overview of some of the key contributions of the early chemists, and of modern 20th century
biochemists who have lead the discipline to where it is today. Research endeavors such as the
human genome project ultimately owe their success to basic discoveries about the structure of
the DNA "double helix" by Watson & Crick and the development of DNA sequencing methods
by Fredrick Sanger.
II. The chemical basis of life.
The biomolecules such as proteins that are present in living organisms are carbon-based
compounds. Carbon is the third most abundant element in living organisms (relative abundance
H > O > C > N > P > S). Fig. 1.1. shows the 29 elements found in living organisms. The most
common ions are Ca+2, K+, Na+, Mg+2, and Cl-. The properties of biomolecules, such as shape
and chemical reactivity, are best described by the discipline of organic chemistry.
A. Representations of molecular structures.
Your text will use skeletal, ball & stick, and space-filling models to show molecular
structures. Therefore, you must be familiar with each of these types of representations. Skeletal
and ball & stick models are good for showing the positions of nuclei in organic compounds.
Space-filling models show van der Waals radii of the atoms in molecules, i.e., the surfaces of
closest possible approach by neighboring molecules.
B. Chemical bonding.
If necessary, please review the supplemental notes at the end of this section concerning
the atomic and molecular (bonding) orbitals of carbon, nitrogen, and oxygen. sp3 and sp2
molecular orbitals are the most prevalent in biomolecules. The orientations of bonding orbitals in
space ultimately determine the shapes of biomolecules.
, C. Functional groups.
The chemical reactions of biomolecules are dictated by the functional groups they
contain. Fig. 1.2. shows the general formulas of common organic compounds and functional
groups that will be encountered constantly in the proteins, carbohydrates, nucleic acids and
simple metabolites you will study. You should be familiar with the structure, charge properties,
polarity, and basic chemical reactivity of all of these compounds and functional groups.
III. Many biomolecules are polymers.
The principle biomolecules in cells (proteins, polysaccharides, and nucleic acids) are
polymer chains of amino acids, monosaccharides, and nucleotides, respectively. Biopolymers are
formed by condensation reactions in which water is removed from the reacting monomer units.
Each monomer unit of a biopolymer is referred to as a residue.
A. Proteins.
Most of the chemical reactions of the cell are carried out by proteins. Proteins also are the
major structural components of most cells and tissues. Proteins are often called polypeptides in
reference to the fact that they are composed of amino acids held together by peptide bonds (Fig.
1.3). Peptide bonds actually are amide bonds which are formed by the condensation of the
carboxyl groups and amino groups of consecutive amino acids in the polymer chain. The so-
called peptide backbone of a protein is a monotonous, regularly repeating structure. Projecting
out from the backbone are the R-groups which are the side-chains of the amino acids. In a later
chapter, we will discuss how the R-groups play a significant role in determining the 3D structure
of a protein, i.e., its active conformation.
The enzymes comprise one subclass of proteins. These proteins carry out chemical
reactions with extraordinary specificity and speed (up to 1017-fold enhancement in reaction rate).
Specificity is achieved because the binding site for reactants--the active site--is highly
complementary in shape to the reactants and products. A stereoview of the active site of
lysozyme is shown in Fig. 1.4. This enzyme binds to and cleaves the polysaccharide portion of
the bacterial cell wall. Cleavage leads to osmotic lysis of the affected bacterium. Lysozyme is
present in tears and egg whites where it helps protect against unwanted bacterial growth and
infection. We will discuss the structure and function of many medically and otherwise relevant
proteins and enzymes such as myoglobin, hemoglobin, collagen, trypsin, insulin receptor,
glycogen phosphorylase, plasma lipoproteins, and DNA polymerase in this course. Many of
these proteins and enzymes are the targets of poisons and drugs whose actions also will be
discussed.
B. Polysaccharides.
Polysaccharides are polymers of simples sugars known as monosaccharides (e.g.,
glucose). Different polysaccharides perform either structural (cellulose) or energy storage
(glycogen, starch) functions. Polysaccharide and monosaccharides were some of the first
biomolecules that were studied by organic chemists. You should be familiar with the different
types of representations used to describe the structures of monosaccharides (Fig. 1.5). A
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