Chem 46: Fundamentals of

Biochemistry

Chapter 1
Introduction to Biochemistry

Department of Chemistry
College of Mathematics and Natural Sciences
Caraga State University
Lecture Outline:
− A. Essential Elements for Living Systems
− B. Classes of Organic Compounds
− C. Stereochemistry and Chirality
− D. The Cell Structure
− E. Biomolecular Families
− F. Molecular Forces of Attraction
− G. Amphipathic Molecules, Water and pH
− H. Biochemical Reactions
Intended Learning Outcomes:
Define biochemistry;

Distinguish the difference between living systems and

non-living systems;

Classify the different classes of organic compounds

present in the different biomolecules

Distinguish the composition of the different types of cells

and relate the different biochemical process involved;

Summarize the hierarchy of living systems and

biomolecules involved;
Intended Learning Outcomes:
Converse the value between the significance of water
in the cell and in the living systems;

Illustrate the stereochemistry of substances and

appreciate its significance in the biological world

Identifies the biomolecules for a particular force of

attraction

Distinguish the different biochemical reactions

A. ESSENTIAL ELEMENTS FOR LIVING SYSTEMS
Biochemistry is the study of the chemical substances found in living organisms and the
chemical interactions of these substances with each other.
A. ESSENTIAL ELEMENTS FOR LIVING SYSTEMS

Elements essential to animal life and health. Bulk elements (shaded orange) are structural components of cells and tissues
and are required in the diet in gram quantities daily. For trace elements (shaded bright yellow), the requirements are much smaller:
for humans, a few milligrams per day of Fe, Cu, and Zn, even less of the others. The elemental requirements for plants and
microorganisms are similar to those shown here; the ways in which they acquire these elements vary.
A. ESSENTIAL ELEMENTS FOR LIVING SYSTEMS

Composition of the Earth’s Crust, Seawater, and the Human Body*

A. ESSENTIAL ELEMENTS FOR LIVING SYSTEMS

Levels of structural organization in the

human body. Note the hierarchy from
simple to complex.
B. CLASSES OF ORGANIC COMPOUNDS
B. CLASSES OF ORGANIC COMPOUNDS
C. STEROCHEMISTRY & CHIRALITY

Stereochemistry is the study of the three‐dimensional structure of molecules.

Subdivision of isomers.
C. STEROCHEMISTRY & CHIRALITY
C. STEROCHEMISTRY & CHIRALITY

The cis and trans isomers are forms of stereoisomers, differing structurally only in
the location of the atoms of the molecule in three‐dimensional space. Such
stereoisomers can have different physical and chemical properties.
C. STEROCHEMISTRY & CHIRALITY
A chiral object is one that cannot be superposed on its mirror image.

The mirror image of a right hand is Left and right hands are not
a left hand. superposable.
C. STEROCHEMISTRY & CHIRALITY
A chiral object is one that cannot be superposed on its mirror image.

The glass and its mirror image are superposable.

C. STEROCHEMISTRY & CHIRALITY
A chiral object is one that cannot be superposed on its mirror image.

This mug is chiral because it is not superposable on

its mirror image.
C. STEROCHEMISTRY & CHIRALITY
C. STEROCHEMISTRY & CHIRALITY
C. STEROCHEMISTRY & CHIRALITY
C. STEROCHEMISTRY & CHIRALITY
D. THE CELL STRUCTURE
● All living cells fall into one of three broad categories—Archaea,
Bacteria and Eukarya.

● Archaea and bacteria are referred to collectively as prokaryotes.

As a group, prokaryotes are single-celled organisms that lack
nuclei and other organelles; the word is derived from pro meaning
“prior to” and karyot meaning “nucleus.”

● In conventional biological classification schemes, prokaryotes are

grouped together as members of the kingdom Monera. The other
four living kingdoms are all Eukarya— the single-celled Protists,
such as amoebae, and all multicellular life forms, including the
Fungi, Plant, and Animal kingdoms. Eukaryotic cells have true
nuclei and other organelles such as mitochondria, with the prefix
eu meaning “true.”
D. THE CELL STRUCTURE

This bacterium is Escherichia coli, a member of the coliform group of bacteria that colonize the intestinal tract of humans.
(Photo, Martin Rotker/Phototake, Inc.; inset photo, David M. Phillips/The Population Council/Science Source/Photo
Researchers, Inc.)
D. THE CELL STRUCTURE
D. THE CELL STRUCTURE
D. THE CELL STRUCTURE
How Many Genes Does It Take To Make An Organism?
D. THE CELL STRUCTURE
E. BIOMOLECULAR FAMILIES
F. MOLECULAR FORCES OF ATTRACTION

Weak Chemical Forces and Their Relative Strengths and Distances

 F. MOLECULAR FORCES OF ATTRACTION

● Van der Waals interactions are the result of induced electrical interactions between closely
approaching atoms or molecules as their negatively charged electron clouds fluctuate
instantaneously in time.

Van der Waals packing is enhanced in molecules that are structurally complementary. Gln 121 , a surface protuberance on lysozyme, is recognized by
the antigen-binding site of an antibody against lysozyme. Gln 121 (pink) fits nicely in a pocket formed by Tyr 32 (orange), Phe 91 (light green), Trp 92
(dark green), and Tyr 101 (blue) components of the antibody.
(a) Ball-and-stick model. (b) Space-filling representation.
F. MOLECULAR FORCES OF ATTRACTION

● Hydrogen Bonds – are formed between

a hydrogen atom covalently bonded to
an electronegative atom (such as
oxygen or nitrogen) and a second
electronegative atom that serves as the
hydrogen bond acceptor. Several
important biological examples are given
in the given figure.
F. MOLECULAR FORCES OF ATTRACTION

● Ionic interactions - are the result of

attractive forces between oppositely
charged structures, such as negative
carboxyl groups and positive amino
groups
F. MOLECULAR FORCES OF ATTRACTION

● Hydrophobic interactions - result from the strong tendency of water to exclude

nonpolar groups or molecules

● The formation of oil droplets as hydrophobic nonpolar lipid molecules coalesce in

the presence of water is an approximation of this phenomenon. These tendencies
have important consequences in the creation and maintenance of the
macromolecular structures and supramolecular assemblies of living cells.
G. AMPHIPATHIC MOLECULES, WATER & pH

A single molecule may have both polar (hydrophilic) and nonpolar

(hydrophobic) portions. Substances of this type are called amphipathic.
G. AMPHIPATHIC MOLECULES, WATER & pH

Micelle formation by
amphipathic molecules in
aqueous solution. When
micelles form, the ionized polar
groups are in contact with the
water, and the nonpolar parts of
the molecule are protected from
contact with the water.
 G. AMPHIPATHIC MOLECULES, WATER & pH
● Water is the predominant chemical component of living organisms.

● An excellent nucleophile, water is a reactant or product in many metabolic reactions.

● WATER IS AN IDEAL BIOLOGIC SOLVENT.

G. AMPHIPATHIC MOLECULES, WATER & pH

● Water Molecules Form Dipoles ● Water Molecules Form

Hydrogen Bonds
G. AMPHIPATHIC MOLECULES, WATER & pH

● Water Molecules Exhibit a Slight but Important Tendency to Dissociate

● The ability of water to ionize, while slight, is of central importance for life.
Since water can act both as an acid and as a base, its ionization may be
represented as an intermolecular proton transfer that forms a hydronium ion
(H3O+) and a hydroxide ion (OH−):

H2O + H2O H3O+ + OH-

G. AMPHIPATHIC MOLECULES, WATER & pH

● The term pH was introduced in 1909 by Sörensen, who defined it as the

negative log of the hydrogen ion concentration:

● pH = -log[H+]

A low pH characterizes an acidic solution, and a high pH denotes a basic solution.

H. BIOCHEMICAL REACTIONS

● A biochemical reaction is the transformation of one molecule to a different molecule

inside a cell. Biochemical reactions are mediated by enzymes, which are biological
catalysts that can alter the rate and specificity of chemical reactions inside cells.

● Enzymes are grouped into six major classes based on the types of reactions they
catalyze