Foundations of Biochemistry: The Animal Cell, Biomolecules, and Physical Principles

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Chapter 1: Foundations of Biochemistry

Introduction to Biochemistry

Biochemistry is the study of the chemical processes and substances that occur within living organisms. This field bridges biology and chemistry, focusing on the molecular mechanisms that underlie cellular structure, function, and regulation. In this course, the primary emphasis is on the biochemistry of the animal cell, its structural components, and the chemical properties of biomolecules.

The Animal Cell

Key Structural Components

The animal cell is a eukaryotic cell, typically 10–100 µm in diameter, and contains a variety of organelles with specialized functions. The cell membrane regulates transport, while internal organelles carry out essential biochemical processes.

Nucleus: Contains genetic material (DNA) and controls cellular activities.
Mitochondria: Site of ATP (energy) production via cellular respiration.
Endoplasmic Reticulum (ER): Synthesizes proteins (rough ER) and lipids (smooth ER).
Golgi Apparatus: Modifies, sorts, and packages proteins and lipids.
Lysosomes: Contain digestive enzymes for breakdown of macromolecules.
Cell Membrane: Phospholipid bilayer that controls entry and exit of substances.

Diagram of an animal cell Labeled diagram of animal cell organelles Typical animal cell with organelles and micrographs

The Physical Laws of Life

Application of Physical Principles

All living organisms, including animal cells, obey the fundamental laws of physics and chemistry. These include:

Conservation of Mass and Energy: Matter and energy cannot be created or destroyed, only transformed.
Laws of Thermodynamics: Govern energy changes and the direction of biochemical reactions.
Chemical Kinetics: Describes the rates of chemical reactions.
Principles of Chemical Reactions: Underlie metabolic pathways and cellular processes.

Composition of Biomolecules

Elements Essential for Life

The human body is primarily composed of a small number of elements. The most abundant are carbon (C), nitrogen (N), oxygen (O), hydrogen (H), calcium (Ca), phosphorus (P), potassium (K), and sulfur (S), which together account for nearly 97% of the body's dry weight.

Element	Dry Weight (%)
C	61.7
N	11.0
O	9.3
H	5.7
Ca	5.0
P	3.3
K	1.3
S	1.0
Cl	0.7
Na	0.7
Mg	0.3

Table of most abundant elements in the human body

Other elements, such as titanium (Ti) and cadmium (Cd), have recently been shown to have biological importance. Elements are classified as bulk elements or trace elements based on their abundance and necessity for life.

Periodic table highlighting bulk and trace elements

Classes of Biomolecules

Major Biomolecule Types and Their Functions

Carbohydrates: Main source of energy; includes sugars and starches.
Lipids: Provide stored energy, form biological membranes, and serve as signaling molecules.
Proteins: Serve as enzymes (catalysts), structural components, signaling molecules, and transporters.
Nucleic Acids: Store and transmit genetic information; blueprint for protein synthesis.

Important Functional Groups in Biomolecules

Common Functional Groups and Linkages

Functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. Understanding these groups is essential for studying biochemical reactions.

Compound Name	Structure	Functional Group or Linkage
Amine	R-NH2, R2NH, R3N	Amino group
Alcohol	R-OH	Hydroxyl group
Thiol	R-SH	Sulfhydryl group
Aldehyde	R-CHO	Aldehyde group
Ketone	R-CO-R'	Keto group
Carboxylic acid	R-COOH	Carboxyl group
Ester	R-COOR'	Ester linkage
Thioester	R-COSR'	Thioester linkage

Table of common functional groups in biochemistry

Compound Name	Structure	Functional Group or Linkage
Amide	R-CONH2	Amide group
Imine (Schiff base)	R-CH=NH	Imine group
Disulfide	R-S-S-R'	Disulfide linkage
Phosphate ester	R-O-PO32-	Phosphoester linkage
Diphosphate ester	R-O-P-O-P-O-R'	Phosphoanhydride linkage

Table of additional functional groups in biochemistry

Important Intermolecular Forces

Bonding and Nonbonding Forces

Intermolecular forces are critical in determining the structure and function of biomolecules. They include both bonding (ionic, covalent, metallic) and nonbonding (ion-dipole, hydrogen bonds, dipole-dipole, dispersion) interactions.

Force	Model	Basis of Attraction	Energy (kJ/mol)	Example
Ionic	Cation–anion	Electrostatic attraction	400–4000	NaCl
Covalent	Nuclei–shared e- pair	Electron sharing	150–1100	H2
Metallic	Cations–delocalized electrons	Electron sea	75–1000	Fe

Table of bonding and nonbonding intermolecular forces

Force	Model	Basis of Attraction	Energy (kJ/mol)	Example
Ion-dipole	Ion charge–dipole charge	Electrostatic	40–600	Na+–H2O
H bond	Polar bond to H–dipole charge	High EN of N, O, F	10–40	H2O
Dipole-dipole	Dipole charges	Electrostatic	5–25	HCl
Dipole-induced dipole	Dipole charge–polarizable e- cloud	Induced	2–10	HCl–Cl2
Dispersion (London)	Polarizable e- cloud	Induced	0.05–40	F2–F2

Table of nonbonding intermolecular forces

Thermodynamic Principles in Biochemistry

Thermodynamics of Biochemical Reactions

Biochemical reactions are governed by the laws of thermodynamics. The spontaneity of a reaction is determined by the change in Gibbs free energy ():

First Law (Conservation of Energy): Energy can be converted between forms but not created or destroyed.
Second Law (Entropy): The entropy (disorder) of the universe tends to increase.
Third Law (Absolute Zero): At absolute zero (0 K), the entropy of a perfect crystal is zero.

The Gibbs free energy equation is:

If , the reaction is spontaneous (exergonic).
If , the reaction is non-spontaneous (endergonic).

Example: The decomposition of hydrogen peroxide is a thermodynamically favorable process and can be catalyzed by substances such as manganese dioxide (MnO2) or iron oxide.

Hierarchy of Cell Organization

Levels of Biological Structure

Cells are organized in a hierarchical manner, from simple monomeric units to complex organelles and supramolecular assemblies:

Level 1: Monomeric units (nucleotides, amino acids, sugars, fatty acids)
Level 2: Macromolecules (DNA, proteins, cellulose)
Level 3: Supramolecular complexes (chromosomes, plasma membrane, cell wall)
Level 4: The cell and its organelles

Hierarchy of cell organization from monomers to organelles

Additional info: This foundational overview prepares students for deeper study into the structure, function, and interactions of biomolecules in subsequent chapters.