Cell and Molecular Biology
Cell and Molecular Biology

Cell and Molecular Biology

Lead Author(s): Rolf Prade

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​The objectivity of life is often difficult to grasp! This book is organized from the bottom up and establishes a foundation of cell and molecular biology.

               Cell and Molecular Biology   

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   By ROLF PRADE, Professor of Microbiology
OKLAHOMA STATE UNIVERSITY, STILLWATER OK
 

INTRODUCTION

The objectivity of life is often difficult to grasp! What is it that makes life so beautiful, diverse, exciting and vibrant? Why is it that everything that is alive, a bacterium, a yeast, a fruit fly, a mouse or a human being, shares the same chemistry with inorganic matter? Is there something special about the molecules that makeup living beings (organisms) even though they are built by the same atoms than non-living things (inorganic matter)? Furthermore, if humans are built by atoms, elements and chemicals that are identical to the atoms, elements and chemicals of inorganic matter (a rock) are we therefore required to follow the same physical and chemical principles that guide non-living objects?

The answer to these questions rest on the fundamental observation that living beings constantly order, organize, reorder, resynthesize and assemble complex molecular structures and networks while inorganic matter is structurally inert and decays over time. The expansion of disorder over time justifies the irreversibility of the natural course, and the asymmetry between future and past. Inorganic objects are structurally simple and degrade over time, while live organisms are organic, complex and organized (opposite of decomposed).

While inorganic matter decays over time, increasing the entropy (or disorder) of an isolated system, as predicted by the laws of thermodynamics, living beings organize inorganic elements (hydrogen, carbon, oxygen, nitrogen and phosphorus) into organic compounds, amino acids, nucleotides and carbohydrates, that polymerize creating macromolecules such as proteins, DNA, RNA and polysaccharides, which in turn interact and collaborate with each other to create complex biochemical processes that irrevocably result in cell division, perpetuating living systems.

The laws of thermodynamics are omnipotent rules that apply to the entire universe and cannot be broken and biological systems are no exception. However, the fact remains, biological systems are highly organized and strive for continued organization as the fundamental activity that maintains organisms alive. This constant need to maintain cellular components organized requires the constant input of chemical energy, the solution to drive thermodynamically unfavorable reactions. Thus, living cellular systems are in constant need of a chemical energy source, delivered by the oxidation of sugars. The electrons abstracted from sugar oxidation are shuttled through complex biochemical systems dispensing high-energy packets that power unfavorable chemical reactions. Unfavorable reactions are all those reactions that construct organized molecules, and drive complex biochemical processes. An organism is only as alive as it can harvest adequate chemical energy to fuel its unfavorable metabolism, synthesize macromolecules, power cellular processes such as transcription, translation, replication and coordinate cell division. Once a living cell ceases to organize its intracellular network of macromolecules it dies, decays increasing the entropy of the universe. 

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Figure 1. The perpetual energy driven spiral of life. Living beings organize inorganic elements (hydrogen, carbon, oxygen, nitrogen and phosphorus) into compounds (methane, carbon dioxide, ammonium, phosphate etc.) organic compounds (e.g., amino acids, nucleotides, fats and carbohydrates) that polymerize creating macromolecules (e.g., lipids, polysaccharides, proteins, DNA and RNA), which in turn interact and collaborate with each other (e.g., metabolism, anabolism, photosynthesis) to create complex biochemical processes (e.g., compartments, replication, translation and transcription) that irrevocably result in the creation of cells that divide establishing tissues, organs and systems perpetuating living systems.

Organisms (all living things) use DNA as the informational molecule to permanently store, transmit and propagate genetic information. Genetic information (DNA) is the blueprint needed to make proteins and enzymes a cell requires to drive metabolism, the lipids it needs to construct membranes and organelles and polysaccharides to make cell walls. The genome of an organism (DNA) encodes thousands of genes (informational units) that when expressed and translated yield proteins and other gene products that assemble chemical factories, cellular components and biochemical processes that confer shape, fate and functional determination.

DNA endows uniqueness to organisms. It is the type of genetic data stored in DNA that defines a species, the shape color, fate and function of an organism. Each species has its own DNA blueprint, even though similar but not identical. Moreover, multicellular organisms, a consortium of cells, contain the exact same DNA but do not express (interpret) all their genetic data in the same way, providing functional individuality to each cell-type of an organism. In this way in humans, cells that make up lungs are very different from the cells that make up a liver, an intestine or a brain, but all contain the exact same DNA. Thus, the information stored in the genome of an organism is identical to all cell types and the large variety of cells, its shape, purpose and function as well as the associations we observe in integrative biology are the result of pre-determined spatial-temporal expression of genes that a given organism contains.

This book is organized from the bottom up. We initially recall the big picture of small things, examining the basic composition of matter, regardless of being inorganic or organic (PART I, Chapters 1 and 2). We than try to understand how an amino acid sequence determines protein shape by looking at structure and function of macromolecules and how compartments and the trafficking between them occurs (PART II, Chapters 3, 3.1, 3.2 and 4, 4.1 and 4.2). Next, we try to solve logical chemical reactions and make metabolic reconstructions, based on the examination of energy and chemical transformations in cells; a series of chapters (PART III, Chapters 5, 5.1, 5.2 and 6) dedicated to the cellular chemical reactions that harvest, shuttle and transfer energy from favorable reactions (in accordance with the law of thermodynamics) onto non-favorable reactions (that apparently are non-compliant with the second law of thermodynamics). We than examine the implications of DNA structure as a repository of information and their fundamental outcomes by considering genetic data flow in cells (PART IV, Chapters 7, 8, 8.1, 8.2 and 8.3) and finally evaluate gene regulation mechanisms, create cellular processes, cell division, tissues and organs as well the implications of cancer (PART V. Chapters 9, 10.1, 10.2 and 11, 11.1, 11.2, 11.3 and 12).

While ORGANIC CHEMISTRY and any INTRODUCTORY BIOLOGY (Plant, Animal or Microbial) courses are pre-requisites for CELL & MOLECULAR BIOLOGY other courses are complementary and essential for any PREMED initiative. Here we mention just a few. The study of INTEGRATIVE BIOLOGY (formerly known as Zoology) examines the aggregated phenotype (the comprehensive gene expression profile) of an organism while CELLULAR AND MOLECULAR BIOLOGY attempts to study the sub-organismal components that enables the chemistry of life. The study of GENETICS examines DNA information and DNA processing mechanisms which include the regulation of gene expression. The study of BIOCHEMISTRY examines in detail all the chemical reactions catalyzed by enzymes of biological systems and tries to develop a comprehensive picture on how cells are equipped to provide all that chemical energy to drive the non-favorable reactions that pretend to defy the second law of thermodynamics. The study of PHYSIOLOGY examines chemical relationships that exist within all the diverse chemical pathways within a cell, organism or a society of them, and try to determine the rules and relationships that govern (regulate) large scale cellular processes. The study of METABOLISM, examines the minute nature of cellular chemical reactions including the kinetic properties and reallocation of atoms and electrons, the study of ENDOCRINOLOGY determines the impact of hormones and signaling molecules on metabolic pathways. The study of ANATOMY looks at the shape and morphology of tissues, organs and systems. The study of DEVELOPMENTAL BIOLOGY focuses on how and why cells change cell fate and shape and the studies of EMBRYOLOGY examine the mechanisms that lead a single fertilized cell (embryo) to evolve into a multicellular organism. The study of SIGNAL TRANSDUCTION examines the molecules that signal, transmit and receive signals.

Finally, the study of CELL AND MOLECULAR BIOLOGY tries to develop a universal molecular account of reactions essential to drive primary cellular processes that culminate with cell division and the perpetual maintenance of life. Thus, in several of the above-mentioned fields, this book represents a shortfall in explaining fully detailed chemical processes specifically it fails in addressing the enormous diversity of cellular metabolism capable to adapt to adverse situations and/or respond to stimuli emanated by neurons or environmental conditions.