Fundamentals of Molecular Biology. Part 1: Molecular Cell Biology - A. N. Ogurtsov 2011

Molecular Biology. Subject Matter and Core Sections of the Course
Biomacromolecules

Molecular Cell biology examines biological processes at THE MOLECULAR LEVEL, viewing all cellular "events" as the result of interactions between individual molecules: the synthesis of macromolecules from building blocks, the assembly of macromolecules into complex structures, the catalytic effects driving specific Chemical Reactions, and the reading and utilization of information encoded within macromolecules.

The Cell interior is filled with a dense aqueous "soup" of small molecules (such as simple sugars, Amino Acids, and Vitamins) and ions (including sodium, chlorine, and calcium). The spatial distribution and concentration of these substances at any given point within the cell are regulated by a vast array of Proteins embedded in cellular membranes. These protein pumps, transporters, and channels direct the required molecules to their proper destinations and specific cell Organelles.

Specific small molecules (monomers) can be joined together to form polymers.

The most important of these polymers are Polysaccharides, proteins, and Nucleic Acids, which are commonly grouped under the umbrella term biological macromolecules.

The specific way in which a polymer is constructed from its monomers enables a vital function of macromolecules: the storage and transmission of information.

Proteins serve as the primary cellular "agents" responsible for carrying out most mechanical and chemical transformations within the cell. They are synthesized from 20 standard Amino Acids and typically consist of 100 to 1,000 amino acid residues. Following synthesis, the protein chain spontaneously folds into a defined three-dimensional Structure, which dictates the functional Specificity of that particular protein. The Diversity of protein structures is virtually limitless. Scale models of several protein molecules, along with DNA and The Plasma Membrane lipid bilayer, are shown in Figure 4.

Class="center">

Figure 4 - Models of certain Biomolecules

Such proteins make up distinct Protein Families, with several hundred such families currently known. Proteins perform a multitude of Functions within the cell: they act as Structural components of the intra- and Extracellular matrix, serve as sensors and carriers of chemical signals, catalyze biochemical reactions (as Enzymes), regulate Gene Expression (via protein Repressors and activators), and function as "pumps" that transport other molecules and ions.

Built from a mere 20 amino acids, proteins underpin the entire spectrum of biological functions across all living structures. Since an average protein comprises about 400 amino acids, there are theoretically $20^{400}$ possible distinct protein structures.

It is instructive to estimate the number of proteins a single cell utilizes to sustain its vital activities. Consider, for example, a hepatocyte (Liver cell) with a volume of $3,4\times10^{-9}$cm³ and a density of $1.03$ g/cm³, yielding a cell mass of $3.5\times10^{-9}$ g. Given that proteins account for approximately 20% of the cell's weight, the total protein mass in a hepatocyte is $7\times10^{-10}$ g. The average Yeast protein has a Molecular Weight of 52,700 g/mol, which implies there are on the order of $7.9\times10^{9}$ protein molecules in a hepatocyte ($N_a=6.02\times10^{23}$). A hepatocyte contains approximately 10,000 different proteins, meaning the cell averages roughly 1 million molecules of each specific protein type. Naturally, this is a very rough and approximate estimate, as protein copy numbers vary widely—ranging from relatively scarce Insulin-binding receptors (20,000 molecules) to abundant molecules of the structural protein Actin ($5\times10^{8}$ molecules).

Nucleic acids represent the second major class of biomacromolecules. Deoxyribonucleic acid carries the genetic blueprint dictating how, where, and when specific proteins are synthesized. The three-dimensional structure of DNA is a double helix whose strands are composed of monomer units called NUCLEOTIDES.

Four different nucleotides—adenine, thymine, cytosine, and guanine—pair up complementarily as A–T and C–G, forming a double helix (Figure 5). During Replication, the helix unwinds into two strands, each serving as a template for the synthesis of a complementary daughter strand, resulting in two copies of the original parent helix.

Figure 5 - Diagram of METABOLISM/36.html">DNA replication

Genetic information regarding Protein Structure is stored in DNA as genes—nucleotide sequences encoding a specific protein or RNA, typically ranging from 5,000 to 100,000 nucleotides in length. The bacterial genome (the complete set of all genes) comprises several thousand genes, whereas The Human Genome contains approximately 40,000 genes. Alongside the coding region, genes contain regulatory regions that allow the cell to control gene expression.

Cells utilize a two-step process—Transcription and Translation—to convert genetic information into synthesized proteins (Figure 6).

Figure 6 - Diagram of genetic mechanisms for Protein Synthesis in a Introduction/5.html">Eukaryotic Cell

During transcription, the enzyme RNA polymerase copies the gene into an RNA molecule (pre-mRNA). In Eukaryotic cells, this RNA is processed into functional Messenger RNA (mRNA) via RNA Processing, during which non-coding regions (introns) are removed from the pre-mRNA, and coding regions (exons) are spliced together.

The mRNA moves from The Nucleus into the Cytoplasm, binds to the small and large ribosomal subunits, and translation—the Synthesis of the polypeptide protein chain—begins.

The Regulation of Protein Synthesis is mediated by transcription factors—specific proteins that bind to DNA and stimulate either the activation or repression of gene expression.

The majority of eukaryotic DNA is located within the nucleus and packaged into Chromosomes.

Prokaryotic DNA typically consists of a circular molecule randomly coiled into a nucleoid located in the central region of the cell.