STRUCTURE AND PROPERTIES OF BIOMOLECULES - A. E. Zemlyakov - 2017

01. BIOMOLECULES. CELL STRUCTURE

Organic compounds that make up Living organisms are exceptionally complex and diverse. Even the simplest single-celled organisms consist of a vast array of Different types of molecules. Many of these molecules perform specific biological Functions and are commonly referred to as Biomolecules. For example, the bacterium Escherichia coli (or E. coli for short) contains about 5,000 different organic compounds, including approximately 3,000 Proteins, 1,000 Nucleic Acids, about 50 Monosaccharides, and 40 lipid components.

Ultimately, all biomolecules are derived from simple Inorganic Compounds (such as nitrogen, carbon dioxide, and Water obtained from the environment). These precursors are synthesized into intermediate organic molecules, which serve as monomer building blocks. The blocks then assemble into macromolecules (Biopolymers) and, subsequently, into supramolecular complexes. Several "tiers" of increasing structural complexity can be distinguished within a Cell (see diagram).

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At the intersection of such multifaceted sciences as chemistry and biology, the advancement of natural sciences has given rise to numerous new disciplines dedicated to The Study of biomolecules. These particularly include biochemistry, the chemistry of natural compounds, molecular biology, and bioorganic chemistry. Many living systems are studied simultaneously by several of these scientific fields.

• Bioorganic chemistry — the science concerning the Structure and BIOLOGICAL FUNCTIONS OF the most important components of living nature. Its primary focus is on establishing the correlations between chemical structure and biological activity.

The main objects studied in bioorganic chemistry are conventionally divided into two broad groups:

♦ biopolymers, which include proteins, CARBOHYDRATES, nucleic acids, and mixed biopolymers; and

♦ low-molecular-weight BIOREGULATORS, such as Alkaloids, Antibiotics, Vitamins, Pharmaceuticals, pesticides, pheromones, and other groups of biologically active compounds.

Lipids are also frequently classified alongside biopolymers due to their formation of lipid aggregates, which exhibit physical behavior similar to that of high-molecular-weight compounds.

The principal objectives addressed by bioorganic chemistry include:

- isolation of substances in pure, individual form;

- structural elucidation;

- chemical synthesis and chemical modification;

- investigation of biological activity through in vitro and in vivo assays.

• Biochemistry — the science of the composition and metabolic transformations of compounds that make up living matter during life processes. Biochemistry is traditionally divided into three branches:

■ static biochemistry — investigates the Composition and Structure of compounds found in biological objects;

■ dynamic biochemistry — explores the chemical transformations occurring during vital activity in conjunction with energy changes;

■ functional biochemistry — establishes the relationships between The structure of organic substances, their alterations resulting from biochemical processes, and the functions of Tissues and Organs.

Key Elements of Cell Structure

❖ Cell Classification.

♦ Based on Cellular Organization, Cells are divided into higher (eukaryotes) and lower (prokaryotes).

♦ Based on the mode of carbon acquisition from the environment: autotrophic cells ("self-feeders") capable of assimilating carbon dioxide, and heterotrophic cells ("other-feeders") that obtain carbon in the form of organic compounds.

♦ Based on Energy Sources: phototrophic cells, which utilize light as an energy source, and chemotrophic cells, which derive energy from oxidation-reduction reactions.

❖ Eukaryotes — higher, chromosomal cells. These include Protozoa, microscopic Algae, Fungi, as well as PLANT AND ANIMAL cells. A typical cell has a size of ~20 µm. It is enclosed by a protein-lipid Plasma Membrane. The interior is filled with cytoplasmic fluid—a structured colloidal system containing Enzymes, nutrients, macromolecules, and small cellular components.

Diagram of The Introduction/5.html">Eukaryotic Cell structure

The eukaryotic structure comprises A number of cell Organelles:

✵ Nucleus. Diameter ~5 µm, surrounded by a membrane containing pores. It houses the bulk of the cellular DNA (up to 95%) in the form of Chromatin, which condenses into Chromosomes prior to Cell Division.

✵ Nucleolus contains the major portion of nuclear RNA.

✵ Mitochondria — ellipsoidal organelles up to ~3 µm in length. The outer membrane is smooth, whereas the inner part forms numerous folds known as cristae. Their main function is the generation and transport of intracellular energy in the form of ATP molecules. Different cells contain varying numbers of mitochondria, ranging from 10 in Yeast to several hundred in animal cells.

✵ Lysosomes — cytoplasmic bodies with a diameter of 0.25-0.5 µm, bounded by a membrane. They contain the majority of hydrolytic enzymes. Their primary function is intracellular Digestion.

✵ Peroxisomes — organelles similar to lysosomes (diameter 0.2-0.5 µm). They contain enzymes that generate and break down hydrogen peroxide.

✵ Endoplasmic reticulum — a complex membrane system extending from The Nucleus to The Cell membrane. A large number of Ribosomes are anchored to it. It mediates the Biosynthesis and glycosylation of proteins, as well as lipids, Polysaccharides, Steroids, and other molecules. In some cells, it is closely associated with the Golgi apparatus—a membrane complex responsible for the concentration and transport of biopolymers.

✵ Cytoskeleton is a complex dynamic system responsible for maintaining cell shape, anchoring organelles, and facilitating biochemical reactions. Its main components are Actin filaments formed by the protein actin, Intermediate filaments formed by keratin molecules, and microtubules composed of tubulin proteins.

The structural units of filaments are actin molecules (molecular weight ~42 kDa). In its monomeric state, it is bound to an ATP molecule. In the presence of Mg²⁺ ions, self-assembly of the double-stranded protein macromolecule takes place, accompanied by The conversion of ATP to ADP (analogous to the "GTP/GDP switch").

Tubulin protein units consist of two subunits with a Molecular Weight of 50-55 kDa. Each subunit contains a GTP molecule. Upon Hydrolysis of the nucleotide molecule belonging to the β-subunit into GDP, the tubulin dimer acquires The ability to readily form a supramolecular structure via non-covalent interactions. Conversely, microtubules are capable of rapid depolymerization under certain conditions.

The cytotoxic activity of several antitumor drugs is related to their effect on tubulin. For instance, the alkaloids colchamine and vinblastine block the ability of the tubulin dimer to form microtubules, whereas the diterpenoid taxol inhibits the depolymerization process.

✵ Cell membrane — a dual lipid-protein membrane up to 8 nm thick. It ensures cell integrity and participates in membrane transport, cell-to-Cell Recognition, adhesion, and receptor signaling.

❖ Prokaryotes — lower, non-chromosomal cells. These include Bacteria and blue-green algae. They are significantly smaller in size than eukaryotes, with a diameter of 0.2-1 µm and a length of 0.3-5 µm.

Compared to eukaryotes, they have a simpler structure: they lack a nucleus, an endoplasmic reticulum, and virtually all mitochondria. The prokaryotic nucleoid lacks a membrane and is typically represented as a single circular DNA molecule. Ribosomes are located on the cell membrane.

Most bacteria possess an additional outer envelope outside the membrane, consisting of a Cell wall and a capsule, which provides enhanced cell protection. Based on the structure of their outer envelope, bacteria are divided into Gram-positive (Gr⁺) and Gram-negative (Gr^-) bacteria. This classification stems from the fact that certain bacteria retain a stain proposed in 1884 by the Danish physician H. Gram, whereas others do not.

✵ Gram-positive bacteria have a single-layered cell wall 20-100 nm thick. The Main Components of the wall are peptidoglycan (50-80%) and Teichoic Acids (up to 50%). The cell wall contains virtually no lipids. They produce exotoxins. The cell wall features pores with a diameter of 1-6 nm, which permit The transport of various molecules.

✵ Gram-negative bacteria. The cell wall is bilayered: a rigid peptidoglycan layer 2–3 nm thick and an outer layer featuring a secondary heterogeneous lipid membrane, with a total thickness of 8–10 nm. The cell wall contains little peptidoglycan (5–10%) and typically lacks teichoic acids.

The periplasmic space lies between the outer and Cytoplasmic membranes, containing enzymes and other biomolecules. The outer membrane contains porin proteins that form pores for the passage of substances (sugars, Amino Acids, Peptides), as well as lipopolysaccharides, some of which function as endotoxins.

✵ Bacterial capsules. Capsule-mediated protection is characteristic of most bacteria. It provides defense against external environmental factors and acts as a camouflage mechanism. For instance, the capsule of Yersinia pestis carries Antigens homologous to human Blood group I, helping the bacterium evade the host immune system. Capsular structures possess distinct antigenic properties (K-antigens). In certain bacteria, the capsule directly determines serological Specificity and virulence.

Microcapsules are distinguished by a thickness of up to 0.2 µm, macrocapsules exceed 0.2 µm, and the mucous layer has a thickness significantly greater than the bacterial diameter.

Based on their chemical composition, capsules are subdivided into polysaccharide and polysaccharide-polypeptide types.

✵ L-forms of bacteria. Under METABOLISM/18.html">The Influence of antibiotics, such as penicillin, a bacterium loses its peptidoglycan layer entirely or partially, leading to a dramatic increase in size (up to 50 µm). In pathogenic bacteria, virulent properties acquire a new dimension—mortality rates decrease, while drug resistance increases, and the resulting infections tend to become chronic.

• Autotrophs and heterotrophs. Unlike autotrophic cells, which are capable of assimilating carbon from the environment in the form of carbon dioxide, heterotrophic cells cannot assimilate CO₂ and instead acquire carbon from complex, reduced organic compounds (relative to carbon dioxide), such as glucose. Autotrophs sustain themselves independently, whereas heterotrophs feed on the metabolic products of other cells. All photosynthetic cells and certain bacteria are classified as autotrophs, whereas the vast majority of microorganisms and higher animal cells are heterotrophs.

❖ Phototrophs and chemotrophs. Phototrophs include plant cells, purple bacteria, blue-green algae (cyanobacteria), and green algae. All these cells derive their energy from sunlight.

Chemotrophs are subdivided, depending on The Nature of the electron Donors they use to generate energy, into:

■ organotrophs (eukaryotes, non-phototrophic prokaryotes), for which complex organic molecules (such as glucose) serve as electron donors, and

■ lithotrophs (from the Greek "lithos" meaning stone), which utilize molecular hydrogen, sulfur, or other simple inorganic compounds (such as hydrogen sulfide and ammonia) as electron donors. For example, giant sulfur bacteria Thiomargarita (measuring 0.1–0.75 mm) have been discovered in oxygen-depleted layers deep within the Gulf of Mexico, deriving their energy from The oxidation of hydrogen sulfide.

Chemoorganotrophs (otherwise referred to as heterotrophs) are divided into two major classes:

♦ aerobic cells use molecular oxygen as the final electron acceptor, whereas

♦ anaerobic cells utilize other substances.

Certain cells are capable of surviving under both aerobic and anaerobic conditions; such cells are termed facultative anaerobes. Conversely, anaerobic cells that cannot utilize oxygen and for whom oxygen is toxic are known as obligate anaerobes.

In some organisms, not all cells belong to the same metabolic class. For instance, in higher plants, green cells (containing chlorophyll) are autotrophs that sustain themselves via Photosynthesis, whereas ROOT cells are heterotrophs. Furthermore, in the light, nearly all cells of a green leaf behave as autotrophs, whereas in the dark, they function as heterotrophs.