Comprehensive University Study Notes: Biological Sciences and Plant/Animal Physiology

Biology Fundamentals and Classification

Biology is defined as the science of life forms and living processes. The living world encompasses an amazing diversity of organisms. Early humans could easily perceive the difference between inanimate matter (like wind, sea, fire) and living organisms (plants and animals). Early societies deified some inanimate objects, and a common feature of these early views was a sense of awe or fear invoked by these entities.

Description of living organisms, including human beings, began much later in human history. Anthropocentric views of biology led only to limited progress in biological knowledge. Systematic and monumental description of life forms became a necessity, bringing in detailed systems of identification, nomenclature, and classification. The most profound realization from these studies was the recognition of the sharing of similarities among living organisms, both horizontally and vertically, showing that all present-day living organisms are related to each other and also to all organisms that ever lived on Earth.

The Living World and Taxonomy

Reproduction refers to the production of progeny possessing features more or less similar to those of parents. Many organisms reproduce asexually, such as fungi producing spores, yeast and hydra through budding, and Planaria via true regeneration. However, some organisms, such as mules or sterile worker bees, do not reproduce, meaning reproduction cannot be an all-inclusive defining characteristic. Metabolism—the sum total of all chemical reactions occurring in the body—is a defining feature of all living organisms without exception. While isolated metabolic reactions can occur in vitro, these are not living things but are living reactions.

Diversity and Nomenclature

The number of species known and described ranges between $1.7 \times 10^6$ to $1.8 \times 10^6$ . This refers to biodiversity. For the facilitation of study, scientists have established procedures to assign a scientific name to every known organism. This standardization is called nomenclature. For plants, names are based on the International Code for Botanical Nomenclature (ICBN), and for animals, the International Code of Zoological Nomenclature (ICZN).

Biologists follow universally accepted principles to provide scientific names. Each name has two components: the Generic name and the specific epithet. This system is known as Binomial Nomenclature, pioneered by Carolus Linnaeus. For example, for Mango, the scientific name is Mangifera indica, where Mangifera represents the genus and indica represents the specific epithet. Rules include: 1) Biological names are generally in Latin and written in italics. 2) The first word denotes the genus, the second the specific epithet. 3) Both words are underlined when handwritten or italicized when printed. 4) The genus name starts with a capital letter, and the specific epithet starts with a small letter.

Taxonomic Categories and Hierarchy

Classification is the process by which organisms are grouped into convenient categories based on observable characters. The scientific term for these categories is taxa. All categories together constitute the taxonomic hierarchy. The basic categories are Species, Genus, Family, Order, Class, Phylum or Division (for plants), and Kingdom. As we go higher from species to kingdom, the number of common characteristics decreases.

Biological Classification Systems

Aristotle was the earliest to attempt a scientific basis for classification, using simple morphological characters to classify plants (trees, shrubs, and herbs) and animals (those with red blood and those without). Linnaeus later developed the Two Kingdom system (Plantae and Animalia). However, this system did not distinguish between eukaryotes and prokaryotes, or unicellular and multicellular organisms. R.H. Whittaker (1969) proposed a Five Kingdom Classification: Monera, Protista, Fungi, Plantae, and Animalia. The criteria used included cell structure, body organization, mode of nutrition, reproduction, and phylogenetic relationships.

Kingdom Monera, Protista, and Fungi

Kingdom Monera includes bacteria, which are the most abundant micro-organisms and occur almost everywhere. They are categorized by shape: Coccus (spherical), Bacillus (rod-shaped), Vibrium (comma-shaped), and Spirillum (spiral). This group includes Archaebacteria (living in extreme conditions) and Eubacteria (true bacteria). Cyanobacteria (blue-green algae) are photosynthetic autotrophs. Kingdom Protista includes all single-celled eukaryotes like Chrysophytes, Dinoflagellates, Euglenoids, Slime moulds, and Protozoans. Kingdom Fungi constitutes a unique kingdom of heterotrophic organisms. They are cosmopolitan and occur in air, water, soil, and on animals and plants. They show great diversity in morphology and habitat.

Plant Physiology: Transport and Nutrition

Plants need to move molecules over very long distances. Water taken up by roots has to reach all parts of the plant, up to the very tip of the growing stem. Photosynthates from the leaves must also be moved to all parts, including root tips. Diffusion is a slow process and might be sufficient for short distances, but for long-distance transport, mass or bulk flow systems (Xylem and Phloem) are necessary. Translocation is the term for long-distance transport through the vascular system. Xylem transport is primarily unidirectional (roots to stems/leaves), while phloem transport of organic and mineral nutrients is multidirectional.

Water potential ( $\Psi_w$ ) is a fundamental concept for understanding water movement. It is determined by solute potential ( $\Psi_s$ ) and pressure potential ( $\Psi_p$ ). Pure water has the highest water potential, defined as zero. Adding solutes lowers the water potential, making $\Psi_s$ always negative. Transpiration is the evaporative loss of water by plants, occurring mainly through stomata. It creates a suction force (transpiration pull) that can lift water over $130\text{ m}$ high in a xylem column.

Photosynthesis and Respiration

Photosynthesis is the primary source of all food on earth and is responsible for the release of oxygen into the atmosphere by green plants. The process involves light-harvesting complexes (Photosystem I and II) located in the thylakoid membranes. Photosynthesis leads to the synthesis of carbohydrates using light energy, carbon dioxide ( $CO_2$ ), and water. Respiration involves the oxidation of organic compounds within the cells, leading to the release of energy in the form of ATP. Glycolysis, the breakdown of glucose to pyruvic acid, occurs in the cytoplasm. In aerobic respiration, pyruvic acid enters the mitochondria and is completely oxidized to $CO_2$ and water through the Krebs cycle and the Electron Transport System (ETS).

Animal Kingdom and Human Physiology

The Animal Kingdom comprises a diversity of living organisms. Classification is based on fundamental features like the level of organization (cellular, tissue, organ, organ system), symmetry (radial, bilateral), and body cavities (coelomates, pseudocoelomates, acoelomates). Phyla include Porifera, Coelenterata, Ctenophora, Platyhelminthes, Aschelminthes, Annelida, Arthropoda, Mollusca, Echinodermata, Hemichordata, and Chordata.

In human physiology, digestion involves the conversion of complex food substances into simple absorbable forms. The respiratory system facilitates the exchange of gases ( $O_2$ and $CO_2$ ). The circulatory system includes heart and blood vessels for the transport of nutrients and gases. Excretion involves the elimination of nitrogenous wastes from the body through kidneys, which contain functional units called nephrons.

Biology is defined as the science of life forms and living processes. The living world encompasses an amazing diversity of organisms, with estimates suggesting there are anywhere between $1.7 imes 10^6$ to $1.8 imes 10^6$ different species known. Early humans could easily perceive the difference between inanimate matter (like wind, sea, fire) and living organisms (plants and animals). Some early societies deified inanimate objects, reflecting a common feature in their views: a sense of awe or fear invoked by these entities. The systematic description of living organisms, including human beings, began much later in human history, paving the way for a new understanding of biology based on empirical observations. Anthropocentric views of biology led to limited progress in biological knowledge; however, a more systematic and monumental description of life forms became necessary. This led to the development of detailed systems of identification, nomenclature, and classification, revealing the sharing of similarities among living organisms both horizontally and vertically. It has become clear that all present-day living organisms are related to each other and also to all organisms that ever lived on Earth.

The Living World and Taxonomy

When we try to define 'living', we look for distinctive characteristics exhibited by living organisms: growth, reproduction, ability to sense the environment, and mounting a suitable response. Other features like metabolism, ability to self-replicate, self-organize, and interact are also considered. All organisms grow; an increase in mass and the number of individuals are twin characteristics of growth. While non-living things such as mountains and sand mounds may grow by the accumulation of material on the surface, growth in living organisms occurs from within. Consequently, growth alone cannot be taken as a defining property of living organisms unless the specific conditions under which it can be observed are specified. Reproduction refers to the production of progeny possessing features more or less similar to those of parents. Many organisms reproduce asexually, with fungi producing spores, yeast and hydra reproducing by budding, and Planaria via true regeneration. However, some organisms, such as mules or sterile worker bees, do not reproduce, indicating that reproduction cannot be an all-inclusive defining characteristic. Metabolism—the sum total of all chemical reactions occurring in the body—is a defining feature of all living organisms without exception. While isolated metabolic reactions can occur in vitro, these are not classified as living things but as living reactions.

Diversity and Nomenclature

Biodiversity encompasses the variety of life forms in a specific habitat or ecosystem, requiring distinctions among the known species. Scientists have established procedures to assign a scientific name to every known organism, a standardization known as nomenclature. For plants, names are based on the International Code for Botanical Nomenclature (ICBN), while for animals, the International Code of Zoological Nomenclature (ICZN) is applicable. Biologists follow universally accepted principles to provide scientific names that are vital for clarity and consistency in scientific communication. Each scientific name consists of two components: the Generic name and the specific epithet, reflecting its place within the broader taxonomic hierarchy. This system, known as Binomial Nomenclature, was pioneered by Carolus Linnaeus. For instance, the scientific name for Mango is Mangifera indica, where Mangifera represents the genus and indica signifies the specific epithet. Key rules of nomenclature include: 1) Biological names are generally in Latin and written in italics. 2) The first word denotes the genus, while the second represents the specific epithet. 3) Both words are underlined when handwritten or italicized when printed. 4) The genus name begins with a capital letter, while the specific epithet starts with a lowercase letter.