Comprehensive Biology Study Notes: From the Living World to Plant and Classification to Plant and Human Physiology

The Science of Biology and the Contributions of Ernst Mayr

Biology is defined as the science of life forms and living processes. The living world encompasses an amazing diversity of organisms. Early human civilizations first perceived the difference between inanimate matter and living entities, often deifying components of the environment like wind, sea, and fire. The descriptive study of living organisms, including humans, began much later in history. Societies that adopted an anthropocentric view of biology registered limited progress in biological knowledge compared to those focusing on systematic and monumental descriptions of life forms. Such descriptive studies led to the development of systems for identification, nomenclature, and classification. A significant result of these studies was the recognition that all living organisms share similarities horizontally (among contemporaries) and vertically (with ancestors). The revelation that all current living organisms are related to each other and to organisms that lived on Earth in the past became a humbling realization for humanity, eventually leading to cultural movements for the conservation of biodiversity.

Ernst Mayr (1904–2004), known as the "Darwin of the 20th Century," was one of the 100 greatest scientists of all time. Born in Kempten, Germany, he joined Harvard\'s Faculty of Arts and Sciences in 1953 and retired in 1975 under the title Alexander Agassiz Professor of Zoology Emeritus. Throughout his career, which spanned nearly 80 years, his research covered ornithology, taxonomy, zoogeography, evolution, systematics, and the history and philosophy of biology. He almost single-handedly made the origin of species diversity the central question of evolutionary biology that it is today. Mayr pioneered the currently accepted definition of a biological species. He received the "triple crown of biology": the Balzan Prize in 1983, the International Prize for Biology in 1994, and the Crafoord Prize in 1999. He passed away at the age of 100 in the year 2004.

Defining Characteristics of Living Organisms

When attempting to define "living," scientists look for distinctive characteristics. These include growth, reproduction, ability to sense the environment and mount a suitable response, metabolism, and the ability to self-replicate and self-organize.

Growth is characterized by an increase in mass and an increase in the number of individuals. In multicellular organisms, growth occurs through cell division. In plants, growth by cell division occurs continuously throughout their lifespan, whereas in animals, it occurs only up to a certain age. Unicellular organisms also grow by cell division, which can be observed in vitro by counting cells under a microscope. In higher animals and plants, growth and reproduction are mutually exclusive events. Non-living objects can exhibit growth through the accumulation of material on their surface (e.g., mountains and sand mounds), but in living organisms, growth originates from within. Therefore, growth cannot be taken as an all-inclusive defining property of living beings unless specific conditions are explained.

Reproduction refers to the production of progeny possessing features similar to parents. In multicellular organisms, this refers to sexual reproduction, but organisms also reproduce by asexual means. Fungi produce millions of asexual spores, yeast and Hydra reproduce by budding, and Planaria (flatworms) exhibit true regeneration. Unicellular organisms like bacteria and Amoeba use cell division as a synonym for reproduction. Because some living organisms do not reproduce (e.g., mules, sterile worker bees, infertile human couples), reproduction is not an all-inclusive defining characteristic of life either, though no non-living object is capable of self-replication.

Metabolism is the sum total of all chemical reactions occurring in the body. All living organisms are made of chemicals that are constantly being Made and changed into other biomolecules. No non-living object exhibits metabolism. While metabolic reactions can be demonstrated in cell-free systems outside the body (in vitro), these isolated reactions are considered living reactions but not living things. Therefore, metabolism is a defining feature of living organisms, and cellular organization of the body is the defining feature of life forms.

Consciousness, the ability to sense surroundings and respond to stimuli (physical, chemical, or biological), is perhaps the most technically complicated feature of life. All organisms, from prokaryotes to eukaryotes, respond to environmental cues. Photoperiod affects reproduction in seasonal breeders. Human beings are the only organisms aware of themselves (self-consciousness). Thus, consciousness is a defining property of living organisms. In the case of patients in a coma supported by machines, defining the living state becomes more difficult as they lack self-consciousness.

Taxonomy and the Diversity of Life

The number of species currently described ranges between $1.7$ to $1.8$ million. This is referred to as biodiversity. nomenclature is the process of standardizing the naming of living organisms so that a particular organism is known by the same name globally. This is only possible when the organism is correctly described and identified through identification. For plants, scientific names are based on agreed-upon principles provided in the International Code for Botanical Nomenclature ($ICBN$); for animals, the International Code of Zoological Nomenclature ($ICZN$) is used.

Binomial Nomenclature, a system established by Carolus Linnaeus, provides a name with two components: the Generic name and the Specific epithet. For example, in Mangifera indica, Mangifera represents the genus and indica represents the specific epithet. Universal rules of nomenclature include:

1. Biological names are usually in Latin and written in italics.
2. The first word represents the genus and the second the specific epithet.
3. When handwritten, they are separately underlined; when printed, they are italicized.
4. The genus starts with a capital letter, while the specific epithet starts with a small letter.
5. The author’s name appears in abbreviated form at the end (e.g., Mangifera indica Linn.).

Classification is the process by which organisms are grouped into convenient categories based on easily observable characters. The scientific term for these categories is taxa. Taxa can indicate categories at very different levels (e.g., plants, wheat, animals, mammals, dogs). Taxonomy is the study of classification based on characteristics. Modern taxonomic studies involve external and internal structure, cell structure, developmental processes, and ecological information. The basic processes of taxonomy are characterisation, identification, classification, and nomenclature.

Systematics involves not just classification but also the study of the relationships among organisms. The word is derived from the Latin systema, meaning systematic arrangement. Linnaeus used Systema Naturae as the title of his publication. Systematics eventually incorporated evolutionary relationships between organisms.

Taxonomic Hierarchy and Aids

Classification involves a hierarchy of steps where each step represents a rank or category. The whole system is the taxonomic hierarchy, and each unit is a taxon. The categories in descending order are: Kingdom, Phylum (for animals) or Division (for plants), Class, Order, Family, Genus, and Species.

• Species: A group of individual organisms with fundamental similarities (e.g., Solanum tuberosum for potato).
• Genus: An aggregate of closely related species (e.g., Panthera includes leo, pardus, and tigris).
• Family: Related genera with fewer similarities (e.g., Solanaceae includes Solanum, Petunia, and Datura).
• Order: Higher category based on aggregates of characters (e.g., Polymoniales includes Solanaceae and Convolvulaceae).
• Class: Related orders (e.g., Mammalia includes Primata and Carnivora).
• Phylum/Division: Classes with common features like a notochord.
• Kingdom: The highest category (e.g., Kingdom Animalia).

Taxonomic Aids are techniques and procedures to store and preserve information and specimens:

• Herbarium: A storehouse of collected plant specimens that are dried, pressed, and preserved on sheets. Sheets carry labels with collection data, English/local/botanical names, family, and collector name.
• Botanical Gardens: Collections of living plants for reference (e.g., Royal Botanical Garden at Kew, England; Indian Botanical Garden, Howrah; National Botanical Research Institute, Lucknow).
• Museums: Established in educational institutes; they have collections of preserved plant and animal specimens in jars with preservative solutions or as dry specimens. Insects are kept in boxes after collecting, killing, and pinning. Large animals are stuffed.
• Zoological Parks (Zoos): Enclosures where wild animals are kept in protected environments under human care to study their behavior and food habits.
• Key: Used for identification based on similarities and dissimilarities. It relies on contrasting characters in a pair called a couplet. Each statement in the key is a lead. Keys are generally analytical in nature.

Biological Classification Systems

Aristotle was the earliest to attempt a scientific basis for classification, using simple morphological characters to group plants (trees, shrubs, herbs) and animals (those with red blood and those without). Linnaeus later developed a Two Kingdom system (Plantae and Animalia). However, this system did not distinguish between eukaryotes and prokaryotes, unicellular and multicellular organisms, or photosynthetic and non-photosynthetic organisms.

R.H. Whittaker (1969) proposed a Five Kingdom Classification: Monera, Protista, Fungi, Plantae, and Animalia. The main criteria for this classification were cell structure, body organization, mode of nutrition, reproduction, and phylogenetic relationships.

• Kingdom Monera: Bacteria are the sole members. Shapes include spherical Coccus ($pl. cocci$), rod-shaped Bacillus ($pl. bacilli$), comma-shaped Vibrium ($pl. vibrio$), and spiral Spirillum ($pl. spirilla$). They show extensive metabolic diversity. Many are autotrophic (photosynthetic or chemosynthetic), but the majority are heterotrophs.

  • Archaebacteria: Live in harsh habitats like salty areas (halophiles), hot springs (thermoacidophiles), and marshy areas (methanogens).
  • Eubacteria: "True bacteria" with a rigid cell wall and often a flagellum. Includes Cyanobacteria (Blue-green algae), which have chlorophyll $a$ and can fix atmospheric nitrogen in specialized cells called heterocysts (e.g., Nostoc, Anabaena).
  • Mycoplasma: Organisms that completely lack a cell wall; they are the smallest living cells known and can survive without oxygen.

• Kingdom Protista: Includes all single-celled eukaryotes. Primarily aquatic.

  • Chrysophytes: Diatoms and golden algae (desmids). Diatoms have siliceous cell walls forming two thin overlapping shells (soap box fit). Accumulations form "diatomaceous earth."
  • Dinoflagellates: Mostly marine and photosynthetic; various colors. Some like Gonyaulax cause "red tides."
  • Euglenoids: Mostly freshwater stagnant water organisms; have a protein-rich layer called a pellicle instead of a cell wall.
  • Slime Moulds: Saprophytic protists. Under favorable conditions, they form an aggregation called plasmodium.
  • Protozoans: Heterotrophs living as predators or parasites. Includes amoeboid (use pseudopodia), flagellated (e.g., Trypanosoma), ciliated (e.g., Paramoecium), and sporozoans (e.g., Plasmodium).

• Kingdom Fungi: Heterotrophic organisms with great diversity in morphology and habitat. They are cosmopolitan. Most are saprophytes or parasites. Symbiotic forms include lichens (with algae) and mycorrhiza (with roots of higher plants).

  • Structure: Composed of long, slender thread-like structures called hyphae. A network of hyphae is mycelium. Cell walls are composed of chitin and polysaccharides.
  • Reproduction: Vegetative (fragmentation, fission, budding), asexual (spores like conidia, sporangiospores, zoospores), or sexual (oospores, ascospores, basidiospores). Sexual cycle involve plasmogamy, karyogamy, and meiosis.
  • Classes: Phycomycetes (e.g., Mucor, Rhizopus, Albugo), Ascomycetes (e.g., Penicillium, Yeast, Neurospora), Basidiomycetes (e.g., Agaricus, Ustilago, Puccinia), and Deuteromycetes (Imperfect fungi like Alternaria, Colletotrichum, Trichoderma).

• Viruses, Viroids, and Lichens: These are not included in Whittaker\'s five kingdoms. Viruses are non-cellular organisms characterized by an inert crystalline structure outside the living cell. Once they infect a cell, they take over the machinery to replicate.

  • Virus structure: Protein coat (capsid made of capsomeres) and genetic material (DNA or RNA). Plant viruses usually have single-stranded RNA; animal viruses have single or double-stranded RNA or double-stranded DNA.
  • Examples: Mumps, smallpox, herpes, influenza, and AIDS in humans.
  • Viroids: Discovered by T.O. Diener (1971), smaller than viruses, lacking a protein coat, and composed of free low molecular weight RNA.
  • Lichens: Symbiotic associations between algae (phycobiont) and fungi (mycobiont). They are very good pollution indicators.

Plant Kingdom Characteristics

Kingdom Plantae includes eukaryotic chlorophyll-containing organisms. Systems of classification have evolved from artificial systems (Linnaeus - based on superficial vegetative characters or androecium structure) to natural classification systems (Bentham and Hooker - based on natural affinities, ultrastructure, anatomy, embryology, and phytochemistry). Current systems use Phylogenetic classification (based on evolutionary relationships), Numerical Taxonomy (using computers and observable characteristics), Cytotaxonomy (cytological information like chromosome number), and Chemotaxonomy (chemical constituents).

• Algae: Chlorophyll-bearing, simple, thalloid, largely aquatic organisms. Groups include:

  • Chlorophyceae: Green algae. Pigments: chlorophyll $a$ and $b$. Storage: pyrenoids (protein and starch).
  • Phaeophyceae: Brown algae. Pigments: chlorophyll $a$, $c$, carotenoids, and xanthophylls (fucoxanthin). Storage: laminarin or mannitol. Cell wall has algin. Plant body has a holdfast, stipe, and frond.
  • Rhodophyceae: Red algae. Pigments: chlorophyll $a$, $d$, and r-phycoerythrin. Storage: floridean starch (similar to amylopectin and glycogen).

• Bryophytes: Includes mosses and liverworts. Known as "amphibians of the plant kingdom" because they live in soil but depend on water for sexual reproduction. The main plant body is haploid (gametophyte).

• Pteridophytes: Includes horsetails and ferns. First terrestrial plants to possess vascular tissues (xylem and phloem). The main plant body is a sporophyte. They can be homosporous or heterosporous (producing macro and micro spores).

• Gymnosperms: Plants in which ovules are not enclosed by an ovary wall and remain exposed both before and after fertilization. Includes the giant redwood tree Sequoia. Seeds are not covered (naked).

• Angiosperms: Flowering plants where seeds are enclosed in fruits. They range from microscopic Wolffia to tall Eucalyptus ($100$ meters). Undergo double fertilization (Syngamy + Triple Fusion) forming a diploid zygote and triploid primary endosperm nucleus ($PEN$).

Animal Kingdom and Structural Organisation

Animals are multicellular, heterotrophic eukaryotes that lack cell walls. Classification is based on symmetry (radial or bilateral), levels of organization (cellular, tissue, organ, organ system), presence of coelom (body cavity), and segmentation.

• Phyla include: Porifera (sponges), Coelenterata (Cnidaria), Ctenophora, Platyhelminthes (flatworms), Aschelminthes (roundworms), Annelida, Arthropoda (largest phylum with jointed appendages), Mollusca, Echinodermata (spiny skin, water vascular system), Hemichordata, and Chordata.
• Chordata subphyla: Urochordata, Cephalochordata, and Vertebrata.
• Classes of Vertebrata: Cyclostomata, Chondrichthyes (cartilaginous fish), Osteichthyes (bony fish), Amphibia, Reptilia, Aves (birds), and Mammalia (possess mammary glands).

Structural organization in animals involves tissues: Epithelial, Connective, Muscular, and Neural.

• Epithelial: Covers surfaces or lines cavities. Can be simple (squamous, cuboidal, columnar) or compound.
• Connective: Links and supports tissues. Includes loose (areolar, adipose), dense (tendons, ligaments), and specialized (cartilage, bone, blood).
• Muscular: Skeletal (striated/voluntary), Smooth (non-striated/involuntary), and Cardiac.
• Neural: Composed of neurons and neuroglia.

Earthworms (Pheretima), Cockroaches (Periplaneta americana), and Frogs (Rana tigrina) serve as model organisms for studying morphology and anatomy. Earthworms have segments with S-shaped setae for locomotion. Cockroaches have an exoskeleton of chitin and an open circulatory system. Frogs are amphibians with skin and lung respiration, and a three-chambered heart.

Cell: Structure and Function

The cell is the fundamental structural and functional unit of all living organisms. Anton von Leeuwenhoek first saw and described a live cell. Robert Brown discovered the nucleus. The Cell Theory (Schleiden and Schwann, modified by Rudolf Virchow) states that all living organisms are composed of cells and products of cells, and all cells arise from pre-existing cells (Omnis cellula-e cellula).

• Prokaryotic Cells: Lack a membrane-bound nucleus. DNA is genomic and often contains small circular plasmids.
• Eukaryotic Cells: Have a membrane-bound nucleus and organelles (mitochondria, chloroplasts, golgi complex, etc.).
• Cell Membrane: Fluid mosaic model (Singer and Nicolson, 1972) describes it as a bilayer of lipids (phosphoglycerides) with integrated proteins. It is selectively permeable.
• Organelles: Mitochondria (powerhouse/ATP production), Ribosomes (protein synthesis), Endoplasmic Reticulum (Rough for proteins/Smooth for lipids), Golgi Apparatus (packaging and secretion), Lysosomes (digestive enzymes), Vacuoles (storage), Chloroplasts (photosynthesis).

Biomolecules and Enzymes

Living organisms have a high abundance of carbon and hydrogen compared to the Earth\'s crust. Biomolecules can be categorized as micromolecules ($< 800$ Daltons) or macromolecules ($> 10,000$ Daltons).

• Amino acids: Organic compounds containing an amino group and an acidic group on the same carbon. There are $20$ types used in proteins.
• Proteins: Heteropolymers of amino acids. Collagen is the most abundant protein in the animal world, while RUBISCO is the most abundant in the biosphere.
• Polysaccharides: Long chains of sugars (e.g., Starch, Cellulose, Glycogen, Chitin).
• Nucleic Acids: Polymers of nucleotides (Nitrogenous base + Pentose sugar + Phosphate). DNA and RNA.
• Enzymes: Biocatalysts that lower the activation energy of reactions. Most are proteins. Activity is affected by temperature, pH, and substrate concentration.

Plant Physiology: Water and Metabolism

Water is essential for all physiological activities. Water potential ($\Psi_w$) is the measure of free energy of water. Pure water has a $\Psi_w$ of zero. Addition of solute lowers it (solute potential $\Psi_s$), while pressure increases it (pressure potential $\Psi_p$). $\Psi_w = \Psi_s + \Psi_p$.

Transport in plants occurs via:

1. Diffusion: Passive movement.
2. Facilitated Diffusion: Protein-aided passive transport.
3. Active Transport: Uses ATP to pump molecules against a gradient.
4. Long distance transport: Via Xylem (water/minerals upwards) and Phloem (organic solutes bidirectional).

Photosynthesis is the process by which green plants synthesize organic compounds using solar energy.

• Light reaction: Occurs in thylakoids; involves light absorption, water splitting, oxygen release, and formation of ATP and NADPH.
• Dark reaction (Calvin Cycle): Occurs in stroma; uses ATP and NADPH to reduce $CO_2$ to glucose.
• C4 path: Adaptation for dry climates to minimize photorespiration.

Respiration involves the breakdown of complex compounds to release energy.

• Glycolysis: Breakdown of glucose to pyruvic acid in the cytoplasm.
• Krebs Cycle: Occurs in mitochondria; releases $CO_2$ and produces NADH/FADH2.
• Electron Transport System (ETS): Uses oxygen as the final electron acceptor to produce ATP via oxidative phosphorylation.
• Respiratory Quotient ($RQ$): Ratio of volume of $CO_2$ evolved to volume of $O_2$ consumed ($RQ = 1$ for carbohydrates, $< 1$ for fats/proteins).