Comprehensive University Admissions Biology Compendium

THE CONCEPT OF SCIENCE AND THE SCIENTIFIC METHOD

The term science originates from the Latin word meaning to know. It is a form of knowledge that involves a rigorous study of an organized system through actions aimed at obtaining verifiable knowledge about facts to interpret and understand the world and the universe. Biological sciences represent a specific way to interpret the natural world. Science is sustained by research, defined as the search for information and explanations. Ideas and questions drive scientific activity, prompting researchers to obtain data to answer questions and support or refute ideas. This dynamic process is influenced by cultural, social, historical, and technological factors, causing scientific methods to evolve over time.

The scientific method is the foundation of all scientific research and consists of a series of ordered and linked steps. The general formulation includes observation of the environment to generate questions; the formulation of hypotheses, which are evidence-based explanations that can be empirically tested; experimentation or systematic observation to obtain data; the analysis of results, which often requires statistical support to sustain or refute the hypothesis; and the interpretation of results leading to conclusions regarding the validity of the proposed hypothesis.

BIOLOGY AND ITS SPECIALIZED BRANCHES

Biology is the integral study of living beings. Knowledge of life and its diversity is fundamental to cultural development, providing information on food sources, medicines, and organisms that cause harm or disease. It is essential for understanding human interaction with other living beings and the environment. Advances in biology, particularly in cell structure, function, and genetics, allow humanity to confront various diseases. Biological knowledge is also critical for addressing contemporary issues like population growth, epidemics, and projects like the human genome. Ecology, a subset of biology, helps identify causes of environmental damage and conservation measures.

Biology is divided into numerous specialized branches due to the breadth of its study. Botany focuses on plants, while zoology studies invertebrate and vertebrate animals. Taxonomy is based on the classification of living beings into hierarchical groups. Microbiology studies microorganisms including viruses, bacteria, protozoa, and certain fungi. Cell biology examines cell structure, function, and interactions. Genetics studies the nature, expression, and transmission of genes. Evolution explores the processes through which species originated. Anatomy describes the form and composition of organs and systems, while physiology studies their functioning from the cellular level to the systems level. Embriology focuses on the development of a new being from egg fertilization. Biochemistry studies molecular functions, and biophysics examines the interaction between matter and energy in organisms. Paleontology interprets past life through fossils, ecology studies interactions between organisms and their environment, and ethology studies animal behavior such as migration and mating rituals.

THEORIES ON THE ORIGIN OF LIFE

Several theories have been proposed to explain the origin of life. The creationist theory is based on the biblical narration in Genesis, holding that each species was created separately by divine forces and remains immutable; this posture lacks scientific foundations. The theory of spontaneous generation suggested that living beings could arise from inert matter, a concept supported by Aristotle. This was challenged by Francesco Redi in 1665, who demonstrated that flies came from eggs, not rotting meat, and was finally refuted in the 19th century by Louis Pasteur, who proved microorganisms in the air were responsible for organic decomposition.

The Panspermia theory suggests life did not originate on Earth but arrived from outer space as spores, bacteria, or resistant organic molecules transported by meteorites or cosmic dust. The most accepted scientific explanation is the chemosynthetic theory proposed by Alexander Oparin and John Haldane in 1929. It suggests life arose from a complex of molecules after prolonged chemical evolution on primitive Earth. The primitive atmosphere, rich in volcanic gases like water vapor, methane ($CH_4$), ammonia ($NH_3$), carbon dioxide ($CO_2$), hydrogen ($H_2$), and nitrogen ($N_2$), lacked oxygen. Energy from ultraviolet radiation, electric discharges, and volcanic heat triggered reactions producing simple organic molecules like sugars. These collected in primitive seas, or the primordial soup, forming coacervates that eventually evolved into the first cells.

CHARACTERISTICS AND LEVELS OF ORGANIZATION OF LIVING BEINGS

Living beings have an organized structure and perform activities for survival and adaptation. The unit of structural and functional life is the cell. Organisms may be unicellular, like an amoeba, or multicellular. In multicellular organisms, cells form tissues, tissues form organs, and organs form organ systems, which constitute the individual. Beyond the individual, organization includes populations (members of the same species interacting), communities (different species interacting), ecosystems (communities interacting with non-living environments such as soil and water), and the biosphere (the Earth's surface inhabited by life).

Key biological characteristics include homeostasis, which is the self-regulation required to maintain constant internal conditions despite external changes. Irritability, or response to stimuli, allows organisms to identify and react to changes like light or sound. Metabolism is the sum of all chemical reactions, divided into anabolism (building complex molecules from simple ones, consuming energy) and catabolism (breaking down complex molecules into simple ones, releasing energy stored in $ATP$ molecules). Growth refers to the increase in size through cell mass or number, while development involves qualitative and functional changes like differentiation. Adaptation is the adjustment to the environment and evolution is the change in a population's genetic composition over generations, driven primarily by natural selection. Reproduction ensures the transmission of genetic information. Asexual reproduction involves a single parent producing genetically identical offspring through methods like binary fission (e.g., paramecia), budding (e.g., yeast), fragmentation (e.g., starfish), sporulation (e.g., fungi), parthenogenesis (from unfertilized eggs), or vegetative multiplication (e.g., strawberry stolons). Sexual reproduction involves two parents and the fusion of haploid ($n$) gametes (egg and sperm) to form a diploid ($2n$) zygote, involving stages of gametogenesis, fertilization (internal or external), and embryonic development.

CLASSIFICATION AND TAXONOMY OF SPECIES

Biological classification is managed by systematic and taxonomic branches. Systematics studies evolutionary relationships (phylogeny), often represented in phylogenetic trees. Taxonomy establishes rules for naming and classifying species. The binomial system, proposed by Linnaeus in the 18th century, assigns each organism a two-word scientific name in Latin: the first is the Genus (capitalized) and the second is the specific epithet (lowercase), written in italics or underlined. For example, humans are $Homo\,sapiens$. The hierarchical categories from smallest to largest are species, genus, family, order, class, phylum (for animals) or division (for plants), and kingdom.

Modern classification organizes life into three domains: Archaea, Eubacteria (both prokaryotic), and Eukarya. The number of kingdoms has evolved from Whittaker's five (1969) to the current seven. Kingdom Eubacteria includes true bacteria that can be heterotrophic or autotrophic (photosynthetic or chemosynthetic). Kingdom Archaea consists of unicellular prokaryotes in extreme habitats, such as methanogens (no oxygen), halophiles (high salt), thermophiles (near boiling), and acidophiles. Kingdom Protozoa contains primitive eukaryotes like amoebas and paramecia. Kingdom Chromista includes diverse organisms like diatoms and brown algae. Kingdom Fungi includes yeasts and mushrooms. Kingdom Plantae consists of photosynthetic autotrophs with cellulose cell walls. Kingdom Animalia includes heterotrophic, multicellular, and tissue-based organisms (except poriferans), divided into invertebrates and vertebrates.

EVIDENCE AND THEORIES OF EVOLUTION

Evolution is the modification of a population's genetic composition over generations. Scientific evidence includes the fossil record (remains in sedimentary rock), biogeography (past and present geographic distribution), comparative anatomy (similarities in structure), comparative embryology (comparing embryos), and molecular biology (analyzing changes in $DNA$, $RNA$, and proteins). All life is related through a virtually identical universal genetic code.

Lamarck's hypothesis (1809) was based on the principles of use and disuse and the inheritance of acquired characteristics. Charles Darwin (1859) proposed natural selection based on overproduction (more offspring than can survive), variations (heredable traits differ among individuals), and the struggle for survival (favorable variations lead to better success). Over generations, the frequency of genes for advantageous traits increases. The modern synthesis, or Neodarwinism, integrates Darwinian natural selection with Mendelian genetics, identifying the gene as the fundamental unit and recognizing that genetic variation arises randomly through mutations and recombination during meiosis.

RELATIONSHIP FUNCTIONS AND SENSORY PERCEPTION

The relationship function allows organisms to receive information, process it, and execute survival responses through excitability or irritability. A stimulus is an element capable of provoking a reaction. Receptors capture stimuli and translate them into electrical signals. Receptors are classified by origin as exteroceptors (external), interoceptors (internal), or proprioceptors (position/orientation). Based on the stimulus type, they are thermoreceptors (temperature), mechanoreceptors (pressure/vibration), photoreceptors (light), chemoreceptors (chemical), or nociceptors (pain). Responses can be motor (movement) or secretory (glandular release).

In plants, responses include tropisms (growth movements relative to stimulus direction, such as phototropism, geotropism, hydrotropism, thigmotropism, and chemotropism) and nasties (automatic movements independent of stimulus direction, like thermonasty, photonasty, and seismonasty). In animals, stimuli are processed in centers like the brain or ganglia, and effects are delivered to muscles or glands. At the cellular level, the plasma membrane is the primary receptor. Cellular responses include movement (amoeboid displacement), secretion (hormones/enzymes), contraction (using actin and myosin), proliferation (division), differentiation (specialization), and apoptosis (programmed death).

BIOCHEMISTRY AND ESSENTIAL MOLECULES

Approximately 25 of the 92 natural elements are essential for life. The primary four—carbon ($C$), hydrogen ($H$), oxygen ($O$), and nitrogen ($N$)—constitute 96% of living matter. Phosphorus ($P$), sulfur ($S$), calcium ($Ca$), and potassium ($K$) make up the remaining 4%. Oligoelements are required in trace amounts. Inorganic biomolecules include minerals, gases (oxygen $O_2$ and carbon dioxide $CO_2$), and water ($H_2O$). Water makes up 70% of human weight and is polar due to the electronegativity of oxygen relative to hydrogen, leading to hydrogen bonding. Properties of water include cohesion (holding molecules together), adhesion (sticking to surfaces), capillarity, high solvent power, and a high specific heat, which helps regulate temperature.

Organic biomolecules include carbohydrates, lipids, proteins, and nucleic acids. Carbohydrates ($CH_2O$ ratio) provide start-up energy and structural material. They are categorized as monosaccharides (3-7 carbons, e.g., glucose $C_6H_{12}O_6$, ribose, fructose), disaccharides (two units, e.g., maltose, sucrose, lactose), and polysaccharides (e.g., starch for plant energy, glycogen for animal energy, cellulose for plant structure, and chitin for fungal walls and arthropod exoskeletons). Lipids are insoluble in water and include triacylglycerols (fats for energy storage), phospholipids (amphipathic molecules for membranes), carotenoids (pigments for photosynthesis/vitamin A), and steroids (four-ring structures including cholesterol and hormones like cortisol).

Proteins are amino acid polymers joined by peptide bonds through condensation reactions. There are 20 common amino acids, including essential ones for humans: isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and histidine (plus arginine for children). Structural levels include primary (linear sequence), secondary (helices/pleated sheets), tertiary (global shape), and quaternary (multiple chains). Functions include enzymatic catalysis, structure (collagen), reserve (ovalbumin), transport (hemoglobin), regulation (insulin), movement (actin/myosin), and defense (antibodies). Nucleic acids, $ADN$ and $RNA$, are nucleotide chains. Each nucleotide has a pentose sugar (deoxyribose or ribose), a phosphate group, and a nitrogenous base (adenine, guanine, cytosine, thymine, or uracil). $ADN$ stores genetic information and is double-helical, while $RNA$ (messenger, transfer, and ribosomal) participates in protein synthesis.

CYTOPHYSICS AND SOLUTIONS

Biological mixtures include solutions (homogeneous, transparent, small particles), colloids (larger particles that disperse light/Tyndall effect, e.g., cytosol), and suspensions (very large particles that sediment, e.g., blood cells after rest). Diffusion is the movement of solute from high to low concentration. Osmosis is the movement of water across a semipermeable membrane toward higher solute concentrations. Cells in hypotonic solutions (lower external solute) gain water and undergo turgor or cytolysis (bursting); in isotonic solutions, volume is constant; in hypertonic solutions, they lose water and undergo plasmolysis.

The $pH$ scale (0-14) measures acidity (excess $H^+$) or alkalinity (excess $OH^-$). Normal blood $pH$ is 7.35 to 7.45. Deviations lead to acidosis (below 7.35) or alkalosis (above 7.45). Homeostasis is maintained by buffers like the carbonic acid-bicarbonate system. If $H^+$ is in excess, $H^+ + HCO_3^- \rightarrow H_2CO_3$. If $H^+$ is scarce, $H_2CO_3 \rightarrow H^+ + HCO_3^-$.

THE CELLULAR SYSTEM AND ORGANELLES

The Cell Theory states that all organisms are made of cells, the cell is the basic unit of life, and all cells come from pre-existing ones. Prokaryotic cells (Archaea and Bacteria) lack a defined nucleus; genetic material is in a nucleoid. Eukaryotic cells have a true nucleus and complex organelle systems. In eukaryotes, the plasma membrane is a fluid bilipidic layer with proteins and cholesterol. Movement across it includes passive transport (diffusion and facilitated diffusion using permeases) and active transport (requiring $ATP$, e.g., the $Na^+/K^+$ pump). Large molecules move via endocytosis (pinocytosis for liquids, phagocytosis for solids) and exocytosis.

Plant cells have a rigid cellulose cell wall. The cytoplasm contains cytosol and a cytoskeleton (microfilaments, intermediate filaments, and microtubules). Organelles include the endoplasmic reticulum (rough for protein synthesis, smooth for lipid synthesis/detoxification); Golgi apparatus (dictyosomes for packaging/secretion); lysosomes (digestive enzymes/autophagy); peroxisomes (peroxide metabolism); and vacuoles (large central vacuole in plants for homeostasis). Mitochondria produce energy through aerobic respiration, possess their own maternal $DNA$, and multiply by binary fission. Plastids in plants include chloroplasts (chlorophyll for photosynthesis), chromoplasts (pigments), and leucoplasts (storage, e.g., amyloplasts for starch). The nucleus contains the genome within a double membrane (karyotheca) with pores. It includes the nucleoplasm, nucleolus ($RNA$/ribosome synthesis), and chromatin ($DNA$ and histones). Chromatin condenses into chromosomes during division, featuring sister chromatids, centromeres, and telomeres. Human somatic cells are diploid with 23 pairs of chromosomes, while gametes are haploid.

METABOLISM AND CELLULAR PROCESSES

$ATP$ is the cell's energy currency, composed of adenine, ribose, and three phosphate groups. Aerobic respiration requires oxygen and produces $36-38\,ATP$ through glycolysis (in cytosol), acetyl-CoA formation, the Krebs cycle, and the electron transport chain (in mitochondria). The general equation is: $C_6H_{12}O_6 + 6\,O_2 + 6\,H_2O \rightarrow 6\,CO_2 + 12\,H_2O + \text{energy}$. Anaerobic respiration (fermentation) occurs without oxygen, producing only $2\,ATP$ as either alcoholic fermentation (producing ethanol and $CO_2$) or lactic fermentation (producing lactate).

Photosynthesis uses light energy and chlorophyll to synthesize carbohydrates: $6\,CO_2 + 12\,H_2O + \text{light} \rightarrow C_6H_{12}O_6 + 6\,O_2 + 6\,H_2O$. It has a light phase (in thylakoids, producing energy and $O_2$) and a dark phase (Calvin cycle in stroma, fixing carbon). The cell cycle consists of interphase ($G_1$ growth, $S$ synthesis/replication, $G_2$ final prep) and cell division. Mitosis (prophase, prometaphase, metaphase, anaphase, telofase) produces two identical diploid daughters. Cytokinesis is the physical division of cytoplasm. Meiosis involves two divisions ($I$ and $II$) to produce four haploid gametes, involving crossing-over during Prophase $I$ to increase genetic variation.

GENETICS AND HEREDITY PATTERNS

Genetics is the study of heredity and trait variation. Genes are specific $DNA$ sequences at chromosomal locations called loci. Alleles are different versions of a gene. Genotype is the genetic makeup, while phenotype is the expressed physical trait. Mendel's laws include the Principle of Uniformity ($F_1$ offspring of pure parents are identical), the Law of Segregation (alleles separate during gamete formation), and the Law of Independent Distribution (different traits are inherited independently). Variations include incomplete dominance (blended phenotype) and codominance (both traits expressed, e.g., $AB$ blood type). Human sex is determined by $XX$ (female) or $XY$ (male) chromosomes. Sex-linked traits, like color blindness or hemophilia, are carried on the $X$ chromosome. Mutations are changes in the genotype, classified as point mutations (substitution, insertion, deletion, duplication) or chromosomal mutations (inversion, translocation). Genetic syndromes include Turner (monosomy $X$), Down (trisomy 21), and Klinefelter (trisomy $XXY$).

ECOLOGY AND ECOSYSTEM DYNAMICS

Ecology (from "oikos" meaning house) studies relationships between organisms and their environment. Levels of organization are organism, population, community, ecosystem, and biosphere. Descriptive branches include autoecology (individuals) and synecology (communities/ecosystems). A habitat is the physical space, whereas an ecological niche is the functional role an organism plays. Species interactions include competition, predation, and symbiosis (mutualism, commensalism, and parasitism). Ecosystems comprise biotope (abiotic factors like relief, sunlight, and $pH$) and biocenosis (biotic community). Energy flows through food chains and webs, represented in ecological pyramids. Biogeochemical cycles circulate elements like carbon, phosphorus, and nitrogen. Major biomes include prairies, savannas, deserts, taiga, tundra, tropical forests, and aquatic biomes (oceans and freshwater).

HUMAN SENSORY ORGANS

The sense of sight involves detecting light (400-700 nm). Accessory structures include eyebrows, eyelids (with Meibomian glands), eyelashes, conjunctiva, and the lacrimal apparatus (producing tears with lysozyme). Six extrinsic muscles move the eye. The eyeball wall has three layers: fibrous (cornea and sclera), vascular (choroid, ciliary body, and iris), and retina (pigmented and neural layers). The neural layer contains rods (night vision/rhodopsin) and cones (color). Images form via refraction, accommodation (lens curving), and pupil constriction. The visual path involves the optic nerve, optic chiasm, and the occipital lobe.

 Hearing and equilibrium involve the external, middle, and internal ear. The middle ear contains the ossicles: malleus, incus, and stapes. The internal ear, or labyrinth, contains the cochlea (hearing receptors in the Organ of Corti) and the vestibular apparatus (saccule, utricle, and semicircular canals for balance). Equilibrium is classified as static (head orientation) or dynamic (motion/acceleration). The sense of touch resides in the skin (epidermis and dermis), featuring receptors such as Meissner corpuscles (touch), Pacini corpuscles (pressure), and nociceptors (pain). The skin also regulates temperature and synthesizes Vitamin D. Taste (gustation) identifies five primary tastes: sour, sweet, bitter, salty, and umami, detected by approximately 10,000 taste buds. Smell (olfaction) uses the olfactory epithelium in the nasal cavity, containing millions of bipolar neurons capable of distinguishing 10,000 odors.

HUMAN LOCOMOTOR SYSTEM

The skeletal system performs support, protection, movement assistance, mineral homeostasis, hemopoiesis (blood cell production in red bone marrow), and triglyceride storage (yellow bone marrow). It is divided into the axial (80 bones) and appendicular (126 bones) skeletons. Bone tissue contains types like cortical (compact/Haversian systems) and trabecular (spongy). Bone cells include osteogenic cells, osteoblasts (building), osteocytes (maintenance), and osteoclasts (resorption). Articulations (joints) are classified structurally as fibrous (sutures, gomphosis, syndesmosis), cartilaginous (synchondrosis, symphysis), or synovial (artrodia, ginglymus, trocoid, condylar, saddle, enartrosis). Functionally, they are synarthroses (immobile), amphiarthroses (slightly mobile), or diarthroses (highly mobile).

Muscle tissue includes skeletal (striated, voluntary), cardiac (striated, involuntary), and smooth (non-striated, involuntary). Skeletal muscle fibers contain sarcolemma, sarcoplasm, and miofibrils with actin and myosin. Properties include electrical excitability, contractility, extensibility, and elasticity. Major skeletal muscles include the occipitofrontal, orbicularis, masseter, sternocleidomastoid, diaphragm, rectus abdominis, deltoid, biceps braquial, and gastrocnemius.

NERVOUS AND ENDOCRINE CONTROL

The nervous system coordinates functions via sensory, integrative, and motor pathways. The tissue consists of neurons (multipolar, bipolar, unipolar) and glia (astrocytes, oligodendrocytes, microglia, ependymal, Schwann cells, satellite cells). Communication occurs at synapses (mostly chemical via neurotransmitters). The system is divided into Central (brain and spinal cord) and Peripheral (nerves and ganglia). The brain includes the brainstem, cerebellum, diencephalon (thalamus, hypothalamus), and cerebrum (cortex with functional areas). Protective meninges are pia mater, arachnoid, and dura mater. The Autonomic Nervous System has Sympathetic (fight-or-flight/noradrenaline) and Parasympathetic (rest-and-digest/acetylcholine) divisions.

The endocrine system uses hormones circulating in the blood to regulate metabolism and development. Key glands include the hypothalamus (control center), hypophysis (master gland with anterior adenohypophysis and posterior neurohypophysis), thyroid ($T_3$, $T_4$, and calcitonin), parathyroids ($PTH$), adrenals (cortisol, aldosterone, adrenaline), pancreas (insulin and glucagon), and gonads (estrogens, progesterone, testosterone). The pineal gland secretes melatonin to regulate the biological clock.

NUTRITION, RESPIRATION, AND EXCRETION

The digestive system processes food through the track (mucosa, submucosa, muscular, serosa) and accessory organs. Digestion involves mastication, insalivation (using ptyalin), deglutition, chymification (in stomach with pepsin/renin), and absorption (mostly in the small intestine). The cardiovascular system pumps blood through the heart (four chambers: right/left atria and ventricles) and vessels (arteries, veins, capillaries). Blood components include plasma (91.5% water) and formed elements: erythrocytes ($5.4$ million/$\mu l$), leukocytes ($5,000-10,000$), and platelets ($150,000-400,000$). Each cardiac cycle takes about $0.8$ seconds.

The respiratory system performs gas exchange. Structures include the nose, pharynx, larynx (vocal cords), trachea, bronchi, and lungs (alveoli). Ventilation involves inspiration and expiration based on pressure changes. The urinary system filters blood in the kidneys using nephrons ($1.2$ million per kidney). Processing includes glomerular filtration, tubular reabsorption (99% of water), and tubular secretion. An adult produces $1-2$ liters of urine daily, mostly containing water, urea, and electrolytes.

REPRODUCTION AND EMBRYOLOGY

The male reproductive system includes testes (producing sperm and testosterone), ducts (epididymis, vas deferens, ejaculatory duct, urethra), and accessory glands (seminal vesicles, prostate, Cowper's glands). Semen volume is $2.5-5\,ml$ with $50-150$ million sperm. The female system includes ovaries, fallopian tubes, uterus (endometrium, myometrium, perimetrium), and vagina. The reproductive cycle ($28$ days) involves the menstrual, preovulatory, ovulation, and postovulatory phases, regulated by $GnRH, FSH, LH$, estrogen, and progesterone.

Development begins with fertilization of the ovocyte by sperm in the fallopian tube to form a zygote ($2n$). Cleavage produces blastomeres, forming a morula and then a blastocyst which implants in the uterus after 7 days. The second week forms a bilaminar disc, and the third week involves gastrulation into three germ layers: ectoderm (nervous system/skin), mesoderm (muscles/bones), and endoderm (internal linings). The embryonic period lasts until the eighth week, followed by the fetal period until birth. Labor stages include dilation ($6-12$ hours), expulsion ($10$ minutes to hours), and the placental stage ($5-30$ minutes).