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COURSE STRUCTURE : BIOLOGY, CHEMISTRY AND PHYSICS
Biology is the natural science that involves the study of life and living organisms, including their physical structure, chemical composition, function, development and evolution. Modern biology is a vast field, composed of many branches. Despite the broad scope and the complexity of the science, there are certain unifying concepts that consolidate it into a single, coherent field. Biology recognizes the cell as the basic unit of life, genes as the basic unit of heredity, and evolution as the engine that propels the creation of new species. Living organisms are open systems that survive by transforming energy and decreasing their local entropy to maintain a stable and vital condition defined as homeostasis. See glossary of biology.
|Biology deals with the study of life and organisms.
Foundations of modern biology
Human cancer cells with nuclei (specifically the DNA) stained blue. The central and rightmost cell are in interphase, so the entire nuclei are labeled. The cell on the left is going through mitosis and its DNA has condensed.
Cell theory states that the cell is the fundamental unit of life, that all living things are composed of one or more cells, and that all cells arise from other cells through cell division. In multicellular organisms, every cell in the organism’s body derives ultimately from a single cell in a fertilized egg. The cell is also considered to be the basic unit in many pathological processes. In addition, the phenomenon of energy flow occurs in cells in processes that are part of the function known as metabolism. Finally, cells contain hereditary information (DNA), which is passed from cell to cell during cell division. Research into the origin of life, abiogenesis, amounts to an attempt to discover the origin of the first cells.
Natural selection of a population for dark coloration.
A central organizing concept in biology is that life changes and develops through evolution, and that all life-forms known have a common origin. The theory of evolution postulates that all organisms on the Earth, both living and extinct, have descended from a common ancestor or an ancestral gene pool. This universal common ancestor of all organisms is believed to have appeared about 3.5 billion years ago. Biologists regard the ubiquity of the genetic code as definitive evidence in favor of the theory of universal common descent for all bacteria, archaea, and eukaryotes (see: origin of life).
The term “evolution” was introduced into the scientific lexicon by Jean-Baptiste de Lamarck in 1809, and fifty years later Charles Darwin posited a scientific model of natural selection as evolution’s driving force. (Alfred Russel Wallace is recognized as the co-discoverer of this concept as he helped research and experiment with the concept of evolution.) Evolution is now used to explain the great variations of life found on Earth.
Darwin theorized that species flourish or die when subjected to the processes of natural selection or selective breeding. Genetic driftwas embraced as an additional mechanism of evolutionary development in the modern synthesis of the theory.
The evolutionary history of the species—which describes the characteristics of the various species from which it descended—together with its genealogical relationship to every other species is known as its phylogeny. Widely varied approaches to biology generate information about phylogeny. These include the comparisons of DNA sequences, a product of molecular biology (more particularly genomics), and comparisons of fossils or other records of ancient organisms, a product of paleontology. Biologists organize and analyze evolutionary relationships through various methods, including phylogenetics, phenetics, and cladistics. (For a summary of major events in the evolution of life as currently understood by biologists, see evolutionary timeline.)
Evolution is relevant to the understanding of the natural history of life forms and to the understanding of the organization of current life forms. But, those organizations can only be understood in the light of how they came to be by way of the process of evolution. Consequently, evolution is central to all fields of biology.
A Punnett square depicting a cross between two pea plants heterozygous for purple (B) and white (b) blossoms
Genes are the primary units of inheritance in all organisms. A gene is a unit of heredity and corresponds to a region of DNA that influences the form or function of an organism in specific ways. All organisms, from bacteria to animals, share the same basic machinery that copies and translates DNA into proteins. Cells transcribe a DNA gene into an RNA version of the gene, and a ribosome then translates the RNA into a sequence of amino acids known as a protein. The translation code from RNA codon to amino acid is the same for most organisms. For example, a sequence of DNA that codes for insulin in humans also codes for insulin when inserted into other organisms, such as plants.
DNA is found as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. A chromosome is an organized structure consisting of DNA and histones. The set of chromosomes in a cell and any other hereditary information found in the mitochondria, chloroplasts, or other locations is collectively known as a cell’s genome. In eukaryotes, genomic DNA is localized in the cell nucleus, or with small amounts in mitochondria and chloroplasts. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the nucleoid. The genetic information in a genome is held within genes, and the complete assemblage of this information in an organism is called its genotype.
The hypothalamus secretes CRH, which directs the pituitary gland to secrete ACTH. In turn, ACTH directs the adrenal cortex to secrete glucocorticoids, such as cortisol. The GCs then reduce the rate of secretion by the hypothalamus and the pituitary gland once a sufficient amount of GCs has been released.
Homeostasis is the ability of an open system to regulate its internal environment to maintain stable conditions by means of multiple dynamic equilibrium adjustments that are controlled by interrelated regulation mechanisms. All living organisms, whether unicellular or multicellular, exhibit homeostasis.
To maintain dynamic equilibrium and effectively carry out certain functions, a system must detect and respond to perturbations. After the detection of a perturbation, a biological system normally responds through negative feedback that stabilize conditions by reducing or increasing the activity of an organ or system. One example is the release of glucagon when sugar levels are too low.
Basic overview of energy and human life.
The survival of a living organism depends on the continuous input of energy. Chemical reactions that are responsible for its structure and function are tuned to extract energy from substances that act as its food and transform them to help form new cells and sustain them. In this process, molecules of chemical substances that constitute food play two roles; first, they contain energy that can be transformed and reused in that organism’s biological, chemical reactions; second, food can be transformed into new molecular structures (biomolecules) that are of use to that organism.
The organisms responsible for the introduction of energy into an ecosystem are known as producers or autotrophs. Nearly all such organisms originally draw their energy from the sun.]Plants and other phototrophs use solar energy via a process known as photosynthesis to convert raw materials into organic molecules, such as ATP, whose bonds can be broken to release energy. A few ecosystems, however, depend entirely on energy extracted by chemotrophs from methane, sulfides, or other non-luminal energy sources.
Some of the energy thus captured produces biomass and energy that is available for growth and development of other life forms. The majority of the rest of this biomass and energy are lost as waste molecules and heat. The most important processes for converting the energy trapped in chemical substances into energy useful to sustain life are metabolism and cellular respiration.
Study and research
Schematic of typical animal cell depicting the various organelles and structures.
Molecular biology is the study of biology at the molecular level. This field overlaps with other areas of biology, particularly those of genetics and biochemistry. Molecular biology is a study of the interactions of the various systems within a cell, including the interrelationships of DNA, RNA, and protein synthesis and how those interactions are regulated.
The next larger scale, cell biology, studies the structural and physiological properties of cells, including their internal behavior, interactions with other cells, and with their environment. This is done on both the microscopic and molecular levels, for unicellular organisms such as bacteria, as well as the specialized cells of multicellular organisms such as humans. Understanding the structure and function of cells is fundamental to all of the biological sciences. The similarities and differences between cell types are particularly relevant to molecular biology.
Anatomy is a treatment of the macroscopic forms of such structures organs and organ systems.
Genetics is the science of genes, heredity, and the variation of organisms. Genes encode the information needed by cells for the synthesis of proteins, which in turn play a central role in influencing the final phenotype of the organism. Genetics provides research tools used in the investigation of the function of a particular gene, or the analysis of genetic interactions. Within organisms, genetic information is physically represented as chromosomes, within which it is represented by a particular sequence of amino acids in particular DNA molecules.
Developmental biology studies the process by which organisms grow and develop. Developmental biology, originated from embryology, studies the genetic control of cell growth, cellular differentiation, and “cellular morphogenesis,” which is the process that progressively gives rise to tissues, organs, and anatomy. Model organisms for developmental biology include the round worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, the zebrafish Danio rerio, the mouse Mus musculus, and the weed Arabidopsis thaliana. (A model organism is a species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in that organism provide insight into the workings of other organisms.)
Physiology is the study of the mechanical, physical, and biochemical processes of living organisms function as a whole. The theme of “structure to function” is central to biology. Physiological studies have traditionally been divided into plant physiology and animal physiology, but some principles of physiology are universal, no matter what particular organismis being studied. For example, what is learned about the physiology of yeast cells can also apply to human cells. The field of animal physiology extends the tools and methods of human physiology to non-human species. Plant physiology borrows techniques from both research fields.
Physiology is the study the interaction of how, for example, the nervous, immune, endocrine, respiratory, and circulatory systems, function and interact. The study of these systems is shared with such medically oriented disciplines as neurology and immunology.
Evolutionary research is concerned with the origin and descent of species, and their change over time. It employs scientists from many taxonomically oriented disciplines, for example, those with special training in particular organisms such as mammalogy, ornithology, botany, or herpetology, but are of use in answering more general questions about evolution.
Evolutionary biology is partly based on paleontology, which uses the fossil record to answer questions about the mode and tempo of evolution, and partly on the developments in areas such as population genetics. In the 1980s, developmental biology re-entered evolutionary biology after its initial exclusion from the modern synthesis through the study of evolutionary developmental biology. Phylogenetics, systematics, and taxonomy are related fields often considered part of evolutionary biology.
A phylogenetic tree of all living things, based on rRNA gene data, showing the separation of the three domains bacteria, archaea, and eukaryotes as described initially by Carl Woese. Trees constructed with other genes are generally similar, although they may place some early-branching groups very differently, presumably owing to rapid rRNA evolution. The exact relationships of the three domains are still being debated.
The hierarchy of biological classification’s eight major taxonomic ranks. Intermediate minor rankings are not shown. This diagram uses a 3 Domains / 6 Kingdoms format
Multiple speciation events create a tree structured system of relationships between species. The role of systematics is to study these relationships and thus the differences and similarities between species and groups of species.However, systematics was an active field of research long before evolutionary thinking was common.
Traditionally, living things have been divided into five kingdoms: Monera; Protista; Fungi; Plantae; Animalia. However, many scientists now consider this five-kingdom system outdated. Modern alternative classification systems generally begin with the three-domain system: Archaea (originally Archaebacteria); Bacteria (originally Eubacteria) and Eukaryota (including protists, fungi, plants, and animals) These domains reflect whether the cells have nuclei or not, as well as differences in the chemical composition of key biomolecules such as ribosomes
Further, each kingdom is broken down recursively until each species is separately classified. The order is: Domain; Kingdom; Phylum; Class; Order; Family; Genus; Species.
Outside of these categories, there are obligate intracellular parasites that are “on the edge of life” in terms of metabolic activity, meaning that many scientists do not actually classify such structures as alive, due to their lack of at least one or more of the fundamental functions or characteristics that define life. They are classified as viruses, viroids, prions, or satellites.
The scientific name of an organism is generated from its genus and species. For example, humans are listed as Homo sapiens. Homo is the genus, and sapiens the species. When writing the scientific name of an organism, it is proper to capitalize the first letter in the genus and put all of the species in lowercase. Additionally, the entire term may be italicized or underlined.
The dominant classification system is called the Linnaean taxonomy. It includes ranks and binomial nomenclature. How organisms are named is governed by international agreements such as the International Code of Nomenclature for algae, fungi, and plants (ICN), the International Code of Zoological Nomenclature (ICZN), and the International Code of Nomenclature of Bacteria (ICNB). The classification of viruses, viroids, prions, and all other sub-viral agents that demonstrate biological characteristics is conducted by the International Committee on Taxonomy of Viruses (ICTV) and is known as the International Code of Viral Classification and Nomenclature (ICVCN). However, several other viral classification systems do exist.
A merging draft, BioCode, was published in 1997 in an attempt to standardize nomenclature in these three areas, but has yet to be formally adopted. The BioCode draft has received little attention since 1997; its originally planned implementation date of January 1, 2000, has passed unnoticed. A revised BioCode that, instead of replacing the existing codes, would provide a unified context for them, was proposed in 2011. However, the International Botanical Congress of 2011 declined to consider the BioCode proposal. The ICVCN remains outside the BioCode, which does not include viral classification.
Animalia – Bos primigenius taurus
These are the main branches of biology: For a more detailed list, see outline of biology.
- Aerobiology – the study of airborne organic particles
- Anatomy – the study of organisms structures
- Histology – the study of cells and tissues, a microscopic branch of anatomy
- Astrobiology (also known as exobiology, exopaleontology, and bioastronomy) – the study of evolution, distribution, and future of life in the universe
- Biochemistry – the study of the chemical reactions required for life to exist and function, usually a focus on the cellular level
- Bioengineering – the study of biology through the means of engineering with an emphasis on applied knowledge and especially related to biotechnology
- Biogeography – the study of the distribution of species spatially and temporally
- Bioinformatics – the use of information technology for the study, collection, and storage of genomic and other biological data
- Biolinguistics – the study of the biology and evolution of language.
- Biomechanics – the study of the mechanics of living beings
- Biomedical research – the study of health and disease
- Pharmacology – the study and practical application of preparation, use, and effects of drugs and synthetic medicines
- Biomusicology – the study of music from a biological point of view.
- Biophysics – the study of biological processes by applying the theories and methods traditionally used in the physical sciences
- Biotechnology – the study of the manipulation of living matter, including genetic modification and synthetic biology
- Synthetic biology – research integrating biology and engineering; construction of biological functions not found in nature
- Botany – the study of plants
- Phycology – scientific study of algae.
- Plant physiology – concerned with the functioning, or physiology, of plants.
- Cell biology – the study of the cell as a complete unit, and the molecular and chemical interactions that occur within a living cell
- Cognitive biology – the study of cognition
- Comparative anatomy – the study of evolution of species through similarities and differences in their anatomy.
- Conservation biology – the study of the preservation, protection, or restoration of the natural environment, natural ecosystems, vegetation, and wildlife
- Cryobiology – the study of the effects of lower than normally preferred temperatures on living beings
- Developmental biology – the study of the processes through which an organism forms, from zygote to full structure
- Embryology – the study of the development of embryo (from fecundation to birth)
- Gerontology – study of ageing processes.
- Ecology – the study of the interactions of living organisms with one another and with the non-living elements of their environment
- Environmental biology – the study of the natural world, as a whole or in a particular area, especially as affected by human activity
- Evolutionary biology – the study of the origin and descent of species over time
- Genetics – the study of genes and heredity.
- Epigenetics – the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence
- Hematology (also known as Haematology) – the study of blood and blood-forming organs.
- Integrative biology – the study of whole organisms
- Marine biology (or biological oceanography) – the study of ocean ecosystems, plants, animals, and other living beings
- Microbiology – the study of microscopic organisms (microorganisms) and their interactions with other living things
- Bacteriology – the study of bacteria
- Mycology – the study of fungi
- Parasitology – the study of parasites and parasitism
- Virology – the study of viruses and some other virus-like agents
- Molecular biology – the study of biology and biological functions at the molecular level, some cross over with biochemistry
- Nanobiology – the study of how nanotechnology can be used in biology, and the study of living organisms and parts on the nanoscale level of organization
- Neuroscience – the study of the nervous system
- Population biology – the study of groups of conspecific organisms, including
- Population ecology – the study of how population dynamics and extinction
- Population genetics – the study of changes in gene frequencies in populations of organisms
- Paleontology – the study of fossils and sometimes geographic evidence of prehistoric life
- Pathobiology or pathology – the study of diseases, and the causes, processes, nature, and development of disease
- Physiology – the study of the functioning of living organisms and the organs and parts of living organisms
- Phytopathology – the study of plant diseases (also called Plant Pathology)
- Psychobiology – the study of the biological bases of psychology
- Radiobiology – study of the action of ionic radiation on living things.
- Quantum biology – the study of quantum mechanics to biological objects and problems.
- Sociobiology – the study of the biological bases of sociology
- Systems biology – the study complex interactions within biological systems through a holistic approach
- Structural biology – a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules
- Theoretical biology – the branch of biology that employs abstractions and mathematical models to explain biological phenomena
- Zoology – the study of animals, including classification, physiology, development, and behaviour, including:
- Ethology – the study of animal behaviour
- Entomology – the study of insects
- Herpetology – the study of reptiles and amphibians
- Ichthyology – the study of fish
- Mammalogy – the study of mammals
- Ornithology – the study of birds