REVIEWER IN GENERAL BIOLOGY I. BIOLOGY: THE SCIENCE OF LIFE ARNEL S. JARDINEL, LPT, MAED General Biology BIOLOGY- science of life Bio, means life - study of living things logus, means to study - Deals with the investigation of the origin, history, structure, function, identification, distribution, development, inheritance, and significance of living things as well as their relationships and inheritance with the environment. DEVELOPMENT AS A SCIENCE Copernicus to Newton, the focused was physical science VAN LEEUWENHOEK (1674) on microscopy VESALIUS (1543) on human anatomy SCHWANN (1838), SCHLEIDEN (1839) and VIRCHOW (1858) on cell theory HARVEY (1628) on circulation of blood “All organism are made up of cells, and these cells come from pre-existing cells.” MALPHIGI (1661) on blood capillaries MENDEL (1868) on genetics HOOKE (1665) on cell KNOLL and RUSKA (1935) on electron microscope VAN LEEUWENHOEK (1674) on microscopy WATSON and CRICK (1953) on DNA CHARLES DARWIN, an English naturalist, published “The Origin of Species” in 1859, modern era of biology. Evolution “All living things have common ancestors and are adopted to a particular ways of life.” PASTEUR (1865), French chemist and microbiologist renowned for his discoveries of the principles of vaccination, microbial fermentation and pasteurization. Biogenesis (Pasteur 1865) “Life comes only from life.” Gene (Mendel 1866; Wilkins, Francklin, Watson & Crick 1953) “Organisms contain coded information that dictates their structures, function and behavior.” METHOD OF BIOLOGY Scientific method is logical process or learning facts through observation and experimentation from which, certain conclusions or theories are drawn. Steps in scientific method 1. Identification of the problem - starts with observation using all the senses, from observation a problem may be identified 2. Formulation of Hypothesis (Hypothesis is a preliminary conclusion or a scientific guess about the problem) -a set of assumptions or possible explanations to the problem may be formulated 3. Experimentation or testing of hypothesis - experiment is a special procedure used to test the hypotheses. - 2 sets of experiments- the control set- up and the experimental set-up - Experimental set-up is similar to the control in every aspect except the presence of variable -The variable is the factor or parameter to be tested 4. Analysis and Interpretation of data and results - data/ results must be gathered during and after experimentation - data include while making observations during an experiment - records of observation is using tables and graphs 5. Generalization or formulation of conclusion -a theory maybe formulated supported by experimental evidence - theory is conclusion derived from actual experiences or experiments formed to explain certain phenomena and the relationships between them. - this theory maybe developed into scientific law or into scientific principle. - scientific law is a statement of what occurs in nature as found by observation and series of experiments to be true; it is formed to explain the relationship between cause and effect. - scientific principle is a law of nature which other laws are based; its is established with certainty inference from adequate factual information. Limitations of the scientific method 1. Existence of God 2. Beauty appreciation 3. Moral issues 4. Value Judgement Branches of Biology According to method or aspect of study Cytology – cells Histology – tissues Organology – organs Anatomy – dissection of body parts Morphology – gross structure Physiology – functions Embryology – development of the embryo Genetics – Heredity Pathology - diseases Ecology – interactions and relationships within an ecosystem Evolution – origin of species Paleontology – fossil/ evidence of the past Systematics – classification and phylogeny Taxonomy – classification Nomenclature – naming/ assigning of scientific name Biogeography – distribution of living things Ontogeny – developmental history of an individual Phylogeny – fresh water habitats Oceanography – marine water habitats According to type of organisms Microbiology – microorganism Bacteriology – bacteria Parasitology – parasites Virology – viruses Protozoology – protozoans Phycology – algae Mycology – fungi Botany (Phytology) – plants Bryology – mosses Zoology – animals Helminthology - worms Carcinology – crustaceans Malacology – mollusks Entomology – insects Ichthyology – fishes Herpetology – reptiles and amphibians Ornithology – birds Mammalogy - mammals Nature of Life Theories on the origin of life Divine Creation Theory - based on the book of genesis - life believed to have created by the Almighty God. Cosmozoic or Interplanetary Theory - a protoplasm in the form of a resistant spore originated from outer planets propelled by radiation pressure - the spore reached the earth and started the first form of life Philosophical theory of Eternity - life has no beginning and no end; life has been here right from the very beginning of time Abiogenesis or Spontaneous Generation Theory - life originated spontaneously from non living things - disproved by Francesco Redi, an Italian scientist in 1668, and Louise Pasteur, a French chemist in 1865. Big Bang Theory - also called physic- chemical or cosmological theory - most scientific and most accepted theory - developed in 1940’s by G. Gamow and R. Alpher - heavenly bodies, including the earth, originated from the explosion of hot rotating gas and eventually life was formed from chemical evolution of different compounds present in the primitive earth. Life - organisms are open systems that maintain homeostasis, are composed of cells, have life cycle, undergo metabolism, can grow, adapt to their environment, respond to stimuli, reproduce and evolve. Characteristics of Living Things Metabolism - refers to all the chemical and energy transformations that occur in cells a s they carry out life’s processes - could be anabolism (building up processes) or catabolism (breaking down process) - a must in order to maintain their organization, and to grow and reproduce. Growth - refers to an increase in size - accomplished through complex series of processes - occurs when constructive activities occur at a faster rate than destructive activities Irritability - refers to the ability to react to any environmental change or stimulus that often results in movement - another form of response is when living things find energy and nutrients by interacting with their surroundings - the ability to respond helps ensure the survival of the organism Reproduction and Development - life comes only from life - in order for life to continue, living things must be able to produce other living things of their kind (reproduction) - reproduction could be asexual or sexual Adaptation - refers to modification that promote the likelihood of survival - living things not suited to a new condition either move to a better environment or change (evolution) - a change cannot occur in one generation but over many generations. - results in unity and diversity of life Organization - parts of living things are arranged in a particular way - there are levels of biological organization- biochemical, structural, physiological and ecological organization Assimilation - process of converting inorganic and organic molecules into living cell that can be done inside a living cell Definite form and size - living things produce offspring similar to themselves - all organism belonging to the same species are alike with certain degree of variations or differences Definite chemical composition - all organisms are basically made up of similar inorganic (water, minerals, gases) and organic molecules (carbohydrates, lipids, proteins, nucleic acid) ________________________________________________________________________________________________________________________ II. CHEMICAL BASIS OF LIFE ATOMS AND MOLECULES ATOMS- smallest particle of matter non-divisible by chemical means. Composed of protons ( + ) and neutrons (neutral) in the nucleus and electrons ( - ) outside the nucleus. -the smallest unit of an element to enter into chemical reactions. -all atoms of an element have a particular number of protons (atomic number). -electrically neutral because the number of protons equals to the number of electrons. -atomic weights depends on the number of protons and neutrons in the nucleus. -chemical properties depend on the number of electrons in the outer shell. MOLECULES -form when two or more atoms of the same element react with one another or combine another with atoms of another element. -the smallest part of a compound that still has the properties of that compound -could be inorganic or organic molecules COMMON ELEMENTS IN LIVING THINGS Oxygen (O) -65 % of human body weight Carbon (C) -18 % Hydrogen (H) -10 % Nitrogen (N) -3 % Sodium (Na) -0.15 % Magnesium (Mg) -0.05 % Phosphorus (P) -1.1 % Sulfur (S) -0.25 % Chlorine (Cl) -0.15 % Potassium (K) -0.35 % Calcium (Ca) -2 % Iron (Fe) -0.004 % Iodine (I) -0.0004 % CHEMICAL BONDING -interactions involving atoms of element combining with one another. -the attractive force that binds atom together to form molecules -determined by the electrons that surrounds the nucleus -an atom may bond with another atom by either gaining, losing or sharing of electrons. TYPES OF CHEMICAL BONDS COVALENT BOND – electrons are shared; characteristics of most chemical in living things; smallest particle formed are called molecules. IONIC BOND – an electron is transferred from one atom to another; ions (charge particles) are formed – cations, when electrons is lost; anions, when electron is gained. HYDROGEN BOND – when hydrogen combines with oxygen or with another electronegative atom; weak and can easily be formed or broken; very important in biological system; important in determining the structure of DNA and protein. INORGANIC MOLECULES -usually contain positive and negative ions -atoms are usually held together by ionic bond -usually composed of short chains -often associated with non –living things -includes water, acids and bases, salts, and gases WATER -the most abundant component of the protoplasm -inorganic compound composed of two atoms of hydrogen an atom of oxygen PHYSICAL PROPERTIES OF WATER -universal solvent -high specific heat and latent heat of vaporization -high degree of thermal conductivity -immiscible with lipids -neutral pH -liquid in form at room temperature -high surface tension PHYSIOLOGICAL PROPERTIES OF WATER -dissolves or holds in suspension the materials of the protoplasm -furnishes a medium for some vital processes and substances (nutrients, wastes, and hormones) moistens surfaces for gas diffusion -regulates body temperature -helps in the functions of the sense organs -serves as lubricant for movable surfaces -serve as cushion for the brain and spinal cord ACID AND BASES -ACIDS are molecules that raise the hydrogen ion (H+) when added to a solution, such as HCl. -BASES are molecules that lower the (H+) when added to a solution, such as NaOH. -pH scale is used to measure the acidity and alkalinity of a solution -as the pH number decreases, acidity increases -as the pH number increases, alkalinity increases. -most organism maintain a neutral pH (pH 7) -a much higher or lower pH may cause illness SALTS -formed from neutralization of acid and a base -occur in the form of soluble chlorides, sulfates, phosphates and carbonates of sodium, calcium, potassium, and magnesium -important in vital processes such as irritability of muscles and nerves, growth and repair of tissues, etc. -act as buffers or regulators of acid- base balance GASES -important in oxidation of food molecule in order to release energy -two important gases are OXYGEN and CARBON DIOXIDE ORGANIC MOLECULES -Always contain carbon and hydrogen -Atoms are usually held together by covalent bond -Usually composed of long chains -Usually associated with living things -Includes carbohydrates, lipids, proteins, and nucleic acids A. CARBOHYDRATES -Composed of carbon, hydrogen, and oxygen in a definite ratio 1:2:1, with a general formula of CH2O -The main source of energy in the body -Building blocks are glucose molecules TYPES OF CARBOHYDRATES 1. MONOSACCHARIDES -simple sugar - important source of energy - sub-units of which most polysaccharide are made a. Glucose- blood sugar or dextrose b. Fructose – fruit sugar c. Galactose – milk sugar 2. DISACCHARIDES -double sugar - two monosaccharide bonded together - principle sugar transported throughout the bodies of land plants a. Lactose – milk sugar: glucose + galactose b. Maltose – malt sugar: glucose + glucose c. Sucrose – table sugar: glucose + fructose 3. POLYSACCHARIDE - complex sugar - many monosaccharide (usually glucose) bonded together a. Cellulose – structural materials in plants b. Starch – energy storage in plants c. Glycogen – energy storage in animals B. LIPIDS -composed of carbon, hydrogen, and oxygen with no definite ratio, the number of oxygen atoms is very much less compared to hydrogen atoms -Storage of energy and important component of the cell membrane -Building blocks are fatty acids and glycerol TYPES OF LIPIDS 1. SIMPLE LIPIDS (TRIGLYCERIDES) - composed of three fatty acids bonded to glycerol - include oil and fats, stearin, palmitin, olein and waxes 2. COMPOUND LIPIDS - composed of lipids found in combination with other compound a. Lipoproten – protein b. Glycolipids – with carbohydrates c. Phopholipids – with phosphoric acid 3. STEROIDS - includes cholesterol, a common component of membranes of eukaryotic cells. C. PROTEINS -Composed of carbon, hydrogen, oxygen, and nitrogen plus other elements such as sulfur, iron, iodine, etc. -For growth and repair of tissues, component of the cell membrane, act as organic buffer, and play a major role in chemical reactions as enzymes, in protection of the body as antibodies -Building block are amino acids. Types of Protein 1. Fibrous protein - polypeptides are arranged parallel along a single axis produce long fibers of sheets. a. keratin- principal component of hair, skin and nails. b. Silk- pleated sheet protein produced by silk moths and spiders. 2. Globular protein - the polypeptide is so tightly folded into spherical or globular shapes, such as hemoglobin, the component of vertebrate blood used to transport oxygen. 3. Conjugated protein - simple proteins in union with other substances. a. Nucleoprotein- with nucleic acids, e.g. histones b. Glycoprotein- with carbohydrates, e.g. Mucin c. Lipoprotein- with fatty acids, e.g. serum and brain tissue d. Chromo protein- with pigments, e.g. cytochrome D. NUCLEIC ACIDS -Composed of carbon, hydrogen, oxygen, nitrogen and phosphorus -Important in protein synthesis as RNA, and are in heredity as DNA -Building blocks are nucleotides, which are made of pentose sugar (ribose or deoxyribose), a nitrogen base (pyrimidine or purine), and phosphoric acid -In DNA, purine are adenine and guanine; pyrimidines are cytosine and thymine in RNA, thymin is replaced by uracil. ________________________________________________________________________________________________________________________ III. NATURE OF CELL HISTORICAL BACKGROUND ROBERT HOOKE (1665), British Scientist- observed mass of tiny cavities from thin slices of cork with his selfmade microscope, he named these structures “CELLS” since these structures reminded him of the small rooms in a monastery. ANTON VON LEEUWENHOEK (1674), Dutch scientist- made pioneering discoveries concerning protozoa, red blood cells, capillary systems, and the life cycles of insects, he also perfected the construction of the compound microscope. ROBERT BROWN (1831), British botanist- observed plant cells with a distinct central part (nucleus); described the streaming movement of the cytoplasm (Brownian movement) DUJARDIN (1835), French biologist- observed that cells were not empty but filled with thick, jelly-like fluids (protoplasm) MATTHIAS SCHLEIDEN, (1838), German botanist-concluded that plants are composed of cells and formulated the plant cell theory THEODORE SCHWANN (1839), German zoologist- concluded that animals are composed of cells and formulated animal cell theory RUDOLF VIRCHOW (1858), German pathologist- concluded that all cells must come only from pre-existing cells MAXX KNOLL and ERNST RUSKA (1932), German engineers- built the first transmission electron microscope. JAMES WATSON, American biochemist and FRANCIS CRICK, British biophysicist (1953)- discovered the structure of DNA that ushered in the era of molecular biology CELL THEORY – (Schleiden, Schwann and Virchow established cell theory) -All organisms are made up of cells, and a cell is the structural and functional unit of organisms. -Cells are capable of self-reproduction, and cells come only from pre-existing cells. CELL, SIZE AND SHAPE -Smallest cell, a bacterium known as MYCOPLASMA- 0.0001mm in diameter -Largest cells are the NERVE CELLS in a giraffe’s neck- 3.0m in length -In human, variety of sizes, from small Red blood cells that measure 0.00076mm to liver cells that maybe ten times larger, about 10,000 average-sized human cells can fit on the head of the pin -common unit of measures in the study of cells is MICROMETER (um) = 1/ 1,000,000 meter -Smaller cell has more surface area per volume than does a large cell -The shape of the cell is related to its functions; long for contraction (MUSCLE CELL), with protoplasmic processes for conduction of impulses (NERVE CELL), concave disc for distribution of oxygen (RED BLOOD CELL) -Ideal shape of an isolated cell is SPHERICAL -Factors affecting variations in cell shapes: elasticity or rigidity of cytoplasm, surface tension, viscosity of cytoplasm, pressure exerted by neighboring cells and functional adaptation TYPES OF CELL PROKARYOTIC CELLS (Greek pro, before, and karyon, nucleus) -Cells without a true nucleus -Characteristics of bacteria with a size ranging from 1 to 10 um -Outer boundary is composed of cell wall and plasma membrane -Cytoplasm contains ribosomes, thylakoids and innumerable enzymes -Nucleoid contains single chromosome (DNA only) EUKARYOTIC CELL (Greek eu, true and karyon, nucleus) -Cell with true nucleus -Characteristics of protist (unicellular), fungi, plants and animals (multicellular) -Consist of PLASMA MEMBRANE, CYTOPLASM and a DISTINCT NUCLEUS -Outer membrane is composed of plasma membrane made up of phospholipids bilayer with embedded proteins -Nucleus is membrane-bounded containing multiple chromatin -Cytoplasm contains compartmentalized organelles IV. CELL STRUCTURE AND FUNCTION Cells -Smallest living unit -Most are microscopic -Discovery by Robert Hooke (mid-1600s) -Observed sliver of cork -Saw “row of empty boxes” -Coined the term cell Cell theory (1839) Theodor Schwann & Matthias Schleiden “all living things are made of cells” (50 yrs. later) Rudolf Virchow “all cells come from cells” Principles of Cell Theory -All living things are made of cells -Smallest living unit of structure and function of all organisms is the cell -All cells arise from preexisting cells (this principle discarded the idea of spontaneous generation) Characteristics of All Cells -A surrounding membrane -Protoplasm – cell contents in thick fluid -Organelles – structures for cell function -Control center with DNA TYPES OF CELL 1.Prokaryotic -First cell type on earth -Cell type of Bacteria and Archaea -No membrane bound nucleus -Nucleoid = region of DNA concentration -Organelles not bound by membranes 2.Eukaryotic -Nucleus bound by membrane -Include fungi, protists, plant, and animal cells -Possess many organelles 2.Eukaryotic -Nucleus bound by membrane -Include fungi, protists, plant, and animal cells -Possess many organelles Bacteria-Like Organelles Derived from symbiotic bacteria Ancient association Endosymbiotic theory -Evolution of modern cells from cells & symbiotic bacteria Plasma Membrane -Contains cell contents -Double layer of phospholipids & proteins Phospholipids Polar -Hydrophylic head -Hydrophobic tail Interacts with water Movement Across the Plasma Membrane A few molecules move freely -Water, Carbon dioxide, Ammonia, Oxygen Carrier proteins transport some molecules -Proteins embedded in lipid bilayer -Fluid mosaic model – describes fluid nature of a lipid bilayer with proteins Membrane Proteins 1. Channels or transporters -Move molecules in one direction 2. Receptors -Recognize certain chemicals 3. Glycoproteins -Identify cell type 4. Enzymes -Catalyze production of substance Cell Walls -Found in plants, fungi, & many protists -Surrounds plasma membrane Cell Wall Differences Plants – mostly cellulose Fungi – contain chitin Cytoplasm -Viscous fluid containing organelles Components of cytoplasm -Interconnected filaments & fibers -Fluid = cytosol -Organelles (not nucleus) -storage substances Cytoskeleton Filaments & fibers Made of 3 fiber types -Microfilaments -Microtubules -Intermediate filaments 3 functions: -mechanical support -anchor organelles -help move substances Cilia & Flagella Provide motility Cilia -Short -Used to move substances outside human cells Flagella Whip-like extensions Found on sperm cells Basal bodies like centrioles Cilia & Flagella Structure Bundles of microtubules with plasma membrane Centrioles Pairs of microtubular structures Play a role in cell division Membranous Organelles Functional components Bound by membranes Nucleus Control center of cell Double membrane Contains -Chromosomes -Nucleolus Nuclear Envelope -Separates nucleus from rest of cell -Double membrane -Has pores within cytoplasm DNA Hereditary material Chromosomes DNA Proteins Form for cell division Chromatin Nucleolus Most cells have 2 or more Directs synthesis of RNA Forms ribosomes Endoplasmic Reticulum Helps move substances within cells Network of interconnected membranes Two types -Rough endoplasmic reticulum Ribosomes attached to surface Manufacture protein Not all ribosomes attached to rough ER May modify proteins from ribosomes -Smooth endoplasmic reticulum No attached ribosomes Has enzymes that help build molecules Carbohydrates Lipids Golgi Apparatus Involved in synthesis of plant cell wall Packaging & shipping station of cell Golgi Apparatus Function 1. Molecules come in vesicles 2. Vesicles fuse with Golgi membrane 3. Molecules may be modified by Golgi 4. Molecules pinched-off in separate vesicle 5. Vesicle leaves Golgi apparatus 6. Vesicles may combine with plasma membrane to secrete contents Lysosomes Contain digestive enzymes Functions Aid in cell renewal Break down old cell parts Digests invaders Vacuoles Membrane bound storage sacs More common in plants than animals Contents Water Food wastes Bacteria-Like Organelles Release & store energy Types Mitochondria (release energy) Chloroplasts (store energy) Mitochondria Have their own DNA Bound by double membrane Break down fuel molecules (cellular respiration) -Glucose -Fatty acids Release energy -ATP Chloroplasts Derived from photosynthetic bacteria Solar energy capturing organelle Photosynthesis Takes place in the chloroplast Makes cellular food – glucose Molecule Movement & Cells Passive Transport Active Transport Endocytosis (phagocytosis & pinocytosis) Exocytosis 1.Passive Transport Types of Passive Transport 1. Diffusion No energy required Molecules move to equalize concentration Move due to gradient 2. Osmosis -differences in concentration, Special form of diffusion pressure, charge Fluid flows from lower solute concentration Move to equalize gradient Often involves movement of water -High moves toward low -Into cell -Out of cell Solution Differences & Cells 3. Facilitated diffusion solvent + solute = solution Differentially permeable membrane Hypotonic Channels (are specific) help molecule or ions enter or leave the cell -Solutes in cell more than outside Channels usually are transport proteins (aquaporins Outside solvent will flow into cell facilitate the movement of water) No energy is used Isotonic Process of Facilitated Transport -Solutes equal inside & out of cell -Protein binds with molecule Hypertonic -Shape of protein changes -Solutes greater outside cell -Molecule moves across membrane -Fluid will flow out of cell 2.Active Transport Molecular movement Requires energy (against gradient) Example is sodium-potassium pump Endocytosis Movement of large material Process of Endocytosis -Particles Plasma membrane surrounds material -Organisms Edges of membrane meet -Large molecules Membranes fuse to form vesicle Movement is into cells Forms of Endocytosis Types of endocytosis Phagocytosis – cell eating -bulk-phase (nonspecific) Pinocytosis – cell drinking -receptor-mediated (specific) Exocytosis Reverse of endocytosis Cell discharges material Vesicle moves to cell surface Membrane of vesicle fuses Materials expelled
