1 BOT 1 Lecture Notes by F5XS Science is a systematized knowledge derived from observation and experiment carried on in order to determine

the principles underlying what is being studied. Biology (bios, life + logos, discourse or study) is the branch of science that deals with the study of living organisms; scientific study of life. botany deals with plants zoology deals with animals Branches of Botany (Basic Plant Sciences) morphology external appearance, formation (phenotype) anatomy internal structures & arrangement physiology processes and functions ecology distributions, abundance of plants and their plants and environment [plant] geography spatial distribution of plants [plant] paleontology study of plant fossils paleontology study of plant fossils ethnobotany (economic botany) uses of plants Branches of Botany (Applied Plant Sciences) based on the purposes for which the plants are grown agronomy science and practice of growing field crops forestry managing and harvesting trees for building materials and other products horticulture growing, processing and marketing fruits, vegetables and ornamental plants; landscaping Principles of Plant Biology characteristics that unify all living things order hierarchical level of organization simple to complex structural organization components of biomolecules have genes (hereditary units) metabolism: nothing lives without energy energy is the capacity to do work metabolism generates energy for growth, survival and reproduction growth and development growth is the irreversible increase in size while development is the change in the complexity of the organism reproduction plants give rise to new plants of the same type by either sexual or asexual reproduction responsiveness: sensing and responding detects specific forms of stimuli (external and internal glands) adaptation a trait that gives the individual an advantage in survival or reproduction, under a given set of circumstances evolution

2 BOT 1 Lecture Notes by F5XS Advances in Plant Science plant biology has changed dramatically over the last few decades 1970 1980

Sharp boundaries between biochemistry, genetics, physiology and ecology boundaries between physiology and molecular biology began to disappear absolute need to use molecular techniques in physiology and physiological ecology became evident microarrays and gene sequencing have become common techniques what is true for plant biology before is no longer valid for plant biology today and in the next decades molecular tools will further increase in importance integrated approach to further plant biology is being realized

Theories on the Origin of Life Biblical Theory Spontaneous Generation Theory Comet (Panspermia) Theory Chemosynthetic Theory Chemosynthetic Theory has four stages: 1] abiotic synthesis of simple organic molecules (monomers) 2] polymerization of monomers 3] aggregation of abiotically produced molecules into droplets 4] origin of heredity Stage 1: Abiotic synthesis of monomers proposed by Al Oparin and JBS Haldane in 1920s; conditions of primeval Earth favored chemical reactions that synthesized compounds the earth had a reducing atmosphere life most likely emerged under high-temperature conditions exact conditions are unknown ample availability of hydrogen atoms very little oxygen high radioactivity and ultraviolet radiation lightnings and volcanic eruptions were very frequent the Miller-Urey Experiment was the supporting evidence for Oparin and Haldanes hypothesis first to show that amino acids and other organic molecules could have been generated on a lifeless Earth Stage 2: Polymerization of Monomers protenoids theory (microspheres: first proteins) proposed by Sidney Fox formed in clays many surfaces for protein formation many positive and negative charges for protein formation iron and zinc served as metal catalysts

3 BOT 1 Lecture Notes by F5XS Stage 3: Protobiont formation abiotically produced molecules aggregate into droplets formed from polypeptides, nucleic acids, carbohydrates membrane-bound incapable of reproduction but multiplies by budding or fission Stage 4: Origin of heredity RNA fragments were the first replicating system RNA act like enzymes to assemble new RNA molecules called ribozymes which might have constituted the primordial self-replicating system Thomas Cech, 1980 synthesized simple organic molecule that act as a template to produce copies of itself nucleic acid genes were preceded by simpler hereditary systems Amino Adenosine (AA) + Ester (E) Amino Adenosine Triacid Ester (AATE)

The Cell Theory all living things are composed of one or more cells cells are the basic units of structure and function in an organism cells come only from preexisting cells Cells are diverse both in size, shape and internal organization. Cells are small to promote: transport cell volume to surface area ratios favor small size control nucleus to cytoplasm consideration metabolic requirements All cells have: plasma membrane (plasmalemma) genetic material cytoplasm ribosomes Note: The genus Mycoplasma has the smallest bacteria that are from 0.1m to 1m

Fluid Mosaic Model conceived by SJ Singer and Garth Nicolson in 1972 fluid because of its hydrophobic integral components such as lipids and others mosaic because it is made up of many different parts or kinds of macromolecules plasma membrane is a lipid bilayer provides a barrier between internal and external environment of the cell allows certain molecules to go through which makes it semi-permeable made up of phospholipid bilayer with proteins embedded that allow for needed passage of macromolecules Ribosomes (protein factories) sites of protein synthesis are made of rRNA and protein cells with high rates of protein synthesis have many ribosomes

4 BOT 1 Lecture Notes by F5XS Cell Types prokaryotes eukaryotes Genetic Control of the Cell nucleus genetic control of the cell chromosomes location of inherited DNA and programs cells and programs cells synthesis of proteins nucleolus production of ribosomes Cell Wall structural support provides defense against invading pathogens provides pathways for communications between cells composed of cellulose, pectin, proteins and hemicellulose (glue that hold the cellulose fibers together) Growing plant cells produce a primary cell wall which stretches as the cell grows. A secondary cell wall may then be produced inside the primary cell wall. Protoderm Dermal Epidermis Periderm Parenchyma

Procambium

Ground Meristem

Vessels Tracheids Xylem Parenchyma Fibers Vascular Sieve tube members Companion cells Phloem Fibers Parenchyma Parenchyma Collenchyma Sclerids Sclerenchyma Fibers

Meristems regions of cell division main difference between plants and animals makes possible to grow a new plant from cutting Apical Meristems found at the tips of roots and shoots increase the length of a plant gives rise to three primary meristems ground meristem gives rise to ground tissues protoderm gives rise to skin coverings procambium gives rise to the plumbing of the plant Other Meristems: Lateral Meristems secondary growth add girth (width) by producing wood and bark

Apical Meristem

5 BOT 1 Lecture Notes by F5XS Other Meristems: Intercalary Meristem why grass keeps growing back after you cut it grasses and related plants do not have lateral meristems intercalary meristems add to the plants length

Chromista photosynthetic source of alginates Kelp (Alginates) viscous substance extracted from kelp used in paper production, toothpaste and in ice cream Archaeozoa no mitochondria Protista dumping ground Chromista implies pigmentation Eubacteria could be either photosynthetic or heterotrophic with peptidoglycan cell wall antibiotic sensitive Archaea live in extreme environmental conditions Protista eukaryotes that do not fit in the other three eukaryotic kingdoms generally unicellular; some algae are multicellular photosynthetic or heterotrophic Fungi eukaryotic heterotrophs absorptive type of nutrition Animalia eukaryotic multicellular ingestive mode of nutrition Plantae eukaryotic multicellular autotrophic/photosynthetic

Taxonomy is the science of classifying and identifying plants. Scientific Names are names understood by all scientists; common name differs in different parts of the world. Latin is the language usually used for scientific classification. A taxonomist is a person who identifies names and classifies organisms.

6 BOT 1 Lecture Notes by F5XS Aristotle classified organisms based on qualities such as shape, color, ability to do harm and the place where it is found. John Ray defined species as organisms capable of interbreeding and producing fertile species. Karl Von Linne (Carolus Linnaeus) developed binomial classification scheme wherein two latin words are put together to indicate the genus and the species. Writing Scientific Names the first word is the generic name (genus) and the second word is the specific epithet (species) if there are additional words, they indicate the variety or cultivar scientific names are followed by author (unitalicized) usually italicized or underlined The generic name of an organism is placed first and begins with a large letter and has more common with each other than they have with the members of other groups. A species can be defined as a group of organisms that are alike in almost every feature and consistently produce like organisms. The hierarchy of biological classifications eight major taxonomic ranks: Life Domain Kingdom Phylum Class Order Family Genus Species Tagalog Singkamas Talong Sigarilyas Mani Sitao Bataw Patani Kundol Patola Upo Kalabasa Labanos Mustasa Sibuyas Kamatis Bawang Luya Linga English Mexican Turnip Jicama Eggplant Winged Beans Peanuts String Beans Hyacinth Bean Lima Beans Winter Gourd Sponge Gourd Bottle Gourd Squash White Radish Mustard Onion Tomato Garlic Ginger Sesame Scientific Pachyrrhizus erosus Solanum melongena Psolocarpus tetragonolobus Arachis hypogaea Vigna sisquepedalis Dolichos lablab Phaseolus lunatus Benincasa hispada Luffa acutangula Lagenaria siceraria Cucurbita maxima Raphanus sativus Brassica integrifola Allium cepa Lycopersicon esculentum Allium sativum Zingiber officinale Sesamum orientale

7 BOT 1 Lecture Notes by F5XS Junctions are special proteins that connect cells. animals tight junctions adherens junctions gap junctions desmosomes for plants, plasmodesmata are microscopic openings in the cell wall The cell membrane has a unique architectural design Two basic types of embedded proteins: intrinsic/integral proteins are proteins bound within the plasma membrane extrinsic/peripheral proteins are proteins that do not penetrate the membrane Membrane proteins based on functions transport/transmembrane proteins channels are proteins that act as selective pores carriers bind molecule on one side of membrane and release it on the other side pumps is a term for carriers if transport is active enzymes speed up biochemical reactions by lowering activation energy receptor proteins transmit information and induce changes marker proteins give cell identity and are important in cell recognition process adhesion and attachment proteins adhesion of neighboring cells through intercellular connections or junctions attachment of cytoskeletons Diffusion higher to lower concentration uses kinetic energy of the molecules molecules move down a concentration gradient (downhill) will stop reached once equilibrium is

ACTIVE TRANSPORT

Transport processes regulated by plasma membrane passive no energy required simple diffusion mass/bulk flow osmosis active requires energy coupled channel (symport and antiport) proton (H+) pump phagocytosis

Note: Aquaporin is a transmembrane protein that facilitates the movement of water

8 BOT 1 Lecture Notes by F5XS Diffusion in three types of osmotic environment Premise: Water is the one that moves freely isotonic [SO]=[SI] water moves into and out of the cell at equal rates net movement of water is zero no change in cell volume hypotonic the solution has a lower concentration of solutes and a higher concentration of water than inside the cell [SO]<[SI] water moves into the cell cell swells; cell volume increases; the cell might undergo cytolysis, bursting of the cell hypertonic the solution has a higher concentration of solutes and a lower concentration of water than inside the cell [SO]>[SI] water moves out of the cell cell shrinks; cell volume decreases; the cell might undergo plasmolysis, shriveling of the cell Endocytosis is a process in which organisms or fragments of organisms are engulfed by cells. phagocytosis (Gk. phagein, to eat; cytos, cell) cell eating cells engulf large particles (organic matter) pinocytosis (Gk. pinein, to eat; cytos, cell) cell drinking Exocytosis wastes or secretions are expelled from the cell using small sacs/vesicles vesicles fuse with membrane and ejects contents