General Botany PDF

**Organization** -- Living things come in different forms and sizes. They have different structures and functions. - **Unicellular** - consists of a single cell *(i.e., Bacteria, Archaea, Protozoa).* - **Multicellular** -- composed of multiple cells *(i.e., Animals, Plants, Fungi, etc*...

**Organization** -- Living things come in different forms and sizes. They have different structures and functions. - **Unicellular** - consists of a single cell *(i.e., Bacteria, Archaea, Protozoa).* - **Multicellular** -- composed of multiple cells *(i.e., Animals, Plants, Fungi, etc*.). - **Prokaryotic Cell** - without a defined nucleus *(i.e., Bacteria and Archaea)*. - **Eukaryotic Cells** -- have a defined nucleus and membrane-bound organelles *(i.e., Animals, Plants, Fungi, Algae, and Protozoa)*. **Table 1.1 Levels of Biological Organization** **LEVEL** **DESCRIPTION** ---------------------- --------------------------------------------------- Subatomic Particles that make up an atom Atoms Chemical Element Molecules Chemical compound Organelles Membrane-bound structure within a cell Cells The smallest unit of life Tissues Several types of cells that work together Organs Part of organisms with a specific function Organ System Organs that work together Organism One individual of a species Population All individuals of one species in an area Biological Community All populations of all species in a given area Biome All communities within a regional vegetation type Biosphere All living creatures on the planet **Metabolism --** Ability to acquire materials for energy to power life. - The sum of chemical reactions through which living things break down or build up materials. - Living things can convert food into chemical energy that cells use through metabolism. - **Autotrophs ­**-- self-feeders or producers - **Heterotrophs** -- consumers **Plant Metabolism --** complex physical and chemical events of photosynthesis, respiration, and the synthesis and degradation of organic compounds. **Photosynthesis** produces the substrates for respiration and the starting organic compounds used as building blocks for the subsequent biosynthesis of nucleic acids, proteins, carbohydrates lipids, organic acids, and other natural products. The primary metabolism in plants consists of any chemical reactions essential for the plant to live. Moreover, plants undergo secondary metabolism, which products aid in their growth but are not required for the plant to survive but are useful in the long term and give plants characteristics such as color. Secondary metabolism facilitates the primary metabolism in plants thus, secondary metabolism plays a pinnacle role in keeping all the of plants\' systems working properly. **Primary metabolism** -- comprises all metabolic pathways that are essential to the plant's survival. Primary Metabolites -- compounds that are directly involved in the growth and development of plant. Secondary Metabolites -- compounds produced in another metabolic pathway that is important but not essential to the functioning of the plant. They are used to fight off herbivores, pests, and pathogens, anti-feeding activity, toxicity signaling, and regulation of primary metabolic pathways. **Growth and Development** - **Development** -- the progression from earlier to later stages in maturation. It is where tissues, organs, and whole plants are produced. - **Differentiation** -- the process in which generalized cells specialize into morphologically and physiologically different cells. - **Growth** -- the irreversible change in the size of cells and plant organs due to cell enlargement. Determinate -- growth occurs when an organ or part reaches a certain size then stops growing. Indeterminate -- growth happens when cells continue to divide indefinitely. **Maintaining Homeostasis** -- living things are able to maintain a stable internal environment. **Homeostasis** -- The process of maintaining a stable internal environment. **Feedback** -- loops that regulate their physiological and behavioral responses. The 3 components are: 1. Receptor -- monitor and respond to changes in an organism's environment. 2. Control center -- receives the information from the receptor. It determines if the variable sent needs to be monitored thereby, adjustments are made. 3. Effectors -- receive information from the control center and correct or make adjustments to maintain homeostasis using either positive or negative feedback loops. Positive -- increases the effect of change and produces instability. Negative -- reduces the effect of change and helps maintain balance. **Homeostatic regulation in plants seeks to:** 1. Maintain an adequate uptake of water and nutrients from soil into leaves. 2. Control stomatal opening so the water loss is minimized and carbon dioxide is maximized. **Reproduction** -- the process by which living things give rise to offspring and transmit hereditary information *(coded in DNA)*. - Sexual-- hereditary information recombines from two parents of the same species. - Asexual -- offspring came from one parent and is genetically identical. **Gametophytes** -- the sexual phase in the life cycle of plants and algae. They represent the *Haploid (n)* phase meaning they contain a single set of chromosomes. - Produce both eggs and sperm, in others, individual gametophytes produce only one. In seed plants, *pollen- and ovule-*producing structures may be borne together within a single flower, borne separately in different structures on the same plant, or borne on entirely different plants. In both groups of plants, the pattern in which reproductive structures are borne influences the frequency wherein the gametes from unrelated individuals unite in zygotes, and it is a predominant influence on the amount and distribution of genetic diversity found in a species. **Ability to Change over Time** **Evolution** -- a change in the characteristics of populations of living things over time. - Occurs by a process called Natural Selection. **Natural Selection** -- a process where organisms with traits that better suit their environment tend to survive and reproduce more successfully than those without those traits. - Genetic Variation -- individuals have different genetic traits due to mutations, genetic recombination - Genetic Diversity -- the variety of genetic variations within a species or population. - Adaptation - characteristic that helps a population to survive and reproduce in a given environment. - Fitness -- the ability to adapt and survive. - Survival of the Fittest -- organisms that are better adapted to their environment are best suited to survive and reproduce. - Came from ***"scientia"*** which means **knowledge** - Refers to knowledge about natural phenomena known as ***"natural science".*** - any discipline in science aims to search for ***"truth".*** It develops a "theory" from repeatedly tested and confirmed hypothesis. **Principle** or **law** is an explanation that verifies several theories and has a wide range of applications. - Good science must be conducted openly to allow verification by other scientists. This ensures that results are reliable and can lead to paradigm shifts. - Paradigm Shift -- where long-established theories are changed. - Any scientific research intends to come up with logical inferences. **Scientific Reasoning** - Inductive Reasoning -- individual observation to a general conclusion. - Deductive reasoning -- general and predict the specific conclusions. **Scientific** **Method** -- intellectual tool for most scientists to arrive at *"truth"*. It is a systematic approach to investigating phenomena. 1. **Observation** -- observe something in the nature that you want to explain. 2. **Formulating a problem** -- propose a problem from observations. 3. **Proposing a hypothesis** -- an unproven conclusion that is testable. 4. **Experimentations or testing** -- to be able to prove a hypothesis, performing an experiment wherein the variables or factors that can affect the experiment are controlled and tested. 5. **Analysis of results** -- data are gathered and analyzed with appropriate tools. 6. **Stating the conclusion** -- the inferences should be empirical. 7. Writing the results and reporting them. **EXPERIMENTS** 1. It must have a control variable that doesn't include the tested variables. 2. The treatments allow the control of the factors. 3. The dependent variable is the affected component by the independent variable *(i.e IV- Temperature, DV- Plant Growth).* 4. Independent Variables or *"experimental variables"* can be manipulated. 1. **Economic** **Botany** -- the study of plants of economic use or value 2. **Phytochemistry** -- plant secondary chemistry and chemical processes. 3. **Phytopathology** -- plant diseases 4. **Plant** **Anatomy** -- cell and tissue structure 5. **Plant** **Biotechnology** -- present technology used in different subdisciplines of plant science. 6. **Plant** **ecology** -- the role of plants in the environment 7. **Plant** **Morphology** -- structure and life cycle 8. **Plant** **Physiology** -- Life functions of the plant 9. **Plant** **systematics** -- classification and naming of plants. **Characteristics of Plants** **Plants are multicellular organisms made up of eukaryotic cells** - It is made up of many cells. The cell is the basic unit of life. - It belongs to the eukaryotic domain whose building block is the *eukaryotic cell*. **Plants have multiple pigments with multiple functions** - Pigments are insoluble in water but soluble in alcohol, ether, and acetone. - **Chlorophyll** -- light-trapping pigment, that utilizes the trapped sunlight to produce food. - It is organized inside the chloroplast. - Mixture of Chlorophyll a *(chl a)* which is blue-green and 72%. Chlorophyll b *(chl b)* is yellow-green and 28%. - The production is more affected by the intensity of light than the wavelength. - Medium intensity is more favorable. - Produced rapidly between 18° C- 30° C - Contains C, H, O2 , N, Mg - Carbohydrates are needed to form. - **Anthocyanin** -- deep red, purple, and blue pigments and is anti-inflammatory. Absorbs blue, blue-green, and green light. - **Carotenoids** -- yellow and orange. They act as Photo-protectors, anti-oxidants, etc. Absorbs blue-green and violet lights. - **Phytochrome** -- from dark-grown plants is blue and absorbs red light. - Used to measure the length of the dark period (nighttime). If the last night is longer than the night before (autumn). If the last night is shorter than the night before (spring). - **Cryptochrome** -- blue-light-photoreceptor. - Photoreceptors -- specialized light-detecting cells that allow plants to differentiate between red and blue. - **Photoautotrophs** -- organisms capable of synthesizing their own food in the presence of light, requiring only water, minerals, and air to survive. **Cell walls are nonliving matrices outside the plant cell membrane that house and/or perform a variety of functions** - **Cell wall** -- composed of cellulose as its building block. - Active site for cell secretion - It can grow, expand, and adjust to mechanical stress. - **Cellulose** -- composed of multiple units of simple sugars *(glucose).* **Plants are non-motile** - Non-motile means not able to move by itself. - Plants are in a fixed position *(sessile)* but can sense their environment. - Plant movement is the changes in spatial orientation or conformation *(i.e., the movement towards light, opening, and closing of flowers, and growth of developing roots in search of water and nutrients).* **The plant life cycle alternates between a haploid (n) gametophyte stage and a diploid (2n) sporophyte stage.** - **Alternation of generations** -- alternate between 2 different stages in their life cycle. - The haploid gametes fuse at fertilization and produce a *zygote*, which is then diploid, and subsequent division by mitosis gives rise to the *sporophyte* generation. - **Sporophyte phase** -- a diploid *(having 2 sets of chromosomes)* plant body grows and eventually produces spores through meiosis. These spores divide mitotically to produce haploid gametophytes. - **Sporic**-- life cycle that plants process. - Plants are the basic food for other living organisms. The major source of oxygen and food on earth. - Plants are used as a national emblem *(i.e., Narra is the national tree because it's sturdy and has a hard and strong wood)*. - Cash crops produce income for farmers. **Plants are Food** - Human nutrition is dependent on plants. - About 7000 species have been used as food for humans. - Animals of livestock which are all herbivores include camels, goats, sheep, pigs, and cows are mostly feed on grasses and cereal plants. **Plants Provide Air and Regulate the Water Cycle** - Plants bring oxygen as a byproduct of photosynthesis. - Act as storage of CO2 from burning fossil fuels - Plants help in purifying and distributing the water of the planet. - Helps in moving water from the soil to the atmosphere through *'transpiration'* **They are Important to Science** - Plants have industrial applications - Entrepreneurs apply plants to provide biodegradable and sustainable products. - The rings of trees serve as a record of climates from the past and are an important dating method in Archaeology. - The *ethnobotany* field studies the use of plants by indigenous culture which helps in discovering new medical plants and in conserving endangered species. **Cell** -- is the basic unit of life. It was first coined after Robert Hooke (1665) observed a thin slice of cork. **Cell Theory** -- Schleiden (1838), Schwann (1839), and Virchow (1858). It states, ***"All organisms are made up of one or more cells, within which the life process of metabolism and heredity occur."*** A diagram of a plant cell Description automatically generated Plant cells contain a *cell wall* and a *large central vacuole*, which animal cells lack. **Indeterminate growth *(meristems)*** -- induced to undergo division. **Totipotent** -- the ability of plant cells to give rise to an entire nuclear genome programme of differentiated cells. **The cell is made up of cell membrane, cytoplasm, and nucleus.** a. The cell unit membrane encloses the cytoplasm, also called protoplast or hyaloplasm, and is continuous with the cell's internal membrane system. - Protoplast -- entire cell without cell wall - Hyaloplasm *(cytosol)* -- fluid part of the cytoplasm. b. The protoplast is the living matter within the cell. Where membrane-bound organelles are dispersed. c. The nucleus is the control center of eukaryotic cells. **Plant cell** - comprises 70% water and 26% macromolecules 4% ions and small molecules. **Biological properties of water** 1. **Cohesion** -- bind with another water molecule 2. **Adhesion** -- bind with molecules except water 3. **Temperature** **Buffer** -- high specific heat and heat of vaporation 4. **Metabolite** -- Physiological reactions 5. **Solvent** -- dissolves most substances. **Hydrophilic** -- "water-loving" substances that dissolve or mix well with water. They are polar or have charged molecules. Can interact with water by hydrogen bonding or ionic interactions. **Hydrophobic**- "water-fearing" substances are repelled by water because they are nonpolar.  **Carbohydrates** -- commonly known as "sugars" Vector set of three categories of carbohydrates -- monosaccharide, disaccharide and polysaccharide. The simplest sugars, two monosaccharides linked together, polymers containing more monosaccharides. Stock Vector \| Adobe Stock  a. **Monosaccharides** - This is the *simplest form* of sugar and is made up of two or more hydroxyl groups, which cannot be broken down through a hydrolysis reaction. b. **Disaccharides** -- it is formed through dehydration synthesis of aldehyde or ketone with any hydroxyl group (-OH) on the second sugar. When 2 monosaccharides are bonded together. c. **Polysaccharides** - These are simple repeating sugar subunits *(\>10 monosaccharides)* forming large linear and branched molecules known as *polymers*. d. **Oligosaccharides** -- The polymer formed is *(3-9 monosaccharides)*. It includes glycolipids and glycoproteins. **Lipids** -- insoluble in water but soluble in organic solvents. They exist as fats and oils (triacylglycerol or triglycerides) formed by the dehydration synthesis of 3 fatty acids to glycerol through ester bonds. - **Saturated Fats** -- with double bonds, commonly solid at room temperature. - **Unsaturated Fats** -- 1 or more double bonds in hydrocarbon tails, commonly liquid at room temperature. Phospholipid Bilayer- Structure, Types, Properties, Functions **Proteins** - constitute most of the plant cell dry biomass. - Monomer is Amino acid.  - Amino acids form proteins through a condensation reaction. - Proteins form peptide bonds by releasing water molecules. - **Primary structure** -- the sequence of amino acids in a polypeptide chain *(i.e., Insulin).* - **Secondary structure** -- patterns like alpha-helices and beta-sheets formed by hydrogen bonds between backbone atoms *(i.e., keratin, collagen, silk fibroin)*. - **Tertiary Structure** -- The 3d folding of the protein due to side chain interactions *(i.e., Myoglobin)* - **Quaternary structure**- Multiple polypeptide chains interact to form a functional protein, such as enzyme or ion channels *(i.e., Hemoglobin)* 8: Levels of organizations of proteins \| Download Scientific Diagram - Proteins like enzymes, promote chemical reactions and are highly specific catalysts. - **Enzymes** have specific active sites that bind substrates, while cofactors in the site help break and form bonds.  **Importance of Proteins in Plants** 1. Structural components that form channels and pumps in the membrane 2. Carry messages from one cell to another 3. Act as signal receptors 4. Moving parts and propel organelles within the cytoplasm 5. Act as hormones, toxins, anti-freeze molecules, etc. **Nucleic Acids** - Long chainlike biomolecules vital for plant life. - The monomer is a nucleotide and is composed of the: - phosphate groups (PO4-2) - nitrogenous base - pentose (5C) sugar - **Nitrogenous Bases** - Pyrimidines (1 ring)- C, T, U - Purines (2 rings) -- G, A, - Adenosine Triphosphate (ATP) is the most common nucleotide in plant cells and acts as an energy carrier. - **Ribonucleic Acid (*RNA*)** -- single-stranded molecule - Involve in protein synthesis (mRNA, tRNA, rRNA) - Catalyzes biological reactions, controls gene expression, and responds to cellular signals. - **Deoxyribonucleic Acid (*DNA*)** -- Double helix formed by two strands of nucleotides. - Stores genetic information - Direct synthesis of proteins via transcription. - Replicates for cell division. **Plasma Membrane**  A diagram of a cell membrane Description automatically generated - Also called "*plasmalemma*" it encloses the cell and acts as a barrier between the cell and the surrounding environment. - The unit membrane is a fluid mosaic made up of a phospholipid bilayer, containing different proteins. It is semi-permeable means that it allows certain substances to pass through while blocking others. - The membrane proteins form pores, channels, or pumps to transport ions and large molecules. - **Osmotic Potential** -- the potential of water to move from hypotonic to hypertonic solution. **Cell Wall**  - A strong outermost layer of plant cells is found external to the plasmalemma. - It gives the shape, provides protection, and rigidity (inability to be bent or forced out of shape), and controls cell expansion. - Consists of cellulose infused in hemicellulose matrix, pectin, and other soluble proteins (primary cell walls). Lignin is subsequently accumulated which adds protection and strength to secondary cell walls. Sure! Here's a concise version: 1\. **Cellulose**- Structural polysaccharide providing strength to plant cell walls. 2\. **Hemicellulose** **Matrix**- Branched polysaccharides linking cellulose fibers, enhancing wall integrity. 3\. **Pectin** - Complex carbohydrate that binds cells together and adds flexibility. 4\. **Soluble Proteins (Primary Cell Walls)** - Easily dissolved proteins in primary walls, involved in structure and signaling. 5\. **Lignins** - Organic polymers that strengthen and waterproof secondary cell walls. 6\. **Secondary Cell Wall** - Thicker layer inside the primary wall, made of cellulose, hemicellulose, and lignin for added support. **Plasmodesmata** - A plasmodesma is a membrane-lined pore connecting the cytoplasm of two plant cells, allowing the intercellular passage of substances and signals between them. **Middle Lamella**  - is a layer of pectin that holds the primary walls of two plant cells together. It forms from the cell plate during cell division. - Singular form = lamellum **Nucleus** What is Plant Cell Nucleus? Meaning, Structure, Parts & Functions - Biology Reader - Located at the *periphery* as large central vacuole occupied most of the cytoplasm. - **Periphery** - outer edge or boundary - Contains the DNA that is separated by porous - **Nuclear Membrane or envelope**- separates the nucleoplasm or karyolymph to the cytoplasm. - **Karyolymph** -- jelly-like substance inside the nucleus, like cytoplasm. - **Nucleolus** -- responsible for the arrangement of ribosomes and modification of tRNA during translation. **Vacuoles** - It's a large, centrally located organelle, that can only be found in Plant Cells. - **Tonoplast** -- surrounds the vacuole and separates the vacuole's contents or cell sap from the cytoplasm. - **Cell Sap** - pigments, cellular waste products, excess mineral ions, and others inside the tonoplast. - Helps maintain osmotic pressure, keeping the plant turgid (firm) and helps it maintain structure. **Endomembrane System** A diagram of a structure Description automatically generated - a group of organelles in eukaryotic cells that works together to modify, package, and transport lipids and proteins. - It includes endoplasmic reticulum (ER), nuclear membrane, Golgi apparatus, vacuoles, endosomes, plasmalemma, and vesicles. a. **Endoplasmic Reticulum** - a network of tubules connected to the nuclear envelope and plasmalemma, synthesizing and storing proteins and lipids. It also stores calcium in plant cells.  1. **Smooth ER (SER)**: Lacks ribosomes; synthesizes carbohydrates, lipids, and hormones, and stores calcium. 2. **Rough ER (RER)**: Has ribosomes; synthesizes and modifies membrane and secretory proteins. b. **Golgi Apparatus/Dictyosomes** Golgi apparatus \| Definition, Function, Location, & Facts \| Britannica - Composed of small stacks of **cisternae** throughout the cytoplasm. - Each cisterna is a flattened, membrane-bound sac with fenestrated margins and surrounded by **vesicles**. - **cis-Golgi**: Interacts with the ER and acts as a receptor for secretory materials. - **trans-Golgi**: Associated with various vesicles. - **Primary roles include:** - Glycosylation of proteins. - Synthesis of polysaccharides for cell wall construction. - Packaging and targeting products to vacuoles or the cell surface. c. **Endosomes** - It is a vesicular structure that is primarily involved in sorting and/or trafficking of proteins and lipids from the Golgi apparatus to the vacuole or plasmalemma. **Mitochondria**  - The **mitochondrion** is a double-membrane organelle. - The outer membrane allows small molecules to pass through. - The inner membrane is impermeable and has folds called **cristae** to increase surface area. - **Cristae** use the electron transport chain to pump protons and produce **ATP** (energy). - The space between cristae, called the **matrix**, contains enzymes that generate energy-rich molecules like ATP, **NADH**, and **FADH2** through oxidation. - Plant mitochondria have their own ribosomes (**mitoribosomes**) and DNA (**mtDNA**), which are mostly linear but can also be circular or branched. This DNA comes from ancient endosymbiotic events. - Mitochondria are believed to have originated from free-living aerobic prokaryotes that were engulfed by larger anaerobic cells, forming a symbiotic relationship. - This ability to use oxygen for energy gave the host an advantage to survive in oxygen-rich environments, leading to the evolution of mitochondria. - The inner membrane is thought to have been the plasma membrane of the aerobic prokaryotes, while the outer membrane came from the anaerobic host during endocytosis. Chloroplast Chloroplast \| CK-12 Foundation - This organelle is enclosed by two-unit membranes namely, the **outer membrane** and **inner membrane**. The membranes are organized into a series of stacks, the **grana** (singular, *granum*), of discs (***thylakoids***) that are embedded in the **stroma**. - The thylakoid disc is a closed membrane cisternum that separates the outer **stromal phase** from the inner lumen. - The lumen has a close connection with the lumen of **stroma lamellae** and to all other thylakoids in all the grana stacks of the chloroplast. - It contains the green pigment **chlorophyll** that traps light energy and transforms it into chemical forms of energy through **photosynthesis**. - Like mitochondria, chloroplasts contain their genetic system but possess circular DNA. It is generally accepted that chloroplasts are originally derived from a free-living photosynthetic prokaryote, which follows the same mechanism (endosymbiosis). - Chloroplast evolved later than mitochondrion. **Microbodies**  - Single-membrane organelles containing crystalline proteins. - Involved in photorespiration, nitrogen metabolism, and fat conversion. - **Peroxisomes** produce toxic peroxides that can be broken down into water and oxygen. - **Glyoxysomes** convert lipids to carbohydrates during seed germination. **Pigments** - **Chlorophyll** - Main photosynthetic pigment; absorbs blue and red light, reflects green. - **Carotenoids** - Accessory pigments and oil-soluble; absorb violet and blue light and reflect yellow and orange. - **Phycobillins** - Water-soluble pigments; phycoerythrin (red, in red algae) and phycocyanin (blue, in cyanobacteria). - **Phytochrome** - Regulates plant growth; absorbs red light (reflects blue-green) and far-red light (reflects light green). - **Flavonoids** - Water-soluble receptor pigments in vacuoles; anthocyanins (red, purple) and flavins (light yellow). - **Betalains** - Nitrogen-containing, water-soluble pigments; betacyanin (blue-violet to red) and betaxanthin (yellow, orange to orange-red). **Cell Inclusions** - These are substances found in plant cells as products of metabolism - In most cases, they are waste products and come in the form of (1) ergastric substances, (2) reserve foods (i.e. starch grains), (3) excretory products (i.e. crystals, calcium oxalates, calcium carbonates), and (4) secretory products (i.e. lipid droplets, spherosomes, volatile oils). **Microtubules** - long and thin tube-like structures within the plasma membrane, made of a protein subunit called tubulin. - seen in spindle fibers during cell division and plate formation after mitotic division. - Microtubules maintain cell shape, assist in chromosome separation during division, transport organelles, and guide cell wall growth.