General Botany Lec Notes PDF

GENERAL BOTANY SEMESTER 1 | 2024-2025 l POPULATION GROWTH, NATURAL RESOURCE WRITING A LABORATORY REPORT CONSUMPTION, AND ENVIRONMENTAL https://docs.google.com/document/d/14...

GENERAL BOTANY SEMESTER 1 | 2024-2025 l POPULATION GROWTH, NATURAL RESOURCE WRITING A LABORATORY REPORT CONSUMPTION, AND ENVIRONMENTAL https://docs.google.com/document/d/14oX8Usy4fp54FB DEGRADATION VIVoTYJ9iuWUgS6I-vP5x-LyYrGBE/edit?usp=sharing 1. In many less developed and moderately developed countries, individual resource use is MICROSCOPY: THE COMPOUND LIGHT MICROSCOPE small. However, a rapidly increasing number of https://docs.google.com/document/d/1VWbov4okQ28hiy people tends to overwhelm and deplete these RHR86cFu_ytdSXAEUm9RmRnrxgFhY/edit?usp=sharin countries’ soils, forests, and other natural g resources. 2. In highly developed countries, individual TOPIC 1: INTRODUCTION TO BOTANY resource demands are large, far above the minimum requirements for survival. To satisfy their desires rather than their basic needs, people in more affluent countries exhaust natural resources and degrade the global environment through extravagant consumption and “throwaway” lifestyles. A single child born in a highly developed country such as the United States has a greater impact on the environment and on resource use than a dozen or more children born in a country such as Nigeria. BIOLOGICAL DIVERSITY all the different kinds of life you'll find in one area—the variety of animals, plants, fungi, and PLANT BLINDNESS even microorganisms like bacteria that make up Plant blindness refers to the phenomenon where our natural world. people fail to notice or appreciate plants in their Affected by several human disturbances environment It also refers to failing to recognize the role of WHAT IS A SUSTAINABLE ENVIRONMENT? plants on earth and believing that plants are Allows humans and other organisms to survive somehow inferior to animals and thrive without compromising the ability of future generations to meet their needs. THE ROLE OF PLANTS The men waved life jackets next to PALM FRONDS SPELLING THE WORD ‘HELP’ on the island of Fanadik, where they were stranded for three days. Photograph: US navy/Reuters THE HUMAN POPULATION AND PLANTS Oxygen Production: Plants produce oxygen Human Population will through photosynthesis, essential for human increase to 9.74 billion by and animal life. the year 2050 Carbon Sequestration: They absorb carbon dioxide, helping to mitigate climate change. EFFECTS OF A Food Source: Plants provide fruits, vegetables, CONSTANTLY INCREASING grains, and nuts, forming the basis of our diets. POPULATION Medicinal Benefits: Many plants are sources of Environmental Deterioration pharmaceuticals and traditional medicines. ○ Increased population leads to greater Habitat and Biodiversity: Plants support resource consumption, resulting in ecosystems by providing habitat for countless deforestation, loss of biodiversity, species. pollution, and climate change. Hunger Soil Health: They prevent soil erosion, enhance soil fertility, and contribute to the water cycle. ○ Higher demand for food can outpace agricultural production, leading to food Climate Regulation: Plants influence local scarcity and malnutrition, especially in climates by regulating temperature and vulnerable population. humidity. Persistent poverty Aesthetic and Cultural Value: Plants contribute ○ Rapid population growth can strain to beauty, inspire art, and hold cultural economic resources, making it difficult significance in many societies. for governments to provide adequate Mental Health Benefits: Green spaces and plants jobs, education, and social services, have been shown to improve mood and reduce perpetuating cycles of poverty. stress. Health issues Economic Value: Plants are vital to agriculture, ○ Overcrowding and inadequate forestry, and industries like landscaping and infrastructure can lead to the spread of pharmaceuticals. diseases, limited access to healthcare, and increased pressure on healthcare SCOPE OF BOTANY systems, exacerbating public health Effects of Global climate on plants challenges. Molecules that make up plant cells Producing enough food to support the ever-expanding world NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 population Plants take in and use energy Identification of future drugs to treat diseases ○ Through photosynthesis, plants convert such as cancer or AIDS. sunlight into chemical energy, using it Plants that are in danger of extinction and to grow and sustain their metabolic keeping these organisms from disappearing processes. forever from our planet Plants respond to stimuli The effect of human-produced pollution on ○ Plants can react to environmental plants factors such as light, gravity, and touch, enabling them to adapt their growth and DISCIPLINES OF BOTANY orientation for survival. Molecular Biology Plants grow and develop Study the structures and functions of ○ Plants undergo growth throughout their important biological molecules such as proteins and life cycle, increasing in size and nucleic acids. complexity, from germination to maturity. Plant Biochemistry Plants reproduce ○ Plants can reproduce sexually (via seeds The study of the chemical interactions within and flowers) or asexually (through plants, including the variety of chemicals that plants methods like cloning), ensuring the produce. continuation of their species. Plant DNA transmits information from one generation to the next ○ Plant DNA carries genetic information that is passed down from one generation to the next, guiding their development and traits. Plant populations undergo genetic changes over time ○ Plant populations can evolve through genetic variation and natural selection, leading to adaptations that enhance survival in changing environments. (warning: word for word na notes HAHHSAHHA) Plant Cell Biology Encompasses the structures, functions, and life TOPIC 2: CHEMISTRY OF LIFE processes of plant cells. CHEMICAL BASIS OF PLANT LIFE Plant Anatomy It is inevitable that before we study the plant Microscopic plant structure (cells and tissues) cellular function, we should first understand the Plant Morphology structure and properties of the major types of biological molecules. Refers to the structures of plant parts such as Remember that the morphological and leaves, roots, and stems, including their evolution and physiological characteristics of cells as well as development other cellular structures are derived directly Plant Physiology from the activities of the molecules of which Study different processes such as photosynthesis they are composed. and mineral nutrition to understand how plants function. Thus, for us to understand the basis of plant life, Plant Genetics we should be provided the necessary basic Plant Heredity and variation information about the chemistry of life. Plant Ecology The Study of the interrelationships among MAGBASA KA SA GENZOO NOTES KO MAS MAGEGETS MO plants and between plants and their environment. BASIC ANATOMY OF AN ATOM AND HOW THEY FORM Plant systematics TO BECOME A MOLECULE encompasses the evolutionary relationships ATOMS among different plant groups. ➔ Basic units of matter and the defining structure Plant taxonomy of elements a subdiscipline of systematics, deals with the ➔ The nucleus of every atom, except the hydrogen, description, naming, and classification of plants consists of both positively charged protons and Paleobotany electrically neutral neutrons. is the study of the biology and the evolution of plants in the geologic past OTHER SPECIALIZATIONS OF BOTANY ➔ Bryology - The study of mosses and similar plantsfor ➔ Agronomy- field crops and soils ➔ Horticulture- Ornamental plants and fruit and vegetable crops ➔ Forestry - forest conservation and forest products such as lumber ➔ Economic Botany - Plants with commercial ATOMIC NUMBER importance ➔ The number of protons in an atom, which equals the number of electrons, resulting in no net CHARACTERISTICS OF PLANTS charge Plants are highly organized ◆ Because it is the electrons that mean the ○ Plants exhibit a complex structure, with chemical behavior of an atom, all the specialized cells and tissues that atoms of a given element have the same perform various functions, such as atomic number. photosynthesis, nutrient transport, and support. NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 NEUTRONS ➔ Neutrons are uncharged subatomic particles of As seen in the essentially the same mass as protons. figure, Ionic bonds ➔ They contribute to the structural stability of the play an important role nucleus. in binding protein ➔ Because of neutrons, an element can exist in molecules to DNA several physically distinguishable but chemically molecules. It is identical forms, which is called ISOTOPES. formed between positively charged CHEMICAL BONDS nitrogen atoms in the The atoms that make up a molecule are joined by protein and the chemical bonds. negatively charged Atoms can attain a more stable arrangement of oxygen atoms in the electrons in their outermost shell by interacting DNA. with one another. The DNA molecule itself consists of two separate COVALENT BOND strands held together by noncovalent hydrogen bonds. A covalent bond is Hydrogen bonds form between abundant electronegative formed when atoms, such as oxygen and nitrogen, which bears a electrons are partial negative charge and abundant hydrogen atoms, shared between which bears a partial positive charge. two atoms. Covalent bonds are ★ As mentioned earlier, a single noncovalent bond strong bonds is relatively weak and easily broken, but large between the atoms numbers of these bonds between two molecules that make up a make the overall complex quite stable molecule. The formation of a WATER covalent bond Plant life, as well as between two other organisms, is atoms is governed totally dependent on by the water. fundamental Although it only principle that an contains one molecule atom is most stable when its outermost electron of oxygen and two shell is filled. molecules of hydrogen, Consequently, the number of bonds an atom can a water molecule has a form depends on the number of electrons needed unique structure that to fill its outer shell. gives extraordinary ○ In most cases, two atoms can be joined properties. by bonds in which more than one pair of electrons are shared. First, water is a highly asymmetric molecule DOUBLE BOND with an oxygen atom at one end and two A bond in which two hydrogen atoms at the opposite end. pairs of electrons are Second, the covalent bonds that form in the shared between two water molecule are highly polarized. atoms. Lastly, each molecule joined transiently with TRIPLE BOND hydrogen bond lattice. A bond in which three ○ each water molecule can form hydrogen pairs of electrons are bonds when the partially positive charge shared between two hydrogen of one water molecule atoms. becomes aligned next to a partially negative charge oxygen of another Interactions between molecules are also molecule. Hydrogen bonds would be governed by a variety of weaker linkages, which is called formed. Consequently, this extensive the noncovalent bonds. NONCOVALENT BONDS do not hydrogen bonding produces a highly depend on shared electrons, but rather it is attractive for interconnected network of water forces between atoms, having an opposite charge. molecules. Individual noncovalent bonds are weak, and they are readily broken and reformed. PROPERTIES OF WATER IMPORTANT TO PLANT LIFE IONIC BOND TEMPERATURE BUFFER Water acts as a temperature buffer because of its An ionic bond is high specific heat capacity, high heat of formed when vaporization, and high latent heat of fusion. electrons transfer ○ High heat specific capacity means that from one atom to the when water is heated, most of the other. thermal energy is consumed in Although individual disrupting hydrogen bonds rather than noncovalent bonds contributing to molecular motion. As are weak, large water receives rapid temperature numbers of them fluctuations that adds stability to the acting together create plant body. additive attractive ○ When we are talking of high heat of forces. vaporization, it means that water Taken as a whole, molecules would require so much energy ionic bonds provide to convert the water from its liquid state considerable stability to its gaseous state by breaking the to structures. NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 hydrogen bonds that hold one molecule ROLE OF WATER IN PLANT to another water molecule. That this Major components in plant cells high heat of vaporization would make ○ almost 70% of the plant cell is composed the water resist evaporation and that of water would be the cause of the cooling effect An excellent solvent for the uptake and transport on plants. of substances within the plant body. ○ On the other hand, when we are talking Good medium and react in many biochemical about the latent of fusion, it is the reactions reverse of heat of vaporization wherein a Temperature stabilizations water molecule takes a lot of energy to Provide structural support via turgor pressure convert it from solid to a liquid state. In ○ specifically the same manner, a lot of energy must the one that be released from water to freeze, thus you can find the water receives the plant body from in the leaves freezing. of the plants Plays a vital role in CAPILLARY ACTION cell elongation and plants use capillary action to bring up water up growth to the roots and stems to the rest of the plant body So molecules can be The molecules of the water are attached to the categorized based on how they molecules of the inside of the stem and this respond to water molecules. It attraction is used to help force the water up from can either be hydrophobic or hydrophilic molecules. the ground and dispense it throughout the plant body. This capillary action happened because of the property of water that is cohesive, adhesive property and high surface tension. ○ When we are talking of cohesion, it is the ability of one water molecule to bind with another water molecule. So the hydrogen bonds between the water molecules make liquid water self-sticky and the hydrogens of one water molecule are attracted to the oxygen from other water molecules. ○ And when we are talking about adhesion property, it refers to the attraction of water molecules to non-water hydrophilic substances. So this property of water gives it the ability to climb the walls of any container it is in. ○ Water’s high surface tension, resulting from cohesive forces, allows it to form a continuous column in plant vessels, HYDROPHOBIC MOLECULES facilitating upward movement. sometimes called as hydrophobes Surface water molecules bond they are nonpolar molecules that are more strongly to each other water-fearing, thus do not dissolve in water than to air, creating a "skin" since these molecules are uncharged, and usually effect. form few or no hydrogen bond at all When the hydrophobic molecules are added to water, they would form what we call micelle to SOLVENT have minimal contact with water. The hydrogen bonds that are formed at the water ➔ Micelles are clamped that form a cage molecules can be able to dissolve more different where hydrogen bonds between the kinds of solutes than any other solvents. water molecules are broken down, thus A small volume of aqueous fluid present within a formed by means of what you call an plant cell would contain a remarkably complex endothermic reaction that would cause mixture of dissolved substances but water is the entropy of the system to decrease more than just a solvent. It also determines the hydrocarbon groups. structure of biological molecules and the types of Interactions that occur between hydrophobic interaction in which they can engage. molecules are what we call Van der Waals Moreover, it is chemically inert that water will interactions. not react unless they are enzymatically designed Oils and fats are some of the hydrophobic to react. molecules that are found in the body. Also water is also the medium to reach materials moved from one compartment of the cell to HYDROPHILIC MOLECULES another. Sometimes they are called hydrophiles. They are polar molecules that are water-loving, TRANSPARENT TO LIGHT thus they can be dissolved in the polar molecules One of the important properties of water to the of water. plants is their transparency to light. Hydrophilic molecules can form hydrogen bonds The chloroplasts inside the cytoplasm of the cell with water molecules, and this mixing is are surrounded by water and the light that exothermic, thus the entropy of the system penetrates in water can be absorbed by the would be increased. thylakoids. Salts and ions, which are molecules with charged particles, are examples of hydrophilic molecules found in the plant body. NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 release is generally stored in CLASSIFICATION OF BIOLOGICAL MOLECULES BY high energy bonds of FUNCTION intermediate-energy carrier In plant cells, the organic molecules are divided into four molecules, which is called categories based on the role in metabolism adenosine triphosphate or ATP. Macromolecules Building blocks of macromolecules Metabolites HOW THE CHEMICAL REACTIONS WOULD TAKE Miscellaneous functions PLACE? The cell starts with a compound A and converts MACROMOLECULES it to compound B, then to compound C and so Contains carbon atoms on, until the functional end product is produced. ○ these are molecules that are highly The biochemical reactions in the conversion of organized with carbon atoms. one molecule to another may either be in the Its shape and size would vary depending on its dehydration synthesis or hydrolysis. function. Some macromolecules form the structure of the cells, as well as carry out the activities of cells DEHYDRATION SYNTHESIS with great precision and efficiency. In the dehydration synthesis, the monomers Macromolecules can be divided into four major that are made from a single subunit would categories, combine with each other via the covalent bond ➔ carbohydrates to form polymers. ➔ Proteins The reactions would allow the monomers to ➔ lipids ➔ nucleic acids release water molecules as by products. These macromolecules are constructed from As additional monomers would join through monomers through the process of multiple dehydration synthesis reactions, the polymerization. chain of repeating monomers begin to form what we call now a monomer. BUILDING BLOCKS OF MACROMOLECULES So different types of monomers can combine in many configurations, which makes the diversity The macromolecules found within the plant cell of macromolecules found within the cell. have a short lifetime, as compared with the cell itself, except the deoxyribonucleic acid or the DNA, which continuously breaks down and being HYDROLYSIS replaced by newly synthesized macromolecules. In hydrolysis reactions, the polymers are broken Consequently, cells maintain a pool of low down into monomers by using water molecules molecular weight precursors that are readily and catalyzed by an enzyme. available to form macromolecules. As the polymer is broken into two components, one part would gain a hydrogen atom and the other gains a hydroxyl group from the split of the water molecule. However, in ionized molecules, one part gains two hydrogen atoms and a positive charge while the other part gains one oxygen atom and a negative charge. This takes note that there are some compounds The macromolecules are the monomers, and this that are formed along the metabolic pathways includes the simple sugars, which are the leading to the end products that might have no precursors of polysaccharides, the fatty acids, function per se and these compounds are called which are incorporated to form into lipids, the metabolic intermediates. amino acids, which are precursors or protein, and the nucleotides, which are the precursors for the formation of the nucleic acids. METABOLIC INTERMEDIATES (METABOLITES) The molecules found in the cell are synthesized in a step-by-step sequence, beginning with the specific starting material, and this is called the METABOLIC PATHWAY. The series of chemical reactions can either be catabolic reactions or anabolic reactions. ○ CATABOLIC REACTION Energy-releasing processes. Break down complex metabolites into simpler ones ○ ANABOLIC REACTION Energy-consuming processes. Build up new molecules. When chemical bonds are broken, energy is released, which drives anabolic reactions to form new bonds, the energy NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 CLASSIFICATION OF BIOLOGICAL MOLECULES BY atoms is present in the sugar, while FUNCTIONS doubling the amount of hydrogen atoms, thus we have the formula of C6H12O6. So each sugar molecule is made of carbon atoms, backbone and are linked together in a linear array in a single hydroxyl group, except for those that contain carbonyl groups. If the carbonyl group is located at the internal position to form a ketone group, the sugar is called ketose. On the other hand, when the carbonyl group is located at one end of the sugar, it forms the aldehyde group and the sugar is called an aldose. ➔ Contains 3 carbons are known as trioses ➔ Contains 4 carbons are known as tetroses ➔ Contains 5 carbons are known as pentoses ➔ Contains 6 carbons are known as hexoses Bulk of the dry wheat of a cell is made out of ➔ Contains 7 carbons are known as heptoses macromolecules and their direct precursors. The molecules of miscellaneous function would include the Some of the common aldoses and ketoses are ➔ vitamins, which are substances that primarily ★ Aldose (O=C-H) function adjuncts to proteins ○ Glyceraldehyde (triose) ➔ hormones, which are signal molecules that ○ Ribose (pentose) would affect the plant growth ○ Glucose (hexose) ➔ ATP which are molecules that are involved in ★ Ketoses (C=O) energy storage ○ Dihydroxyacetone (triose) ➔ it could be regulatory molecules such as cyclic ○ Ribulose (pentose) adenosine monophosphate or what we call the ○ Fructose (hexose) cyclic AMP ➔ the other metabolic waste that are produced in SUGAR LINKAGE the cell such as the urea In the two monosaccharides, either an aldose or a ketose, are linked together, they form what we call now PLANT BIOLOGICAL MOLECULES disaccharides. The sugar linkage between sugars to form larger molecules is called covalent glycosidic bond. This bond is formed by the reaction between carbon one of one sugar and the hydroxyl group of another sugar, which generates carbon, oxygen, carbon or COC linkage between the two sugars. ○ Sugar 1 (C1) + Sugar 2 (-OH) EXAMPLES OF DISACCHARIDES Sucrose (glucose + fructose) ○ The sucrose, which is commonly known as table sugar, is a disaccharide. ○ we all know that sucrose is a major So the four types of biological molecules or what we call component called a plant sap that biomolecules found in plants are the carries chemical energy from one part of ➔ Carbohydrates the plant to another. ◆ carbohydrates are found in the cell wall Maltose (glucose + glucose) of the chloroplasts Lactose (galactose + glucose) ➔ Lipids ➔ Proteins Sugar can be a simple repeating sugar subunit, ◆ proteins are found in the plasmalemma forming large linear and branched molecules. (plasma membrane), nuclear and below ribosomes, microtubules and DNA OLIGOSACCHARIDES ➔ nucleic acids the sugar is linked together to form short or small chains CARBOHYDRATES Mostly oligosaccharides are covalently attached to proteins and lipids, hence they are converted into glycoprotein and glycolipids respectively. These oligosaccharides are commonly found projecting from the surface of the plasmalemma that would function in distinguishing one type of cell from another, as well as they are used to facilitate the cell's interaction with the surroundings. Carbohydrates are sometimes called glycans. It consists of carbon atoms, hydrogen atoms and POLYSACCHARIDES oxygen atoms. are long chains of repeating sugar subunit The simplest sugar is also known as the In plants, the most common polysaccharides are monosaccharide. cellulose and starch. The general formula of carbohydrates is (CH2O)n, ○ Cellulose molecules are unbranched and wherein the number of hydrogen atoms is highly extended and are bundled doubled depending on the number of carbon together into tough fibers and assume atoms. the structural stability of the plant cell. ○ For example, glucose has six carbon atoms, then the same number of oxygen NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 ○ On the other hand, the starch molecules Moreover proteins are responsible in carrying have a helical arrangement and used by messages from one cell to another and they the cell for storage of energy would act as membrane signal receptors and the third would mean how the cell would react to a particular substance. Moving parts and propel organelles within the cytoplasm ○ Proteins can also be used for the machinery or they are responsible for the machinery to various biological So in summary, carbohydrates function movements such as the cyclosis which is primarily as source and storage of chemical energy in the the streaming movement of the cell. It is also important in supplying the carbon atoms in chloroplasts that is found in the building materials needed by the cell during their hydrolysis. Proteins are the ones that are metabolism, thus carbohydrates would play a vital role responsible for the movement of this as a structural component of the cells. chloroplast in the periphery of the hydrilla cell. Furthermore, proteins can act as hormones, LIPIDS toxin or antifreeze molecules that would Lipids are a diverse group of non-polar probably control and coordinate various molecules that can be dissolved in organic biological activities. solvent and they are unable to dissolve in water. It consists of one molecule of glycerol that is AMINO ACIDS linked with ester bonds to three fatty acids. That amino acids are the monomers of proteins is why they are sometimes called triacylglycerol So each polymer of protein has a unique or triglycerides. sequence of amino acids that give them So the fatty acids are long and branched chains characteristically different from one another. with a single carboxyl group at one end. So the Amino acids are organic molecules that would hydrocarbon chain is hydrophobic while the contain both the carboxyl group and the amino carboxyl group is hydrophilic. Since they both group which are separated from each other by a have hydrophobic and hydrophilic regions, they single carbon atom which is called the alpha are termed as AMPHIPATHIC MOLECULES. carbon. So fatty acids differ from one another in the ○ So the R group or what we call the side length of their hydrocarbon chain and the chain is bonded to the alpha carbon and presence or absence of double bonds. they are highly variable to the ○ Saturated Fatty Acids: commonly used 20 amino acids in the Lack of double bonds. construction of proteins, specifically Typically solid at room those that are encoded by the temperature. deoxyribonucleic acid or the DNA. ○ Unsaturated Fatty Acids: Possess double bonds. Usually liquid at room temperature (oils). PHOSPHOLIPIDS 2 fatty acids + 1 glycerol ○ These molecules would resemble a triacylglycerol but have only two fatty acid The amino acids are classified into four groups based on chains thus they are also called the their characters of their side chain diacylglycerol. 2 -OH groups in glycerol linked to fatty acids 3rd -OH group linked to phosphoric acid ○ The third hydroxyl of the glycerol is covalently bonded to a phosphate group which is covalently bonded to a small polar group. ○ So the head of the possible lipids that contain the phosphate group is hydrophilic while the two fatty acid tails are hydrophobic. Phospholipids are the main structural components of the plasmalemma and the characteristic feature of the phospholipids which have hydrophobic and hydrophilic properties makes the plasmalemma a selectively permeable membrane. PROTEIN Macromolecules that play a vital role in all cell activities (huhuuhu wala ako mahanap sa net kaya blur) They can act as an enzymes that would catalyze the rate of metabolic reactions ➔ POLAR CHARGED So in the plasmalemma of the plant cells ◆ Polar charge amino acids would include proteins form channels and pumps and they also aspartic acid act as transporters of various substances. So this glutamic acid probably would be the reason for being lysine selectively permeable to materials that move Arginine inside or taken out of the cell. histidine NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 ◆ They contain side chains that are to physical and other relatively strong organic acids and bases chemical stresses. thus they become fully charged. ◆ They can form ionic bonds with other PROTEIN STRUCTURE charged species in the cell. For example the passively charged arginine residues The structures of the proteins can be described at of histone proteins are linked by the four levels of organization, namely the primary ionic bonds to the negatively charged structure, the secondary structure, the tertiary structure phosphate groups of the DNA. and the quaternary structure. The primary structure is the amino acid sequence of a protein while the three ➔ POLAR UNCHARGED other structures refer to the molecular organization. ◆ polar uncharged amino acids would include Asparagine Glutamine Threonine Serine Tyrosine ◆ The side chains of these amino acids have a negative or positive charge and they can form hydrogen bonds with other molecules that would include the water. ➔ NONPOLAR ◆ non-polar amino acids would include Alanine Valine Leucine Isoleucine Methionine phenylalanine Tryptophan PRIMARY STRUCTURE ◆ The side chains of these non-polar the primary structure of a protein refers to the amino acids are hydrophobic and are not linear number and order of amino acids present capable of forming electrostatic bonds or The convention for the designation of the order they cannot interact with water. of amino acid is that the n-terminal end, the one ◆ Moreover these non-polar amino acids that would bear the residue with a free alpha lack oxygen and nitrogen. amino group, is the first amino acid and is found to the left side of the chain. ➔ SIDE CHAINS WITH UNIQUE PROPERTIES The end of the chain, which is found of course in ◆ have unique properties that would the rightmost part, is the c-terminal end where separate them from the other categories amino acid has a residue that would contain a Glycine free alpha carbonyl group. ○ side chains consist of SECONDARY STRUCTURE only hydrogen and When we are speaking of the secondary structure provide a site where the of a protein, it describes the conformation of a backbones of two portion of the polypeptide chain. polypeptides can ○ When we are talking of conformation, approach one another we are referring to the very closely three-dimensional arrangement of Proline atoms and its spatial organization ○ a unique amino acid of So there are actually two proposed conformation having the alpha amino of proteins, namely the alpha helix conformation group as part of the ring and beta pleated sheet conformation. and does not readily fit ○ ALPHA HELIX CONFORMATION into an ordered The backbone of the polypeptide secondary structure that assumes the form of a would often produce cylindrical twisting spiral form. kinks or hinges The backbone lies on the inside Cysteine of the helix while the side chains ○ One interesting feature are projected upward. of cysteine is the The helical structure is presence of a reactive stabilized by hydrogen bonds sulfhydryl group that is between atoms of one peptide often linked to another bond and those situated just cysteine residue, what above and below it are along the we call the disulfide spiral. bridge. ○ BETA PLEATED SHEET ○ This side disulfide the backbone of each segment of bridge would help polypeptide assumes a folded or stabilize the intricate in a pleated conformation shapes of proteins that wherein they are lying side by are usually found on the side. surface of the So it is characterized by extracellular hydrogen bonds that are environment subjected oriented perpendicular to the long axis of the polypeptide NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 chain that project across from one part of the chain to another. TERTIARY STRUCTURE When we are talking about the tertiary structure, we are referring to the complete three-dimensional structure of the polypeptide units of a given protein. It is stabilized by an array of non-covalent bonds between the side chains of the protein. The tertiary structure also refers to the spatial relationship of the different secondary structure to one another within a polypeptide chain and how these secondary structures would fold into each three-dimensional form of a protein. QUATERNARY STRUCTURE So if a protein would contain two or more ACTIVATION ENERGY different polypeptide chains that are held in energy input required to begin the chemical association by the non-covalent forces and reactions stabilize the tertiary structures of protein, this level or the structure of protein is what we call So the energy is needed to break existing bonds quaternary structure. before new bonds can be formed. It requires large So a protein that is composed of two identical amount of activation energy as shown by the red line in subunits is called homodimer, while those the graph to pursue the reaction as compared with a proteins that are composed of two unidentical catalyzed mediated reaction as shown by the blue line in subunits are called heterodimer. the graph.So which means that enzymes would decrease the required activation energy that would allow a reaction to proceed at a much faster rate. So virtually all metabolic reactions would require enzymes, otherwise it will proceed very slowly. HOW DOES THE ENZYMES WORK TO CATALYZE THE REACTION? LOCK AND KEY MODEL So initially, the lock and key model was first proposed wherein it says here that the active site of an enzyme and the active site would be the location on the surface of the enzyme where substrate would bind would have a specific shape and only the substrate will fit into it like a lock and a key. ○ substrate are those molecules upon ENZYMES which an enzyme would act with one of the most important proteins Enzymes are biological catalysts that lower the ➔ So in the image shown, the substrate is the activation energy for reactions. The lower the ribulose bisphosphate or RUBP and this only activation energy for a reaction, the faster rate of shows that the enzymes are very specific to the reaction would occur. substrates that they are interacting with and Thus enzymes increase the rate of chemical each substrate have their own specific type of reactions that would take place within the enzymes with active site that conform to the non-living cells by lowering the activation shape of a particular type of a substrate. energy. ➔ So for example, if the enzyme is amylase, it only ○ For example, the reaction of glucose and accepts the sugar amylose but not the sugar ATP to produce the byproducts 6 glucose lactose. On the other hand, if the enzyme is the phosphate and adenosine diphosphate lactase, it only accepts lactose but not amylose ADP as shown in the graph. although they are both sugar in nature. ◆ the name of the enzyme is dependent on the substrate that they are acting with and usually ends with the suffix ASE. ◆ So for our previous example, the amylose would be the substrate so the enzyme is called the amylase. The substrate will be the lactose, so the enzyme is called a lactase. NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 faster at higher temperature rather than the lower temperature. But remember here that the temperature must not be too high, that it could change the shape of the active site or sometimes we call it as the DENATURATION of the protein because high temperature would denature the proteins and that would allow the shape of the active site to be changed and it is not already compatible for the specific substrate in which they should be acting upon weight. INDUCED FIT MODEL Another factor would be the ACIDITY and Updated model ALKALINITY that would depend on the activity of the In this model, the active sites of enzymes change enzyme. Remember that each particular type of enzyme their shape as they interact with the substrate. has an optimal pH or the acidity or alkalinity in order for So once the substrate is fully locked in and them to perform their activity efficiently. already in the exact position in the active site, the catalysis can now begin. NUCLEIC ACIDS This only means that the precise orientation of nucleic acids are long the enzyme required for catalytic activity can be chains of nucleotides induced by the binding of the substrate by which ○ nucleotides conformational shape change may occur in the would be the enzyme's active site in order to precisely feed the monomer of the substrate. nucleic acids Moreover, there is a precise substrate interaction that would occur in the active site and this is There are two types of being stabilized by numerous weak interactions nucleic acids namely the like hydrogen bonds, electrostatic interactions, ribonucleic acid (RNA) and the hydrophobic contacts and Van der Waals forces. deoxyribonucleic acid (DNA). each nucleotide is composed pentose sugar ○ The five carbon sugar or the pentose sugar in nucleotides can either be a ribose sugar or a deoxyribose sugar which is present in the RNA and DNA respectively. ○ So the two sugars are different by the presence of the hydroxyl group on the two prime carbon of the ribose and it is Enzymes need to form complexes with their absent in the two prime carbon of the substrate following what we discussed earlier, the deoxyribose. induced fit model nitrogenous base phosphate group So the substrates in the given example that are shown in the image are the adenosine diphosphate or When sugar and a nitrogenous base come ADP and the phosphoenol pyruvate or PEP while the together, they form a nucleotide. The linkage that would enzyme is the pyruvate kinase. form between the base and the one prime carbon of the ★ When we are speaking of kinases, kinases are sugar is what we call the N GLYCOSIDIC BOND. enzymes that would catalyze the transfer of a phosphate group from high energy, phosphate donating molecules to specific substrates and in this case, it is the phosphoenol pyruvate. ENZYME-SUBSTRATE COMPLEX (ES COMPLEX) the binding of a substrate to an enzyme active site Remember that the formation of the ES complex is dependent on the shape of the active site that would allow the binding of the substrate. So on the other hand the phosphate group is ★ Remember that when the substrate ADP and PEP attached to the five prime carbon of the sugar forming a is already in the active site of the enzyme covalent bond. So this time it is a covalent bond that pyruvate kinase, the conformational shape of the would form between a phosphate group and the sugar. active site changes to fit the two substrates to begin with the reaction. So during the assembly of a nucleic acid strand the During the action of the enzyme, the phosphate hydroxyl group attached to the in the PEP or the phosphoenol pyruvate will be three prime carbon of the sugar transferred to adenosine diphosphate or ADP, thus of one nucleotide becomes forming the byproducts adenosine triphosphate or the linked by what we call now an ATP and pyruvate acid. Secondly, these end products, the ester bond to the phosphate ATP and pyruvate will be released by the pyruvate kinase. group attached to the five prime carbon of the next nucleotide as Remember that there are no changes that you would see in the image. So happen in the enzyme so that the active site can accept the nucleotides of the nucleic another ADP and PEP substrate to pursue another acids are then connected by the reaction. So the activity of enzymes is dependent on its sugar phosphate linkages and environmental conditions depending on their are described as the three prime localization, meaning they have their own specific to five prime phosphodiester optimal conditions. However, the activity of enzymes is bonds since the phosphate atom NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 is esterified to two oxygen atoms from each adjoining RNA AND DNA sugar. The two nucleic acids present in the plants are the DNA and the RNA. THE DIFFERENT TYPES OF NITROGENOUS BASES ➔ PYRIMIDINES ◆ smaller molecules consisting of a single ring ◆.include cytosine, uracil and thymine Cytosine is found in both RNA and DNA while the uracil is only found in RNA and it is replaced by thymine in DNA. ➔ PURINES ◆ Larger molecules with two rings ◆ include the bases adenine and guanine can be found both in RNA and DNA RNA DNA double stranded one strand Much longer; a FUNCTIONS OF NUCLEOTIDES chromosome can be several Generally shorter than DNA Nucleotides do not only function as building blocks of centimeters long when nucleic acids unraveled. Formed in the nucleolus Primarily located in the which is found inside the nucleus; small amounts nucleus, then moves to found in mitochondria specialized regions in the (mitochondrial DNA) and cytoplasm depending on the chloroplasts (plastid DNA). type of RNA that would be Most of the energy used by the plants is derived formed from the nucleotide adenosine triphosphate or Basically there are three the ATP. So the structure of the ATP enables types of RNA that can be them to carry a chemical energy in their easily formed hydrolyzed phospho and hydride bonds which is ➔ MESSENGER RNA formed between each of the three phosphate (MRNA): Carries groups. Remember that ATP consists of three genetic phosphate groups and each three phosphate information from groups are linked together by what we call DNA to phospho and hydride bonds. When one ribosomes. phosphate group is removed by the process of ➔ TRANSFER RNA hydrolysis of this phospho and hydride bond so (TRNA): the energy is released and then the ATP is then Transfers amino converted into adenosine diphosphate or called acids during the ADP. protein synthesis. Another function of the nucleotide is that it is ➔ RIBOSOMAL RNA important to plant metabolism is that they have (RRNA): the ability to combine with other groups to form Component of what we now call a coenzyme. ribosomes. ○ So for example the coenzyme A and this coenzyme A is not at fault for its role in More stable due to the synthesis and oxidation of fatty acids deoxyribose sugar (one less More reactive and they are and the oxidation of pyruvate in the oxygen containing hydroxyl not stable in alkaline citric acid cycle. They form a reactive group), which protects solution. thioester bond between the sulfur atom genetic information. and acetate. So if the thioester bond is Vulnerable to damage from More resistant to UV hydrolyzed it releases large amounts of ultraviolet (UV) light. damage compared to DNA. Gibbs free energy making the acetate molecule more readily transferred to FUNCTIONS OF NUCLEIC ACIDS another molecule. Another function of the nucleotide is that it can also be used for the signal transduction which is evident by the activity of cyclic adenosine monophosphate or the cAMP. So the cAMP is a derivative of ATP that is being used for intracellular signal transduction like As we all know the DNA serves as the genetic transferring into cells and the effects of certain material of all cellular organisms and the hormones that cannot pass through the information stored in the DNA is used to govern plasmalemma. Also cAMP binds to and would cellular activities through the formation of RNA regulate the function of ion channels that are messages. found in the membrane of the cell Moreover RNAs have a catalytic role and they are called the RNA enzymes or the ribozymes. NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 RNAs are also important during the protein ○ Procambium -> vascular tissue system synthesis. Wherein the messenger RNA or the mRNA carries the code in sequences that Every part of the plant such as the leaf, stem, determine the specific amino acid while the and root has a common set of TISSUE SYSTEM. tRNA carries the amino acid the ribosomes during protein synthesis. So the rRNA is DERMAL TISSUE SYSTEM important in forming the cell's ribosomes where Outermost layer, protects the plant. protein synthesis would take place. Dermal cells Sa lab to pero dedma isama ko na rin Includes epidermis (young plants) and periderm (woody plants). THE PLANT CELL Specialized structures: stomata, trichomes, root BODY PLAN OF PLANTS hairs. VASCULAR TISSUE SYSTEM Transports water, nutrients, and food. Xylem: moves water and minerals. Phloem: transports sugars, nutrients, and organic compounds. GROUND TISSUE SYSTEM Makes up the bulk of the plant body. Functions: photosynthesis, storage, support. Types of cells: ○ Parenchyma: thin walls, metabolic functions, storage. ○ Collenchyma: thick walls, flexible support. ○ Sclerenchyma: thick, rigid walls, SHOOT SYSTEM structural support. the part of a plant that grows above ground Vegetative part ○ Stem ○ leaf Reproductive part ○ Flower ○ Fruit ○ seed ROOT SYSTEM Located below the ground Non-photosynthetic Function: anchors the plant body; absorption of water and minerals; storage of food (carbohydrates) PLANT GROWTH AND TISSUE Plant growth begins with seed germination and The distribution and concentration of tissues continues for the lifespan of the plant depends on what part and type of the plant is Plants do not live indefinitely; they do have being observed infinite life spans CELL STRUCTURE CELL WALL Unique and distinguishing structure of plants Outermost part of a plant cell ROOT LATERAL MERISTEM Provides support and strength from mechanical This where the growth of root system starts and osmotic stress to in the cell Secondary growth Prevents cell bursting ○ allows the cell to develop turgor SHOOT APICAL MERISTEM pressure which is the pressure exerted This where the growth of shoot system starts by fluid in the cell that presses the Primary growth plasmalemma to the cell wall Forms the primary meristem that differentiate ○ Plasma membrane is semi permeable, into 3 tissue system fluids can diffuse and when water ○ Protoderm -> dermal tissue/epidermis content is too high it can lead to cell ○ Ground meristem -> ground tissue bursting NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 ○ Turgor pressure makes the plant cell rigid ○ Loss of turgor pressure is indicated and can be observed when parts of the plant are wilted or dry. The rigid structure of plant cell dictates its structure, size, and size Plant cell wall is made up of cellulose, a long linear polymer of glucose that aggregates into fibers called microfibrils Helps prevent osmotic lysis or cytolysis (bursting) which occurs when there is too much fluid in the cell PLASMA MEMBRANE Chloroplast moving around the periphery of the Encloses the cytoplasm cells Semi permeable that regulates the material that Cytoplasmic Streaming or Cyclosis - constant enters and exit the cell flow or circulation of the cytoplasm inside the Function to protect the cell from its surrounding cell environment One of the observable indication that cyclosis is Physical barrier that surround all cell and allow occurring is the movement of chloroplast separate activities to occur inside and outside the together with the movement of cytoplasm in cell circular direction and one direction only CYTOPLASM ERGASTIC BODIES Fluid substance within the cell that also Also known as cell inclusions maintains turgor pressure Non living substances present in plant cells Cytosol They may be present in soluble or insoluble state Organelles and can be organic or inorganic in nature They are raw materials or products of metabolism which is present in components or sub components of cells These substance may be exported or expelled from the cell Can be classified into 3 categories ○ Reserve food – Starch, Lipids, Protein ○ Waste Material – Calcium Oxalate, Calcium Carbonate ○ Other Secretory products – Resin, Volatile Oil cells NUCLEUS Contains the cell genetic information Control center of the cell Nucleolus (singular) / Nucleoli (plural) ○ Visible within the nucleus ○ produces ribosomal RNA ○ appear as dark spots in each nucleus VACUOLE Storage cells Membrane - bound structure and that contains fluids and dissolved substances Filled with liquid that contains that contain Petiole - tangkay variety of materials In the lower portion, there are needle shaped structure, Present in many type of cells but most common those are calcium oxalate crystals (raphides) in plant cells and cells of certain protists Can occupy up to 90% of the volume of the cell TYPE OF PLANT CELLS Dissolved substances – Cell Sap Vacuolar membrane / tonoplast which is the the membrane that surrounds the central or large vacuole of the plant CHLOROPLAST Also defines and unique to plant cell PARENCHYMA CELLS Bean shaped or ovoid shaped Isodiametric / polyhedral in shape Plastid ○ Iso (same), diametric (dimension) = Responsible for photosynthesis same dimensional cell Chlorophyll – green pigment responsible for ○ Have nearly equal diameters absorbing during photosynthesis Primary cell wall meaning it contains mainly cellulose, unlike other types that have secondary Ovoid shaped organelles in plants and occur in cell walls containing lignins variety of shape in algaes ○ Cell wall is not that thick, there is no surrounded by two membranes (inner and outer) thickening Grana/granum – formed by a third set of membrane; stack of thylakoid Thylakoid – contains the chlorophylls NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 Retain ability for future cell division even on maturity which then help in regeneration and wound healing ○ They are capable of cell division even they reach maturity stage ○ Plants also undergo wound healing Contain a nucleus Densely cytoplasmic Determine first the long axis of a plant part to be Have several small vacuoles sectioned/cut: Store food reserves ★ Depending on the plant part to be cut, find first the long axis. COLLENCHYMA CELLS ★ The long axis also points to the apices or terminal Primary walls that are usually thickened ends of a plant part. especially at corners or edges ★ For a vertically oriented plant part of an organ, Thickening takes place in the middle lamella that part logically pointing to the top and the Function to support the stem or leaf part that points to the bottom, then connect the Have thicker cell wall than parenchyma cells top and bottom parts, will form your long axis. ★ For usually horizontally oriented plant parts (leaves or flower structures), those near attachment to the main axis of the plant (stem) is one terminal end and connect this to the other end of the plant part to form the long axis of the plant part. ★ Shown in the figures are the identified long axis of the plant organs with lines ending in arrow heads. TOPIC 3: MITOSIS, MEIOSIS AND PLANT CELL CYCLE GROWTH Dictated by continuous SCLERENCHYMA CELLS generation of new cells Thickened lignified walls Achieved through cell expansion and cell Strong and waterproof division Support types and conducting forms Cell cycle “Telomeres” Usually composed of ○ Sclereids Stone cells CHROMOSOME Isodiametric Thread-like structures in a cell’s nucleus that clumps of these cells give fruits are visible under the microscope only during like apple and guava their cell division distinctive grittiness (sandy Consists of proteins and a single large texture) molecule of DNA that contains hundreds of Spherical, Oval or Cylindrical thousands of different genes Provide stiffness to the plant ○ FIbers Elongated cells in stems, roots and vascular bundles Tapering ends of this fibers interlock that provides maximum support for the plant Provide mechanical strength CHROMOSOME NUMBER The number of chromosomes within a nucleus varies from one species to another, but every somatic cell in an organism of a given species contains a characteristic number of CUTTING OR SECTIONING MAY BE THROUGH: chromosomes. Cross or transverse (a cut at 90 degrees of long axis, Fig. A) ➔ Cabbage: 20 chromosomes per cell (10 Longitudinal (a cut parallel to the long axis, Fig. pairs per cell) B) ➔ Haplopappus gracilis: 4 chromosomes Surface sections (epidermal or paradermal cut per cell (2 pairs per cell) parallel to the long axis but are few-cell thick ➔ Olea europea: 46 chromosomes (23 pairs from the epidermis, Fig. C) per cell) ➔ Ophioglossum reticulatum: 1262 chromosomes per cell (631 pairs per cell) NICOLE ANGELA D. BARRION | PROF. CRISTINE JOY LUNA GENERAL BOTANY SEMESTER 1 | 2024-2025 HOMOLOGOUS CHROMOSOME Interphase: “between phases” Members of a chromosome pair that are similar The cell synthesizes needed materials and grows in size, shape, and genetic constitution. Chromosomes undergo duplication during Carry information governing the same genetic interphase (not readily visible) traits, although is not SUBPHASES: necessarily identical. ○ Gap I Phase (GI Phase) or Pre-synthesis ○ Example: A homologous pair carrying a gap gene that specifies flower color, but each ○ Synthesis phase (S Phase) chromosome may specify different ○ Gap II (GII Phase) or colors of petals. Post-synthesis FIRST GAP PHASE (G1) First stage in Interphase Pre-synthesis phase Cell growth Duplication of organelles Cell’s nucleus contains single nucleolus and light chromatin materials Does not involve DNA DIPLOID VS. HAPLOID replication Diploid (2n) GI checkpoint ○ A cell in which each chromosome occurs in pairs Haploid (n) ○ A cell that has a single set of chromosomes DIPLOID HAPLOID Two chromosomes Single Chromosome Represented by 2n Represented by n Somatic cells Gametes Created by Mitosis Created by Meiosis SYNTHESIS PHASE (S) Second stage of Interphase Duplication of THE CELL CYCLE nucleus Synthesis of DNA The cell cycle is the successive series of and protein events in the life of a dividing eukaryotic cell. “Replicated Often represented as a circle and consists chromosomes”- of two main phases (interphase and M chromosomes after S phase) phase The period between two successive divisions, represented by a complete revolution of the circle, is the generation time. SECONDARY GAP PHASE (G2) Third step, next to S Phase Post-synthesis phase Allows the cells to grow more More proteins and organelles (e.g.mitochondria, chloroplasts, etc.) are being made Larger nucleus; nucleus contains two nucleoli and darker chromatin materials. Prepares the cell for the actual division (M MERISTEM Phase) Localized areas of the plant body where mitosis and cytokinesis take place most of the time. Occur in the shoot and root tips (the apical meristems) and in some plants, in thin cylindrical regions that run the entire lengths of stems and roots except at the tips (the lateral meristems) ○ APICAL MERISTEMS: allows the production and subsequent elongation of new cells, causing an increase to the length of growing stems and roots. ○ LATERAL MERISTEMS: produce additional wood and bark tissues that GAP ZER0 PHASE (G0) add girth to stems and roots of trees and Gap zero phase or Resting Phase shrubs. Cells may opt to enter this phase or may directly enter the G1 phase up to cell division INTERPHASE Intrinsic and extrinsic factors Preparatory phase (resource availability, nutritional deprivation, Performs Cell growth and DNA duplication etc.)