Introduction to Botany

Introduction to Botany

• Botany is the study of plants and is associated with green leaves, stems, roots, and flowers.
• Exceptions to the typical plant appearance exist like cactus, pine algae etc.
• Defining a plant precisely is challenging due to the diverse varieties, causing exceptions to simple definitions.
• Biologists disagree about whether certain organisms should be classified as plants.

Characteristics of Plants

• Plant metabolism follows the principles of chemistry and physics.
• Plants have to store and utilize information.
• Plants reproduce, passing on their genes and information to descendants.
• Genes and the information they hold are subject to change.
• Plants need to survive in their environment.
• Plants are integrated organisms.
• An individual plant shows the interaction of genes and the environment.

Origin and Evolution of Plants

• Life on Earth began around 3.5 million years ago with simple early organisms resembling today's bacteria.
• The Earth had anaerobic conditions at the time.
• Cells increased in complexity through evolution by natural selection.
• Major advancements happened as early organisms became more complex, including the evolution of photosynthesis.
• Cyanobacteria had the ability to perform photosynthesis generating energy from sunlight and the machinery to utilize water as a fuel source by oxidizing it.
• Over time, cell structures developed into more efficient subcellular components known as organelles.
• Organelles are closed bags of membranes that allowed for specialization.
• A evolutionary step occurred when DNA became located in the cell nucleus.
• With the location of DNA, came a distinguishing feature between prokaryotes vs eukaryotes
• Eukaryotes diversified, with some acquiring energy-transforming organelles like mitochondria and chloroplasts, which carry out photosynthesis.
• Organisms with chloroplasts evolved into algae and plants.
• Those without chloroplasts evolved into fungi, protozoans, and animals.

Diversity of Plant Adaptations

• There are more than 400,000 species of plants today.
• All of the plant diversity came about through evolution by natural selection.
• Because of this wide diversity, plants have various ways they are utilized.
• In the Stone Age (30,000 BCE), plants could be used as food.
• In the Bronze Age (3000 BCE), Mesopotamian healthcare involved the use of herbs in medicine.
• Herbs were applied externally as bandages or salves to treat physical symptoms with the help of healing plants and liquids.
• Magical spells and rituals were used to end the supernatural influence behind the physical manifestation of the ailment.
• The Olmecs (1900 BCE) first learned how to prepare the beans of the cacao tree, creating the process of turning cacao into chocolate.
• The Mayans and Aztecs revered chocolate as a gift from a serpent god.
• Cacao beans were prized as currency to buy food and other goods, rewards to soldiers, offerings in rituals, and dowry, being more valuable than gold.
• In the Shang Dynasty (1500-1046 BCE), tea leaves were medicinal: chewed to aid digestion or used in skin and joint salves.
• The earliest account of tea was prepared from Camellia sinensis and consumed as a medicinal beverage.

Origins of Botany

• Aristotle (371-286 BCE) systematically studied biology.
• He studied more animals than plants and his work on botany has been lost.
• Theophrastus, Aristotle's student, wrote hundreds of manuscripts describing plants and is known as the “Father of Botany”.
• His works are the first surviving documents to describe plant parts, reproduction, and sensitivity to climate.
• He classified them as medicinal, edible, herbal.
• In the Columbian Exchange (1492), led by Christopher Columbus, Spain searched for new routes and sources for importing spices from the East.
• This exchange impacted agriculture, ecosystems, and diets worldwide and introduced Europeans to crops like maize, potatoes, tomatoes, cacao, chili peppers, vanilla, beans, tobacco, etc.

Botanical Imagery

• Plants and flowers have symbolic meaning.
• Botanical symbolism originated in the literature of antiquity-where plants are used in metaphors for virtue and vice.
• Carnations, for example, represent love, devotion, and resilience.
• Sunflowers represent warmth, positivity, and orient themselves to light.
• Plants, trees, and flowers are associated with certain gods or goddesses, like Apollo and Daphne.

Principles of Chemistry

• Metabolism is the sum of chemical reactions that provide the body with energy.
• Organic compounds are synthesized from living organisms but they can't be synthesized from inorganic matter.

Vital Force Theory

• Jacob Berzelius theorized that living organisms possessed unique properties not explained by ordinary chemical and physical processes with a vital force.
• The theory says something can only become organic thru a vital force found in living creatures
• The theory was debunked by :
  • Wöhler's Synthesis of Urea 1828 where inorganic chemist Friedrich Wöhler synthesized urea accidentally
  • Pasteur Disproving Spontaneous Generation 1859 with a Swan-neck flask
  • Buchner's Cell-Free Fermentation 1897 with Zymologist that Yeast extract with no living yeast fungi can form alcohol from a sugar solution.
  • Zymase from yeast caused glycolysis
• Atoms, the smallest unit of matter, consist of protons, neutrons, and electrons.
• The number of protons determines the elemental identity.
• Helium has an electron configuration that says the atom is inert and does NOT react with other atoms.
• Hydrogen has one shell with one electron.
• Some elements have outer shells holding fewer electrons than they could.
• Fluorine has 7 electrons in its outer shell, which could hold 8, meaning it tends to attract an electron from other atoms.
• Elements exist as ions because of the stability provided to atoms that lose or gain an electron.
  • Cation: positive ions, more protons, less electrons.
  • Anion: negative ions, less protons, more electrons.
  • Valence electrons: electrons in the outermost shell of an atom that can be transferred from one atom to another, converting each to an ion.
  • Ionic bonds form when one atom donates electrons to another and form between a metal and a nonmetal.
  • Covalent bonds form when one atom shares electrons equally with another and form between two metals.

Properties of Water

• A water molecule usually has electrons that are not shared equally.
• Oxygen has a higher electronegativity than hydrogen.
• Electronegativity refers to the ability of an atom to attract electrons toward itself - Positive charge and negative charge attract each other.
• The negative end of water (oxygen) attracts positive of another water (hydrogen).
• Hydrogen bonding is the attractive force between a hydrogen atom covalently bonded to a very electronegative atom such as N, O, or F atom.
• Hydrogen bonding has a force that is not enough to pull electrons from one to the other or even enough to cause the two molecules to adhere firmly to each other.
• The hydrogen bonds are sufficient to cause water molecules to adhere slightly
• Water's polarity and hydrogen bonding allow it to surround and break apart ions and polar molecules.
• High specific heat capacity is the ability of water to absorb and store large amounts of heat without experiencing a significant increase in temperature.
• The quantity of heat energy is needed to raise a specific volume of water's temperature by one degree Celsius.
• It helps keeps the temperature of Earth moderate.
• High heat of vaporization refers to it takes a lot of energy to change water from a liquid to a gas.
• When water freezes, its molecules arrange themselves in a hexagonal structure, causing ice to be less dense than liquid water - Density level from highest to lowest: cold water > warm water > ice.
• Surface tension is a result of the cohesive forces amongst water molecules giving resistance to outside pressures.
• Cohesion happens when water is attracted to water.
• Adhesion occurs when water is attracted to another surface.

Acids and Bases

• pH scale is the potential of Hydrogen.
• It measures acidity or alkalinity, and the concentration of hydrogen ions in a solution.
• Acidic solutions have a pH < 7.
• Neutral solutions: pH = 7.
• Basic/Alkaline solutions: pH > 7.

Macromolecules

• Large, complex polymeric molecules that are typically made of simple, small organic molecules called monomers.
• Monomers are identical but can bond together in different ways to make up different polymers.
• As the physiology of plants changes, ONLY the assembly of monomers changes, NOT the metabolism.
• As the plant grows, it assembles amino acids to proteins for leaves, stems, and flowers.
• Carbohydrates usually have structures like sugars, fibers, and starches.
• They function in plants for energy storage and structural support and contain carbon, hydrogen, and oxygen.
• The ratio of hydrogen to oxygen is close to 2:1 (CH2O).
• Monosaccharides (or simple sugars) are monomers of carbs:
  • Glucose.
  • Fructose.
  • Galactose.
• Monosaccharides can bond together to make various disaccharides or polysaccharides.
• Their ring formation makes them unreactive and relatively inert molecules is ideal for physiological functions.
• They can be transported from region to region by not reacting with structures.
• They are synthesized in leaves from carbon dioxide (CO2) and water during photosynthesis.
• Once synthesized, carbs can be used where energy is needed.
• Disaccharides have 2 monosaccharides covalently bonded:
  • Sucrose = Glucose + Fructose
  • Lactose = Galactose + Glucose
  • Maltose = Glucose + Glucose
• Dehydration happens when water is formed.
• The bond between two monosaccharides happens from the interaction of -OH groups.
• During bond formation, —OH is removed from one carbon, and hydrogen is removed from the other -OH.
• Hydrolysis is reversal of dehydration that breaks the bond by adding water back.

Polysaccharides

• Polysaccharides have complex sugars with long saccharide chains.
• The 3 polysaccharides formed by plants:
  • cellulose.
  • amylose.
  • amylopectin.
• Starch is the primary form of energy storage in plants, as any excess energy from photosynthesis is stored in the plant tissue as starch.
• Technically known as amylose and amylopectin.
• Starch generally contains 20-25% amylose and 75-80% amylopectin by weight.
  • Amylopectin = branched chains, and if a plant needs to use a lot of glucose molecules, amylopectin is easier to access because it is highly branched, where enzymes in plants are able to break it down easily.
  • Useful when plants need rapid energy release such as during germination or rapid growth phases.
  • Starch is primarily made of amylopectin.
  • Amylose = unbranched chains, helical structure:
  • In plants, enzymes are NOT able to break this down easily, and the glucose is released slowly for maintaining energy supplies over long periods.
• A long polysaccharide is composed ONLY of glucose monomers.
• Amyloplast is a type of plastid responsible for producing, storing, synthesizing, and breaking down starch.
• Cellulose is the main substance in the walls of plant cells, providing strength and rigidity to the cell wall.
• Cellulose molecules hydrogen bond to other polysaccharides and become cross-linked into a complex meshwork known as the cell wall and the wall is relatively inert.
  • Only few organisms have enzymes capable of hydrolyzing the beta-1, 4-glycosidic bond.
  • Those that are able to digest cellulose only do so because their digestive tracts contain microorganisms with the proper enzymes.

Proteins

• Proteins function as biological catalysts, form structural parts, participate in cell reactions, act in immunity, and provide fuel.
• Monomers are amino acids and function from the amount of amino acids that can bond together.
• Polymerization, or the linking of amino acids, is regulated by organelles called ribosomes and the sequence and types of amino acids incorporated must be controlled with precision.
• Primary structure is the sequence of amino acids
• Secondary structure is made up of regular sub-structures or folding and some regions interact with other regions of the same protein forming alpha helices or beta sheets.
• Hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern.
• Tertiary structure: structure is three-dimensional and has the physical shape of a protein in its functional mode (when it is able to carry out biological processes).
• Without the correct primary structure, the protein will not fold into its proper form.
• If the tertiary structure is altered, for example, by mutation, the protein may not function correctly.
• Ex. protein mutation in the waxy gene of corn such as on This gene is responsible for the synthesis of granule-bound starch synthase (GBSS), an enzyme crucial for amylose production in plant starch and The mutation inhibits the regulation of amylose.
• Resulting in starch that is almost entirely made up of amylopectin
  • Anthocyanins: pigment of plant.
  • Mutation in Dihydroflavonol 4-reductase (DFR) leads to different coloring in flowers.
• Quaternary structure: complex of protein molecules, maintained by hydrogen bonding, interaction of hydrophobic regions, or disulfide bridges. It interacts between two or more separate polypeptides.

Enzymes

• Proteins speed up chemical reactions and are accelerated through selective processes.
• Functions:
  • Act as biological catalysts
  • Form structural parts
  • Participate in cell reactions
  • Act in immunity
  • Provide fuel
• RuBisCO: Ribulose-1, 5-bisphosphate carboxylase
  • One of the most abundant and important proteins in plants used to catalyze the first step of carbon fixation.
• Other examples: amylase, cellulase, phosphatase

How Enzymes Function

1. Substrate Binding (Formation of the Enzyme-Substrate Complex)

• The enzyme has a specific active site that matches the shape of its substrate (lock-and-key model) or can adjust to match the substrate (induced-fit model).
• The substrate binds with the enzyme for the enzyme-substrate complex

2. Catalysis (Transition State Formation)

• The enzyme lowers the activation energy needed for the reaction.

3. Product Formation (Substrate Transformation)

• The substrate undergoes a chemical change to form the product(s).

4. Product Release

• The product is released from the active site, leaving the enzyme unchanged and free to catalyze another reaction.

Structural, Defensive, Storage, Receptor, and Motor Proteins

• Structural proteins shape skeletons and structures of cells, tissues, and organisms like Keratin in hair.
• Defense proteins protect against diseases.
• antibodies
• Storage proteins are biological reserves for amino acids.
• Ex. ovalbumin in egg whites
• Receptor proteins detect and receive chemical signals.
• Motor proteins lead movement.
  • Ex. actin and myosin in contracting muscles

Transport Proteins

• Transport proteins are responsible for moving materials within an organism.
  • Ex. hemoglobin in blood

Nucleic Acids

• Nucleic Acids are main information-carrying molecules in the cell
• Monomers are nucleotides that contain only 5 nitrogenous bases fall into two groups:
  • Pyrimidines (single ring) like Cytosine, Uracil, and Thymine
  • Purines (two rings) like Adenine and Guanine There are 2 kinds of nucleic acids:
• Deoxyribonucleic acid (DNA).
• In plant cells, most DNA is found in the nucleus, although chloroplasts and mitochondria also contain part of genetic material.
• Functions:
• Permanent storage place for genetic information
• Acts as a blueprint for building proteins and new cells - Base pairings: - Purine adenine (A) pairs with Pyrimidine thymine (T) - Purine guanine (G) pairs with Pyrimidine cytosine (C)
• Ribonucleic acid (RNA)
• Base pairings:
  • Purine adenine (A) pairs with Pyrimidine uracil (U)
• Central Dogma
  • DNA (genotype) → Transcription → Translation by ribosomes → Phenotype

Lipids

• Lipids are biological molecules that do NOT have any true polymers but not big enough to be macromolecules.
• They share one trait: they mix poorly with water but are the chief storage form of energy and provide structural components of membranes.
• 3 classes of lipids are based on chemical composition: Simple, Complex, Derived
• Structure of an Ester and it requires two oxygen atoms and two carbon atoms but contains a carbonyl group (C=O).
  • Require only one oxygen atom connecting two carbon chains.
• Triacylglycerol is Esters of fatty acids with alcohols and molecules with other groups.
• Cholesterol is derived from simple and complex lipids

Cell Cycle and Mitosis

• Growth and Division of the Cell
  • Cells come from the division of existing cells.
  • Highly regulated processing ensures cells divide.
  • At appropriate times
  • With high fidelity, the daughter cells are very similar to the motherog.
• Cell Cycle
  • 2 events.
    • Cell-cycle control mechanisms do quality control on:
    • Incompletely replicated DNA.
    • Damaged DNA.
• Cell can account for any damage thru checkpoints.
  • GAP Phases.
    • Time for cell growth.
• Monitoring the internal and external environment ensures that their conditions are suitable before cell moves to other stages.
  • G1 Phase.
    • The first stage happens after cell division.
    • The rest of the cell recovers form division and follows normal metabolism
    • The cells gets bigger
  • Most organelles are replicated
• Cellular contents are duplicated except for the chromosomes synthesis of nucleotides needed for the next round of DNA replication
• G1/S Checkpoint: stops G1
• cells that have not yet committed to DNA replication from entering S-phase.
• Regulated by: cyclin dependent kinases (CDK) and cyclins -Major Regulators: Plant Cyclin D (CYCD) & Cyclin-dependent Kinase A (CDKA)
  • Acts as key switch to transition from G1 Phase into S Phase
  • If there is DNA damage -> cell can't commit to synthesis
• CDKA/CYCD complex is inhibited -> cell cycle arrest at G1 Phase
• Kinase: enzyme that catalyzes the transfer of a phosphate group from ATP to a molecule.
• Cyclin-Dependent Kinases: family of kinases essential for cell cycle regulation.
• Activity of the proteins depends on where the protein cyclins are located in the cell

S Phase

• Genes in nucleus are replicated
• Synthesis" bc DNA is being synthesized
• Begins when cell has passed G1 checkpoints and growning enough to contain the DNA
• DNA Synthesis
• Chromosomal DNA replication has requirements similar to other eukaryotes.
  • Faithful duplication uses DNA strategies conserved in all eukaryotes and is pivotal to preserve genome integrity.
• 3 Steps
  • Initiation -Elongation -Termination
• Initiation
  • Origins of replication: chromosomal locations where replication begins.
  • Eukaryotes have multiples origins
    • DNA unwinds
• Certain proteins recognize and bind to the origin of replication then recruit other proteins needed for replication
• DNA Polymerase places nucleotides to grow along 3’ end
• Elongation: Happens as the daughter strands form on a 5' to 3' direction.
• Termination: DNA replication termination occurs when two replication forks meet and finish replicating DNA End result is semiconservative DNA: one part is the daughter & parent strand and acts a conserves part of the strand
• Chromosomes are duplicated- Endoreduplication is when a cell undergoes extra rounds of DNA synthesis
• Endopolyploid creates cells that occur within about 80% of all maturing plant cells & most often in root cells, trichomes & rapidly metabolized cells

Ploidy

• Ploidy: the number of sets of chromosomes in a cell or organism Dipploid: 2 sets of chromosomes (2x) - Triploid: 3 sets of chromosomes (3x) - Tetraploid: 4 sets of chromosomes (4x)
  • G2 Phase: After S Phase as cells prepare for division as they make double check DNA replication error, grow rapidly & make all the organelles that membrane and lipid structure -G2/M Checkpoint allows for cell progression if there arent damaged parts and binds during the transition with other cell membranes
  • Mitosis follows the pattern cells divide where specific partners are triggered to activate and enter division
  • M Phase follows cell divide as a meristems
    • Prophase happens as chromatin condenses into chromosomes- allowing the states in a sister chromatid state as many parts and nuclei start to break down -Metaphase allows microtubules connect to align centromeres
    • Sister chromatids move into equatorial plates as ensured in number of cell production
• Spindle Checkpoint: ensures segregation of cell chromosomes that prevent it as cell progression that aligns and attatch

Anaphase

• Anaphase: Sister chromatids begin to separate and pulled to ends to shorten that fibers as precise division in the mothering cell -Telophase reaches that ends as membraned decondense and disappear. - Cell plates are formed by vesicles that accumlate and fuse to be a plate.
• Cytokinesis divides parts that form new cell walls that creates that cell to the outter wall as it enters.
• Meiosis follows asexual parenting where genetic identical form - Sexual parenting gives off the growth and differentiation where sperm fuses
  • Angiosperms are egg in the ovule which is inside of a carpel (female organ).
  • Gymnosperms are also sperms inside the pollen cones of the male

Reproductive Methods

• Eggs are found inside ovules inside of seed cones; Plant spores develops into organism with eachother that involves fusion where gametes are created - Meiosis gives single give where even numbers happen inside of chromosomal sets - Prophase I follows what starts that break to form homologous structures as the chromatids can make new things by swapping and crossing over - Metaphase I makes the fibers move at its chromosomal location - Anaphase has segregated and halved counts of sets
  • Telophase preps up while a nucleus rearranges and forms Meiosis II separates and becomes spores Prophase II forms structures

Plant Cell Structures

• Membrane parts are responsible as permeable parts to allow movement and assembly
  • Phospholipids help by hydrocarbon and bilayer to allow fluid in a mosaic
  • Amphipathic parts have bilayeres that minimize hydrophobic parts -Peripheral are proteins as membranes and transporters can allow processes in cells
  • Integral always attach receptors with alpha or beta connections
• Classes are signals or transports

List of functions and protein use

• Membranes are transferred as channels to produce parts for interaction and communication
  • Plastocynanin makes proteins for phtoosynthesis as Celluose makes plants stronger.
• Plasmodesmata are transports of function of ER in plants

Endoplasmic Reticulum

• They help synthesize and process storage and secretion
• They add carbs and synthesis where either a rough ER makes protien or smooth with steroids and lipids in the nucleus

Golgi Apparatus

• Golgi have synthesized proteins as directs to arrange polysaccharide structure in the vacuole -vacuoles can fill as compartments that have more than 30% that store protein or recycle as a toxic

Turgor Pressure

• Isotonic- equal solution - Hypertonic - more outside - Hypotonic- more inside as a nucleus stores and separates stuff

Types: Nucleolus & Chromatin

• Nucleolus helps generate cells that transcribe genetic structure that are called ribosome or RNA that help encode ribosomal or transfer factors called nucleus

Plastids

• Plastids evolves for synthesizing -Proplastids has other precursor that matures and transforms
• Pregranal develops more to light

Etioplast

Plastids will get stopped if there is no light - lack the production that light needs as chorophyll is made with synthesis to begin.

• Chloroplast has photosynth as it captures energy: synthesize , absorbs, encodes with interna types in membraes in the Grana

  • Chlorophyll- aborbs while reflecting rays -Photosystems have proteo structures

• Chomoplasts are pigment in cell as carotene makes orange types or xanthophylls are produced with chloroplast.

Amyloplasts

• Amyloplast have grainy structures that helps with gravitorsim.
• Elaioplast gives out storage
• Proteinoplast give strength to cell

Meristmatics are actively dividing to make potent ones that diffirentate as apicals, lateral and intercalary

Mitochondria

• Mitochondria make all the enzymes for the electro transfer component with 2 chambers
  • Cristae will make surfaces higher in the autono
    • The transfer codes for transfer factor

Cell Wall

Cell Was give protective walls and can be wall sugars as hemicullous pectin and cell plate as it forms or merges to generate walls in meristems for their final sizes

• Primary (initial formation) or secondary (final stages) formed
  • It builds to give that structural shape of cell wall