BIO 215 FINAL

Monosaccharides - Primary Metabolite

Simple sugars which provide the cell with quick energy - examples such as glucose and fructose

Accessory pigments

Since chlorophyll b expanding the wavelengths absorbed by chlorophyll a, it is referred to as an accessory pigment These pigments can NOT transfer light into the photosynthetic pathways Instead they collect that energy and pass that energy to chlorophyll a (primary photosynthetic pigment) since it alone has the qualities to start the photosynthetic process Function: The increase range of visible light which is given by accessory pigments provides an adaptive advantage Meaning certain plant groups are able to take advantage of a variety of habitats (shade, sun, water) Types of accessory pigments Chlorophyll b Carotenoids (Carotenes and Xanthophylls)

Primary and secondary cell walls

Some plants calls can have more than one cell wall At maturity, plants can have either a plant cell wall or both a primary and secondary cell wall

External factors for energy transduction reactions

Sometimes environmental conditions extra energy is needed to be pulled from the energized chlorophyll a electron cyclic phosphorylation Makes extra ATP but no NADPH and water is not split In one case, the photosystem I chlorophyll a electrons go back and run through the electron transport system which connects the two photosystems together a second time thus removing more of the remaining electron energy

Motor proteins

- These proteins move along the microtubule by converting chemical energy into movement Pulls the organelles and vesicles along the microtubules like a train moving cargo Each motor protein has a distinct motion -Kinesin - associated with microtubules, has a slow and steady motion (ex. Golgi vesicles traveling in cytoplasm -Dynein - associated with microtubules, has a sliding motion (flexing of motion) - Myosin - associated with microfilaments (used in both plant and animal cells) Humans use it to move skeletal muscle In plants, it is responsible for moving things across the cytoplasm (cytoplasmic streaming) and cell division

Fructans - polysaccharide

- These relate to plant fruits - Polymers (long chains) of fructose (not glucose as in starch) - Their storage form is in fruits (grains)

Plastids

Plant cells can have a variety of different plastids with not all of them being chloroplasts Shared characteristics of all plastids 2 membrane bound organelles Contain their own DNA, RNA, and ribosomes which is more similar to prokaryotic NOT EUKARYOTIC Plastids also have circular DNA unlike eukaryotic linear DNA This is significant as it means plastids do not undergo mitosis but rather increase numbers by dividing into two through binary fission - much like prokaryotic cells

Phenolics - Secondary metabolites

Multiple roles in plant lives - coloration of fruits - interacting with growth regulators (phytohormones) - interacting with certain enzymes - signaling gene expression in a plant - protecting plant parts from chemical oxidation - Applying strength agents and waterproofing cells Ex. Lignin, Flavonoids, Salicylic acid

Secondary cell wall

NOT ALL CELLS HAVE A SECONDARY WALL These are only present in certain cells whose main function is to strengthen, support, or manage water (only be in certain areas of a plants body) The secondary wall will only develop after the primary cell wall has fully developed it is located internal to the primary cell wall - closest to the plasma membrane (middle lamella combines two different primary plant cell walls together with the secondary wall located towards the inside of the cell) Functions: Lots of cellulose cables with large amounts of hemicellulose (strengthening agent) and low amounts of pectin (flexibility agent) Secondary cell walls are lignified: water is chemically removed from the cell wall and replaced with the secondary metabolite Lignin (provides rigidity and waterproofing) Arraignment Not random as they are in the primary wall Highly organized into 3 distinct layers of cellulose cables unlike the random layers of the primary cell wall S1, S2, S3 Each of the layers has a cross patterning which further strengthens and limits gaps in the secondary cell wall (making it super strong, rigid, and leak proof)

Secondary metabolites

NOT all plants will produce secondary metabolites Plants that do produce secondary metabolites will only produce it on specific parts of their body, not the entire plant Most secondary metabolites are made in response to environmental stimuli Responding to environmental stimuli with chemical signals gives the plant a survival advantage (and sometimes signals nearby plants of a dangerous situation) -Substances used by plants to keep plants alive, communicate between plants, defense , cell signaling - these help maintain proper gene expression to support metabolic process in order to keep plants alive - Specialized molecules that mostly are made in response to an environmental trigger - the concentrations of the compounds being produced vary within a 24 hour period Ex. A secondary metabolite might be produced in low concentrations in the morning and not produced at all at night Functions: 1. Defense (herbivores, pathogens, competitors) 2. Solar protection (protect cells from damaging rays of light) 3. Aid in dispersal of reproductive structures (animals eating fruit containing seeds, seeds are then discarded in new locations for growth 3 categories of secondary metabolites based on chemistry (all members in each of the categories have a shared structural foundation) - Terpenoids - Alkaloids - Phenolics

Botany

Plant biology Scientific investigation and analyses of photosynthetic eukaryotes Plants survive adaptations to their environments with their structural functionalities Phylogenies: evolutionary relationships among plant groups

Plant and animal metabolic processes comparison

Plants do both photosynthesis and cellular respiration Animals only do cellular respiration Because of this, photosynthetic eukaryotes (plants) can survive without animals, but animals can not survive without photosynthetic eukaryotes

Chlorophylls

Plants look green to us and that tells us that they have chlorophyll All chlorophyll molecules share the same fundamental chemical structure (a porphyrin ring anchored around a central magnesium) Outside the ring, there are slight chemical differences which result in more than one type of chlorophyll

Plasmodesma

Plants use plasmodesma as a way of communicating with other cells They are tiny cytoplasmic tunnels which run from the protoplasm of one adjacent cell, through the cell wall, middle lamella, the adjacent cell wall to protoplasm of the adjacent cell Each of these tunnels are lined with endoplasmic reticulum , This allows for protein regulated information molecules to relay messages from one cell to one another

Endosymbiotic Theory

Plastids have originated as free-living prokaryotic cells - which were then engulfed by a host cell that overtime, genetically assimilated (written them) into their DNA making plastids a useful organelle

What are the five kingdoms of life?

Prokaryota, Protoctista, Fungi, Plantae, Animalia

Crystals in vacuoles

Raphide crystal - long needle like crystals Druse crystals - star shaped crystals

Disaccharides - Primary Metabolite

- 2 monosaccharides combined together example is sucrose which is the primary sugar transport in plants made by bonding fructose and glucose - Sugars are bonded into sucrose (table sugar) before being transported long distances around the plant body (like when sugars from photosynthesis in leaves have to be sent to the lower parts of the body) Ethnobotany: Sucrose = table sugar (heavily consumed in USA) Sucrose is used as a transport form of sugar by plants While very few plants store sugars as sucrose (Sugar beets and sugar cane)

Ligin (Phenolics - Secondary metabolites)

- 2nd most abundant organic compound on Earth (gives extreme strength and decreases water loss from the cells) - Found in the cell wall of some cells - Strengthens the cell wall and waterproofs it - acts as an anti-decaying agent - which chemically prohibited organisms from eating the cells and tissues of a plants body - extremely rigid and waterproof compound, leaving the cell wall with an abundance of strength and prevents water loss from the cells Growth significance of Lignin -Allowed trees to become tall and develop branching complexity (making trees structurally sound and develop branch systems for more leaves) Being tall is an advantage as tall plants are better able to capture solar energy - Lignin makes the entire tree stronger and able to support more branch systems, meaning with more leaves there would be more efficient photosynthetic and reproductive potentials - Tall plants can keep their reproductive structures at the top so that they are most exposed to wind, which will carry seeds for further reproductivity (pollen release and seed dispersal)

Microfibrils into Macrofibrils (Cellulose framework formation)

- Cellulose microfibrils are bundles together to build a larger microfibril - the bundle is then twisted and tightened like tightening the fibers of the rope - This process of twisting increases the tensile strength of the macrofibril (stronger than steel!) These strong macrofibrils are what form the basic foundation of the cell wall

Flavonoids (Phenolics - Secondary metabolites)

- Chemical messengers in cell signaling pathways - Essential plant pigments (colored organic compounds) ex. Anthocyanin's - purple compounds produced in some cells with high light intensity - act as UV filtration and protect plant mechanisms from damage (photoprotection) Nitrogen fixation - Plants are unable to use nitrogen as it exists in the atmosphere or in the soil - therefore the chemical makeup has to be altered to a usable structure through nitrogen fixation - soil microbes live on plant roots in specialized locations acting as mechanisms for nitrogen fixation to occur - formation and maintenance of these locations is managed by phenolics Ethnobotany Ex. Flavonoid foods: beet root, cherry tomato, frozen blueberry, oranges provides anticancer, anti-fungal, antibacterial, antiviral, and antioxidant benefits

types of chlorophyll

- Chlorophyll a This type of chlorophyll is required for the photosynthetic process to be started (all photosynthetic organisms will have this - plants, algae, and cyanobacteria) Primary photosynthetic pigment without this organisms can't be photosynthetic, even if it has other molecular forms of chlorophyll Range Max absorption in blue-violet (high energy short wavelengths) Red (low energy long wavelengths) All photosynthetic prokaryotes and eukaryotes have chlorophyll a - Chlorophyll B - only plants and green algae have this type of chlorophyll All other photosynthetic algae (algae that is NOT green) will have chlorophyll a plus other molecular forms of chlorophyll The slight differences in chlorophyll structure results in different chlorophyll types having different absorption spectrums This type of chlorophyl is used to expand their range of light within the visible light spectrum - it is then referred to as "accessory to chlorophyll a" Range Max absorption blue - slightly lower energy than a Orange-red - slightly higher energy reds than chlorophyll a Chlorophyll a and b absorb light at opposite ends of the visible light spectrum, with little to no absorption in the center (green and yellow wavelength) The green wavelength being reflected making the plant look green

Kingdom Protoctista

- Exclusion kingdom - none of it's members fall in line with plants, animals, fungi, or prokaryotes - Difference between individuals yet all eukaryotic - Exists as single cells or groups of similar single cells Different types Protozoa: animal like cells- no cell wall (paramecium) Algae: those that have plant-like cells - cellulose cell wall and chloroplasts

Kingdom Prokaryota

- Exists as single cells or small groups of cells - Do not have a membrane bound organelles, therefore no nucleus. - DNA is contained in a circular "chromosome" with smaller molecules of DNA called Plasmids - Ribosomes are smaller than eukaryotic cells - Contain pepitdoglycans in their cell wall, not cellulose - May be split into Archaea and Bacteria

Kingdom Animalia

- Multicellular organisms with specialized cells to perform a variety of different tasks - Animals feed heterotrophically, cells do not have cell walls or chloroplast, however, they may have cilia of flagella

Kingdom Plantae

- Multicellular organisms with specialized cells to perform a variety of different tasks - cell walls are made of cellulose and can come in different shapes and sizes to improve structure and rigidity - Undergoes photosynthesis - autotrophs which transfers light energy (photons) into chemical energy (food)

Biological significance of plants

- Soil types Plants play a role in the creation and maintenance of soil types. Without plants, soils would be limited to small amounts produced by physical rock weathering Soil and soil types regulate ecological succession and erosion control - Biogeochemical cycling Plants play an important role in all of the cycles that keep the Earth healthy. such as the water cycle, nitrogen cycle, etc. - Ecological interactions Play roles in food webs, symbioses, and coevolution relationships - Ethnobotany The study of plant use by humans and the role of plants in society and economics Ethnobotanical examples Commercially plants are essential in agriculture, forestry, pharmaceuticals, medicine, fossil fuels, etc. - Aesthetics Psychological connections to nature and universe EX. flowers had such an effect on the Mayans that they copied the structure of flowers in the structure of their houses

Polysaccharides - Primary Metabolite

- The combination of many sugars bonded together in plants - Fundamental use is for structure in plants - Ex Cellulose, Starch, Fructans

Cellulose Framework formation (cellulose synthase complex)

- UDP glucose (Uridine Diphosphate glucose) which exists in the cytoplasm of the cell combines into a long chain to form a cellulose molecule the molecules are spun to form the smallest of the cable, the microfibril - UDP glucose goes into a mobile enzyme complex called the Cellulose Synthase Complex. Here, UDP glucose is bonded to form cellulose which is then spun by the CSC into tight microfibrils - Multiple CSCs move along the plasma membrane collecting UDP glucose from the cytoplasm and spinning it into cellulose microfibrils

Endomembrane system

-An interconnected network of proteins adjacent to the plasma membrane which are responsible for moving organelles and other structures - Cytoskeletal fibers are tiny tubes of proteins called microtubulules and microfilaments They act as the "rail road tracks" where organelles and vesicles are pulled The different protein composition plays a role in the specific functionality of these cytoskeleton fibers

Kingdom Fungi

-Feeds heterotrophically on the remains of dead plants and animals - Does not perform photosynthesis -Fungi cells do not have cilia or flagella, there cell wall is not made out of cellulose but chitin - Fungi have a simple unicellular body form made up of long threads (hyphae) which may not have cross walls

Salicylic acid (Phenolics - Secondary metabolites)

-Keeps plants from getting sick - mediates specific protein production during metabolic function - protection from specific pathogens through mediating responses by protein production - keeps metabolic process going when fighting pathogens, such as photosynthesis or transpiration Ethnobotany Ex. - We use salicylic acid as it has painkilling properties (analgesic properties) Ancient greeks and Native Americans brewed tea from willow bark - today we take it in the form of aspirin

Photosynthesis carbon fixation

After the plant transformed photon energies into biologically usable forms, the resulting molecules ATPs and NADPHs are used to drive the production export of carbohydrates These reactions are the carbon fixation reactions (calvin cycle)

Lipids - Primary Metabolite

1) Fats, oils, and waxes - Lipids are an important component of the bilayer membrane - therefore all cells rely on lipids - play critical roles in water maintenance as plants rely on water management systems in order to maintain physical structure and metabolic health - Lipids have hydrophilic (water loving) head and hydrophobic (water repelling) tails - Lipids work to waterproof areas of plants to maintain structure and to keep the metabolic process requiring water to stay active Cutin and Suberin are two examples of lipids that water-proof plants by forming layers over and between cell walls A plant cuticle is a waxy layer made of cutins Ethnobotany example we use lipids as waxes to protect our floors or in products Corks are made of dead cells made of suberin - waterproof cork is used in sustainable flooring - seeds contain large amounts of lipids which are used as long term energy storage - while an abundance of energy can be gained from lipids, it costs more to release energy from lipids than it does to release energy from carbohydrates 2) Phytosterols (plant steroids) - function to stabilize a plants structure - such as the components of the cell membrane Sitosterol: most abundant plant steroid in green algae and plants - some act as hormones like to control the length of stems

Functions of the cell wall

1. Strengthens cell, tissue, and the plant body (makes up majority of a plant's body mass) 2. Influences individual cell shape (not all plant cells are the same shape) 3. support protoplast (living contents of the cell) in response to changes osmotic stresses 4. allows for the movement of water and other solutes through the permeable membrane structure (permeability allows for the distribution and circulation of H2O) *not selectively-permable like the cell membrane*

5 benefits of trees

1. Tree's produce oxygen as a by-product of photosynthesis 2. Trees reduce pollutants by absorbing them along with CO2 and converting them to non-harmful compounds after biochemical processes 3. Trees prevent humid haze by giving off water vapor which will trigger heavy air molecules to rise and become clouds so that a proper cycle can continue 4. Trees prevent dust storms as they hold the soil to the ground and make the soil moist, preventing the wind from blowing dust 5. Tree's act as natural air purifiers

Plasma membrane

A selectively-permeable phospholipid bilayer forming the boundary of the cells which contain proteins, carbohydrates, and lipids on its surface *Plants have integral membrane proteins which are embedded in the phospholipid bilayer* - These are transportation molecules which allow for the transport of specific molecules - this can give certain advantages to plants growing in different environments Ex. insectivorous plants who grow in low nitrogen rich soil will capture and digest insects using a tube with sugary water and enzymes This attracts insects as a nitrogen source After the insects are digested and nitrogen is picked up from their cells, the nitrogen goes through the ergastic (non-living) cell wall and gets collected by the integral transporter membrane proteins for nitrogen, allowing the plant to maintain homeostasis Because of the function of these insectivorous plants, they can inhabit locations low in nitrogen rich soil that most other plants can't

Carotenoids (Carotenes and Xanthophylls) Accessory pigments

About 600 different forms of carotenoids which range from a variety of different colors yellows, oranges, browns, and reds Plants, algae, and bacteria may have carotenoids Plants have carotenoids in their chloroplasts and also chromoplasts (any color except green) 2 most common types of carotenoids 1. Carotenes - some shade of orange 2. xanthophylls - some shades of yellow Carotenoids expand the energy (light) absorption range of plants by capturing wavelengths in the turquoise range Picking up the blue range wavelengths that chlorophyll a and b can't absorb Function When in CHLOROPLAST ONLY, carotenoids function to capture solar energy (collect light) and participate in the passage of energy to chlorophyll a Photo protection - carotenoids regulate energy transfer and are anti-oxidants meaning they prevent damage to chlorophyll a molecules Ethnobotany - like animals, plants need vitamins to stay healthy, such as vitamin A beta-carotene is a precursor for making vitamin a plants can make beta-carotene while humans can't

Photosystems

After plants capture solar energy, they need to manage it, transform it, and store it in the bonds of organic molecules. This process of transforming energy and storing it is done in the photosystems Photosystems are discrete physical locations embedded in the thylakoid membrane They are composed of discrete physical grouping, such as - pigment molecules - electron acceptor molecules - proteins Photosystems have 2 regions 1. Light harvesting complex - where accessory pigments capture, collect and transfer photon energy to the other distinct region called the reaction center 2. reaction center - where the primary photosynthetic pigment (chlorophyll a) is located There are two molecules of chlorophyll a here along with numerous proteins in the reaction center This is where the light processing chemical reactions of photosynthesis occur How the energy transfer happens Accessory pigments are organized so peripheral pigments capture higher energy shorter wavelengths than those near the center energy is passed in vectorial fashion towards the reaction center The energy transfer is accomplished using Resonance The excited electron energy migrates from one molecules to the next from higher to lower successive energy states

Terpenoids - Secondary metabolites

All based on isoprene units ex: isoprene - creates the blue haze in mountain regions which prevent trees from overheating Terpenoids are components of pigments (colored organic compounds), which create certain colors in molecules They also form - membranes - growth regulators - electron carrier molecules Ethnobotany Ex. Rubber - material made from terpenoids harvested from the hevea tree Essential oils - camphor Taxol - medicine used in fighting breast cancer

Alkaloids - Secondary metabolites

All of these molecules are basic in their pH (7<x) (alkaline) These secondary metabolites function as defensive molecules Ethnobotany Ex. Very important to humans Caffeine - produced by plants as a bitter deterrent to herbivores (cocoa) Morphine - highly addictive pain-killer alkaloid found in the fruit of the opium poppy Cocaine - pain killer effects, prohibits altitude sickness (Erythroxylum) Nicotine - pain killer, defensive alkaloid Atropine - Nightshade plant - deadly toxin in low concentration - used in very very small amounts for medicinal properties Use to be used by eye doctors to dilate the pupils of patients

Respiration

Animals RESPIRE while plants PHOTOSYNTHESIS AND RESPIRE

Chromoplast

Any color other than green - These lack chlorophyll but they synthesize carotenoids (yellow, orange, reds) Common in tomato, red pepper, and some flowers like marigolds also responsible for the colors we see in aging leaves

Interphase - Plant Cell Cycle

As nucleus moves to the center of the cell, the large central vacuole must move out of the way The microtubules and motor protein actin help swing the vacuole held by cytoplasmic strands out of the way

3 possible energy alternatives from excited electron

As the energy leaves the excited electron as it falls back to its ground state, there are 3 possible things that can happen to that energy. 1. Fluorescence: The energy slowly leaves the electron as low wavelengths of light (red light) This is examined in lab conditions if we grind up a leaf to break cells and chloroplast membranes and remove only the chlorophyll We can then shine light on the green pigment chlorophyll extract, the photon energy will be captured by the chlorophyll pigment electrons, therefore it comes off as heat and low energy wavelengths (red light) These electrons will then become energized and move to higher orbitals. But they can't maintain their state and fall back to a stable state, the energy leaving the chlorophyll can't be picked up by cellular mechanisms 2. Cellular mechanisms can capture energy from an excited electron as it returns to its ground state using an electron transport system Here, the excited electron is passed from one electron acceptor molecule to the next down a successive chain of molecules As the excited electron moves through each electron acceptor, the energy is captured at each step until the electron reaches it's stable energy state 3. Resonance Energy transfer The energy from an excited electron moves from one molecule to the next, based on the amount of energy successive molecules can capture (the electron doesn't move, just it's energy) Along with the electron transport system, this plays an essential role in energy management in the photosynthetic process

Oxygen

By product of photosynthesis which is given off to the atmosphere and oceans this is responsible for the present day 21% oxygen levels in the atmosphere Photosynthetic organism pull carbon dioxide out of the atmosphere and use it to produce the carbohydrate which all eukaryotes rely on for cellular energy O2 is required for specific metabolic needs (i.e. cellular respiration) Cellular respiration requires oxygen in order to release ATP from food so cells can do work and the organism lives

Cytokinesis - Plant Cell Cycle

Cell plate forms at this stage It starts forming at the center of the cell along the equatorial plate Perpendicular (vertical) Microtubules direct the Golgi vesicles during cytokinesis to deliver the parts necessary for a cell wall and membrane Perpendicular microtubules - Phragmoplast Its orientation is an evolutionary difference when compared with photosynthetic protists, animals, and fungal cells It is crucial for the plant cell wall/ cell plate to before as it ensures the division between the daughter nuclei *ensuring that each daughter cell will have one nucleus in each cell*

Centrioles ABSENT IN PLANT CELLS BESIDES MOTILE SPERM CELLS

Centrioles are absent in plant cells The only plant cells that have centrioles are the sex cells of the plant (modal sperm cell) The centrioles of the plant sperm cell anchor the flagella in place In n

Types of Plastids

Chloroplast (green color) Chromoplasts (any color other than green) Leucoplast (no color at all) - Amyloplast -Elaioplast - Proteinoplast

Chloroplast amino acid building - Chemical Reduction Reactions

Chloroplast modify sulfer and nitrogen compounds to form specific amino acids Amino acids such as Methionine Cysteine Glutamine Aspartic acid These amino acids have many life sustaining functions such as creating chlorophyll, a necessary pigment for photosynthesis As well as anthocyanins which act as sunscreen for plants

Primary cell wall

EVERY single cell will always have a primary cell wall - this is the wall created when cells are grown and accompanies cell growth The cube shaped cells have to enlarge and differentiate after mitosis/cytokinesis and have to be stretchy - Made up of cellulose, hemicellulose, and pectin - Unlike secondary cell walls, primary cell walls exhibit great flexibility, therefore have a higher concentration of pectin (flexible substances) compared with hemicellulose (strengthening substance) More pectin, the more flexible the cell wall To further enhance flexibility, cellulose fibrils are laid down in a random fashion

Intercellular spaces

Each body of living cells need a supply of atmospheric gasses and water vapor in order to run life supporting biochemical reactions There for there are cells that lack middle lamella (usually at the junction where 3 or 4 cell corners meet) These gaps are intercellular spaces Functions: Act as aeration - exchanges of gases and water vapor Acts as passive transport

Pigments absorbing and reflecting light

Each type of pigment has it's own absorption spectrum = wavelength pattern absorbed by a specific pigment This means a given type of pigment is only capable of absorbing a specific range of wavelengths within the visible light spectrum With one. range of wavelengths being absorbed by the pigment, other wavelengths are reflected from the molecule Each pigment type has a specific color based on the wavelength it absorbs vs. those it reflects We see the reflected wavelengths as color, NOT the color of the wavelength absorbed Ex. We see the color red because red wavelengths of light are reflected not absorbed We see the color black when all wavelengths of light are absorbed We see white when all wavelengths of light are reflected In green plants, the green wavelength is reflected while others are absorbed giving off the green color

Reaction center (photosynthesis process)

Energy reaches the reaction center through resonance energy transfer of one excited electron to another The reaction center is a pigment protein complex where pure energy of an excited state electron is transformed The chemical environment gives it two special chlorophyll a molecules - they have the ability to use photon energy for photochemical reaction

Collenchyma - Plant cell type

Found in only some tissues of some plant bodies These cells are alive at maturity and only have primary cell walls However, the cell wall is unevenly thickened, a key indicator of a collenchyma cell Function: BOTH strength and flexibility is then applied to the tissue Ex. These types of cells are located on the petiole (which attaches a leaf to a stem) This is responsible for holding the leaf out in the air to capture sunlight The breeze can snap the petiole it the construction is too rigid, therefore it needs to sway but be strong enough to hold the leaf level Collenchyma cells accomplish this by being both flexible and strong

Proteins (Non-cellulose intermatrix)

Glycoproteins (proteins covalently attached to carbohydrates)

Proteins - Primary Metabolite

Have structural functions - Linear polymers (long chains) of amino acids Proteins act as metabolites for structural functions - Protein acts as long term storage energy within plant seeds

Chloroplast

Identified by their green color Like all plastids, they are bound by two membranes Internally they are traversed by a network of membranes that form into flattened sacs called thylakoids Stacks of thylakoids are known as Grana (Granum) These Grana contain green colored chlorophyll pigments and other photosynthetic molecules Everything inside the chloroplast except for the thylakoid system is called the stroma DNA, RNA, and other essential ribosomes are located within the stroma The stroma can often contain starch grains and oils Functions: Chloroplasts are the main sites for photosynthesis (solar energy being converted into chemical energy "food") Chloroplasts are also involved in Chemical Reduction Reactions through amino acid building

Preprophase Band - Plant Cell Cycle

Just before prophase, there is a narrow band of microtubules which form around the equator of the cell This band is the preprophase band - this marks the area where the cell wall will eventually form - This disappears after the formation of mitotic spindle

Central Vacuole

Large, fluid-filled sac (90% of cell volume) - This is a single membrane bound, fluid organelle that is translucent - Various ions are within the central vacuole H2O, Ca2+, K+, Cl-, Na+, Due to the ions, the vacuole becomes acidic and in some cases very acidic, such as citrus fruits Some cells have water soluble pigments which impart color Ex. - If u cook red beets, the dark red pigment in the vacuole will break down and seep out into the cooking water Sugars are also stored within the vacuoles Vacuoles can also be used as defense compounds They contain bitter secondary metabolites, such as tannins which can kill certain animals if ingested Crystals also exist as a form of physical protection inside the vacuole Function: Vacuoles maintain turgor pressure (water pressure within a cell) and the entire plant body If the vacuole loses H2O the plant wilts as plants do not have a skeletal structure, they will rely on the tugor pressure to maintain their structure and posture Vacuoles operate as storage for primary and secondary metabolites, old worn out organelles, and macromolecules Vacuoles break down old organelles and macromolecules and recycles the material it can use to support homeostasis processes It stores these products in forms non-toxic to the plant Remove toxic secondary metabolites from the cytoplasm Vacuoles store unwanted material in the forms of crystals which is the result of the trash compaction system

Leucoplasts

Leuco means white These plastids have no color at all but are distinguished from each other depending on what they store Ex. Amyloplast, Elaioplast, and Proteinoplast Amyloplast - synthesize and store starch in non photosynthetic organs (potatoes that grow in the ground and don't get sunlight) Lugol solution - detects starches turns blue Elaioplast - synthesize and store oils (avocados) Proteinoplast - synthesize and store proteins

Photons

Light energy from outer space energy travels to the earth in small discrete amounts called photons "packet of energy" Each photon carries a fixed amount of radiant energy *not every photon has the same amount of energy* The energy in the photon will vibrate and oscillate to make waves, we measure this movement of a given amount of energy from a photon as a wavelength wavelength is the distances moved by.a photon during one complete vibration, measured by the crest of one wave to the crest of another. This distance in meters designates the amount of energy as a wavelength The amount of energy that a photon carries is inversely proportional to its wavelength longer the wavelength (more distance between crests) = the less photon energy shorter the wavelength (less distance between crests) = the greater amount of energy the photon has

Microfilaments - Cytoskeleton Fiber

Made up of two intertwined strands of actin

Problem of photorespiration

On hot, dry days, plants are forced to use mechanisms to slow down excess water loss from their bodies This process stops CO2 from entering the plants body CO2 levels drop, flipping the ratio of CO2 to O2 - due to photosynthesis uses up the CO2 at a rapid rate Rubisco still does it job of connecting carbon from carbon dioxide to RuBP even when CO2 runs out When it is short of CO2, it switches to connect oxygen to RuBP instead of carbon This however creates a compound that is toxic to the plant Instead of producing 2 PGA molecules, only 1 PGA is produced plus a toxic 2-C molecule (phosphoglycolate) For survival, the plant needs to use up valuable energy to neutralize the toxic chemical It must get rid of the phosphoglycolate converted to glycolic acid (removing the phosphate group) It is converted to glycine in the peroxisome, then serine in the mitochondria, and then eventually other molecules (conversions cost energy and result in a net energy loss)

Primary metabolites

Organic molecules which are required to sustain life and are found in EVERY single living cell of the plant's body - nucleic acids - carbohydrates - proteins (amino acids) - lipids and fats Compounds which form the general structure and shape of a plant such as proteins, sugars, and polysaccharides, supports the plant as it starts to grow. Both primary and secondary metabolites function synergistically Meaning they produce more than one effect by working together

Ozone layer

Oxygen is also required for the production of OZONE this shields the Earth from harmful UV radiation from the sun These rays can cause cellular mutations that often lead to cancer and death Without oxygen or the ozone layer, no life can exist in terrestrial environments

What benefit does oxygen have for the atmosphere? (hint: O3)

Oxygen is released to produce the Ozone layer which protects Earth from harmful UV radiation

Pectin (Non-cellulose intermatrix)

Pectin is what fills the gaps between cellulose fibrils and the hemicellulose bridges - Hydrophilic polysaccharide - water loving material - Pectin combines with Calcium ions and Water to from a jelly like matrix Pectin + Ca2 + H2O = Jelly like matrix (we use pectin to make jelly candy) Pectin acts to make the cell wall flexible Higher concentration of pectin vs. hemicellulose = more flexibility Higher concentration of hemicellulose vs. pectin = less flexibility During cytokinesis, the young cell will have its shape and size determined by the composition of the cell wall

Photosystem I (Energy transduction reactions)

Photons strike the light harvesting region energy is captured by accessory pigments transfered to the reaction center of photosystem I The photosystem I chlorophyll a molecules then become energized - boosting the electrons off of the chlorophyll a The chlorophyll a molecules are now positively charged and needs electrons The lost electrons are replaced with the electrons that have went through the electron transport chain from photosystem II With the low energy stable electrons sent through the electron transport chain from Photosystem II, the chlorophyll a molecules in photosystem I are now stabilized The chlorophyll a electrons that LEFT photosystem I are sent to the final electron transport chain As they move down the chain, their removed energy is used to reduce NADP to NADPH

Nucleic Acids - Primary Metabolite

Storage and expression of genetic information - same in all eukaryotic cells

Carbohydrates - Primary Metabolite

Sugars and chains of sugars that are burned by the cell in order to produce energy - energy that is stored in the bonds of carbohydrates is releases as the bonds are chemically broken then converted into ATP used for cellular functions

Composition of cell wall

The architecture of the cell wall allows it to perform it's crucial functions for the plant - The cell wall is made up of a cellulose framework (cable-like structure that forms fibrils and microfibrils) - The cellulose cables are connected through a non-cellulose crosslink matrix (these are the in between spaces between the cellulose framework)

Light: The Electromagnetic spectrum

The electromagnetic spectrum: the entire range of radiation(light) that reaches the Earth from outer-space The electromagnetic spectrum travels in waves Frequency describes how many waves per second a wavelength produces Longest wave with lowest frequency - radio waves

electron transport chain (Energy transduction reactions)

The energized chlorophyll a electrons that leave photosystem II into the electron transport system (connects the 2 photosystem complexes together) The excited electron is then passed through the electron transport chain one after the other - with energy removed at each step Most of the removed energy is packaged in ATP molecules - a process called phtotophosphorylation This uses an enzyme complex, as well, as an electrochemical gradient As protons are driven from the thylakoid lumen through the ATP synthase enzyme complex to the stroma by the electrochemical gradient The phosphate is added to ADP molecules and the energy is stored as ATP

photosynthetic pigments

The energy wavelengths involved in the photosynthetic process are captured in a plant's cellular pigments All of these pigments are embedded in the plants thylakoid membranes of the chloroplasts

The visible light spectrum

The human eye is able to detect certain wavelengths of light Specifically photons with wavelengths ranging between 380 to 750 nanometers (the visible light spectrum) (We see these as the colors of the rainbow which are a range of long through short wavelengths) Red 700 nm orange 620 nm yellow 580 nm green 530 nm blue 475 nm violet 400 nm The visible light spectrum comprises about 1% of all the total light (electromagnetic radiation) that reaches the Earth Red wavelengths have the lowest frequencies and the longest wavelengths of visible light As you move from Red to violet, the wavelengths shorten and the frequency increases

Metabolism

The life of a cell, therefore an entire organism, is sustained by metabolism Metabolism = sum of all biochemical reactions within a cell The two metabolic processes that manipulate energy in plants to perform life sustaining functions is ' Photosynthesis and cellular respiration

Middle Lamella

The middle lamella is the region between the primary cell wall of two adjcent plant cells The cementing agent is made up of highly hydrated pectins (allows for flexibility) with calcium or magnesium as a firming agent Sometimes in regions where water management is an issue lignin is added for waterproofing

The 2 photosystems

The thylakoid membranes have a multitude of photosystems embedded within them with all thylakoids working simultaneously However two photosystems must work in one after the other in order for the photosynthetic reactions to be successful photosystem 2 comes BEFORE photosystem 1 both connected by an electron transport system Differences PS II and PS I differ based on the sources of their low energy electron supply and to where they deliver their electrons

The cell wall

The outer most layer of a plant cell - Ergastic (non-living structure) which is external to the plasma membrane, creating a barrier between the plasma membrane and the outside environment or adjacent cells Plants use dead cells for many important functions and even genetically program some cells to die at maturity to serve as functional units

Starch - polysaccharide

The principle form of carbohydrates in ANIMALS is glycogen Instead of glycogen, PLANTS store their carbohydrates in STARCH Specifically alpha 1,4 glucan (amylose starch) - Type of polysaccharide - This is how plants store their carbohydrates - This is a long chained molecules which tend to form concentric rings, so as more starches form they build on top of one another forming starch grains - Glucose monosaccharide units which are joined by glycoside bonds - We can test for starch using Lugol solution, it will test dark blue or purple if tested positive for starches

G3P

The true end product of photosynthesis is G3P (not glucose) G3P is a versatile carbohydrate and it can readily, with very little energy cost to the plant, can be chemically rearranged into whatever carbohydrate the plant needs at a given time Some G3P is regenerated into RuBP so the cycle can be repeated Some G3P can be rearranged into fructose or glucose for quick energy that the cell can do it's daily work If the cell has enough energy to complete it's metabolic duties, it will store the extra G3P as starch grains - right where it makes it in the chloroplast stroma Non-photosynthetic parts of the plant also need energy to stay alive, so G3P must be exported to these sites The exported form of carbohydrates is sucrose, so some G3P must be rearranged to sucrose before transport

Sclerenchyma - Plant cell type

These are found in only SOME tissues of some plant bodies - specifically in organs that provide strength and support for the plant (bamboo likely has sclerenchyma to support it's upright structure) Function: mechanical support - supports the plant body In order to lend mechanical support, they must be strong and light weight Sclerenchyma will often have a primary and an evenly thickened often lignified secondary cell wall - the second cell wall has lignin to impart rigidity and strength Sclerenchyma cells are dead at maturity and hollow in the center (no living cytoplasm) allowing the cell to be very light weight SPECIALIZED SCLERENCHYMA CELLS Fibers are extremely long sclerenchyma cells which can reach 1m long They increase the mechanical support by bundling and lending strength, hardness and rigidity to tissue/organ Sclereids are irregular in shape and occur singly or in groups Some are shaped like stones, tooth-like, or heart shaped (found in pears, numerous groups of sclereids called stem cells) Functions: mechanical support and herbivore deterrents

Non-cellulose cross-linked matrix

These are molecules which surround cellulose fibrils and connect them to one another so they don't float around 3 interconnecting matrix molecules molecules: Hemicellulose - most functionally critical Pectin - most functionally critical Glycoproteins

Brypohytes

These are plants who have a gametophyte dominant life cycle which are grouped together Oldest known plants on the planet, first successful group of plants to colonize the land Bryophytes are grouped within three phylum (3 different lineages) 1. Phyla Marchantiophyta (liverworts) 2. Phyla Anthocerotophyta (hornworts) 3. Phyla Bryophyta (mosses) All gametophyte dominant with an alternation of generations life cycle - The sporophyte part of a gametophyte dominant plant's life cycle is ephemeral (short lived) The short lived sporophyte grows attached and dependent upon the long-lived gametophyte individual No sporophyte is capable of producing enough photosynthetic products (G3P) to support itself nutritionally, so for the entire life cycle, until the sporophyte plant produces and disperses spores, it relies on the gametophyte to provide nutrition All bryophytes are very small (3-6 mm average) Largest is a moss 60cm tall located in New Zealand

Photosynthesis and cellular respiration cycle

These metabolic processes work together Products of photosynthesis (Food molecules and oxygen) Are the requirements for the chemical reactions of cellular respiration The by-products of cellular respiration (CO2 and H2O) Are required to run photosynthetic processes These two processes sustain and process the biosphere (living ecosystem of Earth)

Photosystem II (Energy transduction reactions)

These reactions occur within photosystems 2 and I embedded in the thylakoid membranes inside the chloroplast Photosystem II functions first - Photons are captured by the accessory pigments of the light harvesting region - Electrons become energized and due to resonance energy, the photon energy is transferred to chlorophyll a in the reaction center ( 2 chlorophyll a molecules in reaction center do the same thing) The transfered energy energizes the chlorophyll a electrons, this excites them so much that they leave the chlorophyll a molecule This excited electron gets picked up by the electron transport chain which connects photosystem 2 and photosystem 1 The loss of 2 electrons leaves each of the 2 chlorophyll a molecule oxidized and positively charged, this means it is unstable and can not leave again without being stabilized The lost electrons are replaced through a process called photolysis (light to split) Light is used to split water and remove it's electrons The 4 electrons from water then replace the lost photosystem II electrons 4 protons are pumped across the thylakoid membrane to set up a chemiosmotic gradient (cellular battery) and 1 molecule of Oxygen is releases into the atmosphere The energized chlorophyll a electrons that leave photosystem II into the electron transport system (connects the 2 photosystem complexes together) PRODUCTS OF PSII ATP has been produces Water is split Oxygen is given off as a byproduct

Hemicellulose (Non-cellulose intermatrix)

This is a polysaccharide (multiple sugars) - Hemicellulose establishes the 3D network of the cell wall by bridging fibrils together Hemicellulose connects the cellulose fibrils together in a relatively rigid manner - adds strength and rigidity to a cell wall this means the amount of hemicellulose in a cell wall will affect how much the cell is able to grow, since it regulates how stretchy the cell wall will be

Parenchyma - Plant cell type

This is found in every plant body - basic ground tissue - makes up all or most of the plant body - Living, active cells with a thin primary cell wall - If you see a cell with a nucleus and other organelles, it is a Parenchyma cell - Multiple Parenchyma cells form Parenchyma tissue - Because of the thin primary cell wall, the cells are loosely packed causing intercellular space - Because parenchyma cells contain living organelles, they carry out the required metabolic activity Functions: Basic metabolic activities - Photosynthesis occurs in parenchyma cells - growth of the plant body also relies on these cells as they are the ONLY cell type capable of undergoing mitosis - Storage of starch grains and lipids

Microtubule Organizing Centers (MTOC) - Plant Cell Cycle

This organize the mitotic spindle in plant cells *remember there are no centrioles in regular plant cells*

Microtubules - Cytoskeleton Fiber

Tube like structures in the endomembrane system which are made of a protein called tubulin.

Photosynthetic process

Two sets of chemical reactions that make up the photosynthetic process 1. energy transduction reactions Photosystems 2 and 1 are the sites of the energy transduction reactions (absorption and management of photon energy) 2. carbon fixation reactions The energy derived from the carbon fixation reactions is then used to drive the carbon fixation reactions These are the biochemical reactions which make the carbohydrate ( the storing of the transformed energy into the bonds of an organic molecule that is usable by the cell)

Cellulose - polysaccharide

Type of polysaccharide - is a product of many glucose molecules bonded together (UDP glucose) - Cellulose is the principle component of the cell wall Gives cell wall form and strength - provides mechanical strength - protection from decay (enzymes to break down starch and glycogen) - protection from harmful microbes and insects (however termites have a special enzyme that can break down cellulose) *Most abundant organic compound on Earth* 50% of all organic carbon on Earth is in cellulose Ethnobotany We use cellulose in many things such as wood, paper, textiles, cotton, etc.

End result of Energy transduction reactions

Unidirectional electron flow from H2O to NADPH results in 6 ATP and 6 NADPH for every 6 electrons These are used to run the reactions of the carbon fixation reactions The reactions then perform energy transformation to drive the biochemical reaction of the carbon cycle Summary of events Light energy used to from ATP from ADP Photolysis (splitting) of H2O Reduced electron carrier molecule (NADP+ to NADPH) ATP and NADPH used to provide energy for driving biosynthetic carbon-fixation pathways

Pigments and visible light

Visible light photons carry the correct amount of energy to excite electrons of organic molecules capable of absorbing light energy These special organic molecules are called pigments

Pigment molecule gets excited

When pigment molecules absorbs photons, the energy carried by the photon temporarily energizes the electrons of the pigment molecule Photons give energy to the pigment molecule exciting it's electrons This boost the electrons to a higher energy level (energized electrons are in an excited state) The energized electron can not obtain this excited state As the absorbed energy is given off from the electron, the electron returns to the ground state (stable state)

Carbon-Fixation reaction (Calvin Cycle)

only known biological pathway used to produce carbohydrates from CO2 These reactions occur in the chloroplast stroma (regions around the thylakoid) While the energy transduction reactions occur in the thylakoid membrane (discovered in 1961 by Dr. Melvin Calvin) ATP and NADPH drive the carbon fixation reactions to build a carbon based molecule called G3P this carbohydrate is the molecule from which other molecules like simple sugars are then reduced The Calvin cycle begins and ends with RuBP (ribulose 1,5- bisphosphate) RuBP is a simple 5 carbon sugar that is always available in the stroma (always available because its regenerated at the end of the Calvin cycle RuBP is the sugar to which the carbon from carbon dioxide gets attached the carbon dioxide enters the plant in different ways depending on the type of plant Once the CO2 is inside the plant, it diffuses into the cell and into the chloroplast The carbon from the carbon dioxide is then attacked to RuBP using the enzyme rubisco rubisco is arguably the most important enzyme on Earth The addition of carbon to RuBP produces a highly unstable 6 carbon compound that immediately breaks in half - forming two three carbon molecules called PGA PGA is then ultimately reduced to the carbohydrate Glyceraldehyde 3 Phosphate (G3P) through a series of biochemical reactions ATP and NADPH are required for the formation of G3P and its chemical rearrangement into other sugars The end product of photosynthesis is G3P (not glucose)

Plant Cell Types

parenchyma, sclerenchyma, collenchyma (enchyma = primitive liquid which nourishes living tissue) In order to determine the function and identification of cell types, check to see 1. If the cell is alive (does it contain living material) or is it dead at maturity 2. If the cell has only a primary cell wall or both a primary and secondary wall primary cell walls = thin, flexible, relatively porous Secondary cell walls - thick, rigid, often lignified, non porous and water proof Dyes and stains Primary walls will stain blue or blue green Secondary walls will stain red or pink

Photosynthesis

the only way solar energy enters the biosphere as usable, cellular energy (besides a few prokaryotes that are able to process cellular energy using elements like sulfur) Photosynthesis takes the energy of the sun and converts it into chemical energy (food) All living things require this solar energy to make their food (except for chemotropic prokaryotes which are able to use energy bonded in chemical elements to make their food) Maintains balance of Earth's systems Throughout geological time, the entrance, transfer, and manipulation of energy from the sun transformed the planet to allow complex life to become possible This energy now supports our ecosystem At the core, the photosynthetic process is powered by light this light needs to be captured by organic molecules within plant cells

Atmospheric CO2

these are maintained in balance as Photosynthesis removes carbon dioxide and uses it to make chemical energy (food) The Earth relies on the balanced carbon cycle Greenhouse effect Carbon dioxide maintains warmth on Earth The atmospheric carbon dioxide layer functions as the windows of a green house This allows high energy solar rays to escape while bouncing others between the Earths surface and the carbon dioxide layer Thus allowing warm temperatures allowing things to survive on Earth Because of human activity, excess CO2 is sent into the atmosphere causing the CO2 layer to thicken and prevents solar energy from going back into the atmosphere This causes the temperature to increase Climate This is weather overtime Climate changes is directly associated with temperature change Can cause damaging effects such as rise in ocean levels and changes in ocean circulation If the temperature rises to 2ºC above the preindustrial temperature average, the effects will be catastrophic Coral reefs wiped out 10% extinction of Earth's plants and animals Up to 1.5 month increase in heatwaves