LESSON 1: Introduction to Botany Levels of Biological Organization (AMMOC–TOOP–CEB)

• Atoms
• Molecules
Botany
• Macromolecules
• Study of plants
• Organelle
• Also called plant biology
• Cell (Smallest unit of life)
• Tissue
Subdisciplines of Botany • Organ
1. Plant molecular • Structure and functions of biological • Organism
biology molecules (e.g. proteins, nucleic acids like • Population (Same species)
DNA and RNA) • Community (Different species, same area)
• Genome information and how it's seen in • Ecosystem (Abiotic and biotic)
structures, processes, and behavior • Biosphere

2. Plant cell • Plant cells' structures, functions, and life

Characteristics of Living Things (OU–IGR-HE)
biology processes (macro level)
1. Organization – cells are the basic building block
• Plant cells' structure, growth, division,
2. Use of Energy
signaling, differentiation, and death
3. Interaction with Environment – responding to stimuli
3. Plant physiology • Plants' function (e.g. photosynthesis, 4. Growth and Development
mineral nutrition) 5. Reproduction
• Physical, chemical, and biological 6. Heredity – transmit genetic information
functioning of plants 7. Evolution – change or adapt to survive changing
environments
4. Plant genetics • Plant heredity and variation
5. Plant ecology • Interrelationships Three Domains
§ Among plants 1. Bacteria
§ Between plants and their 2. Archaea
environment 3. Eukarya
• Plants' distribution and abundance
• Plants' interactions with the biotic and Six Kingdoms
abiotic environment Kingdoms are broad taxonomic categories of related phyla
§ Abiotic – Non-living 1. Bacteria
§ Biotic – Living 2. Archaea
3. Protista
4. Plantae
5. Animalia
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 6. Fungi 4. Predictable • Predictions can be
tested to determine
Domain Kingdom Food and Energy Other Notes Cell Type
if it is true or false
Mostly heterotrophic
Bacteria Bacteria Some photosynthetic – 5. Testable • Testable through
or chemosynthetic Prokaryotes Unicellular
science processes
Extreme
Archaea Archaea –
environments and controlled
Heterotrophic or Protozoa, algae, experimentation
Protista Either
photosynthetic slime molds
Plantae Photosynthetic Cell walls of cellulose
6. Tentative • Theories subject to • Chromosomes
Eukarya Muscular contraction Eukaryotes Multicellular
revision and were
Animalia Heterotrophic
and nervous system correction numbered 48
Fungi
Heterotrophic or
Cell walls of chitin
Mostly • Might be proven before, but
absorbs nutrients multicellular wrong now it's 46

Species
• Group of organisms:
• With similar structural and functional characteristics
• That breed only with one another
• With close common ancestry

Criteria of Science (CONP–TT)

1. Consistent • Experimental or • Green plants
observational results grow towards a
are the same light source
2. Observable • Can be observed and • Some plants
explained can eat meat
• Limited to basic or
extended senses
3. Natural • Natural • Green plants
cause/mechanism convert
must be used to sunlight to
explain why or how energy
the event happens

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LESSON 2.1: Microscopes Comparison

Light Transmission Scannning

microscope electron electron
microscope microscope
Source Focuses a beam Directs a beam of electrons through
of light through the sample
a sample
Propertie Thin Small enough to Ultra thin
s of fit in the
Specimen chamber of
scope
Image

Color, processes, Internal Surface features

movement structure
Cells Alive Dead

LESSON 2.2: Eukaryotic and Prokaryotic Cells

Types of Cells
Eukaryotic • Has nucleus
• Has membrane-bound organelles
• "True kernel"
Prokaryotic • Lacks nuclei
• Lacks membrane-bound organelles

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LESSON 2.3: The Plant Cell Nucleolus
• Synthesis of ribosomal RNA

Endoplasmic reticulum
• Interconnected network of internal membranes
• Site of enzymic activity
• Synthesizes membranes such as nuclear envelope
• Smooth ER
• Fat or lipid synthesis
• Rough ER
• Protein synthesis
• Called rough because of the ribosomes

Additional: Nucleus and Rough ER

• They are close to each other because of the central dogma
• DNA to mRNA to amino acids
§ Rough ER will be the site for protein processing

Plastids
Organelles • Occurring in photosynthetic eukaryotic cells
• Chloroplast – contains chlorophyll which absorbs sunlight, and
Cell wall produces and stores glucose
• Supporting wall • Chromoplast – contains carotenoids (red, orange, yellow
• Rigid but flexible—so that water pigments); found in flowers and fruits
can be contained without bursting • These colors attract pollinators and predators
• Leucoplast – no pigment, but stores starch
Plasma membrane
• Acts as a selective barrier— Mitochondria
passage of materials into and out • Associated with cellular respiration,
of the cell where chemical energy in fuel molecules
is transferred to ATP
Nucleus
• Contains the DNA

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Ribosome Cytosol and Cytoplasm
• Site of protein synthesis Cytosol Cytoplasm
• Trivia: Not membrane-bound, but
considered an organelle because it has
an important function
Structure • Gel-like aqueous • Region enclosed by
substance the cell membrane
Golgi body
• Mixture of water, ions, EXCEPT the nucleus
• Stack of flattened membranous sacs
and macromolecules
• Packaging center; modifies, packages,
• Produces
and sorts proteins
concentration
• These are then sent to the
gradients, called as
plasma membrane or other
intracellular fluid
organelles
Function • Suspension of • Large-scale processes
organelles like cell divsion
Vacuole
• Small-scale processes
• Large, fluid filled, membrane-bound
like cell signaling
sac
• Solution of salts, ions, pigments, and
waste materials
• Contains calcium oxalate crystals LESSON 2.4: Plant Cells vs. Animal Cells
which cleanses toxic materials and gives off a bitter taste to
avoid predators Plant Cells Animal Cells Both
• Nutrient storage, pH balance, cell pressure maintenance only only
• Plastids • Centrioles • Plasma
Cytoskeleton
• Cell walls • Lysosomes membrane
• Composed of microtubules and
• Large vacuoles • Nucleus
microfilaments
mitochondria
• Maintains the cell’s shape
• Ribosomes
• Helps cells move
• ER
• Involved in cell division
• Golgi apparatus
• Cytoskeleton
Vesicle
• Transport of proteins and other
cellular materials

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LESSON 3: Membrane Transport System • There are also proteins in the phospholipid bilayer.
Peripheral Proteins Integral Proteins
Structure of the Cell Membrane o Peripheral area of the • Passes through the
membrane (on the phospholipid bilayer
surface) • Often involved in
The Fluid Mosaic Model o Often involved as transport
• Fluid refers to the flexible movement of the phospholipids enzymes or receptors
(they move around)
• Mosaic refers to the arrangement of many pieces of Cell Transport
phospholipids and protein
Transport

The Phospholipid Bilayer

Passive Active

Simple Diffusion Facilitated Diffusion

Osmosis

• A phospholipid has a polar head and a non-polar tail

Polar Head Non-Polar Tail
• Hydrophilic • Hydrophobic
• Phosphate- • Fatty acid
containing chains
o Phosphate
has an
empty
shell—this
means it
can form
bonds

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Simple Diffusion Active Transport
• Movement: High Concentration to Low Concentration • Requires energy (from ATP)
• Substances travels down its concentration gradient across the • Movement: Low Concentration to High Concentration
phospholipid bilayer
• Involves small and non-polar solutes (because the interior Sodium-Potassium Pump
region of the membrane is the non-polar tails)
o Examples are oxygen and carbon dioxide

Facilitated Diffusion
• Same as simple diffusion, but requires a membrane protein
• Involves small, charged or polar solutes (Because the polar
head blocks them)

Osmosis
• Movement: High Water Potential to Low Water Potential
o Note: High Water Potential = Low Solute Concentration
and vice versa
§ Solute = Molecules other than water • In summary, energy in the form of ATP releases one
• Passive movement of water through a selectively permeable phosphate. This phosphate attaches to the membrane
membrane protein; the energy allows the protein to change shape. The
protein then allows the substance to pass through.
State of a Plant Cell in Different Solutions • When phosphate detaches from the membrane, the protein
Hypotonic Isotonic Hypertonic channel reverts to its original form, releasing the substance
Solution Solution Solution into the inside of the membrane.

Image

Outside High Water Low Water

Cell Potential Similar Water Potential
Inside Low Water Potentials High Water
Cell Potential Potential

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LESSON 4: Photosynthesis Light Upon Hitting Atom

Four Important Requirements

1. Sunlight
2. Carbon dioxide
3. Water
4. Chloroplast

The Sun and Light Energy

• Energy is released in waves
• Sunlight is a mixture of many wavelengths, wherein shorter
wavelengths mean higher energy
• Only visible light reaches the earth

The Green Color of Plants

• Plant pigments absorb almost every wavelength except green
o Green is mostly reflected back
o Green is sometimes transmitted
• Only absorbed light is useful for photosynthesis
The Site of Photosynthesis
Photosynthetic Pigments
Pigment Function/Description Light Absorbed Leaf
Chlorophyll a Main pigment, most Violet to blue light
abundant and orange to far- Mesophyll Tissue
red
Chlorophyll b Expands the Violet blue to green Chloroplast
absorption spectrum blue and yellow to
red Thylakoid
Carotenoids Shields cell from Blue to green
Photosystem
excessive light,
antioxidative Chlorophyll

• During fall, chlorophyll a & b disintegrate while carotenoids

remain strong. This is why leaves in this season appear red or
orange.
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The Mesophyll Tissue The Thylakoid

• The palisade mesophyll contains the chloroplasts.

• The spongy mesophyll is for carbon dioxide storage. It has air
spaces—that’s why it’s called spongy
• The stoma is where carbon dioxide and oxygen enters. Only
the lower epidermis has this. In plural, stomata
• The stromal lamellae connects one stack of granum to
• Guard cells are considered parenchymal cells
another
• The light-independent reaction occurs in the stroma. The ATP
The Chloroplast synthase will have a role in this one.

The Photosystem

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The Chlorophyll 5. Ferredoxin brings the electron to the cytochrome b6-f
• Light-trapping green pigments complex, a proton pump.
• What really captures the light is the 6. The electron energizes the complex, which causes the complex
magnesium ion, the center of the to pump a proton gradient (high concentration of hydrogen)
chlorin ring into the lumen.
• Captures light energy from the sun a. These hydrogen ions will then exit through the ATP
and uses it to chemically combine synthase. For every 3 hydrogen, a phosphate is
hydrogen from water with CO2 from attached to ADP, producing ATP
the atmosphere to produced 7. Plastocyanin (has copper), another electron carrier, brings the
carbohydrates electron back to Photosystem I. The cycle repeats when the
less energized electron is energized again.

End of Photosynthesis (Part 1) Noncyclic Electron Transport (hi omg pls tell din if may mali)

The Light-Dependent Reaction

Cyclic Photophosphorylation (omg pls say if may mali)

1. Light hits Photosystem II, causing the electron to be excited

1. Light hits Photosystem I, causing the electron to be excited.
2. The excited electron moves to the primary reaction center.
3. The electron moves to the primary electron acceptor, quinone
4. Ferredoxin (has iron), the first electron carrier, takes the
electron—this begins the electron transport chain
a. This electron does not return to Photosystem II
i. Instead, the electron later on will be from the
splitting of water. The hitting of light causes
water molecules to split. This produces
hydrogen, oxygen, and electrons.
2. The electron goes to the primary reaction center and then to
pheophytin, the primary electron acceptor.
3. Plastoquinone, an electron carrier, brings electron to
cytochrome b6-f complex.

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 4. The electron energizes the complex, which causes the complex The Light-Independent Reaction: The Calvin Cycle
to pump a proton gradient into the lumen.
a. These hydrogen ions will then exit through the ATP
synthase. For every 3 hydrogen, a phosphate is
attached to ADP, producing ATP
5. Plastocyanin, an electron carrier, brings electron from
complex to Photosystem I.
6. Light hits Photosystem I, causing the electron to be excited
and energized once again.
7. The electron moves to the primary electron acceptor,
Chlorophyll a0
8. Ferredoxin, an electron carrier, brings the electron is brought
to the NADP reductase
9. The reductase is energized. The NADP reductase allows NADP+
and H+ to bind together. NADPH is formed.
10. NADPH will then be used in the Calvin Cycle.

Understanding the Splitting of Water

• When sunlight hits, the H2O
inside the thylakoid is split.
• For every 2 H2O molecules, 1. Carbon Fixation
the following are produced: a. Ribulose biphosphate (RuBP) and carbon dioxide (CO2)
o 4 hydrogen ions bind with the help of the RuBisCo enzyme to form an
o 2 oxygen atoms, unstable 6 carbon intermediate
which will bind to form oxygen gas (will go out through b. The unstable 6 carbon intermediate eventually splits to
the stoma) form two molecules of 3-Phosphoglycerate (3-PGA)
o 4 electrons 2. Reduction
• The enzyme that actually causes the water to split is the a. 3-PGA receives an additional phosphate from ATP with
manganese-calcium cluster the help of Phosphoglycerate kinase to form 3-
Biphosphoglycerate
Other Notes b. A pair of electrons donated from NADPH reduces 3-
• Enzymes (usually ending in the suffix –tase) are usually Biphosphoglycerate to form glyceraldehyde 3-
meeting places for molecules to bind phosphate (G3P); with the help of G3P dehydrogenase
enzyme
i. Some will exit the cycle to be used by the plant
cell
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 3. Regeneration • 85% of plants
a. Molecules of G3P are rearranged into molecules of • C3 is the type of carbon molecule produced in the Carbon
RuBP. To accomplish this, ATP is needed. Fixation Stage
b. The cycle continues • Photosynthesis occurs in the mesophyll since chloroplasts are
there
• Carbon dioxide enters and oxygen leaves through the stoma
• During high temperature, the stoma closes. This is to prevent
water from evaporating.

• No CO2 enters when the stoma is closed. However,

photosynthesis continues—causes oxygen to accumulate.
Once CO2 is used up, the Calvin cycle will not continue

C4 Plant Cells

End of Photosynthesis (Part 2) pls say if may mali

• Mostly monocots (e.g. grasses)
C3, C4, and CAM Plant Cells • Carbon Fixation occurs in the mesophyll layer
• There is an additional bundle sheet—this sheet has
C3 Plant Cells chloroplasts
o The bundle sheet is additional storage for CO2
§ This means that even if the stoma is closed, the
Calvin Cycle can continue

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CAM Plant Cells

• The time of photosynthesis changes

o At night time, the stoma is open because it’s not too
hot. The plant has time to collect CO2
o At day, the stoma is closed. Calvin Cycle occurs in the
mesophyll.

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