LESSON 1: Introduction to Botany
Levels of Biological Organization (AMMOC–TOOP–CEB)
•
•
•
•
•
•
•
•
•
•
•
•
Botany
•
•
Study of plants
Also called plant biology
Subdisciplines of Botany
1. Plant molecular
biology
•
•
2. Plant cell
biology
•
•
3. Plant physiology
•
•
Structure and functions of biological
molecules (e.g. proteins, nucleic acids like
DNA and RNA)
Genome information and how it's seen in
structures, processes, and behavior
Plant cells' structures, functions, and life
processes (macro level)
Plant cells' structure, growth, division,
signaling, differentiation, and death
•
Plant heredity and variation
5. Plant ecology
•
Interrelationships
§ Among plants
§ Between plants and their
environment
Plants' distribution and abundance
Plants' interactions with the biotic and
abiotic environment
§ Abiotic – Non-living
§ Biotic – Living
•
•
Characteristics of Living Things (OU–IGR-HE)
1.
2.
3.
4.
5.
6.
7.
Plants' function (e.g. photosynthesis,
mineral nutrition)
Physical, chemical, and biological
functioning of plants
4. Plant genetics
Atoms
Molecules
Macromolecules
Organelle
Cell (Smallest unit of life)
Tissue
Organ
Organism
Population (Same species)
Community (Different species, same area)
Ecosystem (Abiotic and biotic)
Biosphere
Organization – cells are the basic building block
Use of Energy
Interaction with Environment – responding to stimuli
Growth and Development
Reproduction
Heredity – transmit genetic information
Evolution – change or adapt to survive changing
environments
Three Domains
1. Bacteria
2. Archaea
3. Eukarya
Six Kingdoms
Kingdoms are broad taxonomic categories of related phyla
1. Bacteria
2. Archaea
3. Protista
4. Plantae
5. Animalia
Page 1 of 13
6. Fungi
Domain Kingdom
Bacteria Bacteria
Food and Energy
Other Notes
Mostly heterotrophic
Some photosynthetic
or chemosynthetic
–
Archaea Archaea
Eukarya
–
Protozoa, algae,
slime molds
Plantae
Photosynthetic
Cell walls of cellulose
Heterotrophic or
absorbs nutrients
Predictions can be
tested to determine
if it is true or false
5. Testable
•
Testable through
science processes
and controlled
experimentation
6. Tentative
•
Theories subject to
revision and
correction
Might be proven
wrong
Extreme
environments
Heterotrophic or
photosynthetic
Fungi
•
Cell Type
Prokaryotes Unicellular
Protista
Animalia Heterotrophic
4. Predictable
Either
Muscular contraction Eukaryotes Multicellular
and nervous system
Mostly
multicellular
Cell walls of chitin
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
observational results
are the same
•
Green plants
grow towards a
light source
2. Observable
•
Can be observed and
explained
Limited to basic or
extended senses
•
Some plants
can eat meat
Natural
cause/mechanism
must be used to
explain why or how
the event happens
•
Green plants
convert
sunlight to
energy
•
3. Natural
•
Page 2 of 13
•
•
Chromosomes
were
numbered 48
before, but
now it's 46
LESSON 2.1: Microscopes
Light
microscope
Source
Propertie
s of
Specimen
Focuses a beam
of light through
a sample
Thin
Comparison
Transmission
Scannning
electron
electron
microscope
microscope
Directs a beam of electrons through
the sample
Small enough to
fit in the
chamber of
scope
Ultra thin
Image
Cells
Color, processes, Internal
movement
structure
Alive
Surface features
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
Page 3 of 13
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
Organelles
Cell wall
• Supporting wall
• Rigid but flexible—so that water
can be contained without bursting
Plasma membrane
• Acts as a selective barrier—
passage of materials into and out
of the cell
Plastids
• Occurring in photosynthetic eukaryotic cells
• Chloroplast – contains chlorophyll which absorbs sunlight, and
produces and stores glucose
• Chromoplast – contains carotenoids (red, orange, yellow
pigments); found in flowers and fruits
• These colors attract pollinators and predators
• Leucoplast – no pigment, but stores starch
Mitochondria
• Associated with cellular respiration,
where chemical energy in fuel molecules
is transferred to ATP
Nucleus
• Contains the DNA
Page 4 of 13
Ribosome
• Site of protein synthesis
• Trivia: Not membrane-bound, but
considered an organelle because it has
an important function
Golgi body
• Stack of flattened membranous sacs
• Packaging center; modifies, packages,
and sorts proteins
• These are then sent to the
plasma membrane or other
organelles
Vacuole
• Large, fluid filled, membrane-bound
sac
• Solution of salts, ions, pigments, and
waste materials
• Contains calcium oxalate crystals
which cleanses toxic materials and gives off a bitter taste to
avoid predators
• Nutrient storage, pH balance, cell pressure maintenance
Cytoskeleton
• Composed of microtubules and
microfilaments
• Maintains the cell’s shape
• Helps cells move
• Involved in cell division
Vesicle
•
Cytosol and Cytoplasm
Cytosol
Structure
•
•
•
Function
•
•
Cytoplasm
Gel-like aqueous
•
substance
Mixture of water, ions,
and macromolecules
Produces
concentration
gradients, called as
intracellular fluid
Suspension of
•
organelles
Small-scale processes
like cell signaling
Region enclosed by
the cell membrane
EXCEPT the nucleus
Large-scale processes
like cell divsion
LESSON 2.4: Plant Cells vs. Animal Cells
Plant Cells
only
•
•
•
Plastids
Cell walls
Large vacuoles
Animal Cells
only
•
•
Centrioles
Lysosomes
Both
•
•
•
•
•
•
Transport of proteins and other
cellular materials
Page 5 of 13
Plasma
membrane
Nucleus
mitochondria
Ribosomes
ER
Golgi apparatus
Cytoskeleton
LESSON 3: Membrane Transport System
•
Structure of the Cell Membrane
The Fluid Mosaic Model
• Fluid refers to the flexible movement of the phospholipids
(they move around)
• Mosaic refers to the arrangement of many pieces of
phospholipids and protein
There are also proteins in the phospholipid bilayer.
Peripheral Proteins
Integral Proteins
o Peripheral area of the
• Passes through the
membrane (on the
phospholipid bilayer
surface)
• Often involved in
o Often involved as
transport
enzymes or receptors
Cell Transport
Transport
The Phospholipid Bilayer
Passive
Simple 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
Page 6 of 13
Active
Facilitated Diffusion
Simple Diffusion
• Movement: High Concentration to Low Concentration
• Substances travels down its concentration gradient across the
phospholipid bilayer
• Involves small and non-polar solutes (because the interior
region of the membrane is the non-polar tails)
o Examples are oxygen and carbon dioxide
Active Transport
• Requires energy (from ATP)
• Movement: Low Concentration to High Concentration
Sodium-Potassium Pump
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
• Passive movement of water through a selectively permeable
membrane
State of a Plant Cell in Different Solutions
Hypotonic
Isotonic
Solution
Solution
•
Hypertonic
Solution
Image
Outside
Cell
Inside
Cell
High Water
Potential
Low Water
Potential
Similar Water
Potentials
•
Low Water
Potential
High Water
Potential
Page 7 of 13
In summary, energy in the form of ATP releases one
phosphate. This phosphate attaches to the membrane
protein; the energy allows the protein to change shape. The
protein then allows the substance to pass through.
When phosphate detaches from the membrane, the protein
channel reverts to its original form, releasing the substance
into the inside of the membrane.
LESSON 4: Photosynthesis
Light Upon Hitting Atom
Four Important Requirements
1.
2.
3.
4.
Sunlight
Carbon dioxide
Water
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
Chlorophyll a
Main pigment, most Violet to blue light
abundant
and orange to farred
Chlorophyll b
Expands the
Violet blue to green
absorption spectrum blue and yellow to
red
Carotenoids
Shields cell from
Blue to green
excessive light,
antioxidative
•
Leaf
Mesophyll Tissue
Chloroplast
Thylakoid
Photosystem
Chlorophyll
During fall, chlorophyll a & b disintegrate while carotenoids
remain strong. This is why leaves in this season appear red or
orange.
Page 8 of 13
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
Guard cells are considered parenchymal cells
•
•
The Chloroplast
The stromal lamellae connects one stack of granum to
another
The light-independent reaction occurs in the stroma. The ATP
synthase will have a role in this one.
The Photosystem
Page 9 of 13
The Chlorophyll
• Light-trapping green pigments
• What really captures the light is the
magnesium ion, the center of the
chlorin ring
• Captures light energy from the sun
and uses it to chemically combine
hydrogen from water with CO2 from
the atmosphere to produced
carbohydrates
5. Ferredoxin brings the electron to the cytochrome b6-f
complex, a proton pump.
6. The electron energizes the complex, which causes the complex
to pump a proton gradient (high concentration of hydrogen)
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
7. Plastocyanin (has copper), another electron carrier, brings the
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.
2.
3.
4.
Light hits Photosystem I, causing the electron to be excited.
The excited electron moves to the primary reaction center.
The electron moves to the primary electron acceptor, quinone
Ferredoxin (has iron), the first electron carrier, takes the
electron—this begins the electron transport chain
Page 10 of 13
1. Light hits Photosystem II, causing the electron to be excited
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.
4. The electron energizes the complex, which causes the complex
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.
The Light-Independent Reaction: The Calvin Cycle
Understanding the Splitting of Water
• When sunlight hits, the H2O
inside the thylakoid is split.
• For every 2 H2O molecules,
the following are produced:
o 4 hydrogen ions
o 2 oxygen atoms,
which will bind to form oxygen gas (will go out through
the stoma)
o 4 electrons
• The enzyme that actually causes the water to split is the
manganese-calcium cluster
Other Notes
• Enzymes (usually ending in the suffix –tase) are usually
meeting places for molecules to bind
Page 11 of 13
1. Carbon Fixation
a. Ribulose biphosphate (RuBP) and carbon dioxide (CO2)
bind with the help of the RuBisCo enzyme to form an
unstable 6 carbon intermediate
b. The unstable 6 carbon intermediate eventually splits to
form two molecules of 3-Phosphoglycerate (3-PGA)
2. Reduction
a. 3-PGA receives an additional phosphate from ATP with
the help of Phosphoglycerate kinase to form 3Biphosphoglycerate
b. A pair of electrons donated from NADPH reduces 3Biphosphoglycerate to form glyceraldehyde 3phosphate (G3P); with the help of G3P dehydrogenase
enzyme
i. Some will exit the cycle to be used by the plant
cell
3. Regeneration
a. Molecules of G3P are rearranged into molecules of
RuBP. To accomplish this, ATP is needed.
b. The cycle continues
•
•
•
•
•
•
85% of plants
C3 is the type of carbon molecule produced in the Carbon
Fixation Stage
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
•
•
•
C3, C4, and CAM Plant Cells
C3 Plant Cells
Page 12 of 13
Mostly monocots (e.g. grasses)
Carbon Fixation occurs in the mesophyll layer
There is an additional bundle sheet—this sheet has
chloroplasts
o The bundle sheet is additional storage for CO2
§ This means that even if the stoma is closed, the
Calvin Cycle can continue
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.
Page 13 of 13