CHEM 26.

1 (ANALYTICAL CHEMISTRY)

Analytical Chemistry: Introduction

Lab Safety Guidelines

Proper Personal Protective Equipment

- Helps protect people from hazards after a hazard assessment for a specific task
- It includes proper lab attire, gloves, safety glasses, face shields, and lab coats
- PPE depends on the specific hazard present (extreme cold, heat, and radioactivity)
- Minimum PPE:
o Long sleeved shirt, Long pants, Closed-toed shoes
o Flame retardant lab coat or rubber apron
o Tied long hair
o Safety glasses or protective glasses with side shields
o No jewelry
- Gloves
o Chemical compatibility chart – shows various glove’s resistance to various chemicals along with its
breakthrough time
o Chemical resistant gloves - butyl rubber, latex, neoprene, nitrile rubber, polyethylene, polyvinyl alcohol,
and polyvinyl chloride
o Cryogenic gloves – nylon out, polyester in
o Basic heat resistant gloves – cotton
o Advanced “ – nitrile rubber or Kevlar
o Cut and puncture resistant gloves – Kevlar or leather
o Impact resistant gloves – padding: foam or gel
o Leaded rubber gloves (difficult to work with) and Gloves lined with other metals (less protection)
- Face and Ear protection
o Ear protection when exposed to noise above 85 decibels
o Ear plugs and Earmuffs – reduces noise by 15 to 30 decibels; use both when noise exceeds 105 decibels
o Respirator – lung protection to fine airborne particles
o Goggles or full face shield – when there are flying sparks
o Shaded glasses/face shields – uv, infrared

Proper Waste Disposal

- Improper waste disposal can endanger public health and the environment
- A waste management system must be devised before a lab activity
- Waste Management
o Keep waste to a minimum by reducing the scale of operation
o Chemicals used should be substituted with less hazardous chemicals
o Store only what will be used in the near term
o Chemical should be recycled or recovered for reuse
o Alternative methods of disposal should be considered including incineration, treatment, and land
disposal
- Waste collection and Storage
o When managing waste, use appropriate PPE
o Collect and store waste near the point of generation in appropriate containers
o Waste containers must be grounded and labeled properly along with chemical compositions, hazard
warnings, and accumulation start date
o Do not mix incompatible waste types
- Sharps disposal (syringes & needles)
o Must be disposed in proper sharps container
- Glass recycling
o Every laboratory must have a separate bin dedicated to glass
o To clean empty glass bottles, it must be triple rinsed with water and acetone in an alternating way

Lab Emergency Guidelines

- Lab emergencies occur due to poor planning or lack of attention

- Better to be proactive than reactive
o Regular lab inspection and equipment maintenance for prevention
- Chemical spills
o Most common
o Caused by improper handling or storage and careless opening
 o Identify spilled chemicals and amount spilled and refer to the chemical’s safety data sheet for hazard
assessments
o Minor spills - <1 gallon of low-hazard chemicals or <20 mL of hazardous ones
o Major spills - >1 gallon of low-hazard chemicals or >20 mL of hazardous ones
o Wash chemicals off of body and remove affected clothing
- Fire/Explosion
o May occur from overheating, leakage, spillage of flammable chemicals, or gases exposed to excessive
heat, an open flame, or electric sparks in the laboratory
o Stop, drop onto the ground with hands covering the face, and roll to extinguish the fire on a person’s
clothes
o Use a wet towel to cover the mouth and nose if there is heavy smoke.

Types of Fire Types of Extinguisher

Class A (ordinary combustible solids) Water and Foam, Multipurpose Dry Chemical
Class B (flammable liquids) CO2, MDC, DC, Clean agent
Class C (electrical equipment) CO2, MDC, DC, Clean agent
Class D (combustible metals) Dry power
Class K (cooking oil and greases) Wet Chemical

- Personal Injuries
o Electric shock, heat burn, bleeding, or poisoning
o Don't move the injured personnel unless imminent danger is present.
o If an individual has received an electrical shock, do not touch the person with bare hands

Chemical Storage: Categories, Hazards, and Compatibilities

- Chemical storage begins with proper chemical labeling, which identifies the chemical and indicates what
chemical hazards are associated to anyone who handles, uses, stores or transports
- Safety Data Sheets provide detailed information of a chemical and the NFPA 704 diamond symbol
o Blue – degree of health hazard
o Red – flammability hazard
o Yellow – reactivity hazard
o White – special hazard; may contain special symbols indicating type of hazard
o Rates include 0 (no risk) to 4 (severe risk)
- The Hazard Communication Standard, 29 CFR 1910.1200 requires labels to contain the following information:

Product Identifier

Signal word
Pictogram

Hazard Statements

Precautionary Statements

Contact Information

o Names can include alternate names, the CAS number, and the product batch number
o Signal words – to indicate level of hazard: Warning (less severe), Danger (more severe)
o There are four types of precautionary statements: prevention, response, storage, and disposal
- SDS is a 16 section detailed document covering more topics relevant to safety than labels
o 1 – Identification 9 – Physical and chemical properties
o 2 – Hazard identification 10 – Stability and Reactivity
o 3 – Composition/info on content 11 – Toxicological information
o 4 – first aid measures 12 – Ecological information
o 5 – Fire fighting measures 13 – Disposal considerations Non-
o 6 – Accidental release measures 14 – Transport information Mandatory
o 7 – Handling and storage 15 – Regulatory information
o 8 – Exposure controls/personal protection 16 – Other information
- Chemicals must then be segregated according to their chemical family or hazard classification, and stored
appropriately without close proximity so that any incompatibility is avoided
 o Basic Hazard groups: Acids, Bases, Flammables, Oxidizers, Toxics, Peroxide forming chemicals,
Pyrophoric forming substances, Water reactive chemicals, Explosives
o Common Hazard groups to separate:
 No acids with bases
 No acids or bases with flammables
 No oxidizers near compressed flammable gases

General Laboratory Techniques

Common Lab Glassware and Uses

- Glassware is a standard equipment used in the laboratory because it is customizable, has a relatively low cost,
has extreme durability, and has specific levels of precision
o Soda-lime/Float glass – standard consumer- grade glass but cracks due to expansion/contraction
o Borosilicate glass (Pyrex) - very low coefficient of expansion, preventing internal stresses but impurities
found in this glass may lead to a limited temp range and low optical quality; long axis is greenish
o Fused Silica/Quartz - used in situations where glass needs to be heated above 450°C or to be
transparent to UV light; pure SO2 with 1600°C melting point; optically clear and colorless
- Beakers and flasks – limited accuracy of measuring volume, typically ±5%; used for holding, transferring, heating,
and mixing reagents
- Volumetric glassware – very accurate and is indicated by:
o volume marking
o temperature at which the glassware is accurate (density & volume of liquid is temperature dependent)
o TD (to deliver) or TC (to contain)
- Stoppers – used to seal glassware
o Septum – variation allowing easy access to needles
o Rubber – sized by # 0 – 10
o Cork – may sometimes have holes for thermometer, stirrers, and tubes
o Glass – joint grease are used for glass to glass connections (sized by diameter and length eg 24/40mm)
 Standard taper, ball and socket, O-ring
 Connector clips/Keck clips can be used (color coded accdng to size of joint) and springs and wire
- Supporting tools
o Metal clamps, chain style (large pieces), water-bath clamps (thermometer)
o Ring stands/retort stand
o Lab Jack and cork ring
- Glassware for Qualitative use
o Beakers © Test tubes – used for observations
o Flasks: Erlenmeyer, Florence © Watch glass – common for crystallization and evaporation
o Test tubes © Crystallization dish – commonly used for bath processes
- Glassware for Measuring - ±1% accuracy
o Graduated Cylinder – more precise than beaker (TD) © Micropipette
o Volumetric Flasks © Burette
o Volumetric Pipettes
- Procedural Glassware
o Round bottom/Boiling flasks – never filled to more than 50% © Ceramics
o Separatory funnel – leads to a stopcock ® Büchner Funnel
o Filter/Büchner Flask ® Crucible
o Funnel ® Mortar and Pestle
 Powder funnel
 Filter funnel – may be used with filter paper

Measuring Mass in the Laboratory

- Analytical balance – highly precise measuring instruments

o Triple beam balance – type of scale that uses counterweights on three rider beams to counterbalance
the sample in the pan
o Modern analytical balance – makes use of electromagnetic compensation method (spring + load cell
sending an electric current)
o Some parts: weighing pan, air or draft shield, tare bar for tarring (setting the scale back to 0)
- Weigh boat or weigh paper (for smaller amounts) is used to hold and protect the substance being weighed
- Spatulas: Microspatula or Scoopula
- Analytical balances are so sensitive that even fingerprints can cause readings to be inaccurate
- Cold samples are heavier causing the measurement to be incorrect

Understanding Concentration and Measuring Volumes

 - Solutions are generally identified by their components and corresponding concentrations
- Concentration is most commonly expressed as molarity. A one molar solution contains one mol of solute per
liter of solution
- moles of solute can be determined from the measured mass of the molecule and its molecular weight
- Solutions can also be prepared and quantified as percent concentrations, weight-volume solution, or volume-
volume solution
- Stock solutions – concentrated solutions of stable compounds
- Parallel dilution - a solution of desired concentration and desired volume prepared from a stock solution of
known concentration. The resulting volume can be diluted to the total volume of the solution to achieve the
desired concentration
- Serial dilution technique - a stock solution can be used to make a dilute solution, which can then be diluted
further to make a more dilute solution and so on until the desired concentration is met
- Quantity sufficient – process of adding the solvent to a solution until it reaches the desired volume
- Meniscus – curve of a liquid due to surface tension
- Always select the smallest device that will accommodate the desired volume to achieve the highest accuracy
otherwise graduated cylinders are the appropriate choice for measuring volumes of liquid above 50 mL

Making Solutions

- Solutions can be described by their solute concentration, a measure of how much solute is present per unit of
solution

BIO 100 (INTEGRATIVE BIOLOGY)

The Cell: Overview of The Cell

- Compartments – distinguishing feature of eukaryotes from prokaryotes

o “Compartmentalize” – isolate into compartments or categories with their own function thus increasing
efficiency of cellular processes

Cytoplasm & Cytoskeleton

- Cytoplasm – region between the nucleus and the plasma membrane; site for most metabolic activities of the cell
o Cytosol – liquid portion of the cytoplasm (contains h20 where proteins, lipids, enzymes, free
polyribosomes/ribosomes, and cytoskeleton are suspended)
- Cytoskeleton – to resist mechanical stress; makes up the cell shape
o Intermediate filaments – provides mechanical strength in the cytoplasm and nucleoplasm
o Microtubules – organize movement in the cell (helps the mitochondrion to be anchored)
o Actin filaments – controls shape and movement of cells; thinnest; abundant in cells with large scale
movements like muscle cells

Nucleus and DNA organization into chromosome

- Nucleus – houses genetic information

o Nucleolus – where DNA resides; rRNA synthesis is found
 rRNA is paired up with certain proteins to produce ribosomes
o Nucleoplasm – like the cytoplasm located between the nucleolus and the nuclear membrane
- DNA Organization
o When DNA is stretched linearly, it extends up to 2 meters
o 5 different levels:
 1st – DNA/double helix
 2nd – nucleosomes – “beads on a string”, helical DNA is wrapped around a spool made up of
histone proteins
 3rd – Chromatin fiber – accomplished by twisting the “beads on a string” structure into a coil;
found within nondividing cell
 4th – Looped domains – formed by having periodic attachments to the protein or RNA scaffold
(found at the center of looped domains)
 5th – Chromosome – highly condensed structure; found in dividing cell (chromatid is one leg of a
sister chromatid)
- Ribosomes/Polyribosomes (poly – whenever mRNA is translated into proteins, many ribosomes participate)
o Free polyribosomes – suspended in the cytoplasm
o Bound polyribosomes – attached to the endoplasmic reticulum/nuclear envelope
o Both mRNA and rRNA are exported from the nucleoplasm to the cytoplasm through nucleopores
throughout the nuclear membrane

Endomembrane system

- A system of membranes of phospholipid bilayers within the cell

o 1 membrane = 2 phospholipid layer called as a phospholipid bilayer
 - Nuclear Envelope/Membrane
o Inner Nuclear Membrane and Outer Nuclear Membrane (studded with bound ribosomes; connected
with the endoplasmic reticulum)
 Fuse at sites where nuclear pores are present
 Perinuclear space – separates the 2 nuclear membranes; connected with the lumen of ER
o Nuclear pore (made up of 30 different proteins called nucleoporins) – regulate the entry and exit of
molecules between the nucleoplasm and cytoplasm
- Members are related through direct contact or by transfer of membrane segments as vesicles
o Rough (flattened sheets) or Smooth (tubular) ER
 Difference in morphology allows for segregation of biochemical processes within the organelle
 RER: Initial synthesis and sorting of proteins, glycosylation:
 Polypeptide (linear chain of amino acids) is being synthesized by a free ribosome
through the instructions of the mRNA. Sugar chains are attached and becomes threaded
into the cavity where glycosylation occurs then is bounded by a transport vesicle,
becoming a glycoprotein
 SER: Detoxification, carbohydrate metabolism, lipid synthesis and modification, phospholipid
synthesis, and stores and releases calcium ions within muscle cells
o Golgi complex – processing, modification, sorting, and packaging of cell products; series of flattened disk
shaped sacs stacked together as interconnected membranes
 Cisternae – each golgi stack named according to their orientation in the cell
 Cis face – membrane facing ER (where transport vesicle is received)
 Trans face – faces the plasma membrane or other golgi (shipping site through secretory
vesicles)
o Lysosome – aids in digestion (breakdown into simpler components) of food and damaged organelle
brought by food vacuole; digestive enzymes (acid hydrolases) made by the RER
o Plasma Membrane – regulates the entry and exit of molecules; phospholipid bilayer: hydrophilic heads,
hydrophobic tails
o Vesicles – connecting the different members of the endomembrane system
- Cell wall – only for plant cells; for protection

Semiautonomous organelles

- Were originally prokaryotes; both are doubled membrane

- Semiautonomous – living autonomously in an autonomous (contains their own DNA and ribosomes) living body
- Mitochondrion (anaerobic) – smooth outer membrane & folded inner membrane forming projections called
cristae; for cellular respiration (makes ATP molecules that provide energy for cellular activities)
- Chloroplast (photosynthetic) – has an additional membrane called thylakoid membrane; type of plastid; contains
the pigment chlorophyll

Other organelles

- Vacuole – has a single membrane called tonoplast

o Contractile vacuole – for locomotion
o Food vacuole/Phagosome – digestion and cell waste management
o Large central vacuole – for storage (plant cells)
- Microbodies
o Peroxisome – for the detoxification of alcohol and breakdown of lipids via beta-oxidation
 Ex: Mammalian liver cells – has large amounts of peroxisomes
- Cilia – microscopic hairlike projections that can move like waves; traps inhaled particles
- Flagella – tail-like structure for locomotion

Cellular Processes: Membrane Transport

Fluid-mosaic model

- All biological membranes are constructed as phospholipid bilayer (a dynamic layer because it contains different
components – a mosaic)

Phosopholipid

- Phosphate + lipid (fat and phosphate group)

- Glycerol – 3 carbon polyalcohol acting as a backbone
- Fatty acids
o Components and length differ in different organisms
o Composed of saturated fatty acids (hydrogen-saturated);
o And unsaturated fatty acids important for kinks – bending structure for membrane to stay fluid
- Phosphate group – composition differs in different taxa
Membrane Proteins

- Intercellular joinings – join cells together

- Enzymatic activity – degrade something, convert something, or act as an enzyme
- Transport – of molecules in and out the cell actively across the concentration gradient or passively obeying the
concentration gradient
- Cell-cell recognition
- Anchorage/Attachment – can attach to certain filaments and can anchor membrane in cytoskeletons
- Signal transduction – binding of neurotransmitter to create a chemical/electrical signal
- Kinds of Membrane proteins:
o Integral/intrinsic – embedded in the hydrophobic region
o Peripheral/extrinsic – embedded outside the hydrophobic region
o Carbohydrates – attached to membrane lipids, forming glycolipids and glycoproteins

Membrane permeability

- Factors affecting membrane permeability:

o Molecular size – the smaller the size, the easier it can pass (CO2, N2, O2)
o Polarity – relative solubility; the more non-polar (hydrophobic), the easier it can pass
o Charge – molecules with no charge can pass easily
- Sometimes polarity and charge are related to each other but most of the time charge refers to ions

Types of membrane transport

1. Unassisted Membrane Transport

a. Passive diffusion – random movement of solute molecules from a high concentration to a low
concentration to reach equilibrium (Brownian motion)
o Factors allowing diffusion:
i. Chemistry of solute – pertains to molecular weight and polarity of solute
ii. Difference in concentration gradient – the higher the difference in concentration gradient, the
faster the movement of molecules
iii. Temperature – the higher the temp, the faster the diffusion
b. Osmosis – movement of water molecules only from high concentration to low concentration regardless
of what other molecules are in the solution
i. Hypotonic, Isotonic, Hypertonic (talks about concentration of water and is reversed when it’s
about solute concentration)
- Higher water concentration, lower solute concentration and vice versa
2. Assisted Membrane Transport
- Transporters:
o Channels – transmembrane passageway for diffusion of molecules
 Ion channels (Sodium, Potassium)
 Ligand-gated channel – responds to binding of a ligand (functional group that binds to a
receptor)
 Voltage-gated – responds to changes in the amount of electric charge (usually happens in
nerves)
o Transporters/Carriers – have binding sites and are more selective; not open simultaneously to both sides
of the cell membrane
 Pump – uses ATP to transport molecules against its gradients (organic molecules, sugars, etc)
 Uniport – only allows transport of 1 molecule
 Cotransport – allows transport of 2 molecules
o Symport – two molecules are transported in
o Antiport – 1 transported out, 1 transported in
a. Facilitated Diffusion – like passive but is being aided by a protein channel or carrier protein
b. Primary active transport – transportation of pumps uphill is powered by ATP hydrolysis
c. Secondary active transport – transport protein does not directly use ATP but uses secondhand energy
stored in the form of sodium concentration gradient built up earlier by a primary active transport
3. Vesicular Transport
a. Endocytosis – out to in
i. Phagocytosis – pseudopods form, encapsulating solid particles; “Cell eating”
ii. Pinocytosis – invagination of pocket; “Cell drinking”
iii. Receptor-mediated endocytosis – has receptors that only binds with specific molecules
b. Exocytosis – in to out to empty its content

Cellular Processes: Photosynthesis

Overview of Photosynthesis
Phototrophs

- Can still use any light source for energy, sunlight is just the main source
- The energy is harvested and converted into a reduced/conserved form of energy
 Conserved form is chemical energy called ATP, NADPH
 Stored in the chemical bonds of sugar (glucose, sucrose)
- Anoxygenic phototrophs – can undergo photosynthesis even without oxygen (hydrogen sulfite H2S)
- Oxygenic phototrophs – undergoes photosynthesis with oxygen (water H2O)

Photosynthesis

- Occurs in chloroplasts
 Consists of 2 membranes: Inner and outer; Thylakoid membrane
o Inner membrane filled with Stroma (space inside the chloroplast)
o Thylakoid membrane
 Grana – disc like structures that are stacked (s: Granum)
 Spaces in the thylakoid act like the intermembrane space of a mitochondrion
 ATP formation in photosynthesis is like the electron transport system in the
mitochondrion during cellular respiration
 A lot of proteins embedded in the thylakoid are involved in the electron transport
system (photosynthetic electron transport system & phosphorylation)
 Where chlorophyll molecules are found
- Process complementary with cellular respiration
- Light energy captured by chlorophyll molecules to help boost energy of electrons
 Electrons get excited – can cause spontaneous combustion for it contains lots of energy
 Unexcited electrons go back to its normal state
o By passing the electron from one machinery to the other while forming ATP
- Two stages of photosynthesis (light & dark) are linked by ATP and NADPH

Light Reaction: Solar Energy into Chemical Energy

Light

- Sunlight contains energy called electromagnetic energy/radiation, which is also available in any other source of
visible light (between UV and infrared)
- Light can behave as a wavelength or as a photon (both contain the same amount of energy nonetheless)

Chloroplasts

- Contain several pigments, which absorb light of different wavelengths

 Chlorophyll a – blue and red (430 – 662)
 Chlorophyll b – blue and orange (453 – 642)
 Carotenoids – between 460nm and 550nm
o Broaden the spectrum of colors that drive photosynthesis, provide photoprotection

Photosystem

- Parts of Photosystem
 Light harvesting complex/Antenna complex – series of pigments responsible for absorbing light energy
 Reaction center complex – initial photochemical reaction takes place (redox reactio); where chlorophyll
is found; electrons become excited
 Primary Electron acceptor – accepts excited electron (Photosystem II)
- Types of Photosystem
 Photosystem II – reaction center: P680
 Photosystem I – reaction center: P700

Photosynthetic Electron Transfer

- Primary electron acceptor

 Photosystem II – Pheophytin
 Photosystem I – Ao
- Protein complexes required for the transfer of electrons (PETS)
 P680 –> Pheophytin, Plastoquinone (PQA, PQB), Cytochrome b6f complex, Plastocyanin (electron carrier)
 P700 –> AO, Ferredoxin, Ferredoxin NADP+ oxidoreductase (final enzyme), NADP+ to NADPH

Photophosphorylation

- Metabolic process of generating ATP by harvesting light energy

- 2 Kinds:
 Non-cyclic – can be found in higher forms of organism
  Cyclic – can be found in lower forms of plants or bacteria
o No photosystem II
o Electron only loops in P700, primary acceptor, ferredoxin, cytochrome complex, plastocyanine,
then reduces the P700
- Used by chloroplasts and utilizes light

Process – occurs in the thylakoid membrane; energy-harvesting process

1. Chlorophyll and other pigment molecules absorb photons and transfer energy, through resonance transfer
(transfer through vibration) to chlorophyll a molecules, the reaction center
 These are organized with other proteins into a complex of proteins known as photosystems
2. Excited electrons are passed on to a reaction center
 P680 oxidation drives Hydrolysis – splitting of water into H2, O (by-product), and electrons
 Photolysis provides electron for P680 to become reduced and go back to its natural state
3. An initial primary electron acceptor accepts electron (primary acceptor is reduced)
4. Electron passes through electron transport chain (Photosynthetic Electron Transport System PETS)
 Proton gradient happens – increase in H+ or movement of H+ from stroma to lumen space of thylakoid
through cytochrome complex, driving chemiosmosis
5. Chemiosmosis generates ATP from ADP + phosphate group in PETS
 Chemiosmosis – caused by the difference in H+ proton gradient; ATPase – enzyme responsible in the
formation of ATP
o As the H+ proton moves to a lower gradient with the help of ATPase, it drives the ATP synthase
to move protons from thylakoid space to stroma and produce ATP
6. Oxidized P700 gets electron from PETS to become reduced
7. Primary electron acceptor becomes reduced and transfers electron to ferredoxin
8. NADPH generated from transfer of electrons from photosystems and H+ from water to the electron carrier,
NADP+ (reduction process)

* LEOGER – lost electron oxidized; gained electron reduced

Products

- NADPH, ATP, and O2

Calvin Cycle: Reducing CO2 to Sugar

- Where the conserved form of energy is made through the process of carbon fixation using the ATP and NADPH
generated by the light reaction
- 3 Carbon Dioxide, 9 ATP, and 6 NADPH are required
- Occurs in the stroma because of the presence of RUBISCO
 Ribulose-1,5-biphosphate carboxylase + oxygenate – enzyme needed to facilitate carbon fixation or
oxygen fixation
- Produces G3P (glyceraldehyde-3-phosphate) (3 carbon molecules) that can be used to make glucose (6 carbon
molecules) or other organic molecules, and water

Process – energy synthesis; must actually need 6 CO2 to from glucose

1. Carbon Fixation
a. Carbon Dioxide (1 molecule) is added to RuBP (5 molecules) with the help of Rubisco to produce a 6
carbon molecule
b. 6 carbon molecule spawned from carboxylation and RuBP is highly unstable
c. Immediately cleaves into two 3 carbon molecule called 3-PGA or 3-phosphoglyceric acid (first stable
product)
2. Reduction
a. Each 3-PGA is phosphorylated with the help of ATP and reduced by NADPH, forming G3P
 As it utilizes ATP, it is broken down into molecules of ADP and a phosphate, and NADPH is oxidized into
NADP+
3. 1 G3P released
4. Regeneration of the starting molecule, ribulose-1,5-bisphosphate (RuBP)
a. Remaining ATP is used for G3P to undergo a series of process until RuBP is formed

Cellular Processes: Cellular Respiration

Cellular Respiration

- the process where cells metabolically convert chemical energy from nutrients to adenosine triphosphate (ATP)
- takes place in the mitochondria in animal cells
- requires glucose and oxygen, producing CO2, H2O, and ATP
a. How do cells extract energy?
 i. Redox reaction or oxidation-reduction reaction of glucose and oxygen
1. Glucose loses hydrogen atoms forming carbon dioxide (oxidized)
2. Oxygen gains hydrogen atoms forming water (reduced)
- Cells are able to make ATP via:
a. Substrate-level phosphorylation – transfer of phosphate molecules to ADP, producing ATP
b. Oxidative phosphorylation – chemiosmosis of H+

Stages of Cellular Respiration

1. Glycolysis
- Occurs in the cytoplasm
- Energy Investment Phase
a. Glucose, 2 ATP, 2 Phosphate, 2 NAD+ is needed
b. Glucose is energized using 2 ATP and is split into two, producing two 3-carbon compounds called G3P
i. 1st ATP forms glucose 6-phosphate
ii. Then, is modified to fructose 6-phosphate
iii. 2nd ATP forms fructose 1,6-bisphosphate
iv. Then, is cut to form 2 glyceraldehyde 3-phosphate (G3P)
- Energy payoff
a. 2 NADH is produced from 2 NAD+ reduction
i. 2 NADH for each initial glucose molecule
ii. Phosphate molecules are added to each G3P, forming two 1,3-Bisphospho-glycerate
b. 2 ATP is produced (substrate-level phosphorylation)
i. 1st ATP formed by attaching (transferring) phosphate molecule from two 1,3-Bisphospho-
glycerate to ADP, producing two 3-phospho-glycerate
ii. Molecules re-arrange to form two 2-phospho-glycerate
iii. Water is then added to form two Phosphoenol-pyruvate (PEP)
iv. 2nd ATP formed by attaching phosphate molecule from PEP to ADP
c. 2 Pyruvic acid (C3H4O3) is produced (fate depends on oxygen)
i. With O2 (Respiration): pyruvate oxidized to acetyl coenzyme A, which enters the Krebs cycle
ii. Without O2 (Fermentation):
1. Pyruvate oxidizes NADH to form lactate (C3H6O3)
2. Pyruvate releases CO2 to form acetaldehyde (C2H4O) and oxidizes NADH to yield
ethanol (C2H5OH)
- Products are 2 NADH, 2 ATP, and 2 Pyruvic Acid

- For glycolysis to continue, NADH is recycled to NAD+ by:

a. Aerobic respiration – oxygen is the final electron acceptor
b. (Anaerobic) Fermentation – oxygen is not available thus is replaced by an organic molecule

2. Pyruvate oxidation and Krebs cycle – has 2 turns

- Happens in the mitochondrial matrix
- Pyruvate enters from cytosol through pyruvate translocase to mitochondrial matrix
- Only pyruvate is allowed to enter the membrane of mitochondria
- Pyruvic acid – large polar molecule thus it cannot easily penetrate the outer membrane of mitochondria
- Transition Reaction (chemical grooming) occurs prior the Krebs cycle
- 1 Pyruvate generates 1 NADH, 1 CO2, 1 Acetyl-CoA
a. Decarboxylation – a carbon compound (CO2) is removed from pyruvate
b. Two-carbon compound remaining is oxidized of 2 electrons and is given to NAD+ forming NADH + H +
c. Coenzyme A is added to produce Acetyl-CoA
- Krebs Cycle/Citric Acid Cycle/Tricarboxylic Acid Cycle
 Named after Hans Krebs, 1930
 Is a successive oxidative decarboxylation reaction
 Completes oxidation of organic molecules
a. Generates 3 NADH, 1 FADH2, and 1 ATP and Releases 2 CO2 per turn
i. Acetyl-CoA releases Coenzyme A, forming a two-carbon compound
ii. 2-carbon compound fuses with Oxaloacetate, a 4-carbon compound, producing Citrate, a 6-
carbon compound
iii. Citrate is oxidized, producing 1st NADH and releasing 1st CO2, forming Alpha-ketoglutarate, a 5-
carbon compound
iv. Alpha-ketoglutarate is oxidized, producing 2nd NADH and releasing 2nd CO2, forming succinate, a
4-carbon compound
a) Succinate will help in production of ATP by allowing ADP and P to fuse together
v. Succinate is oxidized, reducing 1st FADH2 from FAD, forming Malate
vi. Malate is oxidized, reducing 3rd NADH, forming Oxaloacetate
 vii. Cycle repeats

- In total, 6 CO2, 4 ATP, 10 NADH, 2 FADH2 are produced from steps 1 and 2
 NADH, and FADH2 are electron carriers that will proceed to the electron transport chain

3. Electron Transport Chain and Chemiosmosis (oxidative phosphorylation)

- Occurs in the inner mitochondrial membrane
- Involves electron carriers (NADH and FADH2) shuttling electrons to the transport chain embedded in the inner
mitochondrial membrane towards a final electron acceptor
- Composed of 4 protein complexes (Cytochrome I-IV), and 2 mobile carriers (Ubiquinone and Cytochrome C)
- Hydrogen ions in gradient are pumped from the matrix unlike in plant cells where it is moved
- Purpose of ETC is to create a proton gradient in the intermembrane space to be utilized by ATP synthase
- For NADH
a. NADH donates 2 electrons to cytochrome I, which pumps 2 hydrogen ions from matrix to
intermembrane space
i. NADH all produced by glycolysis and Krebs cycle
b. 2 electrons will be transferred by ubiquinone to cytochrome III
c. Cytochrome III pumps 2 hydrogen ions upon receiving electrons and simultaneously
d. 2 electrons will be transferred by cytochrome c to cytochrome IV
e. Cytochrome IV pumps 2 hydrogen ions upon receiving electrons and simultaneously
f. 2 electrons will be donated to ½ O2 (final acceptor), creating water
- For FADH2
a. FADH2 donates 2 electrons to cytochrome II
b. 2 electrons transferred by ubiquinone to cytochrome III
c. Undergoes the same process as NADH but without cytochrome I
- NADH contributes more compared to FADH2
- Chemiosmosis
 ATP synthase
o Membrane bound enzyme that helps the hydrogen ion to diffuse from intermembrane to matrix
o Synthesizes ATP by using the energy of the proton gradient

Energy yields are different for species

- For bacteria, usually 38 ATP; For eukaryotes, 32-36 ATP

- Eukaryotes’ net ATP usually don’t achieve 34-36 ATP
- Variety of yields are due to
 The differences in cell types (ex. In glycolysis)
o NADH molecules produced must pass through the 2 membranes of the mitochondrion through
electron shuttles
a) Malate-aspartate shuttle (can be found on liver, kidney, and heart cells)
a. Transports glycolytic NADH to the matrix as NADH
b) Glycerol 3-phosphate shuttle (found on muscle and brain cells)
a. Transports glycolytic NADH as FADH2
 Leaky inner membrane with regards to the proton gradient, causing the driving force for ATP synthesis
to dissipate

Interrupting Cellular Respiration

Cellular poisons

- Block electron transport chain (Rotenone, Cyanide, Carbon Monoxide)

- Inhibit ATP synthase (Oligomycin)
- Make the membrane leaky to hydrogen ions (DNP)

Anaerobic Respiration

Glucose oxidation occurring without O2

- Anaerobic respiration – use of inorganic molecules as final electron acceptor (Nitrate, Sulfate, Ferric ion,
Carbonate)
- Fermentation (a condition)
 Substitute of electron transport chain and chemiosmosis
 Use of organic molecules as final electron acceptor
 Only a partial oxidation of sugar or metabolites
 Generate 2 ATP per glucose and regenerates NAD+
A. 1st Form: Lactic acid fermentation
i. NAD+ regenerated as 2 pyruvate (end product of glycolysis)
ii. 2 pyruvate obtains 2 electrons from NADH, producing 2 Lactate
 iii. NAD+ is regenerated for glycolysis to produce ATP
nd
B. 2 Form: Alcohol fermentation
i. NAD+ regenerated as 2 pyruvate (end product of glycolysis)
ii. Pyruvate releases 2 CO2 and will be further reduced to produce ethanol
iii. NAD+ regenerated for glycolysis to produce ATP

Connection between metabolic pathways

- Cells use organic molecules for cellular respiration

- ATP is generated using:
 Carbohydrates – sugar (primary source)
 Fats – glycerol fatty acids may contribute to the G3P in glycolysis, or it may be a participatory molecule
in the transition reaction
 Proteins – such as amino acids may participate in glycolysis as pyruvate, may contribute to the pyruvate
molecule being utilized in the pyruvate oxidation, or may be a participatory molecule in the citric acid
cycle

Cellular Processes: Cellular Reproduction

Cell Division and Reproduction

Cell Division

- Reproduction renders genetic immortality

- Overview: Interphase, Karyokinetic Processes (Mitosis & Meiosis), Cytokinesis

Eukaryotic Cell Cycle and Mitosis

Eukaryotic Cells

- Have longer gene sequences that are compartmentalized

 Gene – portion of the DNA stretch that encodes the synthesis of a product (structural proteins,
functional RNAs)
 DNA – a molecule containing instructions needed for the organism to develop, live, and reproduce; a
double-stranded molecule
 Chromatin – condensed and compacted DNA + histone proteins
 Chromosome – even more compacted and condensed state (max: metaphase stage) of chromatin
o Single chromosome or Double chromosome
 Genome – complete set of genetic instructions of an organism
- Before it divides, it duplicates all of its chromosomes, resulting into sister chromatids joined together by
centromere
- When it separates, sister chromatids are separated (now called “single” chromosomes)

Phases of Cell Cycle

1. Interphase: duplication of cell contents

a. G1 – growth, duplication of organelles, increase in cytoplasm
b. S (synthesis) – duplication of chromosomes
c. G2 – growth, preparation for division, checking for replication errors, centrioles show
2. Mitotic Phase: division/karyokinetic process
- Ploidy (# of chromosomes) is the same with the daughter cells
- 2n = 4 – n is # of sets of chromosomes while 4 is the total number of chromosomes
- Mitotic spindle – cluster of microtubules
a. Mitosis – division of the nucleus
i. Prophase
 Duplicated chromosomes are present
 Spindle fibers are beginning to form
 Prometaphase
 Nuclear envelope breaking
 Spindle fibers extend to attach to the chromosomes via the kinetochore (disc-
shaped structure in the chromosomes)
ii. Metaphase
 Chromosomes align at metaphase plate
 Kinetochore would face the opposite poles
iii. Anaphase
 Sister chromatids are separated into daughter chromosomes which will move to the
opposite poles
iv. Telophase
 Cell would continue to elongate
  Nuclear envelope reforms
 Single chromosomes start to uncoil
 Mitotic spindles would disappear
b. Cytokinesis – division of cytoplasm; differs in animal and plant cells
 Cleavage furrow forms – due to contracting ring of microfilaments, interacting with myosin
 In plant cells, cytokinesis occurs as a cell plate forming at the middle

Meiosis and Crossing Over

- 23 pairs of homologous chromosomes (2n = 46)

 Chromosomes are matched in homologous pairs, meaning that chromosome 1 from maternal set is
matched to chromosome 1 from paternal set
 22 pairs of chromosomes are autosomes (same size & genetic comp.); 1 pair is a sex chromosome
(different size & genetic comp.)
 XX – female; XY – male
- Have the full genetic complement

Homologous chromosomes

- Matched in length, centromere position, and gene locations

- Locus – position of the gene (different versions may be found from maternal and paternal)
- Alleles – versions of a gene
- Karyotype – collection of an individual’s chromosome

Meiosis

- Produces haploid gametes in diploid organisms

- Two haploid gametes combine to restore the diploid state
 If 3n happens, an abortus
- Forms 4 unique chromosomes (purely maternal, mostly maternal and partly paternal, purely paternal, mostly
paternal and partly maternal)
1. Interphase
 Chromosomes are duplicated
2. Meiosis I (reductional division): homologs pair up and separate
- Already produces haploid, that’s why it is called reductional division
a. Prophase I
 Chromosomes coil and become compact
 Homologous chromosomes come together as pairs by synapsis
 Each pair with four chromatids is called a tetrad
 Non-sister chromatids exchange genetic material by crossing over in the chiasmata
 Source of genetic variation among organisms
b. Metaphase I
 Tetrads align at cell equator/metaphase plate
c. Anaphase I
 Homologous pairs separate
d. Telophase I
 Duplicated chromosomes would reach the poles
 Nuclear envelope reforms
 Nucleus has the haploid number of chromosomes
3. Meiosis II (equational division): sister chromatids separate
- Still produces haploid, that’s why it is called equational division
a. Prophase II
 Chromosomes become compact
 Nuclear envelope breaks
b. Metaphase II
 Duplicated chromosomes align at cell equator
c. Anaphase II
 Sister chromatids separate
d. Telophase II
 Single chromosomes would reach the pole
 Nuclear envelope reforms
 4 haploid cells are produced

Mitosis & Meiosis

- Both begin with diploid parent cells

- Have chromosomes duplicated in the interphase
- End products differ
  Mitosis – 2 genetically identical diploid somatic daughter cells
 Meiosis – 4 genetically unique haploid gametes

Origins of Genetic Variation

Mechanisms contributing to genetic variation

1. Independent assortment of chromosomes

- There is no pre-determined cell where your chromosomes would sort into
2. Crossing Over
3. Random Fertilization

Cellular Processes: Gene Expression

The Structure of the Genetic Material

- Genetic – something is hereditable

- Reproduction entails biological transfer of information (biological instruction)
- Genetic material in living systems must be one of the biomolecules, or the building blocks of life
 Amino acid
 Nucleotides
 Lipids
 Carbohydrates

Griffith’s experiment (1928)

- One of the first pivotal experiments in the discovery of the characterization of the genetic material
- Frederick Griffith, British bacteriologist
- Conducted experiments using streptococcus pneumoniae and mice
- Used two related strains of streptococcus pneumoniae:
 S strain – forms rounded and smooth colonies; smooth due to a polysaccharide coat produced by the
bacteria that would protect the strain from the immune system of the mouse; virulent
 R strain – forms rough colonies with well-defined edges; non-virulent
- Then tried to inject dead S strain to the mouse; mouse lived
- When harmless R strain were combined with dead S strain; mouse died
 Blood stain of dead mouse contained living S strain
- Concluded that the r strain must have taken up a “transforming factor”

Avery, McLeod, and McCarty (1944)

- They purified the transforming factor, separated it from other cellular components by the use of enzyme
- Suggested that DNA is the “transforming factor”, the genetic material

Hershey and Chase (1952)

- Used bacteriophages (virus that attacks bacterial cells)

 Would attach to a surface of a host bacterial cell and would inject some genetic substance (either DNA
or Protein) to make more phages
- DNA is the genetic material
 1st Characteristic: A polymer of nucleotides which consists of a nitrogenous base, sugar, and a phosphate
group

Erwin Chargaff (1950)

- reported that DNA composition varies from one species to the next
 discovered that DNA is responsible for heredity
 discovered that the amount of purine (adenine and guanine) is equal to pyrimidine (cytosine and
thymine) bases (A + G = T + C); A=T, G=C in all species – Chargaff’s Rule
o Basis for these rules weren’t understood until the discovery of the double helix

Watson and Crick (1953)

- Found the secondary structure of the DNA through deduction of all researches
 Chargaff’s observation
 Rosalind Franklin & Maurice Wilkins’ X-ray crystallography data
 Linus Pauling’s construction of 3-D structures
- DNA is a double-stranded helix (uniformly helical)
 Consisted of 2 polynucleotide strands wrapped into a double helix
o Sugar-phosphate backbone is on the outside
o Strands are antiparallel (ex: 1st – 5prime to 3’; 2nd 3’ to 5’)
a) 3’ end is the only region where another bond can be added
 o Nitrogenous bases are perpendicular to the backbone in the interior
o Specific pairs of bases give the helix a uniform shape
a) A pairs with T, forming 2 hydrogen bonds
b) C pairs with G, forming 3 hydrogen bonds
 This characteristic explains a lot about the behavior of the DNA molecule
o Purine + Purine = too wide
o Pyrimidine + Pyrimidine = too narrow
o Purine + Pyrimidine = width consistent with X-ray data

Components of DNA and RNA

- Difference between DNA and RNA in terms of composition is found in their sugar phosphate backbone and
bases
 DNA sugar component is deoxyribose; RNA is ribose
 DNA thymine; RNA uracil
- DNA and RNA (nucleic acids) are polymers of nucleotides (building blocks of RNA and DNA)
- Nucleotide is composed of a nitrogenous base (ATGC), 5-carbon sugar, and a phosphate group
 Direction of the strands depends on the 3’ and 5’ end or the availability of carbon in sugar
 Pyrimidine – heterocyclic aromatic compound with 1 ring
 Purine – 2 rings

DNA Replication

- Watson and Crick suggested that DNA has a possible copying mechanism found on specific base pairings
- DNA replication follows a semiconservative model
 Two DNA strands separate
 Each strand is used as a pattern to produce a complementary strand, using specific base pairing
o Free nucleotides attach to each separated strand
 Each new DNA helix has one old strand and one new strand, thus semiconservative model
- Speed and accuracy of DNA copying is remarkable; copying error is low
 Copying errors lead to mutations
- More than a dozen enzymes and other proteins participate in DNA replication

1. Separation of the 2 strands

a. DNA replication begins at the origins of replication
i. DNA unwinds to produce a “bubble” or opening
ii. At the end of each “bubble” is a replication fork
- Eukaryotic chromosomes have thousands of origins of replication
o Eukaryotes have longer gene sequences and larger chromosomes, thus longer strands of
DNA
- Replication proceeds in both directions from each origin until entire molecule is copied
- Preparation of the DNA strand is facilitated by enzymes
o Helicases – untwists the double helix at the replication forks
o Single-strand binding proteins – binds to a single strand and stabilizes it while replication is
ongoing
o Topoisomerase – corrects overwinding ahead of replication forks
2. DNA strand synthesis
- DNA molecule needs an RNA primer first before it synthesizes
o DNA polymerase would detect the RNA primer and start the DNA synthesis
- Important enzymes involved
o Primase – involved in the synthesis of the RNA primer
 Can start an RNA chain from scratch and adds RNA nucleotides one at a time
 Starts the point for the construction of the new strand of DNA
o DNA polymerase – catalyzes the elongation of the new DNA at a replication fork
 Can only add nucleotides to the 3’ end, thus direction starts at 3’ of parental DNA
 5’ - 3’ duplication is continuous (leading strand)
 3’ - 5’ duplication is discontinuous, leading to the formation of short
sequences or fragments of daughter strands (Okazaki fragments) thus the
existence of gaps (lagging strand)
 Each nucleotide added is a nucleoside triphosphate (free nucleosides)
 Composed of sugar, nitrogenous base, and 3 phosphate group
 Binding catalyzed by DNA polymerase
 2 phosphate groups are removed
o Ligase – repairs irregularities or breaks in the DNA backbone
 Seals recombination fragments, connects Okazaki fragments, seals repairs in DNA
 o Exonuclease – removes all the RNA primers from both strands of DNA
 DNA polymerase fills in the gaps

The Flow of Genetic information from DNA to RNA to Protein

Gene Expression

- Process by which DNA directs protein synthesis

o Transcription – synthesis of mRNA under the direction of DNA
o Translation – synthesis of polypeptide (proteins) under the direction of mRNA
- Gene
o Nucleotide sequences of a DNA molecule
 Introns – removed during the transcription process as the mRNA matures; sometimes regulate
transcription, and its termination process; part of genome organization; where evolution can
take place
 Exons – spliced together and are the ones expressed

1. DNA Replication: Nucleic

- Non-template strand (5’-3’)
- DNA template strand (3’-5’) – used in transcription
2. Transcription: Nucleic
- Key Players:
o RNA Polymerase – links the RNA nucleotides to the DNA, forming mRNA
o Promoter and Terminator sequences – found in DNA sequence, promotes the attachment of
RNA polymerase, and terminates the end of transcription
- polyribosomes – linked together by an mRNA molecule; constantly transcribing the mRNA molecule
producing proteins
- Transcription unit – stretch of DNA transcribed
a. Initiation
- RNA polymerase attaches to the promoter sequence
- DNA would unwind and RNA polymerase would start to incorporate new bases to the mRNA
transcript
b. Elongation
- RNA grows longer and follows the complementary base pairing rules
- A=Uracil (less energetically expensive); G=C
- Thymine is used in DNA because it offers greater resistance to auto chemical mutation and
degradation
c. Termination
- RNA polymerase reaches a certain signal to end the transcription
- Pre-mRNA produced (5’-3’) has:
o Coding sequence – has the initiator codon (AUG) for protein synthesis and the terminator
codon (UAA, UAG, UGA)
o Untranslated segment – has 5’ UTR and 3’ UTR
 AAUAA – found in 3’ UTR; signal for site of 3’ end trimming and poly A tail addition
d. Processing/Maturation
- mRNA must pass the nuclear envelope first before translation
- mRNA needs extra layer of protection because the cytoplasm is a harsh environment
i. Incorporation of 5’ guanine cap – helps ribosomes binds to mRNA
ii. Incorporation of a 3’ polyadenine tail
o Gets added to the ends of mRNA
o Protects mRNA from cellular enzymes
o Allows mRNA to exit the nuclear envelope
iii. RNA splicing – removing introns and joining exons
o Removal of introns is called spliceosome; intron floats around and is called intron lariat
- Produces a mature mRNA segment
o [5’ cap, Protein-coding segment, 3’ cap]
3. Translation: Amino Acids
- Language of mRNA molecule is translated into the language of the polypeptide
o From language of nucleic acid to amino acid
- Characteristics of the genetic code:
o 61 codons correspond to amino acids
o AUG codes for methionine (start codon)
o 3 “stop” codons – UAA, UAG, UGA
o Redundant and unambiguous
  Some amino acids have more than one codon, but a codon used will never be used
again for other amino acids
o Nearly universal – shared by organisms
o Without punctuation – codons are continuous and has no gaps in between
- Key Players:
o Messenger RNA (mRNA) – encodes amino acid sequences; genetic message is read in 3
consecutive codons
o Transfer RNA (tRNA) – converts nucleic acid language into protein language
 Picks up the appropriate amino acid and;
 Has anticodon (triplet of bases) used to recognize the appropriate codons in the
mRNA
 Has a clover leaf structure (2D), has loops where there are no complementary
pairings, has intramolecular base pairings
 Acceptor stem – amino acid attachment site
o Ribosome – synthesizes polypeptide chain
 Has two ribosomal subunits (large – on top; small – bottom) made up of proteins
and rRNA
 Comes together during translation
 Sedimentation rate of proteins during centrifugation is used for naming the
types of ribosomes
 Ribosomes have binding site for mRNA and tRNAs
o tRNA binding sites in large subunit:
 A site (Aminoacyl-tRNA binding site)
 Amino acids are activated for protein synthesis
 Accepts the incoming tRNA that matches the codon
of mRNA
 P site (Peptidyl-tRNA binding site)
 Peptide bond formation
 E site (Exit)
 Protein growing in the exit tunnel
o mRNA binding site in small subunit
- Building a polypeptide chain
o Phases same as transcription
a. Initiation
- Brings together mRNA, tRNA with 1st amino acid, and 2 subunits of ribosome
i. An mRNA molecule binds to a small ribosomal subunit and tRNA binds to mRNA at the start
codon (mRNA – AUG; tRNA – UAC)
o Called the Preinitiation complex
o GTP hydrolysis allows certain confirmational changes and the binding of large ribosomal unit
 Guanosine Triphosphate
ii. Large ribosomal unit joins the small, allowing the ribosome to function
o First tRNA occupies the P site, which will hold the growing peptide chain
o A site ready to receive the next tRNA
o Called the Translation initiation complex
b. Elongation
i. Codon recognition
o mRNA codon complementary base pairing to the anticodon pairs in the A site
ii. Peptide Bond formation
o New amino acid joins the chain by creating a new peptide bond
iii. Translocation
o tRNA released from the P site, exits in E site, then the ribosome moves next tRNA from A
site to P site
c. Termination
i. Occurs when A site recognizes stop codon (UAA, UGA, UAG)
ii. Release factor binds to A site to detach rRNA, releasing free polypeptide
o Polypeptide undergoes a series of protein folding with the help of enzymes and proteins to
be functional
- Replenishing of tRNA – a certain enzyme combines the amino acid and the tRNA together to form
one unit

Essentially, DNA is translated into Proteins, which provide the molecular basis for phenotypic traits

- Molecular chain of command: DNA in the nucleus to RNA in the cytoplasm to Protein
- DNA sequences provide codes for protein construction
 o Protein construction requires a conversion of a nucleotide sequence to an amino acid sequence
o Certain mutations in DNA are reflected in proteins

Tissues

Botany

- study of plant ultra structures, behaviors, responses, metabolites, etc.

Plant

- Plant – multicellular organisms capable of photosynthesis with the exemption of holoparasitic plants and some
mycoheterotrophic plants
o Chloroplast – most primitive characteristic, where chlorophyll is found
o Adaptations gave way to characteristics that enabled plants to thrive
o Plants opted to move from aquatic environments to terrestrial ones, forcing them to develop structures
that allows them to withstand periods of less water
 Phototropism – reaching towards the sun
 Phygmotropism – roots grew downwards
 Xylem and phloem – specialized conducting tissues to aid nutrient nutrients and moisture
distribution
- Plant body arranged into a hierarchy of organization (Cell, tissue, organs, shoot and root system)
o Shoot System: Flower, Stem, Leaf – organs are derived from the active division of the shoot apical
meristem
o Root System: Root – organs are derived from the active division of the root apical meristem
- Plants’ importance – ability to produce O2, food, medicine, raw materials, carbon synch, and aesthetic value

Meristematic Tissues

Characteristics

- Composed of rapidly dividing cells, in an isodiametric shape/spherical/polyhedral that are smaller than
permanent tissue cells
- Dark stained nucleus
- Intercellular space and vacuole generally absent or tightly packed
- Characterized by a primary cell wall
- Immature and young
- Has low metabolic activity for they are aimed more on the cell division process rather than producing
metabolites
- Contains less dense protoplasm

Categories according to Origin

1. Promeristem
- group of young meristematic cells of a growing organ
- early embryonic meristem from which advanced meristems are derived
2. Primary Meristem
- cells that arose from the promeristem and make up the apical tip of the shoot and root system
3. Secondary Meristem
- Responsible for the secondary growth in plants (growth in girth or thickness)

Categories according to location

1. Apical Meristems (SAM & RAM)

a. Shoot Apical Meristem
 Contains an apical cell or apical initials
 Continuously divide to giver rise to other cells
o Tunica corpus model – characterized by 3 layers of meristematic cells; common for
angiosperms
o A cell initial composed of a single cell is common in vascular plants
 Includes apical dominance – prioritizes this portion of the plant as it will dictate the
development of new leaves, branches, and flowers
 Removing SAM will induce dormant or lateral buds, making the plant robust
 Typically used in horticulture
b. Root Apical Meristem
 Produces the primary root of the plant
 Has a protective portion, known as the root cap, composed of columella and peripheral cells
 Secretes mucilage/mucigel to aid as a lubricant as it traverses the soil substrate
 Derived from the calyptrogen initial, implying that they are not direct derivatives of the RAM
 2. Intercalary Meristems
- Special meristematic region common for grass species can be found mostly near the nodal area of the plant
o Node – part of the plant where leaves or branches emerge
- Aids for fast recovery after herbivory
3. Lateral Meristems

Permanent Tissues

Characteristics

- Not mitotically active but are metabolically active

- Specialized/differentiated – cells have specific functions
- Has various stages of development in their own secondary cell walls called perforations

Tissue Systems

- Composed mostly of simple permanent tissues: parenchyma, sclerenchyma, collenchyma

1. Dermal Tissue
- Composed of epidermis and periderm
o Epidermis – outer protective tissue covering of the primary plant body
 Ordinary epidermal cells – main cell types making up the epidermis
 Living, lack chloroplasts, elongated, have walls with irregular contours
 Guard cells – specialized epidermal cells responsible for opening and closing the stoma which
surround a pore (2 guard cells + pore = 1 stoma)
 Crescent-shaped, contains chloroplasts
 Subsidiary/Accessory cell – forms in close association with guard cells; supports guard cells
 For protection, regulation, to deter herbivory, and for transpiration processes
 Replaced by a thick layer of periderm upon reaching maturation in woody plants
o Periderm – forms corky outer layer of a plant stem during plant secondary growth
 Composed of the phellem (cork), phellogen (cork cambium), phelloderm (cork parenchyma)
 Active division of phellogen pushes cells inwards and outwards
 Phellem – cells pushed outward; phelloderm – cells pushed inward
 With continued deposition of dead cells, rhytidome may be produced on the older stem
2. Ground Tissue
- Serves as sites for photosynthesis, provides support in matrix for the vascular tissue, storage for water and sugar
a. Parenchyma – has living protoplasm with uniformly thin cell walls mainly functions for storage and
translocation
 Chlorenchyma – chloroplast-containing parenchyma
 Storage parenchyma – (Ex. Amyloplasts for starch)
 Transport Cells
b. Collenchyma – consists of living protoplasm with unevenly thick walls primarily functions for support
c. Sclerenchyma – has dead protoplasm at maturity; major supporting tissue due to its thickened cell wall
and in some cases, functions as storage
 Composed of fibers and sclereids
3. Vascular Tissue
- Transports water, sugars, and minerals to different parts of the plant body
- Nutrient and water conducting part of the plant
- Translocation – movement of organic molecules and other materials from one place to another
- Transpiration – release of water through the leaves via the stomata
- Composed of the vascular bundle
a. Xylem
 Mediates water flow and some dissolved solutes through continuous transpiration
 Also conducts dissolved minerals
 Composed of fibers, parenchyma, tracheids, and vessels
 Xylem vessels:
 Arise from individual cylindrical cells oriented from end to end, which dissolves during
maturity and dies to form a duct (xylem vessel)
 In angiosperms, most of the water travels in the xylem vessels
o Walls are thickened with secondary deposits of cellulose and are usually strengthened
by lignin
o Secondary walls are deposited in spirals and rings that are usually perforated by pits
 In woody plants, old xylem becomes the wood; annual ring trees = xylem rings
 Tracheids – individual cells tapered at each end so that that it overlaps with an adjacent cell
 Have thick lignified perforated walls and no cytoplasm at maturity so that water can flow
from one tracheid to another
o Only found in ferns and conifers
 o Smaller than vessels
 Different secondary wall thickenings in tracheid: annular, spiral, scalariform, reticulate,
pitted
b. Phloem
 Primary works for food transport
 Components include:
 Companion cells
 Source cell – cell that contains a big amount of nutrients like a leaf cell
 Sink cell – cell needing nutrition like a root cell
 Sieve elements – sieve plates, pores, and lateral sieve areas/perforations
o Cell contents are pushed sidewards directly through perforations established with the
neighboring companion cell which appears like normal plant cells
o Sieve element and the companion cell functions synergistically in accordance with
gradient
 Nutrients from source cell are first handed over to the companion cell before it is
released to the sieve element
 Nutrient flows through the sieve elements, aided by the perforations and plate
openings
 Nutrient passed again to another companion cell, distributing it to the sink cell
o Overall process mediated by gradient and flow of water
 Phloem fiber cap – aids in mechanical support (sclerenchyma)
 Air space
4. Eudicot vs Monocot Stem
- Dicot forms a ring of vascular bundle around its core; peripheral orientation
- Monocot vascular bundles are scattered all throughout
5. Eudicot vs Monocot Root
- Monocot exhibits a ring-like formation
- Dicot exhibits a cross-like pattern

Organs and Organ Systems: Root System

Roots

- Characterized as the subterranean organ of the plant for it is mostly found beneath the ground for plant
anchorage
- Responsible for the assimilation of nutrients from the substrate
- Downward growth of root influenced by the gravitational pull
o Some modifications are present in other plants

Types of Roots

According to origin

- Primary root – originates from the germination stage of the radical of the seed
- Secondary/lateral roots – emanates from the primary root; creates a branching pattern of the root system and is
relatively finer than the primary root where exchange of nutrients and water occur; increases surface area for
root subvert exchange
- Adventitious roots – roots that form from any non-root tissue and are produced both during normal
development (crown roots, nodal roots) and in response to stress

According to root systems

- Tap roots – (dicot); primary roots grow and become stout; secondary growth from primary root; more
penetrative
- Fibrous roots – (monocot); roots develop from lower nodes; have the same length and diameter; very fine and
form matting most of the time; production of the fine roots is due to the abortion of radicle during the early
stages of vegetative growth
- Adventitious roots – (both) they develop from organs and grow near the surface
o Embryonic development – roots may arise at plant internodes or at junctions between the primary root
and the radicle after the growth of the primary root
o Post embryonic – roots may arise from internodes to provide additional mechanical support
 Brace/prop/stilt roots – provide mechanical support to the upright growth of the plant
 Nodal roots
 May function to aid support in plants through climbing roots emanating from stems of plants
 Pneumatophores – aerial root specialized for gas exchange
o Stress response – help the plant’s anchorage or assimilation

Internal Structure of Roots

Growth Phases

1. Primary growth
- Seed germination – radicle of the embryo forms the root system; tip of the root protected by the root cap
(continuously replaced as the root pushes through the soil with the aid of mucilage)
- Proliferation and differentiation of the RAM organizes cells
 Zones overlap and do not have a clear cut delineation
o Zone of cell division – contains the apical meristem; located immediately behind the root cap where
cells are actively dividing
 Quiescent center – zone where cells stop dividing for the meantime
o Zone of elongation – where newly formed cells are growing or elongating thereby increasing root length;
this requires uptake of water, stretching the cell and increasing their size; rectangular cells
o Zone of cell differentiation/maturation – cells are differentiated or have their functions; become either a
dermal, vascular, or ground tissue; maturation is driven by changes in gene expression
 Cells prior to reaching this zone are totipotent – cells with no fate yet
2. Secondary Growth
- Roots turn woody at maturity for dicots
o Thinner compared to periderm in stems because a thicker outer covering impedes the overall
absorption process of the root
- Initiated by lateral meristems (secondary – vascular cambium, cork cambium; primary – fascicular cambium)
3. Lateral root growth
- Occurs when cells in the pericycle are ruptured thus producing lateral roots
o Pericycle – parenchyma or sclerenchyma in a cylindrical form adjacent to the endodermis; outermost
part of stele
- Layer of the cell surrounding the vascular cylinder begin to divide (periclinal) and form additional cell layers that
push through the outer cell layers of the primary root and ultimately organize a second root meristem
- Design is continuous with the vascularization of the main root

Root hairs – early root trichomes that develops during seed germination; epidermal in nature thus it easily falls of when
the plant matures

Root Cap

- Has its own meristematic cell (calyptrogen) which creates cells with rigid cell walls
- Then, produces statoliths, Golgi apparatus, and mucilage
- Portion at the periphery sheds off as a result of friction due to the downward growth of the root
- Root system of plants are considered as indeterminately growing
- Statocytes – specialized cell found at the root tip in the root cap; contains highly polarized cells that contain
starch filled plastids (amyloplast/statoliths) that sediments to the physical bottom upon plant reorientation
within gravitational field

Function of Roots

Water absorption

- Only takes place in the mature area of the root thus the absorption process only happens in the secondary root
growth
- 2 Main Pathways:
o Apoplastic (non-living) route – pathway providing a route towards the vascular stele through free spaces
and cell walls of the epidermis and the cortex
 additional apoplastic route that allows direct access to the vascular tissues is found along the
margins of secondary routes which developed from the pericycle
 structure characterized by the casparian strip, a suberized layer that forces all assimilated
nutrients to move in the symplast in order to enter the vascular system
o Symplastic (living) route – pathway to the vascular stele involving cell to cell transport through
plasmodesmata (channels of cytoplasm lined by plasma membrane traversing cell wall)
o Transmembrane route – movement across cells and cell walls combining both aforementioned routes;
apoplast may switch to symplast whenever it is convenient

Organs and Organ Systems: Shoot System (Stem)

Shoot System

- Stem, leaves, and reproductive parts of the plant

External Structures

- Nodes – regions where leaves attach to stems

- Internodes – elongated portions between succeeding nodes
 o Length varies depending on the plant type (Rosette type of plants have very short internodes)
- Leaf axil – region wherein the base of the attachment of the leaf and the stem meet; angle between the stem
and the point of leaf attachment
- Buds – young immature tissue giving rise to leaves (foliar bud) or flowers (floral bud)
o Axillary – found in the leaf axil
o Lateral – found below the point of attachment of leaves on the stem
o Termina/Apical – found on top of the stem
o Bud scales – highly cutinized and lignified surrounding each bud to protect immature tissues within
- Branching Patterns:
o Dichotomous – primitive pattern where two equal branches arise from the tip found in lower vascular
plants
o Pseudomonopodial – evolved from the dichotomous where one branch is bigger than the other
o Monopodial – dominant in almost all higher vascular plants where one stem dominates all the branches
 With alternate branching or opposite branching

Internal Structures

1. Primary state of Growth

- Responsible for the elongation of plants vertically
- All plants; Monocots and some dicots
a. Shoot Apical Meristem
o Apical Cell – 1 cell gives rise to all tissues (lower vascular plants)
o Apical initial – group of meristematic cells giving rise to all tissues (higher vascular plants)
b. Primary Meristems – derivatives of apical meristems that change in their shape, density of the
cytoplasm and their sizes
i. Protoderm – epidermis; becomes elongated
ii. Ground Meristem – ground tissue (cortex, pith); highly vacuolated
iii. Procambium – vascular tissues; looks like a strip
c. Primary Tissues
i. Epidermis
 Outermost protective covering of the stem
 Bears trichomes – epidermal appendages; used as protection from desiccation or from
herbivores
 Secretes cutin that forms the cuticles
 Uniseriate (one cell thick) or multiseriate (consists of more than one layer; tissue
specific)
ii. Cortex and Pith
 May or may not appear in plants
 Mostly made up of Parenchyma cells (dominant)
 Collenchyma and sclerenchyma are present to provide additional support
 Endodermis – outermost layer of the ground tissue found in lower vascular plants and in
some higher vascular plants called the starch sheath (implies storage stems)
 Medullary sheath (woody dicots) containing more starch and is more persistent
 Pith – area at the center of the vascular cylinder (forms due to vascular bundles
arranged in a circle)
 Cortex – ground tissue outside the vascular cylinder
 Monocots have no pith and cortex due to random arrangement of vascular bundles
iii. Primary Vascular Tissue
 Primary xylem and phloem
 Protoxylem and protophloem – near axis; bigger
 Metaxylem and metaphloem – towards the outside of the main axis; smaller
 Exarch (centripetal) xylem maturation in roots, while endarch (centrifugal) in stems
 Procambium disappears in stems with secondary growth and becomes the residual
cambium which eventually turns into a fascicular cambium
 Stellar pattern – the arrangement of the vascular bundles in the ground tissue
 Siphonostele – lower v.p.; full vascular ring surrounding completely the pith
 Eustele – higher v.p.; dicots; linear/circular arrangement of vascular bundle
 Atactostele – higher v.p.; monocots; vascular bundles scattered randomly
2. Secondary state of Growth
- Facilitates giving them more girth
- Not all plants for secondary growth gives rise to wood (like woody dicots)
- Residual cambium  fascicular cambium
- Pith parenchyma – pith cells getting pushed in due to the formation of secondary xylem; some parts
dedifferentiate  interfascicular cambium
- Secondary xylem (wood) and secondary phloem (inner bark)
 o Derivative of vascular cambium (formed by the fusion of fascicular and interfascicular cambium)
o Presence of pith implies that the plant body is still young
a. Wood
i. Growth/Annual Rings
 Secondary xylem layers formed in a year which determines the age of the tree
 False annual rings – produced during the interruption of seasonal growth
ii. Wood Types
 Early wood (Springwood) – larger cells produced early in the growing season
 Late wood (Summerwood) – smaller darker cells produced late in the growing season
 Sapwood – near the vascular cambium which are softer and have more water; softwood
 Heartwood – deposition of tannins found at the innermost part of the wood due to dead
xylem cells that lost their capacity to conduct; functions for rigidity of the plant;
hardwood
 Reaction wood
 Tension wood – helps plant survive stressful conditions commonly produced at
the upper branch of woody dicots (whenever branches are swayed by the wind)
 Compression wood – formed on the underside of branches (leaning of branches)
b. Bark
i. Periderm
 Phellem, phellogen, phelloderm
 Lenticels – spherical cells formed from lenticel phellogen which forms intercellular
spaces facilitating the movement of air
 Has filling tissue – loose tissue formed in the lenticel
 Bark – tissue located outside the vascular cambium
 Inner bark – secondary phloem, cortex, and phelloderm
 Outer bark – phellem and phellogen

Function of the stem

1. Transport/Conduction
a. Xylem Transport – water and dissolved minerals
i. Adhesion-cohesion Theory – water adheres to the walls of the xylem and cohesion happens to
prevent backflow
ii. Root pressure – water is pushed by the root pressure formed by the casparian strip
b. Phloem transport
i. Pressure-flow Hypothesis – flow of materials follows difference in pressure gradient; sink (higher
concentration of solute) to source (lower) movement
2. Support
a. Mechanical tissues
i. Collenchyma – usually subepidermal which helps retain shape of the stem that may be
continuous or in patches
ii. Sclerenchyma – scattered amongst the cortical or pith cells
3. Storage
a. Parenchyma and collenchyma
b. Only specialized stems form storage tissues (ex. Tubers)
4. Tropism
- Respond to external stimuli
a. Phototropism – response to light
b. Negative Gravitropism – stem grows against gravity
c. Thigmotropism – plant responds to touch

Different types of modified stems

1. Rhizomes
- Horizontal underground stems that may or may not be fleshy
- Have the ability to produce new plants at the region of their nodes
- Ex. Ginger/turmeric
2. Tubers
- Fleshy underground stems/rhizomes enlarged to store food
- Abundance of food in the stem allows it to grow into a whole new plant when separated from the
original plant
- Ex. Potatoes, sweet potatoes
3. Stolons or runners
- Horizontal stems located above ground
- Exhibits long internode
- Buds that develop at the nodes of stolons grow into new plants that develop their own roots
 - Ex. Strawberry, grasses
4. Tendrils
- Lateral branches that twine around small objects for additional support
- Exhibited by stem with very long internodes
- Ex. Vines, grapes
5. Corms
- Very short vertical stems used for storage of food (main storage) covered with papery leaves
- Falls under the classification of bulbs
6. Bulbs
- Compressed, underground stem that is sometimes called a basal plate
- Has a modified flower bud or other growth point that is surrounded by modified, fleshy leaves (main
storage) referred to as scales
- Ex. Onion

Organs and Organ Systems: Shoot System (Leaf)

Leaf

- Principal appendage borne by the stem

- Flat, expanded organ if not modified
- Functions for absorbing light for photosynthesis
- Earliest sign of leaf formation: leaf buttress or leaf primordia
- Phyllotaxy – leaf arrangement important in terms of shadowing
o One leaf per node
 Alternate – leaves opposite per node
 Spiral – leaves arranged in a circular or spiral manner
o Two leaves per node
 Opposite – leaves opposite each other per node
 Distichous – leaves opposite each other but are parallel to the leaves below it
 Deccusate – leaves opposite each other but are not parallel to the leaves below it
o Three or more: Whorled

External Structures

1. Blade/Leaf lamina
- Flat portion of leaves
a. Simple leaf – one blade attached to the node
b. Compound leaf – 2 or more blades
i. Pinnately compound – leaves attached to a rachis (attachment between petiole and leaflets)
ii. Palmately compound – leaves radiate from tip of petiole
- Petiole (petiolules – attachments between leaves and rachis) – stalk that holds the leaves to the stem
- Epetiolates – common in monocots; possesses a sheathing base for leaf sheaths
- Venation (veins found embedded on the blade)
o Parallel – mostly in monocots; veins parallel to the leaf’s axis
o Reticular/netted
 Palmated – venation starts from a single point then successive veins radiate
 Pinnately net-veined – each vein starts from an axis then branches off

Internal Structures

1. Epidermis
a. Epidermal Cells
o Polygonal in shape (most of time looks rectangular depends on the part of the leaves)
o Bulliform cells (monocots) – modified epidermal cells responsible for rolling of young leaves
 Larger than other epidermal cells, highly vacuolated, contains water
o Myrosin cells – contains fatty acids to catalyze the production of toxic compounds when tissues are
damaged by herbivores; highly species specific
o Lithocyst (cystoliths – outgrowths of epidermal cells) – houses crystals
b. Stomata – classified according to number of subsidiary cells
i. Guard cells – regulates opening and closing of stomata; side inside is thicker
ii. Stomatal pore – where co2 goes in
iii. Subsidiary/accessory cells – numbers vary in different species
o Vary in locations in different species:
 Epistomatic – found on top of the leaves
 Hypostomatic – found below the leaves
 Amphistomatic – found both on top and below
c. Trichomes – epidermal outgrowths (protection, storage, h20 release, secretion)
 i. Simple trichomes, branching trichomes, glandular trichomes
2. Mesophyll
- Space between the epidermal cells
a. Palisade mesophyll
o Normally called chlorenchyma for they are parenchyma cells containing chloroplast
o Highly photosynthetic area made up of compactly arranged elongated cells
o 1 layer – Arranged underneath the upper epidermal layer
o 2 layers – Beneath the upper epidermal layers and before the lower epidermal layer
b. Spongy mesophyll
o Called aerenchyma due to loose and irregularly arranged cells
o Sandwiched between or beneath the palisade layer
o Main function is for gas exchange despite the presence of chloroplast due to big air spaces by loose cells
3. Vascular tissues
a. Veins
o Midrib/Midvein – biggest and middlemost vein where vascular tissues are found
o Lateral veins – branches off from midrib; single file of sieve elements
o Ultimate veins – arises from tip of lateral veins
o Guttation – a process that eliminates water during nighttime done by cells called hydathodes located at
the tip and margins of leaves; happens when soil has too much water absorbed by plants
b. Bundle sheath – single layer of collenchyma cells surrounding small veins for support

Function

1. Photosynthesis
2. Gas exchange
- Occurs in the stomata
a. Opening of the stomata
o Caused by an uptake of K ions in the guard cells
o K influx facilitated by blue light
 Phototropin – detects blue light and activates proton pump (ATP driven) lowering the gradient
of guard cells, allowing osmosis to occur
b. Closing of the stomata
o Abscisic acid (ABA) – binds to protein, causing pH inside the guard cell to increase, stimulating efflux
channels of K ions
 Stimulates loss of chloride and other organic acids, facilitating transfer of calcium ions from the
vacuole to the cytosol, causing electrochemical gradient which releases K ions
3. Transpiration – movement of water due to evaporation
4. Guttation – does not happen in soils with no abundance of water
5. Leaf abscission
- Senescence – aging of the plant body
- Removal of old leaves so that new ones would be provided with more nutrients and energy
- Facilitated by ethylene (hormone)
o With the help of ethylene, certain hydrolases would be produced: calcium pectate  pectic acid 
pectin (loosens cell wall)
- Abscission zone – zone between petiole and stem where the leaf abscises during abscission; possesses a
separation layer made up of delicate layers of tissue
- Main target of enzymes would be the cell walls of the separation layers

Modified Leaves

1. Succulent leaves
- Thick leaves storing a lot of water due to highly vacuolated parenchyma and presence of thick cuticle
- Mostly found in arid areas
2. Spines
- Pointed leaves used for defense
- Mesophyll greatly reduced and remaining cells develop thick walls that becomes impregnated with lignin (makes
structure very sturdy)
- Ex. Cactus, calamansi
3. Bud scales
- For protection; cells secrete colleter – glue-like, keeping the leaves closely approximated with each other
4. Insect traps
- Insectivorous/carnivorous plants
- Some secrete nectar (sugary fluid) while some secrete osmophores (volatile substance) to attract insects
- Glandular trichomes – secretes proteolytic enzymes that slowly digests the victim
5. Tendrils
 - Some are specialized stem while some are specialized leaf (highly species specific)
- More slender and more fragile
- Provides support
- Ex. Cucumber, bitter gourd

Organs and Organ Systems: Shoot System (Flowers and Fruits)

Plant Reproduction

Alternation of Generation/Metagenesis

- Alternation of sexual and asexual phase in the life cycle of an organism

- Two generations are often morphologically or chromosomally distinct
- Pronounced via the gametophyte and sporophyte stages
o Gametophyte (n) – sexual phase of plants where it produces sexual organs and gametes: Antheridia (M)
& Archegonia (F)
 Egg and sperms unite via syngamy to form a zygote  embryo
o Sporophyte (2n) – responsible for the creation of spores
 Sporangium  spore mother cell to commence n stage through meiosis

Flowers

Flower inflorescence

- Cluster of flowers arranged on a branch, system of branches, or stems

- Types according to the arrangement of flowers on a peduncle/main axis
o Corymb – oldest flowers are at the periphery
o Cyme – oldest flowers at the main axis
o Umbel – flowers emanate at a single point; either determinate or indeterminate flowering time
- Types according to flowering time
o Determinate – first flowers to open are at the top or middle; may open all at once when specific
conditions are met
o Indeterminate – flowers may temporarily cease to bloom due to environmental factors; first flowers to
open are at the base

Flower Development

- In angiosperms, plants invest heavily on flower and fruit production

- Florigen – hormone triggering the productions of flowering buds; leaf bud ceases
o Terminal portion of the shoot transforms into a highly structuralized reproductive organ
- Structures:
o 4 major whorls (outermost  innermost)
 1st Whorl: Sepal – acts for protection in the developing flowering bud which may persist during
anthesis (flowering period) or until caducous (shed off after the flowers blooms)
 2nd Whorl: Petals – main display of flowers that attracts pollinators due to its striking colors
 3rd whorl: Stamens – consists of the male reproductive structures
 4th whorl: Carpel – consists of the female reproductive structures
o Pedicel – stalk bearing an individual flower or an inflorescence
o Peduncle – stalk supporting a solitary flower
o Receptacle – found at the base of the flower; may be enlarged in some species, forming false fruits
- Structures in botanical jargons:
o Petals are called Corolla
o Sepals are called Calyx
o Perianth – aggregation of calyx and corolla
o Involucre – refers to a collection of bracts (modified leaf associated with a reproductive structure) that
subtends a corolla
o Hypanthium – cuplike or tubular enlargement of the receptacle of a flower, surrounding the gynoecium
or united with it; used to describe swollen ovary
 Inferior ovary – ovary found as a distinct structure below the perianth
 Superior ovary – ovary found raised above or at the same level with the perianth
o Gynoecium – female part of a flower consisting of 1 or more carpels
- As flowers mature, intricate structures in the organ become more discernible and organized
o Stamen – pollen-producing reproductive organ; Androecium
 Anther – possesses a saclike structure holding pollens (pollen sacs) which cracks (line of
dehiscence) to release pollen grains
 During the early development of the anther, tapetum cells encircle the microspore
mother cells (gives rise to mature pollen grains) for nutrition
  Filament – stem-like structure which holds the anther
o Pistil
 Stigma – 1st receiving portion of the pollen
 Style
 Ovary – orientation of the attachment of seeds via the number of locules (separate cavities in
the ovary) in different species vary
 Ovules – precursors of seeds; contains and produces female reproductive cells; found at
the bottom of a vaselike structure called carpel
o Nucellus – largest part; houses the embryo sac (female gametophyte) and
nutritive tissues
 Nutrients travel through the vascular tissues in the funiculus and outer
integument towards the chalaza and into the nucellus
o Integuments – tough outermost layers (bitegmic) mostly enveloping the embryo
sac
o Micropyle – where integuments do not meet
o Funiculus – stalk connecting an ovule with the placenta or ovary wall
o Chalaza – tissue where the integuments and nucellus are joined
- Ovule Development
o A diploid embryo sac mother cell divides into 4 haploid cells, where 3 will die and 1 will proceed as a
megaspore which will then undergo growth through mitosis and becomes the female gametophyte
/embryo
o Cells within the embryo sac further divide to give rise to specialized cells: 3 antipodal cells (situated at
the top portion), 2 polar nuclei (fuses), and 2 synergid cells (ovum found between)
o Mature embryo sac containing 6 haploid cells and 1 diploid cell is formed just before fertilization
- Pollen Development
o 2 Main Processes:
1. Microsporogenesis – happens before the production of a tetrad; comprises the events leading to the formation
of the n unicellular microspore
a. Diploid sporogenous cell (microsporocyte) undergoes meiosis, giving rise to a tetrad
b. Divides to form 4 haploid microspores
2. Microgametogenesis – events lead to the progressive development of the unicellular microspores into mature
microgametophytes containing the gametes
a. Expansion of the microspore associated with the formation of a single large vacuole (60-70%)
b. Vacuolation is accompanied by the displacement of the microspore nucleus to an eccentric position
against the cell wall
c. Cell undergoes 1st pollen mitosis which results into the formation of 2 unequal cells
d. Generative cell detaches from cell wall, forming a unique cell (bicellular pollen)
e. Cell divides again by 2nd pollen mitosis, producing a pollen with 3 nuclei and forming 2 sperm cells either
before pollen is shed or just within the pollen tube
- Double fertilization – species specific
o Pollen grain received by stigma goes down the pollen tube (secretes digestive enzymes for pollen of
different species)
o Pollen grain produces 2 sperm cells: one fertilizes the egg (ovum), forming the diploid zygote while
another fertilizes the 2 polar nuclei, forming the triploid (3n) endosperm which caters the needs of the
growing embryo
- Structural types:
o Complete flower/Monoecious – when the 4 whorls are present
o Incomplete flower/Dioecious – when a whorl is lacking
o Gynoecious flower – only has ovules
o Perfect flower – has male and female parts
o Imperfect flower – has either male or female parts
- Morphological types:
o Actinomorphic/regular/radially symmetrical – flowers with more than 1 dividing plane
o Zygomorphic/irregular/bilaterally symmetrical – only has 1 symmetrical dividing plane
- Floral diagram and Floral formula
o Floral diagram – gives an idea of the number of structures found among the whorls and how they are
arranged
o Floral formula – infers a representation of a structure of flowers using numbers, letter, and symbols
o Once a floral diagram is drawn, a floral formula can be depicted

Fruit

- Ripened ovary enclosing the seeds

- Fruit varies depending on the life strategy of plants
 o Varies in morphology, seed numbers, colors, texture, taste, etc.
- Provides nutritious food for plants and animals and are rich in vitamins, minerals, and other plant
phytochemicals
- Primarily evolved as a dispersion strategy

Parts of a Fruit

- Pericarp:
o Epicarp – outer skin
o Mesocarp – fleshy, edible carp
o Endocarp – inner stony wall
- Seed – deep within the fruit
o Embryo – baby plant
o Endosperm – reserved food
o Seed coat

Fruit classifications

- Simple fruits – always develop from a single ovary containing 1 or more carpels and may or may not include
additional modified accessory
o Dry
 Dehiscent/Capsular – fruit that cracks open upon maturation
 Indehiscent/Achenial – fruits that do not crack open upon maturation but can be split
 Schizocapric/Splitting – fruits that splits into single seeded parts
o Succulent/Fleshy
 Drupe – fleshy fruit with thin skin and a central stone containing the seed
 Berry – fleshy fruit all throughout
 Pepo – fleshy, watery fruit under the cucumber or melon family; has a leathery rind
(shiny exocarp)
 Hesperidium – fruit of citrus family characterized by fruit pulps and visible locules
 Pome – fleshy, enlarged receptacle and a tough core containing seeds
- Aggregate fruits – fruit formed from several carpels derived from the same flower
- Composite/Multiple fruits – developed from an inflorescence rather from a single flower

Placentation

- Attachment of ovules in the ovary

1. Marginal – attached to a single margin
2. Axile – attached to the axis
3. Free central – resembles the axile but the column is not connected by partitions and no locules are formed
4. Parietal – carpel edges are fused together; ovules develop on the wall or slight outgrowths of the wall
5. Basal – ovule attached to the axis of the pedicel

Seed

- Embryonic plant enclosed in a covering

Parts

- Seed coat – outermost protective covering

- Hilum – visible in most seeds; sometimes referred to as a seed scar for it is a remnant of the point of attachment
of the ovule
- Endosperm – nourishes the embryonic plant especially during germination
- Hypocotyl – embryonic stem
- Epicotyl – the region above the cotyledons
- Radicle – first root of the plant
- Cotyledons – embryonic leaves

Seed dispersal, dormancy, and germination

- Seed dormancy – ensures viability of proliferation when environmental conditions are met; may range from
weeks to years
o Recalcitrant – do not tolerate drying and are short lived (mango, tomato, cocoa)
o Orthodox – can tolerate maturation drying and can be viable for years (cashew, guava, chili);
agriculturally important crops
- Seed germination
o Epigeal – hypocotyl elongates and raises the cotyledons above the surface
o Hypogeal – epicotyl grows and pushes plumule above the ground while hypocotyl remains the same in
length; cotyledons remain below the surface
 - Seed embryology
a. Zygote has undergone transverse cell division forming a large basal cell and a small apical cell
i. Apical cell – produces embryo proper
ii. Basal cell – develops into the suspensor and hypothesis (region between suspensor and embryo)
b. Cell division proceeds from octant to globular stage (has pronounced basal cell and visible procambium
as elongated cells at the center of the embryo) then to triangular stage
c. Triangular stage – enlarged globular stage with triangular apical area
d. Heart stage – due to bilateral symmetry
e. Torpedo stage – enlargement of the cotyledonary lobes, making the cotyledons distinct; ram
pronounced
f. Mature embryo stage – cotyledons recurve, primary meristem production, epidermis well developed

Histology

- tackles animal tissues

- came from the Greek word “histo” meaning “tissue/web”
- study of tissues of the body and how tissues are arranged to constitute organs
- First used by Marie Francois Xavier Bichat

Tissues

- Tissue – group of almost similar cells performing a general function

- Came from the Greek word “tissu” meaning “weave/texture”
- Both cellular and non-cellular components are interconnected so that they form a certain pattern of connection
and to manifest a tissue-like appearance
- Tissues have 2 interacting components
o Cells – cytoskeleton, etc
o Extracellular matrix (ECM) – collagen and extracellular fibers

Epithelial Tissues

- Lines the body cavities/surfaces of certain structures in the animal/human body

- Epithelium – a sheet of cells that covers an external or internal surface
o When found outside the body: protective covering
o When inside a structure: functions as a lining for absorption and secretion pathways
- Important for cellular communication and adhesion, absorption of nutrients, and protection

General Features

1. Cell renewal – capability to actively renew the cell population if it gets damage
2. Avascularity – no blood vessels since diffusion of nutrients is easier
3. Cell packing – closely packed with one another due to the presence of certain proteins
4. Polarity – apical and basal sides are distinct for the cell
5. Diversity – in cells that make up a specific tissue

Tissue types

- Based on General Function: Membrane Epithelium and Glandular

- Based on Cell Shape:
o Squamous – usually flat; width bigger than the height; important for absorption and secretion
o Cuboidal – mostly for secretion
o Columnar – height exceeds the width; movement of substances; rare in absorption and secretion
processes;
- Based on the number of layers
o Simple – one cell layer
o Stratified – two or more cell layers

Connective Tissues

- Tissues underlying other tissue types

- Protection, support, bind other tissues together
- Usually composed of relatively few cells and many extracellular fibers, sometimes with a ground substance
known as the matrix/extracellular matrix

General Features

1. Diversity – the most diverse type of tissue because of its components

2. Function – important in withstanding mechanical forces like pressure
3. Components – cells, fibers, ground substance or matrix
Components

- Cells – a variety of cells can be found suspended in connective tissues

o Fibroblast – one of the most diverse and one of the vital cells for it actively synthesizes most of the
fibers found in those tissues
- Fibers – important to resist tension, torque, and flexion especially for body structures that are mostly moving;
prevents damage caused by movement
o Protein Fibers: Elastic Fiber, Collagen Fiber, Reticular Fiber
- Ground substance – highly hydrated transparent complex mixture of specific carbohydrates and proteins

Tissue Types

- Loose/Areolar – packing material

o Greater amount of ground substance and number of cells (fibroblasts)
o Loosely arranged fibers of collagen and elastic fibers
o They offer less mechanical support and they anchor some of the structures of the animal body (blood
vessels, nerves, body organs)
o Evident in the upper portion of the dermis right below the basement membrane
- Dense – important for formation of tendons, ligaments, and other bands of tissues surrounding skeletal muscles
o Dense Regular – for promoting tensile strength; efficient when structures are involved in contraction;
found in ligaments and tendons
o Dense irregular – for binding and additional source of strength
o Both are often associated together for they are found in very deep lying connective tissues
- Specialized connective tissues
o Adipose – specialized for excess fat storage associated with the loose connective tissue including the
skin and internal lining
 Adipocytes – cells that store additional lipids as fat droplets
 Collagen and Reticular fibers, and few ground substances
o Cartilage – characterized by firmness and resiliency; offers more protection and rigidity in terms of
supporting structures mostly moving/exposed to the environment
 Chondrocytes, collagen fibers, and ground substances made up of sulfated proteins
 Not well vascularized unlike bones with perforating vascular tissues
o Bone – specialized for support, protection, and movement; strongest of all vertebrate connective tissues
for it gets calcified and mineralized; can undergo remodeling and repair due to active cells
 Formed by osteoblasts (precursors; synthesizes bone matrix and differentiates when already
surrounded by the matrix) or osteocytes (mature bone cells housed in the lacuna; has dendritic
processes that link osteocytes via gap junctions called canaliculi)
 Collagen fibers, ground substance
 Well vascularized
o Vascular/Blood – a specialized tissue with different components
 Erythrocytes – lack nucleus and organelles for it needs minimal energy to function and promote
gas exchange (relies on anaerobic glycolysis); filled with hemoglobin (O2 carrying protein);
cannot actively replace defective proteins thus the 120 days lifetime; biconcave shape for a
larger surface area allows larger capacity to hold oxygen molecules
 Plasma (water, proteins, other solutes)
 Buffy coat
 Leukocytes – performs various activities related to immunity
o Granulocytes – has specific granules called Polymorphonuclear (PMN)
leukocytes
 Neutrophil – most abundant; important in phagocytosing bacteria
 Eosinophil – kills parasites; bi-lobe
 Basophil – least abundant; important for allergic reactions serving as
anti-coagulate
o Agranulocytes:
 Lymphocyte – smallest; produces antibodies through glycoproteins
interacting with their corresponding antigens (molecules recognized by
the immune system)
 Monocoyte – largest leukocytes; precursors of macrophages
 Platelets/Thrombocytes – important in promoting blood clotting ; non nucleated,
membrane bound cell fragments

Muscular Tissues

- Contractile elements that function for movement

- Most abundant tissue in the body
- Muscle fiber – technical term for a muscle cell
General Features

1. Function – contraction for locomotion through special proteins: Actin and Myosin
2. Properties – allows for contraction and movement
a. Excitability – cells on resting membrane potential (RMP) can be triggered to achieve its excited state
b. Contractility – ability of tissue to shorten its length
c. Extensibility – property to be stretched
d. Elasticity – ability to stretch and still be able to go back to its original form
3. Diversity – not that diverse

Tissue Types

- Skeletal muscle – striated; usually cylindrical and elongated; largest; multinuclei peripherally located (syncytial
cell); always associated with bones; functions for locomotion, voluntary control, and thermoregulation
- Cardiac muscle – only found in the heart; striated, long, cylindrical, and branching; larger than smooth; uninuclei
centrally located; functions for the movement of the heart, regulated by a collection of nerves called as the
pacemaker; intercalated disc – special feature that connects one cardiac muscle to another
- Smooth muscle – long and tapering; no striations; uninuclei centrally located; found in blood vessels like arteries
and internal organs like intestines; for involuntary control; closely apposed with each other – special feature

Nervous Tissues

- Specialized kind of tissue that acts as a consequence of locomotion (controls)

- Receive, integrate, & transmit information

General Features

- Function
o Impulse conduction – transmission of received information from the environment through short electric
signals between cells
o Stimuli reception – sensory receptors made up of nervous tissue to sense stimuli
- Organization – Central Nervous System and Peripheral Nervous System

Neurons/Nerve Cells

- Neurolemma – plasma membrane of neurons

- Perikaryon (Cell Body) – contains
o Nissl bodies – RER associated with proteins
o Mitochondria – power of the cells
o Neurofilaments & Neurotubules – microtubules important in connecting cells
o Lipofuscin pigments – important for degradation; minor functions
- Dendrites – made up of dendritic spines; cytoplasmic projections; input zone – receives change in action
potential in the CNS
- Axon – cytoplasmic projection which serves as the output zone in the PNS
- Myelin sheath/Medullary Sheath – covers the myelin, facilitating faster transmission of electric impulses via
saltatory conduction; produced by the oligodendrocyte in the CNS and the Schwann cell in the PNS
- Nodes of Ranvier – constrictions within the myelin sheath

Integumentary System

- Support, protection, and movement

- Integument/Skin – one of the largest organs of the body (15% of the total body mass)

Overview of the Integument

Development

- Skin precursors or germ layers delineate at the end of neurulation

o Ectoderm  Epidermis
o Mesoderm  Dermomyotome  Dermatome  Dermis
- Neural crest cells migrate between epidermis and dermis
o Neural Crest cells  pigment cells (melanocytes) and body armor
o Nerves and blood vessels are added for nourishment of skin cells
- Vernix caseosa – milky appearance and texture part of periderm used to protect the skin of the infant in the
womb

Components

- 2 Main Layers: Epidermis and Dermis separated by the Basement Membrane

- Hypodermis – subcutaneous region; not necessarily considered a part of the integument; also called superficial
fascia
Functions

- Protection against mechanical and chemical injury

- Provides moisture due to the glands in the skin
- Vitamin D production by converting chemical substances through the presence of UV Radiation
- Gas exchange, Secretion of Waste, Thermoregulation, Locomotion, and Sensory

Animal Integument

Simplest Integument

- Pellicle – external covering of protozoans; considered as the outer cell membrane of the organism
- Functions for removal of waste and gas exchange

Multicellular Invertebrates

- Generally, a simple columnar epithelium

- Mollusk – contains mucous glands to prevent predation and retain moisture in their body
- Rotifers – have thin and elastic cuticle (Lorica) for locomotion and protection
- Crustaceans, Arachnids, and Insects – thick and rigid cuticle in their exoskeleton for protection and moisture
retention

Vertebrate Integument

- Epidermis – stratified squamous keratinized epithelium

- Dermis – loose connective tissue in the upper layer and deeper dense irregular connective tissue
- Basement membrane – between dermis and epidermis
- Hypodermis – loose connective tissue and adipose tissue

Tetrapod Integument

- Epidermis – stratified epithelium because of the presence of several layers (important for adaptations)
o Keratinization or cornification – cells are replaced within 20-30 days; beta keratin harder than alpha
o Stratum corneum – dead cells with a hard protein envelope containing keratin and surrounded by lipids
o Stratum lucidum – dead cells containing dispersed keratohyalin
o S. granulosum – cells become more flattened due to the lower layers pushing; keratin fibers and lipid-
filled lamellar bodies are hardened by keratohyalin by producing a protein envelope thereby killing the
cells and releasing lipids
o S. spinosum – accumulates keratin fibers and lamellar bodies
o S. Basale – mitotic division of new cells; cells get pushed towards the stratum spinosum due to division
- Glands – derivatives of the skin that functions for secretion
o Exocrine glands – may occur as a tube or as a sap; some are classified in terms of how they secrete their
products
 Merocrine – products are delivered in a membrane bound vesicle towards the apical surface of
the cell where the vesicle fuses with the plasma membrane to release the products in a duct
 Apocrine – products are released in the apical portion of the cell where it accumulates and
pinches off together with some cytoplasm
 Holocrine – products accumulate within the cell which triggers cell death and gets discharged
into the lumen of the gland
o Endocrine glands
- Dermis – 2 strata are found in tetrapods; responsible for elastic texture of the skin because of the presence of
elastin and collagenous fibers produced by fibroblasts
o Papillary region – composed of loose connective tissue
o Reticular region – dense irregular connective tissue
o Other components: Glands, nerve endings, blood vessels, hair follicles, and arrector pili muscles
o A stratum of the dermis of fishes is called a ply
- Basement Membrane – delineates epidermis from dermis; in earlier stages, it guides the cells migrating; can be
thickened
o Basal lamina – composed of epithelial cells and collagen fibers; divided into lamina lucida and lamina
densa
o Reticular lamina – composed of reticular fibers; layer secreted by connective tissue cells
- Hemidesmosome – protein complexes that facilitates the adhesion of the epithelium cells to the basement
membrane; promotes mechanical stability
- Hypodermis – layer directly below the dermis (hard to distinguish)
o Serves to connect the skin to the underlying fascia of the bones and the muscles and acts as a cushion
for the integument
o Well vascularized, composed of loose connective tissue and most of the time, adipose tissue to store fat
and for thermoregulation
Muscular System

Organization of Skeletal Muscles

3 Layers of Connective Tissues that wrap muscles

- Each muscle is wrapped in a sheet of dense irregular tissue called the epimysium, separating it from other
tissues thus allowing it to move independently; also allows powerful contraction
- Fascicle – bundles of muscle fibers surrounded by perimysium (connective tissue)
o Fascicular bundle organization is common in skeletal muscles for this allows the neuro system to trigger
specific movements by activating certain subset of the fascicle
- Muscle fiber – muscle cell or myocytes found inside each fascicle surrounded by the endomysium (layer of
collagen and reticular fibers)

Muscle Striations

- Gives the muscles an alternating light and dark band due to the predominant filament in the area
- A (Anisotropic) band – darker bands; thicker myosin filament
- I (Isotropic) band – lighter bands; thin actin filament; disappears during contraction

Motor Entry Points (MEP)

- Muscular nerve endings – results from the branching of nerve bundles and innervation
o Brain can send signals to the muscle, exciting it and allowing voluntary control
- Axon Terminal/Synaptic Knob/Terminal Button – end portion of nerve
- Synaptic Vesicles – found in synaptic knob that contains neurotransmitters which releases acetylcholine in the
synaptic cleft upon receiving the action potential, triggering another set of reactions (gets accepted by ACH
receptors)
- Action Potential – electrical signal; triggers the release of ca in the T-tubules and Sarcoplasmic reticulum

Skeletal Muscle Fiber

Sarcolemma

- Specialized cell membrane surrounding the striated muscle fibers

- Essentially equal to plasmalemma and myolemma
- Possesses transverse tubules – important in the propagation of the action potential from ACH receptors
o Usually located at the center of the A-I junctions
o Has Dihyropyridine receptors (DHPR) – voltage dependent calcium channels; intracellular ca release
 Part of excitation-contraction coupling

Sarcoplasm

- Essentially the cytoplasm

- Contains glycogen (multi-branched polysaccharide), mitochondria, myoglobin, and lipofuscin pigments

Sarcoplasmic reticulum

- Has a reticulated/netted pattern in triads with T-tubules

- Where calcium is dispersed thus the large surface area
- Ryanodine receptor/Foot protein – ca release channel when triggered by the action potential

Myofibril

- Numerous rod-like organelles that serve as specialized contractile elements

- 90% of the volume of the muscle fiber
- The greater the number of myofibrils, the greater the force that can be produced
- Made up of myrofilaments that is made up of sarcomeres

Sarcomere

- Basic contracting unit; Smallest functional unit of a striated muscle

- “sarco” – flesh; “mero” – part
- 1 myofibril has repeating units of sarcomere defined by the Z line/disc
- M Line – extends vertically in the middle of the A band and the H zone
- H zone – lighter area of the A band where thin filaments do not reach; disappears when muscles are in full
contraction for the actin filaments slide in

Myosin

- Thick filament with 2 identical subunits that are intertwined in a helical fashion each with 2 heads
- Globular heads – has an actin binding site and myosin ATPase site
- Tail ends
Actin

- Made up of spherical actin molecules with binding sites for attachment with myosin cross bridge and troponin
and tropomyosin complex
- Actin helix – molecules are joined together
- Tropomyosin – a threadlike molecule that covers binding sites
- Troponin – 3 polypeptide located at specific intervals in the thin filament; binds to tropomyosin, actin molecule,
and calcium

Role of Calcium in Cross-Bridge Formation

- Cross-bridge formation – when myosin binds with actin

o Relaxed – no formation
o Excited – calcium released due to action potential binds to troponin, creating structural changes thus
allowing tropomyosin to slide away from its blocking position. Actin and myosin can now bind, forming
the cross bridge

Muscular Contraction

1. Excitation – happens on the neuromuscular junctions

- Nerve membranes are normally negatively charged (Resting Membrane Potential -70mV)
- Sodium channels – voltage gated channels; allows the entry of sodium ions, changing the membrane’s charge to
+30/40mV
- Myelin sheath – insulates nerves thus it allows jumping of signals or saltatory conduction in the nodes of Ranvier
until it reaches the axon terminal, triggering the release and binding of ACH
2. Excitation-Contraction Coupling
- Upon binding, action potential is transferred and propagated through the sarcolemma towards the T-tubules
- DHPR and other receptors are triggered, and calcium is released in the sarcoplasmic reticulum and into the
microfibrils
- Calcium binds to the troponin, creating structural changes, allowing the tropomyosin to slip
- Formation of cross bridge between myosin head and actin subunit
3. Contraction – Sliding Filament Theory
- Attachment/cross bridge formation
- Release and Binding of ATP in the ATPase binding site, which leads to the breakdown of ATP into ADP
- Bending of myosin head during breakdown
- Energy released is used for force generation (power stroke)
- Reattachment of cross bridge formation
- Sliding Filament Theory
o During contraction, myosin heads slide past the actin filaments thus muscle shortens
o Titin – elastic protein molecule
4. Relaxation
- Sarcoplasmic reticulum pumps calcium back using calcium-atpase pumps (energy provided by mitochondria)
- Calsequestrin – main calcium binding protein of the sarcoplasmic reticulum; allows concentration of Ca at 20mM
o Gives the ability to contract frequently without fatigue
- Acetylcholine is broken down into acetic acid + choline from neuromuscular junction by the acetylcholinesterase
found in the synaptic cleft through hydrolyzation

Respiratory System

Phases of Respiration

Respiration – exchange of gases

- External Respiration – occurring between the organism or the respiratory organ and the environment
- Internal Respiration – exchange within the organism; between the blood and the tissues
o Oxygen enters the bloodstream, carbon dioxide exits the bloodstream
- Cellular Respiration – utilization of oxygen; between blood and cells
- Phases differ per organism as they exhibit different respiratory surfaces

Respiratory Surfaces

- Another term for respiratory organs due to the fact that not all organisms capable of respiration have
respiratory organs
1. Cell Membrane: Simple Diffusion
- Common in Amoeba and other small organisms; simple diffusion is sufficient for gas exchange
2. Cutaneous Respiration
- In animals living in moist environments (frogs, newts, earthworms, lungless salamander) (Water respirers)
o Well-developed among frogs – obtains 25% Oxygen; 75% from lungs
 o And Lungless salamanders for they rely solely on cutaneous respiration in the skin and buccal-
pharyngeal region
- Also called integumentary respiration since it refers to the exchange of gases across the integument
- Integument Properties:
o Always moist – both O2 and CO2 can only cross cell membranes when dissolved in water
o Richly supplied with networks of capillaries close to the skin to facilitate faster gas exchange
o They have no armor
- Disadvantages:
o Integument has low permeability to gases that is why water is needed
o Integument, even though thin, has a large surface area thus others have evolved organs
3. Tracheal System
- Exhibited by some terrestrial invertebrates (insects, centipedes, some mites, ticks, spiders)
- Refers to a system of air tubes close to the skin which provides direct exchange of gases
- Insect blood plays no direct role
- Composition:
o Trachea – highly branched chitin-lined tubes open to the outside of the body through openings called
o Spiracle – opening with closure devices to prevent water loss
o Tracheole – found at the ends of smaller tracheal tubes and lie closely to cells of the body
4. Gills/Brachia
- Organs formed as outgrowths/invaginations/outfoldings of the body surface specialized for gas exchange
- Water respirers
- Thin filaments where each are highly vascularized or have high concentrations of capillaries
- External gills – outside the body (Axolotl – brachial tufts); has support tissues
- Internal gills – fragile, needing protection thus found inside the body (Operculum – common)
o Each filament contains stacks of lamellae (richly supplied with lamella) or flat platelets
o Flow of blood is always opposite to the flow of water
- Countercurrent gas exchange – opposite flow of blood and water which creates a gradient, enhancing the
exchange of gas between water and blood
5. Lungs
- Respiratory organs adapted for aerial breathers or air respirers – organisms who acquire O2 from the
atmosphere
- Exchange of gases occur in the tiny sacs called alveoli at the end of bronchioles
- Alveoli are lined with simple squamous epithelium and capillary networks; has a moist internal surface; secretes
surfactants that reduces the surface tension between the fluid and air inhaled
- Lung Ventilation – mechanisms in which they make contact to the environment
o Ventilation – mechanism that increases contact between the environment and the respiratory surface
 Inhalation and Exhalation
a. Positive Pressure Pumping Mechanism
 Exhibited by amphibians and reptiles both of which pushes air into their lungs
 Jaw is opened and air is gulped then mouth and nares are closed
b. Negative Pressure Pumping Mechanism
 Air is sucked
 Inhalation – rib cage expands as lungs expand; diaphragm and intercostal muscles contract;
provides lower pressure which allows air from the buccal cavity to move in
c. Negative Pressure Pumping in birds
 One way flow thus more efficient
 Bird lungs are exhibited as tunnel like passages called parabronchi lined with capillaries
 Anterior and posterior to it are the air sacs
 2 Inhalation
 1st: air moves from the outside towards the posterior
 2nd: allows air from the parabronchi to move towards the anterior air sac
 2 Exhalation
 1st: air moves towards the lungs via contraction of the posterior air sac then gas
exchange occurs in the parabronchi
 2nd: air moves from the anterior air sac to exit the bird’s body

Human Respiratory System

1. Air enters the mouth or the nasal openings

2. Then it passes through the nasal chamber lined with mucus-secreting ciliated epithelium
- Air is warmed, moistened, and filtered through ciliated epithelium
3. Then through internal nasal openings that connects the nasal cavity to the pharynx
- Pharynx – tube which branches into 2 openings: to esophagus or to larynx
4. Air encounters epiglottis – flap that folds over the glottis (opening to the larynx)
5. Once the glottis is opened, air passes the larynx or voice box and proceeds to the trachea or windpipe
 - Trachea surrounded by cartilaginous rings to prevent it from collapsing
6. Air passes Bronchi (paired tubes leading to each lung) then bronchioles
7. Air reaches the end of bronchioles which are alveoli or air sacs where gas exchange occurs

Exchange of Gases

Air is a mixture of gases (79% N, 20.9% O, small amounts of water vapor and CO2)

Diffusion of Oxygen and Carbon dioxide will always be due to the difference in partial pressure (High to Low p.)

- Oxygen diffuses from alveoli to blood; from blood to tissues

- Carbon dioxide diffuses from tissues to blood; from blood to lungs

Transport of Oxygen

- In some invertebrates, gases are simply carried as dissolved gases and body fluids
- In many invertebrates and vertebrates, respiratory proteins help carry oxygen and some co2 in the transport
process
- Hemoglobin – iron containing protein composed of 5% heme (iron containing structure which gives off the red
color) and 95% globin (colorless protein)
o Oxygen binds to heme; Hemoglobin binds o2 when o2 concentration is high thus called oxyhemoglobin
 This allows a more radiant red color

Transport of Carbon Dioxide

- Carbon Dioxide diffuses in the blood via 3 interconnected pathways

- Peripheral Tissues – any type of tissue surrounded by systemic capillary
o Carbon dioxide within the cell that has undergone cellular respiration will diffuse towards the plasma of
the blood (low carbon dioxide) in the systemic capillary
o 7% of the CO2 dissolves in the plasma
- Systemic capillary – capillaries found in any organ except for the lungs
o 93% enters the red blood cell
o As it enters the rbc, 23% combines reversibly with hemoglobin forming carbaminohemoglobin
o 70% remaining is converted to carbonic acid with the help of carbonic anhydrase and H2O
o Carbonic acid dissociates into hydrogen and binds with hemoglobin, while bicarbonate ions move out
the rbc via a protein into the blood plasma
- Pulmonary capillary – capillaries surrounding the lungs
o Aforementioned setup is transferred to the pulmonary capillary near the lumen of the alveolus
o The opposite cycle happens: 70% bicarbonate will enter the rbc while chlorine ions will exit
o Bicarbonate ions fuse with hydrogen ions to form carbonic acid
o Carbonic acid dissociates into water and carbon dioxide
o 23% attached to the hemoglobin dissociates itself and fuses with the 70%
o Then it fuses with the 7% in the plasma, forming 100% CO2 that diffuses in the blood plasma towards
the lumen of the alveolus

Nervous Control Breathing

Inhalation and Exhalation are controlled by the nervous system

- Respiratory control is found in the medulla oblongata:

o Sends nerve signals to the intercostal muscles and diaphragm to contract which allows inhalation
 Only possible if body has high concentrations of CO2
o Breathing control center responds to the pH of blood and cerebrospinal fluid
 High concentrations of CO2 mean low pH levels (acidic blood)
o Nerve signals indicate CO2 and O2 levels
 Acidic blood is sensed by sensors in the aorta which sends signals to the medulla oblongata,
triggering the contraction of muscles

BOT 119 (PLANT ANATOMY)

The Plant Body

Overview of The Plant Body

Evolution of The Plant Body

- Theories on the Origin of plant multicellularity

 Cell Theory of Multicellularity – multicellularity is the result of aggregation; cells are the building blocks
 Organismal Theory of Multicellularity – cell subdivides within itself; organism is not a separate unit from
the cell; function of the organism is a result of the coordinated functions carried out by the cells
- How does cell division occur in plants?
 - How is cell to cell communication in plants?
- Evolution of plants

Development of the Plant Body

I. Embryogenesis
- After fertilization, the zygote develops inside the seed and goes through histodifferentiation, cell expansion, and
maturation drying
- Histodifferentiation – also referred to as embryogenesis, characterized by differentiation of the endosperm and
embryo

II. Monocot embryogenesis

- Monocot – more complex embryo structure in the mature seed compared to dicots but similar in early stages
- Proembryo Stage
 First division is asymmetrical and leads to an apical (divides more rapidly; will become the embryo) and
basal cell (becomes the suspensor)
- Globular Stage
 Similar to dicots, except for the difference in the suspensor (less differentiated and has more row of
cells)
 In the late globular stage, the outer epidermal layer is evident and a group of cells on one side divides
rapidly, giving rise to the embryo axis
- Scutellar Stage
 Remnant of the cotyledon (embryonic leaf stored in the seed and is the first to sprout) can be seen.
 Monocots only have one cotyledon called the scutellum
 Scutellum – acts as conductive tissue between the endosperm and embryo axis
- Coleoptilar Stage
 Embryo axis differentiates into the plumule (shoot) and radicle
 Embryo axis has a specialized tissue surrounding the shoot (coleoptile) and root tissue to aid in
emergence (coleorhiza) during germination

III. Dicot embryogenesis

- Proembryo stage
 First division is transverse
 Suspensor functions to push the proembryo in the embryo sac cavity and to absorb and transmit
nutrients to the proembryo
 Suspensor is a column of multiple or single cells
- Globular stage
 Hyphophysis – basal cell derivative which becomes the radicle
 Tissue differentiation becomes evident in the 16-celled globular embryo
- Heart stage -> Torpedo Stage -> Cotyledon stage
 Cotyledon primordium is evident from the heart shaped stage of the embryo
 Then it elongates to give a typical torpedo stage embryo
 Embryo organized to form the apical meristem, radicle, cotyledons, and hypocotyl
- Mature stage
 Embryo is fully formed, cotyledons are evident, a distinct shoot and a root meristem can be seen
 Suspensor and basal cell begins to disappear

The Plant Cell: Protoplast

- Plant cells vary in their components depending on their function

- Organization of structures in plant cells vary

Cell wall – distinguishing feature of the plant cell; first thing discovered in plant cells

- Most cell walls are comprised of multiple layers:

 Primary wall – first formed layer produced by protoplast following mitosis and formation of middle
lamella (layer outside primary wall which cements 2 adjoining plant cells together)
o Compound middle lamella – middle lamella + 2 adjacent walls
 Secondary cell wall – after formation of primary wall and cell growth has ceased; deposited on the inner
surface of the primary wall; has 3 distinct layers
o S1, s2, s3 – differentiated based on the arrangement and orientation of cellulose microfibrils
- Plasmodesmata – gaps in the cell walls; microscopic channels that connect the cytoplasm of 2 adjacent primary
walls such that small molecules may be transported from one cell to the next; reason why organismal theory is
prevalent in plant cells because plants are connected through plasmodesmata

Protoplast – everything inside the cell wall (cell membrane, cytoplasm, nucleus)

- Organelle – membrane-bound subcellular components

 - Plastids – only in plant cells; self-replicating organelles containing their own DNA
 Classified based on their color/on their pigments they contain
 Chloroplasts – green
o Sites of photosynthesis
o Containing chlorophyll and carotenoid pigments
 Chromoplasts – red and orange
o Contains only carotenoid pigments
o Functions as attractants
 Leucoplasts – non pigmented
o Lack elaborate system of inner membranes
a) Proteinoplast – protein storage
b) Elaioplast – fat storage
c) Amyloplast – starch storage
 All plastids are developmentally related and come from the same precursor, called proplastid
o Small, colorless or pale green, undifferentiated plastids found in meristematic cells of roots and
shoots
- Vacuole – bounded by tonoplast
 Sometimes so large that it occupies 90% of cell space; primary component is water
 Storage organelles for primary metabolites or lytic compartments
 Separate toxic secondary metabolites from the cytoplasm
o Secondary metabolites are toxic to pathogens, parasites, and herbivores, playing an important
role in plant defense
 Sites of pigment deposition (anthocyanin – water soluble pigment responsible for blue, violet, dark red,
and scarlet colors of plant cells)
o Frequently confined in epidermal cells and serve to attract animals for pollination and seed
dispersal
 Without vacuoles, plants will wilt for they are important for internal pressure and maintaining tissue
rigidity
 Increase in size as the cell enlarges
- Peroxisomes (microbodies)
 Bounded by a singular membrane with granular interior
 one of their important functions is peroxidase activity
 Types according to their functions:
o Leaf peroxisomes – in green leaves; play a role in the glycolate pathway of photorespiration
a) Photorespiration – converts oxygen into co2; it reduces photosynthetic efficiency of
plants affecting their growth
b) With the help leaf peroxisomes, carbon is recycled to be used for photosynthesis
o Glyoxysomes – in endosperm/cotyledon of germinating seeds; converts fats to carbohydrates
through the glyoxylate cycle (fuels seedling growth)
o Unspecialized peroxisome
 Each peroxisome can transform directly to another type of peroxisome
- Cytoskeleton – network of protein filaments that give shape, structure, and organization to the cytoplasm
 Cell division (mitosis & cytokinesis)
 Cell expansion and differentiation
 Cell-cell communication
 Movement of cytoplasmic components (cyclosis/cytoplasmic streaming)
o Enables exchange of material
 Two types: Microtubules and Actin filaments/microfilaments

The Plant Cell: Cell Wall

Mechanical Properties

1. Plasticity
2. Elasticity – the ability to go back to its normal structure even after force is exerted
3. Tensile strength – the capacity to withhold maximum tensile stress

Function of Cell Wall

- Structure, Growth, Defense, Signaling, Cell-cell adhesion

Cellulose

- Basic unit is the cellulose molecule

- Cellulose molecules are then cross linked or bonded to other molecules through hydrogen bond to form
cellulose microfibrils
- Cellulose microfibrils are bundled up to form macrofibril
 - As the cell grows, cellulose in its structure also increases

Non-cellulosic components

- Cellulose microfibrils are embedded in cross-linked matrix of non-cellulosic molecules

- Polysaccharides
- Proteins
- Lignins
- Lipids

Meristems: Apical Meristem

Concept of a Meristem

- Localized groups of undifferentiated cells capable of continuous cell division and growth
- Meristems are restricted to certain parts of the plant body
- Have not been modified to carry out a particular task apart from dividing
- Important for survival because it allows adaptations
- Initials – cells that maintain the meristem as a continuing source of new cells
- Derivatives – specialized cells produced from the division of the initials
- Final position of the plant cells determines what type of cell they will become in the future

Classification

- According to position
 Apical
o Found at the tips of the plant body
o Initiates primary growth (length)
o SAM and RAM – established during the development of the embryo thus are inactive until the
seeds germinate
 Lateral
o Found parallel with the sides of the axis
o Initiates secondary growth thus are often secondary meristems (girth)
o Cork cambium and Vascular cambium
 Intercalary
o Derived from the apical meristems and inserted between non meristematic tissues
- According to origin
 Promeristem – (in some) direct descendants of embryonic tissue while primary meristem is derived from
the promeristem; region of shoot apex which refers to the initials and their most recent derivatives
which are not yet differentiated
 Primary
o Derived from promeristem
a) Protoderm – gives rise to the epidermal cells
b) Procambium –provascular meristem; gives rise to the vascular tissues
c) Ground meristem – gives rise to the ground tissues
 Secondary
o Originate from differentiated cells that resumed meristematic activity
- Patterns of Growth
 Different growth patterns
o Periclinal division – line division parallel to the nearest surface of cylinder; increase of cells in
rows
o Anticlinal division – line division perpendicular to the nearest surface of cylinder
a) Radial anticlinal – line division parallel to the radius of cylinder; increase of cells
circumferentially and rows remain the same
b) Transverse anticlinal – line division perpendicular to longitudinal axis of cylinder; adds to
length of the organ due to increase in cells longitudinally parallel to the axis
 Mass – division occurs in all planes (perpendicular and parallel)
 Plate – radial anticlinal; surface of SAM; divides towards the sides within 1 layer
 Rib – transverse anticlinal; found in the body of SAM and RAM

Cytological characteristics

- Small cells, thin cell walls, large cell nuclei, absent or small vacuoles, proplastids, no intercellular spaces

Apical Meristem

Theories on Apical Organization

1. Apical-Cell Theory (Nageli, 1845)

 - First theory that explained the apical organization in plants
- Asserts that there is a single morphologically distinct initial cell at the shoot apex and is responsible for the shoot
formation and the successive growth of plants
- Theory exhibited by higher algal groups but not in seed plants
2. Histogen Theory (Hanstein, 1868)
- Asserts that the shoot and root apices consist of 3 distinct meristematic zones called a histogen
 Dermatogen – epidermis
 Periblem – composed of isodiametric cells; cortex
 Plerome – stele or vascular cylinder
- Rejected because tissues destined to be produced by a histogen asserted by the theory was seen produced by
another histogen
3. Tunica-Corpus Theory (Schmidt, 1924)
- Developed from observations of angiosperm shoot apex
- Tunica Layer – refers to one or more peripheral layers of cells that undergoes anticlinal division
 Cells are relatively smaller and layers are denoted by L#
 Produces the epidermis, leaf, axillary bud primordia
- Corpus layer – below the tunica where cells divide in various planes
 Several layers deep and cells are bigger, contributing to volume growth
 Produces cortex, vascular tissue, pith
- Applicable to most angiosperms but botanists weren’t able to observe it independently
4. Cytohistological zonation theory
- Based on cytological histological differences
- Apart form exhibiting the tunica corpus layer, angiosperm SAM exhibits cytohistological zones
- Central Zone – enlarged initial cells found at the summit of the stem apex divide less rapidly and are relatively
bigger with a prominent nucleus and highly vacuolated
- Rib zone/Pith meristem – derived from central zone; appears directly below the central zone; forms the
intermediate region between the initial cells and the partially differentiated cells; becomes the pith
- Peripheral zone – surrounds the rib and central zone; cells are most mitotically active, has densest protoplast,
and has the smallest cell dimensions; produces the procambium, cortex, and leaf primordia

Shoot Apical Meristem

- Found at the shoot apex

- Gives rise to tissues of stem and leaves

Meristems: Lateral and Intercalary Meristem

Lateral Meristem

- Tissues responsible for the formation of the secondary plant body (secondary growth)

Types

- Vascular Cambium – gives rise to the secondary phloem and xylem (periclinal)
- Cork Cambium/Phellogen – gives rise to the secondary dermal tissues: cork parenchyma/phelloderm and
cork/phellem (periclinal)
- Vascular cambium and cork cambium giving rise to more initials (anticlinal)

Vascular cambium

- Location and Distribution:

 Found in the stem and roots undergoing secondary growth; found in veins of leaves and petioles
undergoing secondary growth; found in conifer needles
 Found between bundles between phloem (smaller circles) and xylem (larger circles located near the
pith)
o Interrupted vertically by parenchyma
 Continuous ring when bundles fuse
- Types
 Fascicular – found between xylem and phloem; responsible for secondary growth but are primary
meristems
 Interfascicular – found between vascular bundles; are secondary meristems
- Cell division*
 Initials are described as bifacial
o one side gives rise to the phloem (outer portion of initial) through periclinal division
o one side gives rise to the xylem (inner portion of the initial) through periclinal division
 Cambial initial usually produces more xylem for water is the most limiting nutrient for plants
- Cambial initials
 Initials are present but hard to identify thus it is identified along with the cambial zone*
 o Each radial file only contains 1 initial while the rest are derivatives*
 Has 2 forms (unique)
o Fusiform – spindle-shaped or has 2 tapering ends; name is derived from morphology
o Ray – isodiametric in longitudinal sections but ray-like in cross sections; found between bundles
of fusiform initials
 Structure of initials reflected in their derivatives
o Xylem fusiform gives rise to tracheary elements (major pipes), fibers, axial parenchyma cells
o Phloem fusiform gives rise to sieve elements, “, “
o Ray gives rise to the transverse components of the xylem and the phloem: ray parenchyma cells

Cork Cambium

- Derivatives (periclinal):
 Cork Parenchyma (phelloderm) – relatively larger cells found near the interior
 Cork (phellem) – rectangular or tabular in form found near the exterior
 Epidermis indicates that an organ is in its initial stage of secondary growth
o Extensive meristematic activity pushes epidermis and is eventually be removed
- Cell division
 Bifacial
o Interior portion of division – cork parenchyma
o Outer portion of division – cork
- Cork Cambial Cells – initials

Intercalary Meristem

- Only limited to certain representatives of monocots

- Meristem inserted between more or less differentiated tissue regions
- Has no initials
- Derived from the apical meristem as the shoot grows

Location

- Found at the base of internodes (space between nodes)

- Found in the lowermost region of leaf sheaths (common feature in grasses)

Other notes

- Cell differentiation is triggered by differential gene expression – difference in genes expressed

 Set of processes followed by a cell to form a specific cell type
- Cellular determination is due to inductive signaling between cells
 One cell produces a special type of inductive signal (a molecule called ligand) which moves to a second
cell and influences the 2nd cell to undergo cellular determination in order to differentiate or specialize
 3 Mechanisms of inductive signaling: diffusion, direct contact, gap junctions

Tissue Differentiation

Concept of Tissue Differentiation

Plant Development

- sum total of events that progressively form an organism’s body; all the processes and changes giving rise to the
plant body
- defined as:
o Growth – irreversible increase in size accomplished by a combination of cell division and cell
enlargement
o Morphogenesis – process by which a plant assumes a particular shape or form
o Differentiation – process by which cells arising from a common precursor become different from one
another and from their cell origin
- Senescence – series of changes in a living organism that leads to its death; believed to be genetically controlled
o Ex: When leaves change color due to declining chlorophyll content, when trees shed their leaves, fruit
ripening, removal of root cap, removal of suspensor in embryogenesis
o Consequence of environmental cues and hormonal signals the plant receives
o Can be stress-induced
- Aging – accumulation of changes that lower the vitality of a living entity without being lethal
o Aging can lead to senescence (age-related senescence) but senescence

Differentiation

- Successive changes in form, structure, and function of the progeny of meristematic derivatives and their
subsequent organization into tissues and organs
 - Coordinated and regulated process to attain a specific form
- Levels
o Cellular
o Tissue (histogenesis)
o Organ (organogenesis)
- Depends on the control of gene expression
o Different types of cells synthesize different proteins because they express certain sets of genes not
expressed by other types of cells
- Fate of plant cell determined by its final position
- Specialization – structural adaptation to a particular function
o Specialization is the concept of cells having different forms and functions while differentiation is the
actual process of cells becoming specialized
- Determination – where a cell chooses a particular fate through cell signaling or through the nature and pattern
of cell division; progressive commitment to a specific course of development that brings about a weaking or loss
of capacity to resume growth
o Once cells are determined, they commit to their fate and lose their capacity to return to their previous
form
- Competence – ability of a cell to develop in response to specific signals
o Cells need to be competent first before it undergoes determination
o Not all cells are similar in their degree of competence

Transdifferentiation

- Capacity of plant cells to convert from one cell type to another

- Some cells in the plant are capable of resuming meristematic activity to differentiate into another type of tissue
- Processes involved:
o Dedifferentiation – loss of previously acquired characteristics
o Redifferentiaion – acquisition of new characteristics

Cellular Basis

Cellular changes in differentiation

- During differentiation, histological diversity results from the changes in the characteristics of individual cells and
also from changes in the relationships between the cells
o Ex. Increase in vacuolar sap, development of plastid from proplastids
o Endopolyploidy – when chromosomes replicate without karyokinesis
 Observed in differentiating cells but has no functional significance
 Increases level of gene expression and promotes rapid cell growth
o Unequal increase in cell size

Histological feature of differentiation

- Cell arrangement – may be determined early by the growth of its meristem

- Appearance of intercellular spaces – profoundly modifies the appearance of tissues in some cells
- Wall growth
o Symplastic/coordinate growth – walls of adjacent cells do not separate and grow in unison
o Intrusive/interpositional growth – adjacent walls separate, and growing cells occupy the space formed
by the separation (tracheids, sclereids)
o Protruding growth – growth takes place away from the plant surface thus not limited by neighboring
cells (trichomes)

Causal Aspects

Factors that can influence differentiation in plants:

Polarity

- Establishment of polarity is essential because it fixes the structural axis of the plant body
- Related to the phenomenon of chemical gradience in plant
- Seen in embryogenesis, with the differentiation of apical cells from basal cells

Position

- Fate is determined by its final position in the developing organ

- Cells differentiate into a cell type appropriate to its new position

Hormones

- Act as chemical messengers or signals between cells

 o Chemical signaling is a crucial function of plant as cells do not have the ability to move
o Helps long distance communication throughout the plant body
- (auxin, cytokinin, ethylene, abscisic acid, gibberellins)

Environmental Signals

- Course of development in plants is largely influenced by environmental signals

- (quantity and quality of light, gravity, temperature, wind)

Plant Tissues: Ground Tissues

Parenchyma

- Sometimes referred to as the ground tissue because it is where the other tissues are embedded
- Fundamental tissue because it serves as the foundation of the plant body in the sense of ontogeny and
phylogeny
o Ontogeny – gametes are parenchymatous in nature
o Phylogeny – link between organisms affected by evolution can be inferred due to their parenchymatous
natures

General Structures and Characteristics

- Presence of an intact or living protoplast

- Living at maturity even after differentiation thus having the capability to resume meristematic activity
- Totipotent – can give rise to all other cells and even to a whole organism
o Plant takes advantage of this through wound healing, regeneration, and the formation of adventitious
organs
o Applied in tissue culture and plant propagation
- Has thin primary walls
o Can have secondary walls in rare cases (sclerified parenchyma)
- Has primary pit fields
- Morphologically and physiologically are less specialized

Distribution and Function

- Performs the bulk of the “housekeeping” activities within the plant body
o Photosynthesis, storage of materials, respiration, secretion and excretion, and movement of water and
food substances
- Specializations may be based on the morphology or shape of cells or based on their functions
o Shape: polyhedral, isodiametric (ground tissues of the stem), lobed (gymnosperm mesophyll),
irregular/branched (dicot spongy mesophyll), elongated (palisade mesophyll)
 Usually differs in distribution
o Specializations:
 Chlorenchyma – parenchyma with numerous chloroplasts functioning for photosynthesis; highly
vacuolated with extensive system of intercellular spaces; seen in mesophylls, cortex of the stem,
secondary xylem tissue, and the pith
 Secretory – found in secretory ducts and secretory channels; dense protoplast, rich ribosomes,
may either have an extensive Golgi bodies or massively developed ER
 Storage – starch storing parenchyma cells with abundant amyloplasts (common in roots);
protein and oil storing thus the abundance of proteinoplasts and elaioplasts (common in seeds);
pigment storing thus in the form of chromoplasts or anthrocytes; water storing cells (tissues of
succulent plants)
 Aerenchyma – has large intercellular air spaces developed by lysigeny (burst) or schizogeny
(adjacent cell walls separate); well developed in aquatic angiosperms for oxygen deficiency to
produce more ethylene used in programmed cell death
 Transfer – characterized by the presence of wall ingrowths, increasing cell surface area of the
plasma membrane thus allowing a greater surface area for transport in short distances; seen in
phloem tissues
 Idioblast – contains resin, crystal (truse), oil, pigment, and tannin; larger than transfer cells
- Form of cells vary because of its respective functions
- Found in the bulk of ground tissues (larger cells; loose) and within vascular tissues (smaller cells; compactly
arranged)

Collenchyma

General Structures and Characteristics

- Thick, non-lignified cell walls due to additional pectin and hemicellulose

- Isodiametric cs, elongated ls
 - A simple tissue – composed of only 1 cell type
- Has a complete protoplast capable of resuming meristematic activity
o Has more restrictions due to their thick cell walls, unlike the parenchyma cells
- body
- Patterns of Wall Thickening
a. Lamellar/Plate – tangential walls (parallel to the surface) are thicker than radial (parallel to the radius)
walls
b. Angular – thickening localized on sides
c. Lacunar – similar to angular but there are spaces found at the corner
d. Annular – uniformly thickened cell walls

Distribution and Function

- Found at the periphery of a plant organ sub-epidermally – immediately beneath the epidermis
o Provides mechanical support to the plant
o Continuous: may be interrupted by parenchyma (beneath stomata)
o Strand: bundles or axial strands separated by parenchyma (strand peripheral parenchyma)
- Found in actively elongating regions of the plant body
o Facilitates expansion of organs
- Fascicular/Perivascular – found associated with the vascular tissues
o Can act as a defense barrier
o Supracribral – borders the vascular bundle at the phloem pole
o Infraxylary – borders the vascular bundle at the xylem pole
o Circumfascicular – completely surrounds the vascular bundle
- Distribution of patterns allows the collenchyma to perform its functions better

Sclerenchyma

General Structures and Characteristics

- Thickest among the rest; lignified secondary cell walls

- Some lose their protoplasts during differentiation
o In some instances, may remain at maturity
- Elongated cells are classified as fibers
o Long, spindle-shaped
o Support plants no longer elongating
o Found solitary or in small groups in ground or vascular tissues (extensive)
o Classifications:
 Xylary fibers – fibers found in the xylem
 Libriform – longer and has thicker walls; has simple pits
 Fiber Tracheid – thinner walls; has bordered pits
 Extraxylary fibers
 All fibers in monocots are considered as extraxylary fibers
 Phloem fibers – found in secondary phloem; arises from parenchymatous sieve
elements
 Perivascular fibers – found at the periphery of vascular tissues, outside the phloem
 Bundle sheaths – appropriate for vascular bundles; can extend to dermal tissues (bundle
sheath extensions)
 Bundle cap – extraxylary fibers surrounding vascular bundles are sometimes incomplete
thus are only found in one side, usually the phloem side
- Shorter cells classified as sclereid
o Shorter lumen – space enclosed by cell wall
o Cell walls typically appear multilayered

Distribution and Function

- More widely distributed relative to the others

- Found sub-epidermally or interspersed within collenchyma tissues
- Found in older or more mature parts of the plant body or non-elongating parts
o Provides mechanical support

Plant Tissues: Dermal Tissues – Epidermis

Epidermis

- Primary functions: limit water loss, control gas exchange, protection for abiotic and biotic stresses

General Characteristics
 - Constitutes the outermost layer of the plant body except for the root
- Complex tissue due to it having different types of cells
- Has living protoplast at maturity thus it is capable of transdifferentiation
o Cork cambium may arise from this
- Cells are compact and have no intercellular spaces between them
- Typically, uniseriate or one cell layer thick
o Some species are multiseriate as a result of periclinal division
o Some have hypodermis which are actually ground tissues
- Has cuticle – coating of waxes and oils that covers the epidermis of the aerial parts of the plants
o Functions: limit water loss, block UV rays, inhibit attachment of pathogens to the plant body
o Major factor in the colonization of plants
o Components: cutin (hydrophobic; cuticular proper), cutan, epicuticular waxes (scatters light as
protection from UV damage)
o Morphology varies depending on the species and the environment

Anatomical Features

1. Pavement cells
- Also called ordinary epidermal cells
- Typically appear tabular but it can also appear elongated with reference to the axis
o Vary depending on their relative position
- Varied shapes in surface view: rectangular, wavy (leaves, petals, ovules)
- Retain protoplast at maturity
o Usually vacuole occupies > 90% of the cell
 Where anthocyanin found – has different protective functions associated with light
- Walls vary in thickness
2. Stomata
- Openings in the epidermis each bounded by a pair of guard cells
o Guard cells – specialized epidermal cells distinguished by their green color and unique shape
 Eudicots have crescent shaped guard cells
 Monocots have dumbbell shaped guard cells
 Lined by cuticle, prominent nuclei, numerous mitochondria, poorly developed chloroplast
 Ability to change shape – most important feature
- Regulate exchange of water vapor and CO2
o Chemical ions involved in closing and opening of the stomatal pore
 Ions from adjacent pavement cells called subsidiary cells
 Differ in size, shape, arrangement, and sometimes in content from ordinary epidermal
cells
 Number of subsidiary cells are species specific
- Stomatal complex = guard cells + subsidiary cells
o Configurations:
 Anomocytic (Irregular) – guard cells and subsidiary cells have no well defined pattern
 Anisocytic (unequal) – has 3 subsidiary cells with different sizes
 Diacytic (cross-celled) – guard cells enclosed by a pair of subsidiary cells
 Paracytic (parallel) – both cells are parallel
 Actinocytic – stoma surrounded by a circle of radiating sub. cells perpendicular to the guard cells
 Gramineous – dumbbell shaped guard cells are surrounded by 2 lens-shaped sub. Cells
 Tetracytic – guard cells enclosed by 4 subsidiary cells
 Cyclocytic – stoma surrounded by 1 or 2 narrow rings of subsidiary cells
- Varies in distribution:
o Amphistomatic (monocots) – stomata found on both surfaces of leaves
o Epistomatic – (hydrophytes) stomata found at the upper surfaces of leaves
o Hypostomatic (eudicots) – found at the lower side of leaves
- Classified based on position (trans view):
o On the same level as the surrounding subsidiary cells
o Raised compared to the surrounding cells
o Sunken – below the surrounding cells
 Has epistomatal chamber above guard cells and;
 Substomatal chamber below the guard cells
 Functions in limiting water loss by trapping water vapor in the chambers
o Stomatal crypt – same function as sunken but trichomes are the one responsible for trapping
- Also varies in density, and relative # on the surface
- Distribution and abundance is affected by light and CO2
3. Trichomes
 - Highly variable appendages arising from protuberances of epidermal cells
- Classifications may overlap due to their high diversity
- Can be uniseriate or multiseriate, or unicellular or multicellular, or unbranched or branched, or glandular
- Can also be described according to their shapes
- Morphology depends on their functions
o Reduce transpiration
o Absorb water and minerals – epiphytic plants
o Secrete salt – for removing toxic salt in plant body
o Protection against UVB damage
o Defense against insects
4. Others
- Silica cells and corks cells
o Found on the epidermal layers of grasses
o Often occur in pairs
o Silica cells provide support to the leaves and increase resistance to various insects and pathogens
- Bulliform cells
o Present in leaves of many monocots
o Large, thin-walled, and highly vacuolated
o Functions in rolling and unrolling of leaves
- Cystoliths
o Composed of calcium carbonate attached to a silicified stalk
o Physiological significance is unclear

Functions

- Reduction of water loss by transpiration (compact arrangement, regulation by stoma, cuticle)

- Regulation of gas exchange
- Mechanical protection (compact arrangement, trichomes)
- Protection against pathogens (compact, cuticle)
- Mechanical support
- Protection against UV radiation (cuticle, trichomes)
- Dynamic compartments of metabolic products
- Absorb water and solutes
- Act as lenses – they concentrate light so that photosynthetic cells just get enough light
- Site of perception involved in circadian leaf movements and photoperiodic induction

Root epidermis

- Called rhizodermis or epiblem

- Differs with the shoot in terms of development, structure, and function
- May develop from a common origin with the cells of the root cap, called the dermato calyptrogen
- May also differentiate from the outermost layer of the cortex
- Cuticle is absent or very thin
- Develops trichoblasts – root hair functioning for absorption which helps expand he surface area of the root

Plant Tissues: Dermal Tissues – Periderm

The Bark

- non-technical term that has different components compared to the periderm

- includes tissues outside the vascular cambium (secondary phloem to phellem)
- Inner bark: Secondary phloem to cork cambium – living cells/living part of the bark
- Outer bark (rhytidome): Phellem and old nonfunctional phloem

Periderm

- Found in secondary plant body (replaces the epidermis)

- Reduces loss of water and solutes from interior tissues
- Protects plant from unfavorable environmental conditions for it is waterproof and the cork is an insulator,
protecting plant body from temperature extremes
- Helps protect plant body from invasion of insects and microorganisms
- Gives additional support to the plant body
- Not all plants have periderm
o Found in surface of roots and stems with secondary growth
o Herbaceous eudicots (oldest part of stem and root) – also called suffrutescent plants
o Abscission zones and surface wounds
- Most monocots do not develop a type of periderm like eudicots
 o Do not produce true secondary growth
o Layers of phellem are separated by suberized undivided cells
o Storied cork – Cork-like layer may be produced due to thickening of epidermis by repeated divisions of
meristematic cells situated at the margin of the cortex
o Protective tissues of monocots
 Extremely hard epidermis due to the lignified tangential and radial walls of epidermal cells
- Monocots do not have ray initials, only fusiform initials that may vary in morphology
o These meristems are called secondary thickening meristems (STM)
- Few monocots possess true periderm and true secondary growth

Phellogen/Cork Cambium

- Comprised of only one type of cell which is rectangular or polygonal in nature that are narrower and vacuolated,
and may contain tannins or chloroplasts
- Only forms one, single continuous layer that divides in a periclinal manner
- Anticlinal division is also observed sometimes to accommodate the increasing circumference of the plant body
- They are living at maturity
- Originates from sub-epidermal cell layer, epidermal layer, cortical parenchyma, tissues near vascular region,
tissue within phloem, or from pericycle

Phellem/Cork Cells

- Nonliving at maturity but they may contain tannins and resins that can be stained under the microscope
- Prismatic in nature but may look elongated in longitudinal sections
- Compactly arranged in radial rows (coincides with phellogen) thus they will not have intercellular spaces
between them
o Exemptions: Tropical trees possess intercellular spaces to enhance gaseous exchange
- May have thick (due to extensive formation of suberin, wax, and cellulose) or thin walls
- Compressible, resilient, resistant to oil, enzymes, and water

Phelloderm/Cork Parenchyma

- Resembles cortical/phloem parenchyma thus it is hard to determine sometimes but one tip involves its radial file
formation
- Cells smaller than cortical parenchyma and have abundant intercellular spaces
- Cell walls thinner than phellem cells due to lack of suberin, cellulose, and wax
- Living at maturity and may contain crystals
- May undergo sclerification

Lenticels

- Function similar to epidermis – which is for gas exchange

- Arises beneath the stomata; lenticels are where guard cells existed when plant was still under primary growth
- Product of active phellogen activity
- Cannot regulate opening
- Lenticel phellogen – relatively more active than phellogen cells
o Produces complementary/filling cells – loosely arranged cells which allows abundance of intercellular
spaces for gaseous exchange, and which makes up most of the lenticels
- Closing Tissue – compact suberized layer of phellem cells that holds the loose nonsuberized complementary cells
in place; identical to phellem cells
o Compactly arranged due to their function

Plant Tissues: Vascular Tissues – Xylem

Vascular Tissue System

- Consists of an interconnected network of cells and tissues that function for water and food transport throughout
the entire plant body
- Also transports hormones and other signaling molecules
- Pivotal moment in the transition of plants to terrestrial biomes
- Found in vascular bundles in the stem and leaves, or a group at the center or near the center of the root known
as the vascular cylinder
- Includes complex tissues – made up of different types of cells: Xylem and Phloem
o Xylem – transport of water and dissolved ions upwards
o Phloem – transport of metabolites from source to sink

Xylem

- transport of water, dissolved ions, mineral nutrients, plant hormones, and regulatory signals upwards
- provides most of the mechanical support for the upright posture and general architecture in vascular plants
 - Transition from protoxylem to metaxylem happens gradually
- Primary Xylem
o Protoxylem
 Differentiates in parts of the primary plant with incomplete growth
 Relatively few tracheary elements
 Vessel elements exhibit annular and spiral thickenings
o Metaxylem
 Differentiates in still growing primary plant body but matures largely after elongation is
complete
 Wider tracheary elements and may contain fibers
 Vessel elements exhibit scalariform, reticulate, and pitted thickenings
- Secondary xylem
o Wood is another term for secondary xylem
o Has 2 systems that are interconnected by means of plasmodesmata:
 Axial
 Derived from fusiform initials
 Includes tracheary elements, fibers, as well as axial parenchyma cells
 Ray
 Derived from ray initials
 Includes ray parenchyma cells and other living cells
 Connects xylem with the living cells of the pith, phloem, and cortex
o 3 sections of wood – studied due to the presence of the 2 systems
 Transverse section – perpendicular to the long axis of the stem; reveals growth rings
 Radial – parallel to the longitudinal axis and runs through the center of the stem; reveals side
view of rays
 Tangential – parallel to the long axis but off center
o Growth rings – because of periodic activity of vascular cambium
o As wood becomes older, it gradually becomes nonfunctional in conduction and storage
 Sapwood – where most of the transport of water and minerals take place
 Heartwood – formation is due to programmed cell death
 Softwood vs hardwood – main difference is based on the taxa; hardwood is more complex
 Types of hardwood based on pores
o Diffuse porous – uniform size and distribution of vessels throughout the growth
rings
o Ring porous – pores of earlywood are larger than those of latewood
o Semi-ring/diffuse porous – intermediate between these 2
 Reaction wood – develops in branches and stems in an effort to counteract the force and
straighten the branch of stems
 Compression wood (conifers, gymno) – develops on the lower side of the branch/stem
where compressive stress is very high and pushes the stem upright
 Tension wood (angio) – develops on the upper side of the stem/branch where large
tensile stress exists and pulls the stem upward

Components and Function of Xylem

- Tracheary elements
o Most well-known
o Conduction of water and transport of solutes
o Derived from the term trachea
o Types
 Tracheids
 More primitive than vessel elements
 Found in both angiosperms and gymnosperms
 Elongated, tapering, and imperforate, containing pits (bordered)
 Vessel elements
 Evolved later than tracheids
 Wider, elongated, but shorter than tracheids, and are connected end-to-end
 Common in angiosperms but rare in gymnosperms
 Perforations at their walls called perforation plates
o Simple
o Scalariform – perforations are elongated and are arranged in a parallel of series
o Reticulate – resembles a net
o Foraminate – group of approximately circular holes
 Vessels are multicellular pipes while vessel elements are individual cells comprising it
 o More or less elongated
o Lignified secondary walls showing several patterns
 Differences in pattern are based on the timing of their formation
 Annular and spiral patterns – characteristic of tracheary elements that form with primary xylem
of organs that are still elongating
 Scalariform and pitted – found in vessel members after elongation of organ has ended; found in
late forming primary xylem or secondary xylem
o Contain pits
 Bordered pits show 3 main types of arrangements:
 Alternate – pits arranged in diagonal rows
 Opposite – oval-bordered pits arranged horizontally
 Scalariform - pits elongated transversely and are arranged in ladder-like series
o Dead at maturity
 Before cells die the cell walls are lignified
- Xylem fibers
o Support of the xylem tissues and sometimes storage
o Long with commonly lignified secondary cell walls that are thicker than tracheids
o Retains protoplasts at maturity
o Types of fibers
 Libriform
 Longer than tracheids with thicker walls and simple pits
 Fiber-tracheids
 Bordered pits with lenticular slit-like apertures and thin cell walls
 Intermediate form between tracheids and libriform fibers
- Xylem parenchyma
o Storage of fat, starch, tannins, and crystals, and translocation of various substances
o Living cells present in both primary (thin primary cell wall) and secondary xylem (often have secondary
wall)
o Occurs in 2 form in secondary xylem:
 Axial Parenchyma and Ray Parenchyma

Plant Tissues: Vascular Tissues – Phloem

Functions

- Food-conducting tissues for it acts as a conduit for the transfer of sugars, amino acids, and lipids
- It also transports hormones, hormone-like molecules like florigen, proteins, and RNA thus called the information
superhighway

Phloem elements

Sieve-tube elements (A)

- Pipe of sieve elements

- Acts as major conducting cells in angiosperms
- Elongated, shorter but wider diameter compared to the sieve cell, with tapering ends (gymnosperms) which
becomes transverse (angiosperms) upon differentiation
- Only exhibit the presence of primary walls but may appear thick and lignified in other species
- All cell walls are characterized by sieve areas or perforations in their walls that are much more prominent at
transverse walls (thus called sieve plate)
- Living but no nucleus or are found as remnants
- Contains S- or P-plastid (presence of starch or protein)
- Contains P-protein after the precursor of the sieve tube element has divided to give rise to 1 or more
neighboring companion cells
o Act as slime clogs to seal one end of the sieve tube element to prevent pathogenic invasion
- Abundant in wound callose

Sieve plates (A)

- Sieve areas found at the end of transverse walls

- 2 Types
o Simple – there is only a single sieve area in one sieve tube end wall (Angiosperm)
o Compound – One sieve tube element contains two or more sieve areas in one end wall
- Gymnosperms do not have sieve plates because they do not have end walls

Sieve Cell (G)

- Sieve tube elements of gymnosperms

 - Elongated, relatively longer, smaller diameter, have tapering ends
- Contains sieve pores traversed by a tubular ER
o Similar to desmotubules of plasmodesmata
o Tend to be numerous in regions that overlap with other sieve cells but are not continuous
- Living at maturity but eventually loses nucleus through nuclear degeneration or pyknotic degeneration –
chromatin condenses and forms a very dense mass before nuclear envelope ruptures
- Also loses ribosomes, golgi bodies, actin filaments, microtubules, and tonoplast
o Lost due to selective autophagy – disorganization and disappearance of most cellular components
- Lack p-protein and callose

Companion Cells (A)

- Specialized parenchyma cells

- Function as a life support system for sieve tube elements only by delivering informational molecules and ATP
- Right next to sieve tube elements brought about by their ontogeny (arise from the same precursor)
o Also associated in terms of their function – companion cells have primary walls with plasmodesmata
that are continuous with the pores of the sieve tube elements
- A single sieve tube element has 1 or more companion cells
- Nucleated, denser protoplast, smaller than sieve tube elements, usually also elongated but can vary

Strasburger Cells (G)

- Also known as albuminous cells

- Acts as a life support system in sieve cells thus it is only found in gymnosperms
- Presumed to have the same role and characteristics as the companion cells
- Not ontogenically related to sieve cells

Parenchyma Cells (A and G)

- Found in primary and secondary phloem

- Acts as a storage of substances like starch, tannins, and crystals
- Differs in distribution between primary and secondary phloem (ray and axial systems)
- Walls in contact with the sieve tube members are not lignified while walls in contact with fibers or sclerenchyma
are lignified
- Undergoes sclerification once the phloem loses its functionality
- Phellogen formed by phloem/ray parenchyma is grouped with parenchyma cells

Sclerenchyma

- Can exist as
o Fibers – more common, living/non-living, found at the outermost portion (phloem fiber cap in young
dicots)
o Sclereids – form from sclerification (development of secondary walls and may or may not have
lignification) of parenchyma cells
o Fiber-sclereids – a combination of the two; originate from the axial parenchyma of the phloem

Primary Phloem

Protophloem

- First functional food conducting tissue

- As the plant increases in size, protophloem will be stretched until it is destroyed and becomes nonfunctional
- Has sieve elements, parenchyma, and fibers as major components
- Lacks companion cells

Metaphloem

- Matures after growth in length of surrounding tissues is completed and replaces the nonfunctional protophloem
- May become inactive after secondary phloem
- Persists as the conducting tissue in plants (herbaceous dicots and monocots) that do not form secondary phloem
- Sieve elements are longer and wider and contains components the same as protophloems
- Has companion cells
- Usually lacks fibers in dicots

Secondary Phloem

- Axial System: sieve cells (gymnosperm), sieve tube elements + sclereids (angisoperms), companion cells,
parenchyma cells, fibers
o Arrangement in different taxa of gymnosperms may differ
- Radial System: ray phloem, parenchyma
 o Continuous with the radial system of xylem
o Characteristics may differ in conifers (uniseriate, contains strasburger cells) and angiosperms (diverse
patterns, presence of sclereids, secretory elements, crystal forming cells, and diverse patterns of fibers)

Nonconducting Phloem

- Formation of a callose at the sieve areas

- Parenchyma cells, Strasburger cells, and companion cells are dead
- May remain open after death, leaving an air space
- Tylosoid – protrusion in the sieve element coming from contiguous parenchymatous cells
o Protrusions may invade the space of dead sieve elements or may simply push the wall of the sieve
element at one side, causing its collapse
- Crystal/tannin deposition

Secretory Structures

Secretion

- Complex phenomenon wherein there is a separation of substances from the protoplast:

o Removal of substance towards the surface of the plant body or into internal spaces
o Accumulation of secreted materials in some parts of the cell

External Secretory Structures

1. Salt Glands
- Present in plants living in saline habitats
- Regulates salt content through holocrine secretion (substances secreted are produced in the cytoplasm and are
eventually released through the rupturing of the cell membrane)
- Prevents movement of water outside of the plant because of the difference in osmotic gradient
- Salt bladder – has a large vacuole; when vacuole is filled, it ruptures, and ions are released which eventually exits
the plant body
- May also exist as microhairs or multicellular glands
2. Nectaries
- Nectar – aqueous fluid containing high amounts of sucrose, glucose, or fructose
- Restricted to the epidermis via ordinary epidermal cell, trichomes, or stomata
- May also be found several layers deep but not substantially deep
- Types:
o Floral – found in floral parts such as the in the sepal, petal, stamen, ovaries, or on the receptacle
 Directly associated with pollination and it primarily functions to attract pollinators
o Extrafloral – occur on vegetative parts such as at the petiole, pedicel of the flower, and on the outer
surface of floral parts (indicating that they have a different function which is to attract insects that help
them defend from prey)
 Represented by glandular hairs/epidermis
 Alluring glands – found in carnivorous plants that are used to attract insects as their prey
3. Colleters
- Secrete sticky substances that are either mucilaginous or resinous and are water-insoluble
- They may also secrete terpene – for protection of young buds, bud scales, or bud leaves
- Not that persistent – eventually dries up and sheds off
- Resemble trichomes but are entirely different even though they emerged from both epidermal and sub
epidermal tissues
4. Osmophores
- Special glands that secrete volatile substances which may be in the form of terpenoids or aromatic substances
which gives off the fragrance of the flower thus also called as floral fragrance glands
- Attracts pollinators of flowers
- Precursors for sex pheromone
- Located several layers deep with the epidermis as the outer layer
5. Glandular Trichomes
- Varying group of external secretory structures
- Secretes lipophilic structures – substances that dissolve in lipids (terpenoids, fats, waxes)
- Secreted by subcuticular activities
- Serves as a deterrent from herbivores while some attract pollinators
a. Hydathodes
- Loose arrangement of parenchyma cells which secrete water, or other substances dissolved in the water
(salt, sugar, organic substances)
- Secretion is known as guttation, which is an active process (different from dew drops via condensation)
- Found at the margins and tips of leaves
 - Can be active – water is actively secreted by the parenchymatous cells not connected to the tracheary
elements
- or passive – involves water “pull” through tracheary elements  intercellular spaces of parenchyma cells,
called epithem  and exit via stomata (smaller and always open)
b. Digestive Glands – secrete substances that digest insects caught by carnivorous plants
c. Stinging Hairs – produce toxic substances stored in vacuoles

Internal Secretory Structures

1. Internal Secretory Cells

- Called as secretory idioblasts
- Parenchymatous cell that is extremely large and often elongated thus it appears to be tube-like or sac-like
- Produces and stores chemical that deters herbivores and foraging animals
- Other types classified based on their cell contents:
o Crystal-containing cells – may look like parenchyma but in some cases are more distinct
o Myrosin cells – contains myrosinase which functions for defense common in cabbage family
o Pellucid glands/oil glands – under the family of citrus, this is a distinguishing feature found on leaves and
rinds; cell cavity is attached to a point on the inner wall of the cell
o Mucilage cells – secretes a thick glue-like substance to the outside of the plasma membrane; cell usually
differentiates near meristematic regions (common in dicots)
o Tannin idioblasts – secretes and stores abundant tannin in the cytoplasm (common secondary
metabolite – chemical substances produced which are not directly involved with growth processes but
are rather used for defense processes)
2. Secretory Ducts and Cavities
- Both ducts and cavities deposit terpenoids and carbohydrates into large intercellular spaces lined by epithelial
cells or secretory cells
- Cavities are relatively shorter while ducts are much longer
- Cavities are formed in a schizogenous way (splitting or separation of cells)
- Ducts are formed in a schizogenous way, lysogenous way (lysis of cells), or a combination of both (cells that
separate undergo lysis)
- Formation of ducts can also be affected by trauma, injury, mechanical pressure, attack of insects and
microorganisms, and physiological disturbances
3. Laticifers
- May either occur as single cells or may form a series of cells
- Secretes latex – a colloidal suspension of carbohydrates, oils, alkaloids, organic acids, enzymes which are usually
white or colorless
- Colloidal suspension of latex may also contain crystals, starch grains, and enzymes such as cellulase
- Used to deter herbivores
- May be classified based on their form or structures:
o Articulated/laticiferous vessels – forms by fusion brought about by the dissolution of common cells
o Non-articulated – originate from single cells; cynocytic – has multiple nuclei due to multiple nuclear
divisions; tube-like in structure and may also be branched or unbranched

Chem 26 (ANALYTICAL CHEMISTRY LECTURE)

Analytical Chemistry

Measuring Property of the Analyte

- Analyte – the one you are looking for (ex: Nickel in Nickel ore)
- X = kA where x – signal; A – amount of analyte; k – constant

Processing of Data

- Raw Data -> 1. Calculation 2. Statistical Analysis -> Processed Data -> Interpreting results

BIO 101 (STATISTICS)

Introduction to Statistics

- Used by the state before for data gathering that’s why it came from the latin word Statista, which means
politician
- Used before to monitor demographic info, military recruitment, and tax collection
- It is now the analysis and interpretation of data with a view toward objective evaluation of the reliability of the
conclusions based on the data
- Science of collecting and analyzing numerical data in large quantities especially for the purpose of inferring
proportion of a whole from representative samples
 Descriptive
o Provides a way to organize, summarize, and describe data
 o Does not allow us to make a conclusion about our hypothesis
o Measures of central tendency, measure of dispersion/variability
 Inferential/Inductive
o Provides a way to make conclusions, generalization, predictions, and estimations based on data
from samples
o Helps us to objectively select which hypothesis offers the best explanation
o Comparisons between 2 populations, between 2 or more experimental treatments
- Variable – any characteristic, number, or quantity that can be measured or counted
 Quantitative – numeric (discrete or continuous)
 Qualitative – non-numeric
- Data – any possible value or measurement that any variable can assume
- Populations – all items that are being studied; entire collection of measurements
 Large – best to set limitations (ex: fruitflies in baguio); avoid making generalizations
 Small – best to measure the entire group (ex: bio 101 class)
 Imaginary/Hypothetical – how many children u and ur children will have; an organism exposed to high
levels of salinity
- Samples – subset of all measurements in the population; used when population is too large
 Sampling to get sample characteristics and interpret population characteristics
- What are statistics? – often used synonymously with “sample data”; summaries or collections of numbers that
describe a sample

Population parameters vs. Sample statistics

- Population mean uses myu

- Sample mean use x with a bar on top
- As the sample size (n) approaches the value of the population size (N), the sample mean approaches the value of
the population mean
 Increasing the sample size tends to get a closer value to the real population parameter

Biological data

- There is a lot of variation in the data = more difficult to get conclusive results with highly variable data
- Sources of variability:
 Intrinsic variation – the characteristic being measured varies between organisms/within the same
organism
 Experimental or measurement error – caused by measurement through different
experimenters/instruments
- How is variability handled?
 Describe and measure the extent of variability
o Consistent is better
 Determine a probability of the correctness of the conclusion we make about the data
o Determined by the error bar
- Scales of measurements
 Ratio Scale (ordered data)
o Constant size interval between units and Existence of a true zero point
o Ex. Egg numbers, gill slits, spores, branches, digits
 Interval Scale (ordered data)
o Constant interval size but no true zero point
o Ex. Temperature, time of the day, compass points
 Ordinal Scale (ordered data)
o Deals with relative differences rather than quantitative differences
o Contains less information than ratio or interval data
o It gives an idea of order or ranking
o Ex. Relative size, relative growth rate, relative light intensity or brightness
 Nominal Scale (categorical data)
o Variable/attribute under study is classified by some quality it possesses rather than by a
numerical measurement
o Ex. Eye color, taxonomic affiliation, habitat type
- Numerical Data
 Continuous data
o Variables that could have any conceivable value within any observed range
o There is a possible value between any other two possible values
o Ex. Weight, height, growth rate
 Discrete data
 o Variable can take on only certain values; do not necessarily take on values of consecutive
integers
o Ex. Acad load, number of teeth, leaves, seeds

Descriptive Statistics: Frequency Statistics and Graphical Representation of Data

How to Present Data

- Through tables, graphs (bar graphs, line graph)

- Scatterplot – best to use when comparing two variables
- Pie chart – best to use for proportions
- Box plot – best to use for quartiles
- Prevent false impressions
- Always start at 0
- Histogram has no gap between bars compared to a bar graph

Frequency Distribution

- Tables that show and summarize the frequency or count of occurrences of values
- When you have too many categories, trim it down to several groups without loss of info
 2k > n rule where n is the number of samples and k is the ideal number of groups
 After determining the number of groups, determine the width of a class or grouping
o Let w = width/range of each class
a) W = largest value minus smallest value divided by the number of classes or groups
o Midpoint – highest value minus lowest value divided by two
- Cumulative Frequency – can either start with low values or high values; can be used to assess something

Descriptive Statistics: Measures of Central Tendency

Measures of Central Tendency (finding the center of the data)

1. Arithmetic Mean or Average

- Capital X – measurements taken from a population (mean unit is μ)
- Small x – values measured from a sample (mean unit is x̄ )
- N or n – sample size

2. Median
- Middle measurement in an ordered (chronological) set of data
- best used when there are extreme values than the mean for the mean tends to pull the data up or down
- found somewhere between the lower half and the upper half of the data set
- M = X(n+1)/2 where n is the sample size and X is the sample
 If n is odd, the subscript will indicate the middle measurement
 If n is even, the subscript will be a half integer indicating 2 middle values (median is midpoint)
o Midpoint is (X1 + X2)/2
- Use interpolation when there are tied observations
- M = (lower limit of interval) + [(0.5n – cum. Freq.)/observations within interval)](interval size)
 Lower limit of interval – calculate midpoint
 Cumulative frequency – how many data points are there before you reach the probable location of
median?
 Interval Size – look at the increment

3. Quantiles
- Measures that divide a group of ordered data into equal parts
- A generic term
- Quartiles (4), quintiles (5 parts), deciles (10), centiles (100)
- Important in some biological data
- For Q1, use formula for median but divide it by the quantile needed (ex. 4 for Quartiles)
- For Q2, use median formula in general
- For Q3, X(n+1) minus subscript of x for Q1
- For tied observations, use formula of median but substitute 0.5n with .25n for 1 st quartile and .75n for 3rd
quartile
- Percentile – Index Point(i) = Percentile (P)n/100

4. Mode
- Most frequently occurring measurement in a set of
- Equal frequencies = no mode
- Two modes = bimodal
 5. Graphical Representation
- Symmetrical – Mode = Median = Mean
- Bimodal – Mode 1 < [Median = Mean] < Mode 2
- Positively or right skewed – higher frequency in the lower values; Mode < Median < Mean
- Negatively or left-skewed – higher frequency in the higher values; Mean < Median < Mode

6. Other Measures
- Midpoint or Midrange
- Geometric mean – nth root of the product of n data
- Harmonic Mean
- Weighted Mean – average score multiplied by the weight of every group

Descriptive Statistics: Measures of variability

Variability – measures of dispersion of data around the mean

- Mean gives us no idea of the values’ frequency

- Variation is inevitable in biological measurements
- Measurements that are more concentrated around the center = low dispersion/variability otherwise they have
high dispersion/variability

Measures of Dispersion

Range = maximum – minimum

- Difference between largest and smallest observation in data

- Disadvantages:
 Sensitive to outliers/extreme values
 Relies on two extreme observations, invalidating the rest of the data points

Total deviation

- Positive or negative distance from the mean, which results to 0 that is why;
- Sum of all the absolute deviations from the mean is used
- Shows how far each of the data points are from the mean
- Disadvantages:
 Value increases as n increases
 Not useful when comparing 2 groups of different n

Mean deviation = |sum of all the deviations from the mean| / number of items in sample (n)

- Not dependent on the sample size

- Disadvantages:
 Does not describe a parameter in the population

Variance

- To eliminate the negative signs, square the deviations and get the mean
- Population variance = sum of all the squared deviations from the mean / number of items (N)
- Sigma2
- Sample variance =sum of all the squared deviations from the mean / one less than number of items (n-1)
- S2
- Why the squared deviations?
 Eliminates the signs of the deviation from the mean
 Helps derive an important statistic, called the standard deviation
- Why n-1?
 Gives an unbiased estimate of the population variance
 Degrees of freedom
o # of values used in the calculation that are free to vary

Standard deviation = Square root of the variance

- Population standard deviation & Sample standard deviation

- Sd, S, Sigma
- Cannot be calculated from the mean of unsquared numbers
- Depends on large differences from the mean being given more importance than small differences
- Can be represented by box plots
- Standard Deviation Worths Scale
 Expresses how many standard deviations a particular data point is away from the mean
 The farther a data point is from the mean, the less likely it is to be encountered
Coefficient of variation = divide standard deviation by the mean x 100

- Standard deviation expressed as a proportion/percentage of the mean

- Useful when comparing between data sets with different units or different means

Sampling and Sampling Techniques

Sampling Techniques

Sample

- Subset of a population
- Proper sample enables us to draw conclusions about the characteristics of the population it was taken from
- Also used when population is too large
- Imaginary/Hypothetical/Potential populations
- Incorrect sampling leads to wrong conclusions
 Sample is not a good representative of the population
 Not all elements of the population were given an equal chance of being sampled
- Sample must be selected at random

Common sampling techniques

Disadvantages:
1. Convenience sampling
- Convenience/Grab/Opportunity sampling - Inherent bias
- Sample is selected from units of the population that are easy - Characteristics within the
to reach population might be patchily
2. Haphazard sampling distributed, making it easier to miss
- Follows no established system in identifying a sample - “edge effects” – differences in outer
- Forgivable when the object of study appears homogenous but and inner portions of habitats
occurs in patches
3. Random Sampling
- All units are given equal and independent chances of being selected
 Simple random sampling
o Generate random numbers by using
a) Random number generators
o Vulnerable to sampling error
 Systematic sampling
o Population is arranged according to some ordering scheme
o Then, samples are selected in regular intervals
o Involves a random start and then proceeds with the selection of every kth element from then
onwards
a) K = population size divided by sample size
 Stratified sampling
o Used when populations have distinct categories, or strata
o Ensures that each stratum is proportionally represented
 Mechanical sampling
o Typically used for solids, liquids, and gases
o Performed with mechanical devices

Sampling schemes/frameworks

1. Sampling with replacement

- Sample is put back in the population after sampling, thus it might be chosen again
2. Sampling without replacement
- Sample is taken out of the population after sampling

How large should the sample be?

- Size of the sample depends on the variable being sampled

- The greater the variability of the population, the more samples needed to make good inferences
- Depends how large the variability is trying to be shown

Probability

- Branch of mathematics that formalizes concepts of likelihood, predictability, and certainty

- Replaces informative yet imprecise words by a number between 0 and 1

History

- Studies on probability has been around since the 16th century by Girolamo Cardano and Galileo Galilei
 - Theory was formalized during the mid-17th century by Blaise Pascal and Pierre de Fermat (French
mathematicians)

Fundamental Counting Principle

- k = total number of outcomes

- If event A can occur in K1 possible ways, and event B can occur in K2 possible ways, then there are K1 x K2
possible ways both events can occur (outcomes)

Permutations

- Arrangement of objects in a specific sequence

- n (before P) – number of objects

Linear arrangements

- Factorial! Is used (ex: 4! = 1 x 2 x 3 x 4) = nPn formula

- If there are n linear positions to fill with n objects:
 1st position may be filled in any one of n ways
 2nd position in any one of n-1 ways
 3rd in n-2 ways, and so on

Circular arrangements

- No starting positions in circular arrangements

- nP’n formula = n! / n = (n-1)!

Fewer than n positions – linear

- If there are n objects but fewer than n positions in which to place them
- nPr formula = n! / (n-r)!
- read as a number of linear permutations of n objects taken r at a time
 r – grouping of n

Fewer than n positions – circular

- if there are n objects but fewer than n positions in which to place them in a circle
- nP’r formula = n! / (n-r)!(r)

If some objects are indistinguishable

- nPn1, n2,…nk formula = n! / n1!n2!...nk!

 where nk represents the number of like individuals in category k
 cancel numbers if possible

Combinations

- concerned with how objects are grouped

- ABCD has 4 permutations but is only considered 1 combinations because all have the same elements
- nCr formula = n! / r!(n-r)!
 number of combinations of n objects taken r at a time

Definitions

Sets

- Defined collection of items

 Outcome set/Sample Space (S) – set containing all the possible outcomes in an experiment
 Diagram: Written in curly brackets or brace, written inside a rectangle

Event

- Any subset A of the sample space (S)

- Any possible outcome within an outcome set or sample space
 Diagram: written inside a circle within the sample space
o If there are 2 different events: a venn diagram of A may be written

Conjoint

- Talks about event composition and event relations

- Conjoint: 2 sets, A and B (Events), are said to be conjoint when they have at least one element in common
 Represented by overlapping circles
- Disjoint: when no mutually exclusive elements in common
 Represented by respective circles
Union

- Union of A and B (A u B) is the set of elements that belong to either A or B or to both

- Diagram: Venn diagram shaded with the same colors

Intersection

- Intersection of A and B (A n B) is the set of elements that belong to both A and B

General Operations used in Probability Analysis

- Probability is denoted by P followed by the event A

 If P(A) = 0, event is never happening
 If P(A) = 1, event is certain to happen

Approaches to Assigning Probabilities

1. Empirical Probability – probability is determined by repeating the experiment a large number of times with a
formula of P(A) = # of time A occurred / # of times experiment was repeated
 Probability is determined after the event has occurred
 Relative Frequency – proportion of the total observations of outcomes that an event represents
o Relative frequency = frequency of the events (f) / total # of all events (n)
o May be represented in a percentage
2. Classical Probability – probability is determined even before the experiment is performed using the formula P(A)
= # of sample points in A (n) / # of sample points in S (N)
 Forms theoretical basis for statistical tests

Adding Probabilities

- If A and B are two events that are mutually exclusive, P (A or B) = P(A) + P(B)
- If A and B are conjoint events, P (A or B) = P(A) + P(B) – P(A n B)
- If A, B, and C are not mutually exclusive,
 Add all probabilities of 3 events, subtract probability of each 2-way intersection, and add the probability
of the 3 way intersection
 P (A or B or C) = P(A) + P(B) + P(C) – P(A and B) – P (A and C) – P(B and C) + P(A and B and C)

Multiplying Probabilities

- If 2 or more events intersect, the probability associated with the intersections if the product of the probabilities
of the individual events
 P(A and B) = P(A) x P(B)
 P(A and B and C) = P(A) x P(B) x P(C)
- Start with multiplying the probability of the individual events, then multiply all event probabilities together

The Normal Distribution

- A particular pattern of distribution of numbers around the mean

- Demonstrates a natural variation that often occurs
- Provides a statistical skeleton key for data analysis and testing hypothesis

Overview

Distributions – Also called frequency distributions; measures the frequency of occurrence of the different numbers or
events in a population

- Probability distribution P(x) or P(X=x)– describe all possible values or outcomes that a random variable can take
within a given range

Random Variables – values are based on a random outcome

- Discrete – can assume a countable number of possible values

- Continuous – can assume any value in an interval on the real number line

Normal Distribution

- Type of continuous probability distribution where the values of a random variable cluster around the mean
- Characterized by a bell shape hence a normal curve is called a bell curve
- Also referred to as Gaussian distribution named after German mathematician, Yohan carl Fredrich gauss
- Applicable to many real-world examples in relation to proportions and probabilities
- Unimodal, peak is position of the mean, mean = median = mode, symmetrical (thus the +/- standard deviation)
- Has points of inflexion (mirror s-shaped curves on either side of the mean, where convex around the mean
changes to convex towards the extremes)
- Has tapered tails
 - Characterized by the mean and the standard distribution
 Mean – determines the position of the distribution
o When a set of normally distributed data is adjusted, resulting into a shift of the mean, the rest of
the values will follow given their tendency to group around the center
 Standard deviation – signifies how spread out the data is (shown by the lateral change of the curve
compensated for by its height); gives an estimate of the relative frequency of a number occurring in a
sample
o The more SD worths the observation is away from the mean, the rarer its frequency
- Total area under the curve is equal to 1 or 100% (Empirical rule)
 Area within 1 SD away from the mean is equal to .68 or 68%
 Area within 2 SD away from the mean is .95 or 95%
 Area within 3 SD away from the mean is .997 or 99.7%
 Curve never reaches 0

Relevance on Biological Data

1. Biological data are frequently not normally distributed

- Peak usually to the left (positively skewed) with a long thin tail of high values (typical for random or clumped
data)
- Calculating a symmetrical sd is impractical
2. Estimates of the sd of the population remain as estimates
- Sd of sample will not be equal to the actual sd of the population
- Number of samples have a bearing on how well the population was estimated
 Sd inflates when too few samples are taken
 Erroneous conclusions are due to too few samples
 Waste of time and resources = too many

Checking for Normality

- Large data – there should be equal numbers of observations on either side of the mean
- Few observations - there should be no relationship between the magnitude of the mean and its standard
deviation
 If small means show less variation than large means, then a non-normal distribution is indicated
o Increase difficulty in analyzing data
a) Difficulty in extracting conclusions about the population
b) Difficulty in comparing populations

Data transformation

- Deals with non-normality

- Large samples
 Determine whether asymmetry causes the peak to lie above or below the mean
 Change horizontal scale to nonlinear scale to help normalize the data prior to further statistical testing
- Methods:
 Log transformation
o Y = log10(x+1)
a) Y – transformed data point
b) X – untransformed data
c) Addition of 1 to untransformed data is useful for data sets that contain 0 values
o Natural logarithm can also be used
 Square root transformation
o For highly clumped data where var > mean
o Y = sq(x+constant)
a) Constant = 1 to make the lowest numbers positive
 Inverse transformation
o Used when sd of groups of data are proportional to the square of the means of the groups
a) Y = 1/x
 Angular or arcsine transformation
o Used to normalize percentage data especially when extremes are involved
a) Y = sin-1x
 Power transformation
o Data is transformed using a power function

Factors affecting the number of samples needed

1. Variability of the biological material or target population

- Usually determined from preliminary sampling
 2. Size difference targeted
3. Detection of size difference targeted
- 100% certainty of detection is almost impossible however knowing the chances allows a more practical
workload

Number of samples

- Necessary to estimate the number

 No point in doing an experiment that cannot yield results or results that can be statistically supported
 To determine the variation can be controlled using data transformation

Hypothesis Testing

- Difference between two means are statistically significant if it can be shown that the difference did not arise due
to mere chance
- Errors bars – measure of the spread of data based on a form of uncertainty (sd)
o When error bars overlap, this is an early indication that means are not significantly different from each
other
- Major goal of statistical testing is to draw inferences about a population by examining a sample from that
population
- Ho – null hypothesis, means that the means of 2 populations are equal or there is no significant difference
between 2 population
- HA or H1– alternate hypothesis, mean that the means of 2 populations are not equal or that the mean of
population 1 is either less than or greater than population 2

T-Test

- Most important statistical test in relation to biological variability; encountered the most in studies
- Objective: to determine if 2 sample means are estimates of the same population mean
- Method: compares the means with the standard error of difference between means (s.e.d.m.)
o If P > 0.05, means are equal
o If P < 0.05, means are statistically different (there is 1 in 20 chance that the means come from the same
pool of number or possible outcomes)
 0.05 is an arbitrary choice for there are other levels of probability that can show other results of
interest

Helps answer the question “is the difference between the means big enough?”

- For very large samples (n >= 60), it should be > 1.96 or 2 SE (95% confidence limits)
- For small samples, the factor 1.96 is amplified to compensate for the increasingly poor estimate of the true
variance
o Amplification factors for different size samples (n-1) can be found in the table of “t” values compiled by
William Gossett

1-tailed vs 2-tailed

- 1-tailed test
o Ho: means are equal
o HA: mean 1 greater than mean 2
- 2-tailed test
o Ho: means are equal
o HA: means are unequal; mean 1 either greater than or less than mean 2

Standard t-test

- Appropriate to sample sizes of 30 or less

- May be applied to large samples where the variation around the 2 means is similar
- In testing hypothesis, it is standard to state the null hypothesis and the alternate hypothesis
- SE is an SD referring to the means of the groups being compared
- Assumes that two means being compared come from normal distributions with the same variances thus, here,
we are testing whether the two means could have been sampled from the same population

T-test for means associated with unequal variances

- When we are dealing with 2 distinct population

- Groups being compared may or may not have the sample size
- Same standard procedure but no pooling of variances

Paired t-test

- When comparing between 2 samples that have a high within-group variability

 - Pooled variance is calculated from the differences between pairs of numbers and not from the variance of
individual observations
- Since the 2 groups are compared in a pair wise manner, sample size must be equal

Z-test

- Moderate to large samples n > 30

- Requires several condition to be met before it can be reliable
- Preferred when population SD Is known

Hypothesis Testing: The Significance level

Significance level – criterion for accepting or rejecting a null hypothesis; expressed by alpha

Alpha

- Probability used as a criterion for rejection (a = 0.05); t value corresponding to alpha is called the critical value of
the test statistic
- For small sized experiments, it is possible that the null hypothesis will not be rejected due to large within-group
variability. This might require a higher level of significance

Statistical errors

- Occasionally, a true null hypothesis will be rejected since we have committed an error in drawing a conclusion
about the population. This is called a Type I error or alpha error
o At alpha = 0.05, it is possible that our null hypothesis would be concluded as false 5% of the time
- A type II error or beta error happens when a null hypothesis is accepted when it is in fact false
- The probability or frequency of us committing that error would be equal to the value of alpha

The power of a test

- Alpha is inversely proportional to beta

o Lower probabilities of committing a type I error are associated with higher probabilities of committing a
type II error
o Minimize type II error by setting a higher alpha
- Power of a test is denoted by 1 minus beta
o This is the probability that the test will correctly reject the null hypothesis when it is false
- Both types of errors can be reduced by increasing the sample size
- For any given alpha larger samples will result in statistical tests with greater power

Striking a balance: Managing errors

- For any given n, both types of errors cannot be minimized simultaneously

- Find an acceptable combination of the 2 types of errors
- In practice, alpha at 0.05 is conservative – significance level is small enough to commit a type I error and to
result in a large chance of committing a type II error
- For environmental scientist, minimizing type II error is more critical

ANOVA: Analysis of Variance

- For experiments with three groups, each should have a null hypothesis with each group
- Each null hypothesis then can affect the alpha and inflate it
- For each hypothesis, the probability that we will incorrectly reject the null hypothesis (Type I error) is given by
o 1-(1-alpha)c , where C = number of possible different pairwise combinations of k samples/groups
- To keep the alpha at 0.05, we must conduct an analysis of variance

ANOVA

- Appropriate for measurements of a variable for 3 or more groups, even with different number of samples
- Factor/independent variable – typically on a nominal or ordinal scale
- Dependent variable – number scale
- ANOVA applicable to factors on a nominal or ordinal scale; regression applicable to ratio or interval scale

Single-Factor ANOVA

- Used for analyzing a single-classification variable

- H0 = all means are equal where k refers to the number of experimental groups
- Experimental design:
o Random sampling
o Approximately equal sample sizes but not necessary
o Factor should be a nominal or ordinal variable
 o Power of test increases when all subjects are as similar as possible in all respects (controlled factors)
except for the experimental factor
- ANOVA aims to detect where the sources of variation are coming from
o Sources of variation from – among groups variation + within-groups variation = total variation
 Among groups: groups sum of squares(ss) – deviation of each group mean from the grand mean;
Degrees of Freedom: (k – 1)
 Within-groups: error ss – deviation of each datum from its own group mean; DF: sum of (sample
size minus 1 of each group)
 Total variation: Total ss; DF: Grand total (N) minus 1
- Hypothesis is tested by getting MS (mean squared deviation from the mean)
o Needs groups ss and error ss
o MS = group/error SS divided by group/error DF
- Testing the hypothesis: how does the variability among groups compare to the variability within groups?
- Uses the F-statistic, named after statistician RA Fisher
o F = groups MS divided by error MS
 Groups MS in the numerator because we are testing the size of the difference between groups
in relation to the size within groups
- We compare F statistic to a critical value: Falpha(1),(k-1),(N-k)
o Where alpha(1) – one tailed sig value, (k-1) – groups DF, (N-k) – error DF
o If F > or equal to critical value, we reject H0
 Probability that the observed data came from the populations described in the null hypothesis is
less than or equal to alpha
 All the k population means are not equal

Two-way ANOVA

- Involves 2 independent and 1 dependent variables

- Looks at difference among cells and within cells
- Aims to detect the effect of each factor on the dependent variable independent to one another
- May involve an interaction effect of the 2 independent variables
o When an interaction between factors is evident, there is another effect present on top of the sum of the
effects of each factor
- Has 3 null hypothesis
o F = group ms/within ms
- Interaction effects – occurs when the magnitude of the effect of one independent variable on a dependent
variable varies as a function of a second independent variable
o Parallel lines of factors in a graph means that there is no interaction
o Factor with fewer levels is plotted
- For unequal replication:
o Use proportional replication = (data per row)(data per column)/N
o Disproportional replication may still be tested
- Can also analyze without replication

Fixed and Random Factors

- Fixed – when the levels under study are the only levels of interest or can be controlled; conclusions made from
the results of the stat tests are restricted to those levels used
o Temperature: 10, 20, 30 degrees
- Random – when the levels under study are a random sample from a larger population and the goal of the study
is to make a conclusion regarding the larger population
o Temperature: Ambient temperatures, average temp for a specified time interval (mean daily temp, mean
hourly temp)

Assumptions of ANOVA

Parametric Tests

- Conventional statistical procedures (T-test, ANOVA); looking at parameters

- A sample statistic is obtained to estimate the population parameter
o Mean, variance, standard deviation
- Certain parametric assumptions are required to ensure all components are compatible with each other

Assumptions of ANOVA

- Departures from one or more assumptions can affect 2 things:

o Level of significance of the test
o Sensitivity of ANOVA to detect real departures from the null hypothesis which minimizes type II errors
 The margin of error can be affected if the assumptions cannot be addressed, which governed
the use of ANOVA
- When assumptions are not met, resort to:
o Data transformations
o Non-parametric tests – able to deal with most data sets (robust) but not as powerful as parametric tests
in detecting differences
- Main Assumptions of ANOVA
o Independence – groups of observations are independent of each other
 Scores in one cell are not dependent on the scores of another cell
 Independent observations:
 Achieved through random assignment of subjects to groups: no selection and
information bias, and no confounding effects
 Subjects are only measured once
 Positively correlated data leads to:
 Inflated standard error – higher variability; difficult to establish significant differences
 Inaccurate p-values – higher chances of committing type 1 or type 2 error
 Correlation can exist as a function of space, time, or an error in relation to experimental design
 Experimental unit – lowest level we can assign a treatment to
 Remedies for correlated data:
 Proper study design and randomization – designs could be implemented that takes
correlation into account
 Look for environmental factors that may be affecting results – add covariates to the
model if they are causing correlation (analysis of covariance; ANCOVA)
 If no underlying factors can be found:
o Use a different model (random effects model)
o Transform the independent variables using a correlation coefficient
o Normality – data are normally distributed; samples or observations should have come from a normal
population
 Check by looking at histograms or standard normality tests in statistical software
 F-test in ANOVA is very robust against non-normal data, especially in a fixed-effects model
(Model I)
 Large sample size will reach normality with a sample size of 50 or more
 Simulations have shown unequal sample sizes between treatment groups magnify any
departure from normality
 A large deviation from normality leads to hypothesis test that are too liberal (might declare
significant differences when there are none) and a decrease in power and efficiency
 Remedies for nonnormality:
 Data transformation
 Modified F-tests: adjust the degrees of freedom, rank F-test
 Randomization test on the F-ratio
 Other non-parametric test if distribution is unknown
o Homoscedasticity – observations in different groups or cells have nearly equal variances; also referred to
as homogeneity of variances or equality of variances
 F-test is very robust against heterogeneity of variances, especially with fixed effects and equal
sample sizes
 For unequal sample sizes, probability of type I error will increase to a degree dependent on the
magnitude of the heterogeneity
 Check if standard deviations of each group are approximately equal
 Quick check: ratio of largest to smallest sample sd must be less than 2
 If various groups do not contain the same number of subjects, researcher is obligated to test the
assumption of equal variances
 Tests to check if variances are equal:
o Bartlett’s chi-square, Hartley’s F-max test, Cochran’s C test, & Levene’s test

Correlation and Regression

Variable

- Any measure or character that is expected to be different from one experimental unit to another
- Establish mathematical relationships to assess measurements of variables

Simple correlation

- Describes the relationship of any 2 variable

- Data does not imply dependence on y or x, which means it does not imply a cause and effect relationship
 - Determines extent of how 2 variable of equal status increase or decrease with each other in a straight line
relationship
- Not concerned with predicting one from the other but we want to know if they are varying in a related way (if
they are correlated)

Pearson’s correlation coefficient (r)

- Formula used to describe a straight line relationship of 2 variables

- Most common correlation coefficient
- Indicated by r for sample, and p for populations
- Measures the amount that the two quantitative variables vary together, considering how much they vary apart
- Range is from -1 to +1 – sign indicates relationship
o Positive correlation – as one variable increases, values of the other variable also increase
o Small or 0 correlation coefficient – no linear correlation which may indicate either randomness or more
complicated relationship is present (ex: a curve) thus best way to determine the relationship is to draw a
scatter plot
o Negative correlation – inverse relationship
- R value does not change when the units of measurement are changed
- Ignores the distinction between explanatory (independent) and response (dependent) variables
- R is strongly affected by outliers
- Rule of Thumb
o 0.8-0.10 – very strong relationship
o 0.0-0.2 – very weak or no relationship
2
- r – coefficient of determination or correlation index
o can be derived from correlation coefficient
o the amount of variability in one of the variables by correlating that variable with the 2 nd variable
 ex: 36% of the variability in x can be explained by the variability in y while 64% of the variability
in x can be further explained by other variables
o expressed in percentage
o useful in determining regression analysis

Assumptions in parametric tests:

- Random sampling
- Independence of observations
- Bivariate normality – both variables are normally distributed
o If non-normal
 Transform 1 or both variables
 Use a more robust measure of correlation (robust is not equal to powerful)
 Spearman’s rank correlation coefficient
 Uses the ranks of the observations

Significance of a correlation coefficient

- The significance of a correlation coefficient is a function of the magnitude of the correlation and the sample size
- Indicates if the calculated r value is different from zero or not
o HO: r = 0
o HA: r is not equal to o
- If you have a large number of data points, even a small correlation coefficient can be significant due to its value
compared to the alpha
- A negative correlation shows an equally strong relationships as a positive correlation

- Interpreting a correlation coefficient: always be wary of assuming that one causes variation in the other
- Being significant is not the same as being important or strong
- Whenever correlation is computed, the accompanying significance value tells us if the r value computed is most
likely real or obtained by chance alone

Simple Regression

Linear regression models

- Assume a linear relationship between a continuous/numerical response variable and a single usually continuous
predictor/explanatory variable
- 3 Major Purposes
a. To describe the linear relationship between x and y
b. To determine how much of the variation (uncertainty) in Y can be explained by the linear relationship
with X; and how much of this variation remains unexplained
c. To predict new values of Y from new values of X (unique to linear regression)
 - Regression line – imaginary line in a graph that has the closest distance to all measured points
o Residual – vertical lines that connect the measured points to the regression line; difference between a
subject’s predicted scored and the actual score
- Least squares method – tries to find the regression line that would minimize the sum of the squared residuals
- Predictive Value: Y = mx + b – general equation for a straight line; y = a + bx
o a represents the value of y when x is 0 – intercept; regression constant
o b represents the slope – slope; regression coefficient
- 95% confidence interval for the slope:
o Take 2 SD above and below the mean/computed slope
o (value – 2A) to (value + 2B)
o Means that there is a 95% chance that the true slope lies between A and B

Adjusted r2

- Squared correlation coefficient corrected for the number of independent variables in the equation
- Adjustment decreases the value of r2
- Difference is typically small
- Becomes larger and more important when dealing with multiple independent variables

Key Points

- Both regression and correlation are strongly affected by outliers

- We can use r to describe how spread out our observations are about the regression line
- Strong relationship between two variables does not always mean that changes in one variable cause changes in
the other
- Relationship between two variables is often influenced by other variables lurking in the background
- Best evidence for causation comes from randomized comparative experiments
o Experiments that use both comparison of 2 or more treatments and random assignment of subjects to
treatments