CO4

Phylogeny and the Tree of Life

Systematics: branch of biology that deals with the classification of organisms
and determining their evolutionary relationships.

 Tools used in determining evolutionary relationships: fossils,

morphology, molecular evidence

Taxonomy: science of classifying and naming organisms on the basis of their

shared characteristics.

 Binomial Nomenclature: “two-term naming system”, makes use of 3. Homology: characteristics in Homologous Structure: similar
the genus and species taxonomic ranking in naming organisms. related species can have underlying anatomy, different function
o Example: Escherichia (genus) coli (species) similarities even though functions
may differ. Analogous Structure: different
anatomy, similar function
Carolus Linneaus: developed this naming system
Embryonic Homologies: similar
 Taxonomic Ranking: relative level of a group of organisms in a early developmental stages
taxonomic hierarchy.
o Dear King Philip Came Over For Good Spaghetti Vestigial Homologies: structures
with little to no use for the organism
Cladistics: is a method of hypothesizing relationships among organisms.

 Cladogram: diagram that depicts patterns of shared characteristics Molecular Homologies: similar DNA
among taxa. and amino acid sequences.
o Clade: group of species that includes an ancestral species and
its descendants Phylogenetic Tree: branching diagram that shows the evolutionary history of
o Shared derived characteristics: evolutionary novelty unique a group of organisms.
to a clade; traits that appeared in the most recent ancestor.
o Shared ancestral characteristics: a character that originated  Parts:
in an ancestor of the taxon.
o Monophyletic: consists of an ancestral species and all of its
descendants.
o Paraphyletic: consists of an ancestral species and some, but
not all its descendants.
o Polyphyletic: includes distantly related species but does not
include their most recent ancestor
  Topology: branching structures of the tree
o Tips: external nodes that represent groups of descendant
taxa
o Internal Nodes: occurs at points where more than one
branch meet and represent ancestral sequences
o Root: represents the most recent common ancestor.
"Humans (red) are more closely related to mice (bright blue) than they are to
lizards (green)." This is because humans share a common ancestor more
recently with mice (ancestor = purple spot) than they do with lizards
(ancestor = dark blue spot).
Example 2:
"Frogs (purple) are more closely related to lizards (green) then they are to fish
(pink)." This is because frogs share a common ancestor with lizards more
recently (ancestor = orange spot) than they do with fish (ancestor = black
spot)."
Example 3: equal relatedness
"Fish (pink) are equally related to mice (bright blue) as they are to frogs
(purple)." This is less intuitive, but if you trace back to the MRCAs you will see
why: mice and frogs share the same common ancestor (black spot) with fish,
so neither species is more closely related to fish.
Remember:
 These interpretations rely on our tree being rooted because the root
is needed to define the direction of evolution and therefore what is
'more recent' in evolutionary time.
 If we rotate the branches to change the topology of the tree then
the tree still has the same biological meaning and evolutionary
relationships.
Five Kingdom System: Animal, plant, protist, fungi, and all prokaryotes are
under monera.
Six Kingdom System: Animal, plant, protist, fungi, Protista, and:
 Eubacteria: normal everyday prokaryotes
 Archaeabacteria: prokaryotes found in extreme environmental
conditions
Three-Domain system: biological classification introduced by Carl Woese
that divides cellular life forms into:
 Archaea: constitutes single-celled organisms, some are prokaryotes
who have no cell nucleus
 Bacteria: biological cells that constitute a large domain of prokaryotic
microorganisms. No peptidoglycan in cell walls
 Eukarya: organisms whose cells are enclosed in cell membranes;
contains multi-cellular organisms. Have peptidoglycan in cell walls.
Molecular Clock: some regions of DNA appear to evolve at constant rates;
 figurative term for a technique that uses the mutation rate of
biomolecules to deduce the time in prehistory when two or more life
forms diverged.
CO5
Plant Cell and Tissues
Characteristics of Organisms under Kingdom Plantae
1. Have cell walls
2. Autotrophs: produces their own food; in this case thru
photosynthesis.
3. Angiosperms: plants that produces flowers and seeds enclosed
within a carpel.
a. Approx. 90% of all pants
b. Key adaptation: flowers and seeds
Plant Tissue Type
1. Dermal tissue: single layer of
closely packed cells that cover the
entire plant that protects against
water loss and invasion of
pathogens.
It contains a cuticle or a waxy layer.
Parts located on the Dermal Tissue:
a. Stomata: opening of the
leaf that helps control
water loss from plants
b. Guard Cells: controls the
opening and closing of the
stomata
c. Trichomes: hair-like
projections on the stem and
leaf that help reduce
evaporation of water from
plants.
2. Vascular Tissue: it’s main
function is for the transport of
water and food throughout the
plant.
Types:
a. Xylem: transports water
from roots to the plant.
Tracheids: tubular cells
tapered at each end.
b. Phloem: made up of
tubular cells joined end to
end that transports sugar to
Illustration
all parts of the plant
Cell types: sieve tubes,
companion cells
3. Ground Tissues: found
throughout the plant that isn’t
dermal or vascular. It is in charge of
photosynthesis, storage, and
secretion.
Pith: inside the vascular tissue
Cortex: Outside the vascular tissue
Parenchyma: thin cell wall;
functions as storage
Collenchyma: uneven thickening of
cell walls; functions as support
Sclerenchyma: even thickening of
cell walls; functions for both
support and protection
 4. Meristematic Tissue: located in Type Illustration
regions of actively dividing cells that Tap Root: one thick, vertical root
produces most of the plant’s new with many lateral roots.
cells.
They are firm anchors and stores
foods.

Table 1. Plant Tissues and their Functions

Plant Growth Fibrous Root: mat of thin roots

spread just below the surface.
Types of flowering plants:
They have increased surface areas
1. Annuals: plants that complete their life cycle within one year and
then dies.
2. Biennials: plants that take two years to complete their life cycle. They
enter a period of dormancy in the cold months
3. Perennials: plants whose lifespans exceed over two years.
Table 2. Root Systems
Meristem: perpetually embryonic tissues.
Stems: supports leaves and flowers and contains vascular tissue to transport
 Apical Meristem: growth at the tips of roots and buds of shoots that materials.
causes primary growth (increase in length)
 Lateral Meristem: growth thickens the roots and shoots which is  May be modified to store food and/or water.
called secondary growth o Succulents: plants that store large amounts of water in their
o Vascular Cambium: produces secondary xylem which is the stems or leaves.
wood.  Arrangement of Vascular Tissues:
 Bark: all tissues outside the vascular cambium. o Monocots: xylem and phloem are scattered throughout the
o Cork Cambium: produces touch covering that replaces stem.
epidermis. o Dicots: xylem and phloem are in circles that form a ring.
 Shoot apical meristem: dome of dividing cells at tip of terminal bud. Part Function
Roots: anchor, absorb nutrients, contain vascular tissue to transports 1. Terminal Bud: growth is Secretes hormones to prevent
concentrated at the top of the stem. growth of axillary buds.
materials.

 Have root hairs that increase surface are of the root. Growth is directed upward towards
light.
2. Axillary Bud: located in between Pinching/pruning: removal of
leaves and stems and forms terminal bud.
branches for lateral shoots.
Rhizomes: an underground stem that usually grows horizontally that is Level of Organization:
capable of producing new shoots and roots.
Cell  Tissue  Organ  Organ System  Organism
 Examples: Iris, ginger, potato
Tissues: are collections of similar cells and the extracellular matrix
Stolons: aboveground stems that run across the soil surface usually growing surrounding them.
horizontally to produce new shoots and roots.
 Histology: study of tissues
 Examples: Strawberries, grass  Four main types of Tissues
1. Epithelial: covers the outside of the body and the lines of
Bulbs: they grow underground.
organs and cavities of the body
 Types: 2. Connective: binds and supports other tissues
o Tunicate: they have a paper outer covering. 3. Muscle: controls body movement
o Scaly: they lack the paper outer covering. 4. Nervous: senses stimuli and transmits signals throughout the
 Parts: animal.
o Scales: modified leaves that store carbohydrates
Epithelial tissues: covers the surface. It has little extracellular material and
o Apical Buds: sits on top of the basal plate that eventually
usually has a basement membrane.
grows to a shoot
o Basal plate: modified stem.  Epithelial cells are either:
o apical,
Leaves: solar energy and CO2 collectors of plants that are responsible for
o lateral surface (attached to other cells)
photosynthesis.
o basal surface (attached to the basement membrane)
 Leaf anatomy  Functions of E. Tissues:
o Epidermis: interrupted by stomata that are flanked by guard o Protection of underlying structures (Skin)
cells. o Acts as barriers (skin)
o Mesophyll: ground tissue between upper and lower o Permitting the passage of substances (epithelium in lungs)
epidermis. o Secreting substances (mucous glands)
o Parenchyma: sites of photosynthesis. o Absorbing substances (epithelial cells in the intestine)
o Petiole: holds the blades of the leaf
o Phyllotaxy: arrangement of leaves on a stem
 Transpiration: loss of water through stomata
 Leaf venation: patterns of veins on the leaves
o Either parallel, pinnate, or palmate

Anatomy: study of biological form or structure of an organism while

physiology: is the study of the biological functions of an organism.

Structure dictates function

 Gland: single cell or multicellular structure that secretes.

 Endocrine glands: do not have ducts; they secrete hormones directly

to the blood
 Exocrine glands: have ducts that secretes onto a surface or a cavity.
They are classified according to structure and how the product leaves
the cell.
o Structure:
 Simple: have one duct
 Compound: have ducts that branch repeatedly
 Tubules: ducts end in small tubes
 Acini: ducts end in saclike structures
 Alveoli: ducts end in hollow sacs
Type Description Function o Secretion types:
Simple squamous Single layer, flattened Filtration, diffusion,  Merocrine: no loss of cellular material
Epithelium osmosis, covers  Apocrine: part of the cell pinches off
surface  Holocrine: entire cell is shed
Simple Cuboidal Single layer, cube Secretion and
Muscle tissues: specialized to contract making movement possible
Epithelium shaped cells Absorption
Simple columnar Single layer, elongated Protection, secretion,  Sometimes called muscle fibers because they often resemble tiny
epithelium cells absorption threads
Pseudostratified Single layer, elongated Protection, secretion,
columnar cells absorption of mucus Type Description
and substances Skeletal Meat of animals
Stratified squamous Many layers, top cells Protections Approx. 40% of person’s body
flattened weight
Stratified Cuboidal 2-3 Layers, cube- Protection Attached to the skeleton that allows
shaped cells for movement
Stratified columnar Top layer of elongated Protection, secretion Voluntary, multinucleated, and
cells, lower layer of striated
cube-shaped cells Cardiac Muscle of the heart
Transitional Many layers of cube- Distensibility, Connected to one another by
shaped and elongated protection intercalated disks
cells Involuntary, striated, and usually
Glandular Unicellular or Secretion have one nucleus per cell
multicellular Smooth Forms the walls of hollow organs
Involuntary, not striated, have a
single nucleus.
Connective tissue: consists of cells separated from each other by an CO6
abundant extracellular matrix
Nervous System
Classification Function
Areolar Connective tissue: loose Fills the space between organs and Central Nervous system: consists of the brain and the spinal cord.
packing material of the body holds organs in place
 It integrates the received information and coordinates and influences
Adipose tissue Stores energy
Pads and protects parts of the body the activity of all parts of the bodies.
Acts as thermal insulator  Brain: most complex part of the human body and it is the central
Dense connective tissue: consists of Capable of stretching and recoiling control module.
a matrix containing densely packed like a rubber band o Parts of the Brain:
fibers  Cerebrum: responsible for information processing
Cartilage Provides support and the right and left hemispheres.
Allows growth of long bones  Corpus Callosum: connects the two
Provides rigidity and flexibility hemispheres of the brain
Bone: has a mineralized matrix Forms most of the skeleton of the  Brainstem: oldest evolutionary part responsible for
body basic autonomic behaviors
Blood: liquid matrix Found in blood vessels and  Medulla Oblongata: responsible for
produced in hemopoietic tissue
breathing, heat and blood vessel activity,
digestion, etc.
Homeostasis: existence and maintenance of relatively constant environment  It transfers information between the PNS
within the body despite fluctuations in either the external or internal and CNS
environment  Cerebellum: coordinate hand movement, balance,
motor skill learning
 Negative feedback mechanism: any deviation from the set point is o Grey matter: neuron cell bodies, unmyelineated axons
made smaller or resisted
o White Matter: fatty, myelineated axons
 Positive feedback mechanism: occurs when the initial stimulus
 Spine: carries information between the brain and the body and is
further stimulates a response connected to the brainstem.
 Three components o It also connected to the nerves of the PNS
o Receptor: monitor value of a variable
o Responsible for reflexive responses
o Control center: establishes set point which a variable is
maintained Peripheral Nervous system: consists of all the neurons that exist outside the
o Effector: can change the value of the variable. brain and spinal cord.

 Connects the CNS and other various parts of the body.

o Parts of the PNS:
 Somatic Nervous System: second functional division
of the PNS. It controls the voluntary muscular
movement of skeletal muscles.
  Autonomic Nervous System: related to all o Interneurons: connect sensory and motor neurons
involuntary visceral activity of the body. Consists of: o Motor Neurons: transmits information from the CNS to the
 Sympathetic Nervous System body
 Parasympathetic Nervous System  Nerves: bundles or collection of neurons
o Contains motor neurons and or sensory neurons
Sympathetic Nervous system: it becomes more active when the body is  Parts of a neuron
stressed in a “fight or flight” response o Cell body: contains the nucleus and organelles
 The SNS can affect the body through the following: o Dendrites: receives incoming messages
o Increase in heart rate o Axon: transmits messages away to other cells
o Widening of bronchial passages o Myelin Sheath: fatty insulation covering the axon that
o Decreases the motility of the large intestine speeds up nerve impulses
o Make blood vessels narrower o Synapse: gap between 2 neurons
o Increase peristalsis o Neurotransmitter: chemical messengers sent across synapse
o Cause pupil dilation o Glia: cells that support neurons
o Piloerection (goosebumps)
o Perspiration
o Raise blood pressure

Parasympathetic Nervous system: works in conjunction with the

sympathetic nervous system to maintain homeostatis.

 It does the opposite of the sympathetic nervous system to balance

each other’s effects.
 The PSNS can affect the body through the following:
o Relaxation of heart
o Narrowing of bronchial passages
o Increase the motility of large intestines
o Constricts eye
o Widening of blood vessels
o Technically the opposite of the effects of the SNS on the
body.

Neuron: functional unit of the nervous system which consists of a dendrite Neurotransmitters: chemicals released from vesicles by exocytosis into
and an axon synaptic cleft
 Types of Neurons:  Functions:
o Sensory: information from the body is transmitted to the o Diffuse across synapse
CNS o Bind to receptors on neurons, muscle cells, or gland cells
 o Broken down by enzymes or taken back into surrounding Spermatogenesis Oogenesis
cells Production of sperm Production of Ova
 Types: Stem cells  spermatids in Before birth:
o Excitatory: speeds up impulses by causing depolarization of seminiferous tubules Oogonia  Meiosis – stops at
postsynaptic membrane Prophase I (primary oocytes)
o Inhibitory: slows impulses by causing hyperpolarization
Puberty:
Circulatory System: moves fluid to tissues and cells for exchange Each month, egg in follicle 
Meiosis I (secondary oocytes) 
 Types: Fertilization  Meiosis II
o Open: blood bathes organs directly in arthropods and Mature and add tail in epidymis 1 ovum + 3 polar bodies
mollusks 4 motile sperms
o Closed: blood is contained in vessels and pumped around the
body
 Types of blood vessels:
o Arteries: carries blood away from the heart
o Capillaries: connect arteries and veins where exchange of
CO2 occurs
o Veins: carries blood back to the heart

Flow of blood summary

1. The right atrium receives oxygen-poor blood from the body and pumps
it to the right ventricle through the tricuspid valve.
2. The right ventricle pumps the oxygen-poor blood to the lungs through
the pulmonary valve.
3. The left atrium receives oxygen-rich blood from the lungs and pumps it
to the left ventricle through the mitral valve.
4. The left ventricle pumps the oxygen-rich blood through the aortic valve
out to the rest of the body.

Valves: prevent the backflow of blood

 Atrioventricular valve: separates each atrium and ventricle Mammalian Fertilization

 Semilunar valves: control blood flow to the aorta and the pulmonary
1. Sperm binds to receptors in zona pellucida (extracellular matrix of
artery
egg)
Respiratory System: series of organs that are responsible for the intake of
2. Acrosomal reaction: sperm releases hydrolytic enzymes to digest z.p.
oxygen and the expulsion of carbon dioxide.
 (Sea Urchins) Depolarization of membrane: prevent other sperm  Functions:
from binding = fast block to polyspermy o They prepare the body to fight disease without exposing it to
the disease’s symptoms.
3. Sperm + Egg Fuse
o Incites memory cells’ production of antibodies at a fast rate
4. Cortical reaction: sperm + egg fusion triggers release of Ca2+ to eliminate foreign bodies.

 cortical granules fuse with z.p.  z.p. hardens to form

fertilization envelope = slow block to polyspermy

5. Ca2+ release also triggers activation of the egg

Gastrulation: rearrange cells to form 3-layered embryo with primitive gut

Ectoderm Mesoderm Endoderm

Skin, nails, teeth Skeletal and muscular Epithelial linings of
systems digestive, respiratory,
excretory tracts
Lens of eye Notochord Live, pancreas
Nervous System Excretory, circulatory
Reproductive System
Blood, bone, muscle

Organogenesis: development of three germ layers into organs

 Notochord: stiff dorsal skeletal rod, forms from mesoderm

 Neural Plate: brain and spinal cord
 Neurulation: forms hollow dorsal nerve chord
 Somites: block of mesoderm arranged along notochord.

Patterns of development

Cytoplasmic determinants: chemical signals such as mRNAs and transcription

factors influence pattern of cleavage

Induction: interaction among cells that influence the change in gene

expression

Totipotent Cells: capable of developing into the different cell types.

Immunizations/Vaccines: induce memory toxin to nonpathogenic microbe or

toxin