Biology II

Taxonomic groups are based on hypothesis regarding evolutionary relationships from systematics
Hierarchical system involving successive levels
Each group at any level is called a taxon
Highest level is Domain
- All life belongs to 3 domains
- Bacteria, Archaea, and Eukarya
  - The Eukarya Domain is often divided into Kingdoms in the next level
    This is typically called the 4 Kingdom concept

Four Kingdoms

Domains Bacteria and Archaea
- Prokaryotic cells
  - Lack nucleus
Kingdom Protista, Fungi, Plantae, Animilia
- Eukaryotic cells
  - True nucleus

Types of cells

Prokaryotic

Lack Nucleus
Lacks membrane-bound organelles
Typically singled celled

Eukaryotic

Well defined nucleus
Membrane-bound organelles
internal membrane system (compartments)

Binomial Nomenclature

Genus name + Specific epithet
- ex. Homo sapiens ('wise humans')
Genus name is always capitalized
Specific epithet is never capitalized
Both names are either italicized or underlined

Phylogenetic Trees

Phylogeny
- Evolutionary history of a species or group of species
To propose a phylogeny, biologist must use the tools of systematics
Trees are usually based in morphological and genetic data
- Subjective vs. Objective data
Diagram that describes the phylogeny
A hypothesis of evolutionary relationships among various species
Based on available information

Monophyletic Group or Clade

Group of species (taxon) consisting of the most recent ancestor and all of its descendants
Smaller and more recent clades are nested within larger clades that have a common ancestor

Paraphyletic group

Contains a common ancestor and some, but not all of its descendants

Over time, taxonomic groups will be reorganized so that only monophyletic are recognized
Reptiles were a paraphyletic group because birds were excluded
In the class and lab, we are going to separate birds and reptiles

Systematics

Morphological Analysis

First systematic studies focused on morphological features of extinct and modern species
Most of early classifications were based upon morphological features

Molecular Analysis

Analysis of genetic data (DNA, Amino Acids, rRNA) to identify and study genetic similarities and propose phylogentic trees
DNA and Amino Acid sequences from closely related species are more similar to each other than sequences from more distantly related species

Horizontal Gene Transfer

any process in which an organism incorporates genetic material from another organism without being the offspring of that organism (by means of asexual reproduction)

Vertical Evolution

Changes in groups due to descent form a common ancestor (sexual reproduction)

Exam 1 - Notes

Chapter 27-31

Prokaryotic Diversity

Prokaryotes dated at 3.5 billion years old
Modern Prokaryotes are most abundant, lacking sexual reproduction

Domain Bacteria

Proteobacteria
- "true bacteria"
Cyanobacteria
- "Blue-Green bacteria"

Domain Archaea

Have and "almost" nucleus
specialized membranes
surrounded by a cell wall
old, can live in extreme conditions

Eukaryotic Diversity (Ch 28)

Kingdom Protista

Earliest eukaryotes in fossil record
most are microscopic and found in moist environments
DNA many separate groups
Most artificial category
- "catch-all" category

Subgroups

Algae

Plant-like organisms
10 groups
autotrophic (self-feeding)
- most are photosynthetic
- few ingest food
cell wall with

Protozoans

Animal-like
mostly netraothrophic (food-eating)

Slime Molds

Fungal-like Protist
Mostly saprothrophic (absorb-feeding)
mostly multicellular

Kingdom Fungi (Ch 31)

Conspicuous portion of the organism in the mushroom/yeast/mold/etc
Saprothrophic (some are heterotrophic)
Natures recyclers
Composed of:
- Mycelium
  - compacted mass of tubular filaments called hyphae
- Fruiting body
  - site of spore production
- Cell wall
  - composed of muramic acid/chitin

Kingdom Plantae (Ch 29 & 30)

>330,000 species
eukaryotic and multicellular
autotrophic (mostly) self-feeding
- capture sunlight to produce energy by photosynthesis
- Food storage copound
  - starch
- cell wall
  - cellulose
Are referred to as "land plants"
fossils dated to ~400mybp (million years before present)
Ancestor stock
- probably a group of algae (green)
Life on land requires special innovation
- Must be able to get water
  - ROOTS!

Phyla (divisions)

10 phyla
Typically combine these into 4 broad categories for convenience

Bryophytes

Phylum Hepatophyta
- Liverworts
- ~6500 species
Phylum Anthocerophyta
- Hornwarts
- ~100 species
Phylum Bryophyta
- Mosses
- ~12,000 species

Referred to as "mosses and their friends"

Characteristics

Reproduce by spores (not seeds)
non-vascular plants
- lack conducting tissues
  - xlem and phloem
Small plants
Require external H2O for reproduction

Pteridophytes

Phylum Lycopodiophyta
- lychophytes
- 1000 species
Phylum Pteridophyts
- Ferns and allies
- 12,000 species

Characteristics

Sporangia
- Where the spores are produce
Reproduce by spores
- no seeds
vascular plants
- xylem
  - water and minerals
- phloem
  - food and solutes
true roots, stem, and leaves
- due to being vascular
vascular allows for larger size
Require external H2O for reproduction

Gymnosperms

Phylum Cycadophyta
- cycads
- 300 species
Phylum Ginkophyta
- Ginko
- 1 species
Phylum Gnetophyta
- gnetophytes
- 300 species
Phylum Coniferophytes
- conifers
- 500 species

Means "Naked seeds"
Seeds are not enclosed

Biggest group are the conifers
(Cone bearing trees)

Oldest
- Bristle cone pine
  - Over 4600 years
Biggest
- Giant Sequoia
  - estimated 600 tons
Tallest
- Coastal Redwood
- 180 meters in height

Characteristics

Vascular
- more advanced that Pteridophytes
Advance seed
- It has more survival value
- Contains:
  - Embryo
    - Offspring
  - Stored food
  - Integument
    - Seed coating
Does not require external H2O for reproduction
- Pollen tubes deliver sperm to egg location

Angiosperms

Phylum Anthophyta
- 300,000 species

Characteristics

Enclosed seed
produces flowers and fruits
most advance vascular tissues
Seeds advance
- Enclosed in a vesses (fruit)
  - no survival value
- Embryo
- Stored food
- 2 integuments
  - Seed coats
Does not require external H2O for reproduction
Flowers
- Attract pollinators
Fruit
- Enclose and protect the seed
- assist with seed dispersal

Exam 1 - Notes

Chapter 32 & 33

Kingdom Animilia

Over 1.5 million species
- Estimated 73 million
35 Phylums
- Over half are insects
More similarities within animal genomes than other kingdoms

Characteristics

Multicellular
Lack of cell wall
Sexual reproduction
- mobile sperm
- larger non-motile egg
Nervous Tissue
- Complexity
- Responsiveness
Hox Genes
- Special clusters of genes associated with the planning of the body

Metazoans

All animals
Multicellular animals
Paratoans
- Sponges
Eumetazoans
- "true" multicellular animals

Classification/Systematics

Old
- Morphology
- Embryonic Development
Recent
- Molecular genetics

Body Plans

Morphological and Developmental Features

Body Symmetry
Number of tissue Layers
Patterns of Embryonic development

Symmetry

Eumetazoa
- Divided by symmetry
Radiata
- Radial symmetry
- Often Circular or tubular
Bilateria
- Bilateral symmetry
- Dorsal
  - Back
- Ventral
  - Front
- Anterior
- Posterior
- cephalization
  - enlarged head

Tissues

Metazoa
- all animals
- divided on weather or not they have specialized tissues
Parazoa
- Porfera
  - sponges
  - may have distinct cell types
Enmetazoa
- more than one type of tissue
- organs
- all other animals

Germ Layers

Radial
- 2 layers
- Diploblastic
  - endoderm
  - ectoderm
Bilateral
- 3 layers
- Triploblastic
  - endoderm
  - ectoderm
  - mesoderm

Embryonic Development

Protostome
- Blastopore becomes mouth
- cleavage is determinate
  - fate of embryonic cells are determined early
Deuterostome (second opening)
- Blastopore becomes anus
- cleavage is indeterminate
- each cell produced by early cleavage can develop into a complete embryo

Other Morphological Characteristics

Used in classification

Presence or absence or coelom
Body segmentation

Molecular data suggest these features are unreliable in terms of understanding evolutionary history

Body Cavity

Coelom

- a fluid-filled body cavity
Coelomate or eucolemate
- true coelom
- coelom completely lined with mesoderm
Pseudocoelom
- coelom only partially lined with mesoderm
- rotifers and roundworms
Acoelomate
- lack of a body cavity and instead have mesenchyme
- flatworms

Flatworm has no mesoderm

Functions of the Coelom

Cushions internal organs
Enables movements and growth of internal organs independent of the body wall
Fluid acts as a simple circulatory system

Segmentation

Body may be divided into regions called segments
occurs in annelid worms, arthropods, and chordates
allows specialization of body region

DO NOT worry about the number of species

Molecular views of Animal Diversity

Scientist now use molecular techniques to classify animals
- Compare similarities in DNA, rRNA, and Amino Acids
- Closely related organisms have fewer differences than those more distantly related
Advantages over morphological data in that genetic sequences are easier to quantify and compare
- Example: A,T,G, and C in DNA

Genes used in Molecular Systematics

Studies often focus on ribosomal RNA (rRNA)
- Universal in all organisms
- changes slowly over time
Hox genes also studied often
- Found in all animals
- duplications in these genes may have led to evolution of body form
Phylogenies constructed using rRNA and Hox genes are similar and often agree with those based on morphology

Invertebrates

"without backbone"
+95% of all species

Phylum Porifera

Sponges
lack tissues (organs)
multicellular
pores
- filter H2O and food
Invertebrates

Phylum Cnidaria

Jelly fish, corals, anemones
Diploblastic development
- Two tissue layers
Mesoclea
- gelatinous covering
Nerve net
- interconnected nerve cells
- no brain
One opening with gastrovascular cavity
Protostomes
Invertebrates
Radial symmetry
Salt and fresh water
Stingers

Phylum Ctenophora

Comb jellies
Same characteristics as Cnidaria
Strictly salt water
No Stingers

Phylum Platyhelminthes

Flatworms, tapeworms, flukes
Triploblastic
Organs and organ systems
Enhanced nerve net
- 2 cerebral ganglia
One opening with gastrovascular cavity
Protostomes
invertebrates
bilateral symmetry
Acoelomate

Phylum Rotifera

rotifers
pseudocoelomate
Triploblastic
Two openings
- complete gut tract
- alimentary canal
Protostomes
Corona
simple brain
invertebrates

Phylum Mollusea

Snails, slugs, oysters, octopus, squid, clams, muscles
Triploblastic
Eucoelomate
Complete gut tract
Protostomes
Invertebrates
Three part Body
- Foot
- Visceral mass
- Mantle
  - Many have outer shells

Phylum Annelida

Segmented ring worms
Triploblastic
Eucoelomate
Complete gut tract
Protostomes
Enhanced nervous system
Invertebrates

Phylum Nematoda

Roundworms
Triploblastic
Pseudocoelomate
Complete gut tract
Protostomes
Invertebrates

Phylum Anthropoda

Insects, crustaceans, spiders, ticks
Highest diversity of animals
- >1.5 million species
Hardened Exoskeleton
Protostomes
Invertebrates
Eucoelomate
Triploblastic
Complete gut tract
Enhanced nervous system
- Insects, in particular, have an enhanced brain
segmented appendages

Phylum Echinodermata

sea stars, urchins, sea cucumbers, sand dollars
Triploblastic
Eucoelomate
Complete gut tract
Deuterostomes
Simple nervous system
Endoskeleton
- series of plates

Phylum Chordata

Deuterstomes
Complete gut tract
Endoskeleton
Few invertebrates
- Mostly vertebrates
Eucloemates
Triploblastic

Four Critical Innovations of Chordate Body Design

Notochord
Dorsal, hollow nerve cord
Pharyngeal gill pouches
Post-anal tail

These four features are exhibited at some point of life history/development
- Only some Fishes exhibit all four

Notochord

Cartilaginous supporting rod along the dorsal axis
Replaced by jointed "backbone"
- Vertebral column of hardened cartilage or bone

Dorsal, hollow nerve cord

Expanded at the anterior end
- Brian
Enclosed/supported/protected by the Notochord

Pharyngeal gill pouches

Gill slits
pharynx
- back of mouth cavity

Post-anal Tail

Tail extends posterior of the anus

Humans

Notochord

replaced by vertebrae
only pieces left are the inter-vertebral discs between vertebrae

Nerve cord

Dorsal, hollow with largest brain capacity (compared to body size)

Pharyngeal Pouches

Embryonic Development
1 pair retained as Eustachian tubes

Post-anal Tail

One vertebra as a tail bone (coccyx)

Subphylum Urochordata

tunicates
invertebrates
~3000 species
Marine
Filter feeders

Subphylum Cephalochordata

Lancelets
Invertebrates
25 species
marine
Filter feeders

Exam 1 - Notes

Chapter 34

Subphylum Vertebrata

Vertebrates
Chordates with a backbone

Chordate features as well as:

Vertebral column
- Series of cartilaginous or bony elements
Cranium
Endoskeleton or cartilage or bone
Hox genes (lots of them)
Neural crest

Cyclostomes

Jawless Fishes

Class Myxini

Hagfishes
lack jaws, eyes, fins vertebrae
skeleton comprised of notochord and cartilaginous skull
covered in slime

Class Cephalospidomorphi

Lampreys
Has notochord, and cartilaginous vertebral column
lacks jaws and appendages (fins)
Oldest fossil records 510 mybp

Class Chondrichthyes

Cartilaginous fishes
Sharks, skates, rays
Cartilaginous skeleton and notochord as adults
jawed fishes
paired appendages (fins)
< 900 species

Class Osteichthyes

Bony fishes
Most diverse vertebrate group with < 26,000 species
Bony skeleton (most do have this)
Jawed
paired appendages (fins)

Tertapod: Gnathastomes

Four limbs with jawed mouth
Transition to land involved adaptions for locomotion, reproduction, desiccation (drying out) prevention, and gas exchange
Sturdy lobe-finned fishes became animals with four limbs
Vertebral column strengthened, ship and shoulder bones braced against backbone
relatively simple changes in gene expression, especially Hox genes

Class Amphibia

>4000 species
Amphibios
- greek - "living double life"
- split their life between aquatic and terrestrial stages
Successfully invaded land but reproduce in water
Lunges are and adaption to semi-terrestrial lifestyle
Three chambered heart
- Fishes only have a two chambered heart
External Fertilization
Larval stages are aquatic
- Undergo metamorphosis
Not completely separated from water

Order Anura

Frogs and toads
Nearly 90% of amphibians
Carnivorous adults
- Herbivorous tadpoles

Order Apoda

Caecilians
Nearly blind tropical burrowers
Secondarily legless

Order Urodela

Salamanders
Often have colorful skin patterns
Most have four limbs

Amniotes

Tetrapods with a desiccation resistant egg
Critical innovation
- Development of a shelled egg
Amniotic egg
- Broke the tie to water
- Three internal membranes
Shell is permeable to Oxygen and CO2
- Birds
  - Hard and Calcareous
- Reptiles
  - Soft and Leathery
- Most Mammals
  - Embryo embeds in uterine wall
  - Only three species lay eggs
    - These eggs are soft and leathery

Other Key Innovations of the Amniotes

Desiccation resistant skin
- contains keratin
Thoracic breathing
- Negative pressure sucks air in
Water conserving Kidneys
- Concentrate waste prior to elimination
Internal fertilization

Class Reptilia

>8000 living species
turtles, crocodilians, lizards, snakes
Can live away from water
thicker skin and scales
larger brain
larger limbs with muscles
enhanced kidneys
Amniotic egg
- "indoor pond"

Vertebrate Reproductive Modes

Oviparous
- Egg laying outside of the body
Ovoviviparous
- live baring wuth retention of eggs
- No maternal connection
Viviparous
- live bearing with egg retained
- Maternal connection

Class Aves

Birds
Evolved form small dinosaurs
Fossils 150mybp
Adaptions for flight
- Feathers
- Modified front limbs
- Lightweight skeleton
- Organ reduction
- Lungs and air sacs
  - more gas exchange
Oviparous
- all leg layers
Bill beak
- Encloses mouth and nasal cavity
- Adapted for environment

Endothermic

"Internal temperature"
Body temperature is primarily controlled by trapped metabolic heat.
Birds and mammals

Ectothermic

"External temperature"
Body temperature is primarily related to external temperature
Metabolic heat is generated but difficult to capture/maintain the heat
Fishes, amphibious, reptiles

Class Mammalia

Milk producing Amniotes
Evolved from amniote ancestors (reptiles) earlier than birds
>6000 species
Appeared ~ 225mybp
- Evolved from small mammal-like reptiles
After dinosaur extinction, mammals flourished
Range of sizes, body forms, and complexity unmatched

Fish-like mammals
- Marine mammals
Bird-like mammals
- Bats
Reptile-like mammals
- Three egg layers

Distinguishing Characteristics

Mammary Glands
- Secrete milk
All have hair
- In varying amounts
Only vertebrate with multiple dentitions
- Heterodont
  - Different types of teeth
  - incisors, canines, molars, premolars
- Thecodont
  - Teeth with long roots embedded in sockets of jawbone
- Diphyodont
  - Milk teeth that are mostly replaced by "adult" teeth later in life
Pinna
- Flap of cartilage and lose connective tissue to channel and funnel sound
- The "outer ear"
Three middle ear ossicles (bones)
Enlarged Skull
- Brain enlarged in large skull
- Larger Cerebrum
- Single lower Jawbone (Dentary)
Anucleate red blood cells

Order Primates

Primarily tree dwelling species
grasping hands with opposable thumbs
Large brain
Some digits with flat nails
- Not claws
Binocular vision
Complex social behavior and well-developed parental care
Enhanced sense of touch

Taxonomy of Humans

Kingdom Animalia
- Phylum Chordata
  - Subphylum Vertebrata
    - Class Mammalia
      - Order Primates
        
        Suborder Anthropoidea
        
        Superfamily Hominoidae
        
        Family Hominidae
        
        Subfamily Homininae
        
        Tribe Hominini
        
        Genus Homo
        
        Species Homo sapiens

Exam 2 - Notes

Chapter 35

Introduction to Plants

Kingdom Plantae

We will primarily be discussing the angiosperms
- Phylum Anthophyta
Flowers and fruits
- Only group that does/has these things
Advanced traits
- Seeds
- Advanced vascular tissues

From seed to seed

The life of a flowering plant

Seeds
- reproductive structures produced by angiosperms and other seed plants
- usually the result of sexual reproduction
- contains embryos that develop into seedlings upon germination
- has survival value

Alternation of Generations

Exhibited by all plants (and plant-like organisms) that have sexual reproduction
There is an alternation between a diploid (2N) form [sporophyte] and a haploid (1N) form [gametophyte]

Gametophyte (haploid)

Gamete-producing plant fomr
multicellular
microscopic in flowering plants
- female
  - embryo sac with egg
- male
  - pollen grain
grow and develop within flowers of angiosperms
produces gametes by mitosis/cytokineses

Sporophyte (diploid)

multicellular
large "plant" in flowring plant
produces haploid spores by meiosis (reduction)
- called meiospores

The plant embryo

Fertilization (syngamy) results in the formation of a diploid zygote, which undergoes mitosis to form an embryo (multicellular)
the embryo is a sporophyte that lies dormant in the seed with a supply of stored food and a seed coat
may lay dormant for long periods until conditions are favorable

The plant body

Composed of three organ types

stems
leaves
roots

Shoot system

stem
- produce leaves and branches and bear the reproductive structures
leaves
- flattened structure specialized for photosynthesis

Root system

roots
- Provide anchorage in the soil and foster efficient uptake of water and minerals
- can store food

Growth

Indeterminate growth
- increasing in size as long as the plant is alive
grows into a seedling and then a mature plant
Plant growth occurs by 3 means
- Increase in number of cells
  - cellular reproduction
    - (mitosis/cytokineses)
- increase in cell size
  - elongation
- increase in weight/mass

Development

Mature plants produce reproductive structures
- flowers
- seeds
- fruits
flowers and floral buds are reproductive shoots that develop when shoot apical (tip) meristems produce flower parts instead of new tissues and leaves
flowers are produced by determinate growth

Seed coats

Flower tissues enclose and protect tiny male and female gametophytes
- sperm in pollen fertilizes the egg, triggering ovules to develop into seed and flower parts to develop into fruit
fruits enclose seeds and function in seed dispersal
- Angiosperms

Meristems

Seedlings and mature plants produce new tissue from meristems
- cell factories
meristem is a region of undifferentiated cells that produce new tissue by cell division
A dormant meristem occurs at the shoot and root of seed embryos
- activate in seedlings
mature plants have shoot apical meristems (SAM) and root apical meristems (RAM)

Mature sporophyte develop from seedlings

photosynthesis powers the transformation of seedlings into mature plants
provides the ability to produce organic food
plants undergo both vegetative growth and reproductive development

Hierarchy of structures in a mature plant

Specialized cells
tissues
organs
organ systems
- branches, buds, flowers, seeds, fruits
root and shoot systems
plant (the organism itself)

Primary Growth

Elongation of plant organs
roots, stems, and leaves
Occurs in ALL plants
Produces primary tissues from apical meristems (SAM and RAM)

Primary Tissues

Primary xylem
- vascular/conducting tissue
- water and minerals
Primary phloem
- vascular/conducting tissue
- food and solutes
Epidermis
- dermal
  - Outter-most tissue
- protection
- holds water in plant
Support ground tissues
- Parenchyma
  - most abundant type
  - storage
    - water and food
  - part of cortex/pith
- Collenchyma
  - Protection/support of growing plant organs
  - cortex
- Sclerenchyma
  - protection/support of non-elongating organs
  - cortex

Secondary Growth

Expansion of plant organs
- lateral meristems
roots and stems only
- does not occur in leaves
noes not occur in all plants
Produces secondary tissues
- woody tissues

Major groups of Angiosperms

Eudicots

>240,000 species
all have primary growth
most have secondary growth
- for this class we are saying they all have secondary growth

Monocots

>60,000 species
all have primary growth
very few have secondary growth
- for this class we are saying that non have secondary growth
grasses, corn, tulips, lilies

Root system adaptations

Major functions

absorbing water and minerals
anchoring the plant in the soil
storing nutrients and water

Eudicots

Taproots

Monocots

fibrous roots

Three zones of root growth

Region of cell division
- RAM and root cap
- RAM contains cells that ar dividing
- Quiescent center keeps nearby cells undifferentiated
- Root cap embedded in mucigel
  - Mucigel is a slimy substance that covers the root cap of the roots of plants.
Region of elongation
- cells extend by uptake of water
Region of maturation
- root cell differentiation and tissue specialization
- identified by presence of root hair
  - water and mineral uptake

Root Internal Structure

Epidermis of mature roots encloses a cylinder of parenchyma called the root cortex
- One cell thick
- often rich in starch
  - functions as food storage
- many contain inter-cellular air spaces
Endodermis
- selective absorption of minerals
- one cell thick
Meristematic pericycle
- encloses root in vascular tissues
- provides lateral branches
woody roots produce primary vascular tissues followed by secondary vascular tissues

Eudicot root

Monocot Root

The shoot system

Stem and leaf adaptations

Shoots are modular with 4 parts

Stem node
- leaves or branches emerge
Internode
- stem between adjacent nodes
- elongation
Leaf
Axillary Meristem
- generate axillary buds
- can produce flowers or branches
  - Lateral shoots
- New branches bear SAM at their tips

Shoot Tip

Terminal bud
- at the end of each shoot
- includes the SAM and other parts
- scales

Leaf anatomy

Leaf adaptation

Leaf venation

Eudicot

Pinate (feathery)
Palmate (palm)
Netted
- provides more support for the leaves

Monocot

Parallel

Stem

Primary growth

mostly above ground organs,but some modified stems are blow ground
- Irish potato
  - underground stem

Eudicot Stem

ALC
Primary (elongation) and secondary (expansion) growth
vascular bundles (xylem and phloem) form a ring pattern
exhibit both a pith and a cortex
cambium ring produce cells
- provide secondary growth

Lateral Meristems

Produces secondary growth
2 lateral merstems
- both are rings that retain cell division properties and produce secondary tissues to the inside and outside of the cambium ring
Vascular cambium
- produces ring of secondary xylem (wood) to the inside and a ring of secondary phloem (inner bark) to the outside
Cork cambium
- Produces ring of periderm (outter bark) that replaces the epidermis and cortex for external protection

Secondary vascular tissue
- woody plants begin life with only primary vascular systems
  - produces secondary tissues and bark as they mature
- secondary xylem
  - wood
- Secondary phloem
  - inner part
- bark has both outer bark (mostly dead cork cells) and inner bark (secondary phloem)
Secondary growth
- begins late in first year of growth
- eudicot stem after 3 years of growth

Monocot stem

Primary growth (elongation)
vascular bundles (xylem and phloem) are scattered
lacks both pith and cortex

Comparison between Plant types

Leaves

Eudicot

net venation

Monocot

parallel venation

Roots

Eudicot

primary and secondary growth (mostly)
cortex
no pith
core of xylem in the root

Monocot

Primary growth only
both cortex and pith

Stems

Eudicot

primary and secondary growth (mostly)
vascular bundles in a ring pattern around cortex

Monocot

Primary growth only
vascular bundles scattered around
no pith or cortex

Primary Growth

Due to activities of Apical Meristems
- RAM and SAM
Results in production of primary growth

Secondary Growth

Due to activities of lateral maristems
- vascular and cork cambiums
Results in production of secondary tissues

Exam 2 - Notes

Chapter 36

Overview of plant behavioral responses

Behavior is a response of an organism to an internal or external stimulus
types of plant behavior
- movement
  - bending,twisting, or rotating
    - nutation
  - rapid movement as in sensitive plants
    - response to touch
- growth
- seed germination
- seasonal production of reproductive structures
- defensive responses to attacks
  - thorns, spines, chemicals

Responses to internal and external stimuli

Internal

Internal biological clock
- circadium rhythms
chemical signals
- transcriptions factors and other proteins or hormones
- often interact with each other and external signals

External

light atmospheric gases (CO2 and water vapor) temperature, touch, wind, gravity, water, rocks, and soil minerals
Herbivors, pathogens, organic chemicals from neighboring plants, and beneficial or harmful organisms

Plant Behavior

Involves internal and external stimuli

tropism
- growth response that is dependent on a stimuli that occurs in a particular direction
Reception molecules
- located in plant cells
- sense stimuli and cause response

Phototropism

Growth response to light
light causes movement of hormone auxin away from said light
result in unequal distribution of auxin
- causing unequal cell elongation
positive tropism

Gravitropism

growth response to gravity
positive tropism
- roots
negative tropism
- shoots
columella cells in root cap/tip region sense gravity

Thigmotropism

Growth response to touch
roots
- columella cells cause roots to grow around obstacles

Regulation of plant growth

Hormones

chemical messengers that regulate plant growth
- most transported in phloem tissue
- all require an expenditure of energy on part of the plant (ATP) for transport
interact with external environmental stimuli

Hormones control

growth
seed germination
flowering
fruiting
shedding of leaves
color change of leaves

Hormones of two broad categories

growth inhibiting
- mostly fall/winter
- certain times of the year growth is not good
growth promoting
- mostly spring/summer

Auxins

first group of plants hormones to be described
growth promoting
produced in
- shoot tips, seeds, fruits, leaves, stem
- NOT in the roots

Effects of auxin

Promotes

cell elongation
shoot elongation
production of wood
fruit development

Inhibits

lateral bud development
absission (falling off) of leaves, flowers, fruits

Cytokinins

Originally detected in coconut "milk"
growth promoting
prodiced in
- seed, fruits, roots

Effects of Cytokinins

Promotes

cellular division
- named derived from Cytokenesis

Inhibits

senesence
- change of color due to breakdown of pigments

Gibberellins (giberellic acids)

many types
- >200
- more than any other group
growth promoting
found throughout the plant but concentrated in seeds

Effects of Gibberellins

Promotes

stem elongation by cell division and cell elongation

intake of water causes swelling and embryo hydration
embryo secretes gibberellins
gibberellins transported to cells of aleurone layer to secrete enzyme
(alpha-amaylase) for breakdown of endosperm (starchy stored food) to glucose
embryo will respire glucose to produce ATP
embryo is directing the timing of plant germination
Advantage seed plants

Brassinosteriods

growth promoting

Effects of Brassinosteriods

Promotes

cell expansion
shoot elongation
xylem tissue development
stress response

Inhibits

leaf abscission

Abscisic Acids (ABA)

Growth inhibiting
found in large quantities in seeds. mature leaves, and dormant buds

Effects of ABA

Promotes

senesence
production of storage molecules in seeds

Inhibits

cell elongation
alpha-amaylase production

Ethylene

growth inhibiting
actually a gas produced by incomplete metabolism
interacts with the 4 growth promoting hormones to determine cell size and shape

Effects of Ethylene

Promotes

fruit ripening
abscission of leaves, fruits, flowers

Seed germination

requires breaking of dormancy
- combination of internal and external factors

Internal

hormones
stored food
H2O absorption
embryo swelling

External

sunlight
temperature
longer day light
soil moisture

Generalized Seed

Seed coat(s)
as seed coat cracks
Radical comes out first
- then then shoot

Seedling

result of cellular reproduction and increase size
internal development
- cells>tissues>organs>organism

Exam 2 - Notes

Chapter 37

Nutritional resources of plants

Essential elements

Play many roles in plant metabolism
often function as enzyme factors

Macronutrients

required in amounts of atleast 1g per 1kg of dry plant mass

Micronutrients

trace elements
required in amounts at or less than 0.1g per 1kg of dry plant mass

Limiting factors

resources that can limit plant growth
- too little or too much
carbon dioxide
water
other mineral nutrients

Exam 2 - Notes

Chapter 38

Transport of materials in plants

Root system absorbs water and dissolved minerals from the soil
Shoot system takes CO2 from the atmosphere via stomata
Photosynthetic cells use these materials to produce organic compounds needed for growth and reproduction
long-distance transportation occurs withing the plant body using a continuous system of conducting materials
- Xylem
  - transport water and dissolved minerals
  - Only goes up
- Phloem
  - transports food and other solutes (hormones)
  - Goes up and down

Importance of water

Photosynthesis
support of plant organs
conduction
cell elongation
most chemical reactions
Average plant is 90% water
Solvent for most substances
- Solution
  - Solvent
  - Solute

Properties of water

Polar molecule
- neutral
Hydrogen bonding
Cohesiveness
Adhesiveness
Temperature Stabilizer
Transport medium
Best biological solvent
Occurs in all 3 forms of matter within earth's temperature range

Principles of movement

Bulk\Mass flow
- Mass movement of liquid cause by pressure and\or gravity
- Ex: leaching
  - movement of ion though soil to plant roots
- Faster than diffusion
Diffusion
- high concentration > low concentration
- Simple diffusion
  - Movement of molecules through a phospholipid bilayer down a concentration gradient
- Facilitated Diffusion
  - transport of molecules across a plasma membrane down a concentration gradient with the aid of membrane protiens
Osmosis"gatekeeper"
- Diffusion across a selectively permeable membrane in response differences in solute concentration
- simple diffusion of water does not occur rapidly enough for rapid expansion of plant cells
- Aquaporins
  - protein channels that allow facilitated diffusion of water

Tissue-level transport

trans-membrane transport
- export of material via membrane proteins, followed by import of the same substance by an adjacent cell
- Ex. Auxin transport aided by carrier protiens
Symplastic Transport
- Movement from cytosol of one cell to cytosol of another cell via plasmodesmata
  - Cytosol
    - Everything inside the cell wall
Apoplastic transport
- movement along cell walls and inter-cellular spaces
- Ex: water and disolved minerals

Cellular water content

water content of plant cells depends on osmosis, which depends on:
- Solute concentration
- Turgor preassure
  - hydrostatic pressure that increases as water enters plant cells
  - cell walls restrict the extent to which the cells can swell

- Turgid plant cell has cytosol full of water and plasma membrane pushes up against the cell wall
- Plasmolyzed cell has lost so much water that turgor pressure is lost and the plasma membrane no longer presses on the cell wall

Water potential

Potential energy of water
Water moves from highest to lowest water potential
- affected by
  - pressure
  - solute concentration
  - other factors (damage, temperature)
Concept used in 2 ways
- to understand the movement of water into and out of cells (cellular water potential)
- to understand the movement of water between entire plants and their enviroments

Water (and soil mineral) movement through the plant

Transpiration
- Evaporation of water from plant surfaces
- "cost" for the plant to live on land
- capable of pulling water up by bulk flow
- primary form of long distance water transportation in plants

Stomata
- Opening has 2 guard cells
  - control balance of CO2, O2, and H2O inside leaf

Xylem

Flowering plant xylem consists of 4 types of cells

Xylem parenchyma cells
Thick-walled supportive fibers
- may be alive or dead at maturity
vessel elements
- Speacilized water conducting cells and are always dead and empty of cytosol when mature
- Wide tubes
Tracheids
- tracheory elements
  - Rich in lignin which offers strength, durability, and water proofing
- Narrow tubes

Stomata

Plants produce a waxy cuticle to prevent water loss
stomata facilitate gas exchange
90% of water that evaporates from plants is lost through stomata
when stomata are open, O2 and water vapor are released and CO2 is taken up
controlled by guard cell pairs

Mechanisms of Guard cells

Daytime/sunlight
- CO2 is low in leaf
Guard cells "pump" in K (potassium)
- Changes solute concentration
H2O from xylem moves by osmosis onto guard cells
- cells become turgid
Guard cells swell and open stomata
- CO2 diffusion into leaf
"Pump" out K (potassium)
- H2O moves out by osmosis out of guard cells causing shrinking

Pumping
- Expenditure of ATP energy

Causes of water loss

Sunlight energy
- heats up leaf causing evaporating of H2O from mesophyll cells
- Causes a decrease in H2O concentration causing a "pull" of H2O
- This "pull" moves H2O though the "Transpiration stream"

Transpiration Stream

Soil H2O (and nutrients)
root epidermis
root cortex
endodermis
root xylem
stem xylem
leaf xylem
mesophyll
Vapor into atmosphere

Unidirectional movement
Only goes UP!

C-A-T Mechanism

Occurs once the stomata are open
Purely a physical process
"pull" of H2O one molecule at a time
unidirectional movement
Cohesion
- H2O molecules stick together
Adhesion
- H2O adheres to cellulose in cell walls
Tension
- "pull" due to H2O loss from mesophyll
NO ENERGY expended
Only energy is sunlight heating leaf

Solute movement in plants

Translocation
- movement of solutes in plants
food
- dissolved in H2O
- Moved in form of Sucrose
Goes form Source to Sink
- Site with excess of carbohydrate
- Site where the carbohydrate is stored or immediately needed
Bidirectional

Long-distance transport in phloem

Phloem transports sugars from where they are produced and\or stored to other sites where they are stored and/or needed
- Source > Sink
Primary Phloem
- Occurs in the vascular bundles of herbaceous plants
Secondary Phloem
- Occurs as the inner bark of woody plants

Phloem Structure

Phloem of flowering plants in composed of supporting fibers, parenchyma cells, sieve-tube elements, and adjacent companion cells (members)
Sieve-tube members (STM) are arranged end-to-end , and together with companion cells, form a system to transport soluble organic substances
- Sieve-tube members lose their nucleus and most of the cytoplasm to reduce obstruction to bulk flow
- phloem sap passes through sieve plate pores

Pressure Flow Hypothesis

At source

Companion cells "pump" sucrose into STM (STP expended)
As sucrose concentration increases in STM, water potential (concentration) decreases within STM
Adjacent Xylem has higher water potential than STM, H2O moves into STM by osmosis

Bulk flow of Sucrose
Higher Pressure > lower Pressure

At sink

Companion cells unload sucrose (ATP expended)
Sucrose converted into starch for storage in root cortex
Without sucrose, higher H2O potential in STM
H2O moves from STM to adjacent Xylem by osmosis

ATP spent only by companion cells at source (loading) and sink (unloading)
Bulk flow (pressure/potential differences) and osmosis (H2O potential\concentration differences)
- No energy Expended

Similarities Between Translocation and Transpiration

Both involve conduction
both involve physical properties of H2O

Translocation	Transpiration
Phloem Bidirectional Must expend ATP energy by plant	Xylem Unidirectional Sunlight energy (no expenditure by plant)

Exam 2 - Notes

Chapter 39

Reproduction in plants

Most flowering plants display sexual reproduction
- Two gametes fuse to produce offspring with a unique combination of genes
They undergo Alternation of Generations
- Two multicellular life cycle stages
- diploid
  - Spore producing sporophyte
    - produces spores by meiosis
      - a type of cell division that results in four daughter cells each with half the number of chromosomes of the parent cell, as in the production of gametes and plant spores.
- haploid
  - Gamete producing gametophyte
    - produces gametes by mitosis
      - a type of cell division that results in two daughter cells each having the same number and kind of chromosomes as the parent nucleus, typical of ordinary tissue growth.
Egg is Female
Sperm is Male

Evolutionary Trends in the Plant Kingdom

Sporophyte has become larger, more complex
- Flowering plants
  - Sporophyte independent
  - Dependent gametophyte is only a few cells contained within flowers
Gametophyte has become smaller, less complex
- Moss
  - Sporophytes small and dependent on gametohyte (Dominant form)
Female
- 7 cells
Male
- 2-3 cells

Flower and Sexual Cycle

Flowers
- ONLY in angiosperms
- All sizes, shapes, colors, and aromas
Essential process of Sexual reproduction occurs within flowers
- Meiosis/cytokenesis
  - reduces chromosome number
- Syngamy (fertilization)
  - restores chromosome number

"Ideal" Flower

Uses highly modified leaves arranged in whorls (circular) at the tip of a highly modified stem
A flower is a highly modified determinate (short term) shoot system

Pedical, receptical, 4 sets of highly modified leaves are all 2N and part of the sporophyte generation
Pollen (sperm) and eggs of embryo sac are part of the 1N generation
Pedical
- flower stalk
Recepticle
- tip of modified stem with 4 whorls attached

Sexual Cycle

Male

Pollen formation
- occurs within the anther of stamen
Anther
- Bilobed with 2 pollen chambers per lobe

2N microspore mother cell
meiosis/cytokenesis
4 1N microspores
Each: mitosis/cytokenesis
unequal and incomplete
1N Generating cell
1N Tubecell

Male Gametophyte

Pollination

Transfer of pollen from the anther to the stigma
Self-pollination
- Transfer with the same flower or between flowers on the same plant
Cross-Pollination
- Transfer between flowers of other plants

Pollinating Agents

Mechanisms utilized for transfer of pollen

Wind
- small/lightweight pollen
Water
- Transfer with a few aquatic plants
Animals
- Majority of plants
- Utilized as a "trick and reward" system
- nectar, colors, and aromas to attract animals

Female

Ovule Development

Ovule
- future seed
Enclosed within the ovary of pistol (carpel)
One to many ovules per ovary
- ovary will become fruit
Ovule attached to central axis or to wall of hollow fruit
- always enclosed
- angiosperms
within ovule is 1 large 2N cell
- megaspore mother cell

2N megaspore mother cell
meisos/sytokenesis
4 1N Megaspores
3 degrade
2N Functional megaspore
Series of 3 mitosis/cytokenesis cycles
Incomplete and unqueal
7-celled embryo sac
8 nuclei

Female gametophyte

1N Functional megaspore
- 3 mitosis/cytokenesis divisions
One cell with 1 nucleus becomes 8 nuclei but only 7 cells

Embryo sac

8 nuclei, 7 cell structure
female gametophyte
3 antipodal cells (1N)
- opposite end from micropyle
1 central cell with 2 large 1N polar nuclei
2 Synergids (1N)
- Micropyle end on outside
1 egg (1N)
- Middle at micropyle end

Syngamy (fused gametes)

1N egg + 1N sperm = 2N zygote (single fertilized egg)
Pollen grain germination
- tube cells form pollen tube (delivers sperm)
- generative cell divides by mitosis/cytokenesis to produce 2 sperm

Pollen tube enters micropyle
- digests tube cell nucleus
Pollen tube enters one synergid
- releases it's content (sperm)
- synergid ruptures
- mycropyle closes

"Double fertilization" (double fusion)
- 1N egg +1N sperm = 2N zygote
- 1N sperm +2 1N polar nuclei = 3N primary endosperm cell

Post fertilization with ovule
2N zygote grows by mitosis/cytokenesis into 2N multicellular embryo
3N primary endosperm cell grows by mitosis/cytokenesis into 3N multicellular endosperm
- nutrient tissue for embryo

Ovule/ovary with 2N zygote mature/enlarges with sugars/H2O into a fruit (mature ovary) with enclosed seeds (mature ovules)
Seed dispersal (seeds enclosed withing a fruit)
agents
- wind
- water
- animals - majority

Seed germination

Seed with 2N embryo enters period of dormancy
dormancy broken by a combination of internal (hormones) and external factors (environmental)
radical (first root) emerges and grows down
shoot emerges and grows up

Exam 3 - Notes

Chapter 40

Intro to Animal Structure(Form) & Function

Key concepts

organization of animal bodies
the relationship between structure and function
homeostasis

All Animals:

Exchange materials with their surroundings
Obtain energy from organic molecules
synthesize complex molecules
reproduce themselves
detect and respond to signals in their immediate surroundings

Levels of Animal Organization

Cellular
- Phylum Porifera
Tissue
- Phylum Cnidaria
- Phylum Ctehotophora
Organ System
- All advanced animal groups

Internal Organization of Animals

Cells with similar properties group together to form tissues
Tissues combine together to form organs
Organs are linked together to form organ systems
Organ Systems form an organism

Tissues

Tissue

An association of many cells that have a similar structure and function

Types

Epithelial tissue
Connective tissue
Muscle tissue
Nervous tissue

Epithelial

Sheets of densely-packed cells that:
- cover the body or enclose organs
- line the walls of the body cavity and organs
Specialized to protect and secrete/absorb ions and organic molecules
cells have a variety of shapes
- cuboidal
- squamous
- columnar
arranged to form different types of tissues
- simple
  - one layer
- stratified
  - multi layer
- pseudo-stratified
  - one layer, but appears stratified
All are asymmetrical or polarized
- One side rests on the basal lamina (basement membrane)
- the other faces the environment

Types of Epithelial Tissue

Simple squamous
- one layer of flat cells
Simple cuboidal
- one layer of square cells
Simple columnar
- single layer of rectangular cells
Pseudo-stratified columnar
- 1 cell thick with all at basement barrier
Stratified squamous
- multi-layered flattened cells
Transitional
- stretchable tissue

All may be involved with secretions/absorption/protection

Connective tissues

Connect, surround, anchor, bind, & support

For extracellular matrix (ECM) around cells
- provides scaffolds for attachment
- protects and cushions
- mechanical strength
- transmit information
- transport

Types of Connective tissue

Blood
- transport and protection
adipose (fat)
- insulation, protection, support, and storage
bone
- support, protections, and movement
cartilage
- support and flexibility
loose connective tissue
- holds internal organs in place
dense connective tissue
- strength and support

Muscle Tissues

Cells specialized to contract, generating mechanical force

Types of muscle tissue

Skeleton muscle
- attached to bone(via connective tissue) or exoskeleton for locomotion
- elongated fibers
- voluntary control
- striated
Smooth muscle
- surrounds tubes and body cavities for propulsion of contents
- flattened cells
- involuntary control
cardiac muscle
- only in the heart
- elongated fibers
- involuntary control
- striated
- branched

Nervous tissue

complex networks of neurons (nerve cells)
initiate and conduct electrical signals from one part of the body to another
electrical signals produced in one neuron may stimulate or inhibit other neurons
- initiate new electrical signals
- stimulate muscle cells to contract
- stimulate glandular cells to release chemicals
also contains neuro-glial cells
- more numerous than neurons
- provide metabolic support, maintenance, ion balance, and cleaning for the neurons

Organ Systems

10 organ systems that we will cover (not in this order)

Structure and function

organization of structure(form) can predict the function of a structure
we will concentrate of the increasing complexity of structural(form), and thus the increasing complexity of organismal function
most emphasis on vertebrates

Homeostasis

changing variables in environmental:
- air temperature
- water temperature
- food supply
- water supply
- pH
- O₂ Concentration
Process of adjusting to the external environment and maintaining a stable internal environment

Exam 3 - Notes

Integumentary System

Apparently there is no chapter/section for this in the book?

Integument

the skin and all accessory structure (hair, feathers, scales)

Skin

The largest vertebrate organ
major part of the integument system

Vertebrate integument and derivatives

Functions

Protection form abrasion
protects against water loss
barrier to disease causing pathogens
protection from UV light
temperature regulation
contains sensory receptors
excretion (limited)

Vertebrate Integument

skin and all other accessories
skin is the largest organ o vertebrates
skin consists of 2 layers
- epidermis
- dermis

Epidermis

outer layer
nutrients diffuse into the epidermis form the dermis
stratified squamous epithelial cells

Cell types

langerhans cells
- defensive cells
Melanocytes
- produce pigment melanin
- skin coloration
- protect form UV light
Merkel cells
- touch receptors
Keratinocytes
- primary cell type
- produce insoluble protein Keratin
- amount of keratin increases from the inside to outside
- keratin fill cytoplasm and impairs nutrient diffusion, cell dies

Dermis

Inner layer of skin
- thinner than dermis
highly vascularized
contains:
- sensory structures
- vessels
- nerves
- glands
Origin of hair/scales/feathers in vertebrates
Sensory structures
- Meissner's corpuscles
  - light touch
- Pacinian corpuscles
  - deep vibrations

Sweat Glands

temperature regulation
produce sweat (primarily water)
- evaporating cooling
- release of waste ions
2.5 million on the body
release of heat

Sebaceous Glands

all over body, except palms and soles
large on face, neck, and upper chest
produce sebum
- lubricates and soften hair and skin
- water proofing in aquatic mammals

Hypodermis

subcutaneous layer
- below the dermis
not a layer of the skin
contains much adipose (fat) tissue
females have thicker layer of adipose tissue than males

Function

body contour
insulation
support the skin

Exam 3 - Notes

Chapter 45 & 46

Digestive System

Key Concepts

Animal nutrition
general principles of digestion and absorption of food
overview of vertebrate digestive systems
mechanisms of digestion and absorption in vertebrates

Intro to nutrition

nutrient
- any substance taken in by an organism that is needed for:
  - survival
  - growth
  - development
  - tissue repair
  - or reproduction
nutrition
- process of consuming and using food for nutrients
animals receive nutrients by consuming food

Dietary categories

basic similarities in organ system function lead to similarities in nutritional requirements
different animal physiologies can have different nutrient demands

Herbivores
- eat only plants
- digestive system contains micro-organisms that help digest cellulose
Carnivores
- eat only animal flesh or fluid
Omnivores
- eat both

Animals are heterotrophic

Heterotrophs
- ingest feeders
cannot manufacture more food
require already synthesized organic compounds of plants of other animals to supply materials
- survival
- maintenance
- growth
- reproduction

Gut Tracts

Two types

Digestion

the breakdown of large molecules into smaller ones

Digestive enzymes (hydrolases)

carbohydrases
proteases
lipases
nucleases

Food processing in animals

Occurs in Five phases

Ingestion
- food is taken into the body and moves into a digestive
digestion
- food is broken down into smaller molecules
- chemical and mechanical
transport
absorption
- ions, water, and small molecules are transported into the circulatory system
egestion
- undigested materials and other waste are passed from the body
- elimination or exceretion

Alimentary canal

digestive tract or tube
- Gastrointestinal tract
Five regions of food processing
Single tube with opening at each end
contains smooth muscles in walls
lined with epithelial cells
- synthesize and secrete digestive enzymes
- secrete hormones
- transport digestive materials
several specialized regions
- different structures for different processes
- storage area

Structure of GI Tract

some general structure from midpoint of esophagus, to the anus or cloaca
- lumen lined by epithelial and glandular cells
- secretory cells release a protective layer of mucus
- other cells release hormones
- glands release enzymes, acids, water, and ions
Epithelial cells linked by tight junctions and surrounded by layers of tissue made of smooth muscle, neurons, connective tissues, and blood vessels
- neurons activated by sight and smell of food and presence of food in tract

Region of Reception

Buccal cavity

mouth and accessory structures
ingestion site and digestion site
chemical and mechanical
jaws, teeth, cheek muscles, tongue, and salivary glands (saliva)

Pharynx

back of mouth cavity
point that respiratory and digestive system cross paths

Region of Conduction

Esophagus

- tube carrying materials from mouth cavity to the rest of the alimentary canal
- forces/pushes good down
- conducts food from pharynx to stomach
- Peristalsis
  - rhythmic wave-like contractions which propel food forward in the GI tract
- No new digestion here
  - only chemical continuation from buccal cavity

Region of digestion and storage

Stomach (mostly)

- saclike organ evolved for storing food
- muscular nature helps break up food
- partial protein digestion
- regulates rate of emptying into small intestine
Secretions
- hydrochloric acid
  - kills microbes
  - dissolves particulate matter
  - secreted by parietal cells
- Pepsinogen
  - converted to pepsin to begin protein digestion
  - secreted by Chief cells
Epithelium coated with an alkaline mucus
carbohydrate digestion continues from mouth
little lipid digestion happens
lumen (cavity) stomach
- pepsinogen + HCL -> pepsin (for protein breakdown)