Principles of Biology II

Review Final Exam

Chapter 19- Viruses
Draw the structure of a virus. (Show examples)

lytic
cycle




lysogenic cycle
Replicative Cycles of animal viruses- Retroviruses (HIV)





Viroids:
circular RNA molecules (few hundred nucleotides)
infect plants
disrupt growth
Prions
slow acting
indestructible
infectious proteins
transmitted in food
cause brain diseases in mammals
o Mad Cow Disease
o Creutzfeldt-Jakob disease
Humans
o Scrapie
Sheep

Chapter 27- Bacteria and Archaea

Bacteria: Structural and functional
adaptations- Cell-surface structures, motility,
internal and genomic organization.
Reproduction and Adaptation: genetic
diversity in prokaryotes- 1) Rapid
reproduction, 2) Mutation and 3) Genetic
recombination. Conjugation & plasmids.
Diverse nutritional and metabolic adaptations
(photoautotrophy, chemoautotrophy,
photohetero-trophy, and chemoheterotrophy),
prokaryotic phylogeny (Comparison of three
domains). Archaea : Extermophiles, Extreme
halophiles, extreme thermophiles,
methanogens.

Cell surface structures
-Bacterial cell wall
-peptidoglycan, network of sugar polymers cross-linked by polypeptides
-Archaea cell wall
- have polysaccharides and proteins but lack peptidoglycan



Gram Staining
-Remember: PPT (Positive Purple Thick)


-Gram negative bacteria
-have less peptidoglycan
-outer membrane that can be toxic
-Antibiotics target peptidoglycan to damage the wall
-Capsule = polysaccharide or protein layer that covers many prokaryotes
-Fimbriae
-attachment pili
-stick to substrate or other individuals in a colony
-Sex pili
-longer than fimbriae
-allow prokaryotes to exchange DNA
Motility
-Flagella
-Taxis
-ability to move toward or away certain stimuli

Chapter 28 Protists
Endosymbiosis in Eukaryotic Evolution, Five Supergroups of Eukaryotes- list their key
characteristics, and describe some representative taxa. (Red algae and green algae, Life cycle of
plasmodium, Cellular slime molds).
Chapter 29 Plant Diversity I: How Plants Colonized Land
Land plants evolved from green algae, Highlights of plant evolution. Derived Traits of Plants: Protection
of the embryo, Alternation of generations (with multicellular embryos dependent on the parent plant),
Walled spores produced in sporangia, Multicellular gametangia, Apical meristems. The Origin and
Diversification of Plants: Nonvascular plants, vascular plants: seedless vascular plants, seed plants and
their classification. The life cycle of a moss. The ecological and economic importance of moss. The
origin and traits of vascular plants. The life cycle of a fern, Adaptations for life on land, sporophylls and
Spore Variations, The Significance of Seedless Vascular Plants.
Chapter 30 Plant Diversity II: The Evolution of Seed Plants
Seeds and pollen grains, the key adaptations for life on land, Gametophyte/sporophyte relationships in
different plant groups, Heterospory: Ovules and Production of Eggs, Heterospory: Pollen and Production
of Sperm, The Evolutionary Advantage of Seeds, Gymnosperms bear naked seeds, typically on cones,
The Life Cycle of a Pine, The reproductive adaptations of angiosperms include flowers and fruits, The
Angiosperm Life Cycle, Angiosperm Evolution. Major differences between monocots and eudicots.

50 nm
Internal and Genomic Organization
-lack complex compartments
-some have specialized membranes that perform metabolic functions













-have less dna than eukyot.
-Most genome consists of circular chromosome, some also have plasmids
-plasmid
-smaller rings of DNA
-no membrane bound nucleus
-chromosome is located in the nucleoid
-many prokaryotes form metabolically inactive endospores which can remain viable in
harsh conditions for centuries


(a) _______ prokaryote (b) _______ prokaryote
0.2 m 1 m
Reproduction and Adaptation:
genetic diversity in prokaryotes-
1) Rapid reproduction
-binary fission
-divide every 1-3 hours
2) Mutation
-mutations rates = low
-bc of fast reproduction, when mutations do happen, they accumulate rapidly in a
population
-high diversity from mutations allows for rapid evolution
3) Genetic recombination. Conjugation & plasmids.
-makes more diversity
-Transformation
-take up foreign DNA from the environment
-Transduction
-movement of genes btwn bacteria by bacteriophages
-Conjugation
-process where genetic material is transferred btwn bacterial cells
-sex pili = allow cells to connect and pull together for DNA transfer
-Plasmids
-carry antibiotic resistance genes and can be transferred btwn species







-F factor: has genes required for production of pili; can exist as F plasmid or a part of the
entire chromosome
-F plasmid: Plasmid with f factor
-R plasmid: carry resistance genes which code for enzymes that destroy or hinder
antibiotics like tetracycline or ampicillin
Diverse nutritional and metabolic adaptations
-chemoheterotrophic prokyot.
-decomposers
-break down corpses, dead vegetation, and waste
-nitrogen-fixing prokaryotes add usable nitrogen to the environment
Host= larger Symbiont=smaller
Pathogens= parasites that cause disease
Exotoxins
-cause disease even if prokaryotes that make them are not there (Cholera, botulism)
Endotoxins (gram negative bacteria)
-are released only when bacteria die and their cell walls break down


Archaea

-share some traits with bacteria and
others with eukaryotes
Extermophiles
-live in extreme environments
Extreme halophiles
-live in highly salty/saline places (ex: dead sea)
extreme thermophiles
-live in super hot places (ex: you, lolz. And hot springs)
Methanogens
-live in swamps and marshes
-make methane as a waste product
-strict anaerobes and are poisoned by O
2



Chapter 28 Protists
Protist
-informal name
-formal name: Unicellular eukaryotes
-paraphyletic group (dont include all of the descendants of a single common ancestor)
-Kindom Protista = not a valid clade
Valid clade = has ancestral species and all of its descendants
-have organelles
-more complex than prokaryotes
-mostly unicellular
-some colonial/multicellular
-not plants, animals, or fungi
Endosymbiosis in Eukaryotic Evolution
-Mitochondria
-evolved by endosymbiosis of an aerobic prokaryote (gram-negative
proteobacteria)
-Plastids
-evolved by endosymbiosis of a photosynthetic cyanobacterium
-Protists with plastids
evolved into red and green algae
-Red and Green algae
underwent secondary
endosymbiosis, in which they were
ingested by a heterotrophic
eukaryote

Five Supergroups of Eukaryotes- list their key characteristics, and describe some representative
taxa. (Red algae and green algae, Life cycle of plasmodium, Cellular slime molds).
1.) Excavata
-excavated feeding groove
-polyphyletic
-diplomonads
-(modified mitochondria: mitosomes, multiple flagella)
-ex: Giardia intestinalis and parabasalids
-reduced mitochondriae
-ex: hydrogenosomes and Trichomonas vaginalis
-euglenozoans
-includes kinetoplastids and euglenids
2.) Chromalveolata
-monophyletic
-originated by secondary endosymbiosis
-proposed endosymbiont was red alga
-includes alveolates and stramenopiles
3.) Rhizaria
-diverse group of protists defined by DNA similarities
-Amoebas move and feed by pseudopodia (some [not all] belong to clade rhizaria)
-include forams and radiolarians
4.) Archaplastida (plantlike)
-Red & Green algae, and land plants
-land plants descended from green algae

5.) Unikonta
-closely related to fungi and animals
-two clades: amoebozoans and opisthokonts (animals, fungi, etc)

Chapter 29 Plant Diversity I: How Plants Colonized Land
Land plants evolved from green algae
-Charophytes = closest living relatives of land plants
-Embryophytes = Kingdom Plantae
= not free living
= protected by maternal tissue














4 traits they share:
1.) Rings of cellulose-making proteins
2.) Peroxisome enzymes
3.) Structure of flagellated sperm
4.) Formation of phragmoplast (group of microtubules)

4 traits only land plants have:
1.) Alternation of Generations & Multicellular, Dependent Embryos
2.) Walled Spores Produced in Sporangia (multicellular organs that make spores)
3.) Multicellular Gametangia (multicellular organs that make gametes)
4.) Apical Meristems (in shoots and roots)
(More derived traits: Cuticle, secondary compounds)
Gametophyte
-haploid
-makes haploid gametes through mitosis
-w/i organs called gametangia
Female gametangia: archegonia (makes eggs/site of fertilization)
Male gametangia: antheridia (makes sperm)
Sporophyte
-diploid
-makes spores in sporangia
-Sporocytes = diploid cells
-sporocytes undergo meiosis to make haploid spores that grow into gametophyte by
mitosis
-fusion of gametes = new sporophyte
-Diploid embryo is retained w/i tissue of the female gametophyte (i.e. protection nof
embryo)
-Placental transfer cells: where nutrients are transferred from parent to embryo
Embryophytes
-named so because the embryo is dependent on the parent
Symbiosis btwn fungi and land plants may have helped plants w/o true roots to get
nutrients
Origin and Diversification of Plants
-Nonvascular = Bryophytes
-Vascular = most plants are in this
-Seedless Vascular
=Lycophytes
-club mosses and relatives
=Pterrophytes
-ferns and relatives
-Seed Plants
=Gymnosperms
-naked seed plants, inclu. Conifers
=Angiosperms
-flowering plants
-seed = embryo and nutrients surrounded by protective coat

Label which are gametophyte/sporophyte
dominant





Rhizoids
-anchor gametophytes to substrate
-not true roots
Height of gametophytes = constrained by lack of vascular tissues
Bryophyte sporophytes
=not freeliving
=grow out of the archegonia
=smallest and simplest sporophytes of all extant plant groups
Sporophyte parts
=foot
=seta (stalk)
=sporangium (capsule)
-discharges spores
=(have stomata for gas exchange)
Sporophyte examples:
Anthoceros (no seta, only sporangium) Polytrichum commune

Ecological and Economic Importance of Mosses
Mosses
=inhabit diverse, extreme, moist places
=help retain nitrogen in the soil
=Sphagnum (Peat moss)
=makes deposits of decayed organic material called peat
=important global reservoir of organic carbon

Origins and Traits of Vascular Plants
=Fossils=420 mill. yrs old
Living vascular plants
=sporophyte dominant
=tiny gametophytes
=grown on or below the soil surface
=have xylem/phylem
=well developed roots and leaves


Adaptations for land life
=xylem
=water & minerals
=tracheids=dead tube cells
=phloem
=living cells
=sugars, amino acids, & other organic products
=roots
=anchor vascular plants
=enable twater/nutrient absorption from soil
=evolved from subterranean stems
=leaves
=increase surface area
=capture solar energy
=photosynthesis
Sporophylls and Spore Variations
=Sporophylls
=modified leaves with sporangia
=Sori
=clusters of sporangia beneath sporophylls
=Strobili
=cones formed from groups of sporophylls
=Homosporous
=one type of spore that develops into bsexual gametophyte
=Heterosporous
=make megaspores and microspores
=megaspores: female gametophyte
=microspores: male gametophyte


The Significance of Seedless Vascular Plants
=ancestors of modern lycophytes, horsetails, and ferns grew to great heights
=during the Devonian and Carboniferous
=forming the first forests
=increase. Photosynth. = global cooling at end of Carboniferous
=Decaying plants (Carboniferous period) Coal





Chapter 30 Plant Diversity II: The Evolution of Seed Plants
Seeds and pollen grains (key adaptations for life on land)
Common to all seed plants:
=Seeds
-enable production in terrestrial ecosyst.
-made of:
-embryo
-nutrients surrounded by protective coat
=Reduced gametophytes (as few as 3 cells)
=Heterospory
-separate male and female spores/gametophytes
=Ovules
=Pollen (microgametophyte)
Gametophytes
=develop inside walls of spores
=the spores stay inside the tissues of the parent sporophyte
(Know gametophyte/sporophyte relationships in different plant
groups)
Heterospory: Ovules and Production of Eggs
=Ovule
=megasporangium
makes megaspores (meiosis)
megaspores make megagametophytes (mitosis) and one or more
integuments
Integument seed coat



Heterospory: Pollen and Production of Sperm
=Microsporangia
makes microspores
microspores turn into pollen grains (that contain
microgametophytes)
=Pollination
=Pollen Ovules
=eliminates need for water during fertilization
=can be dispersed great distances by air or animals (birds&bees ;)
=Fertilization
=fusion of gametes (egg and sperm)


The Evolutionary Advantage of Seeds
=Seed
-develops from the whole ovule
-sporophyte embryo & food supply
-packaged in protective coat
-can be dormant for days-years
-can be transported by wind or animals

Gymnosperms bear naked seeds (typically on cones)
=Naked seeds are not enclosed by ovaries
=Seeds are exposed in cones
=Seed plants arise ~360 mya
=Living see plants have 2 clades
Gymnosperms and Angiosperms
(Gymnosperms = earlier ~305 mya)
=Progymnosperms
= Transition seedless vascular plants
=Archaeptoris
=heterosporous tree with woody stem
=Conifers
=cone-bearing gymnosperms
=habitat: northern latitudes
Phylum Cycadophyta (Cycads)
=Large cones
=Palm-like leaves
=Thrived during Mesozoic
=few species exist today





Phylum Gingkophyta (Ginkgo biloba)
=single species: Ginkgo biloba
=high tolerance for air pollution
=population ornamental tree



Phylum Gnetophyta (3 genera: Gnetum, Ephedra,
Welwitschia)
=some tropical
=others live in deserts
=natural source of ephedrine (banned supplement) and pseudoephridine


Phylum Coniferophyta (conifers like pine, fir, & redwood)
=largest of the gymnosperm phyla
=most are evergreens (can do photosynthesis all year)


The Life Cycle of a Pine
=Sporophyte dominant
=Seeds develop from fertilized ovules
=Pollination
=small cones make pollen grains (microspores)
=big cones make megaspores that turn into female gametophyte
=Takes ~3 years from cone production to mature seed


The reproductive adaptations of angiosperms include flowers and
fruits
=Angiosperms
=seed plants with fruits & flowers (reproduct. struct.)
=most widespread & diverse
=single phylum: Anthophyta (greek, anthos = flower)
=Flower
=angiosperm structure
=sexual reproduction
=pollinated by insects, animals, or wind
=specialized shoot, up to 4 types of modified leaves
=Sepals
=enclose flower
=Petals
=brightly colored; attract pollinators
=Stamens
=make pollen on anthers
=Carpels
=make ovules
=made of ovary at base and style leading to sticky stigma
=Fruits
=made of mature ovary (and maybe other flower parts. For example, ovary grows into
fruit but its maternal tissue that grows around the seeds)
=protect seeds
=aid in seed dispersal
=can be fleshy or dry
=can be carried by wind, water, or animals
=consumed and pooped
=blow with wind
=stick to fur
=nuts= collected and buried
=(examples: tomato, ruby grapefruit, nectarine, milkweed, hazelnut, wings,
barbs)
The Angiosperm Life Cycle
=Sporophyte flower
=has male and female structures
=Male Gametophyte
=inside pollen grains
=Microsporangia
=make pollen
=found on anthers
=Female Gametophyte
=aka embryo sac
=develops within ovule
=Has mechanisms to ensure cross pollination
=btwn different flowers but same species


Angiosperm Evolution
=305 million yrs ago
=Ancestors of angiosperms and gymnosperms diverged
=Angiosperms originated 140 million years ago
=major ranches diverged during late Mesozoic (ex: Archaefructus)
=Dicot
=historical paraphyletic group
=contained most eudicots & several smaller lineages
=Basal angiosperms
=less derived
=inclu. flowering plants belonging to oldest lineages
=first flowering plants to diverge from ancestral angiosperm
=Amborella trichopoda
=ancestral angiosperm
=water lily
=3 small lineages
=formerly in Dicots
=Magnoliids
=share some traits with basal angiosperms
=more related to monocots and eudicots
=(ex: magnolias, laurels, black pepper)
=formerly in Dicots
=Monocots
=More than 25% of angiosperms
=ex: grasses, grains, bananas, orchids, lilies, etc.
=Eudicots
=More than 66% of angiosperms
=ex: Zucchini flowers, dog rose, California poppy, Pyrenean oak




Major differences between monocots and eudicots

























Chapter 35: Plant Structure, Growth, and Development
=Roots
=multicellular organs
=anchor plant
=absorb minerals and water
=store organic nutrients
=Taproot system
=one vertical roots gives rise to lateral/branch roots
=Adventitious roots
=come from stems or leaves
=Fibrous root system
=seen in seedless vascular plants and monocot
=thin lateral roots
=no main root
=Root hairs
=where absorption of water and minerals happens
=increase surface area
=Dermal
=cover surface
=epidermims
=periderm (in woody plants)
=cuticle
=waxy coating on top of epidermis
=trichomes
=outgrowths of shoot epidermis
=make organ fuzzy
=may be one or multiple cell for insect defense
=physical barrier or secondary metabolites (toxic chem)
=Guard cells
=around stomata
=specialized epidermal cells
=Root hairs
=Vascular
=xylem

=transport
=Ground
=everything thats not dermal/vascular
=Water-conducting cells
=dead at maturity
=tracheids (found in all vascular plants)
=vessel elements
=common in most angiosperms and some gymnosperms
=larger and more edvanced
=aligned end to end
=form long micropipes called vessels
=their presence differentiate hardwoods from softwoods
=Sugar-conducting cells
=sieve-tube elements
=alive at maturity
=lack organelles
=sieve plates
=porous end walls
=allow fluid to flow between cells along sieve tube
=companion cell
=is in each sieve-tube element
=nucleus and ribosomes serves
itself and sieve-tube element

=Ground tissue
=Pith
=internal to vascular tissue
=Cortex
=external to vascular tissue
=Functions
=storage
=photosynthesis
=support
=Parenchyma cells
=thin, flexible walls
=least specialized
=perform most metabolic functions
=retain ability to divide and differentiate
=Collenchyma cells
=grouped in strands
=help support young parts of plant shoot
=elongated cells
=thicker uneven cell walls
=flexible support w/o restraining growth
=(ex: Helianthis stem)
=Sclerenchyma cells
=rigid, thick
=secondary walls strengthened with lignin
=dead at maturity
=Sclereids
=short, irregular in shape
=thick lignified secondary walls
=ex: Nutshell, seed coat, gritty texture of pear
=Fibers
=long and slender
=arranged in threads
=ex: hemp fiber-rope, flax-linen
=Indeterminate growth
=can grow forever
=ex: stem, branch, root
=Determinate growth
=stop growing at a certain size
=ex: flower, leaf
=Annuals
=complete life cycle in a year or less
=ex: corn, wheat
=Biennials
=require two growing seasons
=ex: flower in 2
nd
yr, carrots, beats
=Perennials
=live for many years
=ex: trees, bushes
=Meristems
=forever embryonic
=allow indeterminate growth
=Apical Meristem
=located at tips of roots and shoots and at axillary buds of shoots
=Primary growth
=add length
=apical meristem elongate shoots and roots
=Secondary growth
=add thickness to woody plants
=Two lateral meristems
=vascular cambium
=adds layers of vascular tissue (secondary xylem and phloem)
=cork cambium
=replaces epidermis with periderm (thicker/tougher)
(In woody plants, primary and secondary growth happen simultaneously but in diff. places)

=Primary Growth of Roots
=produces epidermis, ground tissue, and vascular tissue
=root cap
=covers root tip
=protects apical meristem as root pushes through soil
=Growth behind root tip 3 zones
=zone of cell division
=zone of elongation
=zone of maturation
=Stele
=vascular cylinder
=ground tissue fills cortex
=Endodermis=innermost layer of cortex
=Primary Growth of Shoots
=shoot apical meristem
=dome-shaped mass of dividing cells at shoot tip
=Leaf primordial
=where leaves develop
=are along the sides of the apical meristem
=Axillary buds
=develop from meristematic cells at the bases of leaf primordial
=lateral shoots (branches) develop from here



=Tissue Organization of Leaves
=epidermis have stomata
=each stomata has 2 guard cells
=Mesophyll
=ground tissue in leaves
=btwn upper and lower epidermis
=Upper mesophyll = Palisade Mesophyll
=Lower mesophyll = Spongy Mesophyll (gas exchange)
=Vascular tissue of leaf is continuous w/ vascular tissue of stem
=Veins
=leafs vascular bundles
=function as the leafs skeleton
=enclosed by protective bundle sheath



=Secondary growth
=happens in stems and roots of woody plants
=rarely happens in leaves
=consists of tissues produced by the vascular and cork cambium
=doesnt happen in monocots
=only in gymnosperms and eudicots
=Cork Cambium
=makes periderm (periderm is made of cork cambium and the layers of cork cells
it produces)
=Bark
=all the tissues external to the vascular cambium
=Vascular Cambium
=cylinder of meristematic cells between the xylem and phloem
=adds secondary xylem inside
=adds secondary phloem outside
=Secondary xylem accumulates as wood
(Wood consists of tracheids, vessel elements in angiosperms, and fibers)
=Early wood (in spring)
=thin cell walls to maximize water delivery
=Late wood (in summer)
=thick wall cells to maximize stem support
=Tree rings
=where early and late wood meet
=used to estimate trees age
=Dendrochronology
=analysis of tree ring growth patterns
=used to study past climate change
=Growth
=irreversible increase in size
=Morphogenesis
=development of body form and organization
=determines the position of the cell type









The plant body:
Stems: apical bud, axillary bud, node, internode, (Modifications-Rhizomes, tubers,
stolons)
Roots: Tap root, Fibrous root (Storage roots, Pneumatophores, prop roots) and
leaves (Leaf modifications).
Tissue system: Dermal, Vascular, and Ground Tissues.
Vascular tissue system: Xylem,Phloem.
Water-Conducting Cells of the Xylem- tracheids and vessel elements.
Sugar-Conducting Cells of the Phloem: Sieve-tube elements.
Ground tissue system: parenchyma cells, Collenchyma cells, Sclerenchyma cells:
Sclereids, Fibers.
Indeterminate growth, Determinate growth.
Meristems: Apical meristems- Primary growth, Lateral meristem: vascular
cambium, cork cambium- secondary growth.
Primary Growth of Roots: Zone of cell division, Zone of elongation, Zone of
maturation.
Organization of primary tissues in young roots (Eudicot root and monocot root).
Primary Growth of Shoots: Organization of primary tissues in young stems
(Eudicot and monocot stems)
Tissue Organization of Leaves.
Growth, morphogenesis, and differentiation produce the plant body: Genetic
Control of Flowering (ABC model).
Chapter 36 Resource Acquisition and Transport in Vascular Plants
Resource acquisition and transport in a vascular plant, Different mechanisms to transport substances over
short or long distance, diffusion, osmosis, active transport, passive transport, transport proteins, solute
transport across plant cell plasma membranes. Three Major Pathways of Transport: symplastic route,
apoplastic route, transmembrane route. Bulk Flow in Long-Distance Transport, Transpiration derives the
transport of water and minerals from roots to shoot via the xylem, Bulk Flow Driven by Negative
Pressure (Tension) in the Xylem, Pulling Xylem Sap: The Transpiration-Cohesion-Tension Mechanism,
The rate of transpiration is regulated by stomata, Stimuli for stomatal opening and closing, sugars are
transported from sources to sink via the phloem, Bulk Flow by Positive Pressure: The Mechanism of
translocation in angiosperms.
Chapter 37 Soil and Plant Nutrition
Basic physical properties ( texture and composition) of soil, mechanism of cation exchange in soil,
sustainable agriculture, Irrigation, aquifers, subsidence, salinization, Drip irrigation, Fertilization and Soil
pH, soil erosion and ways to control soil erosion, Phytoremediation, essential elements, macronutrients
micronutrients, Plant nutrition and plants relationships with other organisms (mutualistic relations),
rhizosphere, rhizobacteria, Bacteria in the Nitrogen Cycle, Nitrogen fixation in root nodules by
rizobacteria, Fungi and Plant Nutrition, Mycorrhizae: ectomycorrhizae, arbuscular mycorrhizae,
nutritional adaptations that use other organisms in nonmutualistic ways: Epiphytes, Parasitic Plants, and
Carnivorous Plants, examples of each of them.

Chapter 38 Angiosperm Reproduction and Biotechnology
Flowers, double fertilization, and fruits are unique features of the angiosperm life cycle, angiosperm
reproduction: Flower Structure and Function, Development of Male and Female Gametophytes,
Pollination and Double Fertilization. Structure of the mature seed. Seed Dormancy, seed Germination,
and Seedling Development. Fruit Form and Function. Flowering plants reproduce sexually, asexually or
both. Mechanisms of sexual reproduction and asexual reproduction. Vegetative propagation and
agriculture. Plant Biotechnology and Genetic Engineering.