Introductory Biology II – Midterm Review II [Biology notes]

This is a set of revision notes for Introductory Biology II classes at most universities. It may be helpful for IB Biology students who wish to seek more in-depth knowledge in regards to biological concepts. For notes from Midterm I, please refer to this page.

This is also part of an extended series on basic biological facts and concepts. For more notes on introductory biology, refer to the revision notes forMidterm 1, Midterm 2 and final exam for Introductory Biology I.

I apologize for the lack of pictures due to copyright. Many of the life cycle pictures can be obtained through a quick search on Google Images.

A generic alternation of generations life cycle

Lectures 10-12: Protists

• Apicomplexans
  
  • Parasites of animals
    
  • Apex contains a complex of organelles specialized for penetrating a host
    
  • Apicoplast – nonphotosynthetic plastid
    
  • Most have sexual and asexual stages that require two or more different host species
    
    • Eg)
      plasmodium – causes malaria
      
    • Needs both mosquitos and humans to complete life cycle
      
    • 2 million people die/year from malaria
• Ciliates
  
  • Named for use of cilia to move and feed
    
  • Have large macronuclei and small micronuclei
    
    • Micronuclei are used in conjugation, a sexual process that produces genetic variation
      
    • Have oral groove, cell mouth, etc.
• Stramenophila
  
  • Several groups of heterotrophs and algae
    
  • “hairy” flagellum paired with “smooth” flagellum
  • Subcategory diatoms
    
    • Unicellular algae with unique, two-part, glass-like wall of silica
      
    • Usually asexual reproduction, sometimes sexual
      
    • Major component of phytoplankton, highly diverse
      
    • Fossilized diatom walls compose much of the sediments known as diatomaceous earth
      
  • Subcategory golden algae
    
    • Yellow and brown carotenoids
      
    • Typically biflagellated – both flagella at one end
      
    • All are photosynthetic, some mixotrophs
      
    • Most are unicellular, some colonial
      
  • Subcategory brown algae
    
    • Largest and most complex algae
      
    • All are multicellular, most are marine
      
    • “seaweeds” – kelp
      
    • Algal body is plant-like, but lacks true roots, stems and leaves
      
      • Thallus – body
        
      • Holdfast – root like
        
      • Stipe – stem like, anchored by holdfast
        
      • Blades – leaf-like

Lecture 12: Alternation of Generations

• Complex life cycle – alternation of generations
  
• Definition: alternate multicellular haploid and diploid forms
  
• Heteromorphic - generations are structurally different
  
• Isomorphic - generations look similar
  
• Brown algae life cycle

• Cells on the blade develop into sporangia.
• Sporangia produce zoospores by meiosis.
• Zoospores are structurally alike, but half become male gametophytes and the other half turn into female gametophytes. The gametophytes are extremely small filaments that grow on rocks.
• Male gametophytes release sperm, and female gametophytes produce eggs, which remain attached to the female gametophyte. Eggs use chemicals to attract sperm to increase fertilization probability.
• Sperm fertilizes the egg.
• The zygote grows into new sporophytes whilst attached to the remains of the female gametophyte.

Oomycetes (water molds) - biflagellated zoospores

• Include water molds, white rusts, downy mildews
  
• Once considered to be fungi, but actually are protists
  
  • Largely because they have filaments (hyphae) that facilitate nutrient uptake — these maximize usage of surface area
    
  • Have cellulose in cell walls, not chitin like fungi
    
• Most are decomposers / parasites
  
• Eg) Phytophthora infestans (potato blight)
  
• Life cycle – Not alternation of generations because it is unicellular?

• The zoospore lands on a substrate and grows hyphae.
• Several days later, the hyphae form sexual structures.
• Meiosis produces eggs within oogonia.
• On separate branches of the same/different individuals, meiosis produces haploid sperm nuclei contained within antheridial hyphae.
• Fertilization tubes allow the sperm to fertilize the eggs. Zygotes develop.
• Oogonium wall usually disintegrates, and the zygotes germinate and form hyphae.
• The ends of hyphae form tubular zoosporangia.
• Each zoosporangium asexually produces about 30 biflagellated zoospores.

• Rhizarians – amoeba
  

• Pseudopodia – used by amoebas to move and feed – some but not all belong to rhizarians
  
• Have threadlike pseudopodia

• Forams
  
  • Foraminiferans – named for porous, multichambered shells called tests
    
  • Pseudopodia extend through pores in the test
    
  • Foram tests in marine sediments form a fossil record
• Radiolarians
  
  • Also have tests, but fused into one piece and usually made out of silica
    
  • Use pseudopodia to engulf microorganisms
    
  • Pseudopodia radiate from central body (like points of a star)
• Archaeplastida – red algae, green algae, land plants
  
  • Red and green algae are closest relatives of land plants; land plants are considered to have been descended from green algae
    
  • Red algae – produce accessory pigment called phycoerythrin – maximizes amount of light they can photosynthesize with
    
    • Usually multicellular; seaweeds
      
    • Eg) Dulse, Bonnemaisonia hamifera
      
    • FYI: Nori. Red alga Porphyra is the source of seaweed for Japanese food, used in sushi, etc.
      
  • Green algae – grass-green chloroplasts
    
    • Two main groups chlorophytes and charophyceans
      
    • Marine and freshwater
      
    • Eg) Ulva (sea lettuce) or Caulerpa (intertidal chlorophyte)
• Unikonta
  
  • Amoebozoans – amoeba that have lobe/tube-shaped pseudopodia (as opposed to threadlike pseudopodians from Rhizaria)
    
    • Include gymnamoebas, entamoebas, slime molds
      
  • Slime molds
    
    • Once thought to be fungi
      
    • Brightly coloured – yellow or orange
• Protistan ecology
  
  • Some protist symbionts form mutualist relationships with their hosts
    
    • Eg) dinoflagellates – nourish coral polyps that build reefs, get protection from coral
      
    • Hypermastigotes – digest cellulose in the gut of termites
      
  • Some protists form parasitic relationships with their hosts
    
    • Eg) Plasmodium, Pfiesteria shumwayae (dinoflagellate that kills fish)
  • Photosynthetic protists
    
    • Important producers
      
    • In aquatic environments, photosynthetic protists and prokaryotes are main producers

       

Lectures 13-15: Plant Diversity I

• Plant – eukaryote, multicellular, photosynthetic autotrophs
  
• Four groups of plants
  
  • Nonvascular (initial colonization of land)
  • Seedless vascular (development of vascular tissue – xylem and phloem)
  • Gymnosperms (development of seeds – less dependent on water for reproduction)
  • Angiosperms (development of flowers)
• Pros and cons of land
  
  • Pro: unfiltered sun, more plentiful CO2, nutrient-rich soil, few herbivores or pathogens
    
  • Cons: A scarcity of water and lack of structural support
    
• Adaptations enabling the move to land
  
  • Resistant resting structures (seeds)
    
    • Land is harsh and unpredictable
      
    • Less UV radiation compared to water
      
    • Temperature changes are more extreme (water holds heat better than air)
      
  • Specialized body parts and transport systems
    
    • On land, water, light and nutrients are segregated (not in same medium)
      
  • Covered with a waxy cuticle and use stomata for respiration (regulation of evaporation by closing/opening stomata)
    
    • Land is dessicating – evaporation could kill plants
      
  • Plants evolved pollen to disperse more efficiently on land
    
    • Land is dry, so there are problems for reproduction
      
  • Support tissues – thickened cell walls
    
    • Land lacks support because of full force of gravity on large plant structures
      

   

• Land plants evolved from green algae (charophytes)
  
  • Eg Chara species, Coleochaete orbiscularis
    
  • Share several characteristics
    
    • Use chlorophyll a, b, b-carotene for photosynthesis
    • Cell walls made of cellulose
      
    • Store carbohydrates as starch
      
    • Photosynthetic membranes are stacked within organelles
      
    • Cell division forms new walls by similar process
      

       

  • Derived traits of plants (AWMA)
    
    • Appear in nearly all land plants but are absent in green algae (charophytes)
      
    • Alternations of generations (with multicellular, dependent embryos)
      • 2 multicellular stages
    • Walled spores produced in sporangia
    • Multicellular gametangia
    • Apical meristems

       

  • Alternation of generations
    
    • Two multicellular stages
      
    • Gametophyte (n) – produces haploid gametes by mitosis
      
    • Fusion of the gametes creates sporophyte (2n) – produces haploid spores by meiosis

• Spore grows into gametophyte, gametophyte produces gamete. Gametes fuse, produce zygote that grows into a sporophyte.
  
• Sporangia – where the sporophyte produces spores
  
• Sporopollenin – a substance contained in spore walls that make them resistant to harsh conditions
• Gametangia – where gametes are produced
  
• Archegonia – female gametangia that produce eggs and are the site of fertilization
  
• Antheridia – male gametangia that produce sperm and release sperm
  
  • NB: sperm = smaller gamete, egg = larger gamete
• Apical meristems – specialized tissues that are allowing the plant to grow – localized regions of cell division
  
  • Cells from apical meristems differentiate into various tissues

Nonvascular plants – bryophytes

• Mosses are exclusively bryophyta
  
• Most plants have vascular tissue – vascular plants
  
  
• 3 phyla
  
  • Liverworts
    
  • Hornworts
    
  • Mosses
    
• Gametophyte – dominant stage of life cycle
• Gametophytes
  
  • A spore germinates into a gametophyte composed of a protonema and a gamete-producing gametophore
    
  • Rhizoids anchor gametophytes to substrate
    
  • Mature gametophytes produce flagellated sperm in antheridia and an egg in each archegonium
    
  • Sperm must swim in a film of water to fertilize the egg (flagellated)
    
• Sporophytes
  
  • Sporophytes grow out of the archegonium
    
  • A sporophyte consists of:
    
    • Foot
      
    • Seta (stalk)
      
    • Capsule (sporangium)
      
    • Peristome
      
  • A sporangium discharges spores through a peristome
    
    • When things are dry, the peristome opens up so the spores can be dispersed
      
    • When things are wet, the peristomes close up
• Ecology
  
  • Mosses help retain nitrogen in the soil (reduce nitrogen loss)
    
  • Apparently, they pick up nutrients and water form the air in a dense forest
  • Peat – partially decayed organic material formed by Sphagnum in deposits
    
    • Used for fuel, fertilizer, etc.
      
    • Takes a long time to decompose – good carbon sink
      
    • Therefore, sphagnum is an important global resevoir of organic carbon
  • NB: bog mummies are formed when bodies fall into bodies of water that are dominated by Sphagnum – the acidic water helps preserve the body by killing off decomposers

Seedless vascular plants

• Vascular tissue allowed these plants to grow taller by starting to overcome the light/nutrient/water segregation problem
  
• Still have flagellated sperm
  
• Restricted to moist environments usually
• Traits that characterize seedless vascular plants
  
  • Life cycles with dominant sporophytes
    
  • Vascular tissues called xylem and phloem
    
  • Well-developed (true) roots and leaves
  • Bisexual spores that don’t grow into female/male forms (have male and female parts)
    
  • Gametophyte has both the antheridium and archegonium
    
  • Has mechanisms to prevent self-fertilization
    
  • Fiddlehead – baby fern
• Vascular tissues
  
  • Xylem – conducts most water and minerals
    
    • Includes dead cells called tracheids
      
  • Water-conducting cells are strengthened by lignin which provides structural support
    
  • Phloem – distributes sugars, amino acids, other organic products, and consists of living cells
  • Roots – anchor vascular plants
    
    • Enable vascular plants to absorb water and nutrients from the soil (not just structural support like rhizoids)
• Leaves
  
  • Two types
    
    • Microphylls – leaves with a single vein
      
    • Megaphylls – leaves with a highly branched vascular system

• Sporophylls – modified leaves with sporangia on them
  
• Sori – clusters of sporangia on the undersides of sporophylls
• Homosporous – produce one type of spore that develops into a bisexual gametophyte (has both antheridia and archegonia)
  
• Heterosporous – produce megaspores that give rise to female gametophytes, and microspores that give rise to male gametophytes

• Classification
  
  • Phylum Lycophyta – more important millions of years ago
    
    • Includes club mosses, spike mosses, quillworts
      
    • Eg) Selaginella apoda (spike moss), Isoetes gunnii (quillwort), Diphasiastrum tristachyum (club moss)
      
    • Strobili – clusters of sporophylls
    • Giant lycophytes thrived for millions of years in moist swamps
      
    • Surviving members are small herbaceous plants
      
    • Club mosses and spike mosses are not “true” mosses” because they have vascular tissue
  • Phylum Pterophyta
    
    • Includes ferns, horsetails, whisk ferns
      
    • Eg) Athryium filix-femina (lady fern), Equisetum arvense (field horsetail), Psilotum nudum (whisk fern)
    • Ferns are the most diverse seedless vascular plants
      
    • Live in tropical and temperate forests
• Significance
  
  • Important parts of early forests
    
  • Formed first forests in Devonian and Carboniferous
    
  • As they decayed, they eventually became coal
    
  • Increased photosynthesis – produced global cooling at the end of the Carboniferous period
    

Lecture 16-17: Fungi (Ch. 31)

• Introduction
  
  • Fungi are diverse and widespread
    
  • Fungi are multicellular (unlike protists)
    
    • Advantages:
      
    • Cell specialization
    • Division of labour
  • Essential to good ecosystem because they break down organic material and recycle vital nutrients
    
  • FYI: Mushroom is just the fruiting body above ground; very small component of the organism
• Nutrition and ecology
  
  • Fungi are heterotrophs that absorb nutrients from outside of their body
    
  • Enzymes are used extensively to break down complex molecules (alive/dead) into smaller organic compounds
    
    • These enzymes make fungi extremely versatile – an arsenal of enzymes is used, not just one enzyme
      
  • Can feed on both living and dead organisms (living organisms through ingestion)
• Types of fungi
  
  • Decomposers – breakdown and absorb nutrients from nonliving organisms (dead plants, animals and feces) – basically feed on anything that’s nutrient-rich on the ground
  • Parasites – absorb nutrients from a living host (eg. Plant/animal)
  • Mutualists – absorb nutrients from a living host, but also benefit the host in some way (eg. Fungus in a termite gut that allow the termite to digest wood)
• Body structure
  
  • Single cell – yeasts
  • Multicellular
    • Consists of:
    • Mycelia – networks of branched hyphae adapted for absorption that infiltrate (dead) organism’s body
    • Chitin – main component of fungal cell walls
      • Also found in insects, whereas plants use cellulose
• Hyphae structure (morphology?)
  
  • Some fungi have hyphae divided into cells by septa, with pores allowing cell-to-cell movement of organelles
    
    • Eg. Ascomycetes – septate fungus
      
  • Septate – nuclei are generally specific to a compartment, more specialized (but each cell is not completely separated because the septa have holes)
    
  • Coenocytic – nuclei are free-floating
    
    • Eg. Zygomycetes – aseptate fungus
• Specialized hyphae
  
  • Some fungi have fungi that can trap and kill a living host to absorb its nutrients
    
  • More common are haustoria – allow fungi to penetrate the tissues of their host to extract/exchange nturients
    
    • Fungi can grow inside/outside plant root cells
      
    • This relationship is mutually beneficial
      
  • Haustorium – the fingers that grow into the plant cell
  • Mycorrhizae – mutually beneficial relationships between fungi and plant roots
    
  • Mycorrhizal fungi provide phosphate ions and other minerals to the host plant whilst taking organic nutrients (eg. Carbohydrates)
    
  • Ectomycorrhizal fungi – form sheaths of hyphae over root
    
  • Arbuscular mycorrhizal fungi (endomycorrhizal fungi) – extend hyphae through the cell walls of root cells
    
    • Most plants form this kind of relationship
• Reproduction
  
  • Fungi produce spores through sexual/asexual life cycles
    
  • Spores are dispersed through wind or water – animals can consume spores / disperse them through feces
  • Asexual reproduction
    
    • Eg) molds produce haploid spores by mitosis and form visible mycelia (on like expired foods, etc.)
      
    • Yeasts produce asexually and generally inhabit moist, warm environments
      
    • They reproduce asexually by simple cell division and the pinching of “bud cells” from a parent cell
      
    • Advantage: quick, very few problems if environment is nonvariable
    • Asexual reproduction results in rapid growth and dispersion of many molds and yeast
      
      • Many molds and yeast lack a sexual stage
        
      • They are given the name of deuteromycetes – imperfect/second fungi
  • Sexual reproduction
    
    • Fungal nuclei are normally haploid (n) – one copy of parent DNA
      
    • In bad environmental conditions, hyphae will actively seek a different mating strain for sexual reproduction
      
      • To find a different mating type, they use pheromones to find each other
        
      • Advantageous to have genetic diversity in external environment
        
    • Plasmogamy – fusion of hyphae from different mating types
      
    • Haploid nuclei from each parent do not fuse right away; they coexist in the mycelium, called a heterokaryon
      
    • In some fungi, the haploid nuclei pair off two to a cell – dikaryotic (n+n) mycelium
      
    • Karyogamy – nuclear fusion may take a long time, like hours, days or centuries
      
      • Haploid nuclei fuse to produce diploid cells
        
    • In most fungi, the diploid phase is short-lived and undergoes meiosis to produce haploid spores
    • Fungi are haploid dominant, unlike most organisms
  • Origin of fungi
    • Opisthokonts supergroup – contain fungi, animal and their protistan relatives
      
    • 5 groups of fungi from this supergroup (CZGAB)
      
      • Chytrids
        • Diverged early in fungal evolution (older group)
        • Have flagellated spores (zoospores) which “true fungi” lack
      • Zygomycetes
        • Includes fast-growing molds, parasites and commensal symbionts
        • Named for their sexually produced structures – zygosporangia
        • Very resistant to freezing and drying
        • Very efficient at spore dispersal
          • Cow dung species can even ‘aim’ and shoot their spores toward bright light so cows eat the spore-infested grass and disperse the spores through feces
          • Meiosis splits the diploid nuclei into many, many spores
            
          • Predominantly haploid
            
      • Glomeromycetes
        • Once considered zygomycetes
        • Now classified in a separate phylum
        • Nearly all glomeromycetes form arbuscular mycorrhizae
      • Ascomycetes
        • Live in marine, freshwater, terrestrial habitats
          • Include plant pathogens, decomposers and symbionts
        • Sexual spores are produced in saclike asci (singular: ascus) that are contained in ascocarps
          • Ascomycetes reproduce asexually by spores called conidia which form on conidiophores
        • Commonly called sac fungi
        • Lichens – greater than 40% of all ascomycete species live in a symbionce with green algae or cyanobacteria (lichen)
          
          • Lichens are two organisms living together, not just one species
            
        • Some ascomycetes form mycorrhizae with plants
          
        • Some live between mesophyll cells in leaves
          
          • Fungus releases toxic compounds to protect plant against insects
            
          • Plant provides it with carbohydrates
            
          • Mutually beneficial relationship
        • Most of time in haploid stage
          
        • Diploid nucleis undergo meiosis to form 4 haploid nuclei, which undergo mitosis to form 8 spores in the ascus
          
      • Basidiomycetes
        • Include mushrooms, puffballs, and shelf fungi
        • Mutualists, plant parasites
        • Also known as club fungi
        • Basidium – a club-like structure that is a transient diploid stage in the life cycle
        • Life cycle of a basidiomycete usually involves a long-lived dikaryotic mycelium, since it is an efficient form of expanding the hyphae
          
        • In response to environmental stimuli, the mycelium reproduces sexually with fruiting bodies called basidiocarps (what we consider to be mushrooms)
          
          • Many spores are produced, many released through gills – very efficient
            
          • The “mushroom” is a very short portion of the fungi’s lifecycle
            
            • Composed of a mass of tangled hyphae
              
        • In each gill, the numerous basidia in a basidiocarp are sources of sexual spores called basidiospores
        • Two opposite strains come together in plasmogamy
          
        • Dikaryotic mycelium is very good at growing, so it remains in this stage for a long time
          
        • Eventually the basidiocarp (n+n) is produced
          
        • Karyogamy and meiosis result in numerous basidiospores being released
          
• Fungal ecology
  
  • Decomposers
    
    • Can efficiently decompose a wide variety of organic material with their arsenal of enzymes
      
      • Cellulose and lignin (plant cell walls)
        
      • Jet fuel
        
      • House paint
        
      • Bioremediation (cleaning up environmental disasters)
        
    • Perform essential recycling of chemical elements (such as C and N) between the living and nonliving world
      
  • Mutualists
    
    • Form mutualistic relationships with:
      
      • Plants
        
        • Endophytes – harmless symbiotic fungi that plants harbour between the mesophyll layer inside leaves or other plant parts
          
          • Fungus gains carbohydrates and security from plant
            
          • Endophytes make toxins that:
            
            • Deter herbivores from eating plant leaves
              
            • Defend against pathogens
              
            • Increase tolerance to heat, drought or heavy elements
              
      • Algae
        
      • Cyanobacteria (lichen)
        
        • Lichen – symbiotic association between a photosynthetic microorganism and a fungus
          
          • 3 types – fruticose, crustose, foliose
            
        • Fungal component of a lichen is most often an ascomycete
          
        • Algae/cyanobacteria occupy an inner layer below the lichen surface
          
          • Fungus protects it, algae provides carbon compounds from photosynthesis, cyanobacteria can photosynthesize AND fix nitrogen (through heterocysts)
        • Lichen reproduce by fragmentation or the formation of soredia – small clusters of hyphae with embedded algae
          
        • Fungi within the lichen can also reproduce sexually through the formation of ascocarps or basidiocarps
        • Lichen are important pioneers on new rock and soil surfaces, such as burned forest or volcanic flows
          
          • Physically and chemically the substrate – even burned forest or volcanic rock
            
          • Trap wind-blown soil to help establish a topsoil layer
            
          • Some can add nitrogen to the substrate to promote plant growth
        • Lichen are sensitive to pollution, so their death is a warning that air quality is bad
          
      • Animals
        
        • Some fungi share their digestive services with animals
          
          • Eg) break down plant material in the guts of cows and other grazing mammals
            
        • Many species of ants and termites use the digestive power of fungi by raising them in “farms” – because the ants/termites can’t digest the leaves directly
          
          • Eg) leaf cutter ants
  • Pathogens
    
    • About 30% of known fungal species are parasites or pathogens
      
    • Some fungi that attack food crops are toxic to humans
      
    • Mycosis – fungal infection in animals
    • Eg) corn smut on corn, tar spot fungus on maple leaves, ergots on rye
    • Dutch Elm disease – Regina is one of the few places that has any Dutch Elm left
      
      • Caused by a fungus that is spread by insects (like beetles)
        
      • Fungus grows from leaves into the roots and kills the tree
        
      • Fungicides can be used to protect trees, or big sticky bands around tree prevent the beetle from crawling up into the canopy of the tree
  • Uses of fungi
    
    • Used to make many foods
      
      • Eg) cheeses, alcoholic beverages, food
        
    • Fungi produce antibiotics
      
      • The ascomycete Penicillium
        
    • Genetic research on fungi is leading to applications in biotechnology
      
      • Eg) Saccharomyces cerevisiae can produce insulin-like growth factor
        

Lectures 18-19 – Viruses

• Introduction
  
  • Viruses are smaller than bacteria
    
  • Virus – infectious particles consisting of nucleic acid (RNA/DNA) enclosed in a protein coat, or a membranous envelope in some cases
    
  • Viruses are not cells
    
  • Not alive – lack metabolic processes
  • Cannot reproduce by themselves
    
    • Obligate intracellular parasites
      
      • Obligate – have to have it
        
      • Intracellular – in cell
        
      • Parasite – takes something from the host
        
    • Need host cell to replicate
  • Host range – something unique to each virus that specifies the limited set of species that it can infect
• Viral genome
  
  • Viruses can use multiple types of nucleic acid forms
    
    • Eg) Double stranded DNA, double stranded RNA, etc.
      
    • (+) strand of RNA does the coding
    • So, you need to get the negative strand of DNA and then transcribe it to mRNA+ which can be used to translate into proteins
• Viral structure
  
  • Protein coat on outside, nucleic acid on inside
    
  • Capsid – protein shell that encloses the viral genome
    
  • Capsomeres – protein subunits that make capsids
    
    • Two forms: rod and icosahedral (20 sides)
• Membranous envelope
  
  • Viral envelopes surround the capsids of some viruses (eg. Influenza)
    
  • Envelopes help viruses infect hosts because the envelope has specific proteins that allow the viruses to bind to the host cell easier
    
  • The envelopes are derived from the host cell’s membrane – the virus “steals” it when it leaves the cell it was “born” in
    
  • Contains a combination of viral and host cell molecules – combination of proteins that both virus and host have made
  • Virus enters cell, uncoats, releases viral DNA and capsid proteins
    
  • Host enzymes replicate the viral genome whilst host enzymes transcribe the viral genome into viral mRNA, which is used by host ribosomes to make more capsid proteins
    
  • Viral genomes and capsid proteins self-assemble into new viruses that exit the cell
• Evolution
  
  • Viruses likely evolved from other mobile DNA
    
  • Mobile genetic elements
    
    • Plasmids
      
    • Transposons
      
    • Viruses
      
  • Parasitic nucleic acids – “selfish DNA” – some were motile and could move between cells and likely evolved from mobile DNA
    
  • Plasmids – circular mobile DNA – self-replicating
    
    • Requires host’s machinery also, but can sustain itself
      
  • Transposons – jumping DNA
    
    • Can cut itself out and paste itself somewhere else (cut and paste mechanism)
• Bacteriophage (phage)
  
  • Bacteriophage – viruses that infect bacteria
    
  • Probably the best studied of the viruses because experiments could be done on bacteria much easier
    
  • Capsid head encloses DNA
    
  • They inject DNA; virus does not enter the cell; injection, not entry
    
  • A protein tail piece attaches the phage to the host and injects the phage DNA inside
• Reproductive cycles
  
  • Lytic cycle
    
    • Phage infects bacteria (injection)
      
    • Phage reproduces
      
    • Phage escapes by killing cell – has to burst open bacteria cell to release all the phage
    • The assembly process is completely random – they just self-assemble. No directed process.
      
  • Lysogenic cycle
    
    • Phage infects bacteria
      
    • Difference: phage integrates into bacterial chromosome
      
  • Virulent phage – always go through the lytic cycle
    
  • Temperate phage – can do either lytic or lysogenic cycle
    
  • Comparing the two cycles
    

• Defenses against phage
  
  • Only two main stages can be defended
    
  • First stage
    
    • Use a barrier/coating to prevent virus infiltration
      
    • Mutations in binding pocket so virus can’t fit anymore (ie. Lose phage receptor sites or alter their shape)
      
  • Second stage
    
    • Bacteria produce (specific) restriction enzymes that recognize and cut up phage DNA, but not their own

Viral Genomes

• Top strand is (+), bottom strand is (-)
  
• Transcription
  • Synthesize RNA from DNA (or in the case of ssRNA-, synthesize mRNA from RNA)
• Translation
  • Synthesize protein from mRNA

• Viral envelopes
  
  • Found in many animal viruses
    
  • Viral glycoproteins on the envelope bind to specific receptor molecules on the surface of a host cell (“docking” mechanism)
  • Some formed from the host’s cell plasma membrane as the viruses exit
    
  • Others formed from the nuclear membrane or Golgi membrane (may take membranes from different organelles)
  • Viruses steals plasma membrane, then buds off. This ensures that it has a similar envelope that it did when it entered so it can infect other cells easier
• HIV
  
  • HIV is a retrovirus – viral RNA made into DNA (through reverse transcriptase)
    
  • HIV is a provirus – DNA integrates into host genome
    
    • Unlike a prophage, the integration is permanent
      
  • mRNA made from integrated provirus, then proteins are made
    
  • The RNA molecules function both as mRNA for synthesis of viral proteins and as genomes for new virus particles
  • Life cycle is similar, but the DNA that the reverse transcriptase produces is integrated into the nucleus as provirus
• Emerging/re-emerging diseases/viruses
  
  • Emerging viruses – appear suddenly or suddenly come to the attention of scientists
    
    • Eg) SARS – suddenly appeared on the radar
      
    • Swine flu – re-emerging disease
      
  • Outbreaks of “new” viral diseases in humans are usually caused by existing viruses that expand their host range – sometimes caused by humans coming into contact with animals/going into different habitats
    
    • Ie) viruses spreading from animals to humans (zoonisis, plural – zoonoses)
  • Flu epidemics are caused by new strains of influenza virus to which people have little immunity because it’s new

Lectures 20-21: Seed Plants

• Adaptations of seed plants
  
  • Seeds
    
  • Heterospory
    
  • Pollen
    
  • Reduced gametophytes
• Seeds
  
  • Seed – consists of an embryo and nutrients surrounded by a protective coat
    
  • Can remain dormant for months or years

• Gymnosperms bear “naked” seeds
  
  • Naked seeds – not enclosed by ovaries (no fruit)

• Seed plants are heterosporous
  
  • Megasporangia – produce megaspores that give rise to female gametophyte
    
  • Microsporangia – produce microspores that give rise to male gametophytes
• Pollen
  
  • Can be carried long distances
    
  • Microspore develops into a pollen grain = male gametophyte in a pollen wall – resilient structure
    
  • Sporopollenin – present in pollen wall
• Reduced gametophytes
  
  • Gametophytes are microscopic and are retained in the sporophyte
    
  • Protected from UV radiation by sporophyte

Gymnosperms

• Phyla (CGGC)
  
  • Cycadophyta (cycads)
    • Have large cones and palm-like leaves
    • Few species
    • Eg. Cycas revoluta
  • Gingkophyta (one living species: Ginkgo biloba)
    • Single living species
    • Popular ornamental tree since it has high tolerance to air pollution
    • Pollen-producing tree
    • Eg. Ginkgo biloba
  • Gnetophyta (three genera: Gnetum, Ephedra, Welwitschia) – GEW
    • Some tropical, others in deserts
  • Coniferophyta (conifers, like pine, fir and redwood)
    • Largest of all gymnosperm phyla
    • Most are evergreen – photosynthesize year round
    • Eg. Sequoia, Douglas fir
• Evolution
  
  • Were better suited than nonvascular plants or seedless vascular plants to dry environments
    
    • Thus, cone-bearing gymnosperms (conifers) dominate northern latitudes
• Life cycle
  
  • Three key features of the gymnosperm life cycle are:
    
    • Dominance of the sporophyte generation
    • Development of seeds from fertilized ovules
    • Transfer of sperm to ovules by pollen
• Explanation:
  
  • The microsporangium in the microsporangia (2n) in the pollen cone produce microsporocytes (2n) that undergo meiosis to form pollen grains (n)
  • Ovule – produces eggs
    
  • Complete asap – refer to slide notes
• Spore – Haploid cell produced by sporophyte through meiosis
  
• Sporangium – multicellular organ in which meiosis occurs
  
• Sporocyte – diploid cell (spore mother cell) undergoes meiosis to form hapoloid cells
  
• Sporophyte – diploid form, multicellular, produces haploid cells
  
• Sporophyll – modified leaf bearing sporangia
  
• Size: sporophyte > sporophyll > sporangium > sporocyte > spore

Angiosperms

• Angiosperms – seed plants with reproductive structures called flowers and fruits
  
• Most widespread and diverse of all plants
• Flower – specialized shoot with up to 4 types of modified leaves
  
  • Sepals - enclose the flower
  • Petals – brightly coloured to attract pollinators
  • Stamens – produce pollen on their terminal anthers
  • Carpals – produce ovules – stigma is ovary stylish
• Fruit – mature ovary, but may include other flower parts
  
  • Purpose: to protect seeds and aid in their dispersal
    
  • Can be wet or dry protection (fruits vs. nuts)
    
  • Eg) tomato, grapefruit, etc.
  • Various fruit adaptations help disperse seeds
    
    • Can be carried by wind, water or animals
      
    • Animals are attract to the fruit sometimes and transport it, sometimes by eating it (seed passes undigested through digestive system)
      
    • Barbs can be used also
• Angiosperm life cycle
  
  • Male gametophytes are contained within pollen grains produced by microsporangia of anthers
    
  • Generative cell – divides to form two sperm cells
    
  • Tube cell - produces pollen tube
  • Microsporocytes – individual diploid cells that undergo meiosis in the microsporangium. They undergo meiosis to create the microspore that contains the generative cell and tube cell
  • Female gametophyte (embryo sac) – develops within an ovule contained within an ovary at the base of the stigma
    
    • Many mechanisms to ensure cross-pollination between flowers
      
    • Self-fertilization happens, but mechanisms usually prevent it from happening
  • Megaspore – haploid individual cell in diploid megasporangium that leads to formation of female gametophyte, which has several cells inside it; most notably, the central cell and egg
  • A pollen grain that has landed on a stigma germinates and the pollen tube grows down to the oary
    
    • Pollen is produced on the anther of one plant and lands on the stigma of another
      
    • The ovule is entered by a pore called the micropyle
      
    • Double fertilization occurs when the pollen tube discharges two sperm into the female gametophyte within an ovule
      
      • One sperm fertilizes the egg
        
      • The other sperm combines with the two nuclei in the central cell, initiating development of the endosperm (3n) – food storage
        
        • Nourishes growing embryo
          
        • Within a seed – embryo consists of a root and one or two seed leaves called cotyledons
  • Angiosperm diversity – two main groups
    
    • Monocots (one cotyledon)
      
      • 1/4 of all angiosperm species
        
      • Eg) orchids, palms, grain crops – maize, wheat, rice
        
    • Eudicots (two cotyledon)
      
      • Eg) roses, peas, sunflowers, maples, poppies, snow peas
  • Seed plant products
    
    • 6 crops (wheat, rice, maize, potatoes, cassava and sweet potatoes) yield 80% of calories consumed by humans
      
    • The part that we’re harvesting for wheat and rice is largely fruit with the seed
      
    • Modern crops are products of relatively recent genetic change resulting from artificial selection
    • Provide wood
    • Secondary compounds of seed plants are used in medicines
      
      • Something that the plant produces but isn’t involved in the primary metabolic pathway
        
        • Eg) toxins to reduce herbivory
  • Fruit - mature ovary that surrounds seed
    
  • Vegetable – no exact definition

Lectures 22-24: Plant morphology and anatomy

• Plastic plants
  
  • Developmental plasticity – the ability to alter morphology in response to environment
    
  • More marked in plants than animals since it significantly affects whether or not they will survive 
    
  • Determinant growth – exhibited by animals as they stay with shape once they reach adult state
    
  • Indeterminant growth – exhibited by plants as they have no fixed shape or size
    
    • Plant shape is largely determined by interactions on the evolutionary time scale and short-term environmental conditions (eg. Water, sunlight, predators, etc)
• Plant morphology – external structure
  
  • Eg. Arrangement of petals on a flower
    
• Plant anatomy – internal structure
  
  • Eg. Arrangement of cells within a root or leaf
• Morphology?
  
  • Plants have 3 basic organs – roots, stems and leaves
    
    • Organized into a root system and a shoot system (photosynthetic)
  • Organs are composed of different tissues, which are in turn composed of cells
  • Roots
    
    • Multicellular organisms that:
      
      • Absorb water and nutrients
        
      • Provide structural support / anchor the plant
        
      • Store organic nutrients
        
    • Dicots have a taproot system
      
      • Taproot – main root that gives rise to lateral roots
        
      • Eg) Carrots and dandelions – though carrots have been artificially selected to minimize amount of lateral roots
        
    • Monocots have a fibrous root system
      
      • Thin lateral roots, no main root
        
      • Eg) grass
        
    • Adventitious roots – arise from stems or leaves

       

    • Root hairs absorb the majority of water and minerals since the taproot doesn’t absorb a lot
      
      • Root hairs increase surface area since they are extremely fine and thin
        
      • Grow on main root and lateral roots
    • Modified roots
      
      • Prop roots – additional roots that grow out from slightly above the soil, eventually grow down and help anchor the plant down (for fast growing plants like corn)
        
      • Storage roots – store some organic material (beets?)
        
      • Strangling aerial roots – fig trees. Fig sends roots down to the ground and strangle the tree roots, whilst using the tree for support
        
      • Pneumatophores – plants that live in standing stagnant water grow these to do gas exchange. These are roots that stick out of the water since standing water quickly loses oxygen
        
      • Buttress roots – support for extremely large plants
  • Stems
    
    • Stem – an organ consisting of an alternating system of nodes and internodes
      
      • Node – point where leaves are attached
        
      • Internodes – stem segments between nodes
    • Axillary bud – has potential to form a lateral shoot
      
    • Lateral shoot – vegetative shoot that leaves can grow off of
      
    • Apical bud – located near the shoot tip, causes elongation of a young shoot
      
    • Apical dominance – apical bud can regular growth of the rest of the plant with hormones. These hormones tell the plant if it needs to grow laterally or upwards.
      
      • To control direction, you can cut off apical buds. Cut off top apical bud – more lateral growth and vice versa
    • Modified stems
      
      • Stolon – roots growing laterally above ground – basically extensions (eg. Strawberries)
        
      • Tubers – modified stems, not roots – swellings of the rhizomes
        
      • Rhizomes – stolons but underground
        
      • Bulb – garlic/onion with storage leaves
  • Leaves
    
    • Leaf – main photosynthetic organ
      
    • Consists of flattened blade and a stalk called the petiole that joins the leaf to a node on the stem
      
    • Grass – no separate petiole – wrap around each other – leaf coming directly off of it?
    • Monocots and dicots differ in arrangement of veins – main vascular tissue of leaves
      
    • Most monocots have parallel veins
      
    • Dicots have branching veins
    • Attributes of leaves that are useful for classification
      
      • Number of leaves on stem
        • Simple leaf vs compound leaf vs double compound leaf
        • If you ever get confused if it’s a leaflet or actual branch, look at where the axillary bud is–always attached to the main branch
      • Arrangement of leaves on the stem
        • Opposite, alternate, whorled (multiple leaves coming off of the same point)

• Shape of leaves
  • Cordate, lanceolate, triangular, oval
• Vein arrangement

• Parallel, pinnately net-veined (veins that spread out), palmately net-veind (one central vein)
• Types of modified leaves

• Storage leaves – store food
• Reproductive leaves – used in asexual reproduction where specialized leaves fall off plant and grow into new leaf
• Tendrils – sometimes modified stems/leaves that help the plant crawl up/support
• Spines – self-explanatory
• Bracts – leaves that look like flowers, lure in pollinators