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Contents

• The Bacteria
• Archaea and Eukarya
• The Fungi
• Genetics Fundamentals
• Genetic Exchange
• Viruses and Prions
• Genomics

The Bacteria

• Evolution of three domains
  
• Bacterial morphology – very diverse
  
  • These unique features (eg. Flagellum, etc) are used to group/categorize microbes
    
  • There are three major types (which each replicate by binary fission)
    
    • Coccus (round)
    • Bacillus (tube-like, rods)
    • Spiral
• Bacterial replication by binary fission
  
  • Dividing in the centre equally
    
  • Depending on how it happens, you can get different morphologies
    
• Coccus
  

1. Streptococcus – don’t separate, stay joined as they divide
2. Diplococcus – stay in twos
3. Tetrads – divide and stay together in fours
4. Sarcina – divide down longitudinal plane (eight cells, two tetrads that are stacked on top of each other)
5. Staphylococcus – replicate in different planes (random)

• The bacillus (rods) – also divide by binary fission
  
  • Depending on end result, you can get two different types)
    
  • Streptobacillus – chain of bacilli
    
  • Coccobacillus – shortened bacillus structure, combination of coccus and bacillus
    
• Spirals – not based on division, just based on morphology (what they look like)
  
  • Vibrio – comma shaped
    
  • Spirillum – spirals but inflexible (any pic prob)
    
  • Spirochete – flexible spirals (any pic prob)
    
• Bacterial structure has many layers
  
  • Cytoplasm
    
    • Many small molecules (amino acids, nucleotides, ions, cofactors) floating around
      
    • Enzymes/proteins for maintaining the organism
  • Nucleoid
    
    • Nuclear material is concentrated in the nucleoid (no distinct nucleus)
      
    • Not a compartment; just a location
      
    • DNA (a lot) is present in a covalently closed circular duplex (supercoiled)
      

    • The DNA structure is circular, therefore no chromosomes
      
      • Hence, it bundles up in this compact form
        
  • Ribosomes
    
    • Read mRNA, create proteins
      
    • In bacteria, ribosomes form polyribosomes to translate mRNA into protein simultaneously as DNA is being transcribed into mRNA
      
    • Bacteria: 70S ribosomes
      
      • 30S (bottom) subunit and 50S (top) subunit (does not equal 70 = expected)
        
      • S = sedimentation coefficient in centrifugation
        
  • Cytoplasmic membrane – phospholipid bilayer
    
    • Proteins are embedded in the membrane (eg. Transporters)
      
    • Connected to each other with ester linkages between the heads
      
  • Cell wall
    
    • Two major components: peptidoglycan and in some bacteria, outer membrane
      
    • Gram + has a lot more peptidoglycan, Gram – has less but has an outer membrane
      

Gram +ve / Gram -ve

• Gram + cell wall
  
  • Made up of largely peptidoglycan = very thick
    
  • Periplasm – small gap between cytoplasmic membrane and cell wall
    
• Gram – cell wall
  
  • Outer membrane is the outermost layer
    
  • Peptidoglycan is sandwiched between the cytoplasmic membrane and the outer membrane
    
  • Periplasm surrounds the peptidoglycan
    

• Gram staining
  
  • Crystal violet is added and seeps into bacteria – turns everything PURPLE
  • Iodine is added as a mordant
  • Ethanol is used for decolorization
    • Gram + stays purple, Gram – clears
  • Use Safranin, a counterstain, to distinguish between the two types
    • Gram – turns pink
  • Therefore, Gram +ve = purple, Gram -ve = pink
    
• What’s happening in the gram stain?
  
  • Crystal violet penetrates in
    
  • Mordant forms complexes with the ions of crystal violet –> trapping crystal violet in large complexes to make it hard to leave
    
  • Ethanol washes away outer membrane of Gram -ve and dehydrates water
    
    • By dehydrating water, the peptidoglycan SHRINKS
      
    • Gram +ve still has some peptidoglycan left since it had a lot to begin with, but Gram -ve loses almost all of its peptidoglycan
      
    • Crystal violet complex remains in Gram +ve since it’s still stuck on the peptidoglycan and hasn’t been washed away
      
• Peptidoglycan differences
  
  • Gram +ve
    
    • N-acetylmuramic acid (NAM) is bonded to N-acetylglucosamine (NAG)
      
    • Forms long strands and forms bridges with pentaglycine crosslink (glycine residues)
      
  • Gram -ve
    
    • Still have long chains of NAM and NAG
      
    • However, there is a direct crosslink (a direct bond) with no residues in between
      
• Teichoic acid anchors – Gram +ve
  
  • Peptidoglycan is attached to the cell membrane and held together with teichoic acid anchors
    

  • Lipoteichoic acid attaches the peptidoglycan to the lipids in the actual cell membrane
    
  • Teichoic acid anchors hold the peptidoglycan layer together
    
• Lipoprotein anchors – Gram -ve
  
  • Lipoproteins anchor the thin peptidoglycan layer to the outer membrane to provide stability
    

• LPS – Lipid + Sugar (saccharide)
  
  • In humans, the virulence is determined by the O-polysaccharide
    
  • This allows bacteria to attach to the cell
    
  • Eg) E coli has O:157
    

Components (cont.)

• Fimbrae/Pili
  
  • Extend from bacterial cell (can be extended) to attach to a surface
    
  • Bacteria can use the pili to reel themselves in by retracting their pili
    
  • Ie) used to attach / move (via gliding)
    

• Capsule
  
  • An outer layer that forms just around the cell
    
  • Made of extracellular polymeric substances – sugars, proteins (polypeptides)
    
  • Very important for attachment and protects them
    
  • Some bacteria have sheaths – made of sugars and amino acids
    
• Flagellum
  
  • Used in motility
    
  • Variety of different “conformations” and numbers
    
  • Monotrichous – single flagellum from single point
    
  • Peritrichous (perimeter) – multiple flagellum coming out from around the cell
    
  • Amphitrichous (amphibian)- flagella from both ends
    
  • Lophotrichous (mound/hill) – tuft of flagella at one end
    
  • Amphilophotrichous – tuft of flagella at both ends
    
• Flagellum of Gram -ve
  
  • Has evolved to include specific proteins to anchor to the inner/outer membranes and the thin peptidoglycan layer
    
  • Very complex structure
    
• Flagellum of Gram +ve
  
  • Embedding proteins are also adapted
    
  • Anchored in cell membrane also
    
  • Simpler in structure than Gram -ve
    
• Flagellar filament
  
  • Middle is hollow
    
  • Looks like spiral staircase
    
  • Assembly:
    
    • Pieces go through the middle and come out on top – pieces are assembled spirally
      
• Type III secretion system
  
  • Injects virulents into host
    
  • It seems to be related to the flagellum – specialized form
    
    • Seems to have had a common ancestor structure with the flagellum
      
  • The flagellum probably came first because it is more ubiqutous
    
  • Flagellum is hollow inside –> useful structure for adaptation into injection
    

Taxis

• Taxis – movement or orientation directly towards / away from a stimulus
  
  • Eg) magnetotaxis in Magnetospirillum
    
  • Eg) Phototaxis – bacteria align in specific pattern for optimal photosynthesis
    
  • Eg) chemotaxis – move towards chemical / chemical gradient (Agrobacterium tumefaciens)
    
    • Agrobacterium goes towards leaking compounds in soil to find plant
      

Archaea and Eukarya

• Evolution of three major domains: Archaea, Bacteria, Eukarya
  
  • Bacteria are their own distinct domain; Eukarya are considered to be an offshoot of Archaea
    
  • However genetic information was exchanged between all groups
    
• Archaea – general information
  
  • Have layers like bacteria
    
  • Components are very similar to bacteria; similar appearance; small differences in structural components (ie. to allow them to survive extreme conditions)
    
  • Cytoplasm
    
    • Ribosomes
      
    • Macromolecules: DNA, RNA, proteins
      
    • Small molecules: amino acids, nucleotides, ions, cofactors
      
    • Enzymes: metabolic processes
      
    • DNA is found in a nucleoid
      
• DNA of Archaea
  
  • Like bacteria – covalently closed circular duplex (supercoiled)
    
    • Compacting is done so the massive amount of DNA does not fill up the entire cell
      
    • Similar limitations as bacterial DNA
      
  • Supercoiling controlled by gyrase and helicase – introduce + or – supercoiling
    
• Ribosomes of Archaea
  
  • DNA -> mRNA -> proteins (made through ribosomes)
    
  • Simultaneous transcription and translation
    
    • Polyribosomes translate mRNA into protein; attach at gene sequences whilst DNA is being transcribed into mRNA
      
  • Ribosomes are essential for protein synthesis
    
  • 70S ribosomes (like bacteria)
    
    • 50S subunit (top), 30S subunit (bottom)
      
    • They are a bit different even though they are both 70S — same function though
      
    • Ribosomes from Archaea can be substituted with ribosomes from Eukarya, even though Eukarya have 80S ribosomes
      
      • Bacterial ribosomes can not be substituted for Eukaryotic ribosomes!! Only Archaea!!
        
• Plasma membrane = cytoplasmic membrane
  
  • Remember: ester linkages in bacteria
    
    • Major parts: hydrophilic head, hydrophobic tails (unbranched fatty acids)
      
  • Archaeal membrane – lipid bilayer
    
    • Ether linkages
      
    • Different fatty acid (branched)
      
      • Purpose: stronger in extreme environments (where Archaea thrive)
        
  • Archaeal membrane – lipid monolayer
    
    • Still ether linkages and branched fatty acid
      
    • However, fatty acids are directly connected with each other (less sliding)
      
      • WHY? Better stability in extreme conditions and higher bond strength
        
      • Archaea live in high stress (high temp and high pressure) environments so they need stability
        
  • Ether bond is more energetically stable than the ester bond
    
• Comparison of Peptidoglycan in bacteria and archaea
  
  • Bacteria: have NAM and NAG
    
    • Gram +ve – pentaglycine crosslinks
      
    • Gram -ve – direct links
      
  • Archaea cell wall – pseudomurein
    
    • Have NAG still
      
    • Have TAL (N-acetyl-talosaminouronic acid) instead of NAM
      
    • Still the same chain, same orientation of peptidoglycan
      
    • Direct connection, almost like Gram -ve
      
• Many archaea lack a traditional cell wall
  
  • Some use other types of physical structures
    
  • Can have cell wall and/or sheath
    
  • Sheath – like capsule
    
  • S layer – like sheath
    
    • Functions like chain mail – forms a lattice
      
    • Extra reinforcement for extreme environments
      
• Archaeal flagella
  
  • Fimbra/pilus (singular) – used for gliding
    
  • Flagellum may have evolved from archaeal pilus – but it could be the opposite also
    
  • Pili grow from the base – not pushed through hollow tube
    
    • Protein is added closest to the membrane from a single point (like a plant)
      
    • Flagellum of archaea grow in the same way – by adding subunits to base
      
  • Hence, bacterial flagella/pilus are very different from archaeal ones
    
• Comparison: bacterial flagella
  
  • Bacteria have hollow flagella
    
  • Subunits go through hollow tube, added to top (grow at the tip, not the base)
    
  • Type III secretion system – inject virulent proteins
    
  • May have evolved from a protein exporter since bacteria already had a structure to export protein – common ancestor?
    
• Flagella comparisons
  
  • Archaea: assemble from base, solid
    
  • Bacteria: assemble from tip, hollow
    

Eukarya

• Large diverse group (plants/animals)
  

• DNA
  
  • Bacterial DNA: supercoiled, circular
    
    • Most have one copy, some have multiple
      
  • Eukaryotic DNA: chromosomes
    
    • Different packing – wrapped around histones instead of supercoiled
      
    • Not circular
      
    • 2 copies of DNA at least
      
      • Diploid (animals), Polyploid (tetra, hexa, etc. in plants)
        

• Eukaryotes have specialized organelles
  
• Eukaryotes have 80S ribosomes (bacteria/archaea have 70S)
  
  • Archaeal ribosomes work in eukarya, not bacterial ribosomes
    
• Mitochondria
  
  • Involved in cellular respiration -> create energy in the form of ATP (“power plants”)
    
  • Have circular DNA, ribosomes, membranes
    
• Chloroplasts – plants
  
  • Make food for plants
    
  • Harvest energy from light, use CO2 to make sugars
    
  • Have membranes, DNA, ribosomes
    
    • Suggests that mitochondria and chloroplasts are of bacterial origin
      
  • Have very specialized compartments
    
• Photosynthetic bacteria
  
  • Chloroplasts/plant cells resemble cyanobacteria
    
    • However, cyanobacteria have no special compartment, they are the special compartment!
      
  • DO NOT CONFUSE WITH ALGAE
    
    • Some algae are eukarya, some are cyanobacteria
      
• Endosymbiotic theory
  
  • Start off with ancestral prokaryote
    
  • Nuclear area formed in it and it ingested other organisms to survive
    
  • One day, it ingested an ancestral mitochondrion
    
    • It somehow found a way to survive in the cell, as it was beneficial to both organisms
      
    • Efficient energy exchange
      
  • Plants had a second event where chloroplasts were engulfed
    
• Chloroplast ancestor related to the 2 cocci based on DNA (Synechococcus and Prochlorococcus)
  
• Mitochondria ancestor is related to rickettsia
  
  • Pathogen that remains as an intracellular pathogen
    
    • Has pathogen to enter and persist in cells
      
• Eukaryotes – ester linkages (resembles bacteria more than archaea)
  
• Flagella
  
  • Flagella structured very differently in eukarya than bacteria/archaea
    
  • Have microtubules that run the whole way through
    
    • Microtubules can slide within the flagellum for whip-like motion
      
  • Characteristic 9+2 structure for eukarya
    
    • 9 around, 2 in middle
      
  • Flagellum are very long, cilia are shorter and more numerous, like hair
    
• Quick review
  
  • Ester linkage – bacteria, eukarya
    
  • Mitochondria – eukarya only, endosymbiotic theory
    
  • DNA – supercoiled in bacteria/archaea, chromosomes in nuclear region in eukarya
    
  • Ribosomes – 70S in bacteria/archaea, 80S in eukarya
    
  • Flagella
    
    • Bacteria: hollow, built from top
      
    • Archaea: solid, built from base
      
    • Eukarya: (?), 9+2 structure with microtubules through whole length
      

Tree of life

• Three-domain tree – one ancestor into 3 distinct groups
  
• Eocyte tree – eukaryotes evolved from archaea (e. offshot of archaea)
  
  • Eocyte is group within archaea
    
• Web of life – no real ancestor
  
• Ring of life – fusions and mixtures (can’t really trace common ancestor)
  

The Fungi

• Belong in Eukarya
  
• Found virtually everywhere; very diverse
  
• One of the most abundant organisms on the planet
  
• Have medical, agricultural, ecological (nutrient recycling) relevance
  
  • Eg) decimated plant, breaking down wood, ceiling tiles, lichens, yeast infection
    
  • Can form very specific associations with plants (mutualism) – eg. Fungus extending root system
    
• Fungal body
  
  • Mycelium – entire fungal body (singular)
    
  • Mycelia – multiple fungal bodies (plural)
    
• General biology
  
  • Hypha – individual strand in fungal body
    
  • Hyphae – multiple strands
    
  • Mycelium – many hypha
    
  • A fungus has only one type of hyphae, not both (either coenocytic or septate)
    
  • Septum - single wall
    
  • Septa – many walls
    
  • Septate hypha – walls between the cells create individual compartments; seem like individual “cells” with nucleus inside
    
  • Coenocytic hypha – no septa; continuous – nuclei are freely distributed – no physical separation
    
• Fungal growth and reproduction
  
  • Side note: bread mold = usually penicillin
    
  • Fungi spread very quickly from a single point of infection – usually a single spore
    
  • From one spore, they get a single hypha that branches
    
    • Additional hypha and branching from that point give you the whole fungal mycelium
      
  • Hyphae are very good at pushing through a substrate – very strong
    
  • When the mycelium is growing it can produce billions and billions of spores
    
  • Conidia (plural) – Conidium (singular) – asexually produced spores
    

  • A fungal mycelium can take over an entire substrate very quickly (eg. Orange); white parts = growing edge of mycelium, whereas the green = spores
    
• Fungal nutrition
  
  • The fungi spreads throughout the food source
  • Secretes enzymes to break substrate down
  • Enzymes break down specific products
  • Broken down products are absorbed by fungus
  • Enzymes are targeted for specific substrates that they can digest
    

• Fungal identification
  
  • Before DNA… reproductive structure and spore morphology
    
    • Penicillin has “hands” for the reproductive structure
      
• Major fungal groups
  
  • Zygote = resting spore
    
    • Can survive for a long time
      
    • Once conditions are right, they undergo asexual reproduction
      
  • Chytridiomycota (chytridiomycetes)
    
    • Known largely for being parasites and feeding off other organisms
    • Generally aquatic
    • Produce motile spores
    • Responsible for massive die off of frogs
    • Lifecycle:
      
      • Once conditions are right, zygote undergoes asexual reproduction
        
      • Produces structures that look like mycelium (sporangium?) that produce motile zoospores (these infect hosts, like frogs)
        
        • Zoospores move to a source through chemotaxis
          
      • In the host, spores attach and lose their flagellum
        
        • Begin to extend into the host and derive nutrition
          
      • Once somewhat mature, they produce spoers in host
        
      • These spores are gametes (male and female)
        
      • When gametes fuse via conjugation zygote is formed
        
  • Zygomycota – common soil fungi
    
    • Fairly common on fruits, vegetable
    • Do not produce a lot of complex enzymes – can only breakdown simple substrates (simple sugars)
    • Grow very fast and absorb very quickly
    • Coenocytic – no septa in hyphae
    • Worst competitive fungus – colonize only simple sugar substrate, but do not compete well
    • Very thin spore structures
      
    • Common species: Rhizopus, Mucor
      
    • Lifecycle
      
      • Have sexual/asexual cycles
        
      • Sexual cycle involves 2 types that form sexual spores (+ and -)
        
      • Asexual cycle forms more asexual spores that germinate to create a mycelium to repeat the cycle
        
  • Glomeromycota – arbuscular mycorrhizae
    
    • Forms mutualisms – Both partners benefit
    • Endomycorrhizae enter the actual cells
      • Arbuscular mycorrhizae because they send tentacle like structures into cells – that’s where the nutrient exchange happens
      • Forms arbuscules – nodes?
    • Mycorrhizae extends the root system
      • Fungus grows a lot faster than the plant, so it can absorb more nutrients for the plant
      • Under nutrient-limiting conditions, it can make a huge difference (small plant vs large plant grown)
  • Ascomycota – common soil fungi
    
    • Common soil fungus – everywhere
    • Aspergillus – puffy black spores
      • Aspergillus flavus produces aflatoxin
        • Present in canned corn, fresh corn, peanut butter
        • Processed by liver to produce carcinogenic compounds (before processing: not carcinogenic, after processing: carcinogenic)
        • Carcinogenic because it binds to DNA
        • However, it takes a lot to succumb to aflatoxin
    • Alternaria – teardrop with septa spores
    • Penicillium – skeleton hands spores
    • Fusarium – crescent moon shaped spores
    • Trichoderma – overtakes lab plate in a day; runs everything over
      
    • Asexual and sexual reproduction
      
      • One spore forms mycelium which forms even more spores
        
      • 2 types of sexual spores
        
      • Sexual structure is apothecium (cup-like) which produces sexual spores
        
      • Can produce many different structures
        
    • 8 spores (sexual) in ascus
      
    • Nematode-trapping fungi
      
      • Soil fungi that can capture nematodes for extra nutrients
        
      • Nematode comes along, hyphae senses it and rings clasp around nematode
        
      • Hypha tightens, and begins to grow into nematode
        
      • Digests it from the inside out
        
    • Human disease
      
      • Stachybotrys – causes black mould in building
        
        • Loves paper
          
        • Usually growing on paper in drywall – produces cellulase to digest it
          
        • Spores can grow in lungs and spread
          
      • Trichophyton – Athlete’s foot / jock itch
        
        • Loves humans, adapted to skin / nails / hair
          
        • Have keratinase to digest it
          
    • Yeast
      
      • Can produce asca and sexual structures
        
      • Saccharomyces – budding yeast
        
        • Bud off from parent, becomes separate cell
          
      • Schizosaccharomyces – splits into 2 evenly down the middle (binary fission)
        
  • Basidiomycota
    
    • Have asexual and sexual reproduction
    • 2 types that give rise to sexual spores
      • Sexual spores come in form of mushroom
      • Mushroom = sexual structure
      • Underneath the mushroom cap are gills – have millions of spores within
      • Mushrooms can produce hallucinogenic compounds or produce toxins (easily confused)
    • Fairy rings – ring of mushrooms around plant
      
      • Usually a single inoculation point in middle
        
      • Reproduction happens at edge of mycelium -> mushrooms
        
      • Usually around plants, form ectomycorrhizae
        
    • Plant pathogenic fungi
      
      • Rusts
        
        • Often have 2 hosts
          
        • Can produce up to 5 different types of spores
          
        • When plant is infected, infection stays localized to one location
          
      • Smuts
        
        • One host
          
        • Usually 2 different types of spores
          
        • Overtakes entire plant
          
    • Human disease
      
      • Fungi that are found in birds nests are hotspots for 2 pathogens
        
        • Cryptococcus and histoplasma (through inhalation)
          
        • Cryptococcus have outer layer that makes them sticky
          
        • Histoplasma have projections that make it sticky
          
        • Germinate in lungs
          
    • Largest organism
      
      • Armillaria root disease – largest organism on earth
        
      • Almost 10 square kilometres (6000 hockey rinks, 1600 football fields)
        
      • Discovered by finding out that different samples in the area had same DNA
        
• Ectomycorrhizae
  
  • Present in ascomycota, basidiomycota, zygomycota
    
    • Not glomeromycota
      
    • Form on outside of the actual cells to exchange nutrients
      
    • Can also stay in between cells; never enter the actual cell
      
• Batrachochytrium (a type of chytridiomycete)
  
  • The main agent that is killing frogs
    
    • Zoospores swim and penetrate frogs
      
    • Start growing inside frog
      
    • Produce spores in specialized structures
      
    • Motile zoospores are produced again
      
    • Frog eventually dies
      
  • Frogs have a protective slime coating that protects their skin from elements and pathogens
    
    • The chytrid causes the coating to disintegrate, weakening them
      
  • When frog is infected, odd behaviour
    
    • Can’t eat well
      
    • Legs are in odd position -> unable to sit properly
      
    • Lose ability to right themselves (can’t put themselves back up) – succumb to heat, UV
      

Genetics Fundamentals

• Review: basic structure of bacteria/archaea
  
  • Pili, DNA, Ribosomes, Cell Wall, Plasma Membrane, Flagellum
    
• Overview:
  
  • DNA replicates (loop) – 2 copies of DNA, one for each daughter cell
    
  • Transcription to RNA (DNA to RNA)
    
  • Translation to Protein (RNA to protein)
    
• Structure of DNA
  
  • 4 bases: A, T, C, G
    
    • A = T (double hydrogen bond)
      
    • C G (triple hydrogen bond) = stronger bond
      
  • Has major grooves and minor grooves
    
  • Adenine and Guanine are purines (two rings)
    
  • Cytosine and Thymine are pyrimidines (one ring) (both have y in name)
    
• DNA binds in a specific way to form the double helix
  
  • Each sugar bonds to a phosphate on each base
    
    • Direction is determined by which carbon the phosphate binds to
      
    • The phosphate will bind to either Carbon 3 or Carbon 5 on the sugar group
      
    • Start numbering on sugar from where it connects with the nucleotide group
      
  • One strand goes 5′ to 3′, the other goes 3′ to 5′
    
  • Order is always Base -> Sugar -> Phosphate -> Base -> Sugar -> Phosphate
    
• Genetics – Informational Molecules
  

Replication

• Replicate DNA strand to begin transcription and translation
  

• Binary Fission
  
  • As bacteria are dividing, they need to create a copy of DNA for daughter cell
  • Take original DNA -> Separate it into two strands
  • Make copy of each strand (complementary)
• Chromosome Replication
  
  • A bacterial chromosome = circle
  • There is a specific spot called the origin of replication
  • A theta structure is formed as the DNA begins to replicate
    • Bidirectional replication – proceeds in both ways
  • The replicated DNA then “peels off” the original strand = 2 identical molecules formed

1. Replisome
   

• DNA helicase – unwinds DNA at origin
  
  • This creates a lot of winding pressure since the strand is being twisted around
    
• DNA gyrase – unwinds to release winding pressure from helicase
  
• DNA primase – synthesizes RNA primer that serves as starting point of synthesis for new strand
  
• DNA polymerase III does the actual reading of every nucleotide using the dark green strand as template (complementary base)
  
  • DNA polymerase III can read 3′ to 5′ and synthesizes 5′ to 3 for leading strand – CONTINUOUS
    
• For the bottom strand (lagging strand), the template given is already 5′ to 3′ WHICH IS BAD since polymerase needs to synthesize in opposite direction
  
• DNA primase synthesizes RNA primer
  
• DNA binding proteins bind to the primer
  
• Typewriter motion happens
  
  • Ie) Okazaki fragments – piece by piece synthesis
    
  • Does a piece -> lets strand go (to go back) -> synthesizes another piece; DISCONTINOUS
    
  • Synthesizes until it reaches previous RNA primer -> unlatches -> strand scooches in and process repeats
    

• Bidirectional replication – two complexes going in different directions
  
• ALWAYS RESULT IS 5′ TO 3′
  

The Gene

• Gene – many regulation signals that trigger functions
  
• Codon - group of 3 nucleotides, each codes for a single amino acid
  
• Start codon / stop codon – tells translation where to begin and start
  
• Open reading frame – between stop/start codon; includes start/stop codon
  
  • Everything in codons
    
• Promoter region – upstream of start codon
  
  • Activates gene expression
    
  • Turns on during transcription to tell transcription where to begin
    
• Terminator – terminates transcription (turns off gene)
  
• Ribosome binding site – binds the ribosome and interacts with ribosome
  

Open Reading Frame (ORF)

• Start/Stop codon are part of open reading frame
  
• NEEDS TO HAVE START AND STOP CODON
  
• EVERYTHING NEEDS TO BE IN CODONS
  

Transcription

• Promoter
  
  • Upstream of start codon
    
  • A specific DNA strand that activates gene
    
  • Proteins bind to promoter to activate gene
    
  • Sigma factors activate genes – turns them on
    

• How transcription starts
  
  • RNA polymerase (core enzyme) binds to promoter region and gets ready for transcription
    
  • Sigma factor recognizes the DNA strand and binds with RNA polymerase at promoter region
    
  • Sigma factor opens up strands so RNA polymerase can begin its work
    
  • Sigma factor is released (not needed anymore)
    
  • RNA polymerase synthesizes mRNA (from promoter to terminator)
    
    • Final mRNA strand is 5′ to 3′ (like DNA)
      
    • Bottom strand of NDA is used as template
      
    • Therefore mRNA = same as top strand of DNA since bottom strand is the template
      
  • mRNA generated has everything between promoter and terminator, including ribosome binding site
    
• RNA
  
  • Virtually same as DNA, except thymine is replaced by uracil (a pyrimidine)
    
• Quick check – transcription
  
  • Completely ignores start/stop codon and does not check for mutations
    
  • Does not require anything other than promoter or terminator
    

Translation

• Now that we have mRNA, we can translate it to a protein
  
• mRNA to protein
  
  • Ribosome reads mRNA and translate it to a protein
    
  • Also involves rRNA and tRNA
    
  • Ribosome associates with mRNA and reads it codon by codon to make the protein
    
  • Protein detaches and ribosome detaches into its subunits
    
• mRNA = messenger RNA
  
• rRNA = ribosomal RNA
  
• tRNA = transfer RNA
  
• rRNA – functions to help associate ribosome with mRNA
  
  • Ribosome binding site is a specific sequence that helps ribosome bind to a strand
    
  • A sequence on the rRNA will bind to the mRNA
    
• tRNA – transfer RNA
  
  • Helps bring in a specific amino acid for protein synthesis to ribosome
    
  • The amino acid is kept on top
    
  • Anticodon loop on the bottom of the tRNA finds the complementary codon on the ribosome, and then adds the amino acid to the growing polypeptide chain
    
  • tRNA is not as specific as we think – sometimes it might bond with multiple codons, even though they’re not exactly the complementary of its anticodon
    
    • Last position = wobble position = some variance
      
• Wobble position on tRNA
  
  • tRNAs don’t discriminate as much
    
  • For instance, you can get 6 different variations that code for the same amino acid
    
  • Genetic redundancy – 64 codings for 20 amino acids
    

Translation – protein synthesis steps

• Ribosome has 3 sites
  
  • E-site, P-site, A-site
    
  • Exit site, Peptide site, Acceptor site
    

1. Codon is recognized by tRNA on P-site of ribosome
   
2. Second tRNA comes in on A-site
   

• Peptide bond forms between 2 amino acids so far = protein growing
  
  • Protein growing on p-site
    

1. Next amino acid comes in when there is a shift (ie. P-site tRNA moves to E-site, A-site tRNA to P-site) and lands on A-site
   
2. 1st tRNA gets bumped into exit site and exits
   

Protein

• Protein gets released from translation
  
• Stop codon is recognized by termination factor and translation stops
  
• Protein forms 3D structure
  
• In bacteria, transcription and translation is simultaneous
  
  • As the DNA is transcribed into mRNA, polyribosomes read it directly
    

Genetic Exchange

• Gene structure: Promoter -> Ribosome binding site -> Start codon, Open Reading Frame, Stop Codon -> Terminator
  
• Genetic structure = similar in Bacteria/Archaea
  
  • Transcription
    
    • Start: Promoter
      
    • Stop: Terminator
      
    • How it works: RNA uses bottom strand as the template (the 3′ to 5′ strand) IN ORDER to make the mRNA product (5′ to 3′)
      
      • Therefore, mRNA will be identical to top strand except for T and U being interchanged
        
  • Translation
    
    • Start: Start codon / Ribosome binding site (but begins translating at start codon until it reaches stop codon)
      
    • Stop: Stop codon
      
• Eukaryotes have “junk” DNA
  
  • Exons = good (coding)
    
  • Introns = “spacer”
    

  • Still have promoter / terminator signals
    
  • Only exons are coding
    
    • Therefore not a continuous open reading frame because of the introns
      
  • The final mRNA has only exons with introns cut out
    
  • Gene A has introns / exons
    
    • Hence transcription reads the whole gene (from promoter -> terminator)
      
  • 1st mRNA has introns and exons
    
    • Protein cuts out introns and pastes exons (splicing) to create final open reading frame
      
  • Mature mRNA leaves nucleus, exported into ER
    
  • Cap and poly A tail put onto mRNA -> function as export signals
    
  • ER in cytoplasm has ribosomes, which form the mature protein from the mature mRNA
    
• Bacteria – 1 step (simultaneous transcription and translation), whereas eukaryotes have multiple steps because of organelles
  
• 3 domain comparison
  
  • More commonalities between Archaea and Eukarya even though the Archaea have similar appearance to Bacteria
    
    • Although Bacteria/Archaea have circular chromosomes and only one
      
    • Eukarya/Archaea share a lot more replication structures and techniques and share transcription factors
      
  • Eukarya and Bacteria = Ester linkages
    
  • Archaea = Ether linkages (extreme conditions)
    

Mutations

• Bacterial Replisome – Mistakes?
  
  • Mistakes are often made by DNA polymerases whilst transcribing
    
  • It replicates it almost perfectly, but small errors can accumulate
    
  • Eg) add in incorrect bases
    
  • This leads to mutations
    
• Mutations – substitution
  
  • Mistake with existing information (no insertions/deletions) – sometimes detrimental
    
  • Start codon has very little effect (if it is created by a mutation) – the actual start codon has a special addition to it
    
  • Silent mutation – does not change the amino acid, yields normal protein (because of the redundant codon code so same amino acid is produced) (eg TAC -> TAT)
    
  • Nonsense mutation – eg) stop codon in middle of gene (eg TAC -> TAG)
    
    • Transcription is not affected (since it disregards codons), but translation stops
      
    • Creates incomplete protein
      
  • Missense mutation – changes amino acid, creating faulty protein (eg TAC -> AAC)
    
    • By changing the amino acid, the protein might still have some residual activity or it might be completely non-functional
      
• Mutations – Insertions and Deletions (INDELS)
  
  • Usually more harmful because they always change the amino acids / codons
    
  • Original reading frame = 0
    
  • Insertion (+1) – transcription doesn’t care (disregards codons) but translation does
    
    • Ribosome reads codons
      
    • However, all codons move down 1 letter because of the insertion, therefore the amino acids and the resultant protein change
      
  • Deletion (-1)
    
  • Since the amino acids always change, there is a difference in the final protein
    

Operons – complex genetic structure

• Bacteria are always streamlining their genetic code
  
• Compressed such that genes with similar functions are under the control of the same regulatory elements
  
  • Saves a lot of space
    
  • For example, one promoter can serve multiple genes (since transcription starts at promoter and ends at terminator)
    
  • Multiple ribosome binding sites are kept to allow for multiple simultaneous translations which are very efficient
    
• Operons – co-regulated genes
  
• Cistron - gene
  
• Monocistronic – one gene in final mRNA
  
• Polycistronic – multiple genes on same strand of mRNA
  
• Operons and metabolism
  
  • Operons direct the breakdown of nutrients in environment (eg lactose) into simple sugars
    
• Operons – Lactose Inducer
  
  • The Lac operon has 3 genes – lacZ, lacY, lacA (lacI is the repressor gene)
    
    • lacZ produces beta-galactosidase which breaks down lactose
      
  • LacI is on all the time, repressing transcription
    
    • This is very efficient because the lactose genes are on ONLY when there is enough lactose
      
  • Normally the repressor binds to a special area near the lac Promoter to block transcription (since RNA polymerase cannot move)
    
  • Once lactose (inducer) binds to the repressor, the repressor comes off which allows the RNA polymerase to transcribe and translate the strand into proteins
    
  • This prevents the bacteria from producing unnecessary proteins
    
• Operons – Arginine Repressor
  
  • Operon directs the synthesis of arginine which is used in translation
    
  • Transcription proceeds, gene is translated into protein and arginine is made
    
  • You reach a point eventually where you have excess arginine
    
    • The XS arginine binds to repressor and causes repressor to bind to the arg Operator to block RNA polymerase
      
  • Ie) once enough, production is stopped
    
  • Once the concentration dips down again, the arginine dissociates and process resumes
    
    • Arginine constantly in flux
      

Horizontal Gene Transfer – Conjugation

• Horizontal gene transfer = lateral gene transfer
  
• Very common in Archaea/Bacteria to have horizontal gene transfer, rare in Eukarya
  

1. Transformation – DNA from environment
2. Conjugation – Bacteria to bacteria transfer
3. Transduction – transfer mediated by viruses

• Plasmids
  
  • Self-replicating circular pieces of DNA
    
    • Code for various genes
      
    • Can move between bacteria
      
    • Independent of chromosomes
      
  • Multiple copies of plasmids per cell (up to 500 copies) – can also have up to a dozen separate plasmids
    
  • Function independently – have own replication mechanism
    
    • Origin, replication proteins
      
  • Big chunk of genetic info that can be infused into an organism
    
• Plasmid purpose: Symbiosis, Metabolism, Resistance
  
  • Pseudomonas putida – plasmid directs breakdown of benzenes and toluenes
    
  • Yersinia pestis (black plague) – plasmid caused infection (a lot of the Black Plague genes were plasmid-encoded; remove plasmid, remove disease)
    
  • Plasmids carry genes in symbiosis
    
    • To facilitate association with host (+/- relationship)
      
  • Metabolic genes
    
    • Break down compounds, acquire energy
      
  • Resistance genes
    
    • Antibiotic resistant genes can move between bacteria
      
• Conjugation Mechanism
  
  • Direct exchange between 2 cells via physical conduit
    
  • Donor (has plasmid) encounters cell without plasmid
    
  • Pilus connects donor and recipient
    
    • Conduit = pilus (conjugated pilus, not pili for gliding)
      
    • Genes needed to synthesize pilus and the conduit are all coded by the plasmid
      
  • Pilus reels in recipient, retracts
    
  • Pore develops between the two cells
    
  • Plasmid in donor is replicated and one of the strands moves through the pore into the recipient
    
  • Both cells (or just recipient) make the plasmid double stranded again
    
• Plasmids encode surface exclusion proteins and display them on surface (if both have them, the exclusion proteins prevent the pili from forming)
  

Viruses and Prions

• Explain why the answer is not A, B, C, etc.
  
• 70 minutes for exam
  
• Horizontal gene transfer – bacteria picking up DNA from other organisms
  

Transformation

• Homologous (similar) recombination
  
  • Bacteria in environment can pick up pieces of DNA in their immediate vicinity
    
  • DNA is often degraded (nutrition for bacteria), so it doesn’t necessarily remain intact
    
  • However, it is possible that it is not degraded and is incorporated into the DNA of bacteria
    
  • If the DNA is kept (donor DNA), endonuclease (protein) nicks/cuts one strand in the middle
    
  • A single stranded binding (SSB) protein (in replication / DNA synthesis – lagging strand) binds to the single cut strand
    
  • Organism produces RecA protein that helps incorporate unwound DNA donor strand into a host
    
  • RecA helps create a cross-strand junction
    
  • The junction can be cut horizontally or vertically to get 2 double strands
    
• RecA helps incorporation of strand, but it requires the incoming strand to have some similar DNA identity to the recipient
  
• Transformation – Transposons
  
  • Transposons are jumping genes that can cut themselves out of DNA and move to another location (selfish genes)
    
    • Selfish genes because they only reproduce; no obvious advantages
      
    • Too much transposition could be a problem by killing the cell
      
  • 2 types of transposons?
    
    • IS2 (Insertion Sequences / IS Elements)
      
      • Simplest – they have one gene in centre that codes for a transposase enzyme
        
      • Transposase enzyme that is produced can recognize the special borders of the IS elements and cuts at the borders
        
      • The piece is picked up, moved and then reinserted somewhere else
        
    • Multiple IS elements could surround gene
      
      • Transponsase can cleave many different ways (not specific – just cuts as a border)
        
      • The transposon could transpose again only if they still have the functional transposase gene
        
      • Different from IS elements since they carry other genes in addition to transposons (like antibiotic resistance genes)
        
• Transformation – Mechanisms of Transposition
  
  • Conservative transposition - only one copy – cut from original, paste into target (original doesn’t have it anymore, starts to degrade or re-ligased)
    
  • Replicate transposition – copy of original transposon or IS is pasted (both still have the sequence)
    

Transduction

• Involves viruses, especially bacteriophages
  
  • Phage attaches to bacterial host, injects DNA into host
    
  • DNA is then used for:
    
    • Replication (for progeny)
      
    • Transcription and translation (to produce needed proteins)
      
      • All proteins necessary for reproduction are produced by the cell’s machinery using bacteriophage DNA
        

1. Bacterial DNA is chopped up in the process -> pieces of bacterial DNA may be accidentally packaged with phage DNA
   
2. Many bacteriophages are assembled
   
3. Host lyses (bursts) via viral enzymes
   
4. Progeny infects another host
   

• Follows same process, but those progeny inject phage + original host DNA into the new host
  
  • Has introduced new strand of DNA tht may go into homologous recombination if it is similar enough and the new host survives
    

Inheritance

• Horizontal gene transfer - between cells (ie. Incoming DNA)
  
• Vertical gene transfer – happens over course of bacterial reproduction (evolution)
  
  • As species diversify, similar genes are found to be present that are not from horizontal gene transfer in that generation
    
  • Hence, it was acquired through inheritance (ancestors); stays within lineage
    

Viruses

• Have medical relevance
  
• Virus – element that requires a host – similar to IS elements in the sense that they are not really alive
  
• Come in a variety of different flavours
  
  • Naked virus vs enveloped virus
    
• Basic structure: nucleic acid surrounded by protein shell
  
  • Protein shell = nucleocapsid / capsid
    
  • Capsomers – subunits of the protein shell
    
• Enveloped viruses are a nucleocapsid surrounded by a membrane envelope (usually membrane of host)
  

Viral structure

• 2 major viral structures
  
  • Helical – capsomers have specific region where nucleic acid is held inside
    
    • CAPSOMER HOLDS DNA
      
  • Icosahedral - 20 sides
    
    • At each node there are 5 capsomers, everywhere else there is 6
      
    • DNA is inside the protein shell
      

• Viruses are very diverse
  
  • Can have enveloped / naked viruses
    
  • Can have DNA and RNA viruses
    
  • Many combinations
    
• Viral types
  
  • + strand = 5′ to 3′ (top)
    
  • - strand = 3′ to 5′ (bottom)
    
  • Bacteriophage have dsDNA
    
    • Transcription of bottom strand to get mRNA+ -> translation -> protein
      
  • Goal is always mRNA+ from whatever the virus has originally
    
    • Need -ve strand as template
      
  • Eg) ssDNA(+) – cannot use + strand as a template, need bottom strand
    
    • Make other strand, then get dsDNA intermediate and then transcribe bottom strand to get mRNA+
      
  • Eg) dsRNA(+) – directly transcribe bottom strand to mRNA+
    
  • Eg) ssRNA(+) – already mRNA+, no transcription needed
    
  • Eg) ssRNA(-) – transcribe minus strand to get mRNA+
    
  • Eg) ssRNA(+) retrovirus – use own reverse transcriptase enzyme (often very sloppy which generates more beneficial mutations) that takes RNA and converts it into a DNA intermediate. Bottom strand used as template to get mRNA+
    

Bacteriophage (dsDNA)

• Some have just head, some have just head and tail
  
  • Capsid contains DNA
    
  • Tail fibres attach to host membrane
    
  • Tail pins help anchor virus as it infects
    
• Infection mechanism
  

1. Phage attaches to membrane with tail fibres
   
2. Tail pins are used to anchor bacteriophage
   
3. Bacteriophage injects DNA (DOES NOT ENTER CELL)
   
4. Tail lysozyme dissolves through membrane and peptidoglycan
   

• Diagram is a gram negative cell
  
• Once DNA is in, there are 2 routes
  
  • DNA is replicated for progeny
    
  • DNA is transcribed and translated (reproduction / assembly / gene expression)
    
  • Many phage code their own proteins, like transcription enzymes, etc.
    
  • These proteins are used to make more phage DNA – most of it is kept for progeny, some reused for more translation
    

1. Virus assembles spontaneously and becomes mature phage particle
   

• It is a very well timed process – each triggers the next set of events
  
• Three major stages
  
  • Early – start things off
    
  • Middle – replication, sigma factors, translation
    
  • Late – final assembly
    

• Lytic vs lysogenic cycles
  
  • Lytic (most cells DO NOT enter lytic pathway)
    
    • Infection (DNA replication, etc)
      
    • Assembly
      
    • Phage particles lyse cell to get released
      
  • Lysogenic
    
    
    • DNA comes in and integrates into host DNA
      
    • Remains dormant as piece of DNA – prophage
      
    • When cell divides, the prophage is treated as part of the bacterial chromosome
      
  • Eg) cholera toxin encoded by prophage – eliminate phage, no more cholera
    
    • Originally there was no toxin in that bacterium – phage introduced it
      
    • Hence phage are very influential
      
• Plaques – lytic
  
  • Lytic cycle causes lysing of bacterial cells
    
  • Plaques form on lawn of bacteria when they are lysed by the phages
    
    • Ie) holes develop on the plate where bacteria have died because of phage
      

Influenza

• Three types
  
  • A – many animals (seasonal flu)
    
  • B – humans, seals
    
  • C – humans, pigs
    
• Influenza A is very well represented by aquatic birds (eg. Duck, geese) – very prevalent
  
• Influenza A has not jumped very well to humans directly from wild birds because of special unique receptors on human cells
  
  • However, pigs can be infected by wild strains
    
  • Can jump to humans via pigs
    
  • Therefore pigs are reservoirs
    
  • Route from pig to humans is unknown
    
• Evidence that it came from domesticated chickens to humans, not yet from wild birds
  
  • Agriculturally related?
    
• Influenza A virus structure
  
  • Has a nucleocapsid which surrounds the nucleic acids in the middle
    
  • Has envelope (to aid in infection)
    
  • Has 8 different RNAs
    
    • 11 genes scattered on 8 RNAs all over the place
      
  • Outer membrane has H and N proteins
    
• Infection
  
  • H and N are critical for attaching to host and escaping from host
    
  • H bonds to sialic acid sugars on cell surfaces
    
  • Virus enters cell, not injected
    
  • RNA is injected into the cell – 2 routes
    
    • Replicate RNA
      
    • Transcribe and translate genes to get functional proteins
      
  • H and N proteins migrate to cell membrane and embed themselves in it
    
  • Virus buds off cell, taking the H and N proteins as part of its own envelope
    
• Antigenic Drift
  
  • Viruses are prone to mistakes
    
  • Antigenic drift describes mutations (small changes in the nature of the H and N)
    
  • Normally there are 3 H types and 2 N types in humans
    
    • In wild, many different variants between H and N proteins (very different)
      
    • Variants can be combined in any combination
      
    • These variants are known to infect humans
      
    • Eg) H1N1 / H5N1 etc
      
  • In the wild – 16 H variants, 9 N variants
    
    • Antigenic shift – different mixture of H and N
      
    • H1N1 vaccine – immune to H1N1 in that year
      
      • Antigenic drift causes it to change year to year
        
• Influenza Review
  
  • Hemagglutinin (H) binds to sialic acid sugars (receptors) on cell surfaces
  • Virus enters cell and releases RNA into cell
  • RNA takes two paths
    • Replication (progeny need RNA for their structure)
    • Transcription and translation (to make required proteins)
  • Some of the replicated RNA migrate to the cell membrane bud off

  • H and N are transcribed proteins
    
  • They embed in the membrane
    
  • Neuraminidase (N) helps in exit
    
• Antigenic Drift (sloppy replication) – subtle
  
  • Changes in the virus due to mutations
    
  • Mistakes can be made in replication and protein production
    
  • Can get different mutations in different parts of RNA genome
    
  • Leads to antigenic drift -> mutations in RNA
    
  • Mutation helps virus escape the immune system
    
• Antigenic shift – more dramatic
  
  • Switching of the H (16 types) and N (9 types) markers
    
  • Shift describes how viruses mix and match those
    
  • Eg) pigs can be infected by both avian and mammalian flu, therefore pig = reservoir
    
    • Pig might get H5N2 and produce H1N2 and H5N1
      
      • If 2 viruses infect the same cell, mixing and matching happen
        
  • Apparently there is a mechanism that prevents H1H1 or other crazy variants from forming
    
• The next pandemic?
  
  • H1N1 – easily spread, rarely fatal (common)
    
    • H1-H3 bond to sialic acid sugars in nose/mouth since they have specific receptors
      
    • H1 to H3 is usually in humans, not the other ones
      
      • However, there are always mutations and antigenic shift
        
  • H5N1 – spreads slowly, often fatal
    
    • Shouldn’t be in humans, but gets in somehow
      
    • H5N1 is a problem because it is not cell-specific – infects a lot of different tissues
      
    • Spreads very slowly and does not discriminate
      
    • Right now it doesn’t move easily between humans, for now
      

Genomics

• Genomics – study of entire genetic complement of organism (focus on many/all genes)
  
  • Very powerful because you can determine biology, physiology, ecology and evolution from its genomic sequence
    
  • Useful when organism is hard to study directly
    
• Can reveal basic physiology
  
  • Can see entire metabolic sequence based on genome by identifying what proteins are produced and then placing them in the grand scheme of things
    
• Bacterial genome
  
  • Major chromosome = circular
    
  • Plasmids
    
  • Need to take both into account when sequencing
    
• Genome sequencing and assembly
  
  • Construction of DNA library by obtaining bacteria, culturing bacteria and extracting all DNA from bacteria
    • Chromosome is very big, so we cannot sequence it continuously; there is a limit
  • Therefore, DNA is chopped up into smaller sequences so it is easier to process
  • Chopped up sequences are cloned by putting them into cloning vectors (special plasmids)
    • Each vector has a small piece of the original DNA
  • The little pieces are later extracted and then sequenced
• Sequencing
  
  • Each piece sequenced is a fragment of the original, forming a genomic library
    
  • Sequence random pieces and assemble them by looking for an overlap
    • Nowadays, usually done with a software program that will look for overlaps and reconstruct original molecule piece by piece
  • Original strand is obtained (ideally)
  • However, you often just get contigs – a bunch of overlapping sequences
    • Don’t get the whole genome assembling perfectly
    • Need to order the contigs
  • Once you order the contigs, you can put them together to get the original sequence to reconstruct the original circular molecule
• Polymerase Chain Reaction (PCR)
  
  • A method to connect contigs
    
  • Amplifies a specific region of DNA (must have / know part of the sequence already)
    
    • Need to start off with original template
      

1. Heat up DNA to denature it at 94 degrees — the two strands separate
2. Add single stranded pieces of synthesized DNA (primer) –> anneal to corresponding sequence at 50-70 degrees depending on primer
3. Polymerization - (72 degrees) Add in bases (dNTP) and polymerase; the polymerase will add the bases in region between primers until it completes the two strands
4. Strands are constructed, and then used to repeat the cycle again too get many more copies; ie) each new strand becomes a template strand

• Need to do it 30-35x to get lots of sample
  
• Polymerase does 5′ to 3′ synthesis in both cases always
  
• PCR uses dNTP bases
  

• Gel electrophoresis
  
  • Detection limits for DNA are very low, so we need a lot of sample
    
  • Gel is how we visualize DNA
    
  • Left hand side – ladder to measure size of DNA fragmenet
    
  • How this works:
    
    • Gel separates DNA via electricity that causes the DNA to migrate through the gel
      
    • The smaller the fragment, the faster it migrates
      
• ddNTPs vs dNTPs
  
  • Each individual base is connected to the next group with OH in dNTP
    
  • In ddNTP, it’s just H (not OH)
    
• Normally if you have OH it serves as the connection for the next phosphate group to bind to
  
  • The elimination of that O prevents the addition of the next base, terminating the chain
    
  • Useful in sequencing
    

Sequencing – Traditional Sanger Sequencing (max 1000 bases, usually 700-800 is common)

• ddNTP terminates chain
  
• Get 4 tubes of ddNTP for each base (eg. ddGTP, etc)
  • Each tube has all the dNTPs, but they have ONE of each ddNTP

1. In PCR, bases are added
2. Sometimes some of the ddNTPs will be incorporated instead of a dNTP, causing the chain to terminate

• You still get one fragment, but you get distinct bands (completely random) in gel electrophoresis
  
• Band length corresponds to where that particular base is
  
• You can identify the shortest band in gel electrophoresis and conclude that it is one of the first bases (eg if it is T, then one of the first bases should be T) – this corresponds to the DNA
  
• Very slow way of sequencing – one by one almost
  

Modern Sanger Sequencing

• Slight modification
  
• Fluorescent dyes to label bases
  
• Laser reads the fluorescent ddNTPs
  
• Sequencing output
  
  • New output – software does all the work
    
  • Each peak = particular base
    

Annotations

• Once you have the complete DNA sequence, need to annotate it
  
• Annotation – define features in genome and tell where the genes are
  
  • Find open reading frames (start codon to stop codon) in general
    
  • However, not all ORFS are necessarily genes….
    
  • Therefore, the program will find every single start/stop, but there are a bunch of potential starts
    
  • Algorithms will determine which genes are most likely
    
• BLAST – comparison tool that uses central database to determine if your particular sequence has been identified as a gene by someone else
  • Basic Local Alignment Search Tool
  • Paste in DNA, select algorithm, search
  • Typical output: input vs match in gene
    
  • Pretty output: shows bands that represent shared genes between organisms
    
  • Many DNA sequences for microbes added and to be added
    
• Once you have the final annotation, create map of the genes
  
  • Can have genes going forwards and backwards
    
  • Sometimes top strand is coding region, sometimes bottom strand
    

Comparative and Evolutionary Genomics

• Once you have the entire genome, you can do comparisons
  
• Comparative and evolutionary genomics
  
  • Look at different strands and see how they’re evolving through full genome comparisons
    
  • For instance, blocks of same colour indicate that region is the same
    
    • Can detect insertions / deletions / substitutions / inversions
      
    • Can tell if whole regions / genes are acquired or lost – eg) polymerase in all strains, disease or virulence gene in some strains only
      
• Inversions – pieces of DNA may flip between top and bottom strand
  
  • Ie) top strand might become coding region or vice versa
    
• Core region = found in all strains
  
• Flexible region = found in some strains
  
• Genomic islands – came in through horizontal gene transfer because of flexible genome
  
  • Often encode for disease/resistance/biosynthetic/catabolic genes
    
  • Considered to be foreign, and usually can be identified
    
  • Often have IS elements or transposons associated with them
  • GC content (% of G or C) is different in genomic island than in surrounding sequence
  • Inserted near tRNA and scattered throughout genome
    • Addvantage: core gene -> since trNAs are more conserved and are core, this guarantees the success of genomic islands

Functional genomics – DNA microarrays

• Looking at what is happening in the whole organism and all the processes
  
• Microarrays – what’s happening in cell at DNA/RNA levels
  
  • A slide that has tiny spots
    
  • Each spot corresponds to a single gene – can have hundreds or thousands of spots
    
  • Genes are arrayed in single stranded form
    
• Microarrays are used to find out how closely related unknown genome is to known genome by finding genes they have in common
  
  • Extract DNA from organism
  • Make DNA single stranded and wash it over slide – genes will fall into tiny spots
  • Wash over slide of known with unknown
    • If they are similar / complementary, they will bind to each other (hybridization)
  • Use solvent to wash away excess that do not bind
  • Remaining binding spots are shared genes
• If you make a couple of microarrays from a known strain, and wash it over with multiple unknowns, you can easily compare multiple organisms
  

RNA microarrays

• Same approach with RNA
  
• However, point of this is to identify which genes are produced in response to an event or turned in
  
• For instance, bacterial RNA in salt vs no salt environments – which genes are turned on?
  
  • Hybridize both on same microarray
  • If they overlap, they have a certain colour
    • Easily see which genes are turned on under certain circumstances

With the holidays approaching, many IBers and university students are approaching the end of their fall semester. What classes have you picked out for next semester?

Personally, I have:

• Genetics (+ lab)
• Biomedical Ethics
• Introductory Computer Science for the Natural Sciences (+ lab)
• Biochemistry – Metabolism (+ lab)
• Introductory Macroeconomics

Here’s a quick guide for scheduling classes.

As many students in both the IB and university have discovered (or will soon discover), the textbook market is one where your savings can be quickly depleted if you aren’t too careful. There are many overpriced textbooks out there that could cause you to pay a lot more for a textbook than you should have. In my short post-secondary education thus far, I have discovered a couple of tips in finding more affordable textbooks so that I still have some extra money to, you know, eat.

1) Ask your professor if the older version is OK.

In many cases, such as in the liberal arts subjects, the previous version only has minor revisions compared to the old one, and still has most of the many concepts and ideas that will be covered in class. Thus, I would advise emailing your professor before the semester begins to see if the previous version is still acceptable — if it is, ask an upper year student if they want to sell their old copy, or check online for that specific version.

2) Buy used books, rentals or ebooks.

If you really want the current version, you can usually find used ones from a previous semester in your local university bookstore or online that are a bit cheaper than what you would find brand new. Usually I would advise going into your bookstore for a used book — it is always good to check if there is an excessive amount of pink highlighting in the textbook.

If there aren’t any suitable used alternatives, another option would be rental textbooks. Some bookstores and websites (eg. Chegg?) offer textbooks that you can rent for the semester for a significantly reduced price. Once the semester is over, you can just send the textbook back to the supplier. The only drawback is that you won’t be able to keep the textbook around if you need to refer to it in a couple of years.

If there aren’t any used books or rentals available, you could always check to see if an electronic version is available. Not all textbooks have a ebook format, so this is something that you will have to do some Googling for. Some bookstores will sell the codes for the ebooks, so check with them. The advantage is that they are very cheap and can be loaded onto mobile phones, tablets and laptops, but they are a bit harder to study from if you are used to regular paper textbooks.

3) Amazon!

For used books and new books, I often check out Amazon first. Amazon has two basic options for textbooks: the Amazon warehouse or the Marketplace. You can choose to order used/new textbooks from Amazon directly, and they are often priced fairly competitively. Depending on your country, you might even get a gift card from Amazon if you sell it back to them. However, there are instances where the price from Amazon can seem quite intimidating (ie. more than what your bookstore sells it for).

In that case, the other alternative is the Marketplace. With the Marketplace, you can order books from 3rd party companies or users that have listed their books through Amazon. You often have to pay extra shipping for the books in the Marketplace, but they are usually quite a bit cheaper anyway. Do check the reviews on the reseller first — it might not be a good idea to buy from a seller that has a 20% rating!

For example, at the time of publishing, the Lehninger Principles of Biochemistry textbook was sold on Amazon for $177.41, and the lowest Marketplace prices were $159.36 for a new copy and $89.75 for a used copy.

The advantage with Amazon is that you know the copy that is being sold is the same as the one being described on the product page (ie. no international version / old edition mixup).

4) Other students

As I mentioned before, older students usually have spare copies of textbooks that they want to get rid of. Try asking them privately or at your university’s used textbook sales for a price estimate. If they need quick money, they might sell it for an amazing price!

5) Are you absolutely sure you need the textbook?

Sometimes the textbook that is listed on your booklist is not actually required — it might be more of a “recommended reading” book than a “must have this or fail the class” type of book. Email your professor to see if it is actually required. An example would be a student solutions manual for a maths textbook — it would be nice to have, but you don’t need to absolutely have it.

6) Share textbooks!

If you have a close friend or significant other, you could pool your monetary resources and buy one copy for common use. It is a lot more hassle since you don’t have on-demand access to it at all times, but if you need the textbook for just occasional use, this might be the way to go.

7) Buy early and consolidate your purchases

Between semesters, there are often huge sales on certain textbooks online on places like Amazon. A lot of these deals are posted by students or sellers who need quick cash, so they are willing to offer these low prices to get rid of it ASAP. However, these sales usually sell very fast. If you wait until you’re already a month into the semester, it is going to be extremely hard to find good prices because bargain hunters have already bought all of them.

Furthermore, instead of ordering textbooks one by one in separate weeks, it might be worth considering getting several at once. Some websites charge shipping if your purchase is below a certain amount, so it might save you shipping and handling fees if you consolidated your purchases.

 Do you have any more tips? Leave us a comment!

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

As you can see, I’ve begun a new Youtube channel for the purpose of streaming my 1v1 Starcraft 2 matches in 1v1 mode. When this video was recorded, I was just in bronze, so I was trying to improve my game to get into silver.

In this video, I am the red Protoss in the top right, and my opponent is the Terran on the top left. I started off with a standard 3gate build and tried to discreetly get dark templars to warp into his base with the warp prism. I also took the expansion between the two bases to deny the terran of the ability to rebuild his army from there. As you can see, there wasn’t a lot of harassment by either me or the terran–we were both turtled up. My obs revealed that he had a marine marauder ball, so I countered that with some gateway units and immortals, followed later by some colossi once I had expanded. I also got some void rays just in case he got air at a hidden base. I should improve on my keyboard hotkey usage, and get some more upgrades for my units in the future. Extra observers wouldn’t hurt.

In a standard PvT game, you probably want to get some early immortals and colossi to counter the almost inevitable bioball or tank push. However, since this requires early expansion, you should harass them to make sure they remain turtled up in their main base. Do scout early to see if they are going a SCV/marine all-in push in the beginning.

As the game moves on, I tend to get some dark templars even though the terran might have scans with their orbital command. Why? They will eventually run out of energy for scans, and since ravens are rarely used, your dark templars will give you the additional edge to overwhelm their army.

Any comments or suggestions? Leave a comment!

Recently, Sevenoaks, one of the most well-known IB schools in the world, have published a PDF with mark boundaries for this examination session. The mark boundaries show how the raw marks you got in your internal assessments and external assessments were converted onto the 7 mark scale. It can be accessed here.

Discussion related to last year’s mark boundaries (ie. May 2010) is available on one of my older blog posts.

For you May 2011 graduates: how did you do? Did you meet or beat your expectations? How did your fellow classmates do? Leave a comment!

You can also access my results from last year here with complete mark breakdowns.

Scheduling classes in the IB or in post-secondary education is often a skill that is overlooked by prospective students, unfortunately. Even if you managed to pick out the perfect combination of classes that are well-suited to your strengths, a stressful schedule can easily be overwhelming.

Most institutions allow students to register for classes in certain periods or time blocks well in advance of the upcoming semester through either a paper form or an online school website. Once you receive the go-ahead to register, keep some of these points in mind:

• Figure out how many classes or credit hours you need in order to graduate. Determine how many classes you need to take in the upcoming semester to reach that goal (ie. full-time student or part-time student).
• If the classes you are interested in have separate lab components, find out how many there are.
• Once you figure this out, determine what options there are for the classes you plan on taking. Are the classes every day? Mon/Weds/Fri? Tues/Thurs?
• Even if you are an early morning person, try to aim for classes that are later in the morning or in the early afternoon, just in case you sleep in, miss the bus or find out that your car broke down. Try to avoid classes or labs that are in the late afternoon, evening or weekends in general, unless you want your school day/week to be ridiculously long.
• Avoid choosing lectures that are multiple hours in length. Although you will only have the lecture once a week, they become extremely dull, regardless of the subject. Try to find an alternative lecture if possible.
• Determine the locations of your classrooms or lecture theatres. Ensure that you have sufficient time to move between classes so you aren’t late for class.
• Remember to schedule for breakfast/lunch/supper (and breaks, if needed)!
• Make sure that your labs are also scheduled.
• If possible, check when you have final exams for your classes. Try to make sure that you have at least some rest between each final (at least a day, preferably) so you have sufficient time for last-minute cramming or emergencies.

Do you have any other scheduling tips? Be sure to leave a comment!

If you notice any further problems on the website, do contact us via our Contact form.

Congratulations to all May 2011 IB candidates for finishing their exams!