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Summary MGY277 - Final Exam Notes

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Course
MGY277 (MGY277)

Institution
University Of Toronto (U Of T )

Complete and in-depth FINAL EXAM notes for MGY277 for EXAM prep. Kevin has combined notes from his peers and his own work to provide the most complete and comprehensive study guide for all types of students. He has achieved an overall cumulative GPA of 3.95 during his undergrad at the University o...

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MGY277 Final Exam Notes

Unit 1 – Perspectives

Unit 2 – The Bacteria
• Define the terms “magnification”, “resolution”, “contrast”, and “refraction” and apply them when looking at an image from
a microscope.
- Magnification: the increase in the apparent size of the object compared to the size of the actual object
- Refraction: light rays change direction due to change in medium (refractive index – measure of speed of light as it passe
through a medium)
- Resolution: minimum distance at which two points can be distinguished as individuals
- Contrast: the ability to see objects against the background
• Recite the steps of a Gram stain and why the stain can differentiate between different types of bacteria.
1. Crystal violet (primary stain) – bacteria stain purple
2. Iodine (mordant) – bacteria remain purple, cells less soluble now
3. Alcohol (decolourizer) – Gram-positive remain purple, gram-negative become colourless
4. Safranin (counterstain) – gram-positive cells remain purple, gram-negative cells appear pink
• Recall the different types of staining and how they are usefully applied.
- Gram stain: differentiate negative from positive gram cells
- Acid-fast stain: detect small group of organisms that don’t readily take up stain, i.e. Mycobacterium genus
- Capsule stain: capsules stain poorly, negative stain used, or India ink for suspension of carbon particles
- Endospore stain: Bacillus, Clostridium form dormant endospore, resist gram stain; use heat to facilitate uptake o
primary dye – often malachite green – by endospore, counterstain Safranin used to visualize other cells
- Flagella stain where flagella is for prokaryotic motility
• Know what the basic components of the Gram-positive and Gram negative cell envelope are
- Gram-positive: thick peptidoglycan, teichoic acid stick out above peptidoglycan, no outer membrane – hence no porin, n
LPS, sensitive to lysozyme
- Gram-negative: thin peptidoglycan, no teichoic acid, outer membrane – w/ porin, LPS, not sensitive to lysozyme
• Describe the outer membrane of the Gram-negative bacteria
- Outer membrane is unique lipid bilayer embedded with protein; porins and lipoprotein within outer membrane with lipoprotei
attaching to peptidoglycan
• Describe the structure of peptidoglycan: cell wall made of peptidoglycan, subunits N-acetylmuramic acid (NAM) & N
acetylglucosamine (NAG) form glycan chains; glycan chains are linked by tetrapeptide chains (4 AA strings)
- NAG found in mammals, NAG is a derivative of NAM, unique to bacteria
- Wall peptides are short and have unique “D” AA’s (D found in bacteria, L in proteins)
• Describe the basics of how bacteria obtain nutrients
- Trans-membrane highly specific proteins (transport systems) allows for movement of nutrients, small molecules, waste &
other compounds
- Facilitated diffusion: passive transport, not useful in low-nutrient environments & rarely used by prokaryotes
- Active transport: movement against [gradient], requires energy – Proton motive force & ATP (ABC transporter), commonl
used by bacteria
- Group translocation: transported molecule chemically altered upon entry via phosphorylation (i.e. glucose, where energy use
during transport is regained when sugar is broken down)
• Describe how bacteria sense their environment
- Membrane-spanning sensor kinase (SK), transfers a phosphate from ATP to response regulator (RR) – usually found as homo
dimer – RR is transcription factor which turns genes on or off in response
- RR controls response output – RR usually DNA binding protein changing affinity for DNA once phosphorylated
o I.e. Salmonella sense acid to recognize if within host, or sense O2 to regulate genes needed for anaerobic metabolism
• Describe a “typical” bacteria genome
- E. Coli strain CFT073 genome has about 5 million BPs, about 5000 genes
o Other E. coli strains have slight differences in genes they contain, due to frequent gene exchange amongst bacteria
- Contains anywhere from <500 to >8000 genes but only subset expressed at any given time
- Bacteria don’t have histones, introns or exons
• Describe bacterial gene regulation (i.e. how genes are turned on and off)
- Mechanism to control transcription: DNA-binding proteins & alternative sigma factors
- Alternative sigma factors: Standard sigma factor is component of RNA polymerase that recognizes specific promoters fo
genes expressed during routine growth conditions
- Alternative sigma factors can replace the standard factor & recognize different sets of promoters to control expression o
specific groups of genes (i.e. heat shock)

, MGY277 Final Exam Notes

Unit 3 – The Virus
• Describe the physical and genomic features of viruses.
- Viewed as DNA or RNA within protective coating, not alive outside of a cell (not metabolically active or replicating)
- Obligate intracellular parasites – reproduction reliant on intracellular resources
- Can be eukaryotic or prokaryotic (bacteria infected by bacteriophage – don’t infect humans)
- Difficult to study in lab: can’t be grown in pure culture, require live host, EM (expensive) to see
- Small size: 10 – 10000 x smaller than cells they infect (smallest is 17 nm diameter needs 2 genes to replicate), largest i
mimivirus – 2x larger than mycoplasma bacterium
- Virion: nucleic acid + protein coat (capsid), where nucleocapsid comprised of capsid containing genome
- Viruses have spikes for attachment to receptor sites & aid in entry to host cell
- Naked virus: Nucleoplasmid with capsomere subunits & spikes
- Enveloped virus: nucleoplasmid in matrix protein (immediate role during infection), surrounded by envelope w/spikes (oute
bilayer)
- Icosahedral: 20 flat triangles, efficient design using least energy to assemble
- Helical: spiral staircase like helix arrangement, can be short & rigid or long & filamentous
- Complex: intricate structures, i.e. phage w/ icosahedral head and long helical tail w/spikes & tail fibers
- Genomic features: DNA or RNA; linear or circular; double or single-stranded; always segmented; genome sizes vary, DNA
virus typically larger than RNA – large RNA are not stable
• Understand how viruses are classified and grouped, both formally and informally.
- ICVT 2009 report: > 6000 viruses, 2288 species, 348 genera, 87 families & 6 orders
- Formal classification based on: genome structure (ss/ds, RNA or DNA), hosts infected (bacteria, archea, animal, plant o
insect), viral shape & structure (enveloped or naked, icosahedral/helical, dimensions of capsid), disease symptoms
- Families end in –viridae, some names indicate appearance (coronae – crown like appearance), others named for geographi
area first isolated
- Genus ends in –virus (Enterovirus or Herpesvirus)
- Species name often name of disease, i.e. Poliovirus causes poliomyelitis
- Viruses commonly referred to only by species name, in contrast to virus nomenclature of genus, species
- Informal: Epstein-Barr for herpesvirus (Michael Epstein & Evon Barr discovered herpesvirus)
o Based on shared route of infection: Enteric viruses through fecal-oral route, Respiratory viruses through respirator
route, Zoonotic viruses animal to human transmission, Arboviruses spread by arthropods such as ticks & mosquitos
 Arboviruses can infect widely different species, i.e. West Nile encephalitis, yellow fever, dengue fever
- Viral Taxonomy: Nucleic Acid (ds DNA, ss DNA, ds RNA or ss RNA), ss DNA & ds RNA are only naked, revers
transcribing viruses all enveloped
o Nucleic Acid > Outer covering > Family > Members (family have viruses w/ similar structural features, infect simila
host & cause similar diseases)
• 5-step infection cycle for enveloped and non-enveloped viruses.
1. Attachment: > 1 spikes binds specific receptor on plasma – specificity of spike to receptors accounts for resistance
2. Penetration & uncoating: Membrane fusion of enveloped virus, receptor-mediated endocytosis of enveloped + naked virus
a. Membrane fusion leads to nucleocapsid entering cytoplasm & envelope remaining with plasma membrane
b. Receptor-mediated endocytosis: enveloped virus enters intact with enveloped virus staying within endosoma
membrane. Naked virus cannot fuse with endosome of host membrane, must damage endosome & releas
nucleocapsid into cytoplasm
o Virion must localize to site of replication, may be nucleus or cytoplasm
o Uncoating of NA & disassembly of virus may occur simultaneously upon entry, or upon final destination
3. Synthesis of viral proteins & genome replication: Requires viral gene expression + replication
a. DNA viruses: usually replicate in nucleus, requires host machinery for gene expression & DNA synthesis, encode
own DNA polymerase (ss – or ss + to ds ± DNA to ss + RNA (mRNA) to protein)
b. RNA viruses: usually replicate in cytoplasm, require RNA polymerase replicase – enzyme catalyzing replication o
mRNA/+ ss RNA from RNA template (ss – RNA or ds ± DNA)
 Replicase lacks proofreading ability – accounts for genetic mutations where pre-existing immunity ineffective
as seen in seasonal influenza (new vaccine needed due to mutations)
 Segmented RNA viruses undergo re-assortment to alter host specificity, non-human to human transmission
c. Reverse transcribing viruses: encode reverse transcriptase which makes DNA from RNA; retroviruses have ss + RNA
genome, single ds ± DNA complementary strand synthesized => integrated into host genome (can’t eliminate)
4. Assembly: protein capsid must be formed; genome & enzymes packaged within capsid, occurs in nucleus or organelles, man
assemble near plasma membrane close to site of release
5. Release: enveloped virus released via budding (integrates into host plasma membrane upon budding & becomes coate
w/matrix proteins), naked virus released when host cell dies (apoptosis initiated by virus or causing lysis of cell during release

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