MICR271 Midterm

Mods1-3, from scratch

What is a key difference between (Bacteria and Archaea) and Eukaryota?

Bacteria and Archaea don’t have membrane-bound organelles, while Eukaryota do.

What are the 2 different scenarios of the Endosymbiont hypothesis?

1. Symbiogenesis scenario: an archael cell took up a bacterial endosymbiont.

2. Archezoan scenario: a eukaryotic cell took up a bacterial endosymbiont.

What is the Endosymbiont hypothesis?

The hypothesis that mitochondria evolved from bacterial endosymbionts at some point during evolution → supported because they have similarities with bacteria (they have their own DNA and translation system)

Compare/contrast defining characteristics of Archaea/Bacteria/Eukaryota that are monitored in phylogeny.

Bacteria:

• no nucleus

• RNA pol has 3-4 subunits

• 70s ribosomes

• cell wall has murein/PG

Archaea:

• no nucleus

• RNA pol has 8-12 subunits

• 70s ribosomes

• no murein

Eukaryota

• no nucleus

• RNA pol has 12-14 subunits

• 80s ribosomes

• no murein

Distinguish between the Phylogenetic and Phylogenomic Trees of Life, and the Web of Life.

1. Phylogenetic - based on rRNA sequences, show bacteria is different from archaea and eukaryota, which are more similar

2. Phylogenomic - based on entire genome, similar findings ^^

3. Web of Life - accounts for HGT and endosymbiosis

What are the components of a virion?

• Genetic material

• Capsid (protein coat)

• Lipid envelope (only some)

What are the 3 theories of virus origination?

1. Virus-first theory: viruses came first and used to exist as macromolecules (RNA, DNA), and were self-replicating - some evolved into complex cells, some stayed viruses

2. Escape theory: cells came first, some genetic info/cell components leaked out and evolved as a parasite

3. Reduction theroy: cells came first, and viruses came from some cells losing elements until they came to rely on other cells’ machinery (to save E)

Pathogenic vs Commensal bacteria

Pathogenic: infectious

Commensal: non-infectious, most of the bacteria in our gut/body

What are the methods of HGT in bacteria?

1. Transformation: genetic info from environment

2. Conjugation: genetic info directly from another bacterial cell

3. Transduction: genetic info from a virus like a bacteriophage

Is Transposition a method of HGT? Why or why not?

No, Transposition is the transfer of genetic info by transposons between chromosomes of the same organism.

HGT must be between organisms.

How do microbes change genetic material?

1. Mutation

2. Recombination

3. HGT

What are the mechanisms by which bacteria have antibiotic resistance?

1. Target protection: bacteria produces a protein that disrupts target and antibiotic interaction

2. Target modification: amino acid sequence of target site is changed

3. Prevention of intracellular antibiotic accumulation: bacteria has increased efflux mechanisms, lets it take out antibiotics more

4. Antibiotic detoxification: bacteria can change/degrade antibiotic more

What main factors have humans influenced and what do they favour/what effect do they have?

• antibiotic use favours resistant bacteria

• vaccines favour microbes that aren’t recognized by the immune system

• water composition changes determine nutrient availability

• climate change impacts the C cycle and N cycle, and microbe contribution

• spread of people causes the emergence of pathogenic microbes

What is the Peptidoglycan (PG) cell wall made up of?

long sugar chains cross-linked by peptide chains

Compare and contrast Gram+ with Gram-

Gram+

• Thick PG, teichoic acid, small periplasmic space

Gram-

• Thin PG, LPS, large periplasmic space

Compare structures of Bacteria, Archaea, and Eukaryotes

Bacteria

• have PG

• flagella: motility in liquid

• pili: some motility (twitching), conjugation, biofilm

Archaea

• no PG

• diverse outer layers

• some have monolayer (increased stability)

• archaella for motility, pili for attachment

Eukaryotic microbes

• compartmentalization

• cilia and flagella for motility

Compare antigenic drift and shift

Antigenic drift: accumulation of small mutations over time

Antigenic shift: major sudden change

What is one way antigenic shift occurs?

When multiple strains of a virus infect the host at the same time → genome segments from the different strains can be assembled into a new viral particle with new antigen combinations

What do antivirals target?

Either the virus or the host cell to prevent lock and key binding mechanism.

What are the viral antigens + host cell receptors associated with HIV

gp120 on the virus attaches to CD4 receptor on host cells (immune cells)

What is a good target for antibacterial drugs and why?

PG because it’s on the surface, essential fro bacteria, and unique to prokaryotes.

How do antibiotics target the PG of bacterial cell walls, and what is an example of these antibiotics?

• Beta lactams inhibit enzymes that form the cross links between amino acids in different glycan chains

• ex. Penicillin

How do most bacterial cells divide?

Binary fission (can partition damaged stuff to one pole)

Many microbes are chemoautotrophs, what does this mean?

They get Carbon and Energy from organic molecules

What are persister cells?

• metabolically inactive cells in a population of microbes

• harder for antibiotics to target (most antibiotics target metabolic pathways)

• have same genes as population: distinct from antibiotic resistance

• can become metabolically active again once antibiotic is gone

How do bacteria communicate?

Quorum Sensing:

• autoinducers tell bacteria about population density and if the concentration is high enough can change gene expression (like generating biofilm)

• bind to receptors either on the outside of the cell (Gram+) or intracellular (Gram-)

What are the main ways to enumerate microbes and what are their mechanisms?

1. Plating Assay: counts living bacteria → make dilution, add to agar plate, count colonies, 1 original bacterium = 1 colony

2. Plaque Assay: counts infectious viral particles → make dilution, add to monolayer of susceptible host cells → count plaques

3. Hemocytomer: counts cellular microbes → use grid and count cells in grid with microscope

4. Spectrophotometry: increased cells cloud mixture (scatter light) and affect absorbance measurement.

What is the difference between disinfection and sterilization?

• Disinfection: kills all microbes except spores

• Sterilization: kills everything

*difference might just be duration/dose of treatment

What are the methods to control microbial growth?

1. Mechanical (filtration) - removes microbes

2. Chemical - damages cellular components (proteins, membranes)

3. Physical - damages cellular components (heat - proteins, radiation - DNA)

Other than targeting cell walls of microbes, what other metabolic pathway can we target that won’t harm humans?

We can target Tetrahydrofolate synthesis (essential for bacterial DNA synthesis), because we get folate from our diet so we don’t do this.

How do complement proteins work?

They are part of the innate immune system:

• activate inflammatory response

• lyse microbial cells - membrane attack complex

• bind to microbes to help immune system recognize them (opsonization)

What is the process of the adaptive immune response?

• antigens on the surface of phagocytes activate immune cells that recognize them

• B cells = antibodies that recognize antigens (also can turn into memory cells for next time)

• Opsonization, Complement fixation (complement system), Neutralization (block microbes from binding)

• Cytotoxic T cells have receptors to recognize antigens → triggers enzyme to kill infected host cell