MICRB 265 Midterm 1

Who created the first known depictions of microorganisms and is the pioneer of the microscope

Robert Hooke

Who is considered father of microbiology

Antoni van Leeuwenhoek

What concept was prevalent regarding the origin of life for thousands of years?

Spontaneous generation

Who disproved spontaneous generation?

Louis Pasteur

What did germ theory of disease indicate?

Some diseases are caused by microbes

Who provided definitive evidence for germ theory?

Robert Koch

What are Koch's postulates?

Criteria to establish a causative relationship between a microbe and a disease

What does a pathogen mean?

A pathogen is a microbe that can cause disease

What is LUCA?

Last Universal Common Ancestor

What are four features presumed of LUCA?

DNA replication, transcription, translation, cell division

What type of metabolism did LUCA likely have?

Anaerobic (no oxygen) metabolism

What are 3 pieces of evidence of the RNA world hypothesis

-RNA can form intricate, stable structures
- Proteins are still made today using RNA components
- Apparent "relics" from RNA world

Read 1-2 slide 9

Where do microbes get their energy? (For both chemotrophs and phototrophs)

Chemotrophs derive energy from chemical compounds; Phototrophs absorb light

What type of bacteria produced oxygen as a waste product?

Cyanobacteria

What is the endosymbiotic theory?

Eukarya evolved from an archaea-like ancestor that engulfed a bacterium

What did the rise of photosynthetic bacteria lead to?

Oxygen in the atmosphere

What is the role of tRNA?

Transfer RNA used in protein synthesis

What are some evolutionary forces in the RNA world? (List 3)

Improved replication, stability, binding other molecules

What is the primary evidence that supports the endosymbiotic theory?

Mitochondria and chloroplasts evolved from engulfed bacteria.

What is the role of mitochondria?

Efficient energy production.

What type of bacterium became chloroplasts?

Photosynthetic bacterium (cyanobacterium).

What is serial endosymbiosis hypothesis?

Eukarya lineage evolved from an archaea-like ancestor that engulfed an aerobic respiring bacterium

What do mitochondria and chloroplasts have?

Their own genomes, ribosomes, and tRNA.

To which bacteria are mitochondria related?

⍺-Proteobacteria.

To which bacteria are chloroplasts related?

Cyanobacteria

How many microbial cells are in the human body?

Roughly the same number as human cells.

What is a current threat to combating diseases?

Rise of antibiotic resistance.

Define taxonomy

Science of classifying/naming biological organisms

Define phylogeny

Study of the evolutionary relationships between different organisms

What do taxonomists use for classifications?

Genotype, phenotype, and phylogenetic information

How are organisms grouped in taxonomy?

Organisms with similar characteristics are grouped into taxa

What are the levels of similarity in taxonomy?

Hierarchical, from broad to specific

Whar are all the ranks in taxonomy

1. Domain

2. Kingdom

3. Phylum

4. Class

5. Order

6. Family

7. Genus

8. Species

Who developed the system of classification?

Carl Linnaeus

What is a subspecies?

Next finer classification after species

What is a biovar?

Grouping based on physiological or biochemical differences

What is a serovar?

Grouping based on surface antigens

What is a strain?

Genetic variant or subtype, often a specific isolate

List three ways that microbes have been named

• May be descriptive of Characteristics

(e.g. Deinococcus radiodurans - radiation surviving)

• Might honor a scientist

(e.g. Escherichia coli - Theodor Escherich)

• Might describe physical properties/appearance

(Staphylococcus aureus = “Grapes-like”, spherical [cell

appearance], golden [colony colour].

What does taxonomy help us with?

Brings order to diversity and aids communication about organisms

What can taxonomy help predict?

Cell biology, virulence, metabolism of organisms (Based on what we knew about a simlar species)

What is a phylogenetic tree?

Visual representation of lineage and evolutionary relationships

What method is used to determine phylogenetic relationships?

Comparing DNA sequences

What changes over evolutionary time in DNA?

DNA sequences change due to mutations

What indicates closer relatedness in organisms?

Fewer differences in DNA sequences

What type of genes are preferred for comparison?

Highly conserved genes that accumulate mutations slowly

What is commonly sequenced for phylogenetic relationships?

Small subunit ribosomal RNA (SSU rRNA)

True or false:
The ribosome is a conserved feature of all organisms of earth

True

The ribosomal RNA (rRNA, encoded by rDNA) of the small subunit (SSU) of ribosome is commonly sequenced to infer

phylogenetic relationships

________________________ regions useful for identifying relationships, __________________ regions useful for PCR

Variable, conserved

What does the Woese tree of life represent?

Universal tree based on nucleotide sequence similarity in rRNA (Genealogy of all life on Earth)

What is amplified and sequenced in bacterial classification?

16S rDNA

What can increase the power of phylogenetic analysis? (16S rDNA method)

Comparing sequences of multiple conserved genes

What is a limitation of phylogenetic trees?

They are just predictions of evolutionary relationships

What can confuse phylogenetic trees?

Horizontal gene transfer (HGT) (“foreign DNA” mixed in with ancestral DNA)

What can happen during homologous recombination?

Host genes can be replaced with homologous genes from another organism

What affects the mutation rate of DNA in different species?

Selective pressure

What is a major size difference between prokaryotes and eukaryotes?

Prokaryotes are generally much smaller in size.

What do eukaryotes contain that prokaryotes generally lack?

Eukaryotes contain numerous compartments (organelles).

What affects how quickly cells exchange nutrients and waste?

Surface area to volume ratio affects nutrient exchange

Do small cells generally grow (reproduce) more quickly?

Yes (Smaller size/less complexity also means less time/energy to replicate cell)

Historically, morphology has been important for (2)

naming and identifying bacteria (still today, but to a lesser extent)

Shapes dictated by a number of factors (list 3)

(cell wall structure, cell growth/division mechanism, cell differentiation)

What are cocci?

Cocci are spherical prokaryotic cells

What are bacilli?

Bacilli are rod-shaped prokaryotic cells.

What does Salmonella enterica commonly cause?

Food poisoning worldwide

What are Vibrio?

comma shaped (bent rod)

What is Vibrio cholerae known for?

It causes profuse diarrhea and dehydration.

What is Helicobacter pylori associated with? (and what is their mophology?)

It is a common cause of stomach ulcers and stomach cancers. (Helical)

What does Borrelia burgdorferi cause? (and what is their mophology?)

It causes Lyme disease, transmitted by ticks. (spirochetes)

What is Caulobacter crescentus used for? (and what is their mophology?)

It is a model system to study bacterial cell cycle and asymmetric cell division. (Appendaged/ Budding)

What is Chloroflexus aurantiacus studied for? (and what is their mophology?)

To understand the evolutionary origins of photosynthesis. (Filamentous)

What can cell shape affect?

Nutrient access, motility, attachment, biofilm formation, interactions

What is morphogenesis?

Change in shape

What is monomorphic?

One shape; observed in pure cultures of bacteria

What is pleomorphic?

Multiple different morphologies for the same bacterium

What causes different morphologies?

Differentiation, environmental cues, mutations

What is an example of different morphologies during growth?

Arthrobacter crystallopoietes changes shape

What shape does Arthrobacter crystallopoietes take during fast growth?

Rod shape

What shape does Arthrobacter crystallopoietes take during stationary phase?

Coccus shape

What is the cell envelope?

Generic term for structures surrounding the cytoplasm.

What major structures are included in the cell envelope? (4)

Cytoplasmic membrane, cell wall, outer membrane, S-layers.

What are the roles of the cell envelope?

Maintains barrier, protects from stress, transports nutrients and waste, energy conservation.

What is the primary function of the cytoplasmic membrane?

Acts as the primary barrier between the cell and its environment.

What is the structure of the cytoplasmic membrane?

Lipid bilayer with two sheets of phospholipids tail to tail.

What types of molecules interact in the cytoplasmic membrane?

Hydrophilic (water-loving) and hydrophobic (water-fearing) molecules.

What are the components of phospholipids in the cytoplasmic membrane?

Hydrophilic head group and hydrophobic tails.

What is the significance of unsaturated fatty acids in phospholipids?

They increase membrane fluidity and decrease rigidity.

What types of proteins are found in the cytoplasmic membrane?

Peripheral, integral, and transmembrane proteins.

What type of amino acids are typically found in membrane proteins?

Hydrophobic amino acids within the membrane and hydrophilic on the surface.

What are the two faces of the cytoplasmic membrane?

Cytoplasmic face and periplasmic face.

Are the two faces of the cytoplasmic membrane identical?

No, they are not identical; certain proteins face different compartments

What is the primary function of the cell wall?

Prevent cells from bursting due to osmotic pressure

What characterizes Gram-positive bacteria?

Thick cell wall, no outer membrane

What characterizes Gram-negative bacteria?

Thin cell wall, have an outer membrane

What is peptidoglycan?

A lattice-like structure in bacterial cell walls

What are the components of peptidoglycan?

Chains of glycans linked by peptide bridges

What forms the sugar backbone of peptidoglycan?

N-Acetylglucosamine (NAG) and N-Acetylmuramic Acid (NAM)

What type of linkage connects glycan chains?

β(1,4) linkage (glycosidic bond)

What provides additional strength to Gram-negative bacteria?

Outer membrane