Microbial and Animal Diversity

BIOL 227 (continue at protist metabolism)

What is number 9?

Ocular lens

What is number 2?

Nose piece

What are numbers 3, 4, and 5?

Objective lenses

What is number 6?

Stage clips

What is number 7?

Aperture iris diaphragm and condenser

What is number 8?

Light source

What is number 10?

Arm

What is number 11?

stage

What is number 12?

Course adjustment and fine adjustment

What is 13?

Stage controls

What is number 14?

Base

What is the function of the condenser lens?

It converges rays of light to a focal point on the specimen slide

How does light bend as it travels from the light source to the ocular lenses (without oil immersion)?

When the light exits the light source, it get bent by the condenser lens which converges it to a focal point on the slide, which then gets bent by the glass slide, then again by the air, and once more by the lens in the objective lens?

How does light bend as it travels from the light source to the ocular lenses without oil immersion?

The light get converged by the condenser lens, then once more by the glass on the slide, and since oil and glass have the same refractive index, the light only gets bent one last time by the objective lens

What is the magnification of the scanning objective lens?

4X

What is the magnification of the low-power objective lens?

10X

What is the magnification of the high-power objective lens?

40X

What is the magnification of the oil immersion objective lens?

100X

What is the magnification of the ocular lenses?

10X

What is the numerical aperture?

It is the resolving power of each lens

What is Abbé’s equation?

d=\frac{0.5\lambda}{n\sin\theta}

What do each variables in Abbé’s equation mean?

d= resolving power of the objective lens

λ= the wavelength of light

n= refractive index of the medium of the objective lens

θ= ½ the angle of the cone of light entering the objective lens

Why does the resolution improve as we move from scanning to high-power objective lens?

The decreased working distances decreases the angle of the light entering the cone as well as the resolving power of the lens were therefore improves the resolution

How is an increase in resolution is achieved as we move from scanning to high-power objective lenses?

As the distance decreases, the numerical aperture (nsinθ) increases. This causes less light to be scattered after it has converged at the focal point, giving a clearer image

What is dark-field illumination?

A dark-field stop over the condenser unit causes the light to converge at a focal point on the slide at angle beyond that with which can be captured by the objective lens. This causes only the specimens to be illuminated and leave a dark background

What is the oil immersion technique?

It is a technique where a drop of oil is placed on the slide. This creates a uniform media for light to pass through because the refractive index of glass and oil are the same. This stops the light from bending excessively, which would occur in the media shift from glass to air

What is the Koehler illumination technique?

It is a technique that ensures that the rays of light is within the second inverted cone enters directly into the objective lens. It reduces the amount of scattered light that exits the condenser lens which, in consequence, helps us see a clearer image of the specimen

Why is the Koehler technique important?

• It aligns the cone of light for the most light to be focused onto the specimen

• It improves contrast and resolution

Why does the resolution of the image increase when you add a drop of oil?

The oil has the same refraction as the glass and the working distance is decreased therefore when the light passes through the specimen it doesn’t get refracted again by the air

What are prokaryotic cells limited in size?

Due to Fick’s Law of Diffusion and the surface-area-to-volume-ratio, the diffusion time of particles increases as the cell gets larger, therefore, to keep diffusion time at a minimum, having small cells are the best way to do that

Why are prokaryotic cells more susceptible to distress than eukaryotic cells?

Prokaryotic cells lack a developed cytoskeleton which makes them highly sensitive to their environment. To make up for this, they contain a cell wall

What are bacterial cell walls made of?

Peptidoglycan

What does gram-negative bacterial cell walls have and gram-positive cells do not?

Capsule: a slippery layer of polysaccharides to attach to substrates

Fimbriae: allow them to stick to their substrate

Biofilm: slimy extracellular matrix

Flagella

What are the characteristics of a gram positive bacteria?

They have thick peptidoglycan layer, they stain purple, they are highly sensitive to antibiotics like penicillin

What are the characteristics of a gram negative bacteria?

They have a thin peptidoglycan layer, they contain a protective outer layer, they stain pink, they are more resistant to antibiotics like penicillin

What does a thick peptidoglycan wall stain purple?

Because is traps crystal violet die which masks the red safranin dye

What does a thin peptidoglycan wall stain pink?

Crystal violet dye can easily be rinsed away

What three factors contribute to the genetic diverisity of prokaryotes?

1. rapid rates of reproduction

2. mutation

3. genetic recombination

How to prokaryotes reproduce so quickly and still have genetic diverisity?

They reproduce by binary fission and though mutations are rare, because of their rapid reproduction, mutation rapidly accumulate

What are the three methods for genetical recombination in prokaryotes?

1. Transformation

2. Transduction

3. Conjugation

What is transformation?

It is the incorporation of foreign DNA from the surrounding environment

What is transduction?

It is the movement of genes between bacteria and a bacteriophage

What is conjugation?

It is when genetic material is transferred between prokaryotic cells where an F factor (F plasmids) is needed. The F plasmids are transferred from one cell to another by a sex pilus

What are the four different types of metabolism a prokaryote can be?

1. photoautotroph

2. chemoautotroph

3. photoheterotroph

4. chemoheterotroph

How do denitrifiers (or nitrogen reducers) metabolize nitrogen?

They metobolize NO₃^- and organic compounds into N₂

How do nitrifiers metabolize nitrogen?

They metabolize O₂ and NH₃ into NO₂^-

How do nitrosifiers metabolize nitrogen?

They metabolize NO₂^- and O₂ into NO₃^-

How does oxygen affect obligate aerobes?

They require oxygen for cellular respiration

How does oxygen affect obligate anaerobes?

They are poisoned by oxygen and instead use fermentation (anaerobic respiration)

How does oxygen affect facultative aerobes?

They can survive with or without oxygen

What is a biofilm?

A tangled web of polysaccharide fibres that adhere firmly onto substrates 

What is an endospore?

It is a protective layer that protects cell information from harsh conditions until conditions are viable again

Why does the gram negative bacteria stain pink?

When rinsing the slide with alcohol, the complex formed by crystal violet and iodine is rinsed off leaving only the safranin stain

Why does the gram positive bacteria stain purple?

The complex formed by crystal violet and iodine shrinks the pores of the peptidoglycan layer trapping the stain in the peptidoglycan. Rinsing the slide with alcohol will not wash away the stain and therefore leave a purple colour

What are the names of these colony morphologies from top to bottom?

• punctiform

• circular

• rhizoid

• irregular

• filamentous

What are the names of these edge morphologies from top to bottom?

• entire

• undulate

• lobate

• filamentous

• curled

What are the names of these elevation morphologies from top to bottom?

• flat

• raised

• convex

• pulvinate

• umbonate

What are the names of the surface morphologies?

• smooth, glistening

• rough

• wrinkled

• dry, powdery

Name these shapes and arrangements

1. coccus

2. diplococci

3. diplococci encapsulated (pneumococcus

4. staphylocooci

5. streptococci

6. sacrina

7. tetrad

Name these shapes and arrangements

1. coccobacillus

2. bacillus

3. palisades

4. diplobacilli

5. streptobacilli

Name these types of budding and appendages

1. hypha

2. stalk

Name these shapes and arrangements

1. enlarged rod

2. vibrio

3. comma form

4. club rod

5. helical form

6. corkscrew form

7. filamentous

8. spirochete

Describe the effectiveness of Tetracycline

• broad-spectrum antibiotic

• affecting both gram-negative and gram-positive bacteria

• works at moderate to high concentrations

Describe the effectiveness of Penicillin

• only effective against penicillin

• targets cell wall synthesis

• works at low concentrations

Describe the effectiveness of Erythomycin

• only effective against gram-negative

• lipid-soluable therefore it has difficulty passing through lipopolyssacharide outer membrane of gram-negative bacteria

Modes of nutrition for prosists

• Photoautotrophic

• Heterotrophic

• Mixotrophic

Modes of locomotion for protists

• Flagella

• Cillia

• Amoeboid

• Gliding (mucus secretion)

What is conjugation?

It is the decoupling of sex from reproduction where haploid nuclei and genetic material are exchanged

What organisms where born out of primary endosymbiotic events?

• mitochondrion

• chloroplast

• red alga

• green alga

What defines a primary endosymbiotic event?

Engulfing a proteobacterium or cyanobacterium (gram-negative bacteria)

What defines a secondary endosymbiotic event?

Engulfing a primary cyanobacteria (one that already had an endosymbiotic event)

What organisms evolved from the secondary endosymbiont red alga?

• dinoflagellates

• apicomplexans

What organisms evolved from the secondary endosymbiont green alga?

Euglenids and Chlorarachniophytes 

Which organisms are a part of the excavata supergroup?

• Diplomonads

• Parabasalids

• Euglenozoans

Within the excavata supergroup, which ones have not retained their plastids?

Diplomonads and Parabasalids

What are the unique features of the excavates supergroup?

• Specialized feeding grooves for phagotrophic nutrition

• contain a single, paired, or multiple flagella

What are the main characteristics of Diplomonads?

• anaerobic heterotrophs

• two or four equal-sized nuclei and multiple flagella

What are the main characteristics of Parabasalids?

• anaerobic heterotrophs 

• endosymbionts of animals

• moves around by means of its flagella and undulating membrane

What organisms are apart of the Euglenozoan clade?

Kinetoplastids and Euglenids 

What are the key characteristics of Kinetoplastids

• single large mitochondrion 

• Whiplash flagella at the posterior end

• undulating membrane

What are the key characteristics of Euglenids?

• one or two long flagella that emerge from a pocket (the excavated groove) at the anterior end of cell

• eye spot

• slug-like motility

• mixotrophic

What does the SAR Supergroup stand for?

Stramenopiles, Alveolates, and Rhizarians.

What are the observed organisms within the Stramenopiles subgroup?

• diatoms

• brown algae

• oomycetes

What are the observed organisms within the Alveolates subgroup?

• Dinoflagellates

• Apicomplexans

• Cilliates

What are the observed organisms within the Rhizarians subgroup?

• Forams

• Cerocozoans

• Radiolarians

What are the main characteristics of diatoms?

• unique two-part, glass-like wall (frustules) made of silicon dioxide

• mostly non-motile (some species secrete mucilage for movement)

• lost distinguishing flagella

What are the main characteristics of brown algae?

• photoautotrophs

• multicellular

• marine

• contain flagella on sperm and zoospore

• alternation of generations

What are the main characteristics of Oomycetes?

• filamentous protists

• cell wall made of cellulose

• specialized hyphal cells and egg cells

What are the main characteristics of dinoflagellates?

• 2 flagella: 1 transverse and 1 longitudinal

• cell membrane reinforces with cellulose

• autotrophic plankton

What are the main characteristics of apicomplexans?

• parasites

• apical complex (for drilling into cell tissue)

What are the main characteristics of cilliates?

• heterophic

• use cilia all over cell for locomotion

• contractile vacuoles with star-like patterns

What are the key features of the rhizarian clade?

Long thin pseudopods and mineral shells

What are the main characteristics of forams?

• Tests: porous shells made of calcium carbonate

• pseudopodia for feeding and locomotion

• coilling

What are the main characteristics of cerozoans?

• heterotrophic parasites

• descendant of the secondary endosymbiont event involving a green algae

What are the four genomes present in Chlorarachniophytes?

1. Nuclear

2. Mitochondrial

3. Green algal

4. Cyanobacterium

What are the main characteristics of radiolarians?

Pseudopodia that radiate from the centre of the body for nutrition

What organisms are a part of the archaeplastida supergroup?

• red algae

• green algae

• land plants

What are the main characteristics of red algae?

Uses phycoerythrin (red pigment) for photosynthesis

What clades are considered apart of the green algae subgroup?

Charophytes and chlorophytes

What are the main characteristics of charophytes?

• cellulose-synthesizing protein rings embedded in plasma membrane

• phragmoplast