Exam 1 Flashcards

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1
Q

Define microbiology

A

The study of living things too small to be seen with the untrained eye

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2
Q

Define microorganisms

A

an organism of microscopic size

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3
Q

Use the appropriate units when using metric measurements for microorganisms.

A

Meter
100 m
1 m
Centimeter
10-2 m
0.01 m
1/100 m
hundreth of a meter
Millimeter
10-3 m
0.001 m
1/1,000 m
thousandth of a meter
Micrometer
10-6 m
0.000001 m
1/1,000,000 m
millionth of a meter
Nanometer
10-9 m
0.000000001 m
1/1,000,000,000 m
billionth of a meter
Angstrom
10-10 m
0.0000000001 m
1/10,000,000,000 m
ten billionth of a meter
Picometer
10-12 m
0.000000000001 m
1/1,000,000,000,000 m
trillionth of a meter

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4
Q

Recognize the relative sizes of microbes.

A

about 1/10th the size of a typical human cell (7.5 um to 150 um)

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5
Q

Explain the properties of being unicellular vs multicellular

A

Unicellular: a single cell; All prokaryotes are unicellular. Eukaryotes can be unicellular or multicellular

Multicellular: multiple cells that carry out different functions (cellular specialization)

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6
Q

Explain the properties of being autotrophic vs heterotrophic

A

Autotrophs: obtain their energy from inorganic sources (sunlight or chemicals)

Heterotrophs: obtain their energy from the breakdown of organic compounds produced by other organisms

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7
Q

Explain the properties of being prokaryotic vs eukaryotic

A

Prokaryotic: lack a nucleus or other organelles; Bacteria and Archaea

Eukaryotic: contain a nucleus and other organelles; Animals, plants, fungi, protists

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8
Q

Discuss the contributions of Van Leeuwenhoek to the field of microbiology.

A

“Father of Microbiology”
Linen merchant who created high quality magnifying lenses that could magnify 500X
Discovered protozoa and named them “animalcules”
“In all falling rain, carried from gutters into water-butts, animalcules are to be found;…and that in all kinds of water, standing in the open air, animalcules can turn up. For these animalcules can be carried over the wind , along with the dust floating in the air.”
Antoine van Leeuwenhoek, 1702

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9
Q

Discuss the contributions of Redi to the field of microbiology.

A

Used controlled experiments to test whether maggots could spontaneously arise on meat.
Open jars: Maggots on meat
Closed (sealed) jars: No maggots on meat
Jars covered with fine mesh: No maggots on meat

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10
Q

Discuss the contributions of Spallanzani to the field of microbiology.

A

Used controlled experiments to test whether microbes arose from nutrient broth.
Nutrient broth (not heated): Microbe growth
Nutrient broth (heated): No microbe growth

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11
Q

Discuss the contributions of Pasteur to the field of microbiology.

A

Numerous contributions to the field including the process of fermentation, pasteurization, pure culture, the autoclave, and developed the rabies vaccine.
Also, did experiments to test spontaneous generation.
Used an S-shaped flask to test whether microbes are found in the air or generate spontaneously. Microbes are kept out, but air is let in.
Nutrient broth placed in S-flask, heated, not sealed: No microbe growth
Nutrient broth placed in S-flask, heated, then sealed, then neck broken off: Microbe growth

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12
Q

Discuss the contributions of Jenner to the field of microbiology.

A

developed the first vaccine to smallpox.
Demonstrated that inoculations of cow pox could prevent smallpox.

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13
Q

Discuss the contributions of Semmelweis to the field of microbiology.

A

Prior to the 1800, handwashing was not a routine practice in hospitals.
Found that washing hands with a chlorinated lime solution dramatically reduced rates of puerperal fever and death in patients.

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14
Q

Discuss the contributions of Lister to the field of microbiology.

A

introduced the principles of sterile surgery.
Revolutionized surgery in the 1800s.
Introduced carbolic acid (phenol) to sterilize instruments and clean wounds.

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15
Q

Discuss the contributions of Koch to the field of microbiology.

A

developed method to prove microorganism cause of disease.
His major contribution was the Germ Theory of Disease which he developed while studying Bacillus anthracis.

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16
Q

Discuss the contributions of Flemming to the field of microbiology.

A

Discovered naturally occurring antibiotics, including penicillin in 1928.
Discovered lysozyme in 1921.

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17
Q

Discuss the contributions of Hinton to the field of microbiology.

A

Developed widely used, highly accurate tests for syphilis
First black professor at Harvard

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18
Q

Discuss the contributions of Lederberg to the field of microbiology.

A

Considered the “Father of Microbial Genetics”
Discovered that bacteria can exchange genes by transfer of plasmids or by bacterial viruses (phage).

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19
Q

Discuss the contributions of Woese to the field of microbiology.

A
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20
Q

Describe the first organisms on earth, their properties (cell type, metabolism) and how long ago they lived.

A

All life started from the same prokaryotic ancestor, but now there is vast diversity.
Archaea, bacteria, and eucarya
1.3 million species named
Approximately 8.7 million species exist

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21
Q

Explain the impact of the evolution of photosynthesis on the origin of the eukaryotes.

A

Photosynthetic eukaryotes might have emerged around 1.9 billion years ago in freshwater habitats. Eukaryotes are thought to have evolved the capacity of photosynthesis through endosymbiosis, where a protist host encapsulated a photosynthetic cyanobacterium.

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22
Q

Explain the Endosymbiotic theory of the evolution of mitochondria and chloroplasts.

A

Endosymbiotic theory is when the mitochondria and chloroplast in eukaryotic cells were once aerobic bacteria (prokaryote) that were ingested by a large anaerobic bacteria (prokaryote), which explains the origin of eukaryotic cells.
Mitochondria and chloroplasts likely evolved from engulfed prokaryotes that once lived as independent organisms. At some point, a eukaryotic cell engulfed an aerobic prokaryote, which then formed an endosymbiotic relationship with the host eukaryote, gradually developing into a mitochondrion.

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23
Q

Understand the difference between taxonomy and phylogeny.

A

Taxonomy is the science of classifying organisms.
Phylogeny is the study of the evolutionary relatedness of organisms.

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24
Q

Recognize how molecular phylogenetics led to a major change in how organisms are classified.

A

Each species retains some characteristics of its ancestor.
Grouping according to common properties implies that a group of organisms evolved from a common ancestor.
Morphology
Fossils
Molecular data (rRNA)

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25
Q

Compare and contrast three domains relation to their characteristics such as cell type, cell wall composition, plasma membrane composition, antibiotic sensitivity, and ribosome structure.

A

Bacteria: prokaryote, unicellular, hydrocarbon chains attached to glycerol by ester linkages, peptidoglycan, and is antibiotic sensitive.
Archaea: prokaryotic, unicellular, hydrocarbon chains are attached to glycerol by ether linkages, no peptidoglycan (usually S-layer), and not antibiotic sensitive.
Eukarya: Eukaryotic, multicellular, hydrocarbon chains attached to glycerol by ester linkages, no peptidoglycan (cellulose-plants chitin-fungi), and isn’t antibiotic sensitive. Each domain has a unique rRNA structure.

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26
Q

Explain the difference between classification and identification, and why classifying microorganisms is difficult.

A

Classification: Placing organisms in groups of related species. Lists of characteristics of known organisms.
Identification: Matching characteristics of an “unknown” organism to lists of known organisms.
Clinical lab identification
The species of bacteria are not stable. They regularly try to adopt into changed environment by changing their genetic material. So, it is not possible to easily and stable classification of the bacteria at the species level.

27
Q

Understand the different ways we can define species.

A

Biological species concept defines a species as members of populations that actually or potentially interbreed in nature, not according to similarity of appearance. Although appearance is helpful in identifying species, it does not define species.
Multiple factors are used to designate microbial species:
Phenotypic analysis
Molecular analysis
Genomic analysis

28
Q

Relate how we define eukaryotic species, prokaryotic species, and viral species.

A

Prokaryotic species: A group of prokaryotes that have similar characteristics: appearance, physiology, and genes.

Definitions:
Culture: bacteria grown together in laboratory media

Clone: Population of cells derived from a single cell

Strain: Genetically different cells that have been derived from a clone

Eukaryotic
A cell characterized by the presence of a nucleus and other membrane-bound organelles. Eukaryotes can be unicellular (protists) or multicellular (fungi, plants and animals).
Prokaryotic
An organism whose cells do not have an enclosed nucleus, such as bacteria.
viral species
a group of viruses sharing the same genetic information and ecological niche (host)
the two kingdoms Carolus Linnaeus began taxonomy with
Plantat and Animals

29
Q

Explain the difference characteristics used to classify bacteria: morphology (shapes and arrangements), Gram stain (positive vs negative), motility, nutrient requirements (different groups based on oxygen use), antibiotic resistance, and genomics and metagenomics (GC content and 16s rRNA sequencing).

A

Morphology
Coccus: round
Bacillus: rod
Vibrio: curved rod
Coccobacillus: short rod
Spirillum: spiral
Spirochete: long, loose spiral
The ability to move is often accomplished through the presence of flagella, tail like appendages
Obligate aerobes (1)
MUST have oxygen to survive
Facultative anaerobes (3)
Can use oxygen if it is there but can also live without
Microaerophiles (4)
Require a low concentration of oxygen
Obligate anaerobes (2)
Prefer to grow without oxygen
May be harmed by oxygen
Aerotolerant anaerobes (5)
Do not use oxygen but can tolerate it
Antibiotic Resistance: Due to the presence of antibiotics in the environment, some strains have become resistant.
Acquire plasmids carrying antibiotic resistance genes by horizontal gene transfer.
Genomics is the analysis of the complete DNA sequence of an organism.

Gene content and organization
G+C content
DNA-DNA hybridization
Average nucleotide identity (ANI)

DNA extraction and analysis from microbial communities= Metagenomics
Determined 3 domains based on 16s rRNA sequence:
Bacteria
Archaea
Eukarya
Domain is a distinction above kingdom.

30
Q

Know the different morphologies and arrangements of prokaryotic cells.

A
31
Q

Explain how horizontal gene transfer complicates microbial classification.

A

Classification of prokaryotes is complicated by horizontal gene transfer.
1. one bacterium contains a plasmid to be transferred
2. connection forms and the plasmid is copied
3. both bacteria now contain the plasmid
4. the recipient may even integrate the plasmid into its chromosome

32
Q

Describe the ways we identify bacterial species

A

Biochemical tests: Presence of bacterial enzymes and Morphological characteristics: Shape/arrangement of cells, cell structures (more useful for eukaryotic microbes)

33
Q

Understand the difference between selective and differential media

A

Selective media is used to inhibit growth of some organisms, while encourage growth of others

Differential media is used to differentiate closely related or groups of organisms.

34
Q

Describe how biochemical tests can be used to identify bacteria.

A

Mannitol salt agar (MSA)
High salt in media inhibits growth of most bacteria but selects for Staphylococcus species.

Differentiates S. aureus from other species based on their ability to ferment mannitol

Enzyme tests: presence of certain enzymes can be used to identify bacteria.

Examples:
Indole test
Urea broth

Indole test: Hydrolysis of tryptophan by tryptophanase to pyruvate + ammonia + indole

Urea broth: tests for production of the enzyme urease.
Urease breaks down urea.
Urea is a break down product of certain amino acids that is excreted in the waste of many animals.
Urea can provide organisms with a source of nitrogen in the form of ammonia (NH3).

Metabolic tests: tests for presence of a certain metabolic pathway.

Examples:
Phenol red broth: tests for fermentation of carbohydrates.
Different carbohydrates can be tested.

Tests for production of acidic fermentation products and gas.
Phenol red broth results:
Yellow: fermentation
Red/pink: no fermentation

35
Q

Understand why dichotomous keys are used in bacterial identification.

A

Key for identification of organisms based on a series of choices between alternative characteristics.

First characteristic should distinguish between broad categories (such as cell morphology or Gram stain)

Subsequent characteristics should an organism or separate other organisms.

36
Q

Describe the properties of electromagnetic waves: wavelength, amplitude, and frequency.

A

Wavelength: distance from one peak to the next

Amplitude: the height of each peak

Frequency: number of wavelengths/ unit time

37
Q

Describe the following properties of light: reflection, absorbance, transmission, interference, diffraction, refraction, and refraction index

A

Reflection: when light bounces off a material

Absorbance: when a material catches the energy of a light wave

Transmission: when the light wave travels through a material
Opaque vs Transparent

Interference: when light waves interact with each other to make complex motion patterns (like two pebbles thrown in a lake)

Diffraction: when light bends or scatters in response to interacting with small openings or objects.

Refraction: when light waves change direction upon entering a medium

Refractive index: The degree to which a material slows transmission speed.

38
Q

Understand how refraction relates to the function of lenses and how it applies to the usage of fluorescent dyes and phosphorescence.

A

When light passes through a convex lens, it is refracted toward a focal point on the other side of the lens. Used to focus.
A concave lens can be used to redirect the light path in microscopes.
Fluorescent dyes can absorb UV light which is not visible and then use that energy to emit light of a different color. For example, a dye such as Texas red may be excited by blue light but emit red light.
Phosphorescence is when a material absorbs light and then emits it after a delay (like glow-in-the-dark material)

39
Q

Explain the concepts of magnification, resolution, and contrast as they relate to microscopy.

A

Magnification is an increase in size.

Resolution is the ability to see two different points as separate. Determined by:
wavelength (shorter= higher resolution)
numerical aperture (NA): the ability of a lens to gather light (the higher the aperture the higher the resolution)

Contrast is differences is light intensity
How we see things
Most biological material is water
Contrast between the specimen and the background is critical

Different forms of microscopy we will cover:
Light Microscopy
Brightfield
Darkfield
Phase-Contrast
Differential Interference Contrast (DIC)
Fluorescence Microscopy
Confocal Microscopy
Electron Microscopy
Transmission Electron Microscope (TEM)
Scanning Electron Microscope (SEM)

40
Q

Explain the difference between a simple microscope and a compound microscope.

A

Simple: a microscope in which the light only passes through one lens. (van Leeuwenhoek)

Compound: a microscope in which the light passes through two lenses (Galileo)

41
Q

Understand the principles and limitations of light microscopy.

A
42
Q

Discuss special types of light microscopy: brightfield, darkfield, phase-contrast, DIC, fluorescence (including immunofluorescence), and confocal.

A

brightfield: Produces a dark image on a bright background
Can be monocular or binocular
Compound microscopes have two different kinds of lenses
Ocular lens
Objective lens
Need to calculate TOTAL magnification

dark field: Like brightfield with a modified condenser (opaque light stop)

Oblique light reflects off the edges of the specimen

Often better resolution than brightfield

Darkfield allows high contrast, high resolution images without stain.

phase-contrast: Uses refraction and interference to create high-contrast, high resolution images of live samples.

DIC: Differential Interference Contrast Microscopy (Nomarski)
Uses interference patterns to enhance contrast
Live specimens appear 3D.
Can view structures inside cells.

fluorescence: uses fluorescent chromophores. Fluorescent chromophores absorb light (excitation is usually UV) and then emit it as visible light.
Can be natural (chlorophyll) or a stain
Examples: Texas Red and FITC
Creates high resolution images on a dark background
Can do multiple staining at one time
UV is a hazard and can be expensive

Immunofluorescence uses antibodies to visualize specific proteins.
Antibodies are protein molecules produced by the immune system that attach to specific pathogens to kill or inhibit them.
A chromophore can be attached to the antibody to detect the protein in a specimen

Confocal Microscopy takes images at many different z planes, then a computer constructs it into a 3D image.
Fluorescence dyes are often used in conjunction with this technology to increase contrast and resolution.
Useful for resolving all parts of thick samples that can be examined alive
Very complex and expensive instrument

43
Q

Compare and contrast transmission electron microscopy, scanning electron microscopy, and atomic force microscopy.

A

Electron microscopy: Light microscope are limited by the wavelengths of visible light (up 1500X)
Electrons can act like waves with a very short wavelength, so get amazing resolution and can magnify 100000x.
The specimen must be prepared so cannot be alive.
Two main types:
Transmission Electron Microscope
Scanning Electron Microscope

Transmission Electron Microscope: Uses a beam of electrons focused by magnets
Beam passes through a sample and then runs into the detector the captures the image.
Specimens are a very thin section (20-100nm thick)
Good for internal structures

Scanning Electron Microscopy: Creates an image by collecting electron that are knocked off off a specimen with a beam of electrons
Specimens are dried and often coated with gold
Good for looking at the surfaces of larger objects or smaller samples

Atomic force microscopy: can be used in several ways, including using a laser focused on a cantilever to measure the bending of the tip of a probe passed above the specimen while the height needed to maintain a constant current is measure; useful to observe specimens at the the atomic level and can be more easily used with nonconducting samples.

44
Q

Describe the different ways that bacterial cells in culture can be counted.

A

Counting bacterial cells in a culture: In order to study bacteria, scientists often need to know the concentration of bacteria in culture, but this can be challenging. Why?

The cells are very small.
They can be very numerous.

45
Q

Understand the difference between direct and indirect counting methods.

A

Direct counting methods count the number of organisms present in a sample.
Direct microscopic counts using a Petroff-Hauser chamber.
Coulter Counter
Serial dilution, followed by plate count
Most probable number

Indirect counting measure the turbidity (how cloudy) the sample is and is used as as estimation or to compare cultures.

46
Q

Be able to solve serial dilution problems including calculating the OCD of a culture.

A
47
Q

Compare and contrast prokaryotic genome and location from eukaryotic genome and location.

A

The prokaryotic genome is different than the eukaryotic genome.
Prokaryotic genomes are smaller (1/1000 of the human genome) and usually circular.
They are haploid, meaning they only have one copy of every gene.
Prokaryotes often have additional DNA called plasmids, small circular pieces of DNA with non-essential genes.
They are found in the nucleoid and associate with nucleoid-associated proteins that package and organize the DNA.

Eukaryotic cells keep their chromosomes in the nucleus
Have multiple, linear chromosomes
Can be haploid or diploid
DNA is packaged with proteins called histones (also for Archaea).

48
Q

Know how prokaryotes and eukaryotes divide.

A

Prokaryotes divide by binary fission and must replicate their DNA.
Bacteria reproduce by BINARY FISSION

The bacteria chromosome is duplicated (DNA replication)
One copy goes to each daughter.

49
Q

Differentiate horizontal and vertical gene transfer.

A

horizontal gene transfer: when bacterial genetic recombination occurs

Vertical gene transfer is the transfer of genetic information, including any genetic mutations, from a parent to its offspring.

50
Q

Identify and describe the structures in the prokaryotic cytoplasm

A

There are very few structures in the prokaryotic cytoplasm.
1. Nucleoid region with bacterial genome

  1. Ribosomes
    All cells have ribosomes, but the prokaryotic ribosome is a bit different.
    Ribosomes are the protein synthesis machinery made of a mix of RNA and proteins.
    Prokaryotic ribosomes are smaller (70s) than eukaryotic ones (80s).
    Many antibiotics target the prokaryotic ribosome.
  2. Inclusions
    Inclusions allow prokaryotes to store excess nutrients or other materials.
    Not membrane bound
    Usually store nutrients
    Glycogen or starch for carbon stores
    Polyphosphate granules for inorganic phosphate used in metabolism
    Sulfur granules for metabolism in Thiobacilius
    Sometimes can store other things like gas or magnetic iron.
51
Q

Understand the basic structure and function of bacterial endospores

A

Bacterial cells are generally vegetative, undergoing cell division and metabolism, but some can form endospores.
Dormant bodies that are resistant to heat, radiation, and chemicals, freezing, dehydration
Metabolically active vegetative cells can undergo sporulation in response to external stimuli
Found among the Gram positive Bacillales and Clostridiales.
Most well-known genera are Bacillus and Clostridium
Endospores are desiccated and extremely hard to kill.
Consist of several layers and many of the same structures found in vegetative cells
Contain very little water
Can persist in the environment for long periods of time

52
Q

Identify and describe the parts of the cell making up the cell envelope: plasma membrane, cell wall, and glycocalyx.

A

The cell envelope encloses the cytoplasm and internal structures.
Comprised of up to three layers
Cell membrane (inner most)
Cell wall (middle)
Glycocalyx (outer most)

All cells have a plasma membrane which is semi-permeable.
Composed primarily of a bilayer of amphipathic phospholipids, but also has proteins embedded
Structure is described by using the fluid mosaic model.

53
Q

Understand the functions of the cell membrane.

A

Provide a structural permeability barrier
Anchor membrane proteins
Site of energy conservation reactions

54
Q

Describe how molecules move across the plasma membrane by diffusion, osmosis, facilitated diffusion, and active transport.

A

Diffusion is the tendency of molecule to move from an area of high concentration to low.

Osmosis is diffusion of water.
Water will move from areas of higher water concentration to areas of lower water concentration. This inversely corresponds to the solute concentration. Water moves across the membrane to help ‘dilute’ the solute until there is an equivalent % of water to solute on each side.

Facilitated Diffusion: protein helps large, polar and/or charge molecules move WITH their concentration gradient.

Active Transport: protein helps large, polar and/or charge molecules travel AGAINST their concentration gradient. Requires energy (ATP or concentration gradient).

55
Q

Define the terms hypertonic, hypotonic, and isotonic and be able to predict which way water will flow and effect on cell structure.

A

Hypertonic:
Solution with the higher solute concentration
Pulls water towards it (greater pulling power)

Hypotonic:
Solution with lower solute concentration
Water is pulled from it (lower pulling power)

Isotonic:

Same pulling power for water on both sides of membrane

Flow of water is equal in both directions, so the net flow is zero.

56
Q

Understand the general function of membrane proteins and the importance of ABC transporters for bacteria.

A

Functions of membrane proteins: Cell recognition
Transport
Signaling
Enzymatic activity
Adhesion

ABC (ATP-binding cassette) transporters

Play an important roles in bacteria including nutrient acquisition, virulence, pathogenicity, and drug resistance.

Can act as importers or exporters of ions, amino acids, peptides, sugars, and other molecules that are mostly hydrophilic.

57
Q

Compare and contrast the structure and composition of Gram positive and Gram negative cell walls.

A

Gram positive (thick layer of peptidoglycan)
Gram positive bind stain better because they have a thick layer of peptidoglycan.
Stain Purple
Gram-positive bacteria have a very thick cell wall that often contains teichoic acid.

Gram negative (thin layer of peptidoglycan)
Gram negative bacteria only have a little peptidoglycan, so don’t hold on to the stain.
Stain Pink
Gram-negative bacteria have a thin layer of peptidoglycan and an inner membrane (IM) and an outer membrane (OM) separated by the periplasmic space.

58
Q

Describe the use of the acid-fast stain.

A

Acid-Fast Stain: Not all bacteria can be visualized/stained with Gram stain
Mycobacterium and Nocardia
Cell wall contains mycolic acid (a wax) – does not stain well and resists many chemical dyes
Therefore, must use the acid-fast stain to ID important pathogens causing:
Tuberculosis
Leprosy

59
Q

Compare and contrast the cell membrane and cell wall composition and structure of bacteria, archaea, and eukaryotes.

A

Cells walls in Archaea and Eukarya are quite different than in Bacteria.

Archaeal cell walls are not made of peptidoglycan
Usually, pseudopeptidoglycan where NAM subunit is replaced with something else
Could be made of another glycoprotein or polysaccharide
Eukarya cell walls are either made of cellulose (plants) or chitin (fungi)

60
Q

Identify the different types of glycocalyx and describe how the glycocalyx can benefit bacteria.

A

The last part of the cellular envelope is the glycocalyx.

Chemical Composition: Polysaccharides and proteins; thick and gummy
Slime Layer: Unorganized and loosely attached to the cell wall
Capsule: Highly organized and firmly attached to the cell wall

Functions:
Protects bacterium and keeps it from drying out
Facilitates attachment to surfaces
Aides in formation of biofilms

61
Q

Recognize the S-layer as an alternative structure in the cell wall of some organisms.

A

Instead of a glycocalyx, microorganisms can have an S-Layer.

Composed of structural proteins and glycoproteins
Diverse functions including resisting osmotic pressure and contributing to pathogenicity.
Found in most Archaea

62
Q

Describe the structure and function of the three types of bacterial appendages.

A

Many bacteria have filamentous appendages associated with their cellular envelope.

Accessory structures that extend from the surface of the cell.
Not present on all bacteria
Two major subgroups
Fimbriae and pili – allow for specialized attachments
Flagella – provide motility

63
Q

Understand the process of bacterial motility using flagella including the different types of taxis.

A

Flagella allow bacteria to move in response to chemical signals (chemotaxis), light (phototaxis), or changes in temperature (thermotaxis)
Positive –taxis: Movement towards a stimulus
Negative –taxis: Movement away from a harmful stimulus