BIOL 275 Exam 1 Prep Flashcards
(203 cards)
1
Q
How do you isolate a colony of microbes?
A
With solid media, Petri dish, and an inoculating loop. Use the T-streak method to dilute single bacterium so they can form colonies across different areas on a Petri dish.
2
Q
Explain the basic steps in animal virus replication
A
1.) Attachment: like bacteriophages, viral proteins and host cell receptors facilitate attachment. However, animal viruses use glycoprotein spikes or other attachment molecules. (no tails/tail fibers)
2a.) Entry: direct penetration, membrane fusion, or endocytosis
2b.) Uncoating: viruses that enter with capsid or envelope need to remove it to release genome
3.) Synthesis: different strategy and location based on genome type (DNA vs. RNA; ss vs. ds)
4.) Assembly: DNA viruses in nucleus, RNA viruses in cytoplasm (usually)
5a.) Release: enveloped viruses released by budding (taking along portions of cellular membrane coated with viral glycoproteins…which then turns into the envelope)
5b.) Release: naked viruses released by exocytosis or lysing and killing the cell
3
Q
Difference between Bacterial and Archaeal phospholipid bilayers?
A
Bacteria - ester linkages
Archaea - ether linkages
4
Q
What are the general measurement ranges for bacteria and viruses?
A
Bacteria - micrometers
Virus - nanometers
5
Q
What are viroids?
A
Small infectious pieces of RNA (no capsids):
- Viroids infect plants
- Viroid-like agents infect fungi
(Viroid RNA does not code for proteins)
6
Q
When a virus is extracellular (outside a host), what is it also known as?
A
A virion
7
Q
What is osmosis?
A
-Movement of water molecules directly across membrane
-Type of passive transport
8
Q
Why is the synthesis strategy for DNA viruses different than RNA viruses?
A
- Eukaryotic genomes are made of DNA, and not RNA
- DNA viruses usually replicate in nucleus
- RNA viruses usually replicate in cytoplasm
9
Q
Fermentation and pasteurization concepts
A
Fermentation - process that converts sugar to an alcohol or acid
- (Ex. Yeast converting sugar to alcohol, or bacteria converting sugar to acid)
Pasteur invented pasteurization to remove acid producing bacteria from wine
Buchner showed chemical reactions required enzymes, not living cells
10
Q
Explain the effects of water on microbes
A
Pressures exerted on cell
- osmotic (related to concentration of solutes)
- hydrostatic (related to depth)
Water also dissolves enzymes and nutrients
11
Q
What are the types of “light microscopes”?
A
- Bright-field
- Dark-field
- Phase
- Fluorescence
- Confocal
12
Q
How are viruses classified?
A
- Nucleic acid type (DNA or RNA, double or single stranded?)
- Presence of an envelope
- Shape
- Size
(International Committee on Taxonomy of Viruses)
13
Q
How can you improve a poor Bright-field microscope image?
A
A light background with light images and poor contrast can be improved with dyes
14
Q
Eukaryotic cytoplasm contains?
A
- Nucleus (contains DNA and nucleolus, the site of rRNA production)
- Mitochondria (ATP production)
- Ribosomes (protein synthesis, 80S size)
- Cytoskeleton (anchoring organelles, allows movement within cytosol)
- Centrioles and Centrosome (produce spindle fibers for cell division)
- Endoplasmic Reticulum (SER membrane for transport and synthesis of lipids, RER also has ribosomes)
- Golgi Body (modifies and packages cell components)
- Lysosomes (digestion enzymes)
- Peroxisomes (metabolic waste)
- Vacuole (storage)
- Vesicles (storage)
- Chloroplasts (photosynthesis)
15
Q
Examples of endospore forming bacteria that cause diseases?
A
Bacillus anthracis - agent of anthrax
Clostridium tetani - cause of tetanus
Clostridium perfringens - cause of gangrene
Clostridium botulinum - cause of botulism
Clostridiodes difficile - “C. diff” gastrointestinal disease
16
Q
What is transduction?
A
Host DNA is packaged into a viral capsid and transferred into a new host cell
17
Q
This microbe type is similar to animals in its structure and needs/requirements
A
Protozoa
18
Q
Explain “burst time” and “burst size”
A
Burst time - Time it takes to complete replication process from “attachment” to “release”
Burst size - Number of viruses released from each lysed cell
19
Q
Early advocates for prevention of disease:
A
Semmelweis - hand washing procedures
Lister - antiseptics (think of Listerine)
Nightingale - nursing cleanliness
Snow - sourced an epidemic(ology) by tracing cholera epidemic source
Jenner - used cowpox virus for smallpox vaccine
Ehrlich - ‘magic bullets’ kill microbes, not humans
20
Q
Briefly describe the formation of an endospore
A
- DNA is replicated
- Cytoplastic membrane surrounds daughter DNA creating a forespore
- A second membrane surrounds the forespore to create double membrane
- Peptidoglycan layers fill the space between the double membrane (called “Cortex”)
- Spore coat (proteins) is created around double membrane (resistant to heat/chemicals)
- Endospore is released and mother cell dies
21
Q
Name some facts about Protozoa
A
12,000+ species
Mostly harmless in water and soil
Few species are pathogens (yet cause 100s of millions if infections per year)
Pathogen species live on fluids of host/feed on tissues.
Two cycles of pathogenetic protozoa:
- Trophozoite (feeding stage)
- Cyst (resting stage when conditions become unfavorable, this phase spreads disease)
22
Q
Helminths characteristics?
A
- Include tapeworms, flukes, roundworms
- Microscopic when larval stage
- Parasitic helminths spend part of their lives in GI tract
- Reproduce sexually in host’s body
23
Q
What is the difference between positive-sense and negative-sense RNA viruses?
A
- Positive-sense RNA can act as mRNA. Ribosomes can translate proteins directly from positive-sense RNA.
- Negative-sense RNA must be transcribed into positive-sense RNA before translation of proteins can occur.
24
Q
Describe -ssRNA synthesis
A
Genome replication:
- “–ssRNA” viruses carry “RNA-dependent RNA transcriptase” in capsid, released during uncoating
- This enzyme transcribes the -ssRNA into +ssRNA
- Newly created +ssRNA used as template to create more -ssRNA (and to translate proteins)
Protein synthesis:
- Host ribosomes translate proteins directly from the +ssRNA
25
What are some structures that helminths use for attachment?
Suckers, hooks, teeth
26
Active Transport vs. Passive Transport comparison
Active transport:
- Requires/expends energy, requires protein(s)
- Against concentration gradient (low to high)
Passive transport:
- No energy usage
- Down concentration gradient (high to low)
27
Identification is?
Discovering, characterizing/recording traits for taxonomic placement
28
Simple vs. Facilitated Diffusion comparison
- Both are types of passive transport, however....
- Simple diffusion: molecules move directly across membrane
(small or nonpolar/noncharged molecules such as oxygen, carbon dioxide, or lipid soluble chemicals)
- Facilitated diffusion: molecules require aid of channel or carrier protein
(large, or polar/charged molecules such as glucose)
29
What are microbes that cause disease called?
Pathogens
30
Sterile vs. aseptic?
Sterile - free from all microbes
Aseptic - free from pathogens
31
Name microbe types that are eukaryotes
Fungi (mold and yeasts), Protozoa, and Algae
32
Difference between basic and acidic dyes?
Color producing chromophore salts in dyes are positively or negatively charged.
Basic dye - cation (POS charge) and stains acidic structures. Works best in high pH, and used in our lab.
Acidic dye - anion (NEG charge) and stains alkaline structures. Works best in low pH.
(Use dye with the opposite charge of structure)
33
Bacterial species vs. strain/subspecies
Species:
- Group of cells that share a similar pattern of traits
- 70-80% genomic similarity
Strains/subspecies:
- Also 70-80% genomic similarity but have different characteristics
- ex. the various Staphylococcus species and subspecies (due to various antibiotic reactions/growth/appearance)
34
Describe capsid (protein coat) functions
- Provides protection for nucleic acid
- Attachment to host cell (if no envelope)
- Made of: capsomeres
- Determines shape
35
What are some cytopathic effects of viruses?
Viruses can alter or damage host cells:
- Change shape
- Damage intracellular components
- Lysis
Accumulated damage kills most hosts
36
Compare burst time for bacteriophage vs. animal virions
Bacteriophage - about 25 minutes
Animal virions - up to 24 hours
37
Explain the 5 major Lytic replication cycle steps for a T4 bacteriophage with dsDNA
1.) Attachment - after random contact, attachment proteins on the bacteriophage's tail fibers precisely fit with receptors on host's cell wall
2.) Entry - phage releases "lysozyme" enzyme to weaken peptidoglycan in cell wall. The tail sheath contracts like syringe and injects DNA inside cell. Empty virion structure is left behind, still attached. After entry, viral enzymes break apart/destroy host DNA.
3.) Synthesis - the host cell replicates, transcripts, and translates viral DNA (because its own DNA is gone) resulting in viral polymerase, more lysozyme, and components of new virions (such as capsid, DNA, etc.)
4.) Assembly - virion components assemble to form mature virions
5.) Release - lysozyme enzymes break down cell walls and release matured virions, killing host cell
38
Fungi characteristics?
- Non-autotrophic
- Eukaryotic
- Cell walls composed of chitin
(Mold and Yeast)
39
Explain the concept of magnification
Process of refracting light through a glass lens in order to increase the size of an object.
(Electrons through a magnet in electron microscopy).
40
How do microorganisms interact with environment?
- Produce CO2, methane, and nitrogen gas to insulate atmosphere
- Most abundant cellular/acellular organisms in the ocean
- Assist plants obtain nutrients (ex. nitrogen or sulfur cycle)
- Bioremediation
41
Explain the Lysogenic replication cycle for a lambda bacteriophage
(Note: some steps are similar to the Lytic cycle)
1.) Attachment - random contact with host cell results in attachment via the lambda phage's tail
2.) Entry - lysozyme weakens cell wall and phage's tail injects an inactive viral DNA inside cell however, doesn’t destroy host cell's DNA. Empty virion structure is left behind, still attached.
3.) Prophage - the inactive viral DNA (called "prophage") fuses to the host cell DNA to create a single DNA
4.) Replication - the host cell replicates and divides and each daughter cell contains the prophage (inactive viral DNA). (The process of inserting prophage and using host cell replication is known as "lysogeny")
5.) Induction - induction event (radiation, environmental stress, etc.) causes the prophage to be excised (cut) from host DNA and starts synthesis stage
6.) Synthesis - the host cell replicates, transcripts, and translates viral DNA (because its own DNA is gone) resulting in viral polymerase, more lysozyme, and components of new virions (such as capsid, DNA, etc.)
7.) Assembly - virion components assemble to form mature virions
8.) Release - lysozyme breaks down cell walls and release matured virions, killing host cell
42
How can you increase contrast in microscopy?
- Change microscope type
- Adding dye
- Light adjustment
43
What are the growth requirements for microorganisms? (besides physical) What is needed for metabolism?
Nutrients (commonly carbon, oxygen, nitrogen, and hydrogen).
For metabolism, cells need:
- carbon source
- energy source
- source of electrons or hydrogen atoms
44
Cell wall functions?
- Provides structure
- Shape
- Protection from osmotic pressure
- May aid antibiotic resistance in bacteria
45
How is contrast related to image quality?
Contrast is the difference in intensity between two objects/the background.
It can lead to better resolution or quality.
46
Animal virus latency?
- Latent/inactive viruses are known as "proviruses"
- Latency is where animal viruses remain dormant in cells (possibly for years).
- Different from lysogeny because proviruses are not always incorporated into genome
- Incorporated animal viruses become permanent in host's chromosome; lysogenic viruses eventually excise from host DNA
47
Function of Cytoplasmic Membrane
Selectively permeable
-Phospholipid bilayer proteins act as pores, channels, or carriers
-Facilitate active or passive transport
Energy Storage and Production
- In prokaryotes, no organelles like mitochondria to create energy
Maintain concentration and electrical gradient
Control import and export of substances in cell
48
What are Integral Proteins?
Proteins that run all the way through cytoplasmic membrane
49
Define: anaerobic, aerobic, facultative anaerobe
Anaerobic - grows without oxygen
Aerobic - grows with oxygen
Facultative - can grow with or without oxygen
50
What microbes do not require an electron microscope to see?
Bacteria, archaea, fungi, protozoa, and algae
51
Types of stains and general use?
Simple stain (1 dye, usually basic) - increases contrast to help see size, shape, arrangement
Differential stain (2+ dyes) - helps distinguish structure or tell different types of cells apart
Special stains - looks for specific structures
52
Explain the phospholipid bilayer
Phospholipids made of:
- Hydrophilic head (water loving, polar)
- Hydrophobic tail (water fearing, nonpolar)
Arranged into bilayer because of their water loving/fearing properties:
- Polar head faces outwards, nonpolar tails face inward to each other
Phospholipid bilayer also contains:
- Hopanoids (bacteria)
- Cholesterol (eukaryotes)
- Integral proteins
- Peripheral proteins
53
What are the types of viral genomes?
Double-stranded DNA (dsDNA)
Single-stranded DNA (ssDNA)
Double-stranded RNA (dsRNA)
Single-stranded RNA (ssRNA)
54
Algae characteristics?
- Eukaryotic
- Can be unicellular or multicellular
- Photosynthetic (autotroph)
- Cell walls made of: agar or calcium carbonate
55
Name some microbe uses or effects (good or bad)
- food/drink production
- treatment of wounds
- mining of minerals
- can cause disease
- recycling nutrients (carbon, nitrogen, etc.)
- biological warfare
- cleaning up contamination/bioremediation
- research
- antibiotics
- industrial applications
(This list is not the end all be all answer)
56
Serology and immunology are?
Serology - study of blood serum
Immunology - study of body’s defense against pathogens
(Bonus: Fleming discovered penicillin)
57
What is a viral envelope?
- Usually acquired from the host
- It's a phospholipid bilayer membrane that surrounds the nucleocapsid
- Contains proteins - some are viral glycoproteins known as "spikes".
- Provides protection and recognition sites for binding to host cells.
(Virions without envelopes are called "naked virions")
58
How do bacteria and archaea reproduce?
Asexually, through binary fission (ensure you understand general process also)
59
Protozoa characteristics?
- eukaryote
- single celled
- able to move (motile)
- usually in water
- similar to animals in nutrition/structure
60
What is a Symport?
Active transport protein that helps two different molecule to cross membrane in the SAME direction
61
Movement of Eukaryotes? (Note: structures differ from prokaryotes)
Flagella:
- Anchored in cytoplasm
- No Hook
- Undulate, not rotate
- Not hollow
- Made of tubulin rings (9+2 arrangement)
- ATP powered
Cilia:
- Made of tubulin
- Hair-like
- "Beating" movement
62
Name some Prokaryote vs Eukaryote differences?
Prokaryote:
- Lacks membrane bound organelles
- Only unicellular
- DNA, which is circular, freely floats in nucleoid region
- Single chromosome (usually)
- Typically smaller in size
- Reproduce only by binary fission
Eukaryotes:
- DNA (linear) is contained in nucleus
- Multiple chromosomes
- Contains histones
- Contains organelles
- Usually larger in size
- Asexual or sexual reproduction
- Additional active transport mechanisms (endo/exocytosis)
63
What are Cilia?
Short hair-like protrusions used for movement (typically on Protozoa)
64
What is something inside Archaeal cytoplasm that is not found in bacteria?
Histone-like proteins that help fold DNA (like in eukaryotes) that help "keep it safe" in extreme environments
65
What is an Antiport?
Active transport protein that helps two different molecule to cross membrane in OPPOSITE directions
66
Besides dental health, how else are biofilms clinically relevant?
The biofilm protects the bacterial colonies that form on medical items like: catheters, IUDs, pacemakers
67
What is a nucleocapsid?
Consists of the following:
1.) The capsid (protein coat)
2.) The enclosed viral genome (either DNA or RNA)
Note: does not include envelope if there is one.
68
Ribosome function?
Function - protein synthesis
Composed of - rRNA and proteins
*Prokaryotes = 70S
*Eukaryotes = 80S
(antibiotics useful when targeting prokaryotic ribosomes because subunit size difference from eukaryotes)
69
Describe special stains
Negative stains:
- Reveals capsules (surrounding bacteria) by staining background with acidic dye
- Then counter-stains used on bacteria
- Capsules remain colorless and will appear as halo
Flagellar stains:
- Increases contract and thickness of flagella appendages on bacteria
- Allows light microscope to see them
(Bonus: capsules can indicate pathogens and remain colorless due to negative charge)
70
Why might temperature and pH requirements be important to microorganisms?
Both affect important structures such as protein shape, lipid rigidity, and/or hydrogen bonding
71
What temperature does an incubator need to be for growth?
Any temperature that provides optimum condition for a specific microbe to grow
72
Microbe(s) that are usually smaller than eukaryotic cells AND roughly 1 μm (micrometer) in size
Bacteria and archaea (also prokaryotic)
73
Identify the microscope used in the images
74
What is the most important taxonomic category?
How would you write something according to the binomial nomenclature rules?
Species is most significant category.
Binomial rules:
First word = genus (in all italics, with only first letter Capitalized)
Second word = species (all italics, all lowercase)
Once you write it out once, you can abbreviate the genus as "the first letter in italics and Capitalized followed by a period"
75
Review Table 4.2 in textbook. Study guide on reverse side of flashcard.
Important to know (from lecture video):
- Source of magnification (light, electrons, etc.)
- Type of specimens they can see (bacteria, virus, DNA, etc.)
- Specimens living or dead?
- Stain usage needed?
76
Are cell walls present in Eukaryotes?
Yes, only in fungi, algae, and plants
Fungi cell walls = chitin or glucomannan
Algae cell walls = agar, algin, or calcium carbonate
Plant cell walls = cellulose
(No cell walls in animals, protozoa, or helminths)
77
Microscope parts - fill in the blank
(Note: Condenser lens is directly on top of diaphragm and is NOT labelled here)
78
How do we study microbes?
- Rapid reproduction results in growing large populations in labs
- Can’t be seen directly, and are analyzed through indirect means (using microscopes)
79
Physical requirements for growth?
- Temperature
- pH
- Water
80
What are hopanoids?
- Cholesterol-like molecules, enable bacterial cytoplasmic membrane to be fluid and be in extreme high or low temperatures.
- Important in ensuring transport during these extreme temperatures.
81
Brief description of a taxonomic system?
Giving living things a scientific name, and classifying/grouping by structure and order.
Binomial naming (always in italics):
- “Genus” (first letter Capitalized) then “species” (all lowercase)
82
Name some structures that SOME bacteria have
- Flagella, pili, fimbriae
- Outer membrane
- Plasmids
- Endospore
83
Name some of Koch’s contributions
Found rod-shaped bacterium in blood of Anthrax diseased animals. The spore form caused disease.
Developed microbiology techniques:
- simple staining
- first photomicrograph of bacteria and bacteria in diseased tissue
- technique for estimating CFU/ml (colony forming unit)
- use of steam to sterilize media
- use of Petri dishes
- techniques to transfer bacteria
- bacteria as a district species
84
Lipopolysaccharide (LPS, outer membrane) importance?
(LPS only in gram negative bacteria)
Understanding LPS structure:
- O-antigen (outermost part of cell): body's response to antigen helps identify
- Core sugars: help identify genus or species
- Lipid A: endotoxin released by dying bacteria can cause shock
85
Name microbes types that are prokaryotes
Bacteria and archaea
86
Describe quorum sensing
Bacteria communicating with nearby related and unrelated bacteria.
This communication measures their density within an environment
87
What is colony morphology and what do you need to see it?
Method used to describe physical characteristics of a bacterial colony (visible mass originating from a single mother cell) growing on solid media. This can help identify it.
You must grow it before you can look at it.
Use differential stain
88
Describe gram stains (a differential stain)
Distinguishes between two structural types of bacteria (called gram positive and negative):
1. Crystal violet (purple dye #1) stains all bacteria
2. Iodine (mordant, which binds dye #1 to cell walls)
3. Ethanol (decolorizes thin cell wall bacteria)
4. Safranin (pink dye #2) stains thin cell wall bacteria
Purple = gram positive - (thick walls)
Pink = gram negative - (thin walls)
(Bonus: important that cells less than 24 hours old used due to cell wall breakdown)
89
Group bacteria based on the different types of water pressure.
Obligate halophiles - require higher osmotic pressure, up to 30% salt
Facultative halophiles - indifferent to osmotic pressure (2-15% salt)
Barophiles - live under extreme hydrostatic pressure
90
Features of gram negative bacterial cell walls?
- Pink
- Thin walls
- Has outer membrane layer (lipopolysaccharide (LPS))
- Periplasmic space between cytoplasmic & outer membrane (contains dissolved nutrients, ions, enzymes, transport proteins)
91
Describe movement of bacteria and archaea
Flagella cause movement. The basal body (rings) spins like propeller for movement:
"Run" - spins counter clockwise to move in single direction
"Tumble" - spins clockwise to help change direction
"Taxis" (receptors) help to sense attractant/repellant
- Chemotaxis: movement toward chemicals
- Phototaxis: movement towards light
Powered by:
- Hydrogen proton motive force (bacteria)
- ATP (archaea)
92
Label microscope type using image.
93
What are prions?
Infectious protein particles that lack DNA/RNA that affect animals.
Ex.
- PrP is a cytoplasmic membrane protein anchored in rafts
- Normal cellular PrP structure: helices
- Prion PrP contains pleated-sheets that cause cellular PrP to misfold and turn into prion-PrP
- Misfolding proteins causes holes in tissue
94
How do cavities in teeth form?
Biofilms form on teeth, they absorb sugar as nutrients, and then secrete acid that eats away at tooth enamel
95
What does it mean to be autotrophic?
Organism that produces its own food using light, water, carbon dioxide, or other chemicals.
(Photosynthesis is a type of this)
96
What does viral replication rely on?
Viral replication relies on host cell organelles and enzymes.
97
Taxonomy is?
Science of putting organisms into categories/classifying them
98
Hypertonic solution
-More solute (higher concentration) on outside
-Water will flow outward of cell
99
How is wavelength related to resolving power/resolution?
The smaller the wavelength, the increased in resolving power (AKA higher resolution...the ability to distinguish between close objects)
100
What is a Uniport?
Active transport protein that helps one molecule to cross membrane in one direction
101
Virus characteristics?
- Acellular/non-living
- Host required for survival/reproduction (parasites)
- Genes (DNA/RNA) surrounded by protein coat, not surrounded by membrane
- So small they can only be seen with electron microscope
102
Transferring genetic material from one organism to another (deliberately) is possible by?
Recombinant DNA technology
103
Describe +ssRNA synthesis
Genome replication:
- Viral RNA polymerase transcribes +ssRNA into -ssRNA
- The -ssRNA is used as a template to create more +ssRNA
Protein synthesis:
- Host ribosomes translate proteins directly from the +ssRNA
104
Systematics is?
Study of evolutionary relationships
105
Bacterial flagella arrangements?
Endoflagella AKA axial filament - inside of bacteria (corkscrew movement)
Peritrichous - several all around the bacteria
Polar - single
106
What are Peripheral Proteins?
Proteins that are attached to one side/one half of phospholipid bilayer
107
Mold vs. yeast characteristics?
Mold:
- multicellular
- grows in filaments/hyphae
- spores for reproduction
Yeast:
- unicellular
- reproduce by budding
- pseudohyphae
- used in fermentation
108
What are the shapes of virions?
Helical: tube-like
Polyhedral: soccer-ball like sphere
Complex: all other shapes (T4 bacteriophage is made of both, helical and polyhedral shapes, therefore would be considered complex shape)
109
What are the 3 major types of microscopes?
- Light
- Electron
- Probe
110
Name some reasons viruses are not considered living
- They don't grow in size
- They replicate only inside a host (not independently)
- Most cannot metabolize on their own
- Lack cytoplasm or cell structure
111
How do you inspect and identify when culturing microbes?
Inspect colony morphology (shapes) and identify by:
- Appearance
- Metabolism
- Growth requirements (ex. carbon sources, pH, oxygen needs, etc.)
- Energy requirements
- Genetic makeup and immunological characteristics
112
What concepts are important in microscopy?
Microscopy is the magnification of an object using light or electrons
Concepts:
- Wavelength
- Magnification
- Resolution
- Contrast
113
What does “growth” refer to specifically in microbiology?
Increase in the number of population (reproduce)
114
Manipulation of the genetics of microbes, plants, and animals, for the purpose of creating GMOs
Genetic engineering
115
What are the types of "probe microscopes"?
- Scanning tunneling
- Atomic force
116
Simple stain examples?
- Crystal violet
- Safranin
- Methylene blue
117
What organisms can viruses infect?
Typically humans, animals, plants, or bacteria
(Viruses that infect bacteria are called "bacteriophages" or simply "phages")
118
Describe "budding' in enveloped virus release
During the synthesis stage, viral glycoproteins are inserted into the cell membrane. As the virus is released from the cell, this protein coated membrane surrounds the virus and becomes the envelope.
119
Important electron microscope (EM) facts?
- Better resolving power/magnification for viewing: viruses, internal cell structures, molecules, large atoms
- Specimens are dead, dry, stained with metals
- Transmission Electron Microscope - views inside of specimen
- Scanning Electron Microscope - views outside/surfaces of specimen….(”S” for surface)
- Produces 'digital image'
120
Describe dsRNA synthesis
Genome replication:
- dsRNA is transcribed by viral RNA polymerase similar to DNA replication in eukaryotes
Protein synthesis:
- The positive-strand RNA is used by ribosomes for translation
121
Nucleoid description?
Region where prokaryotic the chromosome exists (not sectioned off/partitioned)
122
What are Archaea cell walls made of?
Pseudomuerin:
- Chains of alternating sugars, NAG and NAT (sugars are then held together by beta 1,3 bonds)
- Peptides connect chains
123
What helps facilitate biofilm attachment to surfaces?
- Extracellular Matrix (ECM)
- Pili and fimbreae
- Other proteins
124
Define: culture, medium, inoculum, inoculation
Culture: growth of microorganisms (both the verb and noun)
Media: nutrients for the growth
Inoculum: small sample of microbes
Inoculation: process of putting inoculum onto media to grow
125
Describe a biofilm
Community of different microbe species living on a surface (typically antibiotic resistant and/or immune resistant).
Biofilm can also hide microbes from immune system.
126
Some reasons to culture viruses?
- Isolate
- Identify
- Prepare vaccines
- Perform research on replication, genetics, effects on hosts
127
What is a physical difference between bacteria and archaea?
Archaea does not contain peptidoglycan in its cell walls
128
What are Pseudopods?
Outstretched arm appendages that allow movement (Protozoa)
129
Features of gram positive bacterial cell walls
- Purple
- Thick walls
- Contain teichoic and lipotechoic acids (needed to hold walls together because they are so thick)
130
Mold and yeast fall into this microbe type
Fungi
131
What is probe microscopy?
Using probes for viewing DNA proteins:
- Scanning tunneling - probe over surface creates topography-like image
- Atomic force - probe touching surface produces 3D image
132
How are most viruses grouped?
Most are grouped in families (family -> genus -> species)
133
What the types of "electron microscopes"?
- Transmission
- Scanning
134
What are mycoplasma?
Bacteria without cell walls that are sensitive to osmotic pressure (can burst)
135
Hypotonic solution
-Less solute (lower concentration) on outside
-Water flows inward to cell
136
Are most microbes harmful?
No, most do not cause harm to humans
137
Fluid Mosaic Model explanation?
Model describes the structure of plasma membrane:
Fluid portion:
- Phospholipids aren't attached to one another, they can rotate freely (fluid)
Mosaic portion:
- Contains proteins (integral proteins, peripheral proteins, and sterols/hopanoids)
138
Differential stain examples?
- Gram stain
- Acid-fast stain
- Endospore stain
139
Name some things MOST bacteria have
- Cell wall
- Glycocalyx
140
Plasmid description?
Nonessential small circular pieces of DNA (which can be toxins, drug-resistant genes)
141
Importance of solute concentration for cells (without cell walls)
Mycoplasma don't have cell walls (only have plasma membrane (more stress to osmotic pressure)
-If cell is placed in hypotonic solution, water flow inward could cause cell to burst/be lysed
(Note: animal cells, protozoa, and helminths do not have cell walls either)
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Describe the development of biofilm.
- Free swimming bacteria are vulnerable to environmental stress
- Some land on surface and attach
- Cells build extracellular matrix and secrete quorum molecules
- Quorum sensing triggers cells to change biochemistry
- Other cells may arrive and form biofilm water channels
- Some microbes leave to another surface or become free swimming again
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Shapes of bacteria?
- Coccus (circle)
- Bacillus (rod)
- Spirillus (spiral, caused by endoflagella/axial filaments)
- Vibrio (curved rod like a comma)
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What is resolution dependent on?
Wavelength (lower is better) and numerical aperture (lower is better) of the lens (light-gathering ability, more light is better)
145
What is the wavelength range of visible light?
400nm-700nm
146
Compare and contrast animal viruses vs. bacteriophages
Both:
- Attachment dependent on chemical attraction and exact fitment between viral molecules and host cell's surface
- Same 5 basic steps (attachment, entry, synthesis, assembly, release)
Bacteriophage:
- Typically contain tails and tail fibers
- Needs lysozyme for breaking down peptidoglycan
- Genome is "injected" through cell wall during entry
- Genome replication and protein synthesis always occurs in cytosol (think "prokaryotic" replication)
- No envelopes
Animal viruses:
- Lack tail or tail fibers
- Glycoprotein "spikes" on capsids or envelopes
- Don't require lysozyme because of no cell wall presence
- Entry methods differ (direct penetration, membrane fusion, endocytosis)
- May require "uncoating"
- Genome replication can occur in different locations (DNA - nucleus vs. RNA - cytoplasm)
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Feature of mycobacterium?
- Contains mycolic acid (waxy substance) in cell walls
- Acid-fast stain technique
- Usually looks purple
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Describe acid-fast stains (a differential stain)
Identifies mycobacteria with waxy cell walls (mycolic acid, hard to stain).
1. Carbolfushin (pink dye #1) stains all bacteria
2. Acid alcohol (decolorizes non-waxy bacteria)
3. Methylene blue (#2 dye) stains non-waxy bacteria
Pink = waxy
Blue = non-waxy
(Bonus: mycobacteria cause many human diseases)
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The 5 “I’s” of microbiology are?
Inoculation - adding bacteria to media in order to grow them
Incubation - allowing the time and conditions to reproduce
Isolation - narrowing down a single bacteria/colony
Inspection - looking at appearance to characterize and analyze
Identification - determine type, genetics, requirements, or traits to figure out species
150
Describe some other "light microscopes" (besides Bright-field)
Dark-Field:
- Observes pale objects
- Dark background, light specimen
- No condenser lens (scatters light to create darker background)
Phase:
- Examines living organisms
- In / out of phase light produces contrast in image
Florescent:
- Fluorescent dyes "glow in the dark" under UV light
- Can be used for labelling specific things
Confocal:
- Useful for biofilm study
- Also fluorescent dyes, but use UV lasers instead
151
Fungi uses:
- Essential in decomposing organic matter
- Can help plant roots absorb water and nutrients
- Engineered for antibiotics, alcohol, vitamins
- Eaten by humans
152
What are the two types of viral replication in bacteria?
Lytic Replication Cycle - virus infects host cell, lysis it (burst open to release), and then host dies
Lysogenic Replication - viral genome from bacteriophage (called "prophage") is inserted into host's genome and remains dormant. When the host cell replicates, the prophage does as well (due to it being a part of the host's genome). An event finally triggers the virus to reproduce resulting in lysing and killing the host
153
Cytoskeleton importance?
Important for cell division, cell shape, structure, swimming
154
What are inclusions?
Function: Potential storage areas
Composed of: deposits of chemicals that can be surrounded by protein membrane
Why? Prokaryotes don't have organelles to store
155
What are Coupled Transports?
Two active transport proteins working together to help molecules cross membrane.
(variety of different combinations)
-ex: Three molecules, two directions
156
How are DNA viruses synthesized in animals?
DNA viruses use process very similar to normal dsDNA replication:
- Host cell DNA polymerase replicates the viral dsDNA
- Host cell RNA polymerase transcribes DNA to create mRNA for translation of proteins
(Since normal DNA is double-stranded, ssDNA folds back on itself pretending to be dsDNA for replication and then released as ssDNA)
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Unique Eukaryotic cytoplasmic membrane characteristics?
Function mostly same as prokaryotes except:
Contains steroids like cholesterol
Additional active transports:
- Endocytosis: cell eating/drinking using pseudopods
- Exocytosis: membrane fusion for export of substances
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What is Group Translocation?
Active transport (only in bacteria)
When transported, molecule is chemically modified and stays inside of cell
-ex: glucose being phosphorylated as brought into cell
Assists unicellular organisms living in nutrient-diverse environments
-Nutrient limitations force bacteria to get as many nutrients possible and hoard it
(Often used to transport sugars used for energy)
159
Name some structures that ALL bacteria have
- Cytoplasmic membrane
- Cytoplasm
- Ribosomes
- Chromosome
160
A method for obtaining a pure culture (culture composed of a single bacteria) from a patient?
T-streaking
161
Example of solid vs. liquid media? Uses?
- Solid (ex. Agar for viewing on a plate but not as fast as broth)
- Liquid (ex. broth for growing organisms very quickly but not good for colony morphology)
162
How can we classify bacteria based on optimum growth temperature?
Psychrophiles - low temp, below 20C
Mesophiles - medium temp, 20-40C (most pathogens)
Thermophiles - high temp, above 45C
Hyperthermophiles - extremely high, above 80C
163
Bacterial cell wall composition
- Peptidoglycan chains:
(2 alternating sugars - NAG and NAM)
(sugars linked by beta 1,4 bonds)
- Chains linked by tetrapeptides
164
What is the goal of bacteria? (Like most organisms)
To survive, grow/reproduce
165
Describe endospore stains (a differential stain)
Used to distinguish between endospore and vegetative bacteria.
1. Boil in Malachite (green dye #1) stains endospores
2. Water (decolorizes vegetative)
3. Safranin (pink dye #2) stains vegetative
Green = endospores
Pink = vegetative
(Bonus: endospores can survive extremely harsh conditions and resist stains)
166
What are Flagella?
Tail or whip like structure used for movement
Prokayotes: made of flagellin
Eukaryotes: made of tubulin
167
Name things inside prokaryotic cytoplasm
- Cytosol (liquid portion)
- Circular DNA
- Dissolved ions, carbs, proteins, lipids, waste
- 70-80% water
Also contains:
- Plasmids (circular DNA pieces)
- Inclusions (stored substances surrounded by protein)
- 70S Ribosomes (protein synthesis)
- Cytoskeleton (shape/structure)
- Nucleoid region (DNA location)
168
Describe bacterial endospores characteristics
- Unique structures produced by vegetative (metabolically active) bacteria.
- Bacterial endospores are not metabolically active to be protected against unfavorable conditions (lack of nutrients or extreme physical).
- Once conditions become favorable, the spores will germinate and become active again
- Spores can release deadly toxins that cause fatal diseases like anthrax, tetanus, and gangrene
(Bonus: DNA is protected/preserved by dipicolinic acid and calcium ions)
169
Where are helminths found?
- Helminth sources include: contaminated food, soil, water, or infected animals.
- Infection by oral intake or penetration of tissues
170
This microbe grows in extreme conditions
Archaea
171
What is Bioremediation?
Using living microbes to detoxify polluted environments
172
Fungi morphology?
- Some yeasts look similar to bacteria
- Some yeasts grow in loosely attached filaments
- Some fungi form "hyphae" (long threads) woven together to form "mycelium"
- Fungi can be "dimorphic" (different morphology based on growth conditions)
173
Describe glycocalyx function
Gelatinous outermost layer of cell (usually)
Functions:
- Protect cell from drying out (desiccation)
- Adherence to surfaces or other cells
- Strengthens cell
- Composition (polysaccharides or glycoproteins)
Bacteria and Archaeal note:
- Can hide them from immune system because humans have similar composition
174
What is the function of "reverse transcriptase"?
This enzyme transcribes ssRNA into DNA
175
How were antibiotics discovered?
Fleming accidentally discovered bacteria processing Penicillium mold in small amounts.
Raper found one that produced it in much larger amounts.
176
How were early antibiotics produced?
- Cultured bacteria from soil
- Looked for antibiotic production
- Isolated chemicals
- Tested efficacy and safety
177
Bright-field microscope details?
- Light microscope
- Simple (1 lens) or compound (more than 1 lens)
- Light background, dark specimen
- Total magnification = objective lens x ocular lens magnification levels (i.e. 4 x 10 = 40x)
- Most have condenser lens to focus light through specimen
178
Steps to prepare sample for staining?
Coloring specimen with dye:
- add thin film of microbe to slide (AKA a "smear")
- "fix" (attach) to the slide with heat, air, or chemicals
179
Biofilm Extracellular Matrix composition?
Usually starts with glycocalyx and other bacteria provide more polysaccharides, proteins, and amino acids
180
What type of microscope will we be using in lab?
Compound light microscope
181
Two types of classifying bacteria based on structure?
Bergey's Manuals of:
1.) Systematic Bacteriology - rRNA sequencing
2.) Determinative Bacteriology - based on phenotype
182
What allows "archaeal" attachment or adhering?
- Fimbriae: much shorter than flagella, attachment and twitching
- Hami: hook structures on some fimbriae used for attaching to surfaces (only Archaea)
183
What are the three major domains?
Archaea, Bacteria, Eukarya
184
Why are archaea shaped differently than bacteria?
Due to lack of peptidoglycan in cell wall, the shapes can be bacillus (rod) but are also amorphous (without a clearly defined shape)
185
Explain the 3 animal cell "entry" methods
1.) Direct penetration: (only naked viruses) capsid binds to host cell membrane, sinks in to create a pore, which the genome enters through. Empty structure is left behind on surface
2.) Membrane fusion: viral envelope and cell membrane attach and fuse, releases capsid into cell cytoplasm, uncoats and releases genome. Viral envelope's glycoproteins remain as part of host membrane
3.) Endocytosis: after attachment, viral glycoproteins trigger host cell to engulf the entire virus. Membranes/envelope then removed and uncoating of capsid releases genome
186
Types of media?
- Defined (know exact composition…may include growth factors for fastidious organisms)
- Complex (do not know exact composition, supports variety of microbes…nutrient agar or broth)
- Selective (only favors growth of some microbes, not all)
- Differential (results in visual changes to determine different microbes)
- Anaerobic (contains chemicals to remove free oxygen)
- Transport (used to ensure samples aren’t contaminated/no one else gets infected)
187
Isotonic solution
-Same concentration of solute inside and outside
-No net flow of water
188
What are the challenges of culturing viruses?
They require a live host to replicate, so you are always co-culturing viruses and their hosts
- In-vivo uses the whole animal host
- In-vitro in just the cells/tissues
189
Describe germ theory of disease
Microorganisms are responsible for disease
190
Name some characteristics of viruses
- Acellular/non-living infectious agents containing genetic material (DNA or RNA)
- Replication method depends on type of host (bacteria, animal, etc.)
- Lack cytoplasmic membrane
- Do not grow, respond to environment, or independently carry out metabolism
- Cannot reproduce independently
191
Are all viruses considered human pathogens?
No, bacteriophages are examples that do not cause harm to humans
192
What helps movement of bacteria and archaea?
Is the structure the same for both?
Flagella responsible for movement and the structure differs slightly:
- Bacterial flagella: hollow and grows at tip (powered by Hydrogen proton gradient)
- Archaea flagella: thinner, not hollow, grows from base (powered by ATP)
Parts of flagella:
1.) Filament: tail like structure
2.) Hook: connects to basal body and provides stability
3.) Basal body: rings that anchor in cell wall/membrane and spins like propeller
193
Classify bacteria by pH levels
Neutrophiles - grow in neutral conditions
Acidophiles - lower pH
Alkalinophiles - higher pH
- Bacteria 6.5-7.5 pH
- Yeasts 5-6 pH
194
Describe the structure of virions
Nucleic acid: DNA or RNA, double or single stranded
Capsid: protein coat that surrounds the nucleic acid
Envelope (some viruses): phospholipid membrane (for protection and recognition site for host cells)
(Viral genomes are very small and usually only contain just enough information for replication and nothing else.)
195
Some reasons why there a crisis in treatment of infectious disease? (Related to antibiotics)
- Bacterial resistance (from mutations) to antibiotics
- Antibiotics provide “selection pressure”
- Overuse/misuse of antibiotics
- Few new antibiotics being discovered due to cost
196
Types of glycocalyx
Capsule
- firmly attached to cell surface
- often required for pathogenicity (removal can prevent pathogenicity)
- prevents phagocytosis
Slime layer
- loose and water-soluble
- associated with biofilms
197
What allows "bacterial" attachment or adhering?
- Fimbriae: much shorter than flagella, attachment and twitching
- Pili (only 1-2 per cell): only found in Bacteria...special type of fimbriae for DNA exchange or twitching
198
What magnification do you need to see bacteria?
1,000x (using oil immersion lens which allows more light to enter objective lens)
199
Fungal diseases?
300 fungi species can cause human disease
3 types of fungal disease:
- Community: envionmental pathogens
- Hospital associated infjections: fungal infections
- Opportunistic infections: infections in weakened individuals
Fungal cell walls can cause allergies, and mushrooms can produc toxins
200
What makes Van Leeuwenhoek important to microbiology?
- Invented simple light microscope
- First to visualize microorganisms (he called them "animalcules")
201
What is it meant by incubation period? Why might this be important to a physician?
It is the period of time from initial point of infection until you see symptoms.
Knowing this may help narrow down which organism(s) are causing an illness.
202
What are serotypes?
Classifications within a single species, which are characterized by unique surface structures which cause different antibody responses.
- ex. different O-antigens that triggers different antibody responses
203
Nomenclature is?
Assigning scientific names in taxonomy
