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Final Flashcards

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1
Q

Transcription:

A

DNA produces RNA

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2
Q

Translation:

A

RNA makes protein

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3
Q

Characteristics of Living Systems

A

Metabolism: chemical transformation of nutrients
Reproduction: generation of two cells from one
Differentiation: synthesis of new substances or structures that modify the cell (only in some microbes)
Communication: generation of, and response to, chemical signals (only in some microbes)
Movement: via self-propulsion, many forms in microbes
Evolution: genetic changes in cells that are transferred to offspring

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4
Q

Most microbial cells are found in

A

oceanic and terrestrial subsurfaces

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5
Q

The role of microbes in cleaning up pollutants

A

Bioremediation

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6
Q

Louis Pasteur

A

Discovered that living organisms discriminate between optical isomers
Discovered that alcoholic fermentation was a biologically mediated process (not abiotic chemistry)
Developed the Germ Theory that proposed and showed that germs cause disease
Developed vaccines for anthrax, fowl cholera, rabies
Disproved theory of spontaneous generation
Led to the development of methods for controlling the growth of microorganisms (aseptic technique)

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7
Q

Koch

A

Demonstrated the link between microbes and infectious diseases
Koch’s postulates
Identified causative agents of anthrax and tuberculosis

Developed techniques (solid media) for obtaining pure cultures of microbes, some still in existence today

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8
Q

Bright-field scope

A

Specimens are visualized because of differences in contrast (density) between specimen and surroundings
Two sets of lenses form the image
Objective lens and ocular lens
Total magnification = objective magnification  ocular magnification

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9
Q

Phase-Contrast Microscopy

A

Phase ring amplifies differences in the refractive index of cell and surroundings
Improves the contrast of a sample without the use of a stain
Allows for the visualization of live samples
Resulting image is dark cells on a light background

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10
Q

Dark-Field Microscopy

A

Light reaches the specimen from the sides
Light reaching the lens has been scattered by specimen
Image appears light on a dark background
Excellent for observing motility

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11
Q

Fluorescence Microscopy

A

Used to visualize specimens that fluoresce
Emit light of one color when illuminated with another color of light
Some cells fluoresce naturally (autofluorescence)
Fluorescent dyes are used
Example: DAPI
Widely used in microbial ecology for enumerating bacteria in natural samples

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12
Q

What is used for phylogeny?

A

Ribosomal RNA (rRNA)

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13
Q

What are the organelles of the endosymbiotic theory?

A 
Chloroplasts
Evolved from phagocytosed
photosynthetic Bacteria
Mitochondria
Evolved from phagocytosed oxygen utilizing Bacteria
Nucleus
Evolved from phagocytosed Archaea
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14
Q

All cells have the following in common

A 
Cytoplasmic membrane
Cytoplasm
Ribosomes
rRNA valuable comparison
Genetic material
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15
Q

Nucleoid

A

Non membrane enclosed, but condensed region of genetic material
Bacteria, Archaea, and organelles

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16
Q

Plasmid

A

Extra chromosomal DNA

All domains, mainly Bacteria and Archaea

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17
Q

Histones

A

Eukaryotes and Archaea
Proteins associated with DNA to compact it
DNA wraps around histones
One human cell’s DNA is 6 feet long, wouldn’t fit without histone coiling

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18
Q

Size of Bacteria and Archaea

A 
Range: 0.2 µm to > 700 µm
Most:  0.5 and 4.0 µm wide and <15 µm long
Average: rod 1 x 2 µm
Smallest: M. pneumoniae  0.2 µm
Largest: T. namibiensis 750 µm
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19
Q

Size of Eukaryotes

A

Range: 10 to >200 µm in diameter

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20
Q

Bacterial vs. Archaeal Membranes

A

Bacteria and Eukarya:
Ester linkages in phospholipids, only
Fatty acids, only
Straight carbon chain, only
Bilayer, only
Archaea:
Ether linkages in phospholipids
Lack fatty acids, have repeating isoprenes instead
Major lipids: glycerol diethers (20C) and teraethers (40C)
Side chains and/or rings (ex: cyclohexyl)
Can exist as lipid monolayers, bilayers, or mixture

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21
Q

At least 3 major classes of transport systems

A 
Simple transport
Single protein
Group translocation
Series of proteins
ABC system
3 components
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22
Q

Three transport events are possible:

A

Uniporters transport in one direction across the membrane
Symporters function as co-transporters
Antiporters transport a molecule across the membrane while simultaneously transporting another molecule in the opposite direction

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23
Q

Lipoteichoic acids

A

teichoic acids covalently bound to membrane lipids

on the outisde of gram positive cell walls

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24
Q

channels for movement of hydrophilic low-molecular weight substances

A

Porins

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25
Periplasm:
space located between cytoplasmic and outer membranes ~15 nm wide Contents have gel-like consistency Houses many proteins
26
Pseudomurein
Polysaccharide similar to peptidoglycan Composed of N-acetylglucosamine and N-acetyltalosaminuronic acid Found in cell walls of certain methanogenic Archaea
27
S-Layers
``` Most common cell wall type among Archaea Consist of protein or glycoprotein Paracrystalline structure Interlocking molecules with ordered appearance Variety of symmetries Hexagonal, tetragonal, trimeric, etc. ```
28
Capsules
Tight matrix excludes India ink | Adhere firmly to the cell wall
29
Slime Layers
Looser matrix does not exclude India ink | Loosely attached to cell wall
30
Biofilm
Thick layer of cells (“multicellular”) | Exopolysacharies play key role in biofilm development
31
Fimbriae
``` Filamentous protein structures Enable organisms to: Stick to surfaces Form pellicles Form biofilms ```
32
Pili
Filamentous protein structures Typically longer than fimbriae Less pili per cell than fimbriae Assist in surface attachment Facilitate genetic exchange during conjugation Type IV pili involved in twitching motility (gliding) Can be conductive of electricity
33
Endospores
Highly differentiated cells resistant to heat, harsh chemicals, and radiation “Dormant” stage of bacterial life cycle Ideal for dispersal via wind, water, or animal gut Only present in some gram-positive bacteria
34
Flagellum (pl. flagella):
structure that assists in swimming Different arrangements: peritrichous, polar, lophotrichous, amphitrichous (two poles) Helical in shape
35
Bacterial Flagellar Structure
``` Consists of several components Filament composed of single type of flagellin Move by rotation – rotary motor Energy required for rotation comes from proton motive force ~1000 protons translocated per rotation Gram negative: L ring, P ring, MS ring, C ring Gram positive: P ring, MS ring, C ring ```
36
Archaeal Flagella
``` Smaller diameter than Bacteria 10-13 nm vs 15-20 nm Lack central channel Great diversity of flagellin proteins Amino acid sequence of flagellin proteins show no phylogentic relationship to Bacterial More similar to type IV pili Powered by ATP instead of protons Flagellin added at base during synthesis ```
37
Eukaryote Flagella
A bundle of nine fused pairs of microtubule doublets surrounding two central single microtubules: “9+2” Axoneme Basal body base (kinetosome) is the microtuble organizing center Flagellum encased within cell’s plasma membrane Powered by ATP
38
Taxis:
directed movement in response to chemical or physical gradients
39
Phototaxis:
response to light
40
Aerotaxis:
response to oxygen
41
Osmotaxis:
response to ionic strength
42
Hydrotaxis:
response to water
43
Magnetotaxis:
response to Earth’s magnetic field
44
Chemoorganotrophs
Obtain their energy from the oxidation of organic molecules
45
Chemolithotrophs
Obtain their energy from the oxidation of inorganic molecules Process not found in Eukaryotes
46
Aerobes
use oxygen to obtain energy
47
Anaerobes
obtain energy in the absence of oxygen
48
Phototrophs
Contain pigments that allow them to use light as an energy source Oxygenic photosynthesis produces oxygen Anoxygenic photosynthesis does not produce oxygen
49
Autotrophs
Use carbon dioxide as their carbon source | Sometimes referred to as primary producers or carbon fixers
50
Heterotrophs
Require one or more organic molecules for their carbon source Feed directly on autotrophs or live off products produced by autotrophs
51
Catabolic reactions (catabolism)
Energy-releasing metabolic reactions
52
Anabolic reactions (anabolism)
Energy-requiring metabolic reactions
53
Defined media:
precise chemical composition is known
54
Complex media:
composed of digests of chemically undefined substances (e.g., yeast and meat extracts)
55
Selective Media
Contains compounds that selectively inhibit growth of some microbes but not others IF it grows or not
56
Differential Media
Contains an indicator, usually a dye, that detects particular chemical reactions occurring during growth HOW it grows in comparison
57
Free energy (G):
energy released that is available to do work
58
Exergonic
Negative G0′ | Release free energy
59
Endergonic
Positive G0′ | Require energy
60
Oxidation:
the removal of electron(s)
61
Reduction:
that addition of electron(s)
62
Electron donor:
is oxidized in a redox reaction
63
Electron acceptor:
is reduced in a redox reaction
64
Delta E
Energy released Difference is reduction potential between donor and acceptor redox couple The further electrons “drop” from a donor before they are “caught” by an acceptor the greater the amount of energy Proportional to ΔG0’
65
NADH dehydrogenases:
Proteins bound to inside surface of cytoplasmic membrane Active site binds NADH and accepts 2 electrons and 2 protons that are both passed to flavoproteins e- AND H+
66
Complex I
NADH is oxidized and e- added to quinone pool ( is reduced)
67
Complex II
Bypasses complex I and feeds e- and H+ from FADH to quinone pool
68
Complex III
e- passed from quinone pool to cytochrome b-c1 complex | e- passed to cytochrome c – an e- shuttle
69
Complex IV
e- passed to cytochromes a and a3 | Terminal oxidase – adds e- to terminal electron acceptor (i.e. O2)
70
proton motive force
The inside becomes electrically negative and alkaline The outside becomes electrically positive and acidic
71
Respiration
ATP produced from proton motive force formed by transport of electrons
72
Aerobic Respiration
O2 is the terminal electron acceptor
73
Anaerobic Respiration
Alternative element as the terminal electron acceptor NO3-, NO2-, Fe3+, SO42-, CO32- Redox tower Respiration generally higher ATP yield than fermentations ATP produced at the expense of the proton motive force, which is generated by electron transport
74
Fermentation:
Substrate-level phosphorylation | ATP directly synthesized from an energy-rich intermediate
75
Glycolysis:
catabolism of glucose
76
Chemolithotrophy
Uses inorganic chemicals as electron donors Examples include hydrogen sulfide (H2S), hydrogen gas (H2), ferrous iron (Fe2+), ammonia (NH3) Typically aerobic Begins with oxidation of inorganic electron donor Uses electron transport chain and proton motive force Autotrophic; uses CO2 as carbon source
77
Phototrophy
uses light as energy source
78
Photophosphorylation:
light-mediated ATP synthesis
79
Photoautotrophs
use ATP for assimilation of CO2 for biosynthesis
80
Photoheterotrophs
use ATP for assimilation of organic carbon for biosynthesis
81
Divisome:
cell division apparatus FtsZ: forms ring around center of cel Fts (filamentous temperature-sensitive) proteins Essential for cell division in ZipA: anchor that connects FtsZ ring to cytoplasmic membrane FtsA: helps connect FtsZ ring to membrane and also recruits other divisome proteins
82
Doubling time
of the exponentially growing population is dt = t/n t is the duration of exponential growth n is the number of generations during the period of exponential growth
83
Growth rate
is calculated as | v = 1/dt
84
Psychrophile
low temperature
85
Mesophile:
midrange temperature
86
Thermophile
high temperature
87
Hyperthermophile
very high temperature
88
Water activity (aw):
water availability; expressed in physical terms Defined as ratio of vapor pressure of air in equilibrium with a substance or solution to the vapor pressure of pure water
89
Xerophiles:
organisms able to grow in very dry environments
90
Osmophiles:
organisms that live in environments high in sugar as solute
91
Aerobes:
require oxygen to live
92
Anaerobes:
do not require oxygen and may even be killed by exposure
93
Facultative organisms:
can live with or without oxygen
94
Aerotolerant anaerobes:
can tolerate oxygen and grow in its presence even though they cannot use it
95
Microaerophiles:
can use oxygen only when it is present at levels reduced from that in air
96
Chemolithoautotophs
As early Earth was anoxic, energy-generating metabolism of primitive cells was exclusively anaerobic and likely chemolithotrophic Obtained carbon from CO2 Obtained energy from H2 (probably) H2 available at deep sea hydrothermal vents H2 is energetic (very positive Eh) H2 promotes high energy redox reactions of anaerobic respiration
97
Virion:
Virus particle Extracellular form of a virus Exists outside host and facilitates transmission from one host cell to another Contains: Nucleic acid genome Surrounding by a protein coat Other surrounding layers (only in some virions)
98
Capsid
the protein shell that surrounds the genome of a virus particle Composed of a number of protein molecules arranged in a precise and highly repetitive pattern around the nucleic acid
99
Capsomere:
subunit of the capsid | Smallest morphological unit visible with an electron microscope
100
Lysozyme
Makes hole in cell wall | Lyses bacterial cell
101
Neuraminidases
Enzymes that cleave glycosidic bonds | Allows liberation of viruses from cell
102
Titer
number of infectious units per volume of fluid
103
Plaque assay
one way to quantify virus infectivity Plaques are clear zones that develop on lawns of host cells Lawn can be bacterial or tissue culture
104
Phases of Viral Replication
Attachment (adsorption) of the virus to a susceptible host cell Entry (penetration) of the virion or its nucleic acid Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus Assembly of capsids and packaging of viral genomes into new virions (maturation) Release of mature virions from host cell
105
Restriction enzymes
Aka restriction endonucleases Cleave DNA at specific sequences Degrades all foreign nucleic acid Have to distinguish self vs non-self Modification of host’s DNA prevents cleavage of own DNA Addition of methyl groups at restriction enzyme recognition sites
106
Lysogeny
state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome
107
Temperate viruses:
can undergo a stable genetic relationship within the host | But can also kill cells through lytic cycle
108
Lysogen:
a bacterium containing a prophage Under certain conditions lysogenic viruses may revert to the lytic pathway and begin to produce and release virions Regulation of lytic vs. lysogenic events in lambda is controlled by a complex genetic switch Regulation of gene expression

Microbiology final (2 decks)

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