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Final Flashcards

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Biology 101 flashcards
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
Q

Periplasm:

A

space located between cytoplasmic and outer membranes
~15 nm wide
Contents have gel-like consistency
Houses many proteins

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26
Q

Pseudomurein

A

Polysaccharide similar to peptidoglycan
Composed of N-acetylglucosamine and N-acetyltalosaminuronic acid
Found in cell walls of certain methanogenic Archaea

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27
Q

S-Layers

A 
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.
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28
Q

Capsules

A

Tight matrix excludes India ink

Adhere firmly to the cell wall

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29
Q

Slime Layers

A

Looser matrix does not exclude India ink

Loosely attached to cell wall

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30
Q

Biofilm

A

Thick layer of cells (“multicellular”)

Exopolysacharies play key role in biofilm development

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31
Q

Fimbriae

A 
Filamentous protein structures
Enable organisms to:
Stick to surfaces
Form pellicles
Form biofilms
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32
Q

Pili

A

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

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33
Q

Endospores

A

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

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34
Q

Flagellum (pl. flagella):

A

structure that assists in swimming
Different arrangements: peritrichous, polar, lophotrichous, amphitrichous (two poles)
Helical in shape

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35
Q

Bacterial Flagellar Structure

A 
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
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36
Q

Archaeal Flagella

A 
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
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37
Q

Eukaryote Flagella

A

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

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38
Q

Taxis:

A

directed movement in response to chemical or physical gradients

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39
Q

Phototaxis:

A

response to light

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40
Q

Aerotaxis:

A

response to oxygen

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41
Q

Osmotaxis:

A

response to ionic strength

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42
Q

Hydrotaxis:

A

response to water

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43
Q

Magnetotaxis:

A

response to Earth’s magnetic field

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44
Q

Chemoorganotrophs

A

Obtain their energy from the oxidation of organic molecules

45
Q

Chemolithotrophs

A

Obtain their energy from the oxidation of inorganic molecules
Process not found in Eukaryotes

46
Q

Aerobes

A

use oxygen to obtain energy

47
Q

Anaerobes

A

obtain energy in the absence of oxygen

48
Q

Phototrophs

A

Contain pigments that allow them to use light as an energy source
Oxygenic photosynthesis produces oxygen
Anoxygenic photosynthesis does not produce oxygen

49
Q

Autotrophs

A

Use carbon dioxide as their carbon source

Sometimes referred to as primary producers or carbon fixers

50
Q

Heterotrophs

A

Require one or more organic molecules for their carbon source
Feed directly on autotrophs or live off products produced by autotrophs

51
Q

Catabolic reactions (catabolism)

A

Energy-releasing metabolic reactions

52
Q

Anabolic reactions (anabolism)

A

Energy-requiring metabolic reactions

53
Q

Defined media:

A

precise chemical composition is known

54
Q

Complex media:

A

composed of digests of chemically undefined substances (e.g., yeast and meat extracts)

55
Q

Selective Media

A

Contains compounds that selectively inhibit growth of some microbes but not others
IF it grows or not

56
Q

Differential Media

A

Contains an indicator, usually a dye, that detects particular chemical reactions occurring during growth
HOW it grows in comparison

57
Q

Free energy (G):

A

energy released that is available to do work

58
Q

Exergonic

A

Negative G0′

Release free energy

59
Q

Endergonic

A

Positive G0′

Require energy

60
Q

Oxidation:

A

the removal of electron(s)

61
Q

Reduction:

A

that addition of electron(s)

62
Q

Electron donor:

A

is oxidized in a redox reaction

63
Q

Electron acceptor:

A

is reduced in a redox reaction

64
Q

Delta E

A

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
Q

NADH dehydrogenases:

A

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
Q

Complex I

A

NADH is oxidized and e- added to quinone pool ( is reduced)

67
Q

Complex II

A

Bypasses complex I and feeds e- and H+ from FADH to quinone pool

68
Q

Complex III

A

e- passed from quinone pool to cytochrome b-c1 complex

e- passed to cytochrome c – an e- shuttle

69
Q

Complex IV

A

e- passed to cytochromes a and a3

Terminal oxidase – adds e- to terminal electron acceptor (i.e. O2)

70
Q

proton motive force

A

The inside becomes electrically negative and alkaline
The outside becomes electrically positive and acidic

71
Q

Respiration

A

ATP produced from proton motive force formed by transport of electrons

72
Q

Aerobic Respiration

A

O2 is the terminal electron acceptor

73
Q

Anaerobic Respiration

A

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
Q

Fermentation:

A

Substrate-level phosphorylation

ATP directly synthesized from an energy-rich intermediate

75
Q

Glycolysis:

A

catabolism of glucose

76
Q

Chemolithotrophy

A

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
Q

Phototrophy

A

uses light as energy source

78
Q

Photophosphorylation:

A

light-mediated ATP synthesis

79
Q

Photoautotrophs

A

use ATP for assimilation of CO2 for biosynthesis

80
Q

Photoheterotrophs

A

use ATP for assimilation of organic carbon for biosynthesis

81
Q

Divisome:

A

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
Q

Doubling time

A

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
Q

Growth rate

A

is calculated as

v = 1/dt

84
Q

Psychrophile

A

low temperature

85
Q

Mesophile:

A

midrange temperature

86
Q

Thermophile

A

high temperature

87
Q

Hyperthermophile

A

very high temperature

88
Q

Water activity (aw):

A

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
Q

Xerophiles:

A

organisms able to grow in very dry environments

90
Q

Osmophiles:

A

organisms that live in environments high in sugar as solute

91
Q

Aerobes:

A

require oxygen to live

92
Q

Anaerobes:

A

do not require oxygen and may even be killed by exposure

93
Q

Facultative organisms:

A

can live with or without oxygen

94
Q

Aerotolerant anaerobes:

A

can tolerate oxygen and grow in its presence even though they cannot use it

95
Q

Microaerophiles:

A

can use oxygen only when it is present at levels reduced from that in air

96
Q

Chemolithoautotophs

A

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
Q

Virion:

A

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
Q

Capsid

A

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
Q

Capsomere:

A

subunit of the capsid

Smallest morphological unit visible with an electron microscope

100
Q

Lysozyme

A

Makes hole in cell wall

Lyses bacterial cell

101
Q

Neuraminidases

A

Enzymes that cleave glycosidic bonds

Allows liberation of viruses from cell

102
Q

Titer

A

number of infectious units per volume of fluid

103
Q

Plaque assay

A

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
Q

Phases of Viral Replication

A

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
Q

Restriction enzymes

A

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
Q

Lysogeny

A

state where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome

107
Q

Temperate viruses:

A

can undergo a stable genetic relationship within the host

But can also kill cells through lytic cycle

108
Q

Lysogen:

A

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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