Midterm #1 Flashcards
(157 cards)
1
Q
What are the 3 domains of life?
A
Bacteria
Archaea
Eukarya
2
Q
How did diversity of life arise?
A
Evolution
3
Q
What is LUCA?
A
Last Universal Common Ancestor
4
Q
How do we know when O2 appeared in our biosphere?
A
Oxygen interacting with iron which precipitates into sediments
5
Q
Robert Hooke
A
1665- first book devoted to microscopic observations
6
Q
Antoin Van Leeuwenhoek
A
1676- first to see bacteria
7
Q
Ferdinand Cohn
A
~1850’s - first to see bacterial endospores
8
Q
Louis Pasteur
A
1864- disproved spontaneous generation theory
9
Q
Robert Koch
A
germ theory of infectious disease
10
Q
Light microscopy
A
compound light microscope uses light to illuminate cells
- many different kinds
11
Q
What are the two sets of lenses that form an image?
A
objective and ocular
12
Q
Phase-Contrast Microscopy
A
- invented by Fritz Zernike in 1936
- phase ring amplifies difference in refractive index of cell and surroundings
- improves contrast
- allows visuals of live samples
13
Q
Dark-Field Microscopy
A
- light reaches the specimen from the sides
- image appears light on a dark background
14
Q
Fluorescence Microscopy
A
-used to visualize specimens that fluoresce (emit light) whether they do so naturally or with a stain
15
Q
Differential Interference Contrast (DIC) Microscopy
A
- uses polarizer to make two distinct beams of polarized light
- gives structures a 3-D appearance
16
Q
Atomic Force Microscopy (AFM)
A
a stylus helps to generate an image by measuring weak repulsive forces b/w stylus and specimen
17
Q
Confocal Scanning Laser Microscopy (CSLM)
A
uses computerized fluorescence microscope coupled with a laser source to generate 3-D image
18
Q
Transmission electron microscopes
A
electromagnets function as lenses
19
Q
Electron microscopes
A
uses electrons instead of photons to image cells and structures
20
Q
Scanning electron microscopes
A
scattered electrons are collected by a detector and an image is producedx
21
Q
Which two microbials do not live next to each other?
A
cyanobacteria and clostridium
22
Q
Why is seeing images of microbial cells important?
A
to be able to look at structure-function relationship since seeing is believing
23
Q
What are the major cell morphologies?
A
coccus (spherical)
rod (cylindrical)
spirillum (spiral)
24
Q
What cells have unusual shapes?
A
spiroschetes
appendaged bacteria
filamentous bacteria
25
What does morphology not predict?
physiology, ecology, phylogeny of prokaryotic cells
26
Advantages of small cells?
- more surface area
- support greater nutrient exchange
- grow faster
27
Cytoplasmic membrane
thin structure that surrounds the cell and a barrier that separates the cytoplasm from the environment
28
What functions do membranes perform for the cell?
- permeability barrier
- anchor for proteins
- sire for energy conservation (ETC)
29
Integral membrane proteins
membrane proteins that are firmly embedded in the membrane
30
peripheral membrane proteins
membrane proteins where one portion is anchored in the membrane
31
archaeal membranes
ether linkages in phospholipids of archaea
32
What kind of linkages do bacteria and archaea have in phospholipids?
ester
33
What are the three classes of nutrient transport?
simple transport
group translocation
ABC system
34
Simple transport
the nutrient is simply transported by a transporter
35
Group translocation
substance transported is chemically modified during transport across the membrane and requires 5 proteins
36
ABC system
often involved in uptake of organic compounds, inorganic nutrients and trace metals
37
Peptidoglycan
a classification of bacteria
38
Gram-negative
two layers: peptidoglycan and outer membrane
| - appear red
39
Gram-positive
one layer: peptidoglycan
| - appear purple
40
Gram-stain
differential stains separate bacteria into groups (gram positive or negative)
41
What prokaryotes lack cell walls?
mycoplasmas (bacteria) and thermoplasma (archaea)
42
Gram-positive cell wall
90% peptidoglycan
| have teichoic acids embedded or lipoteichoic acids (have a lipid covalently bonded to it)
43
Gram-negative cell wall
~10% peptidoglycan
| composed of outer membrane (LPS)
44
Lipopolysaccharide (LPS)
consists of core polysac and o-polysac
| replaces most phospholipids in outer half of the membrane
45
Endotoxin
the toxic component of the LPS
46
Lipid A
endotoxin that is released when gram-negative cells are lysed
47
Periplasm
space located b/w cytoplasmic and outer membranes
48
porins
channels for movement of hydrophilic low-molecular-weight substances
49
What is different about archaea?
NO peptidoglycan or outer membrane
| pseudomurein
50
pseudomurein
polysac similar to peptidoglycan that is composed of N-acetylglucosamine and N-acetyloamiuronic acid found in cells walls of certain archaea
51
S layer
found in both bacteria and archaea
| made of protein and is present OUTSIDE other cell wall layers
52
Capsule and slime layer
layer of polysac made of carb polymers and assists with attaching to surfaces
53
Pili
filamentous protein structures, longer than fimbriae, assist with surface attachment, and facilitate with genetic exchange bw cells
54
fimbriae
filamentous protein structure that enables organisms to stick to surfaces or form pellicles
55
Carbon storage polymers
poly-B-hydroxybutyric acid and glycogen
56
sulfur globules
composed of elemental sulfur
57
polyphosphares
accumulations of inorganic material
58
carbonare minerals
composed of barium, strontium, and magnesium
59
Gas vesicles
decrease cell density causing buoyancy in planktonic cell composed of GvpA and GvpC
60
Endospores
contain dipicolinic acid and is rich in Ca2+
61
why do some species of bacteria make endospores?
bc highly differentiated cells are resistant to heat, harsh chemicals and radiation
62
flagella
structure that assists in swimming
63
flagella in bacteria
has several components, filament composed of flagellin, moved by rotation
64
flagella in archaea
half the diameter of bacterial, composed of several different proteins, moved by rotation
65
gliding motility
flagella independent, requires surface contact
66
taxis
directed movement in response to chemical or physical gradients
67
chemotaxis
response to chemicals
| attractants and receptors are sensed by chemoreceptors
68
phototaxis
response to light
69
aerotaxis
response to oxygen
70
asmotaxis
response to ionic strength
71
hydrotaxis
response to water
72
metabolism
the breaking down of 'food' for energy and building up of cell components
73
catabolism
the breaking down and release of energy
74
anabolism
the building up of cell components requiring energy
75
What do you need to consider when growing a culture of microbes?
nutrient, temp and atmosphere requirements and pH
76
Microorganisms grouped into energy classes
- chemoorganotrophs
- chemolithotrophs
- phototrophs
- heterotrophs
- autotrophs
77
Exergonic
reactions with a negative G that RELEASE free energy
78
Endergonic
reactions with a positive G that REQUIRE energy
79
Free energy formation
how to calculate free energy yield of a reaction
80
oxidation
removal of electrons from a substance
81
reduction
addition of electrons to a substance
| always works in pairs - donor or acceptor
82
electron carriers
common link to diverse enzyme reactions
83
prosthetic groups
electron carrier that is attached to enzymes
84
coenzymes
electron carrier that is diffusible
| - NAD+ and NADP
85
Glycolysis
a common pathway for catabolism of glucose (anaerobic with 3 stages)
86
Fermentation
substrate-level phosphorylation
| ATP is directly synthesized from an energy-rich intermediate
87
Respiration
oxidative phosphorylation
| ATP is produced from PMF formed by transport of electrons
88
Aerobic respiration
oxidation using O2 as the terminal electron acceptor and has higher ATP than fermentations
89
NADH dehydrogenases
proteins bound to inside surface of cytoplasmic membrane
| active site bind NADH and accepts 2 electrons and 2 protons that are passed to flavoproteins
90
Flavoproteins
contains flavin prosthetic group (FMD, FAD) that accepts 2 electrons and protons but donates the electrons only to the next protein in the chain
91
Cytochromes
proteins that contain heme prosthetic groups
| accept and donate a single electron via the iron atom in heme
92
Iron-sulfur proteins
contain clusters of iron and sulfur
reduction potentials vary depending on number and position of Fe and S atoms
carry electrons
93
Quinones
- hydrophobic non-protein containing molecules that participate in electron transport
- accept electrons and protons but pass along electrons only
94
Proton motive force
electron transport system in cytoplasmic membrane so that electrons are separated from protons
95
ATP synthase
complex that converts PMF into ATP
96
F1 of ATPase
multiprotein extramembrane complex that faces cytoplasm
97
F0 of ATPase
proton-conducting intramembrane channel
98
CAC and glyoxylate cycle
organic acids can be metabolized as electron donors and carbon sources by many microbes
99
Anaerobic respiration
the use of electron acceptors other than oxygen (NO3-,Fe3+,SO42-, CO32-)
less energy released compared to aerobic
100
Chemolithotrophy
uses inorganic chemicals as electron donors (H2S, H2, Fe2+, NH3) and is typically aerobic
101
Phototrophy
uses light as energy source
102
photophosphorylation
light-mediated ATP synthesis
103
photoautotrophs
use ATP for assimilation of CO2 for biosynthesis
104
Photoheterotrophs
use ATP for assimilation of organic carbon biosynthesis
105
Adenosine diphosphoglucose (ADPG)
precursor for glycogen biosynthesis
106
uridine diphosphoglucose (UDPG)
precursor for glucose biosynthesis
107
Rho-dependent termination
rho protein recognizes specific DNA (RNA) sequences and causes a pause in the RNA polymerase
108
Unit of Transcription
unit of chromosome bounded by sites where transcription of DNA to RNA is initiated and terminated
109
Ending translation
translational termination occurs when the ribosome reaches a "stop" codon
110
Signal sequences
found on proteins requiring transport from cell
111
The Tat system
proteins to be exported, that fold in the cytoplasm, are exported by a transport system distinct from Sec, called the Tat protein export system (Fe-S proteins and redox proteins)
112
Batch culture
a closed-system microbial culture of fixed culture of volume
113
What are the 4 phases of the growth curve for a closed system of cells?
1. Lag phase
2. Exponential phase
3. Stationary phase
4. Death phase
114
Continuous culture
an open-system microbial culture of fixed volume
115
Chemostat
most common type of continuous culture
- if dilution rate too HIGH = organism WASHED out
- if dilution too LOW = organism DIE
116
Dilution rate
rate at which fresh medium is pumped in and spent medium is pumped out (controls growth rate)
117
Flow cytometer
a second method for enumerating cells in liquid reproducing population using laser beams, fluorescent dyes and electronics
118
Viable counts
measurement of living, reproducing population
119
Spectrophotometry
turbidity measurements are indirect, rapid, and useful methods of measuring microbial growth
120
Optical density (OD)
measurement used for turbidity
121
What conditions affect growth?
- temp
- pH
- osmolarity
- oxygen availability
122
Cardinal temperatures
the minimum, optimum, and maximum temperatures at which an organism grows
123
Extremophiles
organisms that grow under very hot and very cold conditions
124
Psychrophiles
organisms with cold temperatures optima and inhabit permanently cold environment
125
Psychrotolerant
organisms that can grow at O C but have optima of 20-40 C and more widely distributed in nature than psychrophiles
126
Thermophiles
organisms with growth temperature optima b/w 45-80D
127
Hyperthermophiles
organisms with optima greater than 80C
128
Neutrophiles
organism that grow optimally at pH 5.5-7.9
129
Acidophiles
organisms that grow best at low pH (<5.5)
130
Alkaliphiles
organisms that grow best at high pH (>or = 8)
131
Osmosis
water diffuses from high to low concentrations
132
Aerobes
requires oxygen (respiration) and grow at full oxygen tension (~21%)
133
Microaerophiles
can use oxygen only when it is present at levels reduced from that in air due to limited respiration or oxygen sensitivity
134
Facultative organisms
can live with or without oxygen
135
Anaerobes
cannot respire oxygen
136
Aerotolerant anaerobes
tolerate oxygen and grow in its presence even though they cannot respire
137
Obligate anaerobes
inhibited or killed by oxygen (ex: some bacteria and archaea, fungi, protozoa)
138
Metabolic Regulation
metabolic activity of a cell = expressed proteins
139
what are the different types of metabolic regulation?
- degradation
- modification
- allosteric regulation
140
Negative control
gene that are negatively controlled have a default of ON
141
Positive control
genes that are positively controlled have a default of OFF
142
induction
= loss of repression
143
Repressor gene
a protein that binds the transcription start site of a negatively controlled gene
144
Global control systems
regulate expression of many different genes simultaneously
145
Catabolite repression
ex of global control and is the synthesis of unrelated catabolic enzymes is repressed if glucose is present in growth medium
146
Diauxic growth
two exponential growth phases
147
Cyclic AMP and CRP
in catabolite repression, transcription is controlled by an activator protein and is a form of positive control
148
CRP
activator protein
149
Cyclic AMP
is a key molecule in many metabolic control systems and is derived from a nucleic acid precursor
150
Sensor kinase
detects environmental signal and autophosphoylates (in cytoplasmic membrane)
151
Response regulator
DNA-binding protein that regulates transcription (in cytoplasm)
152
Phototaxis
movement toward light, light sensor replaces MCP's
153
aerotaxis
movement toward oxygen, redox protein monitors oxygen level
154
Quorum sensing
mechanism by which bacteria assess their population density and ensures that a sufficient number of cells are present before initiating a response that to be effective, requires a certain cell density
155
Acyl homoserine lactone
the first autoinducer to be identified
156
Heat shock response
largely controlled by alternative sigma factors
157
Heat shock proteins
counteract damage of denatured proteins and help cell recover from temp stress
