EXAM I MICROBIO Flashcards
1
Q
Microorganisms inhabit
A
different environments/ habitats
-are ubiqotous (found everywhere)
2
Q
yeast fermentation yields
A
ethanol and CO2
3
Q
microbial fermentation yields
A
sugars –> CO2 + organic acids
4
Q
beneficial microbes
A
improve food safety, preserve foods
5
Q
beijerick and winogradsky have shown that
A
bacteria help recycle vital elements between soil and atmosphere
bacteria + fungi –> decomposing –> environment
6
Q
plants and animals require what compounds
A
nitrogen
carbon
phosphorous
oxygen
sulfur
7
Q
bioenhancers
A
nitrogen and phosphorous plant fertilizers
-increase in oil-degrading bacteria
8
Q
bioaugmentation
A
genetically modified bacteria
9
Q
legumes convert
A
atmospheric nitrogen (N2) into ammonia (NH3)
10
Q
legumes form
A
nodules (tiny factories that fix atmospheric nitrogen for plants to use)
11
Q
nitrogen increases
A
protiens
12
Q
ammonia produces
A
its own fertilizers
13
Q
bacillus-thurogenesis
A
protects plant
-produces a toxin protien
-infects/ kills digestive system of the rodent/bug
14
Q
crown gall cancer is caused by
A
Agrobacterium tumefaciens
15
Q
naturally-occurring microorganisms
A
antibiotics, enzymes, chemicals
16
Q
microbes present in the human body
A
microbiota
17
Q
complex carbohydrates are digested by
A
gut microbiome
18
Q
microbiota
A
prevents pathogens
synthesize vitamins
break down complex carbs
19
Q
from stomach to small intestine
A
increase in microbiota (in colon)
20
Q
clostridium dificile
A
leading cause of HAIs
21
Q
age of the earth
A
4.6 billion years
22
Q
first microbial cells appeared
A
3.7-4.3 billion years
23
Q
atmosphere was first
A
anoxic
-first phototrophs were anoxygenic
24
Q
cyanobacteria present
A
earliest oxygen producing phototrophs
25
stromatolites (3.5 bya)
layer rocks
fossilized microbial formations (ancient)
cyanobacteria- like fossils (3-3.5 bya) (modern)
26
LUCA
common ancestor of plants and animals
27
stanley miller's experiment
electrical charge through methane, ammonia, hydrogen water --> amino acids
28
early notion of disease
bad air- mismatch odors
"invisible force" causing disease
29
Hippocrates "father of western medicine" found
diseases have NATURAL causes from between patient and their environment
30
Antoine van Leeuwenheoek (1632- 1723)
first to observe microbes including bacteria "animalcules"
31
Louis Paster (1822- 1895)
microbial basis of fermentation
sponatenous generation
developed vaccines (rabies)
32
what did Pasteur use?
broth --> alcohol cells and sour milk
alcohol cells --> yeast
sour milk --> cells -> rod bacteria -> lactic acid
33
Robert Koch (1843- 1910)
first to connect single isolated microbe to a known human disease
34
taxonomy
standard format in naming, consistent terminology
35
Carolus Linneus
system of categorizing and naming organisms using a standard format
-consistent terminology
ex. absence of hair - no tail
presence of hair - tail
36
Linnaeus categorized
animals and plants
37
Ernest Haeckel
wrote General Morphology of Organisms
-animals, plants, protist, monera
38
Robert Whittaker
proposed adding fungi to the tree of life
-animals, plants, protists, monera, fungi
39
Carl Woose
brought further modifications based on small unit rRNA
40
Carl Woose's tree shows
closer evolutionary relationship between archaea and eukaya than they have to bacteria
41
what is the basis of comparing organisms
DNA, protiens, RNA
42
binomial nomenclature
genus and species
genus: capitalized
species: lowercase
43
Haloquadrum walsbyi
halo: salt
walsbyi: discoverer
44
relative size of a flu virus
100 nm
45
prokaryotic microbes
-no true nucleus
-bacteria, archae
ex. vibra cholera - rodlike shape
46
eukaryotic microbes
-true nucleus
-bigger size
-appears more round
-fungi, protozoa, algae
47
bacteria
-prokaryotes
-cell wall contains peptidoglycan
-spherical (cocci), rod (bacillus), curved (spirillum, spirochete, vibrio)
48
coccus
round
49
bacillus
rod-like
50
vibrio
most common shape of bacteria
51
archea
-extremophiles
-lack pathogens or parasites
52
methanogenic archae
-common in guts of animals and humans
-methane production
-located in human GI tract
53
protists
any eukarya that isnt plants, animals or dungi
algae, protozoa
54
algae (protist)
photosynthetic
unicellular or multicellular
cellulose cell walls
55
protozoa (protist)
motility (pseudopods, flagella, cilia)
photosynthetic
56
fungi
eukarya
unicellular or multicellular
chitin cell walls
57
yeasts are
unicellular fungi
-causes bread to rise, bevs to ferment
-diseases: vaginal yeast infections, oral thrush
58
molds are
multicellular fungi
-decomposition of dead plants and animals
-cause mycotoxins (allergies, disease)
59
helminths (eukarya)
multicellular parasitic worms
flatworms, roundworms
microscopic eggs and larvae
60
Dranunculus medinesis (guinea worm)
occurs after a person drinks water containing water fleas infected by guinea- worm larvae
61
virus
*not in tree of life
acellular (no cells)
either DNA or RNA - never both
super small
obligate parasites - only replicates within cytoplasm of host cell (needs its own machinery to replicate)
influenza virus, ebola
62
prion
-acellular, obligate intracellular "parasites"
-misfolded PrPc infectious protien
-causes protiens to misfold, forming plaqies
-TSE (spongiform encephalopathy) in animals and humans -- passed through heredity, contaminated fluids/ meats
63
how prions "mad cow disease" is spread to humans
sheep - scrapies
cow - infected sheep fed -- "mad cow disease"
human- contaminated meats consumed or hereditarily
64
what activities do microbial cells carry out/
metabolism: interact with environment
reproduction: cell division
differentiation: cell structures such as spores
communication: sense + respond to environment
movement: flagellum - flagella or cilia
evolution: horizontal gene transfer - transfer or genetic material between donor and recipient; adapt better to environment
65
What bacteria causes the plague?
-Yestina pestis
-Black death
-urban rats carry these bacteria
-fleas (vector) transmit to animals and humans
66
Yestina pestis structure
gram negative
rod-shaped bacterium
67
Plague is transmitted by
rat flea, main vector
Xenopsylla cheopis
68
where does Y pestis replcate
X. cheopis sucks blood from another organism (host) and transmits it to host via flea bite
69
plague is primary
zoonosis of wild rodents - disease in animals but can be transmitted to humans
humans are accidental hosts, not in the chain but due to fleas looking for hosts humans now become part of it
70
enzootic
endemic
-low level of infection in animal pop.
71
epizootic
epidemic
-high level of infection
72
flea -> human transmission of plague
-flea bites human
-bacteria trapped in human-specific body site
-blood clot forms
-protein activates host plasma
-capsule
-colonization overcomes immune system to cont. replication
73
fatal forms if human plague
bubonic - most common
pneuomonic
septicemic
74
bubonic plague
incubation pd: 2-8 days
bite of infected flea
multiply in lymph node near where bacteria entered
pt develop swollen, painful nodes (buboes), fever, headache
75
pneuonomic plague
incubation pd: 1-3 days
person to person (infectious droplets)
bacteria spreads to lungs
76
septicement plague
rapid spread via bloodstream
severe, causing bleeding into skin and septic shock
77
diagnosis of plague
samples from blood or swollen lymph
-visualize small gram neg. with gram stain
-bipolar staining "safety pin"
ELISA confirms diagnosis
78
prevention of plague
control of rodents and fles
good sanitation practice
repellent
keep fleas off of pets
wear gloves
79
cocci (bacteria)
round
divide to reproduce
80
diplococci
remain in pairs after dividing
81
stretococci
divide and remain in chains
82
staphylococci
divide in planes and form grapelike clusters
83
monomorphic vs pleotrophic
keep one vs changing shape
84
free- living smaller cells
tend to grow faster
higher S to V ratio
exchange is higher
better adapted to its environment
faster rate of nutrient and waste exchange
85
shorter wavelength
greater resolution
higher energy
86
light is
absorbed, reflected or scattered
87
refractive index is affected by
staining
88
oil immersion
immersion oil has same Refractive index as glass
adding oil is like increasing the diameter of objective
89
numerical apenture
light gathering ability of lens
90
Bright- field microscope/ compoound
main microscope used
-stained and unstained specimens
-dark image, bright background
91
Dark- field microscope
bright image, dark background
observes living things
only observes unstained things
observes: internal structures in eukaryotic microorganisms, bacteria
92
Phase- contrast microscope
dark microbe, light background
observes microbial movt, bacterial structures
can observe without staining
-refractive index differ in levels of darkness
rays in phase = higher intensity
out of phase = lower intensity, dark light
93
Fluorescence Microscope
excite a specimen with a wavelength of light that triggers the object to emit fluorescent light
-stained by fluorochromes that absorb light, emit visible fluorescent light of higher energy
94
Electron Microscope
limited resolution bc visible light (low energy) is used
-uses electron beam to create image, with electromagnets as lens
-higher resolution than light microscopt
-subcellular structure/ organelles, viruses
95
Transmission (TEM) Microscope
thin specimens, tissues, subcellular structures
-very detailed
96
Scanning (SEM) Microscope
3D surface details of speciments
-fuzzy
97
wet mount
drop of liquid placed on slide
ie. urine, skin scrape
98
smear
dried preparation of bacterial cells on a slide
99
heat fixation
smear is fixed/ attached on slide by heart or it would be washed away during staining procedure
100
staining
contrast between bacteria and background
emphasizes microbial structures
101
bacterial staining
solvent, colored molecule, chromogen (colored compound, not a stain)
102
basic (cationic stain)
cell is stained
103
acidic (anionic stain)
background is stained
104
differential stains
use two or more dyes that react differently so it can distinguish one from the other
105
gram stains
gram negative
gram positive
106
gram negative appears
pink
107
gram-positive appears
purple-violet
108
color differences in these bacteria are due to
difference in cell walls
109
gram positive bacteria
thick cell wall
C-I
goes IN the cell
110
gram negative
thin cell wall
C+I
goes out of the cell
-alcohol extracts from cell wall
111
gram stain procedure
1. application of crystal violent (purple)
2. application of iodine
--form CI complex, becomes soluble
3. alcohol wash (decolorization)
4. application of safranin (counterstain)
112
color of gram positive cells
primary stain: purple
mordant iodine(CI complex forms): purple
decolorizing alcohol acetate: purple (thick, IN)
counterstain safranin: red
113
color of gram negative cells
primary stain: pink
mordant iodine (CI complex forms): purple
decolorizing alcohol acetate: colorless (thin + Outer membane, OUT)
counterstain safranin: red
114
acid fast stains
mycobacterium
-leprosy, tuberchlosis
-gram positive
-waxy layer: mycolic acid (lipids polysaccharide)
115
structure of gram positive
plasma membrane
peptidoglycan
116
structure of gram negative
plasma membrane
peptidoglycan
outer membrane
117
acid fast (+)
plasma membrane
peptidoglycan
mycolic acid
118
carbol fushin
stains everything strongly
-reddish purple
119
decolorization with acid alcohol
removes stain from acid-fast negative cells
120
methylene blue
counterstains (non-acid fast stains)
121
endospore stain (schaffer- fulton method)
bacteria have the ability to form endospores to protect bacterial genome in a dormant state when the environment in unfavorable conditions by forming layers
-not all bacteria have this ability
122
Bacilius and Clostridum that can form Endospores
C tetani: tetanus
C dificile: pseudomembranous colitis
C perfringens: gas gangrene
C botulinium: botulism
123
positions of endospores within vegetative cell
terminal
sub-terminal
central or medial
124
bacterial spores
-use heat to push primary stain machalite green into the endospore
-endospore retains green stain, then counterstained pink with safranin
125
chemical composition of a stain
benzene: organic colorless agent
chromophere
auxochrome
126
Francesco Redi's experiment
housefly --> eggs --> larvae maggots --> pupae
-maggots were offspring of flies, not the product of spontaneous generation
open container: formation of maggot in meat
cork sealed container: no formation of maggot in meat
gauze-covered container: no formation of maggots in meat
127
John Needham
new microbes arise spontaneously
likely did not boil the broth enough to kill pre-existing microbes
conditions: nutrient broth heated, then placed in a sealed flask
results: microbial growth
argued that life originates from a "life force" that was destroyed during Spallanzani's ext boiling
128
Lazzaro Spallanzani
-suggested microbes were introduced into these flasks from the air
conditions: nutrient broth placed in flask, heated, sealed
results: no microbial growth
129
Louis Pasteur (1862)
*disproves spontaneous generation w swan neck flask experiments
boiled solutions
left flasks exposed to air
result: no growth of microorganisms in swan-neck flasks
found that microbes are present in nonliving matter: air, liquids, solids
130
Swan neck flask experiments
bacteria settles in bend of flask
curve of bend prevents bacteria from entering the main reservoir and contaminating the broth
when neck of flask is broken off, bacteria reaches the sterile broth and organism growth begins
131
before swan neck flask experiments
other proponents can no longer enter
132
now due to swan neck flask experiments
opens it to the air, microbes enter and stay in the bend
133
theory of biogenesis (Rudolf Virchow)
all cells arise from another cell
134
Ignaz Semmelweis
death rates in hospital were high --> handwashing to prevent disease transfer
135
Joseph Lister
use carbolic acid (phenol) spray disinfectant/antiseptic during surgery
-reduce postsurgical infection caused by his techniques
136
Robert Koch (1843-1910)
specific disease is attributed to specific disease
-tuberculosis, anthrax, cholera
Germ theory of disease
137
Koch's postules steps
-microorgansms isolated
-microorganism grown in pure culture
-microorganism incoluated in healthy animal
-disease reproduced in healthy animal
-microorganism is isolated from animal and grown in pure culture
-microorganism is identified
138
Koch's Postules Key Concepts
-specific disease is caused by specific microbe
-determines etiology of disease, first step in treatment and prevention
-microbiologists use these steps to identify causes of emerging disease
treponoma pallidum
139
vaccination
coined by Edward Jenner
-milkmaids who developed cow pox were immune to more serious smallpox
140
Louid Pasteur (late 1800s)
rabies vaccine
-obtained rabies virus from rabid dogs and cultivated the virus in rabbits
-first treat an infected human in 1885
141
first antimicrobial drugs
antiseptics could kill pt
"magic bullet"- antibiotic that kills microbe only
Paul Ehrich speculated about penicillin
142
Salvarsan
arsenic derivative effective against syphillis
143
development of antibiotics
Fleming 1928
"zone of clearing" from mold
Penecillin produced by Penicillium chrysogenum
144
huge breakthrough of powerful antibiotics
started in 2nd half of WWII
-purified penicillin and saved lives
145
Endosymbiotic Theory
1) aerobic bacteria is engulfed
2) eukarya becomes mitochondria
3) photosynthetic bacteria becomes chloroplasts
146
origin of viruses come from
prokaryotes
147
Endosymbiotic Theory is defined as
mitochondria and chloroplasts arose from prokaryote establishing symbiotic relationship within a eukaryotic host
148
mitochondria and chloroplasts resemble bacteria in size and shape
-circular DNA (typical of prokarya)
-reproduce independetly of their host cell
-ribosomes resemble prokarya
-antibiotics that inhibit protien synthesis on -ribosomes in bacteria also inhibit protien synthesis on ribosomes in mitochondria and chloroplasts
149
prokaryotic cell structure
envelope (liposaccharide, outer membrane, cell wall, periplasm, cell membrane)
cytoplasm
nucleoid
150
DNA and binding protiens (nucleoid) bind to
cytoplasm
151
what is the cytoplasm comprised of?
80% water, protiens, inclusions
152
outer membrane
sugars overcome predators
153
peptidoglycan of cell wall
provides shape, structure, protection, strength
154
outside bacterial cell wall
gram-negative bacteria has outer membrane
155
cell envelope of bacterial cell (for gram negative species)
cell membrane
cell wall
outer membrane
156
chromosome is organized within the cytoplasm
looped coils "nucleoid"
157
phospholipids
phospho - core of glycerol, phosphate
lipid - protiens, fatty acid
158
fluid mosaic model
keeps on moving up and down, dynamic
159
glycoprotien
cell to cell communication interaction binding site
160
channel
only small gases (O2, CO2) can travel in and out freely
161
transmembrane protien
spans entire membrane
makes the channel
162
peripheral protien
cytoplasmic (protiens, chemicals for growth); leak-proof
163
plasma membrane structure
barrier to diffusion of most polar or charged substances
-phospholipid bilayer with protiens
164
hydrophilic region
extracellular
phosphate, glycerol
165
hydrophobic region
cytoplasm
fatty acids
166
bacterial membrane proteins
-peripheral and integral membrane protiens
-support for structures that protrude from the cell (pili, flagella)
-transport of substances in and out of cell across membrane
-singaling and communication (legumes and nitrogen-fixing bacteria)
-selective permeability
167
coupled transport
use of energy from one gradient to drive transport up another gradient
-symport, antiport
168
proton motive force
membrane = energized
H+ seperated from OH-
move protons outward across the membrane
169
water molecules pass through plasma membrane by
moving through lipid bilayer (simple diffusion) or through integral membrane protiens (aquaporins) that function as water channels
170
facilitated diffusion
no energy transporter
high - low conc
water channels: aquaporins allows water to move around
171
carrier saturated with substrate
once it hits saturation, rate of solute entry plateaus
172
active transport
symport: same direction movt
antiport
group translocation
ABC transporters
173
symport (active transport)
1. energy is released as one substrate moves down its conc gradient
2.this energy moves a 2nd substrate against its gradient and into the cell
lactate/ H+
174
Antiport (active transport)
1. antiporter binds substrate A on cytoplasmic side of membrane
2.antiporter opens to the outside of the cell where conc of A is lower
3.substrate A leaves its binding site and B binds to the site
4. antiporter (cytoplasm -> outside) opens to the inside of the cell; substrate B is released in exhange for A
175
group translocation
unique to prokarya
PEP
G6P: modified substrate; cant move out
176
cytoplasmic group translocation
Enz I, HPr, Enz 2A
177
peripheral group translocation
Enz 2B
178
transmembrane group translocation
Enz 2C
179
ABC systems
ATP binding cassette
-expel wastes, antibiotics
-efflux transporters
-multidrug efflux pumps
180
Mechanism of ABC Transporter
periplasmic binding protien: high affinity for substrate
membrane-spanning protien: form transport channel
cytoplasmic ATP hydrolyzing protien: supply energy for the transport to get the substrate inside the cell
181
gram negatives have
significant periplasm
182
gram positives have
substrate binding
183
iron transport via
siderophone and ABC transport complex
184
Iron in ABC transport complex mechanism
1. bacteria secretes siderophore that binds iron
2. iron is brought inside
3. iron is released inside the cell
185
myobacterium tuberclosis
colonize lungs and requires iron to grow in lungs
186
iron is locked up in
iron transport protiens and hemoglobins
187
small pox replicates in
cytoplasm
188
smallpox is characterized as
linear
double-stranded
DNA virus
189
small pox varialation
sick individual -> postule -> material -> scraping -> inoculating healthy individuals
190
small pox is a ___ virus
variola
191
small pox is caused by an
orthopoxvirus known as the smallpox (variola) virus
192
smallpox is transmitted via
face to face
cough, sneeze, droplets
contaminated objects
193
clinical presentation of smallpox
incubation pd: 7-19 days
initial symptoms: high fever, head and body aches, rash, scabs
194
measles (rubeola)
negative
single-stranded
enveloped RNA
member of mobillivirus
195
humans are the only natural hosts of measles
true
196
symptoms of measles
CCC: cough, conyza (runny nose), conjuctivitis
197
koplicks spots
white spots on buccal mucosa
on inner cheeks
rash -> hairline on face going downwards
198
spread of measles
highly contagious, lives in nose and throat mucus of infected person
can spread via coughing, sneezing (airborn transmission)
if people breathe contaminated air or touch the infected surface then touch themselves...
199
signs and symptoms of measles
high fever
koplicks spots (white tiny spots inside mouth)
measles rash
200
measles is most risky to
-children under 5
-adults over 20
-pregnant women
-compromised immune systems: leukemia or HIV infection
201
common complications of measles in children
ear infection
202
isolation of smallpox rash
infected ppl should be isolated for 4 days after they develop rash
-airborne isolation
-N95 respirator
203
detection of measles
-IgM antibody
-also passed through urine
204
treatment for measles
no specific anti-viral therapy
-vitamin A administration
-MMR vaccine prevents it
205
Glycolayces (Glycocalyx) and S- Layers
-sticky, gelatinous polymer external to cell wall
-composed of polysacc, polypeptode
-made inside the cell and secreted to outside cell
*disease causing ability
206
capsules
organizes and firmly attached
-resistant to phagocytosis
-protect from desiccation
207
slime layer
unorganized, loosely attached to cell wall
-motility
-porous
-unorganized
208
NAG and NAM
alternating sugars that form carb backbone of the cell wall
209
tetrapeptide
mirror- like image
L and D forms
210
L form
laxorotation
-more common
-used in protein synthesis
211
D form
dextral rotation
-cell wall
-targets antibiotics
212
peptide bridges only form on
NAM
213
alternating NAG and NAM
forms bridges to strengthen the cell wall
214
lysozome
cleaves glycosilic bond
215
peptide cross-bridge formation is blocked by
penecillin
216
interbridge
short stretch of amino acids
g positive
217
gram negative
polysaccharide backbone
218
in gram negative bacteria, cross link forms from
amino group of DAP
-no interbridge is present
219
in gram positive bacteria, cross link forms from
interbridge
220
lysozome is active in
cell wall of gram positive bacteria, making it more vulnerable to lysis
221
gram positive cell walls
-primarily composed of peptidoglycan
-teichoic acids (negative)
222
techoic acids (negatively charged) of gram positive cell walls
--primarily an alcohol (glycerol, ribitol) and phosphate
-maintain cell envelope
-protect from environmental substances (antigenic specificity)
-bind to host cells to initiate infection
223
+Ve ions transport
Calcium, Magnesium
224
why are techoic acids negatively charged?
from the phosphate groups
225
gram negative cell wall structure
complex
thin layer of peptidoglycan
lipopolysaccharide: outer leaflet of outer membrane; lipid A and polysaccharide chains
226
lipid A
endotoxin in lysed cells
227
do gram negative cell walls have techoic acids?
no
228
porin protien
regulates portin size (what goes in and out)
229
lipoprotien
connects cell wall to next membrane
230
phospholipid
lower leaflet
231
inner to outer most
phospholipid - lipoprotien - liposaccharide
232
outer membrane is permeable and small due to
protiens "porins" that act as channels for entrance and exit of solutes
233
nonspecific porins
water-filled channels
234
liposaccharide has 3 parts
lipid A: outer membrane
Core polysaccharide: 10 sugar joined to lipid A
O side chain (O antigen): polysacc that extends out from core
235
functions of LPS
negative charge on cell surface
stabilize outer membrane
permeability barrier
host defense protection
acts as endotoxin
236
mycobacterial envelope
complex cell wall with peptidoglycan and mycolic acid
resistant to staining
considered gram positive but envelopes are too thick and comples including extra layers
237
hopanoids
sterol like molecules
-present in the cytoplasmic membranes of bacteria
238
sterols
rigid, planar molecules that strenghten the membranes of eukaryotic cells
ex. cholerstrol
239
osmotic pressure
cell wall provides protection against changes by preventing flow of water inside the cell
240
isotonic solution
solute conc outside = solute conc. inside the cell
241
hypertonic cell
water moves out of cell
membrane shrinks and detaches from cell wall
-crenation
242
hypotonic solution
water moves into the cell
cell wall counteracts osmotic pressure to prevent swelling and lysis
-expand, lysis
243
myoplasms
lack cell wall
sterols in plasma membrane
244
archae
wall-less
pseudomurein (lack NAM and D- amino acid)
245
what breaks the bond between NAG and NAM
lysozome
246
what cleaves the glycosylic bond: NAG or NAM
NAM
247
penecillin inhibits
peptidoglycan synthesis
248
protoplast
gram positive cell that loses cell wall
-surrounded by plasma membrane, may remain intact if lysis does not occur
249
spheroplast
-gram negative cell that loses cell wall
-wall is not completely destroyed, some of outer membrane also remains
250
what is bacterial DNA organized in?
nucleoid
251
plasmids
replicate independently of bacterial chromosomes
252
nucleoid region is a
condensed area of DNA found within prokaryotic cells
253
DNA interacts with
-NAPs
assist in the organization and packaging of the chromosome
254
NAPs function similar to
histones
255
ribosomes are composed of
protien and rRNA (ribosomal RNA)
256
site of protien synthesis
prokaryotic ribosomes - 70S
S= Sveaberg's unit; rate of sedimentation
257
bacterial ribosomal RNA
16S rRNA in small subunit
23S and 5S in large subunit
258
16S helps in
evolutionary relationship identification
259
23S and 5S help in
microbe identification
260
sedimentation rate
dependent on size, shape, weight
-centrifuge runs in high speed
261
inclusions
separated from the cytoplasm
262
energy reserve inclusions
lipid
sulfur
polysaccharide granule:
glycogen: red
starch: black, blue
263
magnetosomes
common in low O2 environments
264
bacterial endospore
released when bacteria experiences unfavorable conditions
265
bacterial endospore steps
1. dna replicates (spore septum)
2. membrane forms around dna
3.forespore forms more membranes
4.protective cortex forms around spore
5.protien coat forms around cortex
6.spore is released
266
sporulation
process of endospore formation within vegetative cell
-not a means of reproduction
267
stages of endospores
DNA, ribosome, enzymes -> nutrients available -> enzymes break layers -> germination -> cell
268
endospores - sportulation
produces dormant cell - no metabolic activity - until nutrients are available and growth resumes
269
mature spores
contain: Dipicolinic and Calcium ions
270
flagella
motility in bacteria by swimming
-chemotaxis
271
lophotrichous
swims left
272
peritrichous
swims all over
273
filament
made up of flagellin
274
flagellar protien - H antigen
distinguishes diff stain variations within G- species
275
run (rotation of flagella)
flagella bundle, rotate in CCW direction
276
tumble (rotation of flagella)
flagella seperated, rotate in CW direction
277
chemotaxis involves
rotation of flagella that propels cell in response to chemoreceptors
-these sensory proteins bind the chemicals
278
attractant
chemical gradient extends the length of run
279
axial filament
endoflagella - has periplasm, outer sheath
-rotation causes cell to move a spiral motion
280
pili
shorter than flagella
made of pilin protien
281
fimbrae
attachment pili
-attach cells to surfaces
282
conjugation (sex) pilus
transfers of DNA between cells
could be drug resistant
283
surface motility
can swim but different motilities
284
twitching motility
require ATP hydrolysis to extend- retract causing cell to move forward; movt occurs in discrete
-type IV pili
short, intermittent, jerky motion
285
what do twiching motility attach
pathogenic bacteria to their host cells
286
gliding
type IV pili
secrete polysaccharide slime from pores onto outer surface of cell
requires cells be in contact with solud surface
287
nucleolus
site of rRNA synthesis
assembly of ribosomes begin
proteins form then move to cytoplasm
288
nucleosome
dna + histones
289
ribosomes
protien synthesis
290
free ribosomes
synthesize protiens used inside the cell
291
membrane bound ribosomes
attached to RER and make proteins for insertion in cell membrane to proteins for export
292
80s and 70s
processed/ formed in nucleolosis then move to cytoplasm
293
RER
synthesize secretory protiens and membrane molecules
294
SER
unique enzymes involved in biosynthesis of lipids, fats, steroids
detoxifies toxic compounds
295
endomembrane system
attach to each other
-RER
-SER
-Golgi apparatus
-Lysosome
296
Golgi complex
function in concert with ER
chemically modified, destined for secretion
297
glycosylation
common modification by adding sugar residues
298
Endoplasmic reticulum
chemical modifications
transport vesicle
299
golgi complex
secretory vesicle, storage vesicle (lysozome)
300
lysozome (formed from golgi complex)
membrane-enclosed
contain digestive enzymes
degrade damaged organelles, food
phagocytosis- ingest bacteria, contain lys.
301
endocytosis
helps in digestion of food particles
302
vacuole (derived from golgi complex)
space/cavity in cytoplasm of cell
proteins, sugars
endocytosis bring food into the cell
metabolic wastes and poisons
303
peroxisomes
not part of endomembrane system
membrane bound organelle
enzymes that oxidize organic and toxic substances
304
what do peroxisomes generate and degrade
hydrogen peroxide (catalase)
305
what do peroxisomes protect against
other parts of cell from toxic of hydrogen peroxide
306
cytoskelaton
maintains shape
307
microfilament
two strands of actin
amoebid movement
pseudopodia "false feet"
308
intermediate filaments
maintain position of nucleus
keratin
309
microtuble
cell motility: cilia, flagella
hollow tubes composed of proteins A-tubulin and B-tubulin
310
mitochondria
powerhouse of cell
ATP prodicution
mitochondrial DNA and 70S ribosomes (prokarya origin)
-mitochondrial protiens
311
matrix
contains all enzymes
312
chloroplasts
contain chlorophyll
algae, plants
photosynthesis
70s ribosomes, dna
313
plasma membrane
phospholipid bilayer
peripheral protiens
integral protiens
sterols
314
group translocation does not occur in
eukarya
315
cell wall
plants, algae, fungi
carbohydrates
cellulose, chitin (fungi), glucan (yeast), mannan
316
glycocalyx
carbs extending from animal plasma membrane
bonded to protiens and lipids in membrane
317
cytoplasm
inside plasma, outside nucleus
318
cytosol
fluid portion of cytoplasm
319
cytoskelaton
microfilaments
intermediate filaments
microtubules
320
cytoplasmic streaming
moving cytoplasm throughout cells
-one part of the cell to another which helps distribute nutrients
-move the cell over a surface
321
flagella
few, long
constructed of microtubules
322
cilia
short, numerous
constructed of microtubules
rapid, flexible, waving motion
323
prokaryotic flagellum
rotates
324
eukaryotic flagellum
moves in a wavelike manner
325
cilia
rapid, flexible, waving motion due to its shorter length
326
hydrogenosomes
some eukaryotic microorganisms are killed by O2
-live an anaerobic life
-lack mitochondria
-fermentative metabolism
327
Trichomonas vaginalis
anaerobic protist
328
ribosomes in eukarya
80S- cytoplasm, RER
70S- mitochondria, chloroplast
329
SA:V ratio in bacteria and archae
high
330
SA:V ratio in eukaryotes
low
331
cell division of prokaya
binary fission
332
bacteria contains or lacks histones
lacks
333
archae contains or lacks histones
contains
334
membrane lipid composition of prokarya and eukarya
ester-linked
335
cell wall composition of bacteria
peptidoglycan
336
cell wall composition of archae
pseudopeptidoglycan
glycopeptide
polysaccahraide
S layer
337
cell wall composition of eukarya
cellulose
chitin
silica
338
bacteria motility structure
rigid spiral flagella
339
archaeal motility structure
rigid spiral flagella composed of archaeal flagellins
340
eukarya motility structure
flagella and cilia composed of microtubules
341
catabolism: microbial buffet
metabolism: all chemical reactions inside a cell
342
catabolism
breakdown --> energy is released in energy
carbs, lipids, protiens broken down
smaller biomolecules (AA, fatty acid, simple sugars) are produced
343
anabolism
takes and uses energy to synthesize
344
substance oxidized
electron donor
345
substance reduced
electron acceptor
346
redox potential
tendency to donate or accept electrons
347
donors
reduction potential: H2
electrons falling
348
.10 = donor/ acceptor
fumarate
349
acceptor
+.90
350
oxygen is at the ___ of redox tower
bottom
351
oxygen is the strongest __
electron acceptor
352
principal electron carrier originate from
B vitamin group
353
B vitamin group derivates of
NAD+
NADP
FAD
354
ADP is phosphorylated to
ATP
355
adenine
base
356
ribose
sugar
357
NAD+ is
reduced to NADH + H+
358
NADH reduced
produces energy and biosynthesis of ATP
359
C6H12O6 is broken into
CO2 and H20
-energy released, ATP is produced
360
coenzymes
organic helper molecules required for enzyme action
common source: dietary vitamins
361
NADH and ATP
common co-enzymes
provide high-energy electrons or phosphate groups
bind to enzymes by activating them
362
catalysts
speed up chemical reaction without being permanently altered themselves
363
factors that affect reaction rate
pH, temp, conc
364
glycolysis (splitting of sugar)
energy investment phase
uses energy from 2 ATP molecules
2 phosphorylated 3C molecules: G3P
365
energy pay off of glycolysis
energy by oxidizing G3P to pyruvate
366
net gain glycolysis from breakdown of single glucose molecule
2 ATP
2 NADH
2 pyruvate
367
ED pathway
go to pseudonomes
2 pyruvate
ATP
NADH
NADPH
368
Pentose Phosphate Pathway (PPP)
intermediates to biosynthesis
ATP
2NADPH
369
for pyruvate to enter the next oxidative pathway it must be
decarboxylated by pyruvate dehydrogenase to a 2 carbon acetyl group
370
Krebs cycle (TCA) occurs in __ for prokarya
cytoplasm
371
Krebs cycle (TCA) occurs in __ eukarya
mitochondrial matrix
372
Intermediates from Krebs Cycle as Building Blocks for Biosynthesis
amino acids
fatty acids
nucleotides
373
per turn of the cycle
1 CO2
3 NADH
1 FADH2
1 ATP (GTP)
374
2 turns for pyruvate would produce
6 NADH
2 FADH2
2 ATP (GTP)
375
Glycolysis
glucose -> NAD reduced to NADH
pyruvate net gain 2 ATP
either fermented or cellular resp.
fermentation is either aerobic or anaerobic - ETC
376
Respiration
anaerobic: -O2 final acceptor ex. nitrate
aerobic: +O2 final acceptor ex. oxygen
377
Cellular respiration
-catabolism from substrate breakdown to reduction of a terminal electron acceptor ex. O2
-catabolism by donating electrons from NADH to the ETS that stores energy by pumping protons
378
oxidative phosphorylation is used for
hydrogen ions return to cell via ATP synthase
379
ETS (electron transport system)
electrons from NADH and FADH2 passed rapidly from one ETS electron carrier to the next
in aerobic resp: final e- acceptor is OXYGEN and is reduced to water
in anaerobic resp: final e- acceptor is inorganic molecule other than oxygen
380
Pseudomonas aeruginosa
soil bacteria
anaerobic terminal electron acceptor
380
flavoprotien (flavo mononucleotide)
riboflavin B2
380
oxidative phosphorylation
reduction of oxygen to generate high-energy phosphate bonds in the form of ATP
381
coenzyme Q
non-protien
high energy
382
Cytochrome B
Iron contain Gp (heme)
383
as electrons go down ETS
higher electron negativity going down
384
how do inner and outer surfaces of the membrane differ
charge
pH
electrochemical potential
385
Q (guinone)
electron transfer is coupled to pumping H+ ions
carry electrons to another ETS complex pumping H+
386
Electron Transport Chain
series of protein complexes, electron carriers, ion pumps
pump H+ out of bacterial cytoplasm into Extracellular space
387
H+ flows back down the electrochemical gradient
into the bacterial cytoplasm through ATP synthase providing energy for ATP production by oxidative phosphorylation
388
How much ATP is generated
38 ATP
2 ATP glycolysis
2 ATP TCA cycle
10 NADH
2 FADH
389
ETS pumps H+
out of the cell
390
for every 3 H+ that flow through the F0
F1 rotates 1/3rd of the turn
catalyzes ADP conversion to ATP
391
Lithotrophy
alternative route to get electrons for ETS and PMF
unique energy pathway used only by some types of bacteria
392
Litotrophs serve as
electron donor
-Ferrous iron (FE2+)
-Ammonium ion (NH4+)
-Hydrogen gas (H2)
393
what serves as the final electrin acceptor for ETS
oxygen or alternative gas
394
in fermentation
final acceptor is made in the cell
pyruvic acid and electrons carried by NADH are from glycolysis and incorporated into fermentation end-products
395
fermentation
if respiration does not occur, NAD+ reuse as electron carrier for glycolysis
396
fermentation does not involve
ETS
-does not directly produce additional ATP beyond glycolysis by substrate-level phosphorylation
397
common fermentation pathways
alcohol -> ethanol, CO2
beer, bread
398
aerobic respiration
38 atp
glycolysis 2 atp
krebs 2 atp
etc 34 atp
399
anaerobic respiration
5-36 atp
glycolysis 2 atp
krebs 2 atp
etc 1-32 atp
400
fermentation
2 atp
glycolysis 2 atp
401
essential nutrients
microbe cannot make it but must gather it from its immediate environment to grow and divide
402
what are the essential nutrients
carbon
nitrogen
phosphorus
hydrogen
oxygen
sulfur
magnesium
iron
potassium
403
Shigella
growth factor: Nicotinamide (NAD)
disease: bloody diarhea
habitat: human intestina
404
S. auerus
multiple grown factors needed
405
autotrophs
make their own carbon compounds starting with CO2
406
heterotrophs
obtain carbon compounds from other compounds
407
chemotrophs can be either
chemoheterotroph
chemoautothroph
408
CO2 is a
chemoautotroph
409
what do chemoautotrophs do?
oxidize a variety of inorganic compounds
410
organic compounds are
chemoheterotroph
411
if O2 is the final electron acceptor
all animals, most fungi, protozoa, bacteria get it
412
if its an organic compound
fementative
ex. Streptococcus
413
if its an inorganic compound
ETC
ex. Clostridum
414
photoheterotrophs
green nonsulfur bacteria
purple nonsulfur bacteria
415
photoautotrophs that use H2O to reduce CO2
oxygenic photosynthesis (green plants, algae, cyanobacteria)
416
phototrophs that do not use H2O to reduce CO2
anoxygenic photosynthetic bacteria
417
physical requirements for growth
pH, temp, moisture, hydrostatic and osmotic pressure, radiation
418
chemical requirements for growth
carbon, nitrogen, sulfur, phosphorous, trace elements, organic compounds, oxygen availability
419
temperature extremophiles
hyperthermile (above 80 celcius)
thermophile (50-80)
Psychophile (below 15)
420
pH extremophiles
alkaliphile - above 9
neutralaphile- 5-8
acidophile- below pH 3
421
osmolarity extremophile
halophile (high salt, greater than 2 M NaCl)
421
facultative microbe
can grow with or without oxygen
422
pressure extremophile
barophile: high pressure, greater than 380 atm
423
variations in temperature
psychrophiles
mesophiles
thermophiles
424
psychrophile
membranes adapt
cold-loving microbe
425
mesophile
moderate temp loving microbes
in lab, 37 celcius is optimal for growth
426
thermophiles
heat-loving microbes
427
danger zone
15-50 celcius
rapid growth of bacteria, some may produce toxins
428
neutrophile
pH optimal: 7
ex. E coli
429
Acidophile
pH optimal: 5, 3
water drainage, cold mines
430
Alkaphile
pH optimal: 8,9,10
high carbonic soil
industrial commericial use
protease, lipase, laundry detergent
431
Sodium leaks into cytoplasm
ion pumps excrete Na, for K
balances charge and maintains pH
432
pH haemostasis
extracellular: pH
intracellular: macromolecular work
433
variations in pressure
membranes are high in unsaturated fatty acids so it doesnt get out and maintain fluidity
434
barophile
require high atmospheric pressure for growth
435
enzymes produced by barophilic bacteria function at high pressure
useful in bioractors, toxic clean-up in deep sea and high pressure food processors
436
water availability is measured as
water activity (aw)
-between 0 (no free water) and 1 (pure water)
437
halophiles
require high salt conc
438
halotolerant
grow and multiply in presense of high salt but do not require it for growth
439
osmophiles
organisms living in high sugar environment
440
water availability strategies
proton motive force
increase solutes within cytoplasm to counteract water loss
excrete sodium for K and maintain neutrality
441
isotonic solution
net water exchange = 0
solute conc in solute conc = higher
cell wall provides pressure
water comes into cell
442
alkalafile
sodium motive force
for microbe to grow in that env
443
plasmolyzed cell in hypertonic solution
environment is hypertonic
water leaves cell
growth of cell is inhibited
can increase number of AA and sugars
444
obtaining nitrogen
nitrogen fixation converts N2 (nitrogen) to NH4+ (ammonium ions) used for biosynthesis
445
decomposition
decay in plants -> ammonia
ammonification
446
legume -> ammonia
nitrogenase allows this via fixation
447
ammonia - nitrites
nitrification
448
ammonia is used for
synthesis of protiens in plants
449
nitrates
easily reaches roots of plants
450
nitrates to nitrite
denitrification
451
symbiotic
live within plants to help fix nitrogen
-Rhizobium, Bradyrhizobium
452
Assimilation
decay organisms (aerobic and anaerobic bacteria and fungi)
453
binary fission
origin of replication
- cytoplasm separates -> each daughter cell gets parental genome
454
binary fission steps in order
dna replication
cell elongation (growth)
formation of division septum
cell seperation
455
FtsZ
related to tubulin
cell division protein in eukarya
456
FTsZ ring
-anchors to the plasma membrane
-separates cytoplasm of new cells
-pinches cell envelope to separate cytoplasm of 2 cells
-cleavage furrow
457
generation time
time it takes for pop to double one round of binary fission
*depends on type of species
e. coli is quickest to replicate
458
generation time is expressed as
2^n
n= generations
459
lag phase`
very slow, needs to meet requirements
synthesis of AA, nucleotide, metabolite
aged culture -> repair
takes up most nutrients
no increase, just prepating
460
log phase
exponential growth
uses nutrients, has everything ready
quorum sensing
binary fission or mitosis
461
stationary phase
microbial death balance production of new
stress enzymes
decrease in cell size
endospores
increased antibiotic resistance
462
deathor decline phase
wastes and nutrients die off
decrease
463
mature endospore
dehydrated
contain calcium dipicolinate and SASPs
464
dipclonate acid
protects against heat and radiation
465
calcium ions
stabilize DNA
466
steps of sporulation
1. spore septum isolates newly replicated dna and small portion of cytoplasm
2. membrane is isolated
3. spore septum surrounds isolated portion
4. peptidoglycan layer forms between membranes
5. spore coat forms
6. release of endospore
467
population density is controlled by
concentration of limiting nutrient in reservoir
468
growth rate is controlled by
dilution rate
469
chemostat
continuous culture
nutrients are supplied at steady rate
470
culture media
feed: constantly added and
effluent: constantly removed
471
diluting medium increase
limiting nutrient increase
essential nutrient increase
growth increase
472
biofilms
mass of cells adhering to surfaces
start unattached, stick via lipposaccharide and flagella
473
if food is scarce
biofilms will look for another site to attach
474
3D biofilms are viewed via
Confocal microscope
475
multiple cells can overcome the immune system
increased resources lead to growth of pathogens
476
quorum sensing:
-cells find their presence in the environment
-lowest amt that can produce toxins to overcosume the immune system
-autoinducer: as conc increases, gene exp increases more regulatory changes in biofilm
477
planktonic cells
cells swim
twitch, glide: motility to search for nutrients to feed on
478
steps involved in biofilms
1. cellular flagella attach to monolayer
2. microcolonies form
3. cells produce EPS (exopolysaccharide)
4. biofilm matures
5. biofilm dissolves and cells disperse
479
Extracellular polymeric substance (EPS)
-protection against harmful substances
-shield from immune system, phagocytes, antibiotics and grow it in there
-water can go in, wastes go out
480
negatives of biofilms
can stay for months/ years in a host
negative in species
oil spill: biofilm adheres to it
nature
481
agar
complex polysaccharide
not metabolized by mirobes
used as solifying agent for culture media in peti
liquifies at 100 celcius
solidifes at 40 celcius
482
culture media
provides essential nutrients for bacteria
483
chemically defined media
exact chemical composition is known
484
complex media
made up of nutrients
exact chemical composition varies
485
reducing culture media
growth of obligate anaerobes
-sodium thioglycolate combinrd with oxygen
486
selective culture media
supression of unwanted microbes
487
differential
differentiation of colonies of desired microbes from others
488
enrichment
start with one microbe -> more
low -> detectable level of desired microbe
favor growth of particular microbe but not others
489
minimal medium
single carbon source
gene expression
mimics environment
-limited to nutrients organsms need to grow
490
blood agar
differentiate by streaking on diffential media
how they lyse RBCs, identify via complete, incomplete or no hemolysis
491
pure culture
one bacteria gives rise to one colony
streak them on differential media
1000 --> 10-20 via flame
492
isolation
streaking allows separation of colonies into pure cultures
population of identical cells
493
Anaerobe jar
Oxygen removed
Carbon dioxide generated
catalyst in lid and GasPak combine with oxygen so theres no more O2 to produce CO2 and H2 produces water
494
Anaerobic chamber
filled with inert gases
equipped w air locks to introduce cultures and materials
495
molecular oxygen
is not toxic, but O2 can be converted to toxic oxygen by-products
496
aerobic bacteria have to take care of
enzymes to take care of toxic byproducts
497
H2O2 hydrogen peroxide
catalase
498
H2O2 hydrogen peroxide
peroxide
499
O2- superoxide
superoxide dismutase
500
growth zones
aerobic (high oxygen): top
microaerophilic: low oxygen
anaerobic: bottom (no oxygen)
501
more crowding at top
obligate aerobe
+SOD
+Catalase
502
facultative anaerobe
+SOD
+Catalase
503
aerotolerant anaerobe
tolerate O2, fementative
+SOD
NO CATALASE
504
strict anaeribe
no enzymes
no not survive in O2
grow in bottom
505
microaerophile
dust- like O2
grow below rim
needs little bit of O2
506
aerobes
destroy reactive oxygen species with SOD to remove superoxide and peroxidase and catalase to remove hydrogen peroxide
507
mycobacterium lepae
clostridum spp
anaerobic microbe
508
filration method
selective and differential media
grow filter paper
-allows growth of coliform bacteria only
509
direct microscope count via counting chamber
does not yield accurate count of number of live cells
cant distinguish between live, dead and debris of same size under microscope
510
Flourescent labelling
differential staining
-stain only live cell, red are dead cells
511
FACS
count and separate bacterial cells that synthesize a flourescent protien
512
spread plate
early dilutions show confluent growth
each colony on agar plate represents one viable organism
513
pour [plate
heat sensitive bacterial isolates
514
dilute cultures
standard microbiology protocol
30:300
moves until you get isolated colonies
515
viable plate count
expressed as colony forming units
-number of viable or live cells
516
turbidity
measured in real time using spectrophotometer which passes a beam of light through sample of culture
-decrease in intensity of light due to scrattering of light = optical density
OD 600
