midterm 2 Flashcards
(109 cards)
1
Q
4 steps of binary fission
A
cell elongation
chromosome replication and separation
septum formation
cell division
2
Q
4 stages of growth curve
A
lag, log, stationary, death
3
Q
lag length young cells from same medium
A
brief
4
Q
lag length old cells in same medium
A
longer than young
5
Q
lag length damaged cells
A
longer still
6
Q
lag length nutrient rich to nutrient poor
A
longest
7
Q
2 differing explanations for cell loss in the death or senescence phase
A
death but no lysis (original assumption)
viable but nonculturable
programmed cell death
8
Q
deterime generation time
A
use exponential phase data only
population = original # x 2^n
n = # of generations
9
Q
factors that affect generation time
A
nutrient uptake
type of metabolism
what it needs to synthesize
10
Q
hypotonic environment
A
less salt outside
water enters, cell bursts
must decrease osmotic pressure with inclusion bodies
open mechanosensitive (MS) channels - solutes can leave
11
Q
hypertonic environment
A
more solutes outside
water leaves
cell increases internal solutes with compatible solutes
12
Q
compatible solutes
A
K, amino acids, sugars,
not Na
13
Q
halophiles
A
salt lovers
> .2 M NaCl
14
Q
extreme halophiles
A
2 - 6.2 M NaCl
15
Q
halotolerant
A
can withstand large changes in NaCl
16
Q
water activity
A
degree of water availability
1 = straight water
17
Q
osmotolerant
A
able to grow over wide ranges of aw
18
Q
neutrophiles
A
grow at neutral pH (5.5-8)
19
Q
acidophiles
A
low pH
net outward of protons
20
Q
alkophiles
A
high pH
inward of protons (H Na fluxes)
21
Q
temperature classifications
A
psychrophile psychrotroph mesophile thermophile hyperthermophile
22
Q
protective enzymes of oxygen metabolism
A
catalase, peroxidase, superoxide dismutase
23
Q
aerobes
A
need O2
have SOD and catalase
just at top of tube
24
Q
microaerophiles
A
only grow in low levels of O2
have SOD, maybe catalase
just in upper middle of tube
25
facultative anaerobe
can use or not use O2
have SOD and catalase
most at top of tube, less throughout
26
aerotolerant anaerobe
no preference
have SOD
equal throughout tube
27
strict/obligate anaerobe
killed by O2
no SOD or catalase
at bottom of tube
28
barotolerant
tolerate increased pressure
29
barophilic/piezophilic
grow more at high pressure
30
oligotrophic environment
low nutrient concentrations
| microbes more competitive
31
biofilms
growth of complex, slime encased communities
32
biofilm formation
pre conditioning of surface
cell deposition and absorption
matrix formation (excellular polymeric substances)
detachment and sloughing
33
benefits of biofilms to microbes
increase nutrient concentration on surfaces, resistance, gene expression, movement to other locations
34
quorum sensing
communication using small organic molecules (autoinducers)
assess population density
target level induces gene expression
35
quorum sensing example
```
marine bioluminescent bacteria
AHL is autoinducer
squid has light organ that houses bacteria, reach quorum to be effective
microbe provides light
animal provides nutrients/ habitat
```
36
common aspects of metabolism
1st law of thermo, use of ATP and redox reactions, chemical reactions into pathways, enzymes, regulation pathways
37
3 major types of work by cells
chemical - synthesis of macromolecules
transport - take up nutrients, ion balance
mechanical - motility
38
exergonic
favorable, delta G negative, give off energy
| ATP stores energy given off
39
endergonic
not favorable, delta G positive
| ATP drives
40
redox potentials
measured as standard reduction potential in volts
more negative - more likely to reduce compound (e donor)
listed as oxidized/reduced, aceptor/donor
41
delta G 0 prime calculated...
acceptor - donor
42
electron carriers
most negative to most positive
| associated with membranes
43
NAD+/NADP+
2 e, 1 proton
44
FAD/ FMN
2 e, 2 protons
45
coenzyme Q
2 e, 2 protons
46
cytochromes
1 e at a time
47
Fe-S proteins
1 e at a time
48
apoenzyme
protein part
49
co-factor
non protein part of enzyme
50
prosthetic group
firmly attached co factor
51
co - enzyme
loosely attached co factor
52
haloenzyme
complete enzyme
53
allosteric effector
molecules that reversibly binds to regulatory site
positive = activity
negative = inactivity
54
source of carbon
heterotroph - use preformed organic material
| autotroph - use CO2
55
source of energy
phototroph - light
| chemotroph - organic/inorganic oxidation
56
source of electrons
lithotroph - reduced inorganic molecules
| organotroph - organic molecules
57
glycolysis
```
glucose to pyruvate
2 ATPs used
NAD --> 2NADH
4 ATP formed by substrate level phosphorylation
2 pyruvate formed
net 2 ATP
```
58
TCA cycle
```
pyruvate oxidized to 3 CO2
--> 3 NADH
--> FADH2
GTP by substrate level phosphorylation
oxaloacetate regenerated
32 ATP max/glucose
1 pyruvate --> 1 GTP
```
59
TCA cycle connecting reaction
pyruvate --> acetyl CoA and CO2
| --> NADH
60
oxidative phosphorylation
synthesis of ATP from e transport
| oxidation of chemical energy source
61
chemiosmotic hypothesis
some carrier carry e and protons, others only e.
H pumped outside membrane in max 3 places.
results in PMF, voltage and pH gradient across membrane
62
anaerobic respiration
starts with glycolysis, used TCA
other than O2 as final e acceptor
shortened ETC, less protons pumped, less ATP
63
fermentation
```
starts with glycolysis
no TCA or ETC
2 net ATP/glucose
pyruvate final e acceptor
NADH --> NAD+
```
64
chemolithoautotrophs
carbon from CO2
energy from organic/inorganic oxidation
electrons from reduced inorganic molecules
65
cehmolithoautotrophs need...
NADPH and ATP to reduce CO2 to make glucose
most e donors have more + reduction pot. than NAD..use reverse electron flow, e transferred to NAD, not energetically favorable
66
hydrogen oxidizers
oxidize hydrogen gas, use hydrogenase
donor: H2
acceptor: O2, Fe3+, S, CO
ATP by oxidative phosphorylation
67
sulfur oxidizers
oxidize sulfur compounds
donor: sulfur, hydrogen sulfide, thiosulfide, etc.
acceptors: O2, NO3-
sulfuric acid as byproduct
ATP by oxidative and substrate level phosphorylation
68
methane oxidizers
donor: CH4
acceptor: O2
atp by oxidative phos.
69
anaerobic methane oxidizers
acceptor: sulfate
may be most plentiful organism on earth
on bottom of ocean
70
nitrogen oxidizers
donors: NH4+, NO2-
acceptors: O2
atp by oxidative phos.
71
nitrogen fixation
reduction of nitrogen gas to ammonia
72
requirements for nitrogen fixation
```
nitrogenase enzyme
system/structure to protect enzyme from oxygen
ATP
electron carrier (ferredoxin)
regulatory system
```
73
symbiotic nitrogen fixers
Rhizobium: bacteria fixes N, plant provides energy and oxygen free area (root nodule)
74
free living aerobic nitrogen fixers
azotobacter - uses O2 quickly, protein protects nitrogenase enzyme, cysts
cyanobacteria - heterocysts = specialized cells for N2 fixation, only cyclic photosynthesis (no O2 produced)
75
ammonia incorporation
ammonia to organic N (amino acids)
76
nitrification
oxidation of ammonium to nitrate
NH4 + --> NO2- --> NO3-
only chemolithorophic bacteria
atp by oxidative phos.
77
assimilatory nitrate reduction
reduction of nitrate (NO3-) to ammonia (NH3) to organic N
nitrate reductase and nitrite reductase
many plants and microbes
78
dissimilatory nitrate reduction
nitrate (NO3-) to reduced inorganic N (N2, N2O, NO2-)
microbes during anaerobic respiration
nitrate is final e acceptor when O2 not available
79
denitrification
NO3- --> NO2- --> N2 reduce nitrate to nitrogen gas
multistep, 4 enzymes
bacteria using anaerobic respiration
80
annamox reaction
NH4+ + NO2- --> N2 + 2H2O
NH4+ is e donor, NO2- is acceptor
marine bacteria in anoxic water
removes nitrogen from environment
81
2 parts of photosynthesis
phototrophy: light energy to ATP
| reduction and incorporation of CO2 (ATP used to fix CO2)
82
4 groups of bacteria that use photosynthesis
cyanobacteria
purple photosynthetic
green photosynthetic
halophilic archaea
83
chlorophylls
euk. and cyanobacteria = chlorophyll a
| green and purple bacteria = bacteriochlorophhyll (light at higher wavelengths)
84
accessory pigments
protection from UV light, capture broader wavelength of light
85
ATP is photosynthesis formed by
chemiosmosis from PMF
ATP synthase
photophosphorylation
86
to fix CO in photosynthesis..
NADPH generated for reducing power
87
NAD vs. NADP
NAD: catabolic, energy generating reactions, e given off
NADP: synthesis, energy requiring reactions, electrons required
88
oxygenic photophosphorylation of cyanobacteria
non cyclic
Z pathway - 2 membrane bound photosystems
ATP and NADP formed in ETC
e donor: hydrolysis of water, O2 as product
89
Z pathway
light hits PSII, water hydrolyzed, e raised to excited state, travels through ETC, ATPase
lights hits PSI, e travels through ETC, final acceptor is NADP
90
cyclic photophosphorylation of cyanobacteria
no oxygen formed (n fixation)
only PSI
for low light intensity and heterocysts
NADPH not formed, no reducing power
91
anoxygenic photosysthesis
1 PS (cyclic)
H2O not e source, no O2 formed
uses bacteriochlorophylls
different mech. for NADPH
92
photosynthetic purple bacteria
```
similar to PSII
as photoheterotroph (preference) - PS onlly for ATP
as photoautoroph - need reducing power, use reverse e flow and external e donor
```
93
reverse e flow in photosynthetic purple bacteria
e donated from external donor, reverse e flow, NADP+ reduced via energy from proton gradient
94
photosynthetic green bacteria
similar to PSI
to make ATP or NADPH (only 1 or other at a time)
external e donor is NADPH
no reverse e flow
95
rhodopsin-based phototrophy
halobacterium
use membrane protein archaeorhodopsin
in low and high light
light drived proton pump, no ETC
96
types of recombination
homologous - with long regions of identical DNA, strand break and cross over, uses RecA
site specific- not need long regions of DNA homology, at specific DNA target sites, recombinases catalyze
97
transposition
internal recombination
| transposable elements activate/inactivate genes
98
insertion sequences (IS elements)
simplest transposable elements, have gene from transposase, bounded by inverted repeats
99
transposons
carry IS elements + additional gene(s)
100
conjugative transposons or integrative conjugative elements (ICEs)
transposons with transfer genes (conjugation)
101
simple transposition
cut and paste
102
replicative transposition
original transposon stays, copy inserted elsewhere
103
3 types of horizontal gene transfer
bacterial conjugation
transformation
transduction (generalized and specialized)
104
conjugation
```
DNA transfer by direct cell to cell contact
non recipriocal
mediated by plasmid
contact by sex pilus
fertility factor: F + is donor
```
105
transformation
uptake of naked DNA into cell
random, any portion of genome
recipient = competent cell (able to take up DNA)
106
competency
cells in certain stage of growth
have protein complexes to escort DNA across
gram + require competence factor
gram - or artificail = no competence factor, take up closely related DNA only
107
transduction
transfer of bacterial genes by viruses, with bacteriophage
108
generalized transduction
only bacterial DNA packaged into 1 viral capsid by mistake, random fragments
during lytic cycle (virulent)
109
specialized transduction
viral and bacterial DNA packaged into viral capsids, specific portion of bacterial genome
during lysogenic cycle (temperate)
development of prophage, improperly excised
