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MB 302 > midterm 2 > Flashcards

midterm 2 Flashcards

1
Q

4 steps of binary fission

A

cell elongation
chromosome replication and separation
septum formation
cell division

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2
Q

4 stages of growth curve

A

lag, log, stationary, death

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3
Q

lag length young cells from same medium

A

brief

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4
Q

lag length old cells in same medium

A

longer than young

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5
Q

lag length damaged cells

A

longer still

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6
Q

lag length nutrient rich to nutrient poor

A

longest

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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

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8
Q

deterime generation time

A

use exponential phase data only
population = original # x 2^n
n = # of generations

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9
Q

factors that affect generation time

A

nutrient uptake
type of metabolism
what it needs to synthesize

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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

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11
Q

hypertonic environment

A

more solutes outside
water leaves
cell increases internal solutes with compatible solutes

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12
Q

compatible solutes

A

K, amino acids, sugars,

not Na

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13
Q

halophiles

A

salt lovers

> .2 M NaCl

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14
Q

extreme halophiles

A

2 - 6.2 M NaCl

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15
Q

halotolerant

A

can withstand large changes in NaCl

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16
Q

water activity

A

degree of water availability

1 = straight water

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17
Q

osmotolerant

A

able to grow over wide ranges of aw

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18
Q

neutrophiles

A

grow at neutral pH (5.5-8)

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19
Q

acidophiles

A

low pH

net outward of protons

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20
Q

alkophiles

A

high pH

inward of protons (H Na fluxes)

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21
Q

temperature classifications

A 
psychrophile
psychrotroph
mesophile
thermophile
hyperthermophile
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22
Q

protective enzymes of oxygen metabolism

A

catalase, peroxidase, superoxide dismutase

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23
Q

aerobes

A

need O2
have SOD and catalase
just at top of tube

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24
Q

microaerophiles

A

only grow in low levels of O2
have SOD, maybe catalase
just in upper middle of tube

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25
Q

facultative anaerobe

A

can use or not use O2
have SOD and catalase
most at top of tube, less throughout

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26
Q

aerotolerant anaerobe

A

no preference
have SOD
equal throughout tube

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27
Q

strict/obligate anaerobe

A

killed by O2
no SOD or catalase
at bottom of tube

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28
Q

barotolerant

A

tolerate increased pressure

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29
Q

barophilic/piezophilic

A

grow more at high pressure

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30
Q

oligotrophic environment

A

low nutrient concentrations

microbes more competitive

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31
Q

biofilms

A

growth of complex, slime encased communities

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32
Q

biofilm formation

A

pre conditioning of surface
cell deposition and absorption
matrix formation (excellular polymeric substances)
detachment and sloughing

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33
Q

benefits of biofilms to microbes

A

increase nutrient concentration on surfaces, resistance, gene expression, movement to other locations

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34
Q

quorum sensing

A

communication using small organic molecules (autoinducers)
assess population density
target level induces gene expression

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35
Q

quorum sensing example

A 
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
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36
Q

common aspects of metabolism

A

1st law of thermo, use of ATP and redox reactions, chemical reactions into pathways, enzymes, regulation pathways

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37
Q

3 major types of work by cells

A

chemical - synthesis of macromolecules
transport - take up nutrients, ion balance
mechanical - motility

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38
Q

exergonic

A

favorable, delta G negative, give off energy

ATP stores energy given off

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39
Q

endergonic

A

not favorable, delta G positive

ATP drives

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40
Q

redox potentials

A

measured as standard reduction potential in volts
more negative - more likely to reduce compound (e donor)
listed as oxidized/reduced, aceptor/donor

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41
Q

delta G 0 prime calculated…

A

acceptor - donor

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42
Q

electron carriers

A

most negative to most positive

associated with membranes

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43
Q

NAD+/NADP+

A

2 e, 1 proton

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44
Q

FAD/ FMN

A

2 e, 2 protons

45
Q

coenzyme Q

A

2 e, 2 protons

46
Q

cytochromes

A

1 e at a time

47
Q

Fe-S proteins

A

1 e at a time

48
Q

apoenzyme

A

protein part

49
Q

co-factor

A

non protein part of enzyme

50
Q

prosthetic group

A

firmly attached co factor

51
Q

co - enzyme

A

loosely attached co factor

52
Q

haloenzyme

A

complete enzyme

53
Q

allosteric effector

A

molecules that reversibly binds to regulatory site
positive = activity
negative = inactivity

54
Q

source of carbon

A

heterotroph - use preformed organic material

autotroph - use CO2

55
Q

source of energy

A

phototroph - light

chemotroph - organic/inorganic oxidation

56
Q

source of electrons

A

lithotroph - reduced inorganic molecules

organotroph - organic molecules

57
Q

glycolysis

A 
glucose to pyruvate 
2 ATPs used 
NAD --> 2NADH
4 ATP formed by substrate level phosphorylation 
2 pyruvate formed 
net 2 ATP
58
Q

TCA cycle

A 
pyruvate oxidized to 3 CO2
--> 3 NADH
--> FADH2
GTP by substrate level phosphorylation 
oxaloacetate regenerated 
32 ATP max/glucose 
1 pyruvate --> 1 GTP
59
Q

TCA cycle connecting reaction

A

pyruvate –> acetyl CoA and CO2

–> NADH

60
Q

oxidative phosphorylation

A

synthesis of ATP from e transport

oxidation of chemical energy source

61
Q

chemiosmotic hypothesis

A

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
Q

anaerobic respiration

A

starts with glycolysis, used TCA
other than O2 as final e acceptor
shortened ETC, less protons pumped, less ATP

63
Q

fermentation

A 
starts with glycolysis 
no TCA or ETC
2 net ATP/glucose
pyruvate final e acceptor 
NADH --> NAD+
64
Q

chemolithoautotrophs

A

carbon from CO2
energy from organic/inorganic oxidation
electrons from reduced inorganic molecules

65
Q

cehmolithoautotrophs need…

A

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
Q

hydrogen oxidizers

A

oxidize hydrogen gas, use hydrogenase
donor: H2
acceptor: O2, Fe3+, S, CO
ATP by oxidative phosphorylation

67
Q

sulfur oxidizers

A

oxidize sulfur compounds
donor: sulfur, hydrogen sulfide, thiosulfide, etc.
acceptors: O2, NO3-
sulfuric acid as byproduct
ATP by oxidative and substrate level phosphorylation

68
Q

methane oxidizers

A

donor: CH4
acceptor: O2
atp by oxidative phos.

69
Q

anaerobic methane oxidizers

A

acceptor: sulfate
may be most plentiful organism on earth
on bottom of ocean

70
Q

nitrogen oxidizers

A

donors: NH4+, NO2-
acceptors: O2
atp by oxidative phos.

71
Q

nitrogen fixation

A

reduction of nitrogen gas to ammonia

72
Q

requirements for nitrogen fixation

A 
nitrogenase enzyme 
system/structure to protect enzyme from oxygen 
ATP
electron carrier (ferredoxin) 
regulatory system
73
Q

symbiotic nitrogen fixers

A

Rhizobium: bacteria fixes N, plant provides energy and oxygen free area (root nodule)

74
Q

free living aerobic nitrogen fixers

A

azotobacter - uses O2 quickly, protein protects nitrogenase enzyme, cysts
cyanobacteria - heterocysts = specialized cells for N2 fixation, only cyclic photosynthesis (no O2 produced)

75
Q

ammonia incorporation

A

ammonia to organic N (amino acids)

76
Q

nitrification

A

oxidation of ammonium to nitrate
NH4 + –> NO2- –> NO3-
only chemolithorophic bacteria
atp by oxidative phos.

77
Q

assimilatory nitrate reduction

A

reduction of nitrate (NO3-) to ammonia (NH3) to organic N
nitrate reductase and nitrite reductase
many plants and microbes

78
Q

dissimilatory nitrate reduction

A

nitrate (NO3-) to reduced inorganic N (N2, N2O, NO2-)
microbes during anaerobic respiration
nitrate is final e acceptor when O2 not available

79
Q

denitrification

A

NO3- –> NO2- –> N2 reduce nitrate to nitrogen gas
multistep, 4 enzymes
bacteria using anaerobic respiration

80
Q

annamox reaction

A

NH4+ + NO2- –> N2 + 2H2O
NH4+ is e donor, NO2- is acceptor
marine bacteria in anoxic water
removes nitrogen from environment

81
Q

2 parts of photosynthesis

A

phototrophy: light energy to ATP

reduction and incorporation of CO2 (ATP used to fix CO2)

82
Q

4 groups of bacteria that use photosynthesis

A

cyanobacteria
purple photosynthetic
green photosynthetic
halophilic archaea

83
Q

chlorophylls

A

euk. and cyanobacteria = chlorophyll a

green and purple bacteria = bacteriochlorophhyll (light at higher wavelengths)

84
Q

accessory pigments

A

protection from UV light, capture broader wavelength of light

85
Q

ATP is photosynthesis formed by

A

chemiosmosis from PMF
ATP synthase
photophosphorylation

86
Q

to fix CO in photosynthesis..

A

NADPH generated for reducing power

87
Q

NAD vs. NADP

A

NAD: catabolic, energy generating reactions, e given off
NADP: synthesis, energy requiring reactions, electrons required

88
Q

oxygenic photophosphorylation of cyanobacteria

A

non cyclic
Z pathway - 2 membrane bound photosystems
ATP and NADP formed in ETC
e donor: hydrolysis of water, O2 as product

89
Q

Z pathway

A

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
Q

cyclic photophosphorylation of cyanobacteria

A

no oxygen formed (n fixation)
only PSI
for low light intensity and heterocysts
NADPH not formed, no reducing power

91
Q

anoxygenic photosysthesis

A

1 PS (cyclic)
H2O not e source, no O2 formed
uses bacteriochlorophylls
different mech. for NADPH

92
Q

photosynthetic purple bacteria

A 
similar to PSII
as photoheterotroph (preference) - PS onlly for ATP 
as photoautoroph - need reducing power, use reverse e flow and external e donor
93
Q

reverse e flow in photosynthetic purple bacteria

A

e donated from external donor, reverse e flow, NADP+ reduced via energy from proton gradient

94
Q

photosynthetic green bacteria

A

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
Q

rhodopsin-based phototrophy

A

halobacterium
use membrane protein archaeorhodopsin
in low and high light
light drived proton pump, no ETC

96
Q

types of recombination

A

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
Q

transposition

A

internal recombination

transposable elements activate/inactivate genes

98
Q

insertion sequences (IS elements)

A

simplest transposable elements, have gene from transposase, bounded by inverted repeats

99
Q

transposons

A

carry IS elements + additional gene(s)

100
Q

conjugative transposons or integrative conjugative elements (ICEs)

A

transposons with transfer genes (conjugation)

101
Q

simple transposition

A

cut and paste

102
Q

replicative transposition

A

original transposon stays, copy inserted elsewhere

103
Q

3 types of horizontal gene transfer

A

bacterial conjugation
transformation
transduction (generalized and specialized)

104
Q

conjugation

A 
DNA transfer by direct cell to cell contact
non recipriocal 
mediated by plasmid
contact by sex pilus 
fertility factor: F + is donor
105
Q

transformation

A

uptake of naked DNA into cell
random, any portion of genome
recipient = competent cell (able to take up DNA)

106
Q

competency

A

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
Q

transduction

A

transfer of bacterial genes by viruses, with bacteriophage

108
Q

generalized transduction

A

only bacterial DNA packaged into 1 viral capsid by mistake, random fragments
during lytic cycle (virulent)

109
Q

specialized transduction

A

viral and bacterial DNA packaged into viral capsids, specific portion of bacterial genome
during lysogenic cycle (temperate)
development of prophage, improperly excised

MB 302 (3 decks)

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