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CMMB 343 > midterm 2 > Flashcards

midterm 2 Flashcards

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1
Q

is CH4 inorganic or organic? is methanotrophy done by a heterotroph or autotroph?

A

organic therefore methanotrophy is carried out by a heterotroph

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2
Q

methanotrophy

A

using methane as a C source, produces CO2, is aerobic process (needs O2)

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3
Q

inorganic carbon source

A

autotrophy

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4
Q

organic carbon source

A

heterotrophy

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5
Q

organic chemical energy source

A

chemoorganotrophy

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6
Q

inorganic chemical energy source

A

chemolithotrophy

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7
Q

what are the last resort respirations when all other e- acceptors are used up?

A

methanogenesis or acetogenesis

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8
Q

methanogenesis

A

generates methane, anoxic (no O2)

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9
Q

largest fossil fuel, where form is it in greatest abundance

A

methane, frozen

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10
Q

nitrogen assimilation

A

the formation of organic nitrogen compounds like amino acids from inorganic nitrogen compounds present in the environment

NH3 (ammonia) –> NH2
or other inorganic N —> organic N

no redox rxn
done to use as a nutrient

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11
Q

anammox (Brocadia)

A

Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas

lithotrophy, anaerobic

NO2- and NH3 –> N2

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12
Q

denitrification

A

nitrate or nitrite into N2, reduction processes

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13
Q

N fixation

A

N2 into NH3 (ammonia), nutrient acquisition

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14
Q

nitrification

A

reduced forms of nitrogen are oxidised into nitrate (NO3-) or nitrite (NO2-)

could even inlcude NO2- –> NO3-

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15
Q

dissimilatory reduction of inorganic compounds

A

used in anaerobic respiration
ex: using N as a terminal e- acceptor

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16
Q

assimilatory reduction of inorganic compounds

A

using inorganic compounds, reducing them into nutrients

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17
Q

inorganic forms of N

A

N2 gas, nitrate NO3- , nitrite NO2-, ammonium NH4+, ammonia NH3

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18
Q

what rxn (anabolism or catabolism) synthesizes new cell material?

A

anabolism (energy input needed, endergonic)

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19
Q

do autotrophs or heterotrophs require more electrons to reduce their carbon sources?

A

autotrophs, need a lot of e- to reduce CO2

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20
Q

electrons will move ___ the redox tower during rxns, the greater the fall the greater the ____

A

down

energy yield is

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21
Q

what are 2 ways to produce ATP in a chemotroph

A

sub level phosphorylation
oxidative phosphorylation

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22
Q

When O2 is the terminal electron acceptor for energy generation, an organism is carrying out ?

A

aerobic respiration

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23
Q

using a terminal e- acceptor other than O2 for energy generation processes?

A

anaerobic respiration

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24
Q

fermentation

A

when the energy substrate is both the redox (e-) donor and acceptor

rearranges substrate into a lower energy state -> product

-uses pyruvate to regenerate more NAD+ for glycolysis

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25
what are the 4 steps in aerobic resp?
- glycolysis - Krebs cycle / CAC - ETC - ATP formation via F1F0 ATPase (pmf)
26
which steps of aerobic respiration are defined as oxidative phosphorylation?
ETC and making ATP using ATPase (atp pump)
27
2 atp are added during the ____ stage of glycolysis
activation stage
28
in glycolysis what are the e- acceptor and donor?
donor = G3P (previously glucose just broken up) acceptor = NAD+
29
what 2 products of glycolysis contain most of the energy of glucose?
NADH and pyruvate
30
is there substrate-level phosphorylation going on in the CAC?
yes, the step where ATP is made
31
what high energy products are made in the CAC that can be fed into the ETC? what do they do in the ETC?
FADH2, NADH, NADPH can act as e- donors (even primary one ->NADH)
32
one glucose turns the CAC ___ times
2 times (total 2 ATP produced)
33
ETC
-flow of electrons down a redox gradient is linked to the formation of a proton gradient -2 protons also consumed in the cytoplasm in the final step -the terminal electron acceptor in aerobic respiration is O2
34
one cycle (or 3 conformational changes) of the F1F0 ATPase generates how much ATP?
1 ATP
35
thru aerobic resp, one glucose molecule gets you how many ATP?
38 ATP (net)
36
ATP in fermentations is solely produced by ?
substrate-level phosphorylation
37
*what is the order of major e- acceptors????
1. O2 2. NO3- 3. Fe3+ 4. SO42- 5. CO2
38
where does a phototroph's reducing power come from?
H2O
39
where is H2S produced in the Win column?
the bottom by sulfate-reducing bacteria SO4 --> H2S (e- acceptor)
40
___trophs make up most of the Win column?
PHOTOTROPHS
41
anoxygenic phototrophs like purple or green sulfur bacteria get their reducing power from?
H2S (not O2)
42
what is the least and most oxidized nitrogen compound?
most reduced (-3) is organic N most oxidized (+5) is NO3-
43
biodegradation in the N cycle is?
ammonification organic N --> NH4+
44
denitrification is a _____ process
reduction
45
what process involving N, uses N as terminal e- acceptor in anaerobic respiration?
DISSimilatory reduction of N
46
anaerobic resp vs lithotrophy
anaerobic resp involves reduces inorganic compounds (not O2) to use as terminal e- acceptors lithotrophy involves OXIDIZING inorganic compounds to use as an ENERGY SOURCE
47
what are 2 things required for nitrification?
ATP and electrons
48
what things do the plant supply the rhizobium bacteroids with?
organic acids (succinate, malate, fumurate --> pyruvate) leghemoglobin brings O2
49
DNA in prokaryotes exists as ?
circular chromosomes, compacted through supercoiling (by gyrase)
50
primary function of fermentation
provides the cell with a mechanism to regenerate the oxidized form of electron carriers, allowing glycolysis to continue
51
function of NADH in fermentation
NADH provides the electrons to reduce pyruvic acid to either an organic acid or ethanol.
52
second-generation benefits vs first-gen (sanger sequence)
lower cost higher throughput
53
Potential ORFs are identified by locating
start and stop codons
54
The net energy gain from complete aerobic oxidation of one glucose molecule is:
38 ATP
55
multiple genes w similar functions under the control of a single promoter
an operon
56
genes in an operon cotranscribed into a ?
polycistronic mRNA
57
regulon
multiple operons all controlled by one signal molecule
58
prokaryotic gene expression steps
-Sigma 70 + DNA Pol = holoenzyme to initiate transcription -Sigma falls off = core enzyme, elongation of RNA strand -Termination stem-loop forms in newly synthesized RNA strand, termination of transcription
59
which region forms an attenuation stem-loop that leads to termination of transcription?
region 3-4
60
if sRNA binds directly at the 3' end of the mRNA, what happens?
translation will continue (it protects the mRNA from degredation)
61
if sRNA binds close to the RBS but not at the 3' end of the mRNA, what happens?
translation will STOP (it enhances endonuclease activity)
62
subcellular particles that can only replicate w/in a host cell
virus
63
how many sides of an icosahedral?
20
64
what things are the only known group to have an RNA genome?
viruses
65
the adsorption process of a virion
T4 fibers attach to LPS of outer membrane of bacteria
66
describe the eclipse stage
right after virus is added, virus takes over host, early enzymes kick in to produce viral nucleic acid and protein
67
what things are transcribed during early T4 synthesis?
anti-sigma factor proteins that inhibit host sigma factors also phage-specific replisome
68
T4 DNA is?
DOUBLE STRANDED AND LINEAR T4 is also a lytic virus
69
what genome is terminally redundant?
T4
70
how does T4 avoid bacterial host defenses?
it modifies its cytosine residues changes to a 5-hydroxymethylcytosine (swaps a H for C2HOH) called glucosylation
71
bacteriophage lambda
TEMPERATE PHAGE, linear dsDNA
72
whats a lysogen? wb a prophage?
prophage is the viral DNA integrated into a host genome the host w the prophage in its genome is now called a lysogen
73
what does a lambda tail attach to on the host during adsorption?
host maltose transport protein
74
most infections result in ___ infection
lytic
75
what represses cl gene
cro
76
true or false: both T4 and lambda progeny have unique genomes due to random cut sites during replication in hosts
false, lambda progenies all have the same genome cuz the concatemers are cut at cos sites during rolling circle replication
77
not all ____ are transducing, and not all _____ are transducible
not all phage are transducing, and not all prokaryotes are transducible
78
phage conversion is done by a ?
temperate phage during multiple lysogenic infections
79
are animal or plant viruses usually naked? which cells are harder to infect?
plant viruses are naked and plant cells are harder to infect
80
a naked virus with a broad host range is most likely?
a plant virus
81
what are the (+) virus classes?
class I and VII, class III, class VI 1, 3, 5, 6
82
what are the DNA viruses??
class I, II, VII 1, 2, 7 remember 12
83
the only double stranded virus genomes are in which classes?
class I and VII, class III 1, 7, 3
84
what is parvovirus?
class 2 ssDNA (+)
85
what is rotavirus
class 3 dsRNA (+)
86
what viral classes are negative?
ONLY CLASS 5 U MORON (V)
87
whats poliovirus homie??
class IV (4 u dummy) ssRNA (+) can be used directly as mRNA
88
whats the only viral class that can be used directly as mRNA
CLASS IV ex: poliovirus
89
rabies and influenza are (+) or (-)?? also are they ds or ss, RNA or DNA?
(-) ssRNA
90
which class includes the bacteriophages phi and M13?
class 2
91
mRNA only made from ___ sense DNA
negative
92
the most common human viruses belong to class?
4 (IV) these are (+) ssRNAs
93
coronavirus is class?
(IV) four it is (+) ssRNA
94
phage T4 would be in what class?
class 1 dsDNA
95
which virus contains VPg protein to help w ribosome bonding and yields a polyprotein
polio
96
what is veryyyyy small, naked, icosahedral, (+) ssRNA virus?
poliovirus
97
whats a virus transmitted via aerosols?
influenza
98
which virus is (-) ssRNA and has a broad set of hosts?
influenza
99
what virus has multiple capsids surrounding its genome? what class is it in?
rotavirus (diarrhea) dsRNA class 3

CMMB 343 (3 decks)

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