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CMMB 343 > midterm 2 > Flashcards

midterm 2 Flashcards

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
Q

what are the 4 steps in aerobic resp?

A
  • glycolysis
  • Krebs cycle / CAC
  • ETC
  • ATP formation via F1F0 ATPase (pmf)
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26
Q

which steps of aerobic respiration are defined as oxidative phosphorylation?

A

ETC and making ATP using ATPase (atp pump)

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27
Q

2 atp are added during the ____ stage of glycolysis

A

activation stage

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28
Q

in glycolysis what are the e- acceptor and donor?

A

donor = G3P (previously glucose just broken up)

acceptor = NAD+

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29
Q

what 2 products of glycolysis contain most of the energy of glucose?

A

NADH and pyruvate

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30
Q

is there substrate-level phosphorylation going on in the CAC?

A

yes, the step where ATP is made

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31
Q

what high energy products are made in the CAC that can be fed into the ETC? what do they do in the ETC?

A

FADH2, NADH, NADPH

can act as e- donors (even primary one ->NADH)

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32
Q

one glucose turns the CAC ___ times

A

2 times (total 2 ATP produced)

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33
Q

ETC

A

-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

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34
Q

one cycle (or 3 conformational changes) of the F1F0 ATPase generates how much ATP?

A

1 ATP

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35
Q

thru aerobic resp, one glucose molecule gets you how many ATP?

A

38 ATP (net)

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36
Q

ATP in fermentations is solely produced by ?

A

substrate-level phosphorylation

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37
Q

*what is the order of major e- acceptors????

A
  1. O2
  2. NO3-
  3. Fe3+
  4. SO42-
  5. CO2
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38
Q

where does a phototroph’s reducing power come from?

A

H2O

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39
Q

where is H2S produced in the Win column?

A

the bottom by sulfate-reducing bacteria

SO4 –> H2S (e- acceptor)

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40
Q

___trophs make up most of the Win column?

A

PHOTOTROPHS

41
Q

anoxygenic phototrophs like purple or green sulfur bacteria get their reducing power from?

A

H2S (not O2)

42
Q

what is the least and most oxidized nitrogen compound?

A

most reduced (-3) is organic N

most oxidized (+5) is NO3-

43
Q

biodegradation in the N cycle is?

A

ammonification
organic N –> NH4+

44
Q

denitrification is a _____ process

A

reduction

45
Q

what process involving N, uses N as terminal e- acceptor in anaerobic respiration?

A

DISSimilatory reduction of N

46
Q

anaerobic resp vs lithotrophy

A

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
Q

what are 2 things required for nitrification?

A

ATP and electrons

48
Q

what things do the plant supply the rhizobium bacteroids with?

A

organic acids (succinate, malate, fumurate –> pyruvate)
leghemoglobin brings O2

49
Q

DNA in prokaryotes exists as ?

A

circular chromosomes, compacted through supercoiling (by gyrase)

50
Q

primary function of fermentation

A

provides the cell with a mechanism to regenerate the oxidized form of electron carriers, allowing glycolysis to continue

51
Q

function of NADH in fermentation

A

NADH provides the electrons to reduce pyruvic acid to either an organic acid or ethanol.

52
Q

second-generation benefits vs first-gen (sanger sequence)

A

lower cost
higher throughput

53
Q

Potential ORFs are identified by locating

A

start and stop codons

54
Q

The net energy gain from complete aerobic oxidation of one glucose molecule
is:

A

38 ATP

55
Q

multiple genes w similar functions under the control of a single promoter

A

an operon

56
Q

genes in an operon cotranscribed into a ?

A

polycistronic mRNA

57
Q

regulon

A

multiple operons all controlled by one signal molecule

58
Q

prokaryotic gene expression steps

A

-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
Q

which region forms an attenuation stem-loop that leads to termination of transcription?

A

region 3-4

60
Q

if sRNA binds directly at the 3’ end of the mRNA, what happens?

A

translation will continue
(it protects the mRNA from degredation)

61
Q

if sRNA binds close to the RBS but not at the 3’ end of the mRNA, what happens?

A

translation will STOP
(it enhances endonuclease activity)

62
Q

subcellular particles that can only replicate w/in a host cell

A

virus

63
Q

how many sides of an icosahedral?

A

20

64
Q

what things are the only known group to have an RNA genome?

A

viruses

65
Q

the adsorption process of a virion

A

T4 fibers attach to LPS of outer membrane of bacteria

66
Q

describe the eclipse stage

A

right after virus is added, virus takes over host, early enzymes kick in to produce viral nucleic acid and protein

67
Q

what things are transcribed during early T4 synthesis?

A

anti-sigma factor proteins that inhibit host sigma factors
also phage-specific replisome

68
Q

T4 DNA is?

A

DOUBLE STRANDED AND LINEAR
T4 is also a lytic virus

69
Q

what genome is terminally redundant?

A

T4

70
Q

how does T4 avoid bacterial host defenses?

A

it modifies its cytosine residues
changes to a 5-hydroxymethylcytosine (swaps a H for C2HOH)
called glucosylation

71
Q

bacteriophage lambda

A

TEMPERATE PHAGE, linear dsDNA

72
Q

whats a lysogen? wb a prophage?

A

prophage is the viral DNA integrated into a host genome
the host w the prophage in its genome is now called a lysogen

73
Q

what does a lambda tail attach to on the host during adsorption?

A

host maltose transport protein

74
Q

most infections result in ___ infection

A

lytic

75
Q

what represses cl gene

A

cro

76
Q

true or false: both T4 and lambda progeny have unique genomes due to random cut sites during replication in hosts

A

false, lambda progenies all have the same genome cuz the concatemers are cut at cos sites during rolling circle replication

77
Q

not all ____ are transducing, and not all _____ are transducible

A

not all phage are transducing, and not all prokaryotes are transducible

78
Q

phage conversion is done by a ?

A

temperate phage during multiple lysogenic infections

79
Q

are animal or plant viruses usually naked? which cells are harder to infect?

A

plant viruses are naked and plant cells are harder to infect

80
Q

a naked virus with a broad host range is most likely?

A

a plant virus

81
Q

what are the (+) virus classes?

A

class I and VII, class III, class VI

1, 3, 5, 6

82
Q

what are the DNA viruses??

A

class I, II, VII
1, 2, 7

remember 12

83
Q

the only double stranded virus genomes are in which classes?

A

class I and VII, class III

1, 7, 3

84
Q

what is parvovirus?

A

class 2
ssDNA (+)

85
Q

what is rotavirus

A

class 3
dsRNA (+)

86
Q

what viral classes are negative?

A

ONLY CLASS 5 U MORON (V)

87
Q

whats poliovirus homie??

A

class IV (4 u dummy)
ssRNA (+)
can be used directly as mRNA

88
Q

whats the only viral class that can be used directly as mRNA

A

CLASS IV
ex: poliovirus

89
Q

rabies and influenza are (+) or (-)??
also are they ds or ss, RNA or DNA?

A

(-) ssRNA

90
Q

which class includes the bacteriophages phi and M13?

A

class 2

91
Q

mRNA only made from ___ sense DNA

A

negative

92
Q

the most common human viruses belong to class?

A

4 (IV)
these are (+) ssRNAs

93
Q

coronavirus is class?

A

(IV) four
it is (+) ssRNA

94
Q

phage T4 would be in what class?

A

class 1
dsDNA

95
Q

which virus contains VPg protein to help w ribosome bonding and yields a polyprotein

A

polio

96
Q

what is veryyyyy small, naked, icosahedral, (+) ssRNA virus?

A

poliovirus

97
Q

whats a virus transmitted via aerosols?

A

influenza

98
Q

which virus is (-) ssRNA and has a broad set of hosts?

A

influenza

99
Q

what virus has multiple capsids surrounding its genome? what class is it in?

A

rotavirus (diarrhea)
dsRNA
class 3

CMMB 343 (3 decks)

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