midterm 2 Flashcards
is CH4 inorganic or organic? is methanotrophy done by a heterotroph or autotroph?
organic therefore methanotrophy is carried out by a heterotroph
methanotrophy
using methane as a C source, produces CO2, is aerobic process (needs O2)
inorganic carbon source
autotrophy
organic carbon source
heterotrophy
organic chemical energy source
chemoorganotrophy
inorganic chemical energy source
chemolithotrophy
what are the last resort respirations when all other e- acceptors are used up?
methanogenesis or acetogenesis
methanogenesis
generates methane, anoxic (no O2)
largest fossil fuel, where form is it in greatest abundance
methane, frozen
nitrogen assimilation
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
anammox (Brocadia)
Anaerobic ammonia-oxidizing (anammox) bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas
lithotrophy, anaerobic
NO2- and NH3 –> N2
denitrification
nitrate or nitrite into N2, reduction processes
N fixation
N2 into NH3 (ammonia), nutrient acquisition
nitrification
reduced forms of nitrogen are oxidised into nitrate (NO3-) or nitrite (NO2-)
could even inlcude NO2- –> NO3-
dissimilatory reduction of inorganic compounds
used in anaerobic respiration
ex: using N as a terminal e- acceptor
assimilatory reduction of inorganic compounds
using inorganic compounds, reducing them into nutrients
inorganic forms of N
N2 gas, nitrate NO3- , nitrite NO2-, ammonium NH4+, ammonia NH3
what rxn (anabolism or catabolism) synthesizes new cell material?
anabolism (energy input needed, endergonic)
do autotrophs or heterotrophs require more electrons to reduce their carbon sources?
autotrophs, need a lot of e- to reduce CO2
electrons will move ___ the redox tower during rxns, the greater the fall the greater the ____
down
energy yield is
what are 2 ways to produce ATP in a chemotroph
sub level phosphorylation
oxidative phosphorylation
When O2 is the terminal electron acceptor for energy generation, an organism is carrying out ?
aerobic respiration
using a terminal e- acceptor other than O2 for energy generation processes?
anaerobic respiration
fermentation
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
what are the 4 steps in aerobic resp?
- glycolysis
- Krebs cycle / CAC
- ETC
- ATP formation via F1F0 ATPase (pmf)
which steps of aerobic respiration are defined as oxidative phosphorylation?
ETC and making ATP using ATPase (atp pump)
2 atp are added during the ____ stage of glycolysis
activation stage
in glycolysis what are the e- acceptor and donor?
donor = G3P (previously glucose just broken up)
acceptor = NAD+
what 2 products of glycolysis contain most of the energy of glucose?
NADH and pyruvate
is there substrate-level phosphorylation going on in the CAC?
yes, the step where ATP is made
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)
one glucose turns the CAC ___ times
2 times (total 2 ATP produced)
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
one cycle (or 3 conformational changes) of the F1F0 ATPase generates how much ATP?
1 ATP
thru aerobic resp, one glucose molecule gets you how many ATP?
38 ATP (net)
ATP in fermentations is solely produced by ?
substrate-level phosphorylation
*what is the order of major e- acceptors????
- O2
- NO3-
- Fe3+
- SO42-
- CO2
where does a phototroph’s reducing power come from?
H2O
where is H2S produced in the Win column?
the bottom by sulfate-reducing bacteria
SO4 –> H2S (e- acceptor)
___trophs make up most of the Win column?
PHOTOTROPHS
anoxygenic phototrophs like purple or green sulfur bacteria get their reducing power from?
H2S (not O2)
what is the least and most oxidized nitrogen compound?
most reduced (-3) is organic N
most oxidized (+5) is NO3-
biodegradation in the N cycle is?
ammonification
organic N –> NH4+
denitrification is a _____ process
reduction
what process involving N, uses N as terminal e- acceptor in anaerobic respiration?
DISSimilatory reduction of N
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
what are 2 things required for nitrification?
ATP and electrons
what things do the plant supply the rhizobium bacteroids with?
organic acids (succinate, malate, fumurate –> pyruvate)
leghemoglobin brings O2
DNA in prokaryotes exists as ?
circular chromosomes, compacted through supercoiling (by gyrase)
primary function of fermentation
provides the cell with a mechanism to regenerate the oxidized form of electron carriers, allowing glycolysis to continue
function of NADH in fermentation
NADH provides the electrons to reduce pyruvic acid to either an organic acid or ethanol.
second-generation benefits vs first-gen (sanger sequence)
lower cost
higher throughput
Potential ORFs are identified by locating
start and stop codons
The net energy gain from complete aerobic oxidation of one glucose molecule
is:
38 ATP
multiple genes w similar functions under the control of a single promoter
an operon
genes in an operon cotranscribed into a ?
polycistronic mRNA
regulon
multiple operons all controlled by one signal molecule
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
which region forms an attenuation stem-loop that leads to termination of transcription?
region 3-4
if sRNA binds directly at the 3’ end of the mRNA, what happens?
translation will continue
(it protects the mRNA from degredation)
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)
subcellular particles that can only replicate w/in a host cell
virus
how many sides of an icosahedral?
20
what things are the only known group to have an RNA genome?
viruses
the adsorption process of a virion
T4 fibers attach to LPS of outer membrane of bacteria
describe the eclipse stage
right after virus is added, virus takes over host, early enzymes kick in to produce viral nucleic acid and protein
what things are transcribed during early T4 synthesis?
anti-sigma factor proteins that inhibit host sigma factors
also phage-specific replisome
T4 DNA is?
DOUBLE STRANDED AND LINEAR
T4 is also a lytic virus
what genome is terminally redundant?
T4
how does T4 avoid bacterial host defenses?
it modifies its cytosine residues
changes to a 5-hydroxymethylcytosine (swaps a H for C2HOH)
called glucosylation
bacteriophage lambda
TEMPERATE PHAGE, linear dsDNA
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
what does a lambda tail attach to on the host during adsorption?
host maltose transport protein
most infections result in ___ infection
lytic
what represses cl gene
cro
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
not all ____ are transducing, and not all _____ are transducible
not all phage are transducing, and not all prokaryotes are transducible
phage conversion is done by a ?
temperate phage during multiple lysogenic infections
are animal or plant viruses usually naked? which cells are harder to infect?
plant viruses are naked and plant cells are harder to infect
a naked virus with a broad host range is most likely?
a plant virus
what are the (+) virus classes?
class I and VII, class III, class VI
1, 3, 5, 6
what are the DNA viruses??
class I, II, VII
1, 2, 7
remember 12
the only double stranded virus genomes are in which classes?
class I and VII, class III
1, 7, 3
what is parvovirus?
class 2
ssDNA (+)
what is rotavirus
class 3
dsRNA (+)
what viral classes are negative?
ONLY CLASS 5 U MORON (V)
whats poliovirus homie??
class IV (4 u dummy)
ssRNA (+)
can be used directly as mRNA
whats the only viral class that can be used directly as mRNA
CLASS IV
ex: poliovirus
rabies and influenza are (+) or (-)??
also are they ds or ss, RNA or DNA?
(-) ssRNA
which class includes the bacteriophages phi and M13?
class 2
mRNA only made from ___ sense DNA
negative
the most common human viruses belong to class?
4 (IV)
these are (+) ssRNAs
coronavirus is class?
(IV) four
it is (+) ssRNA
phage T4 would be in what class?
class 1
dsDNA
which virus contains VPg protein to help w ribosome bonding and yields a polyprotein
polio
what is veryyyyy small, naked, icosahedral, (+) ssRNA virus?
poliovirus
whats a virus transmitted via aerosols?
influenza
which virus is (-) ssRNA and has a broad set of hosts?
influenza
what virus has multiple capsids surrounding its genome? what class is it in?
rotavirus (diarrhea)
dsRNA
class 3
