Week 5 Flashcards
(188 cards)
1
Q
When did microbes appear?
A
Potentially biogenic carbon preserved in a 4.1-billion-year-old zircon
2
Q
How diverse are microbe habitat?
A
Very range from hydrothermal vents, to inside of organisms
3
Q
What does a microbe need to be to be well travelled?
A
Bacteria such as E. coli must adapt to a broad range of conditions including temperatures, UV light, low pH, salinity,
4
Q
What is the life cycle of E.coli ending up in humans?
A
Either:
Contamination of environment, wildlife, and agriculture from environment –> transmission between production animals (can be reverable) –> transmission to person
Or:
Contamination of environment, wildlife, and agriculture transmission of food and water to person transmission to person to person and to and from domestic animals
5
Q
What is an example of a bacteria with a large turnover time?
A
16-million-year-old sediments contain bacteria with estimated turnover times (lifespan) of 22 years
6
Q
What is an example of an extreme environment that prokaryotes can live?
A
Prokaryotic cells of the deep sub-seafloor biosphere identified as living bacteria
7
Q
What are the main stages of the bacterial life cycle when grown in a lab?
A
An initial lag period followed by exponential-phase growth. After remaining at high density for 2 or 3 days, cells enter death phase
8
Q
What happens after most bacterial cells die?
A
After ~99% of the cells die, the survivors can be maintained under long-term stationary-phase culture conditions for months or years
9
Q
What is a key feature of bacteria that means that they can survive along time?
A
Bacteria can survive for years in an environment without additional food.
10
Q
What does life need?
A
Life requires energy (i.e. keep electrons moving)
11
Q
What are the sources of energy?
A
Originally assumed that all life required sunlight
Many examples of environments that don’t need sunlight.
Environments for animals include sealed caves and deep-sea hydrothermal vents
Bacteria can live in even more extreme environments
12
Q
What sustains life on earth?
A
Life on earth is sustained by 2 sources: (1) sunlight (2) the earths molten core
13
Q
What are the processes that sustains life on Earth?
A
Photosynthesis and Chemosynthesis
14
Q
What is the overview of the hydrothermal vent ‘Black Smokers’?
A
First observed in 1977
Produce hydrogen sulphide (black smoke)
Sulfide and oxygen provide energy for bacteria on surface
Bacteria form the start of a food chain around the smoker
15
Q
What is an example of another organism living around ‘black smokers’?
A
‘Red worms’ use the bacteria to generate organic nutrients. Technically parasites, the worms can grow over 2m
16
Q
What is the overview of the hydrothermal vent ‘The lost city’?
A
Alkali hydrothermal vent
Found in 2000
Emits methane and hydrogen
90 foot chimneys contain thick biofilms of archae using methane and hydrogen as energy sources.
Serpentine mineral structure consists of interconnected chambers about 1micron across. Possible start of life?
17
Q
What is a potential location for extra-terrestrial life?
A
Europe, frozen moon, with cracks of iron, underneath are oceans. The recipe for life
18
Q
What is LUA?
A
Last universal ancestor
19
Q
What is believed to be the first compounds to except electrons for early prokaryotic life?
A
Fe(III)
S0
Nitrogen compounds (NO, N2O, NO3-, SO4- and DMSO)
Later oxygen
20
Q
When do they believe water-splitting enzyme appeared?
A
Around 1 billion years after life evolved allows for oxygenic respiration which led to increase in oxygen
21
Q
What was the famous quote by Alber Szent-Gyorgyi?
A
Life is nothing but an electron looking for a place to rest
22
Q
What chemicals and elements are needed for life?
A
Carbon
Oxygen
Nitrogen
Sulphur
Phosphorus
Trace elements like Fe
23
Q
What are the energy sources to survive and grow?
A
Phototropic - sunlight generates organisms
Chemotropic – breakdown of molecules generates energy
24
Q
What are the energetic demands of higher organisms?
A
Need lots of energy
Obtained from O2 and high energy carbon sources
Plants use high energy wavelength of light
25
What are the overall energy demands of bacteria?
Bacteria are more versatile
Various molecule can be used instead of ¬O2 and carbon sources
Photosynthetic bacteria can use different energy wavelength
26
What is the main energetic source in all life?
ATP – adenosine triphosphate
This is broken down into adenosine diphosphate
27
How much energy is released from the breaking down of ATP?
~45 kJ/mol
28
What are the functions of ATP?
Transport, sensing and synthesis eg condensation reactions in peptide bonds DNA synthesis
29
What is the main source of reductive energy in all life?
Nicotinamide adenine dinucleotide hydride (NADH) is oxidised to form Nicotonamide adenine dinucleotide (NAD+), this takes 2 electrons away.
An alternative form (NADPH) is also used
30
How much reductive energy is gained from the reduction of NADH)?
Energy of -0.3V or ~60 kJ/mol
31
What is done to increase the efficiency of cellular energy?
Chemical and electrical energy are linked within the cell to maximise efficiency during metabolism
32
What are the two forms of metabolism?
Catabolism – energy yielding reactions
Anabolism – biosynthetic metabolism
33
What happens to NAD+ and ADP in catabolism?
ATP and NADH are formed
34
What happens to NADH and ATP in anabolism?
ADP and NAD+ are formed
35
What are the process that occur in anabolism?
Taking in external nutrients
Intracellular precursor pool
Forming biosynthetic intermediates (eg amino acids)
Forming biopolymers
36
What happens to lipids to produce energy?
Lipids --> Fatty acids --> Acetyl-CoA (using NADH and FADH2) --> The citric acid cycle --> NADH + FADH2 ATP
37
How can you produce lipids?
Convert fatty acids using ATP
38
What happens to polysaccharides to produce energy?
Polysaccharides --> Carbohydrates --> Pyruvate (In glycolysis using NADH) --> Acetyl-CoA --> The citric acid cycle --> NADH + FADH2 --> ATP
39
How can polysaccharides be produced?
The conversion of carbohydrates to polysaccharides using ATP
40
How can proteins be converted to ATP?
Proteins --> Amino acids --> Pyruvate --> Acetyl-CoA --> The citric acid cycle --> NADH + FADH2 --> ATP
Amino acids can go straight to the TCA cycle
41
How can proteins be produced?
Conversion of amino acids to proteins using ATP
42
What happens if there is an overabundance of a compound in the central metabolic pathway?
All pathways are reversible, so the metabolic balance in the cell can be maintained
43
How are ATP and NADH produced?
ATP and NADH are made (directly or indirectly) by oxidation of energy rich modules
44
What happens in oxidation?
Oxidation releases electrons
45
What is a feature of electrons for energy?
They can’t be stores indefinitely
46
What is used to couple oxidation of one substrate to another?
Fermentation and respiration
47
What is respiration for electrons?
Metabolic pathways where unconnected electron donors and acceptors exchange electrons
48
What is fermentation for electrons?
Electron donors and acceptors are apart of the same metabolic pathway
49
What is the difference between ATP and NADH when produced?
NADH is produced directly form donor oxidation and ATP is produced indirectly
50
How is chemical energy obtained?
Chemical energy is obtained from the movement of electrons (redox reactions)
51
How can you calculate Gibbs free energy?
GFE (delta G) = -nF deltaE
52
What do the letters in the formula for gibbs free energy mean?
N = number of moles of electrons
F = Faraday constant
DelatE = change in energy for redox
53
What is the faraday constant?
96.4 J mV-1 mol-1
54
What happen in aerobic respiration and how much energy is yielded?
Glucose + 6O2 --> 6CO2 + 6H2O
Energy yield DeltaG = -2870 kjmol-1 (~30 ATP)
55
What happen in anaerobic respiration using nitrate and how much energy is yielded?
Glucose + 6NO3- --> 6NO2- + 6CO2 + 12H+
Energy yield DeltaG = -1930 Kjmol-1 (~20 ATP)
56
What happen in lactic acid fermentation and how much energy is yielded?
Glucose --> 2 C3H5O3 (lactate or lactic acid)
Energy yield DeltaG = -195 Kjmol-1 (~2 ATP)
57
Where is all the NADH and ATP kept?
Inside the cytoplasm
58
Where is all the quinone/quinol kept?
Inside the cytoplasmic membrane
59
Where are the two places energy can be generated?
Inside the cytoplasmic membrane
Across the cytoplasmic membrane
60
What is an overview of energy production in the cytoplasm?
Seen in fermentation
Also called Substrate label phosphorylation
61
What is an overview of energy production across the cytoplasmic membrane?
Eg oxidative phosphorylation
Respiration
62
What is an overview of quinone and quinol?
Exist as a mixed population of quinols and quinones in living cells
Hydrophobic molecules located in the inner (cytoplasmic) membrane
Can carry 2 e and 2 H+ without changing charge
Used to transport electrons and protons across membrane
Types include Ubiquinol (aerobic), Menaquinol & Duroquinol (anaerobic)
GFE of -10 kJ/mol
63
What is the function of quinone/quinol?
Allows for the generation of a proton motive force
64
What happens to quinone during respiration?
NADH + H+ --> NAD+ + 2H+ causes quinone to be reduced to quinol
Quinol will be oxidised back to quinone effectively moving 2 electrons and hydrogens form the cytoplasm to periplasm
65
What allows for the function of quinone/quinol?
Diffusion throughout the cell membrane
66
What happens to the protons build up on the periplasm side of membrane?
They can diffuse through an ATP synthase to allow the production of ATP from ADP
67
What is important about energy conservation in the module?
Microbes must obtain energy to survive and grow
ATP and NAD(P)H are universally used for energy conversion
Energy must come from environment
(e.g. Light or reduced molecules)
During homeostasis the cellular components balanced are in equilibrium.
* NAD+/NADH equilibrium
* Quinol/Quinone pool equilibrium
* Proton motive force equilbrium
68
What is the way organisms obtain energy from chemical compounds?
Chemotrophy eg Respiration and Fermentation
69
What is a way of organisms obtaining external energy?
Phototrophy eg Photosynthesis an Photophosphorylation
70
What is a brief overview of the broad mechanism of respiration?
Substance X is oxidised which produces energy. This also produces an electron to remove it substance Y gets reduced. This can potentially release energy as well
71
What is the difference between aerobic and anaerobic respiration?
Aerobic is when the reduced substance is O¬2
Anaerobic is when the reduced substance is anything but O2 eg Fe3+ or NO3
72
What is fermentation?
Is when a single substance is sequentially oxidised and then reduced
73
What is an overview of fermentation?
Electron shuttles (typically NADH) are reduced and then oxidised
Fermentation does not yield as much energy as respiration
Historically described as metabolism of oxygen, sometimes used simply to describe microbiological growth
Important biotechnological process
74
What are the different glucose metabolic pathways in microbes?
Glycolysis (same as humans)
Pentose phosphate pathway
Enter-Doudoroff pathway
75
What connects the 3 different glucose metabolic pathways together?
All 3 connect at Glyceraldehyde-3P to produce different amounts of ATP, NADH or NADPH
76
What is an overview of glycolysis?
Catabolic pathway
Found in microbes, plants, and higher animals
No net loss of carbon
77
What is produced in glycolysis?
2 ATP
2 NADH
2 Pyruvate
78
What initially happens to the glucose in glycolysis?
It is activated though ATP, so becomes phosphorylated. This happens twice to produce Fructose-1,6-di-P
79
What happens to the Fructose-1,6-di-P in glycolysis?
It is converted into Glyceraldehyde-3-P and potentially Dihydroxyacetone phosphate (DHAP) (though this is converted back is Glyceraldehyde-3-P)
80
What happens to glyceraldehyde-3-P inn glycolysis?
It is oxidised using 2NAD --> 2NADH to form 1,3-di-P-Glyceric acid which is then you get ATP out to form 3-P-Glyceric acid
81
What happens to the 3-P-Glyceric acid in glycolysis?
It is converted into 2-P-Glyceric acid this is turned into PEP which released 2ATP when being converted into Pyruvate
82
What is key about all the steps between Glyceraldehyde-3-P and pyruvate in glycolysis?
They are all 3 carbon molecules, so this happens twice per molecule of glucose
83
What is an overview of Enter-Doudoroff pathway?
An alternative to glycolysis (mainly by gram negative bacteria
Uses KDPA (2-keto-3-deoxyg-6-phosphogluconate) as an intermediate
84
What are the products of the Enter-Doudoroff pathway?
1 NADPH
1 NADH
1 ATP
2 pyruvate
85
How is glucose converted into KDPA in the Entner-Doudoroff pathway?
Glucose is phosphorylated to form Glucose-6-P. This is then oxidised to form 6-P-Gluconic acid. This is oxidised from the reducing of NADP to NADPH. 6-P-Gluconic acid is then converted to KDPA
86
What does the KDPA produce?
Pyruvate and Glyceraldehyde-3-P
87
What happens to the Glyceraldehyde-3-P to Pyruvate in the Enter-Doudoroff pathway and the pentose-phosphate pathway?
The same as in glycolysis releasing 2 ATP and when oxidised it releases NADH
88
Why does the Enter-Doudoroff pathway produce less ATP?
As a molecule of pyruvate is produced meaning you don’t get the ATP produced from converting Glyceraldehyde-3-P to Pyruvate
89
What is an overview of the pentose-phosphate pathway?
Found in both prokaryotes and eukaryotes (plants)
Can form glycolysis intermediates - Glyceraldehyde-3-P
90
What is the process of completely oxidising glucose-6-P into Glyceraldehyde-3-P?
Glucose-6-P is oxidised to form 6-P Gluconic acid, this is further oxidised to form Ribulose-5-P. These process cause 2 molecules of NADP+ to be reduced to form 2 NADPH. The ribulose-5-P is then converted into Ribose-5-P which is then converted into Glyceraldehyde-3-P
91
What are the 2 NADPH formed in the pentose-phosphate pathway used for?
Anabolic reaction that require electrons
92
What are the Ribulose-5-P formed in the pentose-phosphate pathway used for?
Can be sent to the Calvin-Benson cycle
93
What are the Ribose-5-P formed in the pentose-phosphate pathway used for?
Can be used for the synthesis of nucleotides and nucleic acids
94
What is an overview of fermentation for microbiologists?
An ancient mode of metabolism, and must have evolved with the appearance of organic material on the planet (predates photosynthesis and respiration)
95
What molecular structures are needed in fermentation but not respiration ?
No outside electron acceptors are involved; no membrane or electron transport system is required; No ATP synthase needed
96
What happens during fermentation?
Energy is derived from the partial oxidation of an organic compound using organic intermediates as electron donors and electron acceptors
97
What produces ATP during fermentation
All ATP is produced by substrate level phosphorylation
98
What is an overview of Lactic acid bacteria?
Include Streptococcus and Lactobacillus
Obligately fermentative, aerotolerant, gram-positive bacteria that ferment sugars with lactic acid as the major product
99
What is an overview of Lactobacillus with lactic acid production?
Lactobacill are relatively acid-tolerant growing wel down to pH 4
Lactobacilli are not pathogenic their acid production kills other organisms)
Acid production by Streptococci is a dominant factor in tooth decay
Only lactobacilli and some enteric bacteria have the capacity to metabolise the disaccharide lactose (glucose + galactose)
100
How is Lactic acid produced in fermentation?
Glucose is phosphorylated to produce fructose diphosphate, consuming 2 ATP.
The fructose diphosphate then produces 2 glyceraldehyde-3P.
With the oxidation of this to 2 phosphoglycerate 2 ATP are released and 2 NADH are released
2 more ATP are released when 2 phosphoglycerate is converted to 2 pyruvate
The reduction of 2 pyruvate to 2 lactate using Lactate dehydrogenase released 2 NAD+
101
What is an overview of the function of lactate dehydrogenase?
This disposes the reductant but does not itself generate ATP
This reaction must therefore be linked to glycolytic ATP production
102
What is an overview of yeast?
Examples are Sacchromyces, Candida albicans
Eukaryotic microorganisms --> mitochondria
Capable of aerobic respiration or fermentation
Yeast are facultive anaerobes
103
What is the Pasteur effect?
Yeast in low glucose, high oxygen concentration, fermentation is supressed
104
What is the Crabtree effect?
Yeast in high glucose, low oxygen concentration, aerobic respiration is supressed
105
What is a real world use of Yeast?
Saccharomyces cerevisiae – baker’s yeast
It is used in the production of alcoholic beverages and industrial ethanol
The CO2 produced by fermentation makes bread rise
106
What is the process of making ethanol through fermentation in yeast?
Glucose is phosphorylated to produce fructose diphosphate, consuming 2 ATP.
The fructose diphosphate then produces 2 glyceraldehyde-3P.
With the oxidation of this to 2 phosphoglycerate 2 ATP are released and 2 NADH are released
2 more ATP are released when 2 phosphoglycerate is converted to 2 pyruvate
Pyruvate is turned into acetaldehyde using pyruvate decarboxylase also producing 2 CO2
2 acetaldehyde is turned into 2 ethanol using the enzyme alcohol dehydrogenase also oxidising 2 NADH to 2 NAD+
107
What is the equation for the glycolysis reaction?
Glucose + 2 ADP + 2 Pi + 2 NAD+ --> Pyruvate + 2 ATP + 2 NADH
108
What is the equation for the lactate dehydrogenase reaction?
2 pyruvate + 2 NADH --> Lactate + 2 NAD+
109
What is the overall reaction for lactate production?
Glucose + 2 ADP + 2 Pi --> Lactate + 2 ATP
110
What is the equation for ethanol production?
2 pyruvate + 2 NADH --> Ethanol + 2 NAD+ + 2 CO2
111
What is the overall equation for ethanol production through fermentation?
Glucose + 2ADP + Pi --> ethanol + 2 ATP + 2 CO2
112
What is an example of aerobic respiration?
C6H12O6 + 6O2 --> 6CO2 + 6H2O
113
What are examples of anaerobic respiration?
COO + NO2 --> CO2 + NH3- + 2H2O
CH3CH(OH)COO- (lactate) + Fe3+ --> CH3COOH + CO2 + Fe2+
114
What happens to the pyruvate during respiration?
It binds with CoA to form Acetyl-CoA + CO2
CoA + Pyruvate + NAD+ --> Acetyl-CoA + CO2 + NADH
Which is then fed into the citric acid cycle
115
What are the products of the citric acid cycle?
3 NADH
1 FADH2
1 GTP (same energy equivalence as ATP)
116
What is key in catabolic reactions for making ATP?
Catabolic reactions producing ATP which either organic or inorganic compounds serve as electron donors and organic or inorganic compounds serve as electron acceptors.
These reactions are associated with the cytoplasmic membrane and ATP is generated by oxidative phosphorylation
117
What is an outline for oxidative respiration?
NADH and FADH2 act as a H+ donor which then are transported across the membrane. This is powered by the chemical energy in electrons which are reduce oxygen to form water. H+ then move across an ATP synthase producing ATP
118
What is special about the aerobic respiration in Paracoccus denitrifcans?
A descendant of the common mitochondrial ancestor
Similar to oxidative phosphorylation pathway to eukaryotes
119
What is a rough outline of oxidative phosphorylation in Paracoccus denitrificans?
NADH dehydrogenase removes hydrogen from NADH which is then pumped across the membrane
The electrons bind with a ubiquinone to form ubiquinol
This then goes to a cytochrome bc1 complex allowing for more H+ to go across the membrane through oxidation reduction of ubiquinol
The ubiquinol then goes to a cytochrome C and then to a cytochrome aa3 the electrons then reduce Oxygen to form water pumping more H+ across the membrane
120
What is an alternative aerobic respiration in Paracoccus denitrificans?
Paracoccus denitrificans has a branched respiratory pathway and can use methanol instead od the TCA cycle
This is done through a methanol dehydrogenase and a cytochrome C551 which is tacked onto the cytochrome C. These electrons then go in cytochrome A.
121
What is respiration different in E.coli than in mitochondria?
It takes in NADH hydrogenase which goes to a quinol and the straight to an oxidase. There is no BC1 complex or cytochrome C
122
What is key for respiration in a gut bacterium?
E.coli faces a number of challenges as a gut bacterium
Respiration must be regulated to meet cell demand
123
What happens with respiration in the log phase?
Log phase – High aeration – ATP required, maximise P/O ratio
124
What happens with respiration in the stationary phase?
Stationary phase – low aeration – ATP less important, lower P/O ratio
125
What quinol oxidases are contained in E.coli?
3 quinol oxidases contained
Cytochrome bo3, db1, bd2
126
What quinol is expressed in the log phase?
High aeration
Cytochrome bo oxidase expressed
127
What quinol is expressed in the stationary phase?
Low aeration
Cytochrome bd oxidase expressed
128
What are the differences between cytochrome bo oxidase and cytochrome bd oxidase?
Bo oxidase has a lower affinity for oxygen and a proton pumping mechanism
Bd oxidase has a higher affinity for oxygen and no proton pumping mechanism
129
What happens at the bo oxidase?
NADH dehydrogenase turns NADH to NAD+ the electrons go to a quinone forming a quinol. The Quinol acts as an electron carrier providing energy for H+ to move across. This then oxidises the quinol to form quinone again these hydrogens can go into the periplasm space and can then move across to produce ATP. Water is degraded as an energy source
130
What happens at the bd oxidase?
Similar to the bo oxidase but not proton pumping meaning you make half of the ATP
131
What is the advantages of ATP synthase?
Higher affinity for oxygen means that you can produce ATP in low oxygen environments
Less ATP produced means it will take longer of ATP reserves to fill up. ATP reserves filling up means electrons stop moving if that happens cell dies
132
What happens if there isn’t enough oxygen for respiration?
Multicellular organisms can compete for light and nutrients
Bacteria cant move across environments easily so they diversify their substrate range
133
What are examples of anaerobic respiration?
Metal respiration eg Fe3+ --> Fe2+
Denitrification eg NO3- --> N2
Sulfate respiration eg SO42- --> SH-
Fumarate respiration eg fumarate --> succinate
134
What is the nitrification pathway?
Organic nitrogen --> NH4+ --> NH2OH --> NO2 --> NO3-
135
What is the denitrification pathway?
NO3- --> NO2- --> NO --> N2O --> N2 --> (fixation) NH4+ --> Organic nitrogen
136
What are alternatives to the nitrification and denitrification pathway?
NO2 N2 = Anammox
NO2 Respiration assimilation
137
What bacteria can convert NH4+ + O2 --> NO2- + H2O?
Nitrosomas (aerobic pathway – nitrification)
138
What bacteria can convert 2 NO2- + O2 --> NO3
Nitrobacter (aerobic pathway – nitrification)
139
What can convert R-CHO + 3H+ + NO2 --> CO2 + N2 + 2 H2O?
Paracoccus (anaerobic pathway – denitrification)
140
Why nitrogen fixation important?
Removal of nitrogen contaminants
Deeper anaerobic basins remove nitrates
Shallow aerobic basins remove ammonia
141
What happens with anaerobic respiration of nitrogen in paracoccus denitrificans?
NADH dehydrogenase converts NADH to NAD+. The electrons from this go to ubiquinol. Nitrogen reductase converts NO3- to NO2- . Cytochrome complex 1 pumps H+ across membrane. Nitrite reductase turns NO2- to NO in the periplasm. Nitric oxide reductase turns NO to N2O and then nitrous oxide reductase turns N2O to N2
142
When can nitrogen fixation cause human health human?
Bacteria on food are ingested.
In mouth bacteria are attack by nitrate and toxic nitrite produced by commensal bacteria
In gut – acidic environment – nitrate, toxic nitrite, chemically produced toxic reaction NO, no oxygen
Intestine – nitrate, toxic reactive NO form commensal bacteria, no oxygen
Bacteria fix nitrogen that comes area, providing energy and detoxify surrounding area
143
What is a lithotroph?
An organism that uses inorganic material for catabolism
A lithoautotroph can use inorganic substrates for anabolism
144
What is an example of an assimilatory pathway for carbon?
CO2 + H+ + ATP + NADPH -> Organic carbon
145
What is an example of an assimilatory pathway for nitrogen?
N2 + NAD(P)H + ATP + H+ --> Amines
Requires around 16 ATP
146
What is an example of an assimilatory pathway for oxygen/hydrogen?
H2, O2 or H20 + ATP
147
What is an example of an assimilatory pathway for sulphur/pshosphorus/metals?
Sulphates/phosphates dissolved in water (ATP dependant import and NADH used for reduction assimilation)
148
What is an overview of lithotrophy in life?
Inorganic substrate level phosphorylation most likely first mechanism of ATP generation. E.g. H2, HS-, CH4
However, all known autotrophs use chemiosmosis (Na+ or H+) for ATP production.
Chemiosmosis most like appeared with first true cellular organisms.
149
What are complexities in generating proton motive forces in microorganisms?
Many reaction release or uptake protons on the wrong side of the membrane
Not all reactions generate enough energy for active proton pumping
150
What are 'redox loops' formed by quinones?
Quinol is reduced to quinone through the oxidation of NADH to NAD+
Quinone diffuses across membrane
Quinone is oxidised to quinol by the reduction of a substance causing it donate 2 e- and loss 2 H+
The quinol then diffuses across membrane again restarting the loop
151
What is the function of redox loops?
Redox loops are arranged to generate proton motive force
152
What is an example of a redox loop equations?
HCOOH + Q --> CO2 + QH2
NO3- + QH2 --> NO2- + H2O + Q
153
How have bacteria used the oxidation of formate to increase proton motive force?
The oxidation of formate occurs on the periplasm where protons need to end up
The electrons are them passed through some iron bound clusters and b type haemes. They finish on a quinol binding site on the cytoplasmic side of the membrane
154
What happens to the electrons at the quinol binding site?
They are then used to reduce quinol to quinone using 2H+
155
What happens to the quinone formed in the redox loop?
They move across membrane to a quinone binding site where it is oxidised.
The quinol the moves back across the membrane
The 2H+ are released on the periplasmic side of membrane
The electrons are donated to another b type haeme
156
What happens to the electrons donated to the second b type haeme?
They are moved across the membrane again first through 4 x FS then an FS then a Mo-bisMGD where the nitrate are reduced nitrite and water
157
What is an overview of redox loops?
Redox loops are common in anaerobic bacterial respiration
No proton pumping, just quinol diffusion and H+ uptake/release (about 5 H+ released/transported)
158
What are the different operons encoding for nitrate reductases?
NAR -> membrane cytoplasmic reduction of nitrate
NAP -> membrane periplasmic reduction of nitrate
NAS -> cytoplasmic reduction of nitrate
159
What are the uses of NAR, nitarate reductase?
Membrane bound
Used to generate a PMF to allow growth
160
What are the uses of NAP, nitarate reductase?
Periplasmic
USed to remove electrons from quinol without generating proton motive force
161
What are the uses of NAS, nitarate reductase?
Cytoplasmic
Used to generat nitrite for nitrogen assimilation
162
What is an overview of the history of Fe (III) respiration on earth?
Geochemical evidence that Fe(III) rather than So was the first external electron acceptor of global significance
Fe(III) derived from photochemical oxidation of Fe(II) from Archean seas and hydrothermal vent fluids was abundant on early earth
Fe(III) respiration demonstrated in deep branching hyperthermophilic Archaea and Eubacteria many of which do not respire S0
163
What is an overview of Fe(III) reduction?
Reduction of Fe(III) via long-range electron transfer need not require specific enzymes
Magnetite accumulations attributed to Fe(III)-reducing microorganisms detected in ancient deposits
164
What is a case study of Fe respiration?
Fe respiration on the Titanic
Titanic is 52 million kilos of (mostly) iron
Microbial Fe metabolism causes rusticles on surface
The titanic will disappear within 100 years due to bacterial corrosion
165
What are examples of metal respirers?
Shewanella and Geobacter genera
166
What is an overview of the present of metal reducers in the environment?
Facultative anaerobe Shewanella found in sediments
Strict anaerobe Geobacter found in anoxic soils.
Require organic carbon, so not autotrophic
Preferred electron acceptors are insoluble minerals.
167
What is an overview of mineral respiration?
CHO is oxidised to form CO2
Electron is used reduce a chemical O2 to H2O or NO3- to N2
This is dependant in small molecule diffusion
168
What is a problem with metal respiration?
Metal/ mineral respiration is limited by diffusion
169
What allows metal respiring bacteria to access metal?
Nanowires
170
What is an overview of nanowires?
The surface of metal reducing bacteria are covered in membrane permeating nanowires. They allow for the transport of electrons through them as they are a series of haeme groups which can directly reduce metals
171
What is an overview of shewanella anaerobic respiration?
Shewanella anaerobic metabolism is substrate level phosphorylation AND respiration
172
What happens with lactate in shewanella anaerobic respiration?
Lactate is oxidised to pyruvate
Pyruvate is then converted to acetyl CoA either forming formate or NADH + CO2
The acetyl CoA is phosphorylated to acetyl-P
The acetyl-P bonds with ADP to make ATP + Acetate
All occurs in the cytoplasm
173
What else is formed during the the oxidation lactate to pyruvate?
Electrons are released and along with 2H+ convert menaquinol to menaquinone in the cytoplasmic membrane
174
What happens to the menaquinone?
It is then oxidised into menaquinol which releases 2H+ into the periplasm creating proton motive force
175
What happens to the electrons released form the oxidation of menaquinol?
It travels through the periplasm by being transported to different cytochrome molecules
Through the molecular membrane and is released out of the cell
176
What are the true lithotrophs?
Include acidophiles (Acidothiobacillus) (Leptospirillum) and neutrophiles (Sideroxydans) (Gallionella)
177
What are a key feature of true lithotrophs?
Use Fe2+ and O2 for respiration
Very slow growing (8 hr doubling time)
178
What is the redox potential when grown on oxygen and nitrate?
Redox potential of -0.42V
Enough to generate proton motive force
179
What is the redox potential when grown on oxygen and iron?
-0.33 V
180
How are proton motive forces generated in true lithotrophs?
Fe (II) is oxidised to Fe (III)
The electrons are the transported into cell and then onto an oxidase
The oxidase pumps protons across the membrane through the oxidation of 1/2 O2 + 2H+ --> H2O
181
What happens to the electrons generated in true lithotrophs in reverse redox loops?
Either:
The H+ can be used to generate ATP
They can be added to a quinol oxidase and can be used to make NADH in a reverse quinone/quinol redox loop
182
What are the condition where Sideroxydans lithotrophicus can live?
Occupies the micro-oxic zone in soil
Obligate aerobe
Uses Fe(II) as electron source but Fe(II) chemically reacts with oxygen
183
Where does Sideroxydans lithotrophicus live?
S. lithotrophicus lives at a oxygen concentration where the chemical rate of iron oxidation is slower than the biological rate
184
What is the process of iron oxidation by SIderoxydans lithotrophicus?
Same as the reverse redox loops
Though can make different quinol molecules
185
What is an overview of the Rio Tinto?
The 100 km ‘red river’ is caused by a process known as acid mine drainage (caused by romans)
Red colour comes from high concentrations of iron
High concentrations of sulfur take river pH to < 4
Release of iron and sulfur are caused by Acidophilic iron oxidising bacteria
186
How does Acidithiobacillus make energy?
Acidithiobacillus oxidises pyrite (FeS) into Fe3+ and SO42- using oxygen
187
What is an overview of lithotrophy in Acidithiobacillus?
Proton motive force (ATP) generated by proton pumping of oxidase
NADH generated from quinol pool
CO2 fixed by ATP and NADH.
SO42- lowers pH of environment to less than 1
188
What is the paradox with Acidithiobacillus?
It generates a redox potential of -0.03V
Intracellular oxygen potential is 0.8
Fe3+ to Fe2+ (pH 2) potential is 0.77
