Lecture 8 - principles of bacterial aerobic cellular respiration Flashcards
Growing cells
new biomass dominates total energy requirements
Non growing cells
repair and replacement is all that is possible
Proton motive force
gradient of both concentration and charge that is required even during non growth
3 key molecules that participate and determine the majority of catabolic and anabolic reactions
ATP, NADH and NADPH
Active vs passive transport
Active transport accumulates substrates rapidly and against concentration gradient, but has a higher energy cost than passive
3 transporters are
ABC family, MFS family, group translocation
Protein synthesis has the highest…
Protein synthesis has the highest energy requirement, making new amino acids monomers however would require more energy than protein synthesis
How do food sources get converted into NADH?
Amino acids, glucose, glycerol and fatty acid are monomers
Variety of different nutrient sources that cell can take up such as proteins, sugars and lipids. Idea behind cell metabolism in general is that we are trying to conserve backbones so that we can used conserved pathways to operate on because then you do not have to make millions of different proteins that are really hard to make so you want to make as few proteins as possible whilst still maintaining flexibility
Monomers are entered into various parts of glycolysis or the citric acid cycle//breakdown products ultimately enter the CAC and can be entered into different parts of this conserved pathway depending on the molecule or pathway used initially (see diagram)
Specialised pathways isolate the conserved carbon backbone from molecules to enter it into either glycolysis or TCA cycle
Monomers and how they are converted to NADH
Monomers are entered into various parts of glycolysis or the citric acid cycle//breakdown products ultimately enter the CAC and can be entered into different parts of this conserved pathway depending on the molecule or pathway used initially (see diagram)
Sugars/monosaccharides conversion
(6 carbon rings only)
Converted to glucose-6-phosphate or early precursors of glycolysis
Amino acids conversion
Amino (NH2) group must be removed. Variable entry into TCA
Primarily transaminate NH2 -> glutamate - key in CAC, example of how a specific amino acid can be entered into the CAC which means all the stuff that happened in glycolysis is missed and doesn’t happen and the alternative pathways need to be used
Glutamate alpha-ketoglutarate is tightly regulated by both TCA cycle and urea cycle. Deamination removes excess NH2
Fatty acids conversion
Glycerol can enter into glycolysis with only two enzyme reactions
Beta oxidation: flexibility removes acetyl-CoA or propionyl-CoA from any length fatty acids. Both enter into TCA
Two phases of glycolysis
Energy investment phase and the energy payoff phase
Glycolysis define
Glycolysis is the first of the main metabolic pathways of cellular respiration to produce energy in the form of ATP. … Overall, the process of glycolysis produces a net gain of two pyruvate molecules, two ATP molecules, and two NADH molecules for the cell to use for energy
Energy investment phase
Put in energy
ATP is used to phosphorylate sugar : unstable intermediate
6C sugar ring is broken into two 3C chains
Use ATP to further phosphorylate G6P and modify it into unstable intermediates, essentially glucose is split into two smaller things which go through the rest of the pathway twice
Energy pay off phase
Oxidations and (eventual) removal of phosphate produced ATP and NADH
Subsequent oxidation and reduction reactions to essentially create ATP or NADH, can create ATP directly or can create NADH which is involved in some catabolic steps and then will be used by respiration later
For each molecule of glucose…
2 pyruvate are produced
What happens to the 2 pyruvate produced during glycolysis?
these are then entered into the CAC and essentially the idea is that it is going around in a forward (oxidative) direction and then adding in acetyl-CoA (can come from beta oxidation but pyruvate usually gets converted into acetyl-CoA) and this gets added into some of the conserved intermediates, essentially adding carbons on to the 4C molecule and then later removing carbons to generate NADH molecules
Full cycle operates twice per glucose in glycolysis
Many reactions are reversible
Aerobically the favourable direction is oxidative (forward running cycle)
Driven by dehydrogenases - enzymes that perform oxidation reactions that can produce lots of these energy currencies
NET products produced during glycolysis
2 pyruvate, 2 ATP, 2 NADH
ATP formed and used in glycolysis
4 ATP formed, 2 ATP used, therefore net gain of 2 ATP
Products produced from pyruvate dehydrogenase (PD)
1 NADH
Products produced during 1 full cycle of TAC
3 NADH
1 GTP (can be converted into 1 ATP)
1 FADH2
Total products from the entire process ( 1x glycolysis, 2 x PD, 2 x TCA)
10 NADH, 2 FADH2, 2 ATP and 2 GTP
The two major routes of ATP production
Substrate level phosphorylation and oxidative phosphorylation
Substrate level phosphorylation
Making ATP as a consequence of cytoplasmic reactions
Glycolysis and TCA possess such reactions
Low efficiency but simpler and not limited by electron acceptor
Eventually limited without regenerating NAD+ (e.g. fermentation) - linked to a lot of cytoplasmic reactions that need NAD+
Essentially it is any process in the cytoplasm of the cell that produces ATP, get very low amounts of ATP but can make smaller amounts of proteins in this process
Oxidative phosphorylation
Oxidative phosphorylation is the process by which ATP is synthesized as the result of electron transport driven by the oxidation of a chemical energy source.
Using reducing power (combining NADH and FADH2) to generate ATP
Electron transport chain and ATP synthase
For ETC - oxidises our reducing power, takes the electrons off things like NADH and by taking these electrons down energy levels we make a proton pump, essentially the electron is put on oxygen and this is why we breathe oxygen as humans in order to power this process and get a proton gradient which is then used to power another enzyme called ATP synthase (enzyme that produces ATP)
High efficiency but complex and limited by electron acceptor
Very efficient system and is goof for organisms that require a lot of ATP or for organisms that need to use their carbon source efficiently so indeed persisters and cells that grow slow are found to rely on these processes therefore understand the importance of PMF in stressful environments
Regenerates NAD+ as part of its activity - allows catabolic reactions to continue which is a good way of dealing with the build up of too much reducing power
Linked by proton motive force
Also known as cellular respiration
OXPHOS produces up to _____ times _____ ATP than SLP
10 times more
ATP is required for
anabolic processes (polymer synthesis)
Growth rate of bacteria depends on
ATP yields because you need ATP for anabolic processes
Bacterial and archaeal ETCs vs mitochondrial ETC
Although some bacterial and archaeal ETCs resemble the mitochondrial chain, they are frequently very different. First, bacterial and archaeal ETCs are located primarily within the plasma membrane. Furthermore, some Gram-negative bacteria have ETC carriers in the periplasmic space and even the outer membrane. Bacterial and archaeal ETCs also can be composed of different electron carriers, employ different terminal oxidases, and be branched. That is, electrons may enter the chain at several points and leave through several terminal oxidases. Bacterial and archaeal ETCs also may be shorter, resulting in the release of less energy (and the transport of fewer protons across the membrane). Although microbial ETCs differ in details of construction, they operate using the same fundamental principles.
Order used of reactions
from the first one used … aerobic respiration (oxygen at high pressure), micro aerobic respiration (oxygen at low oxygen pressure), anaerobic respiration (nitrate), anaerobic respiration (fumarate) and fermentation (acetyl-CoA)
Aerobic respiration - Oxygen ( high pO2) - MAX YIELD
38
Microaerobic respiration - oxygen (low pO2) - MAX YIELD
15
Anaerobic respiration - Nitrate - MAX YIELD
15
Anaerobic respiration - Fumarate - MAX YIELD
12
Fermentation - acetyl-CoA - MAX YIELD
3
Reactions that are oxidative phosphorylation and substrate level phosphorylation
aerobic respiration (oxygen at high pressure), micro aerobic respiration (oxygen at low oxygen pressure), anaerobic respiration (nitrate), anaerobic respiration (fumarate)
Reactions that are only substrate level phosphorylation
Fermentation - acetyl-CoA
Why is oxygen so important in OXPHOS?
Redox (reduction) potentials
Molecules can inherently have high energy electrons within them
Main principle behind OXPHOS
Electrons in redox active molecules have an inherent energy, measured as a voltage
Tendency of a molecule to accept or release electrons
More negative = more likely to release electron. Electron in higher energy orbital/state (itself will be oxidised and it will reduce something else)
Energy release from transferring electrons can be used to do work, coupled to proton pumping
Oxygen is the lowest energy electron acceptor in biological systems
Oxygen is the ______ _______ electron acceptor in biological systems
lowest energy
Redox potentials
More negative = more likely to release electron. Electron in higher energy orbital/state (itself will be oxidised and it will reduce something else)
Aerobic respiration
oxygen is used as terminal electron acceptor
Anaerobic respiration
no oxygen available so bacteria use an alternative electron acceptor
Electron transport chain
Series of membrane bound proteins AND cofactors
Catalyse the redox reactions that usually make a PMF
Bacteria = highly modular, but the mitochondrial configuration is the most efficient. Flexible
Key features of ETCs
1 - A membrane = a physical barrier is needed to create a concentration gradient
2- Oxidative protein complexes that liberate electrons from reducing power and may pump H+
3 - Cofactors that transfer electrons between enzymes
4 - Reductive protein complexes that finally transfer electrons to a terminal electron acceptor and may pump H+
Electron liberating complexes list
Complex I Complex II Quinone Cytochrome C Complex III Complex IV
Complex I
Complex 1 - NADH dehydrogenase. Large multi-subunit enzyme
Oxidises NADH and reduced coenzyme q (ubiquinone)
Induces structural/conformational changes that pump proton
s
Electron liberating complexes
complex II
Complex II - Succinate dehydrogenase (none protein pumping enzyme), the same enzyme from CAC
FAD is in fact covalently bound intermediate. Succinate oxidised and quoin directly reduced
Generally does not pump protons
Electron liberating complexes
Quinone
Small lipophilic chemical with aromatic headgroup that accepts electrons
Small molecule that freely diffuses through the membrane at least by the standard model to fo to the terminal acceptors on the enzyme
Many types with different redox potentials
e.g. coenzyme Q / ubiquinone
E.g. vitamin K2/ Menaquinone
Called a quinol when reduced
Electron transferring cofactors
Cytochrome C
Cytochrome = protein with heme
Small protein that contains a heme group that accepts electrons
Generally only associated with oxidase enzymes that perform oxygen reduction
Not to be confused with other heme containing enzymes like cytochrome P450, that perform reactions
Electron transferring cofactors
Complex III
Cytochrome bcI. Transfer electrons between quinol and cytochrome C
Indirectly transfer protons using electron carrier acid/base chemistry (not a proton pump)
Linked to complex IV, in many bacteria they are a super complex
Electron donating complexes
Complex IV
Cytochrome C oxidase. Electrons from cytochrome C used to terminally reduce oxygen
Protons taken up during catalytic intermediate and pumped
Electron donating complexes
ETC features - a membrane
A membrane = a physical barrier is needed to create a concentration gradient
ETC features - oxidative protein complexes
Oxidative protein complexes that liberate electrons from reducing power and may pump H+
ETC features - cofactors
Cofactors that transfer electrons between enzymes
ETC features - reductive protein complexes
Reductive protein complexes that finally transfer electrons to a terminal electron acceptor and may pump H+
