Lecture 7 - The balance of anabolic and catabolic reactions Flashcards
Energy source
Catabolic reactions and anabolic reactions
New cells means new _____
polymers
Making new monomers =
huge energy investment
Percentage of total energy that goes into making new monomers
95%
Percentage of the 95% of energy that goes into making each monomer for the polymers
Proteins > 50% (of that 95%)
Lipids~20%
RNA ~ 13%
DNA only ~ 2%
Percentage of the 95% of energy that goes into making proteins
Proteins > 50% (of that 95%)
Percentage of the 95% of energy that goes into making lipids
Lipids~20%
Percentage of the 95% of energy that goes into making RNA
RNA ~ 13%
Percentage of the 95% of energy that goes into making DNA
DNA only ~ 2%
Assembling monomers into polymers is _______
Less costly
Percentage of total energy that foes into assembling monomers into polymers
5% of the total energy
Percentage of the 5% that goes into forming proteins
greater than 90% of the 5%
Are other nutrients needed for monomer synthesis?
Yes e.g. nitrogen/sulfur sources
Is polymer synthesis more difficult under anaerobic conditions?
Yes
When a bacteria is just trying to survive…
Replacement and repair of existing macromolecules is essential during persistence
A surviving microbe must make …
Proteins that repair DNA
Proteins that stabilise RNA
A proton (or sodium) motive force
What the top two do is that they stabilise transcription and preserve the genetic code
For how many years can a microbe stay metabolically active but not continue to grow?
~500,000 years
Proton motive force is an
electrochemical gradient
Proton motive force
Energy stored in a build up of H+ ions and other ions in the periplasm
Drives many transporters. Uptake carbon/energy sources
Required for high efficiency ATP synthesis
Even fermenters need a PMF
Some bacteria use sodium ions instead of protons
For long term survival
For long term survival you need to replace all you macromolecules - so think of it as that essentially there are many factors required for growth that are still needed but are all needed at slower rates and need to be balanced accordingly
Long term persistance
Long term persistence = it looks like the cells are not growing but if we dig into these cells and sequence their genomes they are actually accumulating mutations over time, there are essentially lineage that are appearing and disappearing even though from the data point of view they do not look like they are growing
Catabolism
Catabolism= breakdown of high energy molecules to release energy or directly power other reactions
Anabolism
Anabolism = assembly of cell macromolecules, driven by cellular energy supplies
Catabolism:anabolism
Catabolism:anabolsim is finely balanced according to environmental conditions (i.e. energy in vs energy need)
ATP is an…
energy rich molecule (high energy phosphate bond)
ATP features
Energy from phosphate hydrolysis powers other reactions
Covalent reactions/intermediates
Produced by oxidative phosphorylation
Produce ATP by the oxidative phosphorylation process and then it is used as one of the energy currencies in anabolism for building up these reduced biosynthetic products (polymer etc.)
NADH is an …
electron rich molecule
NADH features
Allows redox chemistry
Produced during central carbon metabolism (the citric acid cycle/glycolysis)
Powers oxidative phosphorylation and many central metabolic reactions
Use the high energy electrons in NADH to drive the oxidative phosphorylation process and catabolism is really all about producing molecules like NADH or NADH itself, electron rich molecules are used in many processes but we are specifically going to talk about its involvement with oxidative phosphorylation
All persisters are
metabolically active and primed for regrowth
NADPH is
another electron rich molecule
NADPH features
NADH with an extra phosphate on it
Phosphorylated form of NADH
Enzymatic produced from NAD+ or NADH
Powers reduction reactions that form polymers
Distinct molecule, separates its redox chemistry away from NADH and essentially it is maintained at a differed ratio of oxidised and reduced and we instead use it to power reactions that create the reduced macromolecules
NADH to NADH
reduction
NADPH to NADH
oxidation
NADH vs NADPH
A redox cofactor
Being reversible, easier to reroute certain reactions backwards than with ATP
Phosphorylation = a simple solution to create two separate redox pools
Pools maintained at different rations
The two enzymes allows the addition of further level of regulation in terms of these 2 redox cofactors
The balance of all such ratios is known as redox reactions - messing up redox balance, really messes up the system so a lot of the antibiotics are aimed at messing up the redox balance
NAD(P)H or related molecules = reducing power/equivalents
NAD+/NADH normally high…
NAD+/NADH - Normally high, more NAD+ to promote catabolism - drive these reactions forward, wanna break down molecules and receive the energy from them in terms of electrons, accept the electron and acquires the extra proton in the process therefore the NADH is in its reduced form
NADP+/NADPH normally low ….
NADP+/NADPH - normally low, more NADPH to promote anabolism - trying to feed electrons in to create these reduced biosynthetic products, making more electrons available to allow for the production of more complicated molecules by reducing these bonds and basically adding phosphate is a very simple adaptation to create these 2 different pools of very similar molecules for different reasons
How electron carriers are used …
When the organic energy source is oxidized, the electrons released are accepted by electron carriers such as NAD+ and FAD. When these reduced electron carriers (e.g., NADH, FADH2) in turn donate the electrons to an electron transport chain, the metabolic process is called respiration and may be divided into two different types. In aerobic respiration, the final electron acceptor is oxygen, whereas the terminal acceptor in anaerobic respiration is a different oxidized molecule such as NO3- , SO42- , CO2, Fe3+ , or SeO42- . Organic acceptors such as fumarate and humic acids also may be used. As just noted, respiration involves the activity of an electron transport chain. As electrons pass through the chain to the final electron acceptor, a type of potential energy called the proton motive force (PMF) is generated and used to synthesize ATP from ADP and phosphate (Pi). In contrast, fermentation uses an electron acceptor that is endogenous (from within the cell) and does not involve an electron transport chain. The endogenous electron acceptor is usually an intermediate (e.g., pyruvate) of the catabolic pathway used to degrade and oxidize the organic energy source. During fermentation, ATP is synthesized almost exclusively by substrate-level phosphorylation, a process in which a phosphate is transferred to ADP from a high-energy molecule (e.g., phosphoenolpyruvate) generated by catabolism of the energy source.
How do bacteria acquire energy sources when they finally become available?
Transporters are integral transmembrane proteins - enzymes are sitting inside a cell membrane, transports molecules into the cell’s cytoplasm
Transporters can either be importers (e.g. nutrient uptake), or exporters (e.g. drug efflux). Some are reversible
Classes of bacterial transporters (3)
ATP-binding cassette (ABC) family
Major facilitator superfamily (MFS)
Group translocation e.g. phosphotransferase system (PTS)
Transport is ____ or ______
active or passive
Passive transport
molecules diffuse according to concentration gradient (molecules move from a region of higher concentration to a region of lower concentration)
active transport
an energy source is used to rapidly accumulate against a concentration gradient (move solute molecules to higher concentrations)
Primary active transport
ATP or similar is hydrolysed for energy
Secondary active transport
co-transport of another molecule is the energy source (cotransport = the ion whose gradient powers transport and the substance being moved across the membrane)
Advantages of active transport
High affinity: more competitive for scarce, low concentration resources
Rapidly responds to a fluctuating environment
Allows cells to accumulate against a concentration gradient - keeps intracellular enzymes saturated with substrate
Disadvantages of active transport
Energy cost and more complex proteins required
Facilitated diffusion
Facilitated diffusion is where substances move across the plasma membrane with the assistance of transport proteins that are either channels or carriers.
ATP binding cassette (ABC) superfamily
Know how to draw
Performs primary active transport using ATP as the energy source
Can be exporters (drug pumps) or importers (solute uptake) (exporters tend to not have the binding protein)
Multi-subunit. 7 different subtypes exist with varying transport mechanisms
Periplasmic binding protein - solutes/molecules can be bound by these binding proteins in the periplasm that can either be physically attached or diffused and then interact with the complexes and then transport ultimately the molecules after ATP has been hydrolysed
ABC superfamily stands for
ATP binding cassette superfamily
Major facilitator superfamily (MFS)
Facilitated diffusion of ions/solutes that do not otherwise cross the cell membrane
Either passive or secondary active (aka cotransport)
Transport is power by concentration gradients
Uniport, antiport or symport
MFS stands for
Major facilitator superfamily
Uniport
Passive for MFS. Driven by the concentration gradient of the main solute
Unidirectional import or export which is concentration gradient based
MFS 3 types
Uniport
Antiport
Symport
Antiport
MFS
Active. Concentration of another molecule moving in the opposite direction is used
Something being exported across its concentration gradient and this can drive the import in the opposite direction of another molecule
Secondary active transport - using the concentration gradient of another molecule and the movement of it drives conformational/energy changes that allow movement of another molecule
Symport
MFS
Active. Concentration gradient of another molecule moving in same direction is used
Both molecules are moving in the same direction
Secondary active transport
Group translocation (aka phosphotransferase system)
Cascade of phosphate transfer used to trap substrate inside the cell
Energy atom phosphate used to power transport
Substrate is modified during transport. Its own class of active transport - not primary or secondary transport
A lot of these systems are taking up primary carbohydrates such as glucose, fructose
Gradually the cascade gets more specific as you go along
Use an energy source driven by phosphates to bring the glucose in, the phosphate that is released from these high energy molecules gets attached to the glucose and comes into the ell and what this phosphate does is that it changes the glucose and now it cannot diffuse back out of the cell (trapped) which helps to accumulate glucose
Balancing act of anabolic macromolecule synthesis and catabolic energy generation is regulated by …
redox balance
