Lecture 7 - The balance of anabolic and catabolic reactions

Question 1

Energy source

Answer 1

Catabolic reactions and anabolic reactions

Question 2

New cells means new _____

Answer 2

polymers

Question 3

Making new monomers =

Answer 3

huge energy investment

Question 4

Percentage of total energy that goes into making new monomers

Answer 4

95%

Question 5

Percentage of the 95% of energy that goes into making each monomer for the polymers

Answer 5

Proteins > 50% (of that 95%)
Lipids~20%
RNA ~ 13%
DNA only ~ 2%

Question 6

Percentage of the 95% of energy that goes into making proteins

Answer 6

Proteins > 50% (of that 95%)

Question 7

Percentage of the 95% of energy that goes into making lipids

Answer 7

Lipids~20%

Question 8

Percentage of the 95% of energy that goes into making RNA

Answer 8

RNA ~ 13%

Question 9

Percentage of the 95% of energy that goes into making DNA

Answer 9

DNA only ~ 2%

Question 10

Assembling monomers into polymers is _______

Answer 10

Less costly

Question 11

Percentage of total energy that foes into assembling monomers into polymers

Answer 11

5% of the total energy

Question 12

Percentage of the 5% that goes into forming proteins

Answer 12

greater than 90% of the 5%

Question 13

Are other nutrients needed for monomer synthesis?

Answer 13

Yes e.g. nitrogen/sulfur sources

Question 14

Is polymer synthesis more difficult under anaerobic conditions?

Answer 14

Yes

Question 15

When a bacteria is just trying to survive…

Answer 15

Replacement and repair of existing macromolecules is essential during persistence

Question 16

A surviving microbe must make …

Answer 16

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

Question 17

For how many years can a microbe stay metabolically active but not continue to grow?

Answer 17

~500,000 years

Question 18

Proton motive force is an

Answer 18

electrochemical gradient

Question 19

Proton motive force

Answer 19

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

Question 20

For long term survival

Answer 20

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

Question 21

Long term persistance

Answer 21

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

Question 22

Catabolism

Answer 22

Catabolism= breakdown of high energy molecules to release energy or directly power other reactions

Question 23

Anabolism

Answer 23

Anabolism = assembly of cell macromolecules, driven by cellular energy supplies

Question 24

Catabolism:anabolism

Answer 24

Catabolism:anabolsim is finely balanced according to environmental conditions (i.e. energy in vs energy need)

Question 25

ATP is an…

Answer 25

energy rich molecule (high energy phosphate bond)

Question 26

ATP features

Answer 26

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.)

Question 27

NADH is an …

Answer 27

electron rich molecule

Question 28

NADH features

Answer 28

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

Question 29

All persisters are

Answer 29

metabolically active and primed for regrowth

Question 30

NADPH is

Answer 30

another electron rich molecule

Question 31

NADPH features

Answer 31

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

Question 32

NADH to NADH

Answer 32

reduction

Question 33

NADPH to NADH

Answer 33

oxidation

Question 34

NADH vs NADPH

Answer 34

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

Question 35

NAD+/NADH normally high…

Answer 35

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

Question 36

NADP+/NADPH normally low ….

Answer 36

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

Question 37

How electron carriers are used …

Answer 37

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.

Question 38

How do bacteria acquire energy sources when they finally become available?

Answer 38

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

Question 39

Classes of bacterial transporters (3)

Answer 39

ATP-binding cassette (ABC) family
Major facilitator superfamily (MFS)
Group translocation e.g. phosphotransferase system (PTS)

Question 40

Transport is ____ or ______

Answer 40

active or passive

Question 41

Passive transport

Answer 41

molecules diffuse according to concentration gradient (molecules move from a region of higher concentration to a region of lower concentration)

Question 42

active transport

Answer 42

an energy source is used to rapidly accumulate against a concentration gradient (move solute molecules to higher concentrations)

Question 43

Primary active transport

Answer 43

ATP or similar is hydrolysed for energy

Question 44

Secondary active transport

Answer 44

co-transport of another molecule is the energy source (cotransport = the ion whose gradient powers transport and the substance being moved across the membrane)

Question 45

Advantages of active transport

Answer 45

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

Question 46

Disadvantages of active transport

Answer 46

Energy cost and more complex proteins required

Question 47

Facilitated diffusion

Answer 47

Facilitated diffusion is where substances move across the plasma membrane with the assistance of transport proteins that are either channels or carriers.

Question 48

ATP binding cassette (ABC) superfamily

Answer 48

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

Question 49

ABC superfamily stands for

Answer 49

ATP binding cassette superfamily

Question 50

Major facilitator superfamily (MFS)

Answer 50

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

Question 51

MFS stands for

Answer 51

Major facilitator superfamily

Question 52

Uniport

Answer 52

Passive for MFS. Driven by the concentration gradient of the main solute

Unidirectional import or export which is concentration gradient based

Question 53

MFS 3 types

Answer 53

Uniport
Antiport
Symport

Question 54

Antiport

Answer 54

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

Question 55

Symport

Answer 55

MFS

Active. Concentration gradient of another molecule moving in same direction is used

Both molecules are moving in the same direction

Secondary active transport

Question 56

Group translocation (aka phosphotransferase system)

Answer 56

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

Question 57

Balancing act of anabolic macromolecule synthesis and catabolic energy generation is regulated by …

Answer 57

redox balance