BLOCK 3 lecture 1

dominant life forms on earth

what is metabolism

the set of chemical reactions that all cells/organisms use to:

• extract energy from the environment

• synthesise the macromolecules that make up all life

catabolism and anabolism

Delta G less than 0 means a reaction is going to release energy

the metabolic triangle

trophic groups

Classify microbes basically on where they get the stuff from the triangle

metabolism key points

why use oxygen

Glucose sits at the top of the tower - means it has a lot of potential to generate energy

In comparison oxygen is at the bottom - but really wants to take electrons from those at the top

Metabolism has evolved steps so this still happens but we can capture energy before we get to oxygen - through the electron transport chain

basic molecules of life

A lot of crossover of what these look like - ring structure, amino acids, etc

So can produce all of these from a small subset of things - 12 molecules

12 fundamental molecules

Can make all of the above from just these molecules

pathways

A lot of the molecules above come from glycolysis

3 from TCA

Only 2 from pentose phosphate pathway (takes glucose-6-phosphate through, mainly to generate ribose-5-phosphate which is essential - makes up sugar molecules in nucleotides)

But also generates erythrose-4-p which is an important precurosor

Also generates a different energy carrier (NADPH) than glycolysis (NADH)

NADH goes to ETC (so mainly for catabolism), NADPH is mainly for anabolism

anaplerotic reactions

refuel the TCA cycle

Acetyl coA would have nothing to bind to - cycle is stalled

So cells need to be able to regenerate TCA intermediates to refuel and keep it reunning

the two anaplerotic reactions

Both glycolysis intermediates

Through regeneration of oxaloacetate

This is wasting carbon but it is necessary in order to keep TCA running

the glyoxylate cucle

Humans do not have the ability to do this - only microbes

2 steps of decarboxylation - CO2 is released

Input of two carbon but lose two carbon - cycle cannot continue as no net gain

So to avoid this microbes have evolved a shortcut to evolve this steps

They take isocitrate and break it apart using isocitrate lyase into succinate (which is next molecule of TCA so skipped a few steps) and glyoxylate (2C molecule)

2nd step facilitated by malate synthesase which makes malate by condensing a glycoxylate with ann acetyl-CoA

This allows the cycle to continue without the decarboxylase steps 

This doesn’t happen for every molecule - as need to make some succinyl-CoA and alpha ketoglutarate for growth - have to balance how much is going through the shortcut vs not to balance growth versus energy

Aerobic as required ETC even though it may not seem it

other uses for oxygen - degrading BTEX pollutants

These molecules have become abundant quickly - they never were in the past

Microbes have been able to quickly adapt to be able to use these as carbon sources

These molecules only contain carbon and hydrogen

Ring structure is very stable so hard to break down

So bacteria use oxygen to attack these bonds to break them down