bchm module 2

what is the overall reaction for respiration

where are electrons added and removed

glucose is oxidised to form CO2 (electrons removed)

O2 is reduced to form H2O (electrons added)

why is respiration exergonic

why does this make it important to be done in stages

respiration is exergonic because the removal of electrons from glucose is a favorable process that releases energy, allowing glucose to move to a more stable state (lower free energy)

therefore it is important to do it in stages, as releasing all this potential energy at once would cause an explosion, therefore the e transport chain is utilised to release potential energy of electrons gradually, as they are passed between acceptors

4 stages of aerobic respiration

what stages are in anaerobic respiration / fermentation

• glycolysis

• pyruvate oxidation

• citric acid cycle

• oxidative phosphorylation

only glycolysis is in anaerboic respiration

where does respiration occur in prokaryotes compared to eukaryotes

eukaryotes

• glycolysis in cytoplasm

• other stages in mitochondria and across mitochondrial membrane

prokaryotes

• all stages occur in cytoplasm

• for reactions occurring across membranes, the plasma membrane is utilised

what are the inputs and outputs of glycolysis in respiration

• input = glucose, 2ATP

• output = 2 pyruvate molecules, 2ATP, 2NADH

what is substrate-level phosphorylation

this is the formation of ATP from ADP, via enzymes transferring a phosphate group from another molecule, to the ADP, therefore forming ATP

summarise the first and second set of reactions in glycolysis

• two sets of 5 reactions

• in the first set, glucose is phosphorylated twice (using 2ATP), then cleaved, forming 2 G3P (glyceraldehyde-3-phosphate, a 3C sugar)

• this makes glucose more reactive to allow the next reactions to occur, by coupling the hydrolysis of ATP

• in the second set, G3P is oxidised as electrons are removed, which are added to NAD+ to form 2NADH (important for further respiration reactions)

• G3P also undergoes substrate-level phosphorylation twice, to form 2ATP by adding phosphates to ADP, in total forming 4ATP (2 overall, as 2 are used at the start)

• these processes are carried out by various enzymes

what is the enzyme control involved with glycolysis

• allosteric regulation of phosphofructokinase, a key enzyme in glycolysis

• when ATP and citrate are at high concentrations in the cell, they bind to this enzyme’s allosteric sites on its quaternary structure

• this switches off (inhibits) glycolysis, as it signifies the cell has lots of energy

• when these concentrations are low, the allosteric sites will be free, and along with AMP (ATP-2 phosphates, associated with low energy) stimulating their activity, glycolysis will be switched on (done more), as it signifies the cell needs energy

summarise the process of pyruvate oxidation in respiration

what are the inputs and yields

• if O2 is present, pyruvate formed from glycolysis will be transported to the mitochondrial matrix

• a series of reactions are carried out by various enzymes on a complex

• pyruvate is decarboxylised (CO2 removed), and oxidised (electrons removed and added to NAD+ to form NADH)

• it then has the coenzyme A added to it

• per pyruvate, 1Actyl CoA, 1NADH, and 1CO2 is formed

summarise the citric acid / krebs cycle

what are the inputs and yields

what does this mean for glucose now

• Actyl CoA formed in pyruvate oxidation is metabolised in 8 steps into various sugars by various enzymes, in a cyclical fashion so the last product can be added to another Actyl CoA so the cycle repeats

• electrons are removed to form 3NADH from NAD+, and 1FADH2

• a substrate-level phosphorylation occurs to form 1GTP, which is converted to 1ATP

• decarboxylation occurs to produce 2CO2

• so 1Actyl CoA forms 3NADH, 1FADH2, 2CO2, and 1ATP

• thus glucose has been oxidised to form CO2, its electrons have been added to NADH carriers

summarise the electron transport chain process of respiration

include the enzymes involved

• NADH & FADH2 formed previously in respiration, transport their added electron, to 4 protein complexes (where involved enzymes are grouped)

• these complexes have various cofactors & coenzymes, which transport the E between complexes, also aided by mobile E carriers (cytochrome C & Q), until the E is added to O2 (reduced to form H2O)

• this releases free energy from NADH&FADH2, and gives it to the complexes, allowing them to change shape and pump H+ across the membrane (into the intermembrane space - proton pumps)

• this creates an uneven distribution of H+ across the membrane, they want a state of lower free energy so they move back across the membrane (into the matrix), via ATPsynthase

• this couples their release of free energy, with the addition of inorganic phosphate to ADP, forming ATP (oxidative phosphorylation)

• this is done by amino acid residues on the various ATPsynthase subunits, becoming protonated by the H+, causing them to rotate, to allow H+ through, and allow P onto ADP

how does the electron transport chain of respiration transform energy

it tranforms potential energy in the electron carriers (NADH & FADH2), to kinetic energy in the H+ in the gradient, to chemical energy in ATP (formed via the addition of P to ADP)

why can respiration have a varying amount of ATP formed per glucose

due to the different electron carriers (NADH&FADH2), how they can cause differing routes of E through the transport chain, how the E can take varying paths in the transport chains - FADH2’s route release less potental energy

these may result in less potential energy released, so less ATP can form

total ATP formed in aerobic respiration

30-32

how can fats be broken down in respiration too

how does their energy yield and efficiency differ

• fats stored in the body as triacylglerides (glycerol & 3 fatty acid chains), undergo beta oxidation in the matrix, where acyl (CH2CH3) units are sequentially cleaved off the fatty acid chains

• these are each converted to Actyl CoA, so can then be fed into the citric acid cycle (forming 3NADH, 1FADH2, and 1ATP) and go on to produce ATP via the electron transport chain as usual

• this can produce much more ATP, as fat stores more energy/g than carbs (due to hydrophobic, can form globs), and has long chains of acyl units to cleave

• however it is much slower, as the fat must be transported from the storage in the body, and then into the mitochondria

how does aerobic respiration differ in prokaryotes compared to eukaryotes

• they have no organelles, so glycolysis / pyruvate oxidation / the citric acid cycle all occur in the cytoplasm, forming NADH and FADH2 the same

• then the electron transport chain occurs across the plasma membrane instead (no mitochondrial membrane to use), and this proton gradient is formed inside & outside the cell

• otherwise the process is the same

• produces more ATP than in eukaryotes (~40/glucose), as the ATP cost of moving produced ATP out the mitochondria is avoided

how are proteins broken down in respiration to form ATP

what are the disadvantages

• they are broken down into amino acids

• these can then be converted to pyruvate and continue into pyruvate oxidation, or Actyl CoA then continue into citric acid cycle, or be put right into the citric acid cycle

• then they go onto form NADH and FADH2 and do the electron transport chain the same, to do oxidative phosphorylation to form ATP

• this is disadvantageous however, as proteins make up body structures and enzymes, they arent simply stored, so breaking them down for enery will impact survival functions

how does anaerobic respiration (fermentation) occur differently to aerobic respiration

how does this differ in yeasts

why is this not as good as aerobic respiration

• glycolysis occurs as normal to form 2 pyruvate per glycose

• no O2 is present, so pyruvate formed in glycolysis is not transported into the mitochondria (thus fermentation occurs)

• it is instead converted to 2 lactate by adding electrons (Reducing), which it gains from NADH, thus helping glycolysis to continue as NAD+ is regenerated to be used in these reactions

• yeast then convert pyruvate acetaldehyde, which is reduced to ethanol

• this only forms 2ATP / glucose vs 30-32 ATP / glucose in aerobic

what types of organisms do photosynthesis

• marine organisms (80% of O2 produced)

• 50% of these are protists & prokaryotes

• also occurs in green plants

what is the overall reaction in photosynthesis

within this, what are the two phases

• H2O is oxidised to form O2, providing electrons and ATP - these are the light dependent reactions, as energy to split water and transport e is provided by light

• CO2 is reduced to form glucose, from the electrons and ATP created in the light dependent reactions - these are the light independent reactions (Calvin cycle)

where does photosynthesis occur in eukaryotes (specific parts)

• in the chloroplasts

• light dependent reactions occur within the thylakoids, stacks of disc-shaped membranes in the centre - in the chlorophyll pigments embedded in their membranes

• light independent reactions occur within the stroma, the fluid within the chloroplasts, surrounding the thylakoids

where does photosynthesis occur in prokaryotes

is the process of photosynthesis the same for them and eukaryotes?

• within infoldings of the plasma membrane, forming thylakoid membranes (but without the chloroplast organelle)

• this increases the SA for photosynthesis

• otherwise, photosynthesis is energetically and in terms of proteins used, very similar

what are the types of pigments a chloroplast can contain

how do these effect the colour we see plants as, and why?

• can contain pigment molecules like chlorophyll, which does photosynthesis,

• this absorbs blue & red wavelengths of light, and reflects green, so photosynthesising parts of the plant appear green

• can contain accessory pigments like carotenoids

• these absorb and reflect different wavelengths of light, and dont do photosynthesis, so make the plant appear different colours (e.g red, yellow - in autumn)

why do the leaves of deciduous plants turn from green, to yellow/orange/red in autumn before the plant sheds them?

• chlorophyll pigment molecules contain nitrogen, so are recycled prior to being shed, to provide lots of nitrogen for the plant (important for growth)

• other pigments like accessory pigments don’t contain nitrogen, so aren’t recycled, and the leaves appear the colour they reflect, rather than green (as chlorophyll has been lost)

how can chlorophyll pigment molecules absorb light energy, to begin photosynthesis (And the electron transfer processes this includes)

• they contain lots of C-C double bonds, which means that the electrons on the C can be ‘excited’ (Raised) to higher energy levels, with the input of light energy (photons)

• as these electrons return to their ground state, they release heat and light energy

• therefore providing energy to be passed on, to fuel photosynthesis

what are photosystems (in photosynthesis)

how do they transport energy throughout themselves

what is this energy transfer called

• photosystems are complex protein complexes in the thylakoid membrane of chloroplasts

• these contain many chlorophyll molecules embedded within (antennae chlorophyll), which when provided light energy input (photon), an electron within is ‘excited’, and when returning to its ground state, releases energy

• this energy is passed on to neighbouring antennae chlorophyll, causing their electrons to ‘excite’

• the cycle repeats until reaching the final RC chlorophyll (Reaction centre)

• this is called resonance energy transfer

summarise the light dependent reaction phase of photosynthesis

• light energy is passed through antennae chlorophyll in PSII, to RC chlorophyll, whos electron is physically passed to the primary acceptor (is replaced from reducing water via splitting complex)

• this e is then passed through the e transport chain, through PQ to cytochrome complex, which fuels shape changes (As e passes on energy), allowing this to pump H+ into the thylakoid

• this creates a proton gradient, and as H+ moves back through to the stroma, it fuels shape changes in ATP synthase in the membrane it moves through, creating ATP

• meanwhile, PSI antennae chlorophyll do the same thing, and the RC chlorophyll passes its e to the primary acceptor, which is replaced by the e from the transport chain (via PC)

• the e from PSI is passed through another e transport chain (via FD & NADP+ reductase) until NADP+, reducing it to NADPH

• = ATP & NADPH formed for calvin cycle

what are the two processes of forming ATP, involved in photosynthesis

why are there two methods?

• non-cyclic photophosphorylation occurs in the linear route of e, taken through the photosystems, and onto the e transport chain between PSII and PSI, which creates an H+ gradient to fuel ATP synthase to create ATP

• cyclic photophosphorylation occurs when PSI’s primary acceptor passes its e to Fd (feridoxin protein), which instead of reducing NADPH, takes it backwards to cytochrome complex in the e transport chain, where it forms more ATP

• this is because the calvin cycle requires more ATP than NADPH

what are the RC chlorophyll named in PSII vs PSI

• PSII = P680

• PSI = P700

how similar is ATP production in the mitochondria (respiration) vs chloroplast (photosynthesis)

• they are very similar

• both use electron transport chains to create proton gradients, which fuel shape changes in ATP synthase to add phosphate to ADP to form ATP

what is a unique photosynthesis adaptation done by some prokaryotes (e.g. sulfur bacteria)

• they use molecules other than water, to split and act as an electron donor, to replace the lost electron in the oxidised RC

summarise the light independent (Calvin cycle) phase of photosynthesis

• 3CO2 enter a complex cyclical metabolic pathway in the chloroplasts (Stroma), and undergo 3 phases

• carbon fixation uses ATP and NADPH (gained in light depedent reactions) and the CO2, adding this to ribulose bisphosphate, to form G3P (reduction phase - e added from NADPH)

• some of this G3P is siphoned off to then form glucose under further modification (and sucrose, starch, cellulose)

• the rest continues through the pathway, undergoing regeneration phase to add CO2 to form ribulose bisphosphate again (so it can accept a CO2 again)

• is carried out by enzyme Rubisco, and the cycle uses ATP and NADPH

what are the two types of reactions a Rubisco enzyme can catalyse in photosynthesis

which one is favored and why

• Rubisco stands for ‘ribulose bisphosphate carboxylase oxygenase’, so it can do both carboxylase (add CO2) and oxygenase (add O2) activity

• calvin cycle requires it to add CO2, in the regeneration (final) phase, to recover the CO2 acceptor onto G3P, and continue the calvin cycle

• so the carboxylase reaction is favored

• however, if it adds O2, it cannot continue through the calvin cycle, and photorespiration (energy input) must occur to get useful sugar out of the product

• so the oxygenase reaction is not favored

how and why does Rubisco have tightly regulated enzyme activity in photosynthesis

• its activity must be tightly regulated so that ATP and NADPH formed in the light dependent reactions, are actually used for the calvin cycle, rather than ATP from other sources (e.g. respiration)

• therefore, it must be activated when / after the light dependent reactions occur

• otherwise, if Rubisco were just to be active all the time in carrying out the calvin cycle to produce glucose, it would likely use ATP from other sources at some point, which would be futile cycling, as the purpose of the light dependent reactions is to gather ATP for this purpose

• activity is regulated by level of Mg2+ and pH in the stroma, and concentration of reductants (all affected by light dependent reactions)

what determines the type of reaction / activity, that the Rubisco enzyme carries out (in calvin cycle of photosynthesis)

how do plants control this

• the concentration of CO2/O2 ratio in the cell (so therefore in the plant)

• with more CO2, carboxylase takes activity, with more O2, oxygenase takes activity

• since carboxylase reaction is more favorable (allows calvin cycle to continue), plants aim to keep a high CO2 concentration relative to O2 in the leaves

• this is maintained by keeping stomata (gas exchange pores) open, so O2 diffuses out (Waste) as CO2 diffuses in (required)

why may maintaining a high CO2:O2 ratio in plant leaves (so that rubisco carries out calvin cycle efficiently), cause issues in some plants

what are the two types of plants that underwent further evolution to combat this

• maintaining this ratio requires stomata (gas pores on leaves) to stay open, which provides risk of water loss via transpiration (Especially in drier environments

• C4 plants and CAM plants developed special adaptations to combat this issue

what is the difference between C4 and CAM plants

how have they each distinctly evolved?

• CAM plants keep stomata open at night (less water loss), so while photosynthesis ceases to occur, CO2 entering is fixed into organic acids, and stored in vacuoles

• during the day, the stomata close, and CO2 is released from this storage (decarboxylated), to maintain a high CO2:O2 ratio, and fuel calvin cycle

• C4 plants shift the location of the calvin cycle, to specialised ‘bundle sheath’ cells, below the mesophyll, around the vascular tissue - these containing rubisco

• so CO2 enters the mesophyll as normal, and is then fixed to a 4C compound, which is then transported to the bundle sheath cells, where they release CO2, and the calvin cycle occurs as normal

• this maintains a high CO2:O2 ratio where rubisco carries out the calvin cycle (bundle sheath cells)