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)

what types of membranes in the cell, does membrane transport occur in?

• outer plasma membrane (eukaryotes & prokaryotes)

• internal membranes surrounding organelles (eukaryotes)

summarise the structure of cell membranes

• phospholipid bilayer

• two layers of phospholipids (glycerol phosphate head - hydrophilic, lipid tail - hydrophilic)

• they arrange into a membrane layer due to the hydrophilic interactions of head → solution, and the hydrophobic interactions of tail → tail

• is full of proteins embedded within

how do integral membrane proteins (embedded in the membrane), differ in structure from proteins surrounded by cytoplasm?

• they must have specific structure to interact with the hydrophobic lipid inner layer, in order to integrate themselves, along with hydrophilic structures to interact with the cell solution (amphiphatic nature of the bilayer)

• this may involve specific non-polar amino acid residues facing the inner bilayer, while amino acid residues face the inner to interact with their transportees, and hydrophilic residues facing the cell solution

• these are made up of alpha helicies protein structures, that span the membrane

• other proteins would only require hydrophilic structures to interact with the cell solution

what are the 3 general types of membrane transport in focus for this module?

• passive transport

• active transport

• secondary active transport

what is passive membrane transport

which law of thermodynamics does it involve, and why?

name the 4 different types

• passive transport is the movement of molecules across a membrane, requiring no energy, as they move spontaneously down their conc. gradient (high → low)

• this involves the 2nd law of thermodynamics, as these molecules are spontaneously moving across the membrane to achieve equal conc. on either side (equilibrium) - to occupy the lowest energy state

• diffusion; facilitated diffusion (via membrane transport proteins, via ion channels); osmosis

what is the permeability through the plasma membrane like for different types of molecules?

with what methods can each of them passively transport in?

• hydrophobic molecules: very permeable, can rely on simple diffusion

• e.g. O2, N2, CO2, steroids hormones

• small polar molecules (uncharged): permeable but simple diffusion is inefficient for most, so transport proteins utilised

• e.g. H2O, urea, glycerol

• large polar molecules (uncharged): permeable but simple diffusion is very inefficient, so transport proteins utilised

• e.g. glucose, sucrose

• ions: not permeable (due to non-polar inner lipid layer), so ion channels are utilised

• e.g. H+, K+, Na+, Ca2+, Mg3+, Cl-, HCO3-

what is the difference between channel and carrier membrane transport proteins

give an example for each

what type of transport is this involved in

• this is facilitated diffusion (passive transport) - so is spontaneous movement requiring no energy

• channel proteins have a channel that molecules pass through the membrane via, lined with specific amino acid residues to let the target molecule through

• e.g. aquaporins for moving water

• carrier proteins temporarily bind with their target molecule, then change shape so the binding site is on the other side of the membrane, and unbind with it, to allow it to pass through

• these are uniporters (Specific to one molecule), due to specific amino acids on the binding sites to only interact with their target

• e.g. GLUT4 to move glucose into the cell (down its conc. gradient) as it is too large to diffuse efficiently

how is the GLUT4 membrane carrier protein, affected by insulin?

how does this process affected by diabetes?

• the insulin hormone acts as a signal (for insulin receptor on the outside of cells) for GLUT4 carriers to be incorporated into the membrane (via GLUT4-containing vesicles fusing with the membrane) to allow glucose into the cell

• so with diabetes (type 1 = no insulin; type 2 = insulin receptors on cells inactive), GLUT4 isn’t signalled to be incorporated into the membrane

• therefore it cannot take glucose into cells, so it instead remains circulating in the blood where it causes damage

what is osmosis

how does this involve ‘free water molecules’

• osmosis is the passive transport of water, via simple / facilitated (via aquaporin channels) diffusion, from high → low conc. across the membrane

• free water molecules refer to water molecules not associated with sugars (not holding molecules in solution), which control the diffusion of water, as it moves from high → low free water conc. (so that only free water is considered and not water busy in solution)

• this occurs as water molecules cluster around solutes, which cannot permeate the membrane, so these waters cannot pass through either

how does osmosis affect animal cells

• animal cells in isotonic solutions have the same solute concentration as their environment, so water doesn’t rush in or out (equal net movement) - ideal

• while in hypertonic solutions (less water), water will rush out and the cell shrivels, and in hypotonic solution (more water), water will rush in and the cell will burst (lyse) - due to their lack of cell wall

• therefore it is important for animal cells (Especially those producing lots / few sugars), to regulate water movement

• e.g. red blood cells to retain effective shape for movement

• e.g. special mechanisms like in Paramecium protists where contractile vacuoles fill up with water rushing in, and release it (due to high solute concentration from high metabolism)

how does osmosis affect plant cells

• plant cells have cell walls, so they respond to iso/hyper/hypo tonic solutions differently to animal cells

• they typically remain hypertonic with their surroundings (more water in the cell), to remain sturdy (water fills vacuoles and applies turgor pressure, with cell wall preventing bursting by limiting uptake) - favouring water movement into the cell

• so in isotonic solutions, they become flaccid (turgidity lost, water not rushing in - plant wilts), and in hypertonic solutions (surroundings have less water), water will instead rush out, and they will plasmolyse (too much water loss occurs)

• e.g. some plants control turgor, to power rapid plant movement

• (Mimosa leaflets closing and opening to deter predators, fungi releasing spores)

what type of membrane transport are ion channels

what does it mean that they are specific, and sometimes gated

• facilitated diffusion - passive transport (charged ions cannot diffuse through the non-polar inner bilayer)

• they are specific, so only let one type of ion through, due to particular amino acid residues facing the interior of their channel, which only interact with their target molecule

• sometimes they are gated, which means they control opening and closing, usually being closed by default and opening in response to stimuli

• e.g. change in voltage, mechanical stimulation, substrate binding (e.g. ligand)

how is cystic fibrosis involved with ion channels

• cystic fibrosis causes respiratory infections, and gradual breakdown of the lungs due to inflamatory response

• is caused by various mutations causing a defective Cl ion channel, as these usually maintain a certain volume of water in the lungs to coat cillia, so they can function to beat and move mucus and bacteria out of the lungs

• so when defective, this volume of water is too shallow or deep, so they cannot beat or remove foreign material effectively, causing inflamatory response

what is active transport

what carries it out, and how?

• active transport is the movement of molecules across cell membranes, against their conc. gradient (low → high), requiring energy (ATP) as this is non-spontaneous

• is carried out by membrane proteins (pumps)

• these temporarily bind with the solute, then change shape with the input of ATP, exposing the binding site to the other side of the membrane, thus allowing it to move through

• e.g. ion pumps (ATPase - Na+/K+, ATPase - H+, ATPase - Ca2+ = to form ATP (binding of phosphate to ADP))

describe the first function of ion channels in neuron action potentials

• when the membrane potential (electrochemical charge gradient) of a neuron reaches > -55mV, voltage gated Na+ ion channels are stimulated to open, and Na+ passively moves into the cell

• this causes repolarisation as the mV further increase

• shortly after, K+ voltage gated ion channels are stimulated to open, and K+ passively moves out of the cell

• this causes depolarisation as the mV decreases below resting potential

• this is sent progressively down the axon (channels distributed throughout), allowing it to be passed onto other neurons

describe the funciton of active transport in neuron action potentials

• sodium potassium ion pumps move Na+ across their conc. gradient, outside the cell, and K+ across their conc. gradient, into the cell (every 3 Na+ out, 2 K+ in)

• this restores the neuron back to resting potential (membrane chemical / conc. gradient back to normal), progressively down the axon, after the action potential has been sent down

• therefore resetting the neuron to allow it to make more action potentials

describe the second function of ion channels in neuron action potentials

• voltage gated Ca2+ ion channels are in the membrane at the end of the neuron, which are stimulated by the change in voltage along the axon (due to action potential)

• this causes them to open, and Ca2+ diffuses into the cell

• this stimulates vesicles of neurotransmitters to exit the neuron, and release these across the synapse (Gap between nerve cells)

• these act as signals to more ion channels (ligand gated, activated by the NT signals), which cause ion (Na+ and K+) movement in the next nerve cell

• therefore passing this action potential along

what is secondary active transport

what are the two types of systems that can be involved

• where active transport occurs (via ion protein pump), to set up an ion gradient (typically H+ / Na+) across the membrane, by moving these ions across their conc. gradient (ATP input)

• these have an associated membrane protein (cotransporter), which allow facilitated diffusion of these ions back into the cell (passive)

• this provides energy for this protein to then transport a different ion / solute, against its conc. gradient (a similar idea to energy coupling)

• symporter = this cotransporter moves the ions and solute in the same direction

• antiporter = this cotransporter moves the ions and solute in a different direction

what is an example of secondary active transport (e.g. in animals, or plants / fungi)

• animals = proteins couple the Na+ conc. gradient (movement down its gradient into the cell), with the movement of glucose into the cell (up its gradient) - e.g. in kidneys

• plants & fungi = H+ATPase moves 1H+ per ATP to generate a conc. and charge gradient (more H+ & + outside), whose movement back down the gradient is used to drive solute uptake

describe an enzyme’s active site

• this is where the enzyme lowers Ea for a reaction

• reactant molecules temporarily bind with the enzyme via weak H bonds (in its active site, specific amino acid structure to fit the reaction)

• this involves a temporary change in the active site, to fit the substrate tighter (induced fit)

• the enzyme lowers the Ea by various methods, and the reactants are converted to products (reaction completes)

• they are then unbound and released, the enzyme shape changes back to default and can catalyse more ractions

list the 4 ways enzymes lower Ea (enzyme catalysis)

how many occur per catalysis?

1. the enzyme may bind to 2 substrate molecules, and use their specific shape active site to orientate them so reaction is encouraged

2. it may use amino acid residues to create uneven charge in the active site, causing uneven charge (electron redistribution) in the substrate, so reaction is favored

3. it may strain / bend the substrate via the active site’s shape, forcing it to a transition state (bonds between atoms affected) where reaction is more likely

4. can also form covalent bonds with the substrate, and the enzyme active site, encouraging reaction

any combination of 1-4 can be used to lower Ea

describe the enzyme catalysis strategies in lysozyme (found in human tears)

• lysozyme enzyme breaks down oligosaccharides in bacterial cell walls, to kill bacteria and prevent eye infection

• it utilises all 4 enzyme strategies

• it forces oligosaccharide into a strained conformation (enabling acidic amino acid residue to add H+, attacking the sugar bond)

• it positions the oligosaccharide close to water (favoring reaction)

• it uses uneven charge (negative amino acid residues) to polarise water (form OH-) which joins to oligosaccharide’s C

• this breaks a covalent bond formed between an amino acid residue and the C

• this splits the sugar into 4 and 2 C long sugars, and the cell wall is compromised and cannot infect

what factors affect enzyme catalysis rate / activity, and why

temperature

• at optimum temp (37C), highest rate of reaction / enzyme activity occurs

• at below optimum temp, reaction rate decreases, as kinetic E of particles decrease (less collisions between enzymes & substrates)

• at above optimum temp, rate increases until enzyme denatures (bonds holding tertiary structure break, so specific active site unfolds and cannot funciton)

pH

• optimum varies for different cells, here the rate is highest

• at above or below optimum, specific interactions with amino acid residues may be inhibited (e.g. protonate / deprotonate an acid/base), and rate is decreased

• above / below optimum may also cause denature (lower rate)

what are enzyme cofactors

why are they helpful

give some examples

• small molecules that bind to the active site, to help the substrate fit more tightly, or help position the substrates to favor reaction (required for catalysis in some enzymes)

• thus increases enzyme catalysis rate

• e.g. inorganic ions (Fe, Zn, Cu), or coenzymes (complex organic molecules: vitaminds, NAD+, FAD+

what is an enzyme inhibitor

name and describe the 4 types

• molecules that bind to the enzyme and prevent substrates from binding (prevent catalysis)

• e.g. drugs, toxins, metabolites (for enzyme regulation)

• irreversible inhibitors = covalently bond to the enzyme, preventing reaction indefinitely

• reversible inhibitors = non-covalently bond to the enzyme, preventing reaction only temporarily

• competitive inhibitors = bind to the enzyme’s active site so substrate molecules cannot (competing with the susbtrate)

• non-competitive inhibitors = bind to another area of the enzyme, causing shape changes of the active site so substrates cannot bind

describe the enzyme inhibition examples of

• penicillin

• viagra

• penicillin is an irreversible inhibitor of an enzyme that has important function in creating the bacterial cell wall, thus the bacterial cell wall is compromised

• this allows penicillin to kill bacteria

• viagra is a revversible inhibitor of an enzyme that normally breaks down signalling molecules to increase blood flow

• in plants therefoe, it causes pollen tubes to reorientate and grow backwards

what is enzyme control

list the 3 types

this is how enzyme activity is regulated in the cell, to regulate metabolic pathways, reactions, etc

• allosteric control

• genetic control

• covalent control

describe allosteric control of enzymes

how does this cause feedback inhibition

• usually done to control enzymes with multiple polypeptide subunits, which have allosteric binding sites (seperate from active sites)

• allosteric activator molecules bind to the allosteric site, and cause shape changes in the active site to make catalysis more efficient (Switch on reaction - enzyme active form)

• allosteric inhibitors bind to the allosteric site, and cause shape changes in the active site to make catalysis less efficient (switch off the reaction - enzyme inactive form)

• also done as ‘cooperativitiy’, where binding of a substrate molecule to one active site, locks all the other subunits into active state (active sites become efficient)

• feedback inhibition occurs in metabolic pathways, where the product of a pathway, acts as an allosteric inhibitor to an enzyme previous in the pathway

• therefore as more products are produced, earlier enzymes are switched off to regulate product production, but as product is used up, they dissociate from the earlier enzymes to switch on the pathway again

describe genetic control of enzymes

how does feedback inhibition work for this method

• this is done by switching on and off the production of enzymes from the genes that encode them (via transcription, translation, etc) - a slower means

• inactivation is done by molecules binding to specific repressor proteins (upstream of gene), which then bind to the gene’s operator protein (Caused by the shape change due to binding to the repressor)

• this prevents RNA polymerase from moving along the gene, therefore stopping transcription and translation

• activation occurs when this molecule is in lower concentration, so it dissociates with the repressor, which then is forced off the operator, and transcription / translation can occur again

• feedback inhibition is done when an end product of a metabolic pathway is used as this inactivation molecule to prevent expression of enzymes in the pathway

• then when in low conc when more product is needed, it dissociates so switches on again

describe covalent control of enzymes

how does feedback inhibition work for this method

• switching on and off enzymes, by phosphorylation, as kinase proteins transfer phosphate from ATP, to the enzyme covalently - relatively fast method

• then, phosphatase proteins can remove the P

• this causes activation or inactivation of the enzyme, depending on the enzyme, by changing its active site shape

how are enzymes compartmentalised in the cell

how is this a means of control

• in eukaryotic cells where cell compartmentalisation exists via organelles, enzymes are located at the site of the specific reaction they catalyse

• this makes reactions more efficient

• it also controls the enzyme as they can only produce their products in a certain area, for a certain reason

what is enzyme feedback inhibition

• using enzyme control to inhibit enzymes in metabolic pathways, using products of these metabolic pathways, therefore forming a feedback loop of inhibition

• as products decrease, are used up, and more are needed, they stop inhibiting and the enzyme and metabolic pathway switches on again

what is metabolism in cells

what does this allow cells to do

how does this ensure metabolic disequilibrium, and why is this important

• metabolism is all of the metabolic pathways in cells, and metabolic pathways are series of sequential chemical reactions (typically a starting molecule, converted to others, eventually to the product molecule)

• these allow cells to do work, as these chemical reactions involve transforming molecules and energy (usually done via enzymes)

• metabolic pathways prevent cells from coming to equilibrium (as this would kill the cell, preventing work), instead helping reach a state of metabolic disequilibrium (a product of one reaction can be coverted to something else, continuously, in these metabolic pathways)

what are the two types of metabolic pathways

how do these interact

why is this important

• catabolic metabolic pathways break down larger molecules into simpler ones (spontaneous, releases energy)

• anabolic metabolic pathways join simpler molecules to form larger ones (non-spontaneous, requires energy)

• energy coupling couples these two types, so the energy released in catabolic pathways, is converted to cellular energy (e.g. ATP, NADH, NADPH) used to energise anabolic pathways, so both can occur

how and why is metabolism regulated

• is regulated depending on the energetic and material needs of the cell / organism (certain reactions needed more or less at certain times and situations)

• regulated via enzymes (carry out metabolic pathways), which are regulated themselves allosterically, covalently, genetically, or compartmentally

how is the reaction to break down glucose, metabolically controlled, and why

• enzymes catalysing this break down are sensitive to energy status, at low energy they are switched on, therefore forming more energy from breaking down the sugar

• then when enough energy is formed, they switch off to stop producing more energy

• this also causes the switching on of anabolic pathways to form glycogen, to store the glucose instead of breaking it down, for later use in low energy

what is the first law of thermodynamics (the expression most relevant to cells)

how does this link to cells and organisms

• energy in the universe is constant, it cannot be created or destroyed, only transferred or transformed

• so cells and organisms that require energy for work, must get it from somewhere else (e.g. sun, inorganic chemicals, organic chemiclas), and transform it to be useful to them

difference between potential energy and kinetic energy

• kinetic energy is energy in movement, while potential energy is energy stored in the structure / location of things (e.g. electron location in a molecule, chemical bonds, proton gradient, concentrations)

distinguish between

• photoautotrophs

• heterotrophs

• chemoautotrophs

in terms of energy transformation

• photoautotrophs convert light energy (sun) to chemical / potential energy (organic moleclules - food)

• heterotrophs convert chemical / potential energy in glucose (food) into chemical / potential energy that can be used by the cell (ATP)

• chemoautotrophs convert chemical / potential energy of electrons in inorganic chemicals (e.g. S2H, NH3+, Fe2+), to chemical energy that can be used by the cell (ATP)

describe the transformation of energy throughout respiration

• chemical / potential energy in glucose, is converted to kinetic energy (and some potential energy is lost), as the electrons are moved and passed through protein complexes

• this is converted to chemical / potential energy, in the generation of the H+ gradient (uneven charge)

• this is converted to kinetic energy, as H+ move through ATP sythase and cause rotation

• this is converted to chemical / potential energy, as this rotation creates ATP from ADP

• depending on the use of ATP, it is commonly converted back to kinetic energy (e.g. protein movement, muscle contraction)

what is the second law of thermodynamics (the expression relevant to cells)

• each energy transfer / transformation, increases disorder (entropy) of the universe

if cells are so highly ordered, how does their creation (/creation of an organism) abide by the 2nd law of thermodynamics?

• as molecules join to form cells and organisms, heat energy is released (Even with coupling), so while creating this order, disorder is still increased in the universe

what is free energy

what are the two types of associated reactions

• free energy measures the stability of a chemical system, its sponteneity to react

• exergonic reactions are systems with higher free energy in reactants, so are less stable, and tend to spontaneously change to stability (release free energy, forming products with lower free energy)

• endergonic reactions are systems with lower free energy in reactants, so are stable, but reactions are non-spontaneous and require energy input

what is the relevance of free energy, to cells, considering equilibrium

• reactions in isolation will come to equilibrium, they will spontaneously move towards the most stable state, where deltaG = 0

• however for cells, this would prevent work, and they would die

• therefore metabolic disequilibrium is maintained in cells, where spontaneous releases of free energy, are used (coupling) to drive processes maybe with less spontaneity, to release free energy, so deltaG will never =0 (products used as reactants…)

name the 3 types of work in cells

• movement / mechanical work

• membrane transport

• chemical synthesis

give examples of movement / mechanical work in cells

• vesicular trafficking (moving materials to specific locations in the cell, e.g. proteins, organelles, hormones)

• cytoplasmic streaming (‘mixing’ of the cell, distributing organelles, nutrients, ions, solutes, evenly around the cell)

• motor proteins (power intracellular movements, e.g. movement of organelles, vesicles, cells)

• cell motility (movement of entire cells to specific locations in the organism, via the cytoskeleton pushing the front, and pulling the back)

• cillia / flagella (movement of cytoskeleton via microtubule motor proteins, e.g. allowing the cell to swim, move mucus and dust past)

• muscle contraction (movement of the whole body due to coordinated cell activity of motor proteins)

describe the chemical synthesis form of work in cells

• the creation of macromolecules, from monomer subunits

• e.g. sugars to form polysacchardies, amino acids to form proteins