Topic 8 Flashcards
1
Q
Benefits of metabolic pathway
A
- intermediates formed -> controlled reaction
- not a lot of energy lost via heat -> smaller reactions (check this point though)
2
Q
How enzymes work + types of enzymatic reactions
A
- enzyme binds to subs –> stresses and destabilises bonds -> lower Ea
Types:
- Endergonic: in anabolic reactions -> free energy from surr to sys -> energy needed to form bonds between molecules
- Exergonic: in catabolic reactions -> free energy from system to surroundings, energy released when bonds broken
3
Q
Competitive v Non competitive enzyme inhibition (MS based)
A
- C: inhibitor binds to active site, NC: allosteric site
- C: increasing subs [] may overpower the effect of inhibitor; NC: inc subs [] has no effect -> the subs cannot bind to many enzymes anymore
- C: Inh complementary shape to AS, similar shape to subs; NC: not
- C: subs binding prevented because inh occupies AS; NC: Subs binding prevented bc inh changes the AS
- C: pharma use; NC: end-product inhibitor use
4
Q
Competitive inhibition example
A
- Relenza inhibitor of influenza patients
- viruses release virions from infected cells -> enzyme neuraminidse cleaves docking protein
- relenza binds to neuraminidase AS competitively -> prevents cleavage -> no virions released
5
Q
NC inhibition example
A
- cyanide
- prevents aerobic respiration -> cause eventual death
- binds to cytochrome oxidase allosteric site
- ## prevents it from functioning in the ETC
5
Q
NC inhibition example
A
- cyanide
- prevents aerobic respiration -> cause eventual death
- binds to cytochrome oxidase allosteric site
- prevents it from functioning in the ETC
- aerobic resp doesnt happen
5
Q
Feedback inhibition
A
- method of negative feedback in metabolic pathways
- products of metabolic pathways are NC inhibitors of an earlier enzyme (often first step)
- increase in product levels -> enzyme inhibited -> product levels decrease
- decrease in product levels -> pathway uninhibited -> product levels increase
- used to tightly regulated levels of essential molecules
- binding to enzyme is reversible
- isoleucine inhibits threonine to isoleucine pathway by binding to threonine deaminase
6
Q
Isoleucine pathway inhibition example
A
- Isoleucine formed from threonine in 5 step pathway
- threonine deaminase is the first enzyme to convert threonine into intermediate
- isoleu binds to TD allosteric site and prevents this formation
- ensures that isoleu production pathway doesn’t deplete threonine stocks
7
Q
Drug design based on enzyme inhibition
A
- microbe proteome sequenced from genome -> metabolism enzymes identified
- microbe (eg plasmodium for malaria) enzymes are identified -> in plasmodium -> the enzymes needed for metabolism
- inhibitors for that enzyme found via screening through bioinformatic database
- inh made less toxic, with increased binding affinity
8
Q
rational drug design
A
- using computers/software to generate a compound -> will function as an inhibitor for an enzymes AS
- using combinatorial chemistry to make that compound
9
Q
ATP - why it is used for energy, functions
A
- 3 phosphate bonds
- phosphorylation makes compounds less stable, more reactive -> atp readily reacts with other compounds
- on breaking terminal phosphate bond -> lots of enegry released
- functions as the energyb currency -> transfers the phosphate group to other molecules -> releases energy for reactions
- renders other org. molecules less stable
10
Q
2 sources of energy to synth ATP from adp
A
- solar energy (during photosynth)
- oxidative processes (cell respiration)
11
Q
Define cell respiration
A
The controlled release of energy from org. compounds to produce ATP (aerobic -> in pres of O2)
12
Q
Benefits of series of reactions to form one reaction
A
- smaller activation energies -> can occur at normal temperatures and rates,
- less energy loss through heat -> transferred to carrier molecules
- transferred via transfer of H atoms -> energy transferred to electron carriers with protons and electrons
- carriers carry H to the ETC -> used to synth ATP
13
Q
what are the similarities between photosynthesis and respiration
A
- both use double-membrane bound organelles;
- both use an electron transport chain to synthesise ATP;
- both generate proton gradient/involve chemiosmosis/use ATP synthase
- both generate ATP;
13
Q
what are the differences between photosynthesis and respiration
A
- R uses O2, P releases O2
- R releases CO2, P FIXES CO2
- R occurs in the mitochondria/matrix, P occurs in the chloroplast/stroma (for LIR);
- R reduces FAD/NAD, P reduces NADP
- R: chemical energy to usable energy/ATP, P: solar energy to chemical energy;
14
Q
Anaerobic v aerobic respiration definitions
A
AN: the incomplete controlled breakdown of organic molecules to produce a small yield of ATP. No oxygen is not required
A: the complete breakdown of organic molecules to produce a large yield of ATP in the presence of oxygen.
15
Q
How hydrogen/electron carriers work
A
- H+ ions and e- are transferred from organic molecules to the carrier molecules -> energy stored in organic molecules also transferred
- e- carriers carry the e- and 2H+ to the cristae of the mitochon. -> transfer to the ETC
- in the ETC the energy of the e- and H+ are used by ATP synthase to synth ATP
- only in aerobic resp is ATP thats derived using FADH2 and NADH used
16
Q
What happens to pyruvate if oxygen is not present?
A
In humans:
- forms lactic acid
- in the process to form lactic acid it is reduced -> reduced by the electron carriers -> oxidised to OG state to replenish stocks
In microogr/yeast
- forms CO2 and ethanol
- same as above
NAD+ stocks hence replenished so small quantities of ATP can continue to be produced
17
Q
Explain how chemical energy for use in the cell is generated via chemiosmosis and electron transport
A
- electron carriers FAD and NAD+ are reduced in glycolysis/link/krebs BY GAINING 2 H AND 2 E
- reduced FAD and NAD deposit high energy electrongs and H+ ions at the cristae of mitochon at IM proteins
- electrons travel down ETC, from one carrier protein to the next in a series of redox reactions
- as electron travle down they release energy
- this generates energy for H+ ions to be pumped via proton pumps across the membrane into the IMS
- The p+ concentration builds up in the IMS and a proton motive force forms
- the protons travel down this chemiosmotic gradient across the mem through the transmem. protein ATP synthase in inner mitochondrial cristae/mem
- energy released when electrons pass through ATP synthase
- ATP synthase uses the movement of H+ to catalyse the reaction forming ATP from ADP +Pi
- oxidative phosphorylation
- Electrons in the ETC are accepted by O, the final e acceptor, and this ensures the ETC can continue
- chemiosmosis is the use of the movement of H+ ions down a concentration gradient to generate ATP
18
Q
total atp from aerobic
A
38
19
Q
mitochondria adaptations
A
- cristae - large mem area for etc
- matrix has the right enzymes and pH for krebs cycle
- mem proteins: electron carriers and other proteins for the ETC and ATP Synthase. outer membrane has the right transport proteins to transport pyruvate from cytosol
- small IMS - maximise the p+ gradient
20
Q
Electron tomography
A
creating 3d visualisation of a sample
- Imaging using a TEM
- Image of sample repeatedly taken, tilting it at different angles between images
- 3D model generated
- samples must be dehydrated and fixed or frozen
Things discovered:
- IMS is of a consistent width
- the cristae are continuous with the inner mem
- the shape, position and volume of mito can keep changing in active mitochon.
21
Q
Non-cyclic photophosphorylation
A
- Light energy/photons are absorbed
- by PSII
- Energy used in the photolysis of water -> 2H+, O, 2e-
- PSII electrons are excited -> travel down an ETC in the thylakoid membrane -> one carrier to next througha. series of redox reactions
- this movement releases energy
- energy used to pump H+ ions across the thy. mem into the thylakoid space.
- The H+ ion conc increases, generating proton motive force
- H+ ions diffuse down the concentration gradient though ATP Synthase in the thylakoid mem. -> the energy from the diffusion of H+ ions used to synth ATP
- from ADP + Pi
- e- from ETC enter PSI where they are re-excited
- transferred to a protein where they reduce NADP+ to NADPH + H+
- e- lost initially from PSII are replaced by electrons from photolysis of water
- end products: reduced NADP, ATP and O2 as a by-product
22
Cyclic photophosphorylation
- Only the electrons in PSI are excited
- NADP+ is not reduced
- the electrons from PSI undergo the ETC, synthesise ATP and return to the PSI to be re-energised
23
C v. NC photophosphorylation
basic differences: oxygen evolved, PSI and PSII used, water photolysis and NADPH produced for NC
NC is to produce ATP as well as organic molecules for further long term storage. C only produces ATP in presence of sunlight
24
How Calvin cycle was discovered
- algae grown in radioactive C-14 -> C - 14 incorporated into compounds -> light shone of algae so it photosynthesises
- algae run through hot ethanol to kill it
- 2D chromatography used to identify the compound w radioactivity
- radioactive compounds identified using autoradiogrpahy
- experiment repeated by exposing the plant to ligth for different times -> order of compounds determined
25
Chloroplast adaptations
- Thin space within thylakoids: optimise h+ [] grad
- photosystems in the thylakoid membranes for the ETC -> PS maximise light absorption
- suitable enzymes and pH in the stroma for calvin cycle
- grana: thylakoids arranged into stacks to maximise the SA of the thyl. mem.
- lamellae: connects and separates different grana, maximising photosynthetic efficiency
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