BIS2A SS1 Week 3

what two processes are found in oxidative phosphorylation?

electron transport and chemiosmosis

electron transport

passage of electrons from one compound to another (can be between complexes) and the capturing that the free energy released by the transfer reaction

what is the energy released from electron transport used for?

oxidation of a compound/reduction of another pumps hydrogen ions/protons, given there is sufficient energy released from the transfer (resulting in an energized membrane)

two types of carriers that aid in electron movement

e-/H+ carriers (usually carry 2 protons, 2 electrons)

e- carriers

e-/H+ carriers

NAD+_ox (NADP+_ox)/NADH + H+_red (NADPH+H+_red)

Quinones_ox/quinones_red

Flavins (FAD_(ox)/FADH_2(red))

e- carriers

FeS proteins

cytochromes (have a heme prosthetic group)

• NOTE: both of them have an Fe center that can be in +2/+3 oxidation state, depending on if an electron is being carried

primary electron donor, what is the primary electron donors in eukaryotes?

first molecule to donate the electron

in euks, NADH is primary donor (complex I is NADH dehydrogenase)

terminal electron acceptor

the final molecule to receive the electron

aerobic respiration

oxygen is the terminal electron acceptor

combines with 2 protons to make water (waste product)

anaerobic respiration

another compound besides oxygen is the terminal electron acceptor

carriers

transfer of electrons usually involves one or more intermediates between donor and acceptor

donors usually have a lower reduction potential than the acceptors

net energy change

difference between the reduction potential of the primary donors and the terminal acceptor

also the change in free energy

why is the ETC done in steps?

1. to release packets of energy to pump the protons

2. too much energy released at once can harm the cell

what is an energized membrane/electrochemical gradient used for?

to make ATP in ETC and to move other compounds into the cell (like proton symporters)

chemiosmosis

formation of energized membrane that can do work, in this case form ATP

ATP formation is reversible

efficiency of the ETC chain

dependent on the difference in reduction potential from the primary electron donor to the terminal electron acceptor —> larger E₀’ drop = more nrg to pump proton

more H+ translocated/e- donated = more efficient

oxidase vs reductase

oxidase (oxygen involved) — cytochrome oxidase (complex 4 of ETC) reduces oxygen

reductase = no oxygen involved

why was using oxygen as the terminal electron acceptor so revolutionary?

because oxygen has a high tendency to be reduced, it can generate a large ∆E₀’ drop, which increases ATP production

efficiency of aerobic vs anaerobic respiration

aerobic respiration is generally more efficient than anaerobic respiration due to the usage of O₂ as a terminal electron acceptor

complex II of ETC

oxidation of FADH2 by succinate dehydrogenase does not pump any protons across the membrane because the energy drop is not sufficient

complex III of ETC

cytochome c reductase; can pump protons across membrane

complex IV of ETC

cytochome c oxidase; can pump protons across as well; reduces oxygen (the terminal electron acceptor), which combines with 2 protons to make water

what 4 things can happen when an electron gets excited?

1. energy dissipated as heat as electron relaxes

2. energy dissipated at florescence as electron relaxes

3. energy transferred to neighboring molecule (not 100% efficient)

4. energy changes reduction potential so it can become e- donor (coupled to redox)

protoporphryin IX, cytochome heme and bacterial chlorophyll

protoporphyrin IX is the precursor to heme/bac. chlorophyll

heme has an iron center

bac. chlorophyll has a magnesium center and a lipid tail (anchors chlorophyll in membrane)

anoxygenic photosynthesis

does not release oxygen/doesn’t use water as a source of electrons; found in 2 forms (cyclic and noncyclic photophosphorylation)

cyclic photophosphorylation

electron that was excited and moved through the ETC ends up back at the reaction center it started at

generates ATP only

noncyclic photophosphorylation

electron that was excited ends up being donated to NADP+ to form NADPH

needs a source of electrons from reduced compounds (like H₂S)

NADH vs NADPH

NADH is used in catabolic processes

NADPH is used in anabolic processes

chlorophyll a

has a greater reduction potential than oxygen, it can oxidize water as a electron source (releases oxygen as waste)

oxygenic photosynthesis

uses water as electron source and chlorophyll a to capture light energy to excite electron; can pump protons across the membrane to generate ATP AND can reduce NADP+ at the end of this

Z scheme

starts as PSII, electron gets excited and move down through the ETC (pumps H+ across the membrane to generate proton motive force)

electron goes to PSI, gets reexcited and moves through another ETC which generates NADPH using NADP reductase

anoxygenic vs oxygenic photosynthesis

what do CH bonds tell us about how reduced a compound is?

more CH bonds = more reduced

ex. CO2 (which has no CH bonds) is the most oxidized form of carbon available

what is an organic compound?

a compound that contains CHO and is made by another organism (that is alive)

heterotrophs

make carbon building blocks from transforming small organic compounds

autotrophs

make carbon building blocks by reducing the highly oxidized carbon source CO₂ (not organic)

catabolism

all the processes in a cell that generate energy (break down compounds)

anabolism

all the processes that build compounds

metabolism

all the processes in a cell — catabolism + anabolism

central metabolism, what processes are included in central metabolism

the metabolic processes all cells need to do all other processes from the catabolic breakdown of glucose — creates precursors

includes glycolysis, pyruvate oxidation, TCA cycle, pentose phosphate pathway (PPP)

what 3 things do cells need to build other cells (comes from central metabolism)?

1. small molecules for anabolic processes (precursors)

2. reducing power (like NADH/NADPH)

3. energy (like ATP)

steady state

cells do not have to change physiology to do processes (no change in environment = no change in procsses)

OR a constant/equal concentration of metabolites

metabolic hypothesis

metabolism evolved as a means of generating small carbon molecules for anabolic reactions (not as a means to generate energy)

the 12 major precursors created by central metabolism that are required to build cell + what are they produced from

glycolysis - glucose 6-phosphate, fructose 6-phosphate, triose-P, 3-phospho-glycerate, phosphoenolpyruvate, pyruvate

PPP - pentose 5-phosphate, erythrose 4-phosphate

pyruvate oxidation: acetyl-CoA

TCA: alpha-Ketoglutarate, oxaloacetate, succinyl-CoA

13th one in gram negative: sedoheptulose (PPP)

glycolysis

oxidation of glucose into pyruvate

net results of glycolysis

2 ATP from SLP (2 consumed; 4 produced)

2 NADH + H+

produces 6 precursors

2 pyruvates (3 carbon) from one glucose

which key reaction in glycolysis is not reversible

phosphoenolpyruvate —> pyruvate (catalyzed by pyruvate kinase)

the 2 fates of pyruvate

1. fermentation to regenerate NAD+

2. respiration (produce acetyl-CoA)

pyruvate oxidation

each pyruvate is decarboxylated and oxidized to acetyl-CoA

produces 1 CO2 and 1 NADH per pyruvate

net results of glycolysis and pyruvate oxidation

2 ATP from SLP

4 NADH + H+ (2+2)

7 precursors (6+1)

2 acetyl-CoA/oxidized glucose

what happens to acetyl-CoA?

goes to citric acid/TCA/Krebs cycle; completely oxidized to CO2

citric acid cycle

2 carbon acetate enters; is a cycle because it regenerates oxaloacetate (which acetyl gets fixed onto)

produces 3 major precursors: alpha-ketoglutarate, succinyl CoA, oxaloacetate

3 NADH; 1 FADH2; 1 SLP; 2 CO2 per pyruvate

what are the end results of the oxidation of glucose (central metabolism)?

6 CO2

10 NADH (2+2+6)

2 FADH2 (citric acid)

4 ATP via SLP(2+2)

10 precursors (6+1+3)

what 2 key substrates are not produced from glycolysis, pyruvate oxidation, TCA?

pentose 5-phosphate

NADPH + H+ for anabolic reactions

oxidation of glucose in the pentose phosphate pathway

3 glucose 6-phosphate —> 3 6-phosphogluconate (produces 3 NADPH + H+)

3 6-phosphogluconate —> 3 ribulose 5-phosphate (3 NADPH + H+ and 3 CO2)

rearrangments of the pentose 5-phosphate

3 pentose-P —> 2 hexose-P (F6P) + 1 triose-P (G3P)

net results of pentose pathway (per 3 glucose)

6 NADPH + H+

2 precursors (pentose and erthyrol P intermediates)

3 CO2

1 G3P

2 hexose-P

what is the driving force of these reactions?

concentration of metabolites in environment (want to reach equilibrium)

what is one caveat of central metabolism and the 12 central compounds?

we need the enzymes for these reactions (humans don’t have them)

we need to get from outside that are readily available (ex. 9 essential amino acids)

Calvin cycle

RuBP is fixed onto 3 CO2 by rubisco and then broken into 2 3-carbon intermediates

takes 2 turns of the calvin cycle to get 2 G3P (the rest of the 10 G3P regenerate 5 carbon RuBP)

what is used in calvin cycle

9 ATP and 6 NADPH per 3 CO2 (therefore calvin cycle is reductive)

the link between calvin cycle and photophosphorylation

1. light induces pH changes that activate calvin cycle

2. light allosterically modulates enzyme activity by reducing disulfide bonds to activate calvin cycle enzymes

other ways to fix CO2

reductive citric acid cycle

reductive acetyl-CoA pathway

hydroxypropionate pathway

why is CO2 useful?

gets rid of excess carbon

starvation enzymes can bypass decarboxylations to conserve CO2 to make sugars

biomass

amount of carbon in an organism

tree biomass from atmosphere

we exhale CO2 at night (biomass lost overnight)

gluconeogenesis

formation of glucose form cellular substrates in low glucose conditions

need to have alternate pathways to make glucose (ex. PEP to pyruvate is irreversible; use alternative reaction that costs 2 ATP and 2 GTP)

reductive TCA

fixes 2 carbon molecules to make acetyl-CoA in organisms without electron transport chains; allows organisms to make 4 of 12 essential compounds

reactions run in reverse, costs NADPH to reduce CO2

phosphoanhydride bonds

high energy bonds between phosphates that can be hydrolyzed to release energy

how to extract energy from ATP

hydrolyze phosphoanhydride bonds

phosphorylation

adding a phosphate group; used to regenerate ATP

what sugar do hexoses flow to?

glucose!

can hexoses, trioses, pentoses enter at different points of central metabolism?

yes!

for example, a pentose or erythrose sugar can enter in the pentose phosphate pathway

trioses can feed into G3P

deamination reactions

removal of amine group from a molecule

what are deamination reactions used for?

converting amino acids into intermediates of central metabolism by deamination reactions

usually in organisms that eat protein (like humans)

when do amino acids feed into central metabolism?

TCA/end of glycolysis

what’s the problem with getting intermediates from amino acids?

you can only do these reactions if you have the genes to make the enzymes

4 ways to control carbon flow

ATP expended to push reactions

keep product concentrations low (done automatically in pathways)

metabolite concentrations near Km (reversible reactions)

feedback regulation (allosteric regulations)

feedback regulation

small metabolites can allosterically regulate enzymes in that pathways

enzymes are sensitive because working at Km

do substrates activate or inhibit?

activate

do products activate or inhibit?

inhibit

what are the two major ratios can control pathways

NADH: NAD

ATP: ADP and AMP

buildup of NADH/ATP (products) will inhibit

buildup of ADP+AMP/NAD will activate