Glycolysis

what makes ATP

consumption of glucose

is all of the energy from glucose stored from ATP

no; only about 980 kj/mol while glucose has 2840 kj/mol

how does glucose oxidation happen

proceeds in a stepwise manner via enzymatic redox rxns. Not spontaneous combustion allowing capture of free energy in NADH, FADH2 and ATP rather than heat.

how to ATP synthesized

reactive intermediates and through proton gradient 

low energy phosphate compounds 

there is an investment of ATP to make these compounds

G6P

F1,6BP

Glycerol 3- phosphate

cells form ATP via two ways

substrate level phosphorylation and oxidative phosphorylation.

substrate level phosphorylation

substrates are activated to form unstable compounds which can donate a phosphate group to ADP to form ATPphosphate ADP to form ATP

oxidative phosphorylation

electron carriers like NADH and FADH2 drive protons across the membrane, which is used to generate ATP via F1-ATP synthase (active transport run backward).

principles of enzymatic catalysis in glycolysis

Proximity: bringing partners together in correct orientation Protection of reactive intermediates Transition state stabilization Direct functional group catalysis: Acid/base, etc. Covalent enzyme intermediates: Like Ser protease Assistance from cofactors and metals Regulation through feedback mechanisms

structure of NAD+

structure of NADH

structure of FAD

structure of FADH2

how do cofactors help in glycolysis

they help progress glycolysis

structure of acetyl co enzyme A

NAD+/FAD

used as electron sinks for carrying out oxidation reactions

Electrons are used to generate ATP

Acetyl CoA

activate carboxylates as thioesters for rxns at C1 and C2

why are thioesters more reactive

the C-S is less resonance stablized than a C-O bond making the carbonyl more electrophillic

preparatory

Step 1 to 5

payoff

Steps 6 to 10

irreversible steps in glycolysis

1, 3, 10

first step

Glucose to G6P

ATP to ADP

enzyme for first step

hexokinase

second step

G6P to F6P

enzyme for second step

phosphohexose isomerase

third step

F6P to F1,6BP

ATP—> ADP

enzyme for third step

phosphofructokinase-1 (PK1)

step 4

F1,6BP to Glyceraldehyde to Dihydroxyacetone phosphate (GAP and DHAP)

enzyme for step 4

aldolase

structure of glucose

structure of G6P

structure of F6P

structure of f 1,6 bp

energy is consumed in what part of glycolysis

preparatory phase

structure of GAP

structure of DHAP

step 5

DHAP to GAP

enzyme for step 5

triose phosphate isomerase

after step 6 what must you do in order to get a balanced equation

multiply everything by 2

step 6

GAP (x2)—> 1,3 bisphosphoglycerate

2Pi—> 2H+

2NAD+ —> 2NAD+

H in GAP is replaced by phosphate from Pi causing release of H+. H from aldehyde goes to NAD+

enzyme for step 6

glyceraldehyde 3-phosphate dehydrogenase

step 7

1,3 BP glycerate—> 3 phosphoglycerate

2ADP—> 2ATP

enzyme for step 7

phosphoglycerate kinase

step 8

3 phosphoglycerate to 2 phosphoglycerate

enzyme for step 8

phosphoglycerate mutase

step 9

2 phosphoglycerate to phosphoenolpyruvate (PEP)

Release of water

enzyme for step 9

enolase

step 10

PEP to pyruvate

2ADP —> 2ATP

enzyme for step 10

pyruvate kinase

hexokinase

glucose C6 hydroxyl attacks ATP y phosphate forming G6P and ADP

irreversible process

reaction proceeds via an SN2 like phosphoryl transfer stabilized by Mg 2+ (pentavalent TS state)

PGI

interconverts G6P to F6P via a ring opening, proton transfer and base catalyzed ring closing sequence 

Reversible

Active Glu residues alternately act as general acid and base; protonates the carbonyl oxygen; the other abstracts a proton from C2, forming an enediol intermate which will then tautomerize to the ketone.

(aldehyde—> ketone)

PFK

commits the sugar to glycolysis because F 1,6 biphosphate is not in other pathways; it must proceed to pyruvate

PFK catalyzes a second phosphorylation of F6P with ATP.

inhibit PFK

allosterically inhibit ATP

activate PFK

AMP

what is the purpose of the feedback mechanism of PFK

preventing unnecessary glycolysis

Aldolase

cleaves F 1,6 BP to GAP to DHAP via shiff base intermediate. (retro aldol rxn) with an active site composed of lys. The imine promotes the carbon to carbon cleavage

Reversible

TIM

cleaves DHAP into GAP

catalytically perfect because the reaction rate is limited only by substrate diffusion into the activate site

kcat/km= 10^-9 s^-1

Functions via acid-base catalysis and stabilization of enediol transition state. Prevents collapse to methylglyoxal by tight binding of enediol.

GAPDH

oxidizes GAP’s aldehyde to a carb acid level while simultaneously forming a high energy acyl phosphate

hosphorylates GAP to form phosphoanhydride from a reactive thioester interediate on Cys (similar to Ser protease).

NAD+ cofactor captures hydride (H- ) to form thioester, used later for energy

PGK

Phosphoanhydride bond is unstable, can be used to phosphorylate ADP. PGK formation of ATP, first direct energy forming reaction of glycolysis. PGK binds reactive substrates to orient them for reaction and prevent hydrolysis.

PGM

Phosphoglycerate mutase catalyzes isomerization of the phosphate group through covalent catalysis. Product phosphate comes from enzyme. PGM reaction is reversible.

enolase

Enolase generates a better phosphoryl donor for pyruvate kinase. Mg2+ ions are used to stabilize the doubly charged carboxyene intermediate. Lys and Glu sidechains carry out acid-base chemistry

PK

Final direct ATP-generating reaction in glycolysis. Tautomerization (2) to pyruvate drives reaction by preventing reverse step 1.

Allosterically activated by FBP for increased pyruvate at high [glucose]. Mg2+ stabilizes TS for ADP attack on PEP.

Regulated by Mg2+ ions; at high [ATP], Mg2+ is sequestered by ATP in other processes, so PK activity drops.

structure of glyceraldehyde 3 phosphate

structure of 2 phosphoglycerate

structure of PEP

structure of pyruvate