BIOS 202 Glycolysis, Glucogenesis, Pentose Phosphate Pathway, Citric Acid Cycle

steps in the preparatory phase

1) phosphorylation of glucose by hexokinase
2) conversion of D-glucose 6-phosphate to D-fructose 6-phosphate by phosphohexose isomerase
3) phosphorylation into D-fructose 1,6-bisphosphate by phosphofructokinase-1
4) splitting into dihydroxyacetone phosphate and glyceraldehyde 3-phosphate by aldolase
5) isomerization of dihydroxyacetone phosphate to glyceraldehyde 3-phosphate by triose phosphate isomerase

purpose of the preparatory phase

phosphorylation of glucose and lysis into two 3 carbon molecules of glyceraldehyde 3-phospahte

steps of the payoff phase

6) oxidation and phosphorylation of glyceraldehyde 3-phosphate to 1,3-bisphosphoglycerate with inorganic phosphate by glyceraldehyde 3-phosphate dehydrogenase
7) formation of 3-phosphoglycerate by removal of phosphate with phosphoglycerate kinase
8) isomerization into 2-phosphoglycerate by phosphoglycerate mutase
9) enolation of the phosphate by enolase
10) removal of phosphate to create pyruvate with pyruvate kinase

use of pyruvate

besides bacterial exceptions, either oxidized and sent into citric acid cycle, reduced to lactate during lactic acid fermentation, or converted into ethanol through ethanol fermentation

overall equation for glycolysis

glucose + 2NAD+ + 2ADP + 2Pi -> 2 pyruvate + 2NADH + 2H+ + 2ATO + 2H2O

function of phosphoryl groups

1) prevents the sugars from leaving the cell, cell walls generally don’t have phosphorylated sugars
2) conserves energy from metabolism in phosphate ethers (like glucose 6-phosphate, also helps conversion from ADP to ATP
3) helps in binding substrates with enzymes, also lowers AE and specificity when bound

energetics of glycolysis

glucose to pyruvate: -146 kJ/mol, ADP to ATP: 61 kJ/mol, overall -85 kJ/mol, most of energy is stored in pyruvate

thiamine pyrophosphate (TPP)

helps cleave bonds next to carbonyl groups, involved in decarboxylation and transfers of activated acetaldehyde groups, functions through acidic proton on thiazolium ring, deprotonation leads to carbanion which adds to carbonyls, TPP can then act as an electron sink to allow reactions like decarboxylation

thiamine pyrophosphate (TPP) in pyruvate dehydrogenase

attacks ketone carbonyl, decarboxylates pyruvate, covalently bonds to pyruvate aldehyde, on E1, rate limiting step in reaction

pyruvate dehydrogenase complex

cluster of multiple copies of 3 enzymes: pyruvate dehydrogenase, dihydrolipoyl transacetylase, dihydrolipoyl dehydrogenase overall completes an irreversible oxidative decarboxylation, uses 5 cofactors

overall equation for pyruvate dehydrogenase

pyruvate + CoA-SH + NADH+ -> Acetyl-CoA + CO2, cofactors TPP, lipoate, FAD

flavin adenine dinucleotide (FAD)

reduces TPP back to S—S form by accepting hydrides, will donate the hydrides to the electron transport chain

coenzyme A (CoA or CoA-SH)

SH group covalently links to acyl groups, forming thioesters, high acyl group transfer potential, creates an “activated” acyl group for transfer

nicotinamide adenine dinucleotide (NAD)

reduces FADH2 back to FAD so that pyruvate dehyodrogenase complex can be reverted back to original state

lipoate + function in pyruvate dehydrogenase complex

lipoic acid, two thiol groups that reversibly oxidize to a S—S bond, can be an electron hydrogen carrier or an acyl carrier, attaches to amide bond to Lys group on E2, accepts electrons released from oxidation of alcohol into carbonyl from E1 and TTP into S—S bond, breaking it

hexokinase

first step in glycolysis, since it is a kinase, phosphorylates C6 in glucose by turning MgATP2- complex to Mg2+ and ADP, irreversible

phosphohexose isomerase

2nd step in glycolysis, isomerizes glucose 6-phosphate to fructose 6-phosphate with Mg2+, reversible

phosphofructokinase-1

3rd step in glycolysis, phosphorylates fructose 6-phosphate to fructose 1,6-bisphosphate through ATP and Mg2+, irreversible, complex regulatory enzyme which is downregulated by ATP and upregulated by ADP and AMP

aldolase

4th step in glycolysis, cleaves fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate, splits fructose 1,6-bisphosphate into 123, 456 groups, oxygen in ring becomes an alcohol on C5, reversible

triose phosphate isomerase

5th step in glycolysis, isomerizes dihydroxyacetone phosphate to glyceraldehyde 3-phosphate, changes carbonyl form C2 to C3, reversible

glyceraldehyde 3-phosphate dehydrogenase

6th step in glycolysis, first of two energy conserving reactions that lead to ATP formation, aldehyde looses a hydride to NAD+ and is converted to an acyl phosphate, releasing NADH and H+, turns glyceraldehyde 3-phosphate into 1,3-bisphosphoglycerate, reversible

phosphoglycerate kinase

7th reaction in glycolysis, second reaction which helps synthesize ATP, transfers a Pi group from 1,3-bisphosphoglycerate to ADP to make ATP and 3-phosphoglycerate, reversiblephso

phosphoglycerate mutase

8th step in glycolysis, shifts phosphate group, turning 3-phosphoglucerate to 2-phosphoglycerate with Mg2+, goes through a bisphosphorylated intermediate (2,3 BPG), reversible

enolase

9th step in glycolysis, dehydrates 2-phosphoglycerate to form a C=C double bond, makes phosphoenolpyruvate (PEP), reversible

pyruvate kinase

transfers a phosphate from phosphoenolpyruvate to ADP to make pyruvate and ATP with Mg2+ or K+

lactate dehydrogenase

reduces pyruvate to L-lactate in anaerobic conditions to reproduce NAD+, reversible reaction but favors lactate, produces 2 NAD+ for 1 pyruvate, same ratio as glycolysis, two ATP from glycolysis are not consumed, so still a net gain in energy from glucose to lactate

gluconeogenesis

converts pyruvate/other 3-4 C compounds to glucose if the body needs more, in mammalian liver, shares 7 steps with glycolysis using the same enzymes, 3 irreversible glycolysis reactions are catalyzed by different enzymes, has 11 steps to the 10 of glycolysis, needs 6 high energy phosphate compounds (4ATP and 2 GTP)

pyruvate carboxylase

first step of gluconeogenesis, converts pyruvate to oxaloacetate using bicarbonate as a reactant and ATP and biotin as cofactors, carboxylates the methyl on pyruvate, adding a carbon, acetyl-CoA upregulates pyruvate carboxylase

malate dehydrogenase

2nd step in gluconeogenesis, converts oxaloacetate to L-malate so that it can be transported from the mitochondria to the cytosol, uses NADH and H+, once malate reaches the cytosol, it immediately reoxidizes to oxaloacetate

phosphoenolpyruvate carboxykinase

3rd/2nd step in gluconeogenesis, converts oxaloacetate into phosphoenolpyruvate with GTP, creates PEP, CO2, and GDP, reversible

fructose 1,6-bisphosphatase (FBPase-1)

second to last step in gluconeogenesis, hydrolyzes fructose 1,6-bisphosphate to fructose 6-phosphate with H2O

glucose 6-phosphatase

last step in gluconeogenesis, changes glucose 6-phosphate to glucose with H2O, activated by Mg2+

pentose phosphate pathway

oxidation of glucose 6-phohate to pentose phosphates, uses NADP+ to make NADPH, pentoses are later used to make RNA, DNA, ATP, NADH, FADH2, CoA

pentose phosphate pathway steps

1) glucose 6-phosphate to 6-phosphoglucono-gamma-lactone by glucose 6-phosphate dehydrogenase
2) conversion to 6-phosphogluconate by lactonase
3) conversion to D-ribulose 5-phosphate by 6-phosphogluconate dehydrogenase
5) conversion to D-ribose 5-phosphate by phosphopentose isomerase

glucose 6-phosphate dehydrogenase (G6PD)

1st step in phosphate pentose pathway, oxidation of an alcohol on glucose 6-phosphate to a carbonyl to make 6-phosphoglucono-gamma-lactone, uses NADP+

UNFINISHED - PHOSPHATE PENTOSE PATHWAY

stages of cellular respiration

formation of acetyl-CoA, citric acid cycle, electron transport chain

STRUCTURE AND MECHANICAL FUNCTION OF PYRUVATE DEHYDROGENASE COMPLEX NOT INCLUDED

page 604 - 606

steps of the citric acid cycle

1) condensation of acetyl-CoA and oxaloacetate to make citrate through citrate synthase
2) changes to isocitrate by aconitase/aconitate hydratase
3) cleavage to alpha-ketoglutarate and CO2 by isocitrate dehydrogenase
4) oxidative decarboxylation to succinyl-CoA by alpha-ketoglutarate dehydrogenase complex
5) hydrolysis to succinate by succinyl-CoA synthetase
6) succinate is oxidized to fumarate by succinate dehydrogenase
7) hydration to L-malate by fumarase
8) oxidation to oxaloacetate by malate dehydrogenase

citrate synthase

1st step in TCA, binds the methyl carbon of the acetyl group to the middle carbonyl of oxaloacetate to form citroyl-CoA intermediate, which is hydrolyzed to make citrate and CoA, citrate binds to enzyme first, causing conformation change that encourages acetyl-CoA to bind, then conformation change causes bond cleavage. irreversible

aconitase

second step in TCA, aconitate hydratase, adds water to double bond in intermediate cis-aconitate to make isocitrate (adding in other conformation converts back to citrate), reversible

isocitrate dehydrogenase

third step in TCA, alcohol is converted to a carbonyl and then Mn2+ is inserted to stabilize negative changes in intermediate, CO2 is lost, then proton is added to make alpha-ketoglutarate, uses NADP+, irreversible

alpha-ketoglutarate dehydrogenase complex

4th step in TCA. uses CoA-SH and NAD, oxidative decarboxylation like pyruvate dehydrogenase complex, irreversible

succinyl-CoA synthetase

cleaves CoA-SH from succinyl CoA with GDP and phosphate to make succinate, reversible

succinate dehydrogenase

6th step in TCA, uses FAD to remove two hydrides to make the alkene in fumarate, reversible

fumarase

7th step in TCA, hydration of fumarate to L-malate through a carbanion intermediate, very stereo specific enzyme, reversible

malate dehydrogenase

NAD accepts a hydride and creates a proton to oxidize malate alcohol to an oxaloacetate, reversible

REGULATION OF TCA NOT COMPLIED

SKIPPED CHAPTER 15

allosterically regulated TCA enzymes

citrate synthase, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase