Biochem for final+makeup #2

The first step of glycolysis is…

The first step of glycolysis is…

irreversible and driven in direction of G6P by ATP

The second step of glycolysis is

reversible and has a positive deltaG

How is Hexokinase IV different from the other three?

It has low affinity for glucose, higher hill number and no product inhibition

In reaction 3 of glycolysis, ATP is the donor, this means….

this is an irreversible step and is the first committed step

Why is it important to interconvert DHAP and G3P

only glyceraldehyde 3-phosphate is a substrate for the remaining reactions of glycolysis

In the first stages of glycolysis, glucose is converted to…

two molecules of G3P

Key intermediate for the first phase of glycolysis

ATP-dependant phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate

Which step is the first energy yielding step in glycoysis

reaction 6, the foramtion of 1,3-Biphosphoglycerate

net ATP yield of glycolysis up to reaction 7 is…

zero

Sites of regulation in glycolysis

Hexokinase (reaction 1)

PFK-1 (reaction 3)

Pyruvate Kinase (reaction 10)

Reaction 1 of glycolysis

the ATP-dependant phosphorylation of glucose

Reaction 3 of glycolysis

The ATP-dependant phosphorylation of fructose 6 phosphate

Reaction 4 of glycolysis

The cleavage of F-1,6-B into two different triose phosphates

Reaction 5 of glycolysis

Interconversion of dihydroxyacetone phosphate (DHAP) and Glyceraldehyde 3-phosphate (G3P)

Reaction 6 of glycolysis

Formation of 1,3-biphosphoglycerate

Reaction 7 of glycolysis

substrate level phosphorylation of ADP and formation of 3-phosphoglycerate

Reaction 8 of glycolysis

isomerization of 3-phosphoglycerate

Reaction 9 of glycolysis

dehydration of 2-phosphoglycerate

Reaction 10 of glycolysis

substrate level phosphorylation #2 and the conversion of PEP to pyruvate

Pyruvate kinase is allosterically inhibited by

ATP and acetyl-CoA

Pyruvate kinase is allosterically activated by

AMP and fructose-2,6-biphosphate

NAD+ is required in the oxidation of…

glyceraldehyde-3-phosphate to 1,3-biphosphoglycerate

If O2 is available in glycolysis,

NADH is re-oxidized by the electron trnasport chain

If O2 is unavailable in glycolysis

NADH is re-oxidized by the reduction of pyruvate to either lactate or ethanol

Pyruvate is converted to lactate in

anaerobic tissues (NAD+ is recycled in the process)

In some organisms, pyruvate is converted to ethanol in a process requiring...

thiamine pyrophosphate as a coenzyme (NAD+ is recycled)

Glycogen breakdown three steps

1. release of glucose-1-phosphate from glycogen

2. conversion of glucose 1-phosphate to glucose 6-phosphate

   1. “remodeling” of glycogen to facilitate further breakdown

Glycogen breakdown step 1

No ATP involved, catalyzed by glycogen phosphorylase

• product is Glucose-1-Phosphate

Glycogen breakdown step 2

catalyzed by phosphoglucomutase

• product is glucose-6-phosphate

What additonal enzyme is required to completely convert glycogen to glucose

debranching enzyme

The debranching enzyme catalyzes two reactions…

transferase activity and a-1,6-glucosidase activity

Glucose units are added to the…

non-reducing end of glycogen

What adds individual glucose molecules to the non-reducing end of glycogen

NDP-sugar pyrophosphorylase and glycogen synthase

The enzyme glycogenin serves as

both the primer and the catalyst for synthesis of new glycogen molecule

Phosphorylase exists in 4 forms…

Phosphorylase a:

• inactive or less active: taut ot T-form

• active (phosphorylated): relaxed or R-form

Phosphoylase b:

• same as a

glucose binding to the R-form of phosphorylated phos. a causes…

a conformational change exposing the phosphorylated Ser residues to phosphoprotein phosphatase

High glucose decreases the need for….

the cell to breakdown glycogen into glucose

Glycogen synthase exsits in two forms…

a: active form

b: inactive form

On thermodynamic ground alone, gluconeogenesis cannot..

be a simple reversal of glycolysis

Gluconeogenesis reaction 1

conversion of pyruvate to oxaloacetate

Gluconeogenesis reaction 2

conversion of OAA to PEP

Gluconeogenesis reactions 3 to 8

conversion of PEP to Fructose-1,6-biphosphate

Gluconeogenesis reaction 9

conversion of fructose-1,6-biphosphate to fructose-6-phosphate

Gluconeogenesis reaction 10

conversion of fructose-6-phosphate to glucose-6-phosphate

Gluconeogenesis reaction 11

conversion of glucose-6-phosphate to glucose

F26BP

signal in the cell for low energy

F26BP allosterically activates

PFK-1 and allosterically inhibits FBPase-1

Pyruvate can be converted t glucose and glycogen via gluconeogenesis or….

oxidized to acetyl-CoA for energy production

Acetyl-CoA activates/inhibits…

activates: pyruvate carboxylase

inhibits: pyruvate dehydrogenase

Metabolic fates of G6P

substrate for glycolysis, glycogen synthesis, and PPP

Cellualr respiration produces

CO2 from O2

cellular respiration occurs in three stages…

acetyl-CoA production, acetyl-CoA oxidation via the citric acid cycle, electron transfer and oxidative phosphorylation

Three processes that play central role in aerobic metabolism

citric acid cycle, electron transport, and oxidative phosphorylation

Catabolism

oxidative breakdown of nutrients A

Anabolism

reductive synthesis of biomolecules

The citric cycle is amphibolic, meaning….

it plays a role in catabolism and anabolism

(CENTRAL METABOLIC PATHWAY)

In Euk., the Citric acid cycle occurs in

the mitochondria

In Euk., glycolysis occurs in

cytoplasm

In Euk., oxidative phosphorylation occurs in

the inner membrane

Stage 1 of citric acid cycle

Acetyl-CoA production

• oxidation of fatty acids, glucose, and some AA. Yields some ATP NADH and FADH2

oxidative decarboxylation of puyruvate

remaining 2 carbon atoms of pyruvate enter the citric acid cycle as acetyl-CoA and yield energy

• catalyzed by pyruvate decarboxylase complex

Channeling minimizes

side reactions

Stage 2 of citric acid cycle

oxidation of Acetyl-CoA

• generates NADH, FADH2, and one GTP

  • catalyzed by citrate synthase

Conformational change occurs upon…

the binding oxaloacetate

Open conformation

free enzyme does not have a binding site for acetyl-CoA

Closed conformation

binding of oxaloacetate creates site for binding of acetyl-CoA

• reactive baranion is protected in the closed conformation

Citrate

poor substrate for oxidation

elimaination of H2O from citrate gives

a cis C=C bond

Isocitrate

a good substrate for oxidation

Isocitrate dehydrogenase catalyzes…

the oxidative decarboxylation of D-isocitrate to a-ketoglutarate

a-ketoglutarate dehydrogenase complex catalyzes the…

oxidative decarboxylation of a-ketoglutarate to succinyl-CoA

The conversion of pyruvate to succinyl-CoA has resulted in

introduction of 2 carbon atoms as acetyl-CoA, loss of two carbon atoms as CO2

Reaction 5 of citric acid cycle

substrate level phosphorylation of GDP as succinyl-CoA is converted to succinate

Reaction 6 of citric acid cycle

FAD-dependent oxidation of succinate to fumarate

Reaction 7 of citric acid cycle

stereospecific trans hydration of the double bond to form an alcohol

• it is very specific for fumarate and L-malate

Reaction 8 of citric acid cycle

dehydrogenation to give NADH

The most important anaplerotic reaction

the reaction catalyzed by pyruvate carboxylase

pyruvate carboxylase is allosterically activated by

acetyl-CoA

The two major regulatory points of the citric acid cycle

production of acetyl-CoA by the pyruvate dehydrogenous complex

entry of acetly-CoA into the citric acid cycle as catalyzed by citrate synthase

Regulation of pyruvate dehydrogenase complex occurs at tow levels…

allosteric inhibitors and activators (ATP, AMOP, NADH, NAD+…)

phosphorylation

Pyruvate dehydrogenase complex activity is off when

fuel energy is high

pyruvate dehydrogenase complex activity is on when

fuel energy is low

citrate synthase is inhibited by

NADH, Succ-CoA citrate and ATP

citrate synthase is activated by

ADP

isocitrate dehydrogenase is inhibited by

ATP

Isocitrate dehydrogenase is activated by

ADP

Citric acid cycle makes…

GTP and reduced cofactors that could yield ATP

What converts pyruvate into acetly-CoA

pyruvate dehydrogenase complex

Cristae

convolutions of the inner membrane and serve to increase the surface area

Ubiquinone

lipid-soluble conjugated dicarbonyl compound that readily accepts electrons

cytochromes

small, water-soluable, colored, proteins that have important roles in biological redox reactions C

Cytochromes are classified as a, b, or c based on

spectral characteristics

All cytochromes undergo…

one electron reduction/oxidation at heme-based iron

How many redox reactions are involved in transferring electrons from NADH to O2

about 12

The electron transport chain can be divided into discrete segements…

Complex I, II, III, IV, and ATP synthases

Complexes I, III, IV can drive…

ATP synthesis

Complex IV is the link to

O2

Uncouplers inhibit the

phosphorylation of ADP without affecting electron transport

F0 protein

hydrophobic proton channel buried in the inner mitchondrial membrane

F1 protein

projects into the mitochondrial matrix