Chemical Logic of Metabolism: Deconstructing Glycolysis

Metabolism

the collection of biochemical reactions which convert chemical energy into work to maintain cellular operation.

metabolite

small molecule intermediate or product of metabolism.

Catabolism

the sequences of enzyme-catalyzed reactions by which large molecules are broken down.

Anabolism

the reverse process to build complex molecules from simple structures.

Coupling of anabolic and catabolic pathways

Glycolysis

a series of reactions that extract energy from glucose by splitting it into two three-carbon molecules called pyruvates

produce two molecules of ATP

Consists of 10 enzymatic reactions

occurs in nearly all organisms, both aerobic and anaerobic

does not use oxygen (anaerobic) and predates photosynthesis

History of glycolysis

~3.9 billion years old, just after the first cells

Glycolytic metabolites

precursors for a large number of independent pathways, including mitochondrial ATP synthesis.

What does glycolysis accomplish for the cell?

alone can sustain all activity in anaerobic cells (ATP, amino acids, nucleotides, lipids, sugars)

In aerobic organisms, glycolysis feeds into TCA cycle and oxidative metabolism.

What is the overall net reaction of glycolysis?

Glucose + 2 NAD+ + 2 ADP + 2 Pi => 2 Pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O

fate of glucose

controlled by the concentration of glucose and the body’s energy requirement

Lactic fermentation

Under anaerobic conditions (such as muscle cells during exercise), pyruvate is converted to lactate. Some microbes also dothis under anaerobic conditions (Lactococcus lactis produce yogurt/ cheese).

Alcoholic fermentation

Under anaerobic conditions, in some microbes, such as Brewer’s yeast (Saccharomyces cerevisiae), pyruvate is converted to ethanol and CO2.

central energy pathway

Under aerobic conditions, the majority of pyruvate is metabolized by the citric acid cycle and electron transport chain.

Warburg Effect

Metabolism of cancer cells is adapted to facilitate the uptake and incorporation of nutrients into the biomass (e.g., nucleotides, amino acids, and lipids) needed to produce a new cell → strongly favours glycolysis over oxidative phosphorylation → lactate production

energetics of glucose metabolism

investment and generation phases

Coupled Reactions

Favorable metabolic reactions are used as a driving force to make unfavorable reactions proceed through a common intermediate.

ATP hydrolysis/synthesis

Why did nature come up with such an elaborate scheme to burn up glucose?

glucose was present.

Why phosphorylate glucose?

Hexokinase

drive glucose gradient into cell; make sure G6P doesn’t leave cell

GLUT transporter

transporters glucose into cells, conformational change when bound to glucose

Hexokinase

Conformational changes block water from the active site and promote phosphorylation

uses 1 ATP

Hexokinase regulation

(-) G6P - allosteric regulation

Phosphofructoisomerase

general base in enzyme, activates aldolase cleavage

makes F6P

phosphofructokinase-1 (PFK-1)

both cleavage products should be phosphorylated

produces F16BP

aldolase

adjacent carbonyl activates cleavage

iminium - covalent catalysis to enzyme → reduces entropy + favourable cyclic electron arrangement → control of reaction site

produces DHAP and GAP

triose phosphate isomerase

enediol intermediate

10^8 kcat/Km- near perfect

Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH)

use of NAD bypasses toxic metabolites - aldehyde

Phosphoryl group transfer requires oxidation of

the aldehyde

Nicotinamide adenine dinucleotide (NAD+)

cofactor; oxidizing agent; becomes reduced to NADH