Metabolism

Series of chemical reactions Require a set enzymes that carry out different functions Each molecule along its path differs from any other molecule in the pathway. Each substrate transforms into a product that serves as as substrate for another enzyme reaction until a final product (the end product) is generated. Usually run in one direction.

Diagnosis of pathogenic microbes Determination of a diseased state Identification of targets for drugs and vaccines Toxicogenomics, Pharmacokinetics Fundamental biology (e.g. How do we store information in our brains?) Pathways may serve as a tool to trace evolution (Evolution of pathways <=> Evolution of organisms)
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C D X G F C D X Y F BCDXF ACDEF

CD F

Suggested reading: Heymans and Singh (2002). Deriving phylogenetic trees from the similarity analysis of metabolic path PDF-file available on the web.
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mouse
m-h substrate

Enzyme # 1

house
product/substrate u-r

Enzyme # 2

horse
(end)product
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 Anabolic

pathways Catabolic pathways

Catabolic pathways degrade complex molecules to smaller molecules. These pathways generally produce life sustaining energy in the form of ATP and heat.

ADP ATP S

NAD

NADH + H+

P1

P2

Overview of catabolism
Complex metabolites are broken down into their monomeric units Then to the common intermediate, acetylCoA The acetyl group is then oxidized to CO2 via the citric acid cycle while NAD+ and FAD are reduced to NADH and FADH2. Reoxidation of NADH and FADH2 by O2 during oxidative phosphorylation yields H2O and ATP

Anabolic pathways
Anabolic pathways use chemical energy in form of ATP and NADH or NADPH to synthesize cellular components from simple precursor molecules.
ATP ADP NADH + H+ NAD EP

P2

How do living things acquire the energy needed for these functions?
Autotrophs self-feeders (synthesize their own cellular constituents from H2O, CO2, NH3, and H2S) Photoautotrophs - acquire free energy from sunlight Chemolithotrophs obtain free energy from oxidation of inorganic compounds such as NH3, H2S, or Fe2+. Heterotrophs oxidize organic compounds to make

ATP
ATP is the energy carrier for most biological reactions

Organisms can be classified by the identity of the oxidizing agent.

Obligate aerobes: must use O2

Anaerobes: use sulfate or nitrate

Facultative anaerobes: can grow in presence or absence of O2 (e.g. E. coli) Obligate anaerobes: poisoned by O2

Metabolic pathways are series of connected enzymatic reactions that produce specific products. Their reactants, intermediates, and products are called metabolites. There are over 2000 known metabolic reactions see figure to the left.

Hierarchical Nature of Metabolism

Four classes of macromolecules (proteins, nucleic acids, carbohydrates, and lipids) Six primary metabolite groups (amino acids, nucleotides, fatty acids, glucose, pyruvate, acetyl CoA)
Seven small biomolecules (NH4+, CO2, NADH, FADH2, O2, ATP, H2O)

The six major groups of pathways can be subdivided into those responsible for energy conversion, and those involved in the synthesis and degradation of macromolecules.
Moreover, the major groups themselves consist of several metabolic modules, all of which will be examined individually.

1.

What does glycolysis accomplish for the cell? Generates a small amount of ATP which is critical under anaerobic conditions. Generates pyruvate, a precursor to acetyl CoA, lactate, and ethanol (in yeast).

2.

What is the overall net reaction of glycolysis?

Glucose + 2NAD+ + 2ADP + 2 Pi 2 pyruvate + 2NADH + 2H+ + 2ATP + 2H2O

G = -35.5 kJ/mol

3. What are the key regulated enzymes in glycolysis? Hexokinase, Phosphofructokinase 1, Pyruvate kinase 4. What are examples of glycolysis in real life? Glycolysis is the sole source of ATP under anaerobic conditions which can occur in animal muscle tissue during intense exercise. Fermentation also relies on glycolysis which is a process that is used to make alcoholic beverages when yeast cells are provided glucose without oxygen.

Glycolysis is a central pathway that takes glucose generated by carbohydrate metabolism and converts it to pyruvate. Under aerobic conditions, the pyruvate is oxidized in the citrate cycle which generates reducing power for redox reactions in the electron transport system that result in ATP production by oxidative phosphorylation.

In glycolysis (from the Greek glykys, meaning sweet, and lysis, meaning splitting), a molecule of glucose is degraded in a series of enzyme-catalyzed reactions to yield two molecules of the three-carbon compound pyruvate.
During the sequential reactions of glycolysis, some of the free energy released from glucose is conserved in the form of ATP and NADH.

Glycolysis was the first metabolic pathway to be elucidated and is probably the best understood.

Eduard Buchners discovery in 1897 of fermentation in broken extracts of yeast cells until the elucidation of the whole pathway in yeast (by Otto Warburg and Hans von Euler-Chelpin) and in muscle (by Gustav Embden and Otto Meyerhof) in the 1930s, the reactions of glycolysis in extracts of yeast and muscle were a major focus of biochemical research.

By 1940 all of the reactions of the glycolysis pathway were known from the research of Embden, Meyerhof, Parnas and Warburg.

Glycolysis is sometimes known as the Embden-Meyerhof pathway in the older textbooks.

Glycolytic Pathway

The two stages of glycolysis

The ATP investment stage generates the high energy intermediate glyceraldehyde-3-P (GAP) which is then oxidized to produce NADH and 1,3bisphosphoglycerate. The next four reactions lead to the production of FOUR total ATP because each glucose molecule results in the production of TWO pyruvate. The net yield of ATP in glycolysis is therefore TWO ATP.

Stage 1
Investment of 2 ATP Production of 2 Glyceraldehyde-3-P (GAP) The two highly regulated steps are hexokinase and phosphofructokinase 1 (both respond directly or indirectly to energy charge).

Stage 2
Reducing power is captured in the form of NADH; this is a critical step. Phosphoglycerate kinase and pyruvate kinase catalyze a substrate level phosphorylation reaction yielding 4 ATP (2 net ATP). The two pyruvate molecules are further metabolized.

Each molecule of GAP

No loss of carbons or oxygen in glycolysis The six carbons and six oxygens present in glucose are stoichiometrically conserved by glycolysis in the two molecules of pyruvate that are produced. Hydrogen atoms in glucose are lost as H2O molecules and in the reduction of NAD+.

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Oxidation of glucose Products:

2 Pyruvate 2 ATP 2 NADH

Cytosolic

Provide ATP energy Generate intermediates for other pathways

Hexose monophosphate pathway Glycogen synthesis Pyruvate dehydrogenase

Fatty acid synthesis Krebs Cycle

Glycerol-phosphate (TG synthesis)

Glycolysis is an almost universal central pathway of glucose catabolism, the pathway with the largest flux of carbon in most cells. The glycolytic breakdown of glucose is the sole source of metabolic energy in some mammalian tissues and cell types (erythrocytes, renal medulla, brain, and sperm, for example). Some plant tissues that are modified to store starch (such as potato tubers) and some aquatic plants (watercress, for example) derive most of their energy from glycolysis; many anaerobic microorganisms are entirely dependent on glycolysis.

Ten reactions and two stages:

Stage1:Glucose is phosphorylated and cleaved to form two molecules of glyceralbehyde-3-phosphate.The two ATP molecules consumed.
Stage2: Glycerahyde-3phosphate is converted to pyruvate. Four ATP molecules and two NADH are produced. Total reactions: D-Glucose+2ADP+2Pi+2NAD+ 2pyryvate+2ATP+2NADH+2H+ +2H2O Key notes: Fates of pyruvate, energy field, Metabolism of fructose or galactose,regulation of glycolysis

 In aerobic respiration: Pyruvate+NAD++CoA=acetylCoA+CO2+NA DH In anaerobic organism :

Pyruvate+NADH+H+=lactate+NAD+
G=-25.1 kJ/mol

In alcoholic fermentation:
Pyruvate+ H+=acetaldehyde+CO2

Acetadehyde+NADH+H+=ethanol+NAD+

Oxidation of Pyruvate to Acetyl-CoA The Pyruvate Dehydrogenase Complex -- huge -- highly regulated
Activators: ADP, NAD, CoA Inhibitors: ATP, NADH, acCoA
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Hierarchical Nature of Metabolism Four classes of macromolecules (proteins, nucleic acids, carbohydrates, and lipids) Six primary metabolite groups (amino acids, nucleotides, fatty acids, glucose, pyruvate, acetyl CoA) Seven small biomolecules (NH4+, CO2, NADH, FADH2, O2, ATP, H2O)

Krebs Cycle

Reactions Citrate In a Sentence Should Form More Oxaloacetate CIASSFMO

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How does fermentation allow cells to produce ATP in the absence of oxygen? -- detoxifying of pyruvate -- regeneration of NAD What happens to the lactate? Cori-cycle (a little physiology) Lactic Acidosis
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Using NADH to make ATP

Electron transport and oxidative phosphorylation

You should be able to complete a table to calculate energy yields from glucose or fatty acids (of any given length) -- assuming 2.5 ATP per NADH (1.5 per glycolytic NADH) and 1.5 ATP per FADH

From glucose Glycolysis ATP yield ____ NADH x ____ ATP _______ ____ ATP _______ Transition Rx ____ NADH x ____ ATP x 2 pyr Krebs cycle ____ NADH x ____ ATP x 2 pyr ____ FADH x ____ ATP x 2 pyr ____ GTP x ____ ATP x 2 pyr Total 30

_______ _______ _______ _______

From a 12 carbon fatty acid B-oxidation ATP yie ____ FADH x ____ ATP x 6 acCoA ____ NADH x ____ ATP x 6 acCoA Krebs cycle ____ NADH x ____ ATP x 6 acCoA ____ FADH x ____ ATP x 6 acCoA ____ GTP x ____ ATP x 6 acCoA Total 84
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What are the biosynthetic roles Of these pathways?

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1. Anaerobic and aerobic respiration 2. Photosynthesis and carbon fixation 3. Carbohydrate metabolism 4. Lipid metabolism 5. Amino acid metabolism 6. Nucleotide metabolism

Metabolic pathways are highly interdependent and exquisitely controlled by substrate availability and enzyme activity levels. Key to understanding metabolic integration in terms of nutrition, exercise, and disease (e.g., diabetes and obesity) is learning how metabolic flux between pathways is regulated and controlled.

Should WE memorize this chart?

1. What does the pathway accomplish for the cell? 2. What is the overall net reaction of the pathway? 3. What are the key regulated enzymes in the pathway? 4. What are examples of this pathway in real life?

Glucose occupies a central position in the metabolism of plants, animals, and many microorganisms. It is relatively rich in potential energy, and thus a good fuel; the complete oxidation of glucose to carbon dioxide and water proceeds with a standard free-energy change of 2,840 kJ/mol. By storing glucose as a high molecular weight polymer such as starch or glycogen, a cell can stockpile large quantities of hexose units while maintaining a relatively low cytosolic osmolarity. When energy demands increase, glucose can be released from these intracellular storage polymers and used to produce ATP either aerobically or anaerobically.
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The breakdown of the six-carbon glucose into two molecules of the three-carbon pyruvate occurs in ten steps, the first five of which constitute the preparatory phase (See Fig.). In these reactions, glucose is first phosphorylated at the hydroxyl group on C-6 (step 1 ). The D-glucose 6-phosphate thus formed is converted to D-fructose 6-phosphate (step 2 ), which is again phosphorylated, this time at C-1, to yield D-fructose 1,6bisphosphate (step 3 ). For both phosphorylations, ATP is the phosphoryl group donor. As all sugar derivatives in glycolysis are the D isomers, we will usually omit the D designation except when emphasizing stereochemistry.
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Organisms that do not have access to glucose from other sources must make it. Photosynthetic organisms make glucose by first reducing atmospheric CO2 to trioses, then converting the trioses to glucose. Nonphotosynthetic cells make glucose from simpler three and four-carbon precursors by the process of gluconeogenesis, effectively reversing glycolysis in a pathway that uses many of the glycolytic enzymes.