Metabolic Pathways and ATP Production Notes

Metabolism

• Involves all chemical reactions that provide energy and substances needed for growth.
• Consists of:
  • Catabolic reactions: Break down large, complex molecules to provide energy and smaller molecules.
  • Anabolic reactions: Use ATP energy to build larger molecules.

Stages of Metabolism

• Catabolic reactions occur in stages:
  • Stage 1: Digestion and hydrolysis break down large molecules into smaller ones that enter the bloodstream.
  • Stage 2: Degradation breaks down molecules into two- and three-carbon compounds.
  • Stage 3: Oxidation of small molecules in the citric acid cycle and electron transport provides ATP energy.
• Large molecules from foods are digested and degraded into smaller molecules, which are then oxidized to produce energy.

Cell Structure and Metabolism

• Major components of a typical animal cell include:
  • Cell membrane: Separates cell contents from the external environment; contains structures for communication with other cells.
  • Cytoplasm: Cellular contents between the cell membrane and nucleus.
  • Cytosol: Fluid part of the cytoplasm; contains enzymes for many of the cell’s chemical reactions.
  • Mitochondrion: Contains structures for ATP synthesis from energy-releasing reactions.
  • Nucleus: Contains genetic information for DNA replication and protein synthesis.
  • Ribosome: Site of protein synthesis using mRNA templates.

ATP and Energy

• Energy in the body is stored as adenosine triphosphate (ATP).

Hydrolysis of ATP

• Energy from ATP hydrolysis is used for muscle contraction, moving substances across cellular membranes, sending nerve signals, and synthesizing enzymes.
• The hydrolysis of ATP to ADP (adenosine diphosphate) releases 7.3 kilocalories per mole of ATP.
• $ATP \rightarrow ADP + P_i + 7.3 kcal/mole$
• ADP can also hydrolyze to form adenosine monophosphate (AMP) and an inorganic phosphate ($P_i$).
• $ADP \rightarrow AMP + P_i + 7.3 kcal/mole$

Digestion of Carbohydrates

• Stage 1 of catabolism involves the digestion of carbohydrates, which begins in the mouth and is completed in the small intestine.
• Monosaccharides are absorbed through the intestinal wall into the bloodstream and carried to the liver, where fructose and galactose are converted to glucose.

Digestion of Fats

• The digestion of fats (triacylglycerols) begins in the small intestine, where bile salts break fat globules into smaller particles called micelles.

Digestion of Triacylglycerols

• Triacylglycerols are hydrolyzed in the small intestine and re-formed in the intestinal lining, where they bind to proteins for transport through the lymphatic system and bloodstream to the cells.

Digestion of Proteins

• Begins in the stomach:
  • HCl at pH 2 denatures proteins and activates enzymes like pepsin to hydrolyze peptide bonds.
• Moves to the small intestine:
  • Trypsin and chymotrypsin hydrolyze polypeptides to amino acids.
• Amino acids are absorbed through the intestinal walls and enter the bloodstream for transport to the cells.

Oxidation and Reduction

• Oxidation reactions involve:
  • Loss of hydrogen.
  • Loss of electrons.
  • Increase in the number of bonds to oxygen.
• Reduction reactions involve:
  • Gain of hydrogen ions and electrons.
  • Decrease in the number of bonds to oxygen.

Coenzyme NAD+

• (Nicotinamide adenine dinucleotide) is an important coenzyme. The B3 vitamin, niacin, provides the nicotinamide group, which is bonded to ADP.
• $NAD^+$ participates in reactions that produce a carbon–oxygen double bond ($C=O$).

Coenzyme FAD

• (Flavin adenine dinucleotide) is a coenzyme that:
  • Contains ADP and riboflavin (vitamin B2).
  • Is reduced to FADH2 when flavin accepts 2H+ and 2e-.
• Participates in reactions that convert a carbon–carbon single bond to a carbon–carbon double bond ($C=C$).
• In the citric acid cycle, FAD is utilized in the conversion of the carbon–carbon single bond in succinate to a double bond in fumarate.

Structure of Coenzyme A

• Coenzyme A (CoA) contains pantothenic acid (vitamin B5), phosphorylated ADP, and aminoethanethiol.

Coenzyme A

• An important function of coenzyme A is to prepare small acyl groups (represented by the letter A in the name), such as acetyl, for reactions with enzymes.
• The thiol group ($\SH$) bonds to a two-carbon acetyl group to produce the energy-rich thioester acetyl-CoA.

Glycolysis

• Is a metabolic pathway that uses glucose, a digestion product from carbohydrates.
• Degrades six-carbon glucose molecules to three-carbon pyruvate molecules.
• Takes place in the cytoplasm of the cell.
• Is an anaerobic process: no oxygen is required.

Glycolysis: Overall Reaction

• Two ATP add phosphate to glucose and fructose-1,6-bisphosphate.
• Four ATPs are produced during phosphate transfers.
• There is a net gain of two ATP and two NADH when glucose is converted to two pyruvate.

Pyruvate Pathways: Aerobic and Anaerobic

• Pyruvate is converted to acetyl CoA under aerobic conditions and to lactate under anaerobic conditions.

Pyruvate: Aerobic Conditions

• Under aerobic conditions (oxygen present):
  • Three-carbon pyruvate is decarboxylated.
  • Two-carbon acetyl CoA and $CO_2$ are produced.

Pyruvate: Anaerobic Conditions

• During strenuous exercise:
  • Oxygen is depleted, and anaerobic conditions are produced in muscles.
  • Under anaerobic conditions, pyruvate is converted to lactate.
  • $NAD^+$ is produced and used to oxidize more glyceraldehyde-3-phosphate (glycolysis), producing small amounts of ATP.
  • Increased amount of lactate causes muscles to become tired and sore.
• After exercise, a person breathes heavily to repay the oxygen debt and reform pyruvate in the liver.

Citric Acid Cycle

• As a central pathway in metabolism, the citric acid cycle:
  • Uses the two-carbon acetyl group in acetyl CoA to produce $CO<em>2$, $NADH + H^+$, and $FADH</em>2$.
  • Is named for the citrate ion from citric acid ($C<em>6H</em>8O_7$), a tricarboxylic acid, which forms in the first reaction.
  • Is also known as the tricarboxylic acid (TCA) cycle or the Krebs cycle.

Citric Acid Cycle: Overall Reaction

• Overall chemical equation for one complete turn of the citric acid cycle.

Stage 3: From One Glucose

Electron Transport

• In electron transport, or the respiratory chain, hydrogen ions and electrons from NADH and FADH2 are passed from one electron carrier to the next and combine with oxygen to make $H_2O$.
• The energy released during electron transport is used to synthesize ATP from ADP and $P_i$, a process called oxidative phosphorylation.
• As long as oxygen is available for the mitochondria, electron transport and oxidative phosphorylation function to produce most of the ATP in the cell.

Electron Carriers

• Coenzymes NADH and FADH2 are oxidized in enzyme complexes, providing electrons and hydrogen ions for ATP synthesis.

Oxidative Phosphorylation

• In the chemiosmotic model:
  • Each complex acts as a proton pump by pushing $H^+$ ions from the oxidation of NADH and FADH2 out of the matrix and into the intermembrane space.
  • The increase in $H^+$ concentration lowers the pH and creates an $H^+$ or electrochemical gradient.
  • To equalize the pH and charge between the intermembrane space and the matrix, the $H^+$ ions return to the matrix by passing through a protein complex called ATP synthase.
• The process of oxidative phosphorylation couples the energy from electron transport to the synthesis of ATP from ADP.
• $ADP + P_i + energy \xrightarrow{ATP synthase} ATP$

ATP Synthesis

• When NADH enters electron transport at complex I, the energy released from its oxidation is used to synthesize 2.5 ATP.
• $NADH + H^+ \rightarrow NAD^+ + 2.5 ATP$
• FADH2 enters electron transport at complex II, which is at a lower energy level. Thus, FADH2 provides energy to produce 1.5 ATP.
• $FADH_2 \rightarrow FAD + 1.5 ATP$

ATP from Glycolysis

• Glycolysis yields a total of seven ATP:
  • Five ATP from two NADH
  • Two ATP from direct phosphorylation
• $Glucose \rightarrow 2 pyruvate + 2ATP + 2NADH$
• $Glucose \rightarrow 2 pyruvate + 7ATP$

ATP from Oxidation of Two Pyruvates

• Under aerobic conditions:
  • Two pyruvates enter the mitochondria and are oxidized to two acetyl-CoA, $CO_2$, and two NADH.
  • Two NADH enter electron transport to provide five ATP.
• $2 Pyruvate \rightarrow 2 acetyl-CoA + 2 CO_2 + 5ATP$

ATP from the Citric Acid Cycle

• One turn of the citric acid cycle provides:
  • 3 NADH = 3 * 2.5 ATP/NADH = 7.5 ATP
  • 1 FADH2 = 1 * 1.5 ATP/FADH2 = 1.5 ATP
  • 1 GTP = 1 ATP/1 GTP = 1 ATP
  • Total = 10 ATP
• Because each glucose provides two acetyl-CoA, two turns of the citric acid cycle produce 20 ATP.
• $2 Acetyl - CoA \xrightarrow{two turns of citric acid cycle} 4CO_2 + 20ATP$

ATP from the Complete Oxidation of Glucose

• Glycolysis: Oxidation of glyceraldehyde-3-phosphate.
  • 2 NADH = 5 ATP.
    Direct phosphorylation (2 triose phosphate) = 2 ATP. Summary: C6H12O6 yields 2 pyruvate plus 2H2O = 7 ATP.
  • $C<em>6H</em>{12}O<em>6 \rightarrow 2 pyruvate + 2H</em>2O$
• Oxidation and Decarboxylation.
  • 2 pyruvate yields 2 acetyl CoA plus 2 CO2.
  • 2 NADH = 5 ATP
  • $2 Pyruvate \rightarrow 2 acetyl CoA + 2CO_2$
• Citric Acid Cycle (two turns).
  • Oxidation of 2 isocitrate = 2 NADH = 5 ATP.
  • Oxidation of 2 alpha-ketoglutarate = 2 NADH = 5 ATP.
  • 2 Direct phosphate transfers (2 GTP) = 2 ATP.
  • Oxidation of 2 succinate = 2 $FADH_2$ = 3 ATP
  • Oxidation of 2 malate = 2 NADH = 5 ATP
• Summary: 2 acetyl CoA yields 4 CO2 plus 2 H2O = 20 ATP Total Yield: C6G12O6 is glucose. C6H12O6 plus 6 O2 yields 6 CO2 plus 6 H2O = 32 ATP α
  • $2 Acetyl CoA \rightarrow 4CO<em>2 + 2H</em>2O$
  • $C<em>6H</em>{12}O<em>6 + 6O</em>2 \rightarrow 6 CO<em>2 + 6H</em>2O$

Oxidation of Fatty Acids

• A large amount of energy is obtained when fatty acids undergo oxidation in the mitochondria to yield acetyl-CoA.
• Fatty acids undergo beta-oxidation ($\beta$-oxidation), which removes two-carbon segments, one at a time, from the carboxyl end.

Beta-Oxidation of Fatty Acids

• In stage 2 of fat metabolism, fatty acids undergo beta-oxidation, which removes two-carbon segments from the carbonyl end.
• Each cycle in oxidation produces acetyl-CoA and a fatty acid that is shorter by two carbons.

Fatty Acid Activation

• Prepares fatty acids for transport through the inner membrane of mitochondria.
• Combines a fatty acid with coenzyme A to yield fatty acyl-CoA.
• Requires energy obtained from hydrolysis of ATP to give AMP and 2Pi

Reactions of the Beta-Oxidation Cycle

• In the matrix:
  • Fatty acyl-CoA molecules undergo $\beta$ oxidation, a cycle of four reactions converting the $\beta$-carbon ($CH_2$) to a $\alpha$-keto ($-C=O$).
  • Once the $\beta$-keto group is formed, a two-carbon acetyl group can be split from the carbon chain, shortening the fatty acyl chain.

Reactions 1 and 2 of the Beta-Oxidation Cycle

Reaction 1: Oxidation

• Hydrogen atoms removed by FAD from the $\alpha$- and $\beta$-carbons form a carbon–carbon double bond and $FADH_2$.

Reaction 2: Hydration

• $H-OH$ adds across the double bond, forming the \OH adding on the $\beta$-carbon.

Reaction 3 of the Beta-Oxidation Cycle

Reaction 3: Oxidation

• The secondary hydroxyl group (\OH) on the $\beta$-carbon is oxidized to yield a ketone (keto group), while the hydrogen atoms reduce coenzyme $NAD^+$ to $NADH + H^+$.

Reaction 4 of the Beta-Oxidation Cycle

Reaction 4: Cleavage

• The $C<em>{\alpha} - C</em>{\beta}$ bond is cleaved to yield a two-carbon acetyl-CoA and a shorter (8C) fatty acyl-CoA.
• The cleavage is repeated until the fatty acid is completely broken down to form acetyl-CoA.
• The acetyl-CoA produced from the fatty acid can enter the citric acid cycle to produce energy.

Cycles of Beta-Oxidation

• The number of $\beta$-oxidation cycles depends on the length of a fatty acid and is one less than the number of acetyl-CoA groups formed.

ATP from Fatty Acid Oxidation

• In each $\beta$-oxidation cycle:
  • One NADH is produced, generating 2.5 ATP.
  • One $FADH_2$ is produced, generating 1.5 ATP.
  • One acetyl-CoA is produced, generating 10 ATP.

ATP from Beta-Oxidation of Capric Acid

• ATP Production from $\beta$-Oxidation for Capric Acid (10C)
  • Activation: -2 ATP
  • 5 Acetyl CoA: 5 acetyl-CoA * 10 ATP/acetyl-CoA = 50 ATP
  • 4 Beta Oxidation Cycles: 4 NADH * 2.5 ATP/NADH = 10 ATP, 4 $FADH<em>2$ * 1.5 ATP/$FADH</em>2$ = 6 ATP
  • Total: 64 ATP

Oxidation of Unsaturated Fatty Acids

• Many of the fats in our diets, especially the oils, contain unsaturated fatty acids, which have one or more double bonds.
• Since unsaturated fats are ready for hydration, no $FADH_2$ is formed in this step, and the energy from b-oxidation is slightly less.
• For simplicity, we will assume that the total ATP production is the same for saturated and unsaturated fatty acids.

Ketone Bodies

• If carbohydrates are not available:
  • Body fat breaks down to meet energy needs.
  • Ketone bodies form in a process called ketogenesis.
• In ketogenesis, acetyl-CoA molecules combine to produce ketone bodies: acetoacetate, $\beta$-hydroxybutyrate, and acetone.

Formation of Ketone Bodies

• Ketone bodies form:
  • If large amounts of acetyl-CoA accumulate.
  • When two acetyl-CoA molecules form acetoacetyl-CoA.
  • When acetoacetyl-CoA hydrolyzes to acetoacetate.
  • When acetoacetate reduces to $\beta$-hydroxybutyrate or loses $CO_2$ to form acetone, both ketone bodies.

Ketosis

• Occurs in diabetes, diets high in fat, and starvation.
• Accumulation of ketone bodies occurs.
• Acidic ketone bodies lower blood pH below 7.4 (acidosis).

Degradation of Amino Acids

• Proteins provide energy when carbohydrate and lipid resources are not available.
• The carbon atoms from amino acids are used:
  • In the citric acid cycle.
  • For the synthesis of fatty acids, ketone bodies, and glucose.
• Most of the amino groups are converted to urea.

Transamination

• Amino acids are degraded in the liver.
• An amino group is transferred from an amino acid to an α-keto acid, usually α-ketoglutarate.
• A new amino acid and α-keto acid are formed.
• When alanine combines with α-ketoglutarate, pyruvate and glutamate are produced.

Oxidative Deamination

• Removes the ammonium group ($NH<em>3^+$) from glutamate as an ammonium ion, $NH</em>4^+$, and provides hydrogens for the $NAD^+$ coenzyme.
• Regenerates α-ketoglutarate, which can enter transamination with an amino acid.

Urea Cycle

• Removes toxic ammonium ions from amino acid degradation.
• Converts ammonium ions to urea in the liver.
• Produces 25–30 grams of urea daily for excretion in the urine.

ATP Energy from Amino Acids

• Carbon skeletons of amino acids:
  • Form intermediates of the citric acid cycle.
  • Produce energy.
  • Enter the citric acid cycle at different places depending on the amino acid.