Metabolic Pathways

- Metabolism
o Sum total of all chemical reactions in a living organism
o Provide source of energy we need for all our activities
- Two mechanisms
o Catabolism
 Breaking down of large biochemical molecules broken down to smaller ones
 Energy is released/generated during the process
 I.e., oxidation of glucose
o Major pathway: Glycolysis, breakdown of glucose to pyruvate –
Kreb’s cycle
o Minor pathway: Pentose shunt
o Anabolism
 Joining of small biochemical molecules to form larger ones
 Requires energy
 I.e., Protein synthesis
o Amphibolic
 Catabolism with anabolism
 Molecules are broken down and joined back together
 I.e., Kreb’s Cycle
- Metabolic pathway
o Series of consecutive biochemical reactions to generate end product from a startng
material
 Linear
 Straight-forward process
 Independent enzyme-catalyzed reactions
o One product is substrate for the next reaction in pathway
o i.e., Glycolysis
 Cyclic
 Sequence of enzyme-catalyzed steps. Forming a closed loop
 Intermediate are regenerated each turn of the cycle
o i.e., Citric acid cycle
 Spiral
 Uses same set of enzymes repeatedly;
 Shortening or lengthening given molecule
o i.e., Fatty acid biosynthesis
- Cell structure
o Prokaryotic cell
 Single compartment organism
 No nucleus; only in bacteria
 Single circular DNA molecule near center; nucleoid
o Eukaryotic cell
 Multicompartment cell
  DNA present in membrane enclosed nucleus
 Cellular organelles
 ~1000 times larger than bacterial cells
o Mitochondria
 Responsible for generation of energy in a cell
 Outer membrane; preamble to small molecules
o 50% lipid
o 50% protein
 Inner membrane: Impermeable to most substance; folded to increase
surface area (Cristae)
o 20% lipid
o 80% protein
 ATP synthesis in the inner membrane
- Important compounds in metabolic pathways
o Adenosine phosphates (AMP, ADP, ATP, cAMP)
 AMP: Monophosphate
 Structural component of RNA
 One phosphate
 ADP: Diphosphate
o Connected via strained bond (reactive bond)
 Requires lesser energy to hydrolyze
 Key component for metabolic pathway along with ATP
o Phosphate groups connected to AMP by strained bonds.
 Strained bonds: require less energy to hydrolyze
o ATP + H2O  ADP + PO43- + Energy
o ADP + H2O  AMP + PO43- + Energy
 Summary: ATP + H2O  AMP + PO43- + Energy
 Net energy produced used for cellular reactions
 ATP: Triphosphate
 Energy unit
 Key component of Metabolic pathway
 cAMP: Cyclic monophosphate; cyclic structure
o Cellular reactions
 ATP functions as both source of phosphate group and source of energy
 Glucose + ATP –(Hexokinase)-> ADP + Glucose-6-phosphate
o Hexokinase is stimulated by Insulin
o Phosphate from ATP interacts with -OH group on Glucose.
o Governed by Magnesium
o Other Nucleotide Triphosphates in Metabolism
 Uridine triphosphate
 Involved in carbohydrate metabolism
 Guanosine triphosphate
 Involved in protein and carbohydrate metabolism
  Cytidine triphosphate
 Involved in lipid metabolism
o Flavin Adenine Dinucleotide (FAD)
 Oxidizing agent conversion of alkane to alkene
 Coenzyme required in numerous metabolic redox reactions
 Derived from and requires B2 – Riboflavin
 Flavin subunit is the active form
o Accepts and donates electron
 Ribitol is reduced form of ribose sugar
 FAD  FADH2
 FAD – oxidized form
 FADH2 – reduced form
o FAD goes back and forth (equilibrium) from oxidized to reduced
form
 Forms 2 atp in electron transport chain
o NAD+
 Coenzyme and oxidized form
 NADH – reduced form
 B3 – niacin
 3 subunits
 Nicotinamide – ribose – ADP
 6 subunit structure
 Nicotinamide – ribose – phosphate – ribose – adenine
 Cellular reaction NAD+ serves as oxidizing agent, oxidizing a secondary alcohol
to give ketone
 Forms 3 atp units in electron transport chain
o Coenzyme A
 Derivative of Vitamin B5 (pantothenic acid)
 3 subunits
 2-aminoethanethiol – pantothenic acid = phosphorylated ADP
 6 subunits
 2-aminoethanethiol – pantothenic acid = phosphate – phosphate
phosphorylated ribose – adenine
 Active form is sulfhydryl group attachment in ethanethiol subunit
 Acetyl-CoA (acetylated)
- Acetyl CoA
o Fates
 Metabolized to CO2
 Will enter Kreb Cycle and produce: ATP, NADH. FADH2, GTP,
 If energy is not used (Multiple ATP present)
 HMG-CoA reductase convert Acetyl CoA mevalonic acid  Rate
limiting step in production of Cholesterol
 Energy is used (CHO is absent)
 Starvation; Form Ketone bodies;
 - Classification of Metabolic intermediate compounds
o Intermediates for energy storage and phosphate transfer
 ATP
 ADP
 AMP
o Intermediates for transfer of electrons in metabolic redox reactions
 FAD; FADH2
 NAD; NADH
o Intermediates for transfer of Acetyl groups
 HSCoA; Acetyl-s-CoA

High-energy phosphate compounds

- Have greater free energy of hydrolysis

o Contain at least one reactive bond
 Requires less energy to break and gives more energy when broken
o More negative free energy; greater the strain
 Greater than 6.0 kcal/mole
 Represented by ~
- Examples
o Enol phosphates
 I.e., phosphoenolpyruvate
o Acyl phosphates
 i.e., 1,3-biphospholgycerate, acetyl phosphate
o Guanidine phosphates
 i.e., creatine phosphate, arginine phosphate
o Triphosphates
 i.e., ATP
o Diphosphates
 i.e., ADP
o Sugar phosphates
 i.e.,
 Glucose 1-phosphate;
 Fructose 6-phosphate;
 AMP Adenosine + P;
 G6P;
 G3P

Overview of Biochemical energy production

- Energy obtained from food; Involving different catabolic pathways

- Four general stages
o Digestion
o Acetyl group formation
o Citric Acid cycle
 o Electron transport chain and oxidative phosphorylation
- Each stage involves numerous reactions

Steps

- Digestion
o Begins in mouth (Saliva; amylase)
o Continues in stomach (Gastric juice);
o Completed in small intestine
 Pancreatic digestive enzyme p-d; Intestinal mucosal cell
 Maltase
 Sucrase
 Lactase
 Absorption of sugars in the intestinal lining (Villi)
 Contains tiny capillaries to absorb nutrients
 Small molecules can cross the membrane into the blood
o End product
 Glucose and monosaccharides from carbohydrates
 Amino acids from proteins
 Fatty acids and glycerol from fats and oils
- Acetyl group formation
o Small molecules from digestion further oxidized
 Forming Acetyl CoA
o Involves numerous reactions
 In Cytosol (Glucose metabolism)
 In mitochondria (Fatty acid metabolism)
- Citric acid Cycle
o Main goal: Produce energy (ATP)
o First intermediate is citric acid
 Acetyl CoA oxidized to produce CO2
 The carbon dioxide we exhale comes from this stage
 Most energy is trapped in reduced NADH and FADH2
 Some energy produced is lost in form of heat
- Electron transport chain and Oxidative phosphorylation
o Takes place in mitochondria
o NADH and FADH2 oxidized to release H and electrons
 H transported into inter-membrane space in mitochondria
 Reenters mitochondrial matrix and drive ATP-synthase to produce ATP
 Electrons transferred to O2 and is reduced to H2O

Chemical process prior to metabolism

- Digestion
o Breakdown of food by hydrolysis into simpler units
- Absorption
 o Process of getting simpler units into the blood stream and into cells

Importance of ATP

- ATP and ADP cycling in metabolic processes is principal medium for energy exchange
o ADP to ATP
 Life processes (Cellular work)
o ATP to ADP
 Food catabolism (Oxidation of molecules)

Non-ETC oxygen consuming reaction

- More than 90% of oxygen inhaled via respiration is consumed during oxidative phosphorylation
o Remaining O2 are converted to ROS within the body
 Hydrogen peroxide (H2O2)
 Superoxide ion (O2) and Hydroxyl radical (OH)
 Extremely reactive due to unpaired electrons
o ROS or Free radicals can destroy cells causing oxidative damage
 Can be formed due to external influences
 Can also be beneficial
 WBC produce significant amount of superoxide free radicals to destroy
bacteria and viruses
o 2O2 + NADPH  2O2 + NADP + H
 More than 95% of ROS formed are quickly converted to non-toxic
species (5% escape)
o 2O + 2H –(Superoxide dismutase)-> H2O2 + O2
o 2H2O2 –(Catalase)-> 2H2O + O2
 Antioxidant molecules present in the body help trap ROS species
 Vit. K
 Vit. C
 GSH
 Beta-carotine
 Plant products such as flavonoids are also good antioxidants

Pyruvate

o Fate
 Aerobic respiration
 Acetyl CoA for citric acid cycle, Pyruvic acid converted by Pyruvate
dehydrogenase; along with NAD+ (turning to NADH) and HSCoA (turning
to CO2) to get Acetyl CoA
 Anaerobic respiration
 Undergoes fermentation
 Lactate (Lactic acid)
o Causes muscle spasm