Energy, Spontaneity, and Metabolism

Lecture 15: Energy, Spontaneity, and Metabolism

• Spontaneous reactions do not require energy
• A reaction with a high +ΔG can be made spontaneous by coupling it with an exergonic reaction, which releases energy, this energy must come from an outside source
• Positive ΔG assumes non-spontaneity, endergonicity (requires energy input), and unfavorability
• Negative ΔG assumes spontaneity, exergonicity (releases energy), and favorability
• Metabolism has two components: catabolism and anabolism
• Catabolism breaks down large molecules into smaller ones to release energy
• Anabolism builds smaller molecules into larger ones, requiring energy in the form of redox reactions
• Reduction is the gain of electrons
• Oxidation is the loss of electrons
• OILRIG stands for oxidation is loss, reduction is gain
• A reducing agent is a substance that gets oxidized and becomes positive
• An oxidizing agent is a substance that gets reduced and becomes negative
• NAD+ acts as a reducing agent because it gets oxidized
• NADH functions as an oxidizing agent as it gets reduced
• Coupled reactions have an overall negative ΔG
• Reducing agents tie to oxidation
• Oxidizing agents tie to reduction
• ATP is the energy currency of the cell
• ATP is a high-energy compound due to the high-energy bonds of its three phosphate groups

Lecture 16: Sugar Stereochemistry and Structure

• D stereoisomers have the OH group on the right side of the highest numbered carbon
• L stereoisomers have the OH group on the left side of the highest numbered carbon
• Sugars exist in the D form in nature
• Sugars have a cyclic ring structure
• Ring structures are distinguished by the number of carbon atoms in the structure
• Furanose is a cyclic sugar with a 5-carbon ring and a flat pentagon shape
• Pyranose is a cyclic sugar with a 6-carbon ring and a chair formation that is not flat
• Alpha (α) linkage is below the plane of the ring, pointing down, and is visible
• Beta (ß) linkage is above the plane of the ring, pointing up, and is not visible
• Sugars can exist as D, L, alpha, and beta stereoisomers
• Common oligosaccharides include sucrose, maltose, and lactose
• Sucrose is made of glucose and fructose, linked by an allusion linkage
• Maltose is made of glucose and glucose, linked by an alpha (1,4) linkage
• Lactose is made of glucose and galactose, linked by a beta (1,4) linkage
• Common polysaccharides include cellulose, starch, and chitin
• Cellulose is composed of B-D glucose molecules and found in the cell wall
• Starch is a homopolysaccharide of A-D glucose molecules and found in plant cells
• Amylose and amylopectin are the two forms of starch
• Chitin is composed of B-D glucose molecules and found in the exoskeletons of invertebrates
• Glycogen is composed of A-D glucose molecules and serves as the storage form of glucose
• Cellulose and chitin also make up cell walls

Lecture 17: Glycolysis

• Glycolysis is a method of breaking down glucose to obtain energy in the form of ATP
• Glycolysis has overall products of 2 ATP, 2 NADH, and 2 pyruvate molecules
• Net ATP production in glycolysis is 2
• Gross ATP production in glycolysis is 4
• In glycolysis, glucose is converted into 2 molecules of pyruvate
• Glycolysis is the first stage of glucose metabolism in organisms
• Glycolysis involves enzymes such as Hydrolase, Kinase/Phosphorylase, Dehydrogenase, and Mutase/Isomerase
• Hydrolases use water to break something
• Kinases or Phosphorylases add or remove a phosphate group
• Dehydrogenases add or remove a hydrogen or electron from a substance
• Mutases or Isomerases change the physical structure of a substance, not chemical
• Glycolysis reactions generate cofactors and ATP
• In anaerobic respiration, the primary reaction is the reduction of pyruvate to lactate
• Lactate/ethanol production regenerates NAD+ for glycolysis

Lecture 18: Glycogen, Isomerase, and Gluconeogenesis

• Glycogen is stored glucose when there is a lot of glucose but not a lot of ATP
• Glycogen is found in the liver and muscle cells in animals
• Glucose makes up glycogen
• Glycogen is broken down through debranching enzymes and glycolysis, and made through gluconeogenesis and connected in a branching structure
• A branching structure optimizes glycogen for storage and increases surface area for easy access when needed.
• Isomerase rearranges the functional groups of a compound to yield one with the same chemical structure but different configurations
• Gluconeogenesis makes glucose from pyruvate when there is a lot of ATP but not a lot of glucose
• Gluconeogenesis makes glucose which requires energy, while glycogen breakdown releases energy
• Glycolysis occurs when there is low ATP concentration and high glucose
• Gluconeogenesis occurs when there is high ATP concentration and low glucose
• Reactions in gluconeogenesis that are not a direct reversal of glycolysis: PEP turns into pyruvate and ATP; fructose 6 pyruvate turns into fructose 1, 6 bisphosphate; glucose and ATP turns into glucose 6 phosphate
• Glycolysis and gluconeogenesis are regulated by enzymes and ATP and glucose concentrations
• Hormones stimulate either glycogen breakdown or storage in glycogen metabolism
• Glucagon stimulates glycogen breakdown when glucose levels are low
• Insulin promotes storage of glycogen when glucose levels are high
• The pentose phosphate pathway involves 5-carbon sugars and NADPH

Lecture 19: Citric Acid Cycle

• Direct products of the Citric Acid Cycle (CAC) include 3 carbon dioxide molecules (primary end product), 4 NADPH, 1 GTP, 4 hydrogen ions, and 1 FADH2 molecule

• Pyruvate is the main product of glycolysis

• The conversion of pyruvate to acetyl-CoA involves an oxidation reaction with decarboxylation

• Pyruvate undergoes oxidation to convert into acetyl-CoA

• Pyruvate gets converted into acetyl-CoA and carbon dioxide in the CAC

• Enzymatic activities in the CAC include decarboxylation, oxidation, and isomerization

• Small molecules and cofactors like ATP/ADP and NADH/NAD regulate the CAC by their concentrations and amount present before the cycle begins

• Concentrations of ATP and NADH are low when cells are in a highly active metabolic state

• At low concentrations of ATP and NADH Glycolysis and the citric acid cycle occur

• Concentrations of ATP and NADH are high when cells are in a resting metabolic state

• At high concentrations of ATP and NADH Glycolysis and citric acid cycles are inhibited

• Concentrations of ADP and NADH are high when cells are in a highly active metabolic state, this activates glycolysis and the citric acid cycle

• Concentrations of ADP and NADH are low when cells are in a resting metabolic state

• The glyoxylate cycle is a pathway seen in plants and some bacteria similar to the CAC

• In the reaction involving isocitrate kinase in the glyoxylate cycle, isocitrate is a substrate that catalyses the conversion of isocitrate to glyoxylate and succinate and that forms glyoxylate and succinate products

• In the reaction involving malate synthase in the glyoxylate cycle, glyoxylate and acetyl-coa are substrates, turning them into malate products which function to catalyze the conversion of glyoxylate with acetylcholine into malate

• The glyoxylate cycle is an alternative pathway for the citric acid cycle seen in plants and some bacteria

• Many catabolic processes feed into the CAC, examples include protein, carbohydrates, and fatty acid degradation

• Catabolism is observed in the pathways feeding into the CAC