Sweet Biochemistry

Remembering Structures, Cycles, and Pathways by Mnemonics

Asha Kumari

• Publisher: Academic Press
• Year: 2017
• ISBN:
  9780128144541
• Topic: Biological Sciences
• Subtopic: Biochemistry
• Index: Biological Sciences

Sweet Biochemistry: Remembering Structures, Cycles, and Pathways by Mnemonics makes biochemistry lively, interesting and memorable. by connecting objects, images and stories. Dr. Kumari has converted cycles and difficult pathways into very simple formula, very short stories and images which will help readers see familiar things in complicated cycles and better visualize biochemistry.

• Provides quick, indigenous formulas, mnemonics, figures and short stories to help users simply recollect the study of biochemistry
• Gives unique descriptions of the difficult areas in biochemistry and new ways of remembering a pathway or structure
• Presents original diagrams that resonate and are easy to recall

Chapter 1

Glycolysis

Abstract

Glycolysis is a cytoplasmic pathway which breaks down glucose into two three-carbon compounds and generates energy. Glucose is trapped by phosphorylation, with the help of the enzyme hexokinase. Adenosine triphosphate (ATP) is used in this reaction and the product, glucose-6-P, inhibits hexokinase. Glycolysis takes place in 10 steps, five of which are in the preparatory phase and five are in the pay-off phase. Phosphofructokinase is the rate-limiting enzyme. ATP is generated by substrate-level phosphorylation by high-energy compounds, such as 1,3-bisphosphoglycerate and phosphoenolpyruvate.

Glycolysis is used by all cells in the body for energy generation. The final product of glycolysis is pyruvate in aerobic settings and lactate in anaerobic conditions. Pyruvate enters the Krebs cycle for further energy production.

Keywords

Glycolysis; hexokinase; phosphofructokinase; 1,3-bisphosphoglycerate; aldolase; phosphoenolpyruvate; pyruvate; ATP

Traditional Glycolysis Recap

Glycolysis is a cytoplasmic pathway which breaks down glucose into two three-carbon compounds and generates energy. Glycolysis is used by all cells in the body for energy generation. Glucose is trapped by phosphorylation, with the help of the enzyme hexokinase. Adenosine triphosphate (ATP) is used in this reaction and the product, glucose-6-Phosphate (G-6-P), inhibits hexokinase. This is an irreversible reaction. G-6-P is isomerized into its ketose form, fructose-6-Phosphate (F-6-P), by phosphohexose isomerase.

F-6-P is further phosphorylated by phosphofructokinase to fructose 1,6-bisphosphate (F1,6 bisP). This reaction is irreversible and is the principal regulatory step. Aldolase cleaves F1,6 bisP into glyceraldehyde-3-P and dihydroxyacetone phosphate (DHAP), which are interconverted by the enzyme phosphotriose isomerase.

Glyceraldehyde-3-P is oxidized by NAD+-dependent dehydrogenase forming 1,3-bisphosphoglycerate.

1,3-Bisphosphoglycerate has a high-energy acyl phosphate bond and carries out substrate-level phosphorylation generating ATP. The participating enzyme is phosphoglycerate kinase and 3-phosphoglycerate is formed. Phosphoglycerate mutase isomerizes 3-phosphoglycerate to 2-phosphoglycerate. 2-Phosphoglycerate is dehydrated by enolase to form phosphoenolpyruvate, the second compound capable of substrate-level phosphorylation in glycolysis. Pyruvate kinase transfers the phosphate group of phosphoenolpyruvate to adenosine diphosphate (ADP) and pyruvate is formed.

Pyruvate enters the Krebs cycle in aerobic conditions, and in anaerobic conditions it forms lactate which helps in the generation of NAD+ for the continuation of glycolysis. Pyruvate is converted to acetyl-CoA by pyruvate dehydrogenase complex, which is an irreversible step. Pyruvate enters the Krebs cycle for further energy production.

Glycolysis is one of the basic metabolic pathways, and is crucial for the life of most organisms. We start this book with the pathway showing the reactions, substrates, products, enzymes, and other involved molecules of glycolysis (Figs. 1.1 and 1.2).

Figure 1.1 Glycolysis pathway.

Figure 1.2 A poem to remember the glycolysis intermediates.

Rhyming Glycolysis

The words in the poem in Fig. 1.2 are related to the intermediates of glycolysis. Red-colored letters are taken from molecules or are short forms of molecules. The "P" in peg in the second and fourth lines indicates the phosphate group, it is cut in two to denote the splitting reaction. "BPG," the name of the protagonist, is a short form of 1,3-bisphosphoglycerate. As it is a high-energy compound, the following line gives the description “He is very strong.” "Three two one" indicates that one phosphate molecule is shifted from the third to the second position. "PEP" in red in the next line is phosphoenolpyruvate, and "P" in the last line is for pyruvate (Fig. 1.3).

Figure 1.3 Mnemonic diagram to remember the glycolysis reactions.

Glycolysis Mnemonic Diagram

In glycolysis, glucose (6C) is broken into two pyruvate (3C) molecules.

It has 10 letters in its name and 10 reactions.

Write the word "GLYCOLYSIS" and write the numbers starting from "G" on the left-hand side.

Draw a line at the center of the name dividing it into two parts. The first five are the preparatory steps and the second five are the pay-off or energy-generating steps. Of the preparatory steps, the first three are priming and the subsequent two are splitting steps.

ATP is consumed in steps 1 and 3, so ATP is shown entering at letters "G" and "Y."

The next step is cleavage of fructose 1,6-bisphosphate into glyceraldehyde-3-P and DHAP, indicated by "Cut."

DHAP is isomerized into glyceraldehyde-3-P; this is indicated by the mirror in the "O" of "ISO."

Inorganic phosphate enters along with NAD+ in the following step, therefore "

" is depicted entering "L."

ATP is generated in steps 7 and 10, hence ATP is leaving letters "Y" and "S."

The eighth step is the isomerization reaction in which the molecular formula is "SAME" and only the position of phosphate is changed.

The ninth reaction is dehydration, which is depicted by water coming out of a pipe.

This is how all 10 reactions of glycolysis can be remembered.

Chapter 2

Citric Acid Cycle

Abstract

The citric acid cycle utilizes mitochondrial enzymes. The first step is fusion of the acetyl group of acetyl-CoA with oxaloacetate, catalyzed by citrate synthase. CoA-SH and heat are released and citrate is produced. Citrate is isomerized by dehydration and rehydration to isocitrate. The enzyme aconitase catalyzes these two steps using cis-aconitate as the intermediate. The next two steps are catalyzed by isocitrate dehydrogenase. Dehydrogenation of isocitrate forms oxalosuccinate which decarboxylates to alpha-ketoglutarate. Alpha-ketoglutarate is further oxidatively decarboxylated by alpha-ketoglutarate dehydrogenase—a multienzyme complex. Succinyl-CoA is formed in this unidirectional reaction.

Succinate thiokinase co...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• Dedication
• List of Figures
• List of Tables
• Preface
• Acknowledgments
• Chapter 1. Glycolysis
• Chapter 2. Citric Acid Cycle
• Chapter 3. Electron Transport Chain
• Chapter 4. Beta Oxidation of Fatty Acids
• Chapter 5. Fatty Acid Biosynthesis
• Chapter 6. Cholesterol Structure
• Chapter 7. Cholesterol Synthesis
• Chapter 8. Heme Synthesis
• Chapter 9. Porphyrias
• Chapter 10. Urea Synthesis
• Chapter 11. Urea Cycle Disorders
• Chapter 12. Glycogen Storage Disorders
• Chapter 13. Ceramide Structure and Derivatives
• Chapter 14. Lipid Storage Disorders/Sphingolipidoses
• Chapter 15. Mucopolysaccharidoses
• Chapter 16. Prostaglandin Synthesis
• Chapter 17. Purine Structures
• Chapter 18. Purine de novo Synthesis
• Chapter 19. Pyrimidine Structure
• Chapter 20. Pyrimidine de novo Synthesis
• Exercises
• Further Reading