USMLE - Chapter 1 - Biochemistry
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Chromatin Structure Overview to Histone Deacetylation6Topics
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Nucleoside and Nucleotide Basics to Base Pairing and DNA Stability5Topics
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Introduction to Nucleotide Synthesis Inhibition to Broad-Spectrum Inhibitors and CPS Enzymes5Topics
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Purine Metabolism and Salvage Pathways to Genetic Code: Commaless and Universal6Topics
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DNA Replication Basics to Detailed Lagging Strand Synthesis7Topics
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DNA Repair: Nonhomologous End Joining to DNA Repair: Mismatch Repair5Topics
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Introns vs Exons: Basic Definitions to Visualizing Alternative Splicing and Protein Diversity4Topics
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tRNA Structure Overview to mRNA Stop Codons6Topics
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Introduction to DNA Mutations to Lac Operon Gene Expression States8Topics
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Cilia Structure: Motile Cilia and Basal Body to K+ Pump Inhibition6Topics
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Page 1 — Eukaryotic Gene Overview to Page 1 — RNA Processing: Splicing & Fate8Topics
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Osteogenesis Imperfecta: Genetic Basis to Menkes Disease6Topics
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Eukaryotic RNA Polymerases: Types to Splicing Diagram: Lariat & Mature mRNA7Topics
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Flow Cytometry: Basics and Applications to ELISA: Principle and Uses4Topics
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Protein Synthesis: Initiation Phase to Posttranslational Modifications: Chaperone Proteins6Topics
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Karyotyping: Principles and Applications to Molecular Cloning: Process and Applications4Topics
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Cell Cycle Phases and Regulation to p53 and Apoptosis Induction7Topics
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Introduction to Imprinting Disorders to Visualizing Normal vs. Mutated Chromosomes6Topics
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Rough Endoplasmic Reticulum Functions to Specific Vesicular Trafficking Proteins7Topics
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Autosomal Dominant Inheritance to Pedigree Chart Symbols6Topics
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Peroxisome Functions to Drugs Affecting Microtubules5Topics
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Polyunsaturated Essential Fatty Acids to Water-Soluble Vitamins: Deficiencies and Coenzyme Functions5Topics
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Collagen Introduction and Type I to Collagen Synthesis: Maturation and Fibril Formation6Topics
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Vitamin B7 (Biotin): Function and Deficiency to Vitamin B9 (Folate): Deficiency, Causes, and Prevention3Topics
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Elastin: Structure and Composition to PCR Cycle: Elongation and Repetition8Topics
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Elastin: Structure and Composition
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Elastin Cross-linking and α1-Antitrypsin Deficiency
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Marfan Syndrome: Genetics and Physical Manifestations
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Marfan Cardiovascular Complications & Homocystinuria Overview
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Differentiating Marfan Syndrome and Homocystinuria
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Introduction to PCR: Amplifying DNA
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PCR Cycle: Denaturation and Annealing
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PCR Cycle: Elongation and Repetition
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Elastin: Structure and Composition
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Ethanol Metabolism Overview to Pharmacological Interventions in Alcohol Metabolism5Topics
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CRISPR to Interpreting Southern Blot Results5Topics
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Key Metabolic Locations to Glucose Breakdown and NADPH Production4Topics
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Transgenic Strategies in Mice to Epistasis and Aneuploidy7Topics
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Pyruvate Dehydrogenase Deficiency to The TCA Cycle (Krebs Cycle)3Topics
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Genetic Terms: Dominant Negative & Linkage Disequilibrium to Conditions for Hardy-Weinberg Equilibrium7Topics
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ETC Overview to Fatty Acids in Gluconeogenesis9Topics
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Autosomal Dominant Disorders to CFTR Channel Function Diagram11Topics
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Autosomal Dominant Disorders
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Autosomal Recessive Disorders
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Cystic Fibrosis: Genetics
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Cystic Fibrosis: CFTR Defect
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CFTR Dysfunction and Mucus Thickening
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Cystic Fibrosis: Diagnosis
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CF Pulmonary Complications
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CF Gastrointestinal and Reproductive Complications
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CF Treatment: Mucus Clearance and Inflammation
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CFTR Modulators in Treatment
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CFTR Channel Function Diagram
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Autosomal Dominant Disorders
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Phenylketonuria: Basic Defect and BH4 Deficiency to Alkaptonuria7Topics
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X-linked Recessive Diseases Introduction to Myotonic Dystrophy6Topics
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Fatty Acid Synthesis Overview to Medium-Chain Acyl-CoA Dehydrogenase Deficiency4Topics
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Mitochondrial Diseases: MELAS & MERRF to Trinucleotide Repeat Diseases: Fragile X & Friedreich Ataxia8Topics
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Mitochondrial Diseases: MELAS & MERRF
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Leber Hereditary Optic Neuropathy
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Rett Syndrome Characteristics
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Fragile X Syndrome: Genetics & Premutation
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Fragile X Syndrome: Full Mutation Features
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Trinucleotide Repeat Diseases: Huntington
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Trinucleotide Repeat Diseases: Myotonic Dystrophy
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Trinucleotide Repeat Diseases: Fragile X & Friedreich Ataxia
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Mitochondrial Diseases: MELAS & MERRF
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Hepatic Ketone Body Synthesis to Adipocyte Metabolism: Fed State4Topics
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Autosomal Trisomies & Down Syndrome Overview to Second Trimester Screening & NIPT8Topics
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Metabolic Fuel Use: Initial Exercise to Starvation After Day 3 and Stored Energy Depletion7Topics
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Metabolic Fuel Use: Initial Exercise
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Metabolic Fuel Use: Longer Exercise and Caloric Values
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Fasting and Starvation: Introduction and Fed State
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Fasting and Starvation: Between Meals
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Starvation Days 1-3: Fuel Shifts
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Starvation Days 1-3: Gluconeogenesis and RBCs
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Starvation After Day 3 and Stored Energy Depletion
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Metabolic Fuel Use: Initial Exercise
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Genetic Disorders: Chromosomes 3-7 to Williams Syndrome6Topics
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Dietary Lipid Absorption and Chylomicron Entry to IDL, LDL Formation, and Uptake4Topics
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Vitamin A: Functions and Forms to Vitamin B1: Beriberi Forms7Topics
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Vitamin B2: Function and Deficiency to Vitamin B6 Deficiency Symptoms7Topics
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Vitamin B12: Name, Function, and Sources to Vitamin C: Excess and Toxicity7Topics
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Vitamin D Introduction and Function to Vitamin E Deficiency and Excess Effects6Topics
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Vitamin K Function to Marasmus: Characteristics and Visuals7Topics
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Enzyme Terminology: Kinase & Phosphorylase to Rate-Determining Enzymes: Lipid Metabolism7Topics
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Enzyme Terminology: Kinase & Phosphorylase
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Enzyme Terminology: Phosphatase, Dehydrogenase, Hydroxylase
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Enzyme Terminology: Carboxylase, Mutase, Synthase/Synthetase
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Rate-Determining Enzymes: Glycolysis, Gluconeogenesis, TCA Cycle
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Rate-Determining Enzymes: Glycogenesis, Glycogenolysis, HMP Shunt
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Rate-Determining Enzymes: Nucleotide Synthesis, Urea Cycle
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Rate-Determining Enzymes: Lipid Metabolism
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Enzyme Terminology: Kinase & Phosphorylase
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ATP Production Pathways to Hexokinase vs Glucokinase: Kinetics & Regulation5Topics
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Glycolysis Net Reaction to PDC: α-Ketoglutarate & Arsenic7Topics
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Introduction to Pentose Phosphate Pathway to G6PD Deficiency: Biochemical Mechanism of Oxidative Stress7Topics
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Essential Fructosuria to Galactose Metabolism Pathway & Summary6Topics
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Sorbitol Pathway and Diabetic Complications to Acidic and Basic Amino Acids6Topics
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Urea Cycle Introduction to Hyperammonemia Treatment5Topics
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Ornithine Transcarbamylase Deficiency to Catecholamine Synthesis and Degradation5Topics
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Homocystinuria: Genetic Causes to Methylmalonic Acidemia: Deficiency & Metabolism6Topics
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Glucagon to Glycogen Disorders and Enzymes6Topics
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Introduction to Glycogen Storage Diseases to McArdle Disease (Type V)6Topics
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Lysosomal Storage Diseases Intro & Tay-Sachs to Lysosomal Storage Disease Pathway6Topics
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Key Enzymes in Lipid Transport - Part 1 to Major Apolipoproteins - Part 25Topics
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Lipoprotein Functions: Chylomicron & VLDL to Familial Dyslipidemias: Dysbetalipoproteinemia & Hypertriglyceridemia5Topics
Glycolysis Net Reaction to PDC: α-Ketoglutarate & Arsenic
Content August 26, 2025
Glycolysis Regulation: Key Enzymes
Net glycolysis (cytoplasm):
Glucose + 2 Pᵢ + 2 ADP + 2 NAD⁺ → 2 pyruvate + 2 ATP + 2 NADH + 2 H⁺ + 2 H₂O
Equation not balanced chemically, and exact balanced equation depends on ionization state of reactants and products.
Glycolysis Regulation: ATP Requiring Steps
REQUIRE ATP
Glucose → Glucose-6-P
- Hexokinase/glucokinase (inhibited by Glucose-6-P)
Fructose-6-P → Fructose-1,6-BP
- Phosphofructokinase-1 (rate-limiting step)
- Inhibited by AMP, Fructose-2,6-bisphosphate, ATP, citrate
Glycolysis Regulation: ATP Producing Steps
PRODUCE ATP
1,3-BPG → 3-PG
- Phosphoglycerate kinase
Phosphoenolpyruvate → Pyruvate
- Pyruvate kinase
- Inhibited by Fructose-1,6-bisphosphate, ATP, alanine, glucagon
Regulation by Fructose-2,6-bisphosphate
Fructose bisphosphatase-2 (FBPase-2) and phosphofructokinase-2 (PFK-2) are the same bifunctional enzyme whose function is reversed by phosphorylation by protein kinase A.
#boundingbox
Fructose-2,6-bisphosphate Regulation: Fasting vs. Fed
Fasting state: ↑ glucagon → ↑ cAMP → ↑ protein kinase A → ↑ FBPase-2, ↓ PFK-2, less glycolysis, more gluconeogenesis.
Fed state: ↑ insulin → ↓ cAMP → ↓ protein kinase A → ↓ FBPase-2, ↑ PFK-2, more glycolysis, less gluconeogenesis.
FaBian the Peasant (FBP) has to work hard when starving.
Prince FredericK (PFK) works only when fed.
Pyruvate Dehydrogenase Complex
Mitochondrial enzyme complex linking glycolysis and TCA cycle. Differentially regulated in fed (active)/fasting (inactive) states.
Reaction: pyruvate + NAD⁺ + CoA → acetyl-CoA + CO₂ + NADH
Contains 3 enzymes requiring 5 cofactors:
- Thiamine pyrophosphate (B₁)
- Lipoic acid
- CoA (B₅, pantothenic acid)
- FAD (B₂, riboflavin)
- NAD⁺ (B₃, niacin)
Activated by: ↑ NAD⁺/NADH ratio, ↑ ADP, ↑ Ca²⁺
Pyruvate Dehydrogenase Complex: Comparisons and Clinical Notes
The complex is similar to the α-ketoglutarate dehydrogenase complex (same cofactors, similar substrate and action), which converts α-ketoglutarate → succinyl-CoA (TCA cycle).
The lovely coenzymes for nerds.
Arsenic inhibits lipoic acid. Arsenic poisoning clinical findings: imagine a vampire (pigmentary skin changes, skin cancer), vomiting and having diarrhea, running away from a cutie (QT prolongation) with garlic breath.
Topics Covered:
- Glycolysis Net Reaction
- Glycolysis: ATP Investment Phase
- Glycolysis: ATP Payoff Phase
- Fructose-2,6-BP Bifunctional Enzyme
- Fructose-2,6-BP: Fasting and Fed States
- Pyruvate Dehydrogenase Complex
- PDC: α-Ketoglutarate & Arsenic