AfraTafreeh.

com
TABLE OF CONTENTS

1. Cell Biology
Biochemistry 2. Lysosomal Storage Diseases
3. Connective Tissue
4. Energy Production
5. Carbohydrates
6. One-Carbon Metabolism
7. Oxidative Stress
8. Glycogen
9. Lipid Metabolism
 OUTLINE
1. Cell Trafficking 5. Ubiquitin-Proteasome system
A. Endoplasmic Reticulum A. Overview

Biochemistry:
B. Cell Trafficking to cis-Golgi B. Ubiquitin
C. Golgi C. Proteasome
D. Anterograde Transport from trans-Golgi D. Cell Cycle Regulation

Cell Biology
E. Endocytosis E. Proteasome Inhibitors
2. I-Cell Disease 6. Cytoskeleton
A. Pathophysiology A. Overview
B. Presentation B. Actin
C. Diagnostics C. Intermediate Filaments
D. Management D. Microtubules
E. Complications 7. Primary Ciliary Dyskinesia
F. Differential Diagnoses A. Pathophysiology
B. Presentation
AfraTafreeh.com
3. Signal Recognition Particle
C. Diagnostics
A. Signal Sequence and SRP
B. SRP Receptor and Translocon D. Management
C. Transmembrane Proteins 8. Sodium-Potassium Pump
4. Peroxisome A. Overview
A. Overview B. Pump Mechanism
B. Very-Long-Chain Fatty Acid β-Oxidation C. Applications
C. Branched-Chain Fatty Acid ɑ-Oxidation
D. Peroxisome Synthetic Processes
 AfraTafreeh.com
Biochemistry: Cell Biology Bootcamp.com

Cell Trafficking
• Endoplasmic Reticulum:
• Rough ER: Ribosomes, near nucleus, protein synthesis, N-linked glycosylation
• Smooth ER: No ribosomes, near membrane, lipid synthesis, glucose-6-phosphatase
• Vesicular Trafficking to Cis-Golgi:
• COPII: Anterograde transport → Cis-Golgi
• COPI: Retrograde transport → ER (endocytosis)
• Golgi:
• Post-translational modifications:
• Modify N-oligosaccharides of Asn, add O-oligosaccharides of Ser/Thr
• Sulfation of Tyr
• Addition of mannose-6-phosphate for proteins destined for lysosome
• I-cell disease: Failure to phosphorylate mannose residues → Inclusions
• Anterograde Transport from Trans-Golgi:
• Secretory vesicle to cell membrane → Exocytosis
• Clathrin-mediated transport → Late endosome → Lysosome
• Endocytosis:
• Clathrin-mediated endocytosis → Early endosome → Late endosome
• → Trans-Golgi for retrograde transport to ER (COPI-mediated)
• → Lysosome for degradation
 Biochemistry: Cell Biology Bootcamp.com

I-Cell Disease
• Pathophysiology:
• Golgi normally adds mannose-6-phosphate to proteins destined for lysosome
• Defect in N-acetylglucosamine-1-phosphotransferase → Failure of Golgi to phosphorylate mannose
→ Digestive enzymes NOT tagged for lysosome → Transport of digestive enzymes extracellularly
→ ↑ Lysosomal substances in serum
• Buildup of cell debris inside lysosomes (inclusion bodies)
• Autosomal recessive
• Presentation:
• Young child, developmental delay/failure to thrive
• Coarse facial features, corneal clouding → blindness
• Skeletal deformities/↓ Mobility, kyphoscoliosis, claw hand deformity
• Hepatomegaly, gingival hyperplasia
AfraTafreeh.com
• Diagnostics:
• ↓ N-acetylglucosamine-1-phosphotransferase enzyme activity
• Amniotic fluid/chorionic villi (prenatal) or WBCs (postnatal)
• ↑ Serum lysosomal enzymes, normal urinalysis
• Inclusion bodies and vacuoles in peripheral blood lymphocytes
• Management:
• No cure; symptomatic treatment, nutritional support, physical therapy
• Complications:
• CHF, pneumonia, otitis media, atlantoaxial instability
• Differential Diagnosis:
• Mucopolysaccharidoses (Hurler/Hunter syndromes) → ↑ Urinary glycosaminoglycans
 AfraTafreeh.com
Biochemistry: Cell Biology Bootcamp.com

Signal Recognition Particle

• Signal Sequence and Signal Recognition Particle:
• Signal sequence (SS): String of hydrophobic amino acids on proteins destined for ER
• Export or membrane integration
• SS attracts signal recognition particle (SRP) → Binds SS and stops translation
• (+) Anti-SRP: Polymyositis/dermatomyositis
• (+) Anti-Jo primary diagnostic target
• ↑ Muscle enzymes, symmetrical proximal muscle weakness
• Polymyositis: No cutaneous involvement
• Dermatomyositis: Heliotrope eyelid rash, Gottron papules
• SRP Receptor and Translocon:
• SRP brings nascent protein/ribosome complex to ER membrane, binds SRP receptor
• Ribosome passed to translocon (translocation channel), SRP detaches
• SS opens translocon and binds, translocation continues, threads through as a large loop
• Protein complete → SS degraded by signal peptidase → Translocon closes
• Protein released into ER lumen, escorted to Golgi for vesicular trafficking
• Transmembrane proteins made by changing location of SRP or adding stop sequences
• Failure of SRP → Cytosolic buildup of proteins
 Biochemistry: Cell Biology Bootcamp.com

β-Oxidation Catalase reaction

Peroxisome
• Overview:
• Peroxisomes degrade fatty acids, amino acids, uric acid → Generate peroxide (H2O2)
• Compare to lysosomes and proteasomes
• Lysosomes: Degrade endocytosed materials and cell debris
• Proteasomes: Degrade ubiquitinated proteins
α-Oxidation
• Very-Long-Chain Fatty Acid (VLCFA) β-Oxidation:
• Fatty acids >22 carbons too large to transport into mitochondria, break into medium-chain FAs
• Each cycle cleaves 2C
• Electrons transfer to O2, unlike in the mitochondria (ATP synthesis-coupled) → H2O2 (toxic)
• Catalase reaction degrades peroxide or uses in detox reactions
• Protects cell from oxidative damage
•
AfraTafreeh.com
Catalase (+) bacteria (e.g. Staphylococci) → ↑ Pathogenicity
• Adrenoleukodystrophy: ABCD1 mutation → ↓ VLCFA import → ↓ β-Oxidation → ↑ VLCFA
• Adrenal glands → Adrenal insufficiency
• White matter → Cognitive impairment, neonatal seizures, hearing loss
• Branched-Chain Fatty Acid α-Oxidation:
• Mostly brain and liver, cleaves 1C
• Substrate is phytanic acid
• Refsum disease: Disorder of peroxisome α-Oxidation → ↑ Phytanic acid
• Ascending polyneuropathy, scaly skin, cataracts, shortening of 4th toe, epiphyseal dysplasia
• Peroxisome Synthetic Processes:
• Cholesterol, bile salts, ethanol, amino acids, plasmalogens
• Zellweger syndrome: PEX mutation → ↓ Peroxisome biosynthesis
• ↓ Synthetic function and VLCFA oxidation
• Hypotonia, seizures, hepatomegaly
 AfraTafreeh.com
Biochemistry: Cell Biology Bootcamp.com

Ubiquitin-Proteasome System
• Overview:
• Proteasome degrades endogenous ubiquitinated proteins (specific)
• Misfolded proteins, cell cycle regulation, anti-apoptotic molecules (vs. lysosome for exogenous proteins)
• Ubiquitin:
• Regulatory protein tag added to proteins destined for proteasome, ATP-initiated
• Conjugation cascade by adding ubiquitin (Ub) to lysine residues
• E1: Activation, transfers Ub to E2 (one)
• E2: Conjugation, presents Ub to E3 (several)
• E3: Ligation, facilitates Ub attachment to target (many, specific)
• Process repeats → Poly-Ub chain; Mono-ubiquitination non-degradative
• Proteasome cleaves peptide bonds via ATP hydrolysis
• Ubiquitylation reversible by deubiquitylating enzymes (DUBs)
• Proteasome:
• 26S barrel-shaped catalytic enzyme complex in nucleus and cytoplasm
• Regulatory particles bind, cleave poly-Ub chain, denature target protein, feed to proteolytic core
• Disorders of Lewy Bodies (Parkinson & Lewy Body Dementia): ↓ Ub-proteasome activity → Neurodegeneration
• ↓ Parkin activity (E3) or ↑ DUB activity → ↑ α-synuclein protein → Lewy bodies
• Brainstem: Constipation, depression, fluctuating blood pressure
• Substantia Nigra: Motor symptoms (resting tremor, bradykinesia)
• Cortex: ↓ Memory and executive function
• Cell Cycle Regulation:
• Cyclin B + CDK1 → Entry into M phase
• Ub-mediated proteolysis of Cyclin B → Exit M phase
• Proteasome Inhibitors:
• Inhibition of proteolytic subunit → Cell degradation; Management of multiple myeloma and mantle cell lymphoma
• G2-M phase cell cycle arrest → Induction of apoptosis
• Accumulation of misfolded proteins, more frequent in cancer cells
 Biochemistry: Cell Biology Bootcamp.com

Cytoskeleton
• Overview:
• Cytosolic protein filament network for transport, stability, movement, cell division
• Actin:
• ~7 nm microfilaments in microvilli, stereocilia
• G-Actin monomers + ATP → F-Actin polymers → Double helix
• Migration, cytokinesis, muscle contraction (with myosin)
• Intermediate Filaments (IF):
• ~10 nm filaments for stability (no motor proteins), varying structure, cross-linked by plectin
• Cytokeratin (epithelial cells), vimentin (fibroblasts), desmin (muscle)
• Glial fibrillary acidic protein (glial cells), lamins (cell nucleus); IHC markers detect neoplasm origin
• Microtubules (MT):
•
AfraTafreeh.com
~25 nm filaments in cilia and flagella, mitotic spindle
• Associate with kinesin and dynein for cargo transport
• Dynein: Retrograde (+ → –), used by Clostridium tetani, herpes simplex, poliovirus, rabies
• Kinesin: Anterograde (– → +)
• MT inhibitors: Mebendazole, Griseofulvin, Colchicine, Vinca alkaloids, Taxanes
• ↓ MT polymerization or ↑ stability → Mitotic spindle failure → Neuropathy (Vincristine, Taxanes)

Accessory
Filament Function Size Structure
Proteins

Actin Muscle contraction, cytokinesis, migration Small Double helix Myosin

IF Stability Medium Varies Plectin

MT Movement, cell division Large Cylindrical Kinesin, Dynein

 AfraTafreeh.com
Biochemistry: Cell Biology Bootcamp.com

Primary Ciliary Dyskinesia

• Pathophysiology:
• Normal cilia structure: 9 doublet + 2 singlet microtubules (MTs), triplet centriole in basal body
• Axonemal dynein of MTs links doublets, allows bending
• Defect in dynein → Absent or dysmotile cilia → Dysfunctional ciliated epithelia
• Developmental abnormalities from poor migration
• Normal embryonic nodal cilia rotate in fixed direction → Thoracoabdominal laterality
• Autosomal recessive
• Presentation:
• Chronic productive cough, bronchiectasis; recurrent otitis, sinusitis, nasal polyps
• Failure of ciliary epithelium to clear debris
• Conductive hearing loss on Weber-Rinne test
• Infertility (immotile sperm, ectopic pregnancy)
• Displaced heart sounds (dextrocardia)
• Kartagener Syndrome: Situs inversus, recurrent sinusitis, bronchiectasis
• Diagnostics:
• Screening: ↓ Nasal nitric oxide
• Chest x-ray: Dextrocardia +/- tram-track opacities (bronchiectasis)
• Genetic tests for dynein arm mutations, abnormal cilia on electron microscopy
• Management:
• No cure, management is supportive, maintain airway health
 Biochemistry: Cell Biology Bootcamp.com

Sodium-Potassium Pump
• Overview:
• Active transport, ATP-powered: 3 Na+ out exchanged for 2 K+ into cell
• Generates concentration gradients
• Pump Mechanism:
• Cytoplasmic Na+ binds → ATP phosphorylates → Conformation change → Na+ release
• K+ binds → Dephosphorylation → Return to original conformation → K+ release → Na+ binds, repeat
• Applications:
• IV insulin to manage acute hyperkalemia
• Insulin phosphorylates Na+/K+ pump → ↑ Pump activity → Shift K+ into cells → ↓ Serum K+
• Establish resting membrane potential via leaky K+ channels
• Na+ pumped out, K+ pumped in → K+ leaks out down gradient → (-) Intracellular charge
• + AfraTafreeh.com
Na gradient allows cotransport/antiport of materials (e.g. kidney)
• Na+/glucose cotransport down Na+ gradient → Reabsorption of glucose from urine
• SGLT2 inhibitors: Block Na+/Glucose cotransport → ↓ Glucose reabsorption→ ↓ Blood sugar (Type II DM)
• Na /Ca2+ exchanger: 3 Na in, 1 Ca out; Na/K+ pump → ↓ [Na]i → Na+ enters cell along gradient → Ca2+ exchanged
+

• [Ca2+]i in cardiac myocytes controls inotropy

• Cardiac glycosides: Directly inhibit Na+/K+ pump → ↓ Na+/Ca2+ exchange → ↑[Ca]i → ↑ Inotropy
 AfraTafreeh.com
OUTLINE
1. Intro to Lysosomal Storage Diseases 5. Krabbe Disease
A. Overview of Lysosomal Storage Diseases A. Pathophysiology

Biochemistry:
B. Sphingolipidoses B. Presentation
C. Mucopolysaccharidoses C. Diagnostics
D. Approach to LSDs D. Management

Lysosomal
2. Tay-Sachs Disease E. Differential Diagnosis
A. Pathophysiology 6. Gaucher Disease
B. Presentation A. Pathophysiology

Storage Diseases
C. Diagnostics B. Presentation
D. Management C. Diagnostics
E. Differential Diagnosis D. Management
3. Fabry Disease E. Differential Diagnosis
A. Pathophysiology 7. Niemann-Pick Disease
B. Presentation A. Pathophysiology
C. Diagnostics B. Presentation
D. Management C. Diagnostics
E. Complications D. Management
F. Differential Diagnosis E. Differential Diagnosis
4. Metachromatic Leukodystrophy 8. Mucopolysaccharidoses
A. Pathophysiology A. Pathophysiology
B. Presentation B. Presentation
C. Diagnostics C. Diagnostics
D. Management D. Management
E. Differential Diagnosis E. Differential Diagnosis
9. Summary of LSDs
 Biochemistry: Lysosomal Storage Diseases Bootcamp.com

Intro to Lysosomal Storage Diseases

• Overview of Lysosomal Storage Diseases (LSDs):
• Healthy lysosome degrades cell debris
• Lysosomal enzyme deficiency → ↑ Abnormal metabolic products
• ↑ Ceramide derivative = Sphingolipidosis
• ↑ Mucopolysaccharide = Mucopolysaccharidosis
• Sphingolipidoses:
• Ceramide = Sphingosine + Fatty acid; Ceramide derivative = Ceramide + Head group
• From breakdown of cell membranes
• Lysosomal enzyme deficiency → ↑ Ceramide derivatives
• Galactocerebroside, sphingomyelin, glucocerebroside or precursors (ceramide trihexoside, GM2)
• Mucopolysaccharidoses:
•
AfraTafreeh.com
Mucopolysaccharides (glycosaminoglycans): Disaccharide repeats (Amino sugar + Uronic acid)n
• From breakdown of proteoglycans (ECM) and peptidoglycans (cell wall)
• Lysosomal enzyme deficiency → ↑ Mucopolysaccharides
• Heparan sulfate, dermatan sulfate, common uronic acid (L-iduronate)
• Approach to LSDs:
• Pathway interplay → Symptom overlap
• Vignettes similar, differential rule-out may be more helpful than rule-in
 AfraTafreeh.com
Biochemistry: Lysosomal Storage Diseases Bootcamp.com

Tay-Sachs Disease
• Pathophysiology:
• Healthy lysosome: GM2 ganglioside → Glucocerebroside, enzyme Hexosaminidase A
• ↓ Hexosaminidase A → ↑ GM2
• Gangliosides involved in nerve function → Progressive neurodegeneration
• Autosomal recessive, ↑ incidence in Ashkenazi Jews
• Presentation:
• Developmental delay, weakness, hypotonia in an infant
• Hyperreflexia, hyperacusis, vision/hearing loss, seizures, paralysis
• No hepatomegaly
• Diagnostics:
• Fundoscopy: Cherry-red macular spot
• Biopsy: Onion-skin lysosomes
• Management:
• Supportive care, death in childhood
• Differential Diagnosis:
• Niemann-Pick: Shares cherry spot, Ashkenazi Jewish ↑ incidence, progressive neurodegeneration. Hepatosplenomegaly, older child
• Krabbe: Shares age of onset, vision loss, developmental delay, weakness. No cherry spot, abnormal reflexes
• Metachromatic Leukodystrophy: Shares developmental delay, neurodegeneration, weakness. Ataxia, toddler
• Hurler: Shares age of onset, developmental delay. No weakness, no cherry spot, coarse facies, hepatosplenomegaly
 Biochemistry: Lysosomal Storage Diseases Bootcamp.com

Fabry Disease
• Pathophysiology:
• Healthy lysosome: Ceramide trihexoside (fibroblasts) → Glucocerebroside (cell membrane), enzyme α-galactosidase A
• ↓ α-Galactosidase A → ↑ Ceramide trihexoside
• Vessel endothelium, epithelium of many organs, dermal axons, smooth muscle → Multi-organ system involvement
• X-linked recessive
• Presentation:
• Triad of peripheral neuropathy/pain, hypohidrosis, angiokeratomas
• Corneal clouding, cataracts
• Older child/early adult
• Diagnostics:
• α-Galactosidase A enzyme activity
•
AfraTafreeh.com
Random X inactivation often → false (+) in men or (-) in women → Gene sequencing
• Management:
• Recombinant enzyme therapy, can live into adulthood
• Complications:
• Early TIA/stroke, progressive renal failure, cardiac complications
• Differential Diagnosis:
• Vasculitis, rheumatic disorders, fibromyalgia: Often initial misdiagnoses, not complete symptom triad
• Gaucher’s: Shares age of onset, treatment availability, lack of weakness. Hepatosplenomegaly, bone crises, no rash/hypohidrosis.
• Hurler Syndrome: Shares corneal clouding. Melanocytosis, coarse facial features, developmental delay
 AfraTafreeh.com
Biochemistry: Lysosomal Storage Diseases Bootcamp.com

Metachromatic Leukodystrophy
• Pathophysiology:
• Healthy lysosome: Sulfatides → Galactocerebroside, enzyme arylsulfatase A
• Sulfatides major component of myelin
• ↓ Arylsulfatase A → ↑ Cerebroside sulfate → Neurodegeneration
• Autosomal recessive
• Presentation:
• Weakness, hypotonia, and ataxia beginning ~2yo
• Memory impairment, speech problems, developmental delay, dementia
• Diagnostics:
• ↓ Arylsulfatase A activity, ↑ Cerebroside sulfate
• CNS and peripheral nerve demyelination
• Red-brown vacuoles in macrophage cytoplasm on Toluidine Blue (“metachromasia”)
• Management:
• Supportive, usually death in childhood
• Differential Diagnosis:
• Krabbe: Shares weakness, neuro symptoms only. Infant <6 mo, no ataxia. Globoid cells.
• Tay-Sachs: Shares developmental delay, neurodegeneration, weakness. Cherry spot, presents in infancy.
• Niemann-Pick: Shares weakness, motor symptoms. Hepatosplenomegaly, cherry-red spot
 Biochemistry: Lysosomal Storage Diseases Bootcamp.com

Krabbe Disease
• Pathophysiology:
• Healthy lysosome: Galactocerebroside → Ceramide, enzyme galactocerebrosidase
• Psychosine intermediate
• Galactocerebroside major component of myelin
• ↓ Galactocerebrosidase → ↑ Galactocerebroside, psychosine → Progressive neurodegeneration
• Demyelination of oligodendrocytes → CNS involvement
• Autosomal recessive
• Presentation:
• Neurologic symptoms only, infant
• Progressive weakness, developmental delay, peripheral neuropathy, unusual reflexes, optic atrophy, spontaneous fever
• Diagnostics:
• ↓ Galactocerebrosidase activity
AfraTafreeh.com
• Brain biopsy: Globoid cells (multinucleated, brain tissue, from toxic myelin breakdown)
• Management:
• Stem cell transplant before symptom onset, supportive management, death by age 2
• Differential Diagnosis:
• Metachromatic Leukodystrophy: Shares weakness, neuro symptoms only. ~2yo child, ataxia
• Tay-Sachs: Shares age of onset, vision loss, weakness, developmental delay. Cherry spot, hyperreflexia
 AfraTafreeh.com
Biochemistry: Lysosomal Storage Diseases Bootcamp.com

Gaucher Disease
• Pathophysiology:
• Healthy lysosome: Glucocerebroside → Ceramide, enzyme β-glucocerebrosidase
• ↓ β-Glucocerebrosidase → ↑ Glucocerebrosides in spleen, liver, bones
• Most common sphingolipidosis, ↑ incidence in Ashkenazi Jews, autosomal recessive
• Presentation:
• Hepatosplenomegaly, pancytopenia, bruising
• Osteoporosis, avascular necrosis of femur, bone crises with fever
• Type I most common, minimal CNS dysfunction, older child/young adult
• Diagnostics:
• ↓ Glucocerebrosidase activity, ↑ glucocerebrosides in leukocytes, fibroblasts
• Gaucher cells: Lipid-laden macrophages, “crumpled tissue paper”
• Management:
• Recombinant glucocerebrosidase, can live into adulthood
• Differential Diagnosis:
• Sickle Cell: Shares bone pain, hepatosplenomegaly. Abnormal hemoglobin electrophoresis
• Niemann-Pick: Shares Ashkenazi Jewish ↑ incidence, hepatosplenomegaly, bruising, lipid-laden macrophages.
• Neuro symptoms, cherry spot, foam cells
• Fabry: Shares age of onset, treatment availability, lack of weakness. Angiokeratomas, neuropathy, hypohidrosis
 Biochemistry: Lysosomal Storage Diseases Bootcamp.com

Niemann-Pick Disease
• Pathophysiology:
• Healthy lysosome: Sphingomyelin → Ceramide, enzyme sphingomyelinase
• ↓ Sphingomyelinase → ↑ Sphingomyelin
• Sphingomyelin in myelin → Progressive neurologic symptoms
• ↑ Incidence in Ashkenazi Jews, autosomal recessive
• Presentation:
• Older child, previously healthy, now ↓ motor ability, progressive neurodegeneration
• Hepatosplenomegaly, thrombocytopenia (bruising, bleeding)
• Diagnostics:
• Biopsy: Foam cells (lipid-laden macrophages)
• Fundoscopy: Cherry-red spot
• Management:
AfraTafreeh.com
• No cure, supportive therapy, severe forms → Death in childhood
• Differential Diagnosis:
• Gaucher: Shares Ashkenazi Jewish ↑ incidence, hepatosplenomegaly, bruising, lipid-laden macrophages
• No neuro symptoms, bone crises, no cherry spot
• Metachromatic Leukodystrophy: Shares weakness, age of onset. Ataxia, no hepatosplenomegaly, no cherry spot
• Tay-Sachs: Shares weakness, cherry spot, Ashkenazi Jewish ↑ incidence. No hepatosplenomegaly, presents in infants
 AfraTafreeh.com
Biochemistry: Lysosomal Storage Diseases Bootcamp.com

Mucopolysaccharidoses
• Pathophysiology:
• Mucopolysaccharide: Long chains of disaccharide repeats (amino sugar + uronic acid) from proteoglycans (cell wall)
• Healthy lysosome: Heparan sulfate (HS) and dermatan sulfate (DS) → Amino sugar + L-iduronate
• Iduronate-2-sulfatase and α-L-iduronidase enzymes facilitate
• Mucopolysaccharidosis: ↓ Enzyme activity → ↑ HS and DS
• Hurler syndrome: ↓ α-L-iduronidase; Hunter syndrome: ↓ Iduronate-2-sulfatase
• Hurler: Autosomal recessive; Hunter: X-linked recessive
• Presentation:
• Developmental delay, coarse facies, skeletal abnormalities, hepatosplenomegaly, airway obstruction, infections, melanocytosis
• Hunter milder
• Hurler: Corneal clouding, onset <1yo
• Hunter: Aggression, behavioral problems/hyperactivity, skin pebbling, carpal tunnel, onset 1-2yo
• Diagnostics:
• Dysostosis multiplex (Hurler): Enlarged skull, ribs, thickened diaphyses
• ↑ Urinary mucopolysaccharides (DS and HS), enzyme assay
• Management:
• Supportive care, enzyme replacement therapy, marrow transplant
• Differential Diagnosis:
• I-Cell disease: Shares coarse facies, hepatosplenomegaly. (Hurler shares age, corneal clouding, dysostosis multiplex)
• Urinalysis normal, many lysosomal enzymes ↑ in serum, cytoplasmic inclusions
Biochemistry: Lysosomal Storage Diseases Bootcamp.com

Summary of Lysosomal Storage Diseases

Disorder Enzyme Deficiency Accumulated Substance Vignette DDx

Tay-Sachs Hexosaminidase A GM2 Infant, cherry-red spot, Niemann-Pick

progressive neurodegeneration, onion-skin lysosomes

Fabry ɑ-Galactosidase A Ceramide trihexoside Child/early adult, peripheral neuropathy, Vasculitis, rheumatic
angiokeratomas, hypohidrosis disorders, fibromyalgia

Metachromatic Arylsulfatase A Cerebroside sulfate 2yo, Ataxia, ↓ memory, central/peripheral demyelination Krabbe
Leukodystrophy AfraTafreeh.com
Krabbe Galactocerebrosidase Galactocerebroside, Infant, ↓ oligodendrocytes, peripheral neuropathy, Metachromatic
psychosine optic atrophy, globoid cells Leukodystrophy

Gaucher β-Glucocerebrosidase Glucocerebroside Older child, hepatosplenomegaly, bone crises, femur Sickle Cell,
avascular necrosis, pancytopenia, Gaucher cells Niemann-Pick

Niemann-Pick Sphingomyelinase Sphingomyelin Older child, cherry-red spot, progressive Tay-Sachs

neurodegeneration, hepatosplenomegaly, foam cells

Hurler ɑ-L-iduronidase Heparan sulfate, Infant, corneal clouding, hepatosplenomegaly, coarse I-Cell
dermatan sulfate facies, developmental delay, airway obstruction

Hunter Iduronate-2-sulfatase 1-2yo, Mild Hurler, aggression, no corneal clouding Hurler

AfraTafreeh.com
AfraTafreeh.com
 AfraTafreeh.com

lation lated
AfraTafreeh.com
AfraTafreeh.com
AfraTafreeh.com
AfraTafreeh.com
 OUTLINE
1. Introduction to Energy Production 5. Electron Transport Chain
A. Purpose A. Overview

Biochemistry:
B. Production of Reducing Power B. Physiology
C. Sources of Acetyl-CoA C. Clinical Implications
2. Glycolysis 6. ATP Export and Phosphocreatine

Energy A. Overview A. Overview

B. Key Substrates B. ATP Export
C. Key Enzymes C. Phosphocreatine

Production D. Aerobic vs. Anaerobic Glycolysis D. Creatine Phosphokinase

3. Regulation of Phosphofructokinase E. Creatinine
A. Overview
B. Fructose-2,6-Bisphosphonate
C. Activation of Protein Kinase A
AfraTafreeh.com
D. Hormonal Regulation of Glycolysis
4. Pyruvate Dehydrogenase
A. Overview
B. Pyruvate Dehydrogenase Complex
C. Pyruvate Decarboxylase and Oxaloacetate
D. Pyruvate in the Liver
5. Tricarboxylic Acid Cycle
A. Purpose
B. Key Substrates
C. Key Enzymes
 AfraTafreeh.com
Biochemistry: Energy Production Bootcamp.com

Introduction to Energy Production

• Overview:
• Goal: Create energy in form of ATP
• ATP produced by electron transport chain (ETC)
• ETC requires fuel: Reducing power (electrons)
• Electron shuttles: NADH and FADH2
• Sources of reducing power, signal high-energy state
• Production of Reducing Power:
• Tricarboxylic acid (TCA) cycle main source of NADH, FADH2; Fuels ETC
• TCA cycle: Acetyl CoA → Reducing power
• Extra carbons → CO2, electrons → NAD+/FADH carriers
• NAD+ + 2e- → NADH
• FAD + 2e- → FADH2
• Sources of Acetyl CoA:
• Glucose (glycolysis): Breakdown of sugar
• Fatty acids (β-oxidation): Breakdown of free fats
• Ketone bodies (ketone metabolism): Breakdown of storage form of fats
• Introduction to Metabolism Map:
• ATP production linked to “reverse processes” for energy storage
• Substrate buildup → Shunting to other pathways
• “Road blocks” → “Detours” and “U-turns”
Biochemistry: Energy Production Bootcamp.com

AfraTafreeh.com
 AfraTafreeh.com
Biochemistry: Energy Production Bootcamp.com

Glycolysis
• Overview:
• Purpose: Glucose → Pyruvate + 2 ATP
• Pyruvate → Additional ATP (Tricarboxylic Acid (TCA) cycle), other fates
• Location: Cytoplasm
• Net reaction: Glucose + 2 Pi + 2 ADP + 2 NAD+ → 2 Pyruvate + 2 ATP + 2 NADH + 2 H+ + 2 H2O
• Key Substrates:
• G6P: Feeds into HMP shunt → Nucleotide synthesis, NADPH synthesis (oxidative stress)
• 1,3-BPG: Can be converted into 2,3-BPG, ↓ binding affinity of O2 (↓ O2 compensation)
• Phosphoenolpyruvate (PEP): Gluconeogenesis entry step (de novo glucose production), bypass irreversible PK
• Pyruvate: May be converted to lactate (anaerobic) or Acetyl CoA (aerobic)
• Key Enzymes:
• Hexokinase: ↑ Affinity (↓ Km) → Glucose sequestration, ↓ capacity, irreversible; Inhibited by glucose-6-phosphate (G6P)
• Glucokinase: Liver form of hexokinase, ↓ affinity (↑ Km), ↑ capacity; Insulin-induced, no inhibition by G6P
• No liver/brain competition when ↓ glucose
• Phosphofructokinase-1 (PFK1): Rate limiting step, irreversible, induced by AMP, F26BP, insulin; Inhibited by ATP, citrate
• Glyceraldehyde-3-phosphate dehydrogenase: NADH-producing step
• Phosphoglycerate kinase: ATP-producing step
• Pyruvate kinase (PK): ATP-producing step, irreversible, inhibited by ATP and alanine
• Pyruvate kinase deficiency: ↓ PK → ↓ ATP → ↓ Na+/K+ ATPase → RBC lysis (chronic hemolysis), ↑ Glycolytic intermediates
• Aerobic vs. Anaerobic Glycolysis:
• Aerobic: O2 → Functioning ETC → Favor TCA (↑ ATP)
• Anaerobic: No O2 → Electron transport chain (ETC) failure → Excess NADH → ↓ Tricarboxylic acid (TCA) cycle → Favor lactate
• Reversible: Cori cycle
• Sole energy source in erythrocytes
 Biochemistry: Energy Production Bootcamp.com

Regulation of Phosphofructokinase
• Overview:
• Glycolysis activated in the postprandial (fed) state → Glucose breakdown
• Insulin, glucagon regulate activity of rate-limiting step (PFK1) in liver
• Fructose-2,6-Bisphosphate (F26BP):
• Bifunctional regulatory enzyme, protein kinase A-mediated
• Dephosphorylation → ↑ Phosphofructokinase-2 (PFK2) → ↑ F26BP → ↑ PFK1 → ↑ Glycolysis
• Phosphorylation → ↑ Fructose-Bisphosphatase-2 (FBPase-2) active → ↓ F26BP → ↓ PFK1 activity → ↓ Glycolysis (↑ Gluconeogenesis)
• Feed-forward regulation: ↑ F6P → ↑ PFK2 → ↑ Fructose-2,6-bisphosphate → ↑ PFK1 activity
• Activation of Protein Kinase A
• cAMP pathway: GPCR αs → Adenylyl cyclase → ↑ cAMP → ↑ PKA activity → FBPase-2 phosphorylation → ↓ PFK1 → ↓ Glycolysis
• Hormonal Regulation of Glycolysis:
•
AfraTafreeh.com
Starving state: Glucagon signals ↓ glucose (↓ glycolysis needed)
• ↑ Glucagon → ↑ cAMP pathway → FBPase phosphorylation → ↓ PFK1 activity
• Fed state: Insulin signals ↑ glucose (↑ glycolysis needed)
• ↑ Insulin → ↓ cAMP pathway → ↓ Protein kinase A → Dephosphorylated PFK2 → ↑ PFK1 activity
 AfraTafreeh.com
Biochemistry: Energy Production Bootcamp.com

Pyruvate Dehydrogenase Complex

• Overview:
• Fates of pyruvate: Acetyl-CoA, oxaloacetate (OAA), lactate, alanine
• Pyruvate → Acetyl-CoA in aerobic respiration, enzyme pyruvate dehydrogenase (PDH)
• Pyruvate Dehydrogenase Complex:
• PDH: 3-Enzyme complex, 5 required cofactors (B1, B2, B3, B5, lipoic acid)
• E1 Pyruvate dehydrogenase: Pyruvate → CO2
• E2 Dihydrolipoyl transacetylase (DLAT): CoA-SH → Acetyl-CoA
• E3 Dihydrolipoyl dehydrogenase (DLD): NAD+ → NADH
• Activation by PDH phosphatase; Deactivation by PDH kinase
• Activation: ↑ Glucose, ↑ Insulin
• Inhibition: ↓ Glucose, Acetyl-CoA
• Similarities to α-Ketoglutarate dehydrogenase (TCA cycle): Same cofactors, similar substrate structure, add CoA
• Arsenic Poisoning: ↓ Lipoic acid → ↓ PDH
• Vomiting, “rice water” stools, garlic breath
• Pyruvate Carboxylase and Oxaloacetate:
• OAA + Acetyl-CoA → Start TCA cycle
• ↓ TCA cycle intermediates (other uses) → ↓ OAA → ↓ TCA activity
• Pyruvate carboxylase → ↑ OAA → ↑ TCA activity
• Pyruvate in the Liver:
• Pyruvate ↔ Lactate via lactate dehydrogenase (LDH): Cori Cycle
• Anaerobic glycolysis (e.g. RBCs)
• Pyruvate ↔ Alanine via alanine transaminase (ALT): Cahill Cycle
• Muscle amino groups → Liver
• PDH Deficiency: ↓ PDH → ↑ Pyruvate → Shunting to lactate and alanine
• Lactic acidosis, neurologic defects, ↑ serum alanine in early childhood
• Management: ↑ Ketogenic amino acid intake (lysine, leucine) → Fuel TCA
 Biochemistry: Energy Production Bootcamp.com

Tricarboxylic Acid (TCA) Cycle

• Purpose:
• Create reducing power to fuel electron transport chain (ETC)
• NADH, FADH2 loaded electron carriers
• Location: Mitochondrial matrix
• Other names: Krebs Cycle, Citric Acid Cycle
• Net equation: Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi → 2CO2 + CoA + 3 NADH + FADH2 + GTP
• Regulated by energy status
• Key Substrates:
• Oxaloacetate (OAA) and Acetyl-CoA availability drive TCA cycle
• Acetyl-CoA from glucose, fatty acids, ketones; OAA recycled, pyruvate carboxylase replenishes
• Fumarate: From amino acid breakdown (urea cycle, tyrosine catabolism)
•
AfraTafreeh.com
Succinyl-CoA: Heme synthesis; Made from methylmalonyl CoA via cobalamin (B12)
• Malate: Gluconeogenesis (de novo glucose production)
• Ketoacidosis: Prolonged fasting → ↑ Gluconeogenesis → ↓ OAA → Acetyl-CoA shunts to ketogenesis
• Key Enzymes:
• Irreversible reactions = Important regulatory steps
• Citrate synthase: Combine Acetyl-CoA and OAA, begin cycle (ATP inhibits)
• Isocitrate dehydrogenase: NADH-producing step (ATP and NADH inhibit, ADP and calcium stimulate)
• α-Ketoglutarate dehydrogenase: NADH-producing step (ATP, NADH, Succinyl-CoA inhibit)
• Alcohol consumption: ↑ NADH/NAD+ ratio → ↓ Regulatory enzyme activity → ↑ Acetyl-CoA → Alcoholic
ketoacidosis
• Cofactors: B1, B2, B3, B5, lipoic acid (like pyruvate dehydrogenase complex)
• Wernicke encephalopathy: B1 deficiency → Ataxia, confusion, ophthalmoplegia
• Succinate dehydrogenase (reversible): Also in ETC
 AfraTafreeh.com
Biochemistry: Energy Production Bootcamp.com

Electron Transport Chain

• Overview:
• Purpose: Create ATP via electrochemical H+ gradient (inner mitochondrial membrane)
• Reducing power (electrons: NADH, FADH2) → Redox reaction chain (“oxidative phosphorylation”) → H+ gradient
• Physiology:
• Electrons passed across series of complexes (I-IV) to O2
• Electrons from NADH → Passed along chain
• NADH from glycolysis: Transferred into matrix (malate-aspartate or glycerol-3-phosphate shuttles)
• NADH from TCA cycle and pyruvate dehydrogenase complex: Already in matrix
• Electrons from FADH2 → CoQ “priming” by Complex II
• Produced from succinate dehydrogenase (TCA cycle), already in matrix
• NAD+, FADH recycled to TCA cycle
• Electron carriers: Reduced coenzyme Q (aka ubiquinol, CoQ) → Cytochrome c → O2 (aerobic conditions required)
• Facilitators: Complexes I, III, IV (H+ pumps), Complex II (CoQ “primer”)
• Complex I: NADH dehydrogenase; Complex III: CoQ-Cyt c reductase; Complex IV: Cyt c oxidase
• Complex II: Succinate dehydrogenase
• Electron passing across H+ pumps → H+ gradient in intermembrane space
• ATP synthase (Complex V): H+ flow through (restores membrane H+ equilibrium) → ATP synthesis
• Clinical Implications:
• Cyanide (CN): Binds complex IV → ↓ ETC → ↑ NADH → ↓ TCA cycle → Lactic acidemia
• Flushing → Cyanosis, “bitter almond” breath, tachypnea, tachycardia, headaches, seizures, metabolic acidosis
• Carbon monoxide (CO): Binds complex IV and hemoglobin → ↓ ETC (↓ Complex IV and ↓ O2)
• “Cherry-red” lips/skin, headache, dizziness, nausea, tachypnea, tachycardia
• ATP synthase uncouplers:
• Brown fat: Uncouples ATP synthase from H+ gradient → Energy “wasted” as heat (nonshivering thermogenesis)
• Salicylic acid: Uncoupling (high doses)
 Biochemistry: Energy Production Bootcamp.com

ATP Export and Phosphocreatine

• Overview:
• ATP made in mitochondria (oxidative phosphorylation), used in periphery
• Phosphocreatine (PCr): Creatine + Phosphate (from ATP) = “Storage” ATP
• PCr mobilized for exercise
• ATP Export:
• ATP export by adenine nucleotide translocator (ATP/ADP translocation)
• Phosphocreatine:
• ↑ ATP → ↓ TCA cycle (negative feedback)
• Creatine (Cr): Phosphate carrier, energy storage without ↓ TCA
• Derived from arginine, non-essential
• Cr + ATP ↔ PCr + ADP; Enzyme creatine phosphokinase (CPK)
•
AfraTafreeh.com
Forward reaction at rest, reverse during exercise (mobilize ATP)
• Creatine supplementation: ↑ Cr → ↑ PCr → ↑ Exercise performance (ATP availability)
• Creatine Phosphokinase (CPK):
• Skeletal muscle, brain, heart
• Serum CPK: Measure muscle disease course
• Creatinine:
• Cr spontaneous cyclization → Creatinine → Excreted by kidney
• All filtered creatinine excreted → Estimate kidney function
• Some secretion by tubules → Slight overestimate of GFR
 AfraTafreeh.com
OUTLINE
1. Gluconeogenesis
A. Overview

Biochemistry:
B. Pathway
C. Starting Substrates
2. Malate-Aspartate Shuttle

Carbohydrates A. Overview
B. Fasting State
C. Fed State
3. Fructose Metabolism
A. Overview
B. Pathway
C. Clinical Relevance of Enzyme Deficiencies
D. Fructose, Hyperuricemia, and Gout
4. Sorbitol and the Polyol Pathway
A. Overview
B. Pathway
C. Clinical Implications
5. Galactose Metabolism
A. Overview
B. Pathway
C. Clinical Implications
Biochemistry: Carbohydrates Bootcamp.com

AfraTafreeh.com
 AfraTafreeh.com
Biochemistry: Carbohydrates Bootcamp.com

Gluconeogenesis
• Overview:
• Purpose: De novo glucose production
• Location: Liver, kidneys, enterocytes (no G6Pase in skeletal muscle)
• Pathway:
• Reversible reactions of glycolysis, bypass irreversible steps
• Pyruvate → Oxaloacetate (OAA) via pyruvate carboxylase (PC) in mitochondria
• Requires ATP and B7; Stimulated by acetyl CoA, inhibited by ADP
• Malate-Aspartate Shuttle: No OAA transporters in mitochondrial membrane → Convert to malate for passage
• OAA → Malate → Export from mitochondria → Revert to OAA
• OAA → Phosphoenolpyruvate (PEP) via PEPCK in cytosol and mitochondria
• Requires GTP; ↑ By glucagon, cortisol, epinephrine, thyroid hormone (signal ↑ glucose need); ↓ By insulin, AMP
• Bypass irreversible pyruvate kinase glycolytic reaction, merge for reverse reactions
• Fructose-1,6-Bisphosphatase (FBPase) in cytoplasm: ↑ by ATP and citrate, ↓ by AMP and F26BP
• FBPase-2: Glycolysis/gluconeogenesis regulatory switch
• Glucagon → ↑ FBPase-2 → ↑ Gluconeogenesis
• Glucose-6-phosphate → Glucose via Glucose-6-phosphatase (G6Pase) in ER of hepatocytes; Inhibited by insulin
• Von Gierke Disease: ↓ G6Pase → Hypoglycemia, hepatomegaly, lactic acidosis, hyperlipidemia, hyperuricemia
• Starting Substrates:
• Glycerol: Glycerol → DHAP via Glycerol-3-Phosphate shuttle in fatty acid metabolism
• Lactate: Lactate → Pyruvate via lactate dehydrogenase, requires NAD+
• Alanine: Alanine → Pyruvate via alanine aminotransferase, requires B6 (Cahill cycle)
• Propionyl-CoA: Odd-chain fatty acids, isoleucine, valine → Propionyl-CoA → TCA cycle → Malate
• Glucogenic amino acids: Metabolized into pyruvate, TCA intermediates (Succinyl-CoA, α-Ketoglutarate, Fumarate, OAA)
• Most AAs glucogenic except Leu and Lys (ketogenic)
 Biochemistry: Carbohydrates Bootcamp.com

Malate-Aspartate Shuttle Fasting state

• Overview:
• No NADH or oxaloacetate (OAA) transporters in inner mitochondrial membrane
• Malate ↔ OAA oxidation-reduction reaction coupled with NAD+ ↔ NADH
• Purpose: Leverage redox reactions, transfer OAA and NADH across membrane
• Bidirectional, regulated by energy state
• Synthesis of aspartate
• Location: Cardiac muscle, liver
• Fasting State:
• Favors gluconeogenesis: Move OAA from TCA cycle (mitochondria) → Cytoplasm
• OAA → Malate via malate dehydrogenase (MDH) → Malate export to cytoplasm
• NADH → NAD+ in mitochondria
•
AfraTafreeh.com
Malate → OAA via MDH in cytoplasm; OAA → PEP via PEPCK for gluconeogenesis; NAD+ →
NADH
• OAA also → Asp via aspartate aminotransferase (AST), Asp → Mitochondria → Re-form OAA Fed state
• AST: Glutamate formation in liver → NH3 carrier for urea cycle, liver function test
• Fed State:
• Favors oxidative phosphorylation: Move NADH from glycolysis (cytoplasm) → Mitochondria
• OAA in cytoplasm → Malate via MDH; NADH → NAD+, 2e- loaded onto malate
• Malate → Mitochondria; MDH re-forms OAA, 2e- reduce NAD+ → NADH
• NADH → Complex I in electron transport chain
• Form α-Ketoglutarate in mitochondria (TCA intermediate); Asp → Cytoplasm
 AfraTafreeh.com
Biochemistry: Carbohydrates Bootcamp.com

Fructose Metabolism
• Overview:
• Fructose consumed as simple sugar or in sucrose disaccharide
• Purpose: Convert fructose into usable form for glycolysis
• Location: Liver, Kidneys
• Pathway:
• Sucrose → Glucose + Fructose via sucrase (intestinal brush border)
• Fructose → Enterocytes via GLUT5 → Bloodstream via GLUT2 → Liver, kidneys
• Fructose → Fructose-1-Phosphate (F1P) via fructokinase, ATP investment
• Minor hexokinase activity (low affinity) → F6P alternate product
• F1P → DHAP + Glyceraldehyde via aldolase B
• DHAP glycolytic intermediate
• Glyceraldehyde → G3P (glycolytic intermediate) via triokinase, ATP investment
• Clinical Relevance of Enzyme Deficiencies:
• Fructosuria: Fructokinase deficiency, benign (not aldose → No osmotic pathology)
• Hereditary fructose intolerance: Aldolase B deficiency
• Phosphate sink (ATP investment without payout) → More severe than fructosuria
• Fructosuria, hypoglycemia, hyperbilirubinemia, hyperuricemia
• Fructose, Hyperuricemia, and Gout:
• Fructokinase very fast, no negative feedback, ↑ ADP
• Aldolase B naturally slow → F1P and ADP buildup
• ↑↑ Fructose consumption → ↑ ADP (sink) → ↑ AMP → ↑ AMP deaminase → ↑ Uric acid
• Slow (physiologic) or absent (hereditary) aldolase B → Hyperuricemia → Gout
 Biochemistry: Carbohydrates Bootcamp.com

Sorbitol and the Polyol Pathway

• Overview:
• Chronic hyperglycemia → Hexokinase saturation (glycolysis)
• Polyol pathway: Glucose → Sorbitol → Fructose; Trap glucose in cell, bypass hexokinase
• Differential enzyme expression in tissues → Osmotic effects
• Pathway:
• Glucose → Sorbitol via aldose reductase (AR), NADPH oxidized
• AR present in most tissues
• Sorbitol osmotically active; Sorbitol → Fructose via sorbitol dehydrogenase (SDH), NAD+ reduced
• Fructose → Glycolytic intermediates
• SDH low/absent in lens, retina, kidneys, Schwann cells; SDH present in liver, ovaries, seminal vesicles
• Galactose also an aldose → Glucitol via aldose reductase (osmotically active)
• Clinical Implications:
AfraTafreeh.com
• Diabetes Mellitus: AR in tissues without SDH → Sorbitol accumulation → Osmotic damage
• Lens → Cataracts
• Retina → Retinopathy
• Kidneys → Nephropathy
• Schwann Cells → Peripheral neuropathy
• ↑ AR → ↓ NADPH → ↓ Reduced glutathione → ↑ Reactive oxygen species → Oxidative damage
• Male infertility testing: Seminal vesicles contain SDH; Semen fructose levels measure seminal vesicle function, predict sperm lifespan
 AfraTafreeh.com
Biochemistry: Carbohydrates Bootcamp.com

Galactose Metabolism
• Overview:
• Galactose component of lactose disaccharide
• Purpose: Convert galactose → Intermediates in glycolysis and glycogen pathways
• Location: Liver
• Pathway:
• Lactose → Glucose + Galactose via lactase (small intestine)
• Galactose → Enterocytes via SGLT1 → Bloodstream via GLUT2 → Liver
• Galactose → Galactose-1-phosphate via galactokinase (requires ATP as source of Pi)
• Galactose-1-P + UDP-glucose → UDP-galactose + Glucose-1-P via Galactose-1-phosphate uridyltransferase (GALT)
• UDP-galactose → UDP-glucose via UDP-galactose 4-epimerase
• Glucose-1-P → Glucose-6-P via phosphoglucomutase → Glycolysis
• Galactose substrate for aldose reductase; ↑ Galactose → Galactitol (osmotically active, not substrate of sorbitol dehydrogenase)
• Clinical Implications:
• Classic galactosemia: ↓ GALT → ↑ Gal-1-P (toxic) and galactose → ↑ Galactitol → Osmotic and free radical damage (↓ NADPH)
• Common, autosomal recessive; May be normal at birth; Milk → Jaundice, lethargy, convulsions
• Cataracts, hepatomegaly, galactosemia/galactosuria, intellectual disability
• Management: Stop breastfeeding/milk-based formula (lifelong galactose/lactose restriction)
• Galactokinase deficiency: ↓ Galactokinase → ↑ Galactose → ↑ Galactitol → Osmotic and free radical damage (↓ NADPH)
• Rare, autosomal recessive; Milder than classic galactosemia (no ↑ toxic Gal-1-P)
• Cataracts, ↓ eye-tracking, no social smile, galactosemia/galactosuria; No damage to liver/kidney/brain
• Management: Similar to classic galactosemia
 OUTLINE
1. Absorption of Folic Acid
A. Overview

Biochemistry:
B. Pathway
2. Sources and Uses of One-Carbon Groups
A. Overview

One-Carbon 3.
B. Sources of 1C Groups
C. Uses of 1C Groups
The Activated Methyl Group Cycle

Metabolism A. Overview
B. Activated Methyl Group Cycle
C. Clinical Implications
4. Homocysteine Metabolism
A. Overview
AfraTafreeh.com
B. Transsulfuration Pathway
C. Methionine Oxidation Pathway
D. Clinical Implications
5. Homocystinuria
A. Overview
B. Pathophysiology
C. Presentation
D. Diagnostics
E. Differential Diagnosis
F. Management
 AfraTafreeh.com
Biochemistry: One-Carbon Metabolism Bootcamp.com
 Biochemistry: One-Carbon Metabolism Bootcamp.com

Absorption of Folic Acid

• Overview:
• Dietary folic acid (B9) → Tetrahydrofolate (THF), carrier of one carbon groups
• Purine and pyrimidine synthesis
• Activated methyl group cycle → Catecholamine and creatine synthesis, methylation reactions (DNA, RNA, Lys, Arg)
• Folates stored in liver/kidneys; 3-4 month reserve (Short → Deficiency common)
• Pathway:
• Folate absorption → Duodenal/jejunal enterocytes via proton-coupled folate transporter (PCFT)
• Hereditary folate deficiency: PCFT dysfunction → Megaloblastic anemia, seizures
• Folic acid → Dihydrofolate (DHF) → THF via DHF reductase
• Methotrexate (DMARD): Inhibits DHF reductase → Folates trapped as DHF
• THF → N5N10-methylene-THF (methylation) → N5-methyl-THF (reduced, “active” form) via MTHFR → Bloodstream (bound or free)
•
AfraTafreeh.com
Bound to albumin, soluble receptor, or free
• Peripheral cell uptake (mechanism varies) → Release of 1C into activated methyl-group cycle, liberation of THF
• Polyglutamation of THF via THF synthase → THF trapping in cell
 AfraTafreeh.com
Biochemistry: One-Carbon Metabolism Bootcamp.com

Sources and Uses of One-Carbon Groups

• Overview:
• One-carbon (1C) groups: Source → Carried by tetrahydrofolate (THF) from dietary folic acid → Acceptors
• Sources of 1C Groups:
• Pool of interchangeable THF: N5N10-methylene-THF ↔ N5N10-methenyl-THF ↔ N10-Formyl-THF
• Serine (→ glycine) → N5N10-methylene-THF; Major supplier, serine created de novo from 3PG (glycolytic intermediate)
• Leucovorin and histidine → N5N10-methenyl-THF
• Leucovorin rescue: Methotrexate ↓ DHF reductase (DHFR); Leucovorin ↓ toxicity, provides DHFR-independent folate source
• Formate → N10-Formyl-THF
• Uses of 1C Groups:
• Methanol detoxification (ocular toxicity)
• Methanol → Formaldehyde via alcohol dehydrogenase (ADH), Formaldehyde → Formate via aldehyde dehydrogenase (enzymes ↑ NADH)
• Formate + THF → N10-formyl-THF → CO2 + THF
• Leucovorin for methanol overdose + Fomepizole (ADH inhibitor) or ethanol (↑ ADH affinity)
• Transfer to the activated methyl group cycle (↑ Reactivity → Anabolic pathways)
• Synthesis of creatine, choline, epinephrine
• DNA methylation (inactivation): Parental gene silencing, X inactivation, variable gene expression
• 5’ Methyl-guanosine caps in mRNA (post-transcriptional modifications)
• Protein methylation (Lys or Arg side chains): Histones
 Biochemistry: One-Carbon Metabolism Bootcamp.com

The Activated Methyl Group Cycle

• Overview:
• Formation of S-adenosylmethionine (SAM) → ↑ Methyl group reactivity → DNA/RNA/protein methylation, creatine/epinephrine/choline synthesis
• Overall importance in anabolic pathways
• Activated Methyl Group Cycle:
• N5,N10-methylene-THF (methylated THF) → N5-methyl-THF (reduced, “active”) via methylene THF reductase (MTHFR)
• MTHFR inhibited by SAM
• 1C from N5-methyl-THF + Homocysteine → Methionine via methionine synthase (B12 cofactor)
• Methionine + Adenosine from ATP → SAM
• 1C from SAM → Acceptor via methyl transferases → S-adenosyl homocysteine → Adenosine and homocysteine
• Clinical Implications:
• Creatine formation: Methyl group from SAM + Guanidinoacetate → Creatine (major use of SAM)
•
AfraTafreeh.com
Creatine + ATP ↔ Phosphocreatine + ADP for immediately available energy in muscle
• Phosphatidylcholine formation (membrane lipid): 3x methylation of phosphatidylethanolamine by SAM
• Epinephrine formation: Norepinephrine → Epinephrine via methylation from SAM
• DNA, RNA, protein methylation
• Folate (B9) deficiency: ↓ THF → ↓ Thymine nucleotide synthesis and DNA replication → Megaloblastic anemia
• Cobalamin (B12) deficiency: ↓ B12 → ↓ Methionine synthase → ↓ SAM → ↓ Inhibition of MTHFR → ↑ N5-methyl-THF (folate trap)
• “Secondary folate deficiency”
 AfraTafreeh.com
Biochemistry: One-Carbon Metabolism Bootcamp.com

Homocysteine Metabolism
• Overview:
• Homocysteine → Cysteine in liver (Transsulfuration pathway)
• Homocysteine → TCA cycle (Methionine oxidation pathway)
• Many B vitamin cofactors in both pathways
• Transsulfuration Pathway:
• Homocysteine → Cystathionine via cystathionine β-synthase (B6 cofactor)
• Cystathionine required for brain function
• Cystathionine → Cysteine via cystathionine γ-lyase (B6 cofactor)
• Cysteine involved in metabolism of sulfur-containing compounds, synthesis of glutathione (antioxidant)
• Methionine Oxidation Pathway:
• Methionine → Propionyl-CoA; Propionyl-CoA also intermediate for valine, threonine, isoleucine, odd-chain fatty acids
• Propionyl-CoA → Methylmalonyl-CoA via propionyl-CoA carboxylase (B7 cofactor)
• Methylmalonyl-CoA → Succinyl-CoA via methylmalonyl-CoA mutase (B12 cofactor)
• Clinical Implications:
• Lab testing for folate (B9) and cobalamin (B12) deficiency
• Both: ↑ Homocysteine (↓ Folate → ↓ N5-methyl-THF; ↓ Cobalamin → ↓ Methionine synthase activity)
• B12 deficiency alone: ↑ Methylmalonic acid (↓ Methylmalonyl-CoA mutase activity)
• Classic Homocystinuria: ↓ Cystathionine β-synthase → ↑ Homocysteine, intellectual disability, thromboembolism, lens subluxation
• ↑ Blood methionine, SAM, S-adenosylhomocysteine, sarcosine (N-methylglycine)
 Biochemistry: One-Carbon Metabolism Bootcamp.com

Homocystinuria
• Overview:
• Homocysteine first methyl acceptor in activated methyl group cycle
• Homocysteine → Cysteine in liver for breakdown, use in glutathione synthesis (transsulfuration pathway)
• ↓ Enzymes in activated methyl group cycle or transsulfuration pathway → ↑ Homocysteine (all etiologies autosomal recessive)
• Pathophysiology:
• Classic Homocystinuria: ↓ Cystathionine β-synthase (CBS) → ↑ Homocysteine
• ↓ Affinity of CBS to pyridoxine (B6) → ↓ CBS activity → ↑ Homocysteine
• ↓ Methionine synthase → ↑ Homocysteine
• ↓ MTHFR → ↓ N5-methyl-THF → ↓ Methylation of homocysteine into methionine → ↑ Homocysteine
• ↑ Homocysteine toxic, causes ↓ elastin cross-linking (poorly understood)
• Presentation:
•
AfraTafreeh.com
Failure to thrive, developmental delay, progressive intellectual disability, osteoporosis, megaloblastic anemia
• Marfanoid habitus: Craniofacial features, hand/wrist sign (arachnodactyly), spinal deformities, hyperextensibility, pectus excavatum/carinatum
• Ectopia lentis: Lens subluxation downward and inward
• Cardiac complications: Thromboembolism, arteriosclerosis, coronary artery disease → MI, stroke
• Diagnostics:
• ↑ Homocysteine in urine and serum; Varied serum methionine (↑ in CBS deficiency, ↓ in methionine synthase and MTHFR deficiency)
• Urine sodium nitroprusside test: Orange when ↑ homocysteine
• Differential Diagnosis:
• Marfan Syndrome: FBN1 mutation → Defective fibrillin → ↓ Elastin cross-linking; No intellectual disability, aortic dissection, lenses up and out
• MEN2B: RET gene mutation → Medullary thyroid cancer, multiple neuromas, pheochromocytoma
• Management:
• Betaine (trimethylglycine): Methyl donor for remethylation of homocysteine to methionine (non-B12 dependent)
• Can measure efficacy with sarcosine (methylated glycine acceptor)
• ↓ CBS: ↓ Methionine, ↑ Cysteine, ↑ B6/B9/B12 (↑↑ Cysteine and B6 if ↓ B6 affinity)
• ↓ Methionine synthase: ↑ Methionine
• ↓ MTHFR: ↑ B9
 AfraTafreeh.com
OUTLINE
1. Pentose Phosphate Pathway
A. Overview

Biochemistry:
B. Oxidative (Irreversible) Reactions
C. Nonoxidative (Reversible) Reactions
D. Uses of NADPH

Oxidative Stress
E. Clinical Implications
2. Oxidative Burst
A. Overview
B. Phagolysosome Pathway
C. Neutralization Pathway
D. Clinical Implications
3. Ethanol Metabolism
A. Overview
B. Cytosolic Pathway
C. Endoplasmic Reticulum Pathway
D. Common Pathway
E. Clinical Implications
Biochemistry: Oxidative Stress Bootcamp.com

AfraTafreeh.com
 AfraTafreeh.com
Biochemistry: Oxidative Stress Bootcamp.com

Pentose Phosphate Pathway (PPP)

• Overview:
• Hexose monophosphate (HMP) shunt
• Purpose: Generate NADPH (anabolic reactions, oxidative stress) and ribose-5-phosphate (nucleotide synthesis)
• No ATP used/produced; Occurs in cytosol
• Oxidative (Irreversible) Reactions:
• Glucose → Glucose-6-Phosphate (G6P) via hexokinase (first step of glycolysis)
• G6P → 6-Phosphogluconolactone via G6P dehydrogenase (G6PD), rate-determining; NADP+ → NADPH + H+
• Favored when ↑ G6P
• 6-Phosphogluconolactone → 6-Phosphogluconate via 6-phosphogluconolactonase, requires 1 H2O
• 6-Phosphogluconate → Ribulose-5-phosphate via 6-phosphogluconate dehydrogenase; NADP+ → NADPH + H+, CO2 released
• Nonoxidative (Reversible) Reactions:
• Ribulose-5-P ↔ Ribose-5-P via phosphopentose isomerase
• Ribose-5-P ↔ Fructose-6-P and glyceraldehyde-3-P (glycolysis) via transketolase (requires B1)
• Ribose-5-P also starting substrate for nucleotide synthesis
• Uses of NADPH
• Glutathione reduction inside RBCs: Reduced glutathione detoxifies free radicals
• GSSG (oxidized) + NADPH → 2GSH (reduced) + NADP+ via glutathione reductase
• 2GSH + H2O2 → GSSG + 2 H2O via glutathione peroxidase
• Cholesterol synthesis: HMG CoA → Mevalonate via HMG-CoA reductase requires NADPH (rate limiting step of cholesterol biosynthesis)
• Fatty acid (FA) synthesis: Malonyl-CoA → 2C addition on FA chain via FA synthase requires NADPH reducing agent
• Cytochrome P450: Cyp450 reductase requires NADPH as original e- source
• Respiratory (oxidative) burst: Creation of ROS inside phagocytes to kill bacteria, subsequent neutralization to spare phagocyte
• Clinical Implications:
• G6PD Deficiency: ↓ G6PD → ↓ NADPH → ↓ Glutathione reduction → ↓ Free radical protection → Hemolytic anemia when ↑ ROS
 Biochemistry: Oxidative Stress Bootcamp.com

Respiratory (Oxidative) Burst

• Overview:
• Purpose: Create reactive oxygen species (ROS) within phagocyte for immune response → Neutralize to prevent self-damage
• NADPH (pentose phosphate pathway) required for both ROS creation and neutralization
• Phagolysosome Pathway:
• O2 → Superoxide (O2-•) via NADPH oxidase, requires NADPH
• Superoxide → Peroxide (H2O2) via superoxide dismutase
• H2O2 → Hypochlorite (HOCl•) via myeloperoxidase (Contains heme, blue-green pigmented → Sputum color), requires Cl-
• Invading bacteria also generate H2O2 → Enter pathway here
• Catalase (+) organisms: Bacterial catalase neutralizes H2O2 → H2O + O2
• HOCl• bleach kills bacteria → ↑ Lysosomal enzyme release; Excess H2O2 neutralized by phagocyte
• Neutralization Pathway:
•
AfraTafreeh.com
H2O2 + Reduced glutathione (GSH) → H2O + Oxidized glutathione (GSSG)
• GSSG → Replenished GSH by NADPH; NADPH formed in PPP by G6PD step
• G6PD Deficiency → ↓ Neutralization of ROS
• Clinical Implications:
• Chronic Granulomatous Disease (CGD): ↓ NADPH oxidase → Only use bacterial H2O2 (No oxidative burst)
• Catalase (+) organisms self-neutralize H2O2 → Not usable by phagolysosome → ↑ Infection risk
• ↑ Pyogenic infections (S. aureus, E. coli, Pseudomonas, Serratia, Klebsiella, Nocardia, Candida, Aspergillus)
• (-) Nitroblue tetrazolium test (NADPH oxidase reduces colorless dye → Black)
• Pyocyanin (P. aeruginosa virulence factor): Blue-green, generates ROS (Cytotoxic, competitive advantage)
• Utilizes NADPH → ↑ O2-• and H2O2 → ↑ GSSG
• Directly oxidizes GSH → GSSG
 AfraTafreeh.com
Biochemistry: Oxidative Stress Bootcamp.com

Ethanol Metabolism
• Overview:
• Purpose: Eliminate toxic EtOH
• Standard (cytosolic) pathway and overflow (endoplasmic reticulum) pathways
• Cytosolic Pathway:
• Major (90%) pathway in ↓ EtOH consumers
• Ethanol → Acetaldehyde via alcohol dehydrogenase (ADH), requires NAD+ → NADH
• Zero-order elimination kinetics
• NADH → Mitochondria via malate-aspartate shuttle
• Acetaldehyde forms DNA adducts → Carcinogenic; Vasodilation → Facial flushing, nausea
• Endoplasmic Reticulum Microsome Pathway:
• Minor (10%) pathway in ↓ EtOH consumers, ↑↑ in alcohol use disorder
• Ethanol → Acetaldehyde via CYP2E1 (CyP450 isoform)
• NADPH 2e- from NADPH-CyP450 reductase in ER membrane
• ↑ Km (↓ Affinity) for EtOH vs. ADH → ↑ Activity in chronic ↑ BAC
• ↑ CYP2E1 alters drug metabolism; ↑ CYP2E1 → ↑ Acetaminophen metabolism to NAPQI → ↓ Reduced glutathione
• Formation of superoxide → ROS, oxidative stress
• Common Pathway:
• Acetaldehyde → Acetate via Aldehyde dehydrogenase (ALDH), NAD+ → NADH; Acetate → Blood
• Clinical Implications:
• ↑ EtOH → ↑ Cytoplasmic NADH:NAD+
• ↓ Lactate to pyruvate → Lactic acidosis
• ↓ TCA cycle activity + ↑ Acetate conversion to acetyl-CoA → Alcoholic ketoacidosis, ↑ AMP
• ↑ AMP + ↑ NADH:NAD+ → ↓ Gluconeogenesis (malate-aspartate shuttle “fed state” → ↑ Cytoplasm OAA to malate) → Hypoglycemia
• ↑ Acetyl-CoA shunting to fatty acid synthesis + ↑ Conversion of DHAP to G3P → ↑ Triglycerides → Hepatosteatosis
• Disulfiram: ↓ ALDH → ↑ Acetaldehyde → Alcohol aversion; “Disulfiram-like drug reaction” (e.g. Metronidazole)
• ADH ↑ affinity for EtOH → EtOH for methanol/ethylene glycol poisoning when no fomepizole (ADH inhibitor)
Biochemistry: Oxidative Stress Bootcamp.com

Ethanol Metabolism

AfraTafreeh.com

Malate-Aspartate
Shuttle

Fates of
Pyruvate

Gluconeogenesis

Methanol Metabolism
 AfraTafreeh.com
OUTLINE
1. Glycogenesis and Glycogenolysis 6. Cori Disease
A. Overview A. Overview
B. Glycogenesis B. Pathophysiology

Biochemistry:
C. Hepatocyte Glycogenolysis C. Presentation
D. Muscle Glycogenolysis D. Diagnostics
2. Regulation of Glycogen Metabolism E. Differential Diagnosis

Glycogen A. Overview
B. Glucagon
C. Epinephrine
7.
F. Management
Andersen Disease
A. Overview
D. Allosteric Regulation in Skeletal Muscle B. Pathophysiology
3. Overview of Glycogen Storage Diseases C. Presentation
A. Overview D. Diagnostics
B. Liver Involvement E. Differential Diagnosis
C. Muscle Involvement F. Management
4. Von Gierke Disease 8. McArdle Disease
A. Overview A. Overview
B. Pathophysiology B. Pathophysiology
C. Presentation C. Presentation
D. Diagnostics D. Diagnostics
E. Differential Diagnosis E. Differential Diagnosis
F. Management F. Management
5. Pompe Disease 9. Hers Disease
A. Overview A. Overview
B. Pathophysiology B. Pathophysiology
C. Presentation C. Presentation
D. Diagnostics D. Diagnostics
E. Differential Diagnosis E. Differential Diagnosis
F. Management F. Management
10. Summary of Glycogen Storage
Diseases
Biochemistry: Glycogen Bootcamp.com

AfraTafreeh.com
 AfraTafreeh.com
Biochemistry: Glycogen Bootcamp.com

Glycogenesis and Glycogenolysis

• Overview:
• Purpose: Storage glucose polymer released in hypoglycemia
• Linear α-(1,4) bonds, branched α-(1,6) bonds; Branching ↑ solubility
• Muscle and liver store most
• Glycogenesis:
• Glucose → G6P via glucokinase
• G6P → G1P via phosphoglucomutase (reversible)
• G1P → UDP-glucose via UDP-glucose pyrophosphorylase
• UDP glucose created in galactose metabolism
• UDP-glucose → Glycogen via glycogen synthase (rate-limiting)
• ↑ By insulin, G6P, cortisol; ↓ by epinephrine, glucagon
• α-(1,6) branches added via glycogen branching enzyme
• Hepatocyte Glycogenolysis:
• Glycogen phosphorylase (rate-limiting, B6 cofactor): Phosphorylates 1,4 bonds → Cleaved G1P → “Limit dextrin” (4 glucose on branch)
• G1P → G6P via phosphoglucomutase; G6P → Glucose via G6Pase in liver, kidneys
• Liver phosphorylase ↑ by epinephrine, glucagon, ↓ by insulin; Independent of AMP:ATP ratio (must maintain blood glucose)
• Cleavage/relocation of 3 remaining glucose → Linear linkage via 4-α-D-glucanotransferase debranching enzyme
• Last glucose on branch cleaved by α-1,6-glucosidase debranching enzyme → Free glucose (not phosphorylated) → Blood
• G1P production >> Glucose
• Some glycogen degraded by α-1,4-glucosidase (lysosome)
• Skeletal Muscle Glycogenolysis:
• ↑ By epinephrine, AMP, Ca2+; ↓ by insulin, ATP
• Glycogen → G1P via phosphorylase and debranching enzymes
• G1P → G6P via phosphoglucomutase; G6P → Immediate glycolysis (no G6Pase)
• Muscle phosphorylase dependent on AMP:ATP ratio
• Muscle stores glycogen only for own consumption, regulated by own energy supply
Biochemistry: Glycogen Bootcamp.com

AfraTafreeh.com
 AfraTafreeh.com
Biochemistry: Glycogen Bootcamp.com

Regulation of Glycogen Metabolism

• Overview:
• Hormonal regulation of glycogen metabolism: Insulin, glucagon, epinephrine
• Skeletal muscle stores glycogen → Glycogen consumption (skeletal muscle only)
• Hormonal and allosteric regulation by own energy supply (ATP, AMP, Ca2+)
• Phosphate signals starvation: Phosphorylation ↑ glycogen phosphorylase activity (glycogenolysis), ↓ glycogen synthase (glycogenesis)
• Glycogen phosphorylase kinase: Phosphorylates (activates) glycogen phosphorylase
• Protein phosphatase: Dephosphorylates (activates) glycogen synthase
• Glucagon:
• Indicates starved state (liver only): ↑ Glycogenolysis, ↓ glycogenesis (catabolic)
• Glucagon binds GPCR → ↑ Adenylyl cyclase → ↑ cAMP → ↑ Protein kinase A
• PKA ↑ glycogen phosphorylase kinase → ↑ Glycogen phosphorylase; PKA ↓ glycogen synthase
• Insulin:
• Indicates fed state (liver and muscle): ↑ Glycogenesis, ↓ glycogenolysis (anabolic)
• Insulin binds RTK → ↓ cAMP → ↑ Protein phosphatase → ↑ Glycogen synthase
• Protein phosphatase ↓ glycogen phosphorylase kinase
• Insulin binding directly ↑ glycogen synthase
• Epinephrine:
• Signals maintenance of blood sugar (catabolic)
• Muscle and liver: β-adrenergic GPCR → ↑ Adenylyl cyclase → ↑ cAMP → ↑ Glycogen phosphorylase, ↓ glycogen synthase as with glucagon
• Liver only: α-adrenergic GPCR → ↑ Phospholipase C → ↑ Intracellular Ca2+ via IP3/DAG → ↑ Glycogen phosphorylase kinase
• ↑ Ca2+ → ↑ Ca2+-calmodulin → ↑ Glycogen phosphorylase kinase
• Allosteric Regulation in Skeletal Muscle:
• ↑ Glycogenolysis (catabolic): AMP, muscle contraction (↑ intracellular Ca2+)
• ↑ Intracellular Ca2+ → ↑ Ca2+-calmodulin → ↑ Glycogen phosphorylase kinase as with epinephrine in liver
• ↑ Glycogenesis (anabolic): ATP, glucose-6-phosphate
 Biochemistry: Glycogen Bootcamp.com

Overview of Glycogen Storage Diseases (GSDs)

• Overview:
• Enzyme deficiencies in glycogenesis/glycogenolysis
• Types I-VI, all autosomal recessive
• Liver, muscle, or both
• ↑ Glycogen in affected tissue → (+) Periodic acid-Schiff stain
• Liver Involvement:
• Fasting hypoglycemia, ketosis, hepatomegaly
• GSD types I, III, IV, VI
• Type I: Von Gierke Disease, ↓ G6Pase
• Type III: Cori Disease, ↓ Debranching enzymes
• Type IV: Andersen Disease, ↓ Branching enzyme
•
AfraTafreeh.com
Type VI: Hers Disease, ↓ Liver glycogen phosphorylase
• Muscle Involvement:
• Defective glycogenolysis: Exercise intolerance, cramps, easy fatigability, rhabdomyolysis
• Defective glycogenesis or lysosomal glycogenolysis: Progressive weakness
• Potential cardiac muscle involvement
• GSD types II, III, IV, V
• Type II: Pompe Disease, ↓ Lysosomal acid α-1,4 glucosidase
• Types III and IV above also involve muscle
• Type V: McArdle Disease, ↓ Muscle glycogen phosphorylase
 AfraTafreeh.com
Biochemistry: Glycogen Bootcamp.com

Von Gierke Disease

• Overview:
• Glycogen storage disease (GSD) type I
• Enzyme deficiency → Impaired gluconeogenesis and glycogenolysis (liver)
• Pathophysiology:
• Defective G6PC gene (chromosome 17q) → ↓ G6Pase (Type Ia)
• SLC37A4 gene (chromosome 11q) → ↓ G6P translocase (Type Ib)
• ↓ G6P breakdown → ↑ G6P, ↓ Glucose from glycogen storage
• Presentation:
• Hepatomegaly and renomegaly from ↑ glycogen and lipids; Hepatic adenomas (poorly understood)
• Hypoglycemic tremor, confusion, seizures
• Gout
• “Doll-like facies” (fat accumulation)
• Diagnostics:
• Severe fasting hypoglycemia with lactic acidosis, reliant on fat/protein catabolism
• Hyperlipidemia and mild ketosis
• Hypoglycemia → Sympathetic activation of lipoprotein lipase → ↑ Free fatty acids, oxidation to ketones
• Hyperuricemia → ↑ G6P → ↓ Intrahepatic phosphate → ↑ Purine degradation via AMP deaminase
• ↑ Serum biotinidase (produced by liver), ↑ liver function tests (AST, ALT, ALP)
• Cirrhosis → Nodular liver surface on US, hepatomegaly → atrophy
• Anemia, neutropenia
• Liver biopsy: Periodic acid-Schiff (+) granules
• Gene sequencing, enzyme activity analysis
• Differential Diagnosis:
• Cori Disease (GSD III): Similar presentation, milder than GSD I, normal lactate, muscle findings (weakness, cramps), ↑ limit dextrins
• Management:
• Oral glucose/cornstarch
• Avoid fructose and galactose
 Biochemistry: Glycogen Bootcamp.com

Pompe Disease
• Overview:
• Glycogen storage disease type II
• Enzyme deficiency → Impaired glycogenolysis (muscle)
• Pathophysiology:
• Defective GAA gene (chromosome 17q) → ↓ Lysosomal acid α-1,4 glucosidase
• ↓ Hydrolysis of α-1,4 and α-1,6 bonds (lysosome) → ↑ Glycogen in cardiac muscle
• Presentation:
• Progression: Active voluntary muscles (extremities) → Cardiac muscle →
Diaphragm
• Failure to thrive, proximal myopathy, hypotonia, exercise intolerance
• Hypertrophic cardiomyopathy, cardiomegaly, conduction blocks
• Respiratory failure, early death
AfraTafreeh.com
• Macroglossia
• Diagnostics:
• Muscle biopsy: PAS (+) granules; Electron dense granules inside lysosomes
• Newborn screening for enzyme activity, gene sequencing
• ↑ Creatine kinase, urinary oligosaccharides
• No hypoglycemia
• Differential Diagnosis:
• Muscular dystrophies: Later age of onset
• Management:
• Enzyme replacement therapy
• Pacemaker for conduction defects
• Heart transplantation for severe cardiomyopathy
• Often early death, better prognosis for later onset
 AfraTafreeh.com
Biochemistry: Glycogen Bootcamp.com

Cori Disease
• Overview:
• Glycogen storage disease type III
• Enzyme deficiency → Impaired glycogenolysis (muscle and liver)
• Pathophysiology:
• Defective AGL gene (chromosome 1p) → ↓ Debranching enzymes → ↑ Limit dextrins
• 4-α-D-glucanotransferase and α-1,6-glucosidase
• Functional gluconeogenesis
• Presentation:
• Failure to thrive, generalized muscle weakness, cramps, potential cardiomyopathy
• Hepatomegaly, possible cirrhosis
• Diagnostics:
• Mild fasting hypoglycemia and ketosis with normal blood lactate and uric acid
• ↑↑ Transaminases (often ≥500 U/L, unique to GSD III); ↑ Serum biotinidase
• Hyperlipidemia (sympathetic activation of lipoprotein lipase)
• Ischemic forearm test: No ↑ lactate with exercise under anaerobic conditions
• ↑ Creatine kinase
• Muscle and liver biopsy: PAS (+) granules, ↑ limit dextrin-like structures in cytosol
• Gene sequencing, enzyme activity analysis
• Differential Diagnosis:
• Von Gierke Disease (GSD I): Shares fasting hypoglycemia with hyperlipidemia; ↑ Severity, ↑ blood lactate, no muscle findings
• McArdle Disease (GSD V): Shares ischemic forearm test findings, no liver involvement
• Galactose-1-phosphate uridyltransferase deficiency: Shares hypotonia and hepatomegaly; Cataracts, jaundice, ↑ hypoglycemia, earlier presentation
• Management:
• ↑ Protein diet with cornstarch supplementation
 Biochemistry: Glycogen Bootcamp.com

Andersen Disease
• Overview:
• Glycogen storage disease type IV
• Enzyme deficiency → Impaired glycogenesis (muscle and liver)
• Pathophysiology:
• Defective GBE1 gene (chromosome 3p) → ↓ Branching enzyme → ↓ Branched glycogen
• Presentation:
• Continuum of hepatic and neuromuscular subtypes
• Failure to thrive in early infancy
• Hepatosplenomegaly, cirrhosis
• Hypotonia, cardiomyopathy; Peripheral neuropathy
• Early death
• Diagnostics:
AfraTafreeh.com
• Branching enzyme activity, gene sequencing
• Liver/muscle biopsy: PAS (+) granules
• ↑ Serum biotinidase (produced by liver), ↑ liver function tests (AST, ALT, ALP)
• Cirrhosis → Nodular liver surface on US, hepatomegaly → atrophy
• Hypoglycemia later in disease course
• Differential Diagnosis:
• Von Gierke disease (GSD I): Shares cirrhosis and hepatomegaly with hepatic subtype; Severe, early hypoglycemia, hyperlipidemia, hyperuricemia
• Pompe disease (GSD II): Shares cardiomyopathy, hypotonia; Hypertrophic obstructive findings, no liver involvement
• Management:
• Supportive
• Liver or heart transplantation if warranted
 AfraTafreeh.com
Biochemistry: Glycogen Bootcamp.com

McArdle Disease
• Overview:
• Glycogen storage disease type V
• Enzyme deficiency → Impaired glycogenolysis (muscle)
• Pathophysiology:
• Defective PYGM gene (chromosome 11q) → ↓ Muscle phosphorylase
• Rate-limiting step
• ↑ Glycogen in muscle, ↓ glycogen catabolism
• Presentation:
• Older child/adolescent
• Muscle weakness, cramps, exercise intolerance with “second wind” (↑ blood flow)
• Rhabdomyolysis, myoglobinuria
• Diagnostics:
• Ischemic forearm test: Flat venous lactate curve, ↑↑ ammonia with anaerobic exercise
• ↑ Creatine kinase (CK)
• EKG: Arrhythmia from electrolyte imbalance
• Normal blood glucose
• Enzyme activity, gene sequencing
• Differential Diagnosis:
• β-oxidation defects (carnitine palmitoyltransferase II deficiency), mitochondrial myopathies
• Exercise intolerance with ↑ duration of exercise, no “second wind”
• Pompe Disease (GSD II): Shares exercise intolerance, muscle weakness, arrhythmia; Hypertrophic obstructive cardiomyopathy
• Cori Disease (GSD III): Shares ischemic forearm test findings; Liver involvement, hypoglycemia
• Management:
• Supportive
• Moderate intensity graded aerobic exercise therapy: Maintain aerobic fitness, control CK without ↑ symptoms
• Glucose consumption before exercise
 Biochemistry: Glycogen Bootcamp.com

Hers Disease
• Overview:
• Glycogen storage disease type VI
• Enzyme deficiency → Impaired glycogenolysis (liver)
• Pathophysiology:
• Defective PYGL gene (chromosome 14q) → ↓ Hepatic phosphorylase
• Rate-limiting step
• ↑ Glycogen in liver, ↓ glycogen catabolism
• Presentation:
• Hepatomegaly, hepatic fibrosis
• Poor metabolic control → Short stature, delayed puberty, osteopenia, and osteoporosis
• Diagnostics:
•
AfraTafreeh.com
Mild hypoglycemia with ketosis, gluconeogenesis intact
• ↑ Transaminases, ↓ prealbumin
• Hyperlipidemia
• Ultrasound: Hepatomegaly with diffuse echogenicity
• Liver biopsy: PAS (+) granules
• Gene sequencing, enzyme activity analysis
• Differential Diagnosis:
• Von Gierke Disease (GSD I): Hypoglycemia more severe, ↑ lactate, hyperuricemia
• Cori Disease (GSD III): Muscle findings
• Management:
• Supplement cornstarch, protein
• Supportive
 AfraTafreeh.com
Biochemistry: Glycogen Bootcamp.com

Summary of Glycogen Storage Diseases

Disease Location Defective Enzyme Enzyme Clinical Presentation and Diagnostics
Function

Von Gierke (I) Liver G6Pase G6P → Glucose ● Hepatomegaly, renomegaly

(gluconeogenesis ● Fasting hypoglycemia with mild ketosis, ↑ lactate
and glycogenolysis) ● ↑ Triglycerides, hyperuricemia

Pompe (II) Muscle Lysosomal acid α-1,4 Glycogenolysis ● Cardiomyopathy, conduction blocks
glucosidase ● Proximal myopathy and hypotonia → respiratory insufficiency
● Macroglossia
● PAS (+) lysosomes

Cori (III) Muscle Debranching enzymes Glycogenolysis ● Milder Von Gierke (I), normal lactate, functional gluconeogenesis
(α-1,6 glucosidase, ● Potential muscle weakness, cardiomyopathy
and Liver ● Very elevated transaminases
4-α-D-glucanotransferase)
● Cytosolic limit dextrin-like complexes

Andersen (IV) Muscle Branching enzyme Glycogenesis ● Infant hepatosplenomegaly and failure to thrive
● Hypotonia, muscle weakness, cardiomyopathy
and Liver ● Cirrhosis
● Peripheral neuropathy

McArdle (V) Muscle Muscle glycogen Glycogenolysis ● Muscle weakness, exercise intolerance (second wind)
phosphorylase ● Rhabdomyolysis, myoglobinuria
● Normal blood glucose, flat venous lactate curve with ↑ ammonia

Hers (VI) Liver Liver glycogen Glycogenolysis ● Hepatomegaly, fasting hypoglycemia and ketosis, hyperlipidemia
phosphorylase
 Biochemistry: Glycogen Bootcamp.com

Video Vignettes
Video 8.5:
○ A 5-month-old girl is brought to the ED after a generalized seizure. She reportedly has been lethargic for the past several weeks. She is at the 15th
percentile for height and 10th percentile for weight. Physical exam reveals a rounded face and a distended, nontender abdomen with liver palpable 4 cm
below the right costal margin. Laboratory evaluation is pertinent for serum glucose 32 mg/dL, cholesterol 261 mg/dL, uric acid 9.8 mg/dL, lactate 4.8
mEq/L.
Video 8.6:
○ A 5-month-old boy is brought to the office for a chief complaint of poor feeding for several weeks. His mother reports difficulty holding his head up to
feed, weak suckling, and poor weight gain. He is at the 20th percentile for height and 5th percentile for weight. Physical exam reveals hypotonia in all
limbs, and a high-pitched, crescendo-decrescendo, midsystolic murmur heard best at the left lower sternal border that increases in intensity when the
AfraTafreeh.com
baby strains. CXR reveals cardiomegaly and a muscle biopsy reveals PAS (+) material visible in enlarged lysosomes.
Video 8.7:
○ A 7-month-old girl is brought to the office with a chief complaint of failure to thrive. Her height and weight are at the 10th and 5th percentile, respectively.
Physical examination reveals hypotonia and hepatomegaly; laboratory workup is remarkable for elevated urine ketones, serum glucose of 58 mg/dL,
creatine kinase of 100 U/L, AST of 512 U/L, ALT of 508 U/L, and lactic acid within reference ranges. Liver biopsy shows buildup of abnormally structured
material within the cytosol of hepatocytes on Periodic Acid-Schiff stain.
Video 8.8:
○ A 6-month-old boy is brought to the office with a chief complaint of poor feeding for several weeks. His mother reports difficulty holding his head up to
feed, weak suckling, and poor weight gain. He is at the 20th percentile for height and 5th percentile for weight. Physical exam reveals hypotonia and
hepatomegaly. Laboratory workup reveals a serum blood glucose of 68 mg/dL. Muscle biopsy reveals the presence of PAS (+) granules, and enzyme
activity analysis reveals decreased activity of an enzyme implicated in glycogen formation.
 AfraTafreeh.com
Biochemistry: Glycogen Bootcamp.com

Video Vignettes
Video 8.9:
○ A 14-year-old boy is brought to the office due to several episodes of extreme fatigue and muscle cramping while lifting weights. He states that he
sometimes feels better with a gentle warm up, and feels much better when he drinks a sugary sports drink before beginning his workout. He has noticed
occasional darkening of the urine after strenuous activity. Physical examination is unremarkable. To confirm the diagnosis, a blood pressure cuff is
inflated around his upper arm, and venous blood samples from the forearm are collected at baseline and regular time intervals after exercising the hand;
his venous lactate remains unchanged throughout the testing interval.
Video 8.10:
○ An 11-month-old girl is brought to the office with a chief complaint of abdominal distention. Physical examination reveals a palpable liver 3 cm below the
costal margin. Laboratory workup is remarkable for serum glucose of 64 mg/dL, total cholesterol of 254 mg/dL, elevated transaminases, and a
prealbumin level of 11 mg/dL (ref 16-30 mg/dL).
 OUTLINE
1. Introduction to Lipids
A. Fatty Acids 7. Adipocytes and Lipolysis

Biochemistry:
B. Triglycerides A. Lipogenesis
C. Steroids B. Lipolysis
D. Structural Lipids 8. Fatty Acid Degradation (β-oxidation)
2. Lipid Digestion and Absorption A. FA Transport to Mitochondria

Lipid Metabolism A. Triglycerides

B. Cholesterol
C. Clinical Implications
B. β-oxidation
C. Very Long Chain Fatty Acids
9. Fatty Acid Synthesis
3. Introduction to Lipid Transport Proteins and A. FA Synthesis
Enzymes B. FA Desaturation
A. Lipoproteins 10. Disorders of Fatty Acid Metabolism
B. Enzymes A. Systemic Primary Carnitine Deficiency
C. Apolipoproteins B. MCAD Deficiency
4. Lipid Transport C. CPTII Deficiency
AfraTafreeh.com
A. Triglycerides to Periphery and Liver D. Common Diagnostic/Clinical Features
B. Cholesterol to Liver E. Management
C. Triglyceride and Cholesterol Export from liver 11. Ketone Synthesis and Oxidation
D. Peripheral Cholesterol Activity A. Ketogenesis
5. Hyperlipidemia Pharmacology B. Ketoacidosis
A. Classes C. Ketogenolysis
B. Medications 12. Fed vs. Fasting State
C. Mechanisms and effects on lipoproteins A. Exercise Fuel Sources
D. Adverse Effects B. Energy Sources by Intake
6. Familial Dyslipidemias
A. Type I
B. Types IIa/b
C. Type III
D. Type IV
E. Management
 AfraTafreeh.com
Biochemistry: Energy Production from Lipids Bootcamp.com
 Biochemistry: Energy Production from Lipids Bootcamp.com

Introduction to Lipids
• Overview
• Lipids: Nonpolar organic molecules
• Fatty acids building block for esters (triglycerides, steroids, structural lipids)
• Fatty Acids (FAs):
• Carboxylic acid with linear carbon chain
• Carbon chain length: Short (1-6), medium (7-12), long (13-20), very long (>20), odd-chain
• Saturation: Saturated without double bonds, mono- or polyunsaturated with double bonds (cis- or trans- conformation)
• Trans fats pack tightly, ↓ membrane fluidity → ↑ Risk of CV disease
• ω Nomenclature: Count carbons from methyl (ω) end, identify distance between ω and first carbon of first double bond
• Essential FAs: Polyunsaturated FAs that must be ingested
• ω-3s: ɑ-Linolenic acid, eicosapentaenoic acid, docosahexaenoic acid
•
AfraTafreeh.com
↓ Arachidonic acid in platelet membranes → ↓ Thromboxane production, ↓ platelet aggregation, ↓ CV disease (anti-inflammatory)
• ω-6s: Linoleic acid; ↑ Arachidonic acid → ↑ Prostaglandins, leukotrienes (pro-inflammatory)
• Triglycerides (TGs):
• Fatty acid storage (synthesized in liver, adipose); 3 Fatty acids + 1 glycerol linker (ester)
• Fatty acids liberated → β-oxidation (catabolism)
• Steroids:
• Three 6-sided and one 5-sided carbon rings
• Cholesterol: ↑ Membrane fluidity; Precursor for hormones, bile acids, vitamins; Absorbed and synthesized de-novo
• Cholesterol + Fatty acid = Cholesteryl ester (dietary lipid)
• Structural Lipids:
• Phospholipids, sphingolipids, glycolipids
• Cell membrane components for structure, signalling, receptor function
 AfraTafreeh.com
Biochemistry: Energy Production from Lipids Bootcamp.com

Lipid Digestion and Absorption

• Overview:
• Triglycerides, cholesteryl esters from diet poorly absorbed
• Cleaved by enzymes, absorbed, packaged for transport
• Triglycerides:
• Consumption of fatty meal → Lipases cleave TGs → 2 FAs + Monoglyceride or 3 FAs + Glycerol
• Stomach: Gastric lipase hydrolyzes TGs
• Duodenum: Bile salts emulsify TGs, activate pancreatic lipase
• FAs + Monoglycerides + Bile salts + Fat-soluble vitamins (A, D, E, K) → Mixed micelles
• Bile salts recycled in ileum → Liver for re-secretion
• Absorption of fat-soluble vitamins
• Jejunum:
• Short/medium-chain FAs absorbed into capillary
• Long-chain FAs + Monoglycerides uptake into epithelium → Re-esterify as TGs
• TGs + Cholesterol + Cholesteryl esters + Apoprotein B-48 → Chylomicron (CM) in enterocyte golgi
• CMs present in fed state only
• Microsomal triglyceride transfer protein (MTP) adds apolipoproteins (e.g. ApoB-48) for assembly
• CMs → Extracellular space → Lacteals (Lymphatic thoracic duct → Subclavian vein)
• Gain apolipoprotein C-II, apolipoprotein E in circulation
• Cholesterol:
• Consumption of fatty meal (animal products) → Pancreatic cholesterol esterase cleaves cholesteryl esters → Cholesterol + FAs
• Cholesterol + FAs + Bile salts → Mixed micelles
• Jejunum: Cholesterol absorbed via NPC1L1 transporter, packaged into CMs as above → Lymph → Blood
• Some assembly into cholesteryl esters protected in CM core
• Clinical Implications:
• Abetalipoproteinemia: MTTP mutation → ↓ MTP → ↓ ApoB-48, ApoB-100 → ↓ CMs, VLDL, LDL → ↑ Lipids in intestine and liver (↓ export)
• Steatorrhea/fat malabsorption → Fat-soluble vitamin deficiency, ↓ plasma cholesterol
• Acanthocytes (spiculated RBCs), lipid-laden enterocytes
 Biochemistry: Energy Production from Lipids Bootcamp.com

Introduction to Lipid Transport Proteins and Enzymes

• Overview:
• Chylomicrons loaded with dietary TGs + Cholesterol + Cholesteryl esters + Surface apolipoproteins → Blood
• Chylomicrons emptied by adipose and liver; TGs and cholesterol re-packaged as lipoproteins, exported from liver → Periphery
• Peripheral TGs and cholesterol also returned to liver
• Lipoproteins:
• Lipoproteins: Packages of TGs, cholesterol/cholesteryl esters, proteins, phospholipids
• Chylomicron (CM): Enterocyte golgi packs with dietary TGs and cholesterol
• Most TGs → Adipose, some to liver
• Chylomicron remnant (CMR): Remaining cholesterol after TG depletion → Liver
• Very low-density lipoprotein (VLDL): Hepatic TGs → Periphery (adipocyte, muscle)
• Intermediate-density lipoprotein (IDL): VLDL partially ↓ in TGs, delivers TGs and cholesterol back to liver
• AfraTafreeh.com
Low-density lipoprotein (LDL): IDL further ↓ in TGs, delivers cholesterol → Periphery (“bad cholesterol”)
• High-density lipoprotein (HDL): Cholesterol transport from periphery → Liver (“good cholesterol”)
• Enzymes:
• Pancreatic lipase: Small intestine Apolipo- Function CM CMR VLDL IDL LDL HDL
protein
• Dietary TG breakdown in small intestine
• Lipoprotein lipase: Blood
B48 Chylomicron secretion ✓ ✓
• Cleaves TGs in CMs (→ CMR) and VLDL (→ IDL); ↑ by PPAR-α from enterocytes
• Hormone-sensitive lipase: Adipocytes
• Degrades TGs → FAs and glycerol E Liver uptake ✓ ✓ ✓ ✓ ✓
• Hepatic lipase: Liver
• Cleaves TGs in IDL and chylomicron remnants C-II LPL cofactor ✓ ✓ ✓ ✓
• PCSK9: Peripheral cell
• ↓ LDL receptor → ↑ Serum LDL Binds LDL receptor
B100 ✓ ✓ ✓
• Lecithin-cholesterol acyltransferase (LCAT): Peripheral cell
• Loads HDL with cholesteryl esters
A-I Activates LCAT ✓
• Cholesteryl ester transfer protein (CETP): Blood
• Cholesteryl esters (HDL) ↔ TGs (VLDL)
 AfraTafreeh.com
Biochemistry: Energy Production from Lipids Bootcamp.com

Lipid Transport
 Biochemistry: Energy Production from Lipids Bootcamp.com

Lipid Transport
• Overview:
• Chylomicrons loaded with TGs + Cholesterol + Cholesteryl esters + Surface apolipoproteins → Blood
• Chylomicrons emptied by adipose and liver; TGs and cholesterol re-packaged as lipoproteins, exported from liver → Periphery
• Peripheral TGs and cholesterol also returned to liver
• Triglycerides to Periphery and Liver:
• Adipocytes synthesize lipoprotein lipase (LPL) → Attach to adipocyte capillary endothelium (insulin ↑ expression)
• LPL binds apo C-II (e.g. chylomicrons); TGs → Glycerol (liver uptake) + FAs (mostly adipose uptake, some liver)
• FAs re-esterified into TGs → Storage
• Chylomicron remnants (TG-depleted) → Liver, further TG emptying/FA uptake via hepatic lipase
• Apo E on chylomicron remnant binds receptor (LRP1) on liver → Endocytosis
• Cholesterol to Liver:
• AfraTafreeh.com
Cholesterol/cholesteryl esters still contained in chylomicron remnants, endocytosed into liver (cholesterol → bile salts)
• Cholesterol synthesized in liver de novo:
• Acetyl CoA → Hydroxymethylglutaryl-CoA (HMG-CoA)
• HMG-CoA → Mevalonate via HMG-CoA reductase (rate-limiting step, ↓ by cholesterol and statin drugs)
• Mevalonate → → Cholesterol
• Triglyceride and Cholesterol Export from Liver:
• MTP assembles very low-density lipoprotein (VLDL): ApoB-100 + TGs + Cholesterol + Cholesteryl esters
• “Density” of lipoproteins: Protein:lipid ratio (↑ TGs = ↓ Density)
• Secreted to circulation → Acquire Apo C-II and Apo E
• LPL in adipocyte (insulin-sensitive) and muscle (insulin-independent) capillaries binds apo C-II on VLDL
• LPL ↓ TGs from VLDL → Intermediate-density lipoprotein (IDL) → Hepatic lipase activity further ↓ TGs → Low-density lipoprotein (LDL)
• TGs cleaved → FAs → Adipocytes → Storage as TGs
• LDL ↑ in cholesterol/cholesteryl esters; LDL receptor on cells binds apoB-100 on LDL → Peripheral cholesterol uptake (includes liver)
• Peripheral Cholesterol Activity:
• High-density lipoprotein (HDL): Packed with peripheral cholesteryl esters (lecithin cholesterol acyl transferase (LCAT)), apo A-I surface protein
• Scavenge peripheral cholesterol, return to liver
• Cholesteryl ester transfer protein (CETP): Exchange VLDL and CM TGs with HDL cholesteryl esters → Hepatic lipase ↓ HDL TGs → ↓ HDL
 AfraTafreeh.com
Biochemistry: Energy Production from Lipids Bootcamp.com

Hyperlipidemia Pharmacology
Class Medications Mechanism LDL HDL TGs Adverse Effects

Bile Acid - Colestipol - Binds bile acids in intestinal lumen ↓↓ ↑ ↑ - Abdominal bloating/cramping
Resins - Cholestyramine - ↑ Cholesterol excretion - Fat and fat-soluble vitamin malabsorption
- Colesevelam - Existing cholesterol used for bile acid synthesis - ↓ Drug levels (digoxin, warfarin)
- Cholesterol gallstones

Cholesterol Ezetimibe - ↓ NPC1L1 activity ↓↓ ↑/- ↑/- - Diarrhea

Absorption - ↓ Enterocyte cholesterol absorption - ↑ LFTs
Inhibitors

HMG-CoA Statins - ↓ HMG-CoA → Mevalonate → Cholesterol ↓↓↓ ↑ ↓ - Hepatotoxicity/↑ LFTs

Reductase - ↓ De novo cholesterol production - Myopathy (↑ with fibrates or niacin)
Inhibitors - ↑ LDL recycling

Fibrates - Gemfibrozil - ↑ PPAR-α → ↑ LPL → TG cleavage ↓ ↑ ↓↓↓ - Myopathy (↑ with statins)

- Fenofibrate - ↑ PPAR-α → ↑ HDL synthesis - Cholesterol gallstones
- ↓ 7α-hydroxylase → ↓ Bile acid synthesis
- Supersaturation of bile with cholesterol
(↑ cholesterol:bile acids)

PCSK9 - Evolocumab - ↓ PCSK9 → ↓ LDL receptor degradation ↓↓↓ ↑ ↓ - Myalgia

Inhibitors - Alirocumab - ↑ LDL clearance via ↑ LDL receptors - Neurocognitive effects (delirium, dementia)

Niacin Niacin - ↓ Hormone-sensitive lipase → ↓ Lipolysis ↓↓ ↑↑ ↓ - Prostaglandin-mediated flushing (NSAIDS ↓)

(Vitamin B3) - ↓ VLDL synthesis - Hyperuricemia
- Hyperglycemia

Fish oil/ - Fish oil - Likely ↓ FFA delivery to liver ↑ ↑ ↓ - Nausea

Omega-3s - Marine ω-3 FAs - Likely ↓ Hepatic TG-synthesis enzymes - Poor taste
Biochemistry: Energy Production from Lipids Bootcamp.com

Hyperlipidemia Pharmacology

AfraTafreeh.com
 AfraTafreeh.com
Biochemistry: Energy Production from Lipids Bootcamp.com

Familial Dyslipidemias
• Overview:
• Autosomally inherited defects in lipid transport lipoproteins, apolipoproteins, receptors, enzymes
• Frederickson classification I-V (V rare)
• Hyperchylomicronemia (Type I):
• Autosomal recessive
• ↓ LPL or apo-CII → ↑ Chylomicrons → ↑↑↑ Serum TGs, normal/↑ cholesterol
• LPL: Cleaves TGs in CMs (→ CMR) and VLDL (→ IDL); Apo-CII cofactor for LPL
• Xanthomas (eruptive), hepatosplenomegaly, recurrent pancreatitis; No ↑ atherosclerosis risk
• Overnight plasma: Creamy supernatant
• Hypercholesterolemia/Combined Hyperlipidemia (Types IIa/b):
• Autosomal dominant
• Absent/defective LDL receptor or apoB-100 → ↑ LDL, cholesterol (↑↑↑ IIb); ↑ VLDL, TGs type IIb only
• Xanthomas (tendinous; Achilles tendon xanthoma IIb), xanthelasmas (IIb), early atherosclerosis (MI), corneal arcus
• Dysbetalipoproteinemia (Type III):
• Autosomal recessive
• Defective ApoE → ↑ Chylomicrons, VLDL, TGs, cholesterol
• Xanthomas (tuberoeruptive, palmar), early atherosclerosis
• Hypertriglyceridemia (Type IV):
• Autosomal dominant
• Hepatic VLDL overproduction → ↑↑↑ VLDL, TGs; normal/↑ cholesterol
• Xanthomas (tuberoeruptive), acute pancreatitis (TGs >1000), insulin resistance → hyperglycemia
• Management:
• Statin therapy based on age, LDL levels, and atherosclerotic cardiovascular disease (ASCVD) risk
• Diet/exercise
 Biochemistry: Energy Production from Lipids Bootcamp.com

Adipocytes and Lipolysis

• Overview:
• Fed state → ↑ Insulin → TG storage in adipocytes
• Fasting state → ↑ Glucagon → Hydrolysis of TGs in adipocytes → FAs and glycerol (lipolysis)
• Lipogenesis:
• Fed state: ↑ By insulin; ↓ By glucagon, epinephrine, norepinephrine, ANP, BNP
• LPL cleaves TGs from CMs, VLDL → Glycerol + FAs
• FAs → Adipocyte via fatty acid transport proteins (FATPs)
• FATPs facilitate Acyl-CoA synthetase: FA + CoA → Acyl-CoA
• Acyl-CoA + Glycerol-3-Phosphate → TGs → Storage
• Glycerol-3-Phosphate from DHAP (glycolysis)
• Minor pathway: Acetyl-CoA (glycolysis) → FAs → TGs
• Lipolysis:
AfraTafreeh.com
• Fasting state/exercise: ↑ By glucagon, epinephrine, norepinephrine, ANP, BNP; ↓ By insulin
• Insulin-induced hypoglycemia: ↑ Insulin favors glucose use > FAs/ketones (↓ lipolysis)
• Epinephrine response partial compensation
• TGs → FA + Diglyceride via adipocyte triglyceride lipase
• Diglyceride → FA + monoglyceride via hormone-sensitive lipase
• Monoglyceride → FA + glycerol via monoglyceride lipase
• FA export → Blood (albumin-bound) → Muscle and liver → β-oxidation → ATP
• β-oxidation also within adipocytes
• Glycerol → Blood (unbound) → Liver → Gluconeogenesis
 AfraTafreeh.com
Biochemistry: Energy Production from Lipids Bootcamp.com

Fatty Acid Degradation (β-Oxidation)

• Overview:
• Fatty acids catabolized via β-oxidation in mitochondria of liver/muscle/adipose
• Purpose: Liberate acetyl-CoA → TCA cycle or ketogenesis; Create FADH2 and NADH
• Fatty Acid Transport to Mitochondria:
• Short- and medium-chains (SCFAs and MCFAs): Diffuse freely
• Long-chains (LCFAs): Carnitine-dependent shuttle
• Fatty acid + CoA → Fatty acyl-CoA via fatty acyl-CoA synthetase on outer mitochondrial membrane
• Fatty acyl group transfer to carnitine on outer mitochondrial membrane → Acylcarnitine via carnitine palmitoyltransferase 1 (CPT1)
• CPT1 rate-limiting step of FA catabolism
• ↑ By glucagon; ↓ By malonyl-CoA and insulin
• Acylcarnitine → Mitochondria via carnitine acylcarnitine translocase (CACT)
• Acyl-CoA detached from carnitine via carnitine-palmitoyltransferase II (CPTII); Carnitine recycled, acyl-CoA → β-oxidation
• β-oxidation:
• Cycles of FA chain cleavage (oxidation) at 2-carbon (β-carbon) position
• Liberates 2C acetyl-CoA + FADH2 + NADH each cycle; Remaining Acyl-CoA shortened by 2C → Re-enters β-oxidation
• Even chain termination: Final 4C → 2 Acetyl-CoA (Join OAA → Citrate → Citrate shuttle or TCA)
• Odd chain termination: 3C propionyl-CoA remaining →→ Succinyl-CoA (TCA cycle)
• Very Long Chain Fatty Acids (VLCFAs):
• β-oxidation begins in peroxisomes until octanoyl-CoA (8C) remain → Mitochondria
• Coupled to H2O2 production (toxic)
• Adrenoleukodystrophy: ↓ VLCFA peroxisome import → ↓ β-Oxidation → ↑ VLCFA: adrenal glands (insufficiency), white matter (↓ Cognition)
Biochemistry: Energy Production from Lipids Bootcamp.com

Fatty Acid Degradation (β-Oxidation)

AfraTafreeh.com
 AfraTafreeh.com
Biochemistry: Energy Production from Lipids Bootcamp.com

Fatty Acid Synthesis

• Overview:
• FAs synthesized from excess glucose
• Palmitic acid (16C): Only FA synthesized de novo in humans
• Cytoplasm of liver/adipose/lactating mammary glands
• 8 Acetyl-CoA + 14 NADPH + 7 ATP → Palmitic acid
• Fatty Acid Synthesis:
• Glucose → Pyruvate in cytosol via glycolysis; Pyruvate → Mitochondria → Acetyl-CoA
• Citrate shuttle: Exports Acetyl-CoA to cytoplasm
• Acetyl-CoA + OAA → Citrate → Cytoplasm; Citrate → Acetyl-CoA + OAA via ATP citrate lyase
• Acetyl-CoA → Malonyl-CoA via acetyl-CoA carboxylase (B7, ATP, CO2, NADPH)
• Phosphorylation of Acetyl-CoA regulatory step
• ↑ By insulin, ↑ glucose, ATP, citrate; ↓ By glucagon, ↓ glucose, catecholamines, AMP, acyl-CoA, palmitoyl-CoA
• FA synthase adds 2C units to FA chains until 16C palmitic acid achieved
• Initiation: Acetyl-CoA (2C) + Malonyl-CoA (3C) → Decarboxylation, hydration, reduction with NADPH → 4C FA bound to FA synthase
• NADPH from pentose phosphate pathway
• Elongation: Malonyl-CoA added in similar steps, Malonyl-CoA concentration rate-limiting
• Further elongation to 18-24C using Malonyl-CoA via elongase enzymes (up to 40C in skin, brain, retina, sperm)
• Metabolic reactions with FAs require activation into fatty acyl-CoAs
• Fatty Acid Desaturation:
• Insertion of double bonds at carbons 5, 6, or 9 from carboxyl end; No insertion beyond C9
• Long-chain unsaturated FAs with double bond near ω end → Essential FAs
• E.g. linoleic acid (ω-6), α-linolenic acid (ω-3)
• Essential FAs can be desaturated/elongated like nonessential
 Biochemistry: Energy Production from Lipids Bootcamp.com

Disorders of Fatty Acid Metabolism

• Overview:
• Errors in FA degradation → ↑ of metabolic intermediates, similar clinical features
• Systemic Primary Carnitine Deficiency:
• ↓ Systemic cellular carnitine uptake → ↓ LCFA mitochondrial import via carnitine shuttle → ↑ LCFAs in cytosol (toxic)
• ↑ LCFAs in liver, cardiac, skeletal muscle
• Medium-Chain Acyl-CoA Dehydrogenase (MCAD) Deficiency:
• ↓ MCAD → ↓ Medium-chain FA β-oxidation → ↑ Medium-chain fatty acyl–CoAs in liver
• Carnitine Palmitoyltransferase II (CPT II) Deficiency:
• ↓ CPT II activity → ↑ Long-chain acylcarnitines in liver, heart, skeletal muscle; ↓ Total and free carnitine
• Common Diagnostic and Clinical Features:
• Weakness, hypotonia
•
AfraTafreeh.com
Liver dysfunction (hepatic encephalopathy, hyperammonemia, ↑ aminotransferases)
• Hypoketotic hypoglycemia, lactic acidosis
• ↓ β-oxidation, ketogenesis inside mitochondria
• Primary carnitine and CPTII deficiencies only: Skeletal myopathy, rhabdomyolysis, dilated cardiomyopathy
• Management:
• Systemic Primary Carnitine Deficiency: Avoid fasting, oral carnitine supplementation, acute setting → IV carnitine + dextrose
• MCAD Deficiency: Avoid fasting, ↑ carb/↓ fat diet, acute setting → IV dextrose
• CPTII Deficiency: Avoid fasting, ↑ MCFA/↑ carb/↓ triglyceride diet
 AfraTafreeh.com
Biochemistry: Energy Production from Lipids Bootcamp.com

Ketone Synthesis and Oxidation

• Overview:
• Ketones: Water-soluble energy source during prolonged glucose deficiency (starvation, diabetic or alcoholic ketoacidosis)
• Produced by hepatic mitochondria → Mitochondria of extrahepatic tissues (heart, brain, skeletal muscle, renal cortex)
• Unusable by RBCs (no mitochondria)
• Acetoacetate, β-hydroxybutyrate, acetone (breakdown product of other ketones)
• Ketogenesis:
• Acetyl-CoA + Acetyl-CoA + Thiolase (catalyst) → Acetoacetyl-CoA
• Acetoacetyl-CoA + Acetyl-CoA → HMG-CoA via mitochondrial HMG-CoA synthase (rate-limiting)
• Not cytosolic HMG-CoA synthase (cholesterol synthesis)
• HMG-CoA → Acetoacetate + Acetyl-CoA via HMG-CoA lyase
• Acetoacetate reduction → β-hydroxybutyrate or decarboxylation → Acetone
• Acetone → Exhaled (“fruity odor”)
• Ketoacidosis:
• Fasting, DKA: Oxaloacetate (OAA) (TCA cycle) depleted for gluconeogenesis → ↑ Acetyl-CoA → Divert to ketogenesis
• Alcoholic ketoacidosis: ↑ NADH → OAA conversion to malate → ↓ OAA → ↑ Acetyl-CoA → Divert to ketogenesis
• Polyuria, polydipsia, fruity breath odor, nausea/vomiting, abdominal pain, altered mental status
• ↓ HCO3 (anion gap metabolic acidosis), dehydration → Electrolyte imbalance (hyponatremia, hypokalemia, hypophosphatemia)
• Urine nitroprusside ketone test acetoacetate, blood test β-hydroxybutyrate
• Management: Insulin + Glucose (D5NS)
• Alcoholic ketoacidosis: Precede with thiamine → Prevent Wernicke encephalopathy (ophthalmoplegia, ataxia, confusion)
• Thiamine (B1) TCA cofactor
• Ketogenolysis:
• β-hydroxybutyrate → Acetoacetate via β-hydroxybutyrate dehydrogenase
• Acetoacetate + Succinyl-CoA (TCA cycle) → Acetoacetyl-CoA + Succinate via thiophorase
• Acetoacetyl-CoA → 2 Acetyl-CoA via thiolase, Acetyl-CoA → TCA cycle
 Biochemistry: Energy Production from Lipids Bootcamp.com

Fed vs. Fasting State

• Overview:
• Fed state: Anabolic, insulin-driven; Fasting/starvation state: Catabolic, glucagon/epinephrine-driven
• Energy production pathways change as sources deplete
• Brain must use glucose or ketones; RBCs glucose only (insulin- and glucagon-resistant)
• Carbs and protein: 4 kcal/g; Alcohol: 7 kcal/g; Fat: 9 kcal/g
• Exercise Fuel Sources:
• Stored ATP + Creatine phosphate (Initial seconds) → Anaerobic (<10 sec) → Aerobic (>1 min) + Glycogenolysis/β-oxidation (Minutes to hours)
• Stored ATP immediately released, limited stores
• Creatine phosphate/early anaerobic glycolysis: High rate, low ATP yield (lactate production)
• Anaerobic limited by carbohydrate stores (blood glucose, liver/muscle glycogen)
• Late anaerobic/Aerobic glycolysis: Low rate, high ATP-yield (pyruvate production)
• Overall performance ↓ >10 sec, ↓↓↓ >30 sec
AfraTafreeh.com
• Energy Sources by Intake:
• Fed state (postprandial): Glycolysis, aerobic respiration, triglyceride synthesis
• Short-term fasting (hours): Glycogenolysis-dominant
• Glycogen stores ↓ after ~1 day
• Early starvation (1-3 days): Lipolysis and Gluconeogenesis-dominant
• Adipocytes/muscle/liver: ↑ Lipolysis → ↑ Free FAs (↓ Glucose use) → β-oxidation → Acetyl-CoA for energy production
• Hepatic gluconeogenesis: Lactate, alanine (from peripheral tissue); Glycerol, propionyl-CoA (odd-chain FFAs)
• Brain utilizes glucose from gluconeogenesis, body uses triglycerides
• Late starvation (>3 days): Ketosis-dominant
• β-oxidation produces acetyl-CoA → Ketogenesis → Ketogenolysis
• Gluconeogenesis ongoing
• Brain utilizes glucose and ketones, body uses triglycerides
• End-stage starvation (end of energy stores): ↓ Ketones → Protein degradation for gluconeogenesis → Organ failure
 AfraTafreeh.com
Biochemistry: Energy Production from Lipids Bootcamp.com

Fed vs. Fasting State

Glycolysis and Gluconeogenesis Glycogenolysis

Amino Acid Catabolism

Fatty Acid Metabolism

Ketogenesis
 Biochemistry: Cell Biology Bootcamp.com

References
• Cell Trafficking
• Infographic: Created with BioRender.com
• Inclusion bodies: Unknown photographer, Public domain, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Inclusion_bodies.jpg>
• I-Cell Disease
• Inclusion bodies: Unknown photographer, Public domain, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Inclusion_bodies.jpg>
• Corneal clouding: Vassili Valayannopoulos, Helen Nicely, Paul Harmatz, and Sean Turbeville, CC BY 4.0
<https://creativecommons.org/licenses/by/4.0>, via Wikimedia Commons
• Gingival hyperplasia: Lesion, CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons
• Kyphoscoliosis: Axelrod FB, Gold-von Simson G., CC BY 2.0 <https://creativecommons.org/licenses/by/2.0>, via Wikimedia Commons
• Signal Recognition Particle
AfraTafreeh.com
• Gottron Papules: Elizabeth M. Dugan, Adam M. Huber, Frederick W. Miller, Lisa G. Rider, CC BY-SA 3.0
<https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons
• Ubiquitin-Proteasome System
• Infographic: Created with BioRender.com
• Lewy Bodies: Movalley, CC0, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Immunostaining_(brown)_of_alpha-synuclein_in_Lewy_Bodies_and_Lewy_Neurites_in_the_neoco
rtex_of_a_patient_with_Lewy_Body_Disease.jpg>
• Cytoskeleton
• Cytoskeleton Types Infographic: Adapted from “Cytoskeleton Components (Fluorescent)”, by BioRender.com (2022). Retrieved from
https://app.biorender.com/biorender-templates
• Microtubule Polymerization: Created with BioRender.com
• Primary Ciliary Dyskinesia
• LadyofHats, Public domain, via Wikimedia Commons. <https://commons.wikimedia.org/wiki/File:Eukaryotic_cilium_diagram_en.svg>
 AfraTafreeh.com
Biochemistry: Cell Biology Bootcamp.com

References
• Sodium-Potassium Pump
• Na/K Pump Infographic: Adapted from “Sodium-Potassium Pump”, by BioRender.com (2022). Retrieved from
https://app.biorender.com/biorender-templates
• Membrane Channels Infographic: Created with BioRender.com.
• SGLT2 Inhibitors: Created with BioRender.com.
 Biochemistry: Lysosomal Storage Diseases Bootcamp.com

References
• Tay-Sachs:
• Cherry spot: Jonathan Trobe, M.D., CC BY 3.0 <https://creativecommons.org/licenses/by/3.0>, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Tay-sachsUMich.jpg>
• Fabry Disease:
• Angiokeratoma: Mohammad2018, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Angiokeratoma.jpg>
• Corneal clouding: Vassili Valayannopoulos, Helen Nicely, Paul Harmatz, and Sean Turbeville, CC BY 4.0 <https://creativecommons.org/licenses/by/4.0>, via
Wikimedia Commons. <https://commons.wikimedia.org/wiki/File:Corneal_Clouding_in_MPS-VI_(Maroteaux-Lamy_Syndrome).jpg>
• Metachromatic Leukodystrophy:
• Toluidine Blue: Nephron, CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Vasculitic_neuropathy_-n-_plastics_-_very_high_mag.jpg>
• Krabbe Disease:
• AfraTafreeh.com
Globoid cell: Jensflorian, CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Globoid_cell_leukodystrophy_PAS.jpg>
• Gaucher Disease:
• Tissue paper macrophage: Nephron, CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Gaucher_disease_-_very_high_mag.jpg>
• Niemann-Pick Disease:
• Foam cell: K C Geetika, Talwar OP, CC BY 4.0 <https://creativecommons.org/licenses/by/4.0>, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Histopathology_of_cholesterolosis.jpg>
• Cherry spot: Jonathan Trobe, M.D., CC BY 3.0 <https://creativecommons.org/licenses/by/3.0>, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Tay-sachsUMich.jpg>
• Mucopolysaccharidoses:
• Melanocytosis: Gzzz, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Giant_mongolian_blue_spot_(2).jpg>
• Corneal clouding: Vassili Valayannopoulos, Helen Nicely, Paul Harmatz, and Sean Turbeville, CC BY 4.0 <https://creativecommons.org/licenses/by/4.0>, via
Wikimedia Commons. <https://commons.wikimedia.org/wiki/File:Corneal_Clouding_in_MPS-VI_(Maroteaux-Lamy_Syndrome).jpg>
AfraTafreeh.com
AfraTafreeh.com
 AfraTafreeh.com
Biochemistry: Energy Production Bootcamp.com

References
• Introduction to Energy Production
• Acetyl-CoA: NEUROtiker, Public domain, via Wikimedia Commons. <https://commons.wikimedia.org/wiki/File:Acetyl-CoA.svg>
• ATP: User:Mysid, Public domain, via Wikimedia Commons. <https://commons.wikimedia.org/wiki/File:ATP_structure.svg>
• Energy Production Graphic: Created with BioRender.com.
• Metabolism Map: Created with BioRender.com.
• Glycolysis
• Glycolysis: Adapted from “Glycolysis and Glycolytic Enzymes”, by BioRender.com (2022). Retrieved from
https://app.biorender.com/biorender-templates
• Lactic acid fermentation: Adapted from “Lactic Acid Fermentation”, by BioRender.com (2022). Retrieved from
https://app.biorender.com/biorender-templates
• Regulation of Phosphofructokinase
• Adenylyl cyclase pathway: Adapted from “Activation of Protein Kinase A”, by BioRender.com (2022). Retrieved from
https://app.biorender.com/biorender-templates
• Phosphorylation of PFK2/FBPase-2: Created with BioRender.com.
• Modified glycolysis pathway: Created with BioRender.com.
• Pyruvate Dehydrogenase Complex
• Fates of Pyruvate: Created with BioRender.com.
• Pyruvate Dehydrogenase Complex: Created with BioRender.com.
• TCA Cycle
• TCA cycle: Created with BioRender.com.
• Electron Transport Chain
• Reprinted from “Electron Transport Chain”, by BioRender.com (2022). Retrieved from https://app.biorender.com/biorender-templates
• ATP Export and Phosphocreatine
• Cyclization of Creatine: Iposae, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Cyclization_of_Creatine.svg>
• Phosphocreatine schematic: Created with BioRender.com.
 Biochemistry: Carbohydrates Bootcamp.com

References
• Gluconeogenesis
• Gluconeogenesis Pathway: Created with BioRender.com.
• Malate-Aspartate Shuttle
• Malate-Aspartate Shuttle: Created with BioRender.com.
• Fructose Metabolism
• Fructose Metabolism: Created with BioRender.com.
• Polyol Pathway
• Polyol Pathway: Created with BioRender.com.
• Galactose Metabolism
• Galactose Metabolism: Created with BioRender.com.
AfraTafreeh.com
 AfraTafreeh.com
Biochemistry: Cell Biology Bootcamp.com

References
• Absorption of Folic Acid:
• All images created with BioRender.com.
• Sources and Uses of One-Carbon Groups:
• All images created with BioRender.com.
• The Activated Methyl Group Cycle:
• All images created with BioRender.com.
• Homocysteine Metabolism:
• All images created with BioRender.com.
• Homocystinuria:
• Marfanoid habitus: Mileny ES Colovati1, Luciana RJ da Silva1, Sylvia S Takeno1, Tatiane I Mancini1, Ana R N Dutra 1,Roberta S Guilherme1,
Cláudia B de Mello2, Maria I Melaragno1and Ana B A Perez1, CC BY 2.0 <https://creativecommons.org/licenses/by/2.0>, via Wikimedia
Commons. <https://commons.wikimedia.org/wiki/File:Marfan_Patient.jpeg>
• Pectus Excavatum: Aurora Bakalli, Tefik Bekteshi, Merita Basha, Afrim Gashi, Afërdita Bakalli and Petrit Ademaj, CC BY-SA 3.0
<https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons. <https://commons.wikimedia.org/wiki/File:MarfanChest.jpg>
• Wrist: Staufenbiel I, Hauschild C, Kahl-Nieke B, Vahle-Hinz E, von Kodolitsch Y, Berner M, Bauss O, Geurtsen W, Rahman A, CC BY-SA 2.0
<https://creativecommons.org/licenses/by-sa/2.0>, via Wikimedia Commons. <https://commons.wikimedia.org/wiki/File:Marfan_wrist.tiff>
• Thumb sign: Graziella F. B. Cipriano; Guilherme C. Brech; Paulo A. T. Peres; Cássia C. Mendes; Gerson Cipriano Júnior; Antônio C. C.
Carvalho, CC BY 4.0 <https://creativecommons.org/licenses/by/4.0>, via Wikimedia Commons.
<https://commons.wikimedia.org/wiki/File:Steinberg_and_Walker-Murdoch_tests.jpg>
• Activated Methyl Group Cycle: Created with BioRender.com.
• DDx of Homocystinuria: Created with BioRender.com.
 Biochemistry: Oxidative Stress Bootcamp.com

References
• Pentose Phosphate Pathway:
• All images created with BioRender.com.
• Respiratory (Oxidative) Burst:
• All images created with BioRender.com.
• Ethanol Metabolism:
• All images created with BioRender.com.

AfraTafreeh.com
 AfraTafreeh.com
Biochemistry: Glycogen Bootcamp.com

References
• Glycogenesis and Glycogenolysis
• Glycogen Structure: Boumphreyfr, CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons.
https://commons.wikimedia.org/wiki/File:Glycogen_bonds.png
• Pathway: All images created with BioRender.com.
• Regulation of Glycogen Metabolism
• All images created with BioRender.com.
• Overview of Glycogen Storage Diseases
• All images created with BioRender.com.
• Von Gierke Disease
• All images created with BioRender.com.
• Pompe Disease
• All images created with BioRender.com.
• Cori Disease
• All images created with BioRender.com.
• Andersen Disease
• All images created with BioRender.com.
• McArdle Disease
• All images created with BioRender.com.
• Hers Disease
• All images created with BioRender.com.
• Summary of Glycogen Storage Diseases
• All images created with BioRender.com.
 Biochemistry: Lipid Metabolism Bootcamp.com

References
• Introduction to Lipids
• Fatty Acids: OpenStax College, CC BY 3.0 <https://creativecommons.org/licenses/by/3.0>, via Wikimedia Commons.
<https://upload.wikimedia.org/wikipedia/commons/c/c8/221_Fatty_Acids_Shapes-01.jpg>
• Triglycerides: Wolfgang Schaefer, Public domain, via Wikimedia Commons. <https://upload.wikimedia.org/wikipedia/commons/b/be/Fat_triglyceride_shorthand_formula.PNG>
• Cholesterol: BorisTM, Public domain, via Wikimedia Commons. <https://upload.wikimedia.org/wikipedia/commons/9/9a/Cholesterol.svg>
• Cholesteryl Ester: Leyo, Public domain, via Wikimedia Commons. <https://upload.wikimedia.org/wikipedia/commons/7/79/Cholesteryl_nonanoate.png>
• Lipid Digestion and Absorption
• Triglycerides: Wolfgang Schaefer, Public domain, via Wikimedia Commons. <https://upload.wikimedia.org/wikipedia/commons/b/be/Fat_triglyceride_shorthand_formula.PNG>
• Cholesteryl Ester: Leyo, Public domain, via Wikimedia Commons. <https://upload.wikimedia.org/wikipedia/commons/7/79/Cholesteryl_nonanoate.png>
• Acanthocyte: S Bhimji, MD, CC BY 4.0 <https://creativecommons.org/licenses/by/4.0>, via Wikimedia Commons. <https://commons.wikimedia.org/wiki/File:Human_blood_film_with_acanthocytes_01.jpg>
• Introduction to Lipid Transport Proteins and Enzymes
• All images created with BioRender.com.
• Lipid Transport
• All images created with BioRender.com.
• Hyperlipidemia Pharmacology

•
• All images created with BioRender.com.
Familial Dyslipidemias
AfraTafreeh.com
• Supernatant: Mark-shea at English Wikipedia, Public domain, via Wikimedia Commons. <https://upload.wikimedia.org/wikipedia/commons/8/8d/Hyperlipidaemia_-_lipid_in_EDTA_tube.jpg>
• Xanthoma: Min.neel, CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons. <https://upload.wikimedia.org/wikipedia/commons/9/91/Xanthoma.jpg>
• Xanthelasma: Klaus D. Peter, Wiehl, Germany, CC BY 3.0 DE <https://creativecommons.org/licenses/by/3.0/de/deed.en>, via Wikimedia Commons.
<https://upload.wikimedia.org/wikipedia/commons/2/25/Xanthelasma.jpg>
• Tendinous Xanthomas: Anita A Kumar , Ghanshyam Palamaner Subash Shantha , Yadav Srinivasan , N Senthil , K Rajkumar , Neeta Paunikar and MK Sudhakar, CC BY 2.0
<https://creativecommons.org/licenses/by/2.0>, via Wikimedia Commons. <https://upload.wikimedia.org/wikipedia/commons/2/2f/Multiple_hand_xanthomas_18_yo_case_report.jpg>
• Corneal Arcus: Afrodriguezg, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons.
<https://upload.wikimedia.org/wikipedia/commons/5/5f/Arcus_Senilis_%28cropped%29.jpg>
• Adipocytes and Lipolysis
• All images created with BioRender.com.
• Fatty Acid Degradation (β-Oxidation)
• All images created with BioRender.com.
• Fatty Acid Synthesis
• All images created with BioRender.com.
• Disorders of Fatty Acid Metabolism
• All images created with BioRender.com.
• Ketone Synthesis and Oxidation
• All images created with BioRender.com.
• Fed vs. Fasting State
• Amino Acid Catabolism: Mikael Häggström, CC0, via Wikimedia Commons. <https://commons.wikimedia.org/wiki/File:Amino_acid_catabolism_revised.png>