Cell, Sub-Organelles and Compartmentalisation of Pathways

Metabolic Pathways and Their Locations

Fed → Insulin → Dephosphorylation

Mnemonic: Insulin Hate HSL

so prick with PIN (PGE, Niacin, Insulin)

ㅤ	Fed state	Fasting state
Hormone	• Insulin (anabolic hormone)	• Glucagon • Hypoglycemia in CAMPil • give Glucagon injection
↳ MOA	• Activates phosphodiesterase • ↓ cAMP	• Activates adenyl cyclase → ATP • ↑ cAMP → activates protein kinase A ↳ Glycogen phosphorylase (activated) ↳ Glycogen synthase (inhibited)
ㅤ	ㅤ	Other Counter-regulatory hormones • Epinephrine/norepinephrine • Growth hormone • Glucocorticoids • Thyroid hormones
State	Dephosphorylated	Phosphorylated
Lipase activated	Lipoprotein Lipase (LPL)	Hormone Sensitive Lipase (HSL) Inhibited by • Insulin • PGE1 • Niacin • Insulin hate HSL • so prick with PIN (PGE, Niacin, Insulin)
↳ Function	• Chylomicron TGA → FA + Glycerol • to enter Adipose cells in fed state	• Adipose TGA → FA + Glycerol • for transport to liver in fasting state
ㅤ	Enzymes & Pathways activated	Enzymes & Pathways activated
Pathways activated	• Glycolysis + • Link Reaction + All anabolic pathways • Glycogen synthesis • Cholesterol synthesis • FA synthesis • Protein synthesis	• Gluconeogenesis + All Catabolic pathways • Glycogenolysis • KB synthesis / breakdown • FA (β) oxidation • Peripheral lipolysis • Amino acid oxidation
Enzymes activated	All anabolic + • Glycogen synthase • Acetyl CoA carboxylase • HMG CoA reductase Glycolysis enzymes • Phosphofructokinase • Pyruvate DH Exception ATP Citrate Lyase ↳ FA synthesis ↳ Citrate → Acetyl CoA ↳ activated by insulin ↳ Active in phosphorylated state	All catabolic + Gluconeogenesis enzymes • Fructose 1 , 6 bisphosphate • Glycogen phosphorylase NOTE: • Gluconeogenesis is anabolic • Glycolysis is catabolic
Compartmentalisation	Cytoplasm	Mitochondria
ㅤ	All above pathways + • Glycogenolysis • HMP shunt	All above except Glycogenolysis + • TCA • ETC • PDH
Others	Cholesterol synthesis (Steroids) ↳ Cytoplasm + SER Bile acid synthesis (Steroids) ↳ Smooth Endoplasmic Reticulum	Oxidised in Peroxisomes ↳ Very long chain fatty acid + ↳ Branched chain Fatty acids
Both	ㅤ	ㅤ
ㅤ	• Start in mitochondria • Finish in cytoplasm	PUBG • Pyrimidine Synthesis • Urea cycle • Haem synthesis (blood) • Gluconeogenesis ↳ Oxaloacetate reaches Cyp for gluconeogenesis

Glycolysis:

Only oxidation pathway without Oxygen.

Only pathway generating ATP without Oxygen.

Only oxidation in Cytoplasm.

Glycolysis	ㅤ
Aerobic process	7 ATPs / Glucose (+ 2 Pyruvate )
↳ Hexokinase	Glucose → Glucose 6 Phosphate • [- 1 ATP] • Irriversible
↳ Phosphofructokinase 1	Fructose 6 P → Fructose 1, 6 Bisphosphate • [- 1 ATP] • Irriversible
↳ Glyceraldehyde 3 P dehydrogenase	Glyceraldehyde 3 P → 1, 3 biphosphoglycerate • [+ 2 NADH = + 5 ATP]
↳ Phosphoglycerate kinase	1, 3 biphosphoglycerate → 3 phosphoglycerate • [+ 2 ATP] • Substrate level Phosphorylation
↳ Pyruvate kinase	Phosphoenolpyruvate → Pyruvate • [+ 2 ATP] • Substrate level Phosphorylation • Irriversible
Anaerobic process	2 ATPs / Glucose (+ 2 Lactate)
ㅤ	In Red Blood Cells • RBCs lack mitochondria • Cannot perform aerobic respiration
Link Reaction	Gain 5 ATP / Glucose
ㅤ	Oxidative decarboxylation • Pyruvate (3C) + NAD + CoA →Acetyl CoA (2C) + NADH + CO2
Total ATP at this stage:	7 ATPs + 5 ATPs = 12 ATPs.
TCA Cycle	• Always active (fed/fasting) • Amphibolic Pathway
1. Rate-limiting enzyme / Regulatory Enzymes:	• Irreversible
↳ Citrate synthase	ㅤ
↳ Isocitrate dehydrogenase	1st oxidative decarboxylation
↳ α-Ketoglutarate dehydrogenase	2nd oxidative decarboxylation
2. Substrate-level phosphorylation	• Gain 1 GTP (1 ATP) per Acetyl CoA
↳ Succinate thiokinase	Succinyl-CoA → Succinate
3. NADH Yielding	• Gain 3 NADH (7.5 ATP) per Acetyl CoA
↳ Isocitrate dehydrogenase	Isocitrate → α-Ketoglutarate
↳ α-Ketoglutarate dehydrogenase	α-Ketoglutarate → Succinyl-CoA
↳ Malate dehydrogenase	Malate → Oxaloacetate
4. FADH Yielding	• Gain 1 FADH (1.5 ATP) per Acetyl CoA
↳ Succinate dehydrogenase	Succinate → Fumarate
TCA Cycle Energetics	ㅤ
• Per Acetyl-CoA	10 ATP (Per Cycle x 2 = 20 ATP)
• Per Pyruvate ↳ (PDH + TCA) ↳ Add 2.5 ATP from Link reaction	12.5 ATP
• Per Glucose ↳ (Glycolysis + PDH + TCA)	32 ATP

Ketone bodies:

Products of incomplete fatty acid oxidation.

Complete oxidation:

n-carbon fatty acid yields n/2 Acetyl CoA.
Acetyl CoA enters Citric acid cycle, exhaled as CO₂.

Incomplete oxidation:

Acetyl CoA does not enter Citric acid cycle.
Molecules condense to form ketone bodies.

Three ketone bodies:

Ketone Bodies	Features
Acetone	• Volatile → fruity odour in breath
Acetoacetate	• Primary ketone body • Detected in Urine tests
β-Hydroxybutyrate	• M/c KB utilized (Predominant) • Secondary Ketone Body • Most acidic

Ketone body utilisation KLP

Can’t use ketone bodies:

Cells	D/t absence of
RBCs	Mitochondria
Liver cells	Thiophorase

Don't Confuse “thio” enzymes

Enzyme	Reaction	Relevance
Thiophorase / Succinyl CoA - Acetoaceyl CoA transferase/ β-ketoacyl-CoA transferase	Acetoacetate → Acetoacetyl CoA	• Absent in Liver • Cannot utilize Ketone body
Thiolase	Acetoacetyl CoA → 2 acetyl CoA	• Last steps of β oxidation
Thiokinase	Acyl CoA → Trans enoyl CoA	• Initial steps of β oxidation

Don't Confuse

Fate of Acetyl CoA	Enzyme	Note
↳ Fatty acid synthesis	Acetyl CoA Carboxylase	• Stored as Triacylglycerol
↳ Cholesterol synthesis	HMG-CoA reductase	• In fed state • Stored as Cholesterol ester • RLE in cholesterol synthesis • ⛔ by statins
↳ KB Synthesis	HMG-CoA lyase	• In Starvation

NOTE:

HMG-CoA synthase

Common in both cholesterol and KB synthesis
RLE in ketone body synthesis

Urea cycle (Krebs-Henseleit / Ornithine Cycle)

Converts toxic Ammonia into non-toxic urea.

Ammonia is released from amino acid oxidation.

Site: Liver

Organelle: Cytoplasm + Mitochondria

Enzyme: CPS-I (Rate limiting)

Energetics

CPS-I: 2 ATP
AS synthetase: 2 ATP
Total: 4 ATP used

Contributions

1st Nitrogen: Ammonia

2nd Nitrogen: Aspartate

Carbon atom: Respiratory CO₂

Reactions in Cytoplasm + Mitochondria (PUBG)

Pyrimidine synthesis

Urea cycle

Blood: Heme synthesis

Gluconeogenesis

Urea cycle enzyme Defect	Disorder
CPS I	Hyperammonemia Type I
OTC	Hyperammonemia Type II
AS synthetase	Citrullinemia Type I
Citrin transporter	Citrullinemia Type II
AS lyase	Argininosuccinic aciduria
Arginase	Argininemia
Ornithine transporter	HHH syndrome

Fed and Fasting States diet source

Major sources of plasma glucose during starvation:

Dietary glucose

2 to 2 and half hours

Liver glycogenolysis

Major source of Glucose for 1st 16 hrs of starvation

Gluconeogenesis

Occurs from 6 hours up to 2-3 weeks of starvation.

Stage	Duration After Food Intake	Primary Energy Source
Early Fasting	4–16 hours	Hepatic glycogenolysis
Fasting	16–48 hours	Gluconeogenesis
Prolonged Fasting/ Starvation	48 hours – 5 days	Ketone body synthesis
Prolonged Starvation	>5 days	Muscle proteolysis

Tissue/State	Well-fed State (2 hr)	Fasting (12 - 18 hr)	Starvation (1 - 3 days)
RBCs	Glucose	Glucose	Glucose
White muscle fibers	Glucose	Glucose	Glucose
Neurons	Glucose	Glucose	Ketone bodies
Cardiac muscle	Fatty acids	Fatty acids	Ketone bodies
Red muscle fibers	Fatty acids	Fatty acids	Ketone bodies
Liver	Glucose	FA	FA (Gluconeogenesis → AA, Glycerol)
Adipose	Glucose	FA	FA
Main Fuel	Carbs	Fat	Ketone bodies

Ketone bodies utilized by BHeeM

B (Brain) H (Heart) M (Red Muscle)

Cell and Sub-Organelles

Marker Enzymes of Organelles

Organelle	Marker Enzyme
Nucleus	DNA or RNA Polymerase
Endoplasmic Reticulum MICROSOMES	Glucose-6-Phosphatase
Golgi complex	Glucosyl transferase / Galactosyl transferase Mnemonic: GGG
Mitochondria Outer Membrane	Mono amino Oxidase (MAO) Mnemonic: OM → MAO
Mitochondria Inner Membrane	Complex 2 of ETC/SDH or Complex 5 of ETC/ATP synthase
Cytoplasm	Lactate dehydrogenase
Lysosomes	Cathepsin
Peroxisomes	Catalase

Sub organelles

Peroxisomes:

Functions

Beta oxidation of Very long chain fatty acids.

Oxidation of branched chain fatty acids.

Glycine and Taurine conjugation of bile acids.

Bile acids are derivatives of Cholesterol.

Ether lipid synthesis.

Generate Hydrogen peroxide.

Detoxified by Catalase enzyme.
Pseudocatalase:

Commercial/drug form
Used to treat free radical disorders.

E.g., Vitiligo.

Enzymes produced by peroxisomes

Plasmalogens: Abundant in myelin sheath of nerve fibres.
Luciferase: Responsible for glow in fireflies.

Refsum's disease

Defect: Phytanoyl-CoA oxidase (hydroxylase) deficiency.

Pathogenesis:

↓ α-oxidation of branched chain FA (phytanic acid)

In peroxisomes
Mnemonic: Refsum → Referee for Fight (Phytanic acid) → RIP

accumulation of phytanic acid.

Mnemonic: RIPC

Retinitis pigmentosa
Ichthyosis (scaly skin)

Peripheral neuropathy
Cardiac arrhythmias

Course:

Asymptomatic > symptomatic (worsens with curd/milk).

Management:

Restrict dairy & green vegetables.

Curd, Milk, Goat Meat

Zellweger syndrome

Cerebrohepatorenal Disease

Defect:

Peroxisome targeting sequence (PTS) mutation.
PEX gene mutation ?

PEX codes for peroxins
(Proteins for peroxisome synthesis)

Inheritance: AR

Pathology:

Peroxisomes lack enzymes ("peroxisomal ghost").
Accumulation of VLCFA & phytanic acid

↓ plasmalogens
Neurological damage.

Mnemonic:

Zettle (Zellweger) Down (resemble downs) with brush (Brushfield spots in eye) → Ghost (Ghost peroxisomes)

Clinical features (resembles Down’s syndrome):

Mongoloid facies
Hypertelorism
Unslanting palpebral fissure
Frontal bossing, high forehead
Brushfield spots
Intellectual disability

Adrenoleukodystrophy

Defect in transport proteins.

↑↑ VLCFA's → Neurological impairment.

Lysosomes

Cell's "recycle bin".

Functions

Acid mediated destruction

H+ ATPase acid hydrolase
Acid hydroxylase enzyme

Self-destruction / Suicidal bags / Residual bodies
Autophagy in Starvation

Late stages of starvation
Lysosomes engulf mitochondria
Proteins are released from mitochondria
Undergo metabolism
Energy for survival

Chediak Higashi Syndrome

Normally, CHSI gene produces LYST

Defect:

Mutation in the CHSI gene
LYST gene defect

(Lysocontsomal transport protein)

Lysosomal defect.

No phagocytosis
Phagolysosome fusion doesn’t happen

Microtubule

Note:

Neutrophils contain a high content of lysosomes.
Thus patients are more prone to bacterial infections

Mnemonic: Chediyod Higashikk Lust (lyst → lysosomal) thonni →

Fat () giant () deaf () child with sliver grey hair
Fat

Fever, recurrent infections
Albinism
Thrombocytopenia

Deaf
Giant

Giant (coarse) granules in neutrophils

Mitochondria

Known as the powerhouse of the cell.

Most oxidation processes occur here.

Require Oxygen.

Functions:

Electron transport chain (ETC) complexes:

Located on inner side of inner mitochondrial membrane.

All citric acid cycle enzymes are within mitochondria.

Fatty acids get oxidized in mitochondria.

Part of heme synthesis and urea cycle occurs in mitochondria.

Contain Pyruvate Dehydrogenase (PDH) complex:

Converts Pyruvate to Acetyl CoA.
Links glycolysis to Citric acid cycle.

First step of Gluconeogenesis:

Pyruvate converted to Oxaloacetate.
Catalyzed by Pyruvate carboxylase.

Marker enzymes:

Outer membrane (OM):

Mono amino oxidase (MAO).

Inner membrane:

Complex II of ETC: Succinate dehydrogenase (SDH).
Complex V of ETC: ATP synthase.

Mitochondrial DNA

Mitochondria has own DNA (Endosymbiotic theory).

Inherited from only mother

Has only 1% cellular DNA

Double stranded circular without introns

Not associated with histone proteins

Codes for 13/67 ETC proteins, not all of them

It codes for more than 20% of respiratory chain enzymes

It has 16,000 base pairs

DNA Polymerase: Gamma

10 times more prone to mutations than human DNA (5-10 times)

due to lack of introns

absence of DNA repair enzymes

high production of oxygen-free radicals from ETC

No proof reading

Possesses its own ribosomes for protein synthesis.

Follows a unique genetic code.

Found exclusively in eukaryotes and resembles prokaryotic DNA.

Cannot function without nuclear DNA

To produce enzymes for ATP synthesis

Endoplasmic Reticulum / Microsome

Aka Microsome.

Attached to outer nuclear membrane.

Smooth ER:

Steroid synthesis (e.g., Cholesterol, bile acids).

Rough ER:

ER with Ribosomes.
Protein synthesis.

Microsomal enzyme marker:

Glucose-6-phosphatase.

Involved in gluconeogenesis.

Eukaryote ribosomes

Ribosomes read and translate mRNA.

Involved in protein synthesis and translation.

Eukaryotic ribosomes are 80s.

A → 60s → large subunit.
B → 40s → small subunit.

Functional mRNA

After 3 post-transcriptional modifications,

functional mRNA is formed.

It exits the nucleus and enters the cytoplasm.

Golgi Complex

Has a Cis Golgi (receiving side).

Has a Trans Golgi.

Marker enzymes:

Glucosyl transferase / Galactosyl transferase.

Location

Near RER
SUPRANUCLEAR in position

Functions:

Post-translational modifications.

Proteins from RER enter Cis face of Golgi
Glycosylation

Adds carbohydrate chains
Forms glycoproteins
Glycoproteins have increased stability

Modified proteins stored in vesicles
Released from Trans face upon stimulus

Protein sorting

Decides final destination of proteins
Example:

Protein + mannose-6-phosphate (tag)

By Phosphotransferase

Moves to Lysosome for degradation

I-cell Disease

Inheritance: Autosomal recessive

Category: Lysosomal storage disorder

Absence of phosphotransferase (N-acetylglucosaminyl-1-phosphotransferase)

Features

Coarse facial features
Gingival hyperplasia
Clouded corneas
Restricted joint movements
Claw hand deformities
Kyphoscoliosis
High plasma levels of lysosomal enzymes