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glycolysis metabolic pathway diagram

This pathophysiology diagram illustrates the glycolysis pathway as a therapeutic target for anti-inflammatory strategies. The metabolic flowchart depicts the sequence from glucose entry via the Glut1 transporter through various intermediates including glucose-6-phosphate, fructose-1,6-bisphosphate, and glyceraldehyde-3-phosphate, culminating in pyruvate entry into the Krebs cycle within the mitochondria. Key regulatory interventions are highlighted: 2-DG (2-deoxyglucose) inhibiting hexokinase to treat inflammatory diseases like SLE, RA, and Guillain-Barré; Heptelidic Acid inhibiting GAPDH for neuroprotective and anti-inflammatory effects; and TEPP-46 promoting the tetramerization of Pyruvate Kinase M2 to inhibit pro-inflammatory markers in sepsis, EAE, and AKI. The diagram identifies specific immune cell types affected by these interventions, such as Th1, Th17, macrophages, and NK cells. The educational focus is on how modulating metabolic enzymes can alter immune cell phenotype and manage systemic inflammatory conditions.

This pathophysiology diagram illustrates the metabolic mechanisms of the glycogen pathway in Lactobacillus acidophilus and its role in probiotic functionality. The diagram shows carbohydrate substrates being imported into the intracellular space through membrane-bound carbohydrate transporters. Once inside, these substrates follow two primary pathways: immediate metabolic processing via glycolysis or diversion to the glycogen biosynthetic pathway to form an intracellular 'carbon pool'. A bidirectional red arrow indicates a regulatory feedback loop between glycolysis and glycogen storage to modulate carbon downflow and energy flux. The glycogen pool is shown to serve three critical functions: regulation of metabolic flux, providing energy for maintenance and stress response, and supporting other crucial cellular processes. These physiological roles collectively contribute to the bacterium's clinical and probiotic attributes, including enhanced bile and stress tolerance, prolonged survival and retention in the GI tract, and improved in vivo competitive fitness within diverse environments such as the dairy matrix and processing facilities.

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TCA citric acid cycle Krebs cycle diagram

This pathophysiology diagram illustrates the integration of transcriptomic and proteomic data within the Tricarboxylic Acid (TCA) cycle, comparing diabetic Goto-Kakizaki (GK) and Brown Norway (BN) rat livers. The central circular diagram depicts the metabolic intermediates of the Krebs cycle, including Citrate, Isocitrate, Ketoglutarate, Succinyl-CoA, Succinate, Fumarate, Malate, and Oxaloacetate. Surrounding tables provide comparative data for key enzymes: Citrate Synthase, Aconitase, Isocitrate Dehydrogenase (Idh2), alpha-Ketoglutarate Dehydrogenase complex (Dld/Dlst), Succinyl-CoA synthetase, Succinate Dehydrogenase (Sdha/b/c/d), Fumarate Hydratase, and Malate Dehydrogenase (Mdh1/2). Each table details acetylation levels, microarray expression, and RNA sequencing results. Vertical arrows within the cycle indicate the impact of acetylation on enzyme activity: a green upward arrow for Malate Dehydrogenase denotes activation, while red downward arrows for Isocitrate Dehydrogenase and Succinate Dehydrogenase denote inhibition. This medical infographic serves as a model for systems-level analysis of metabolic regulation, specifically highlighting how post-translational modifications and mRNA expression levels differ in a diabetic state versus a control.

Educational composite detailing metabolic tracing and experimental neurology. Panel A features a Pathophysiology Diagram of the Tricarboxylic Acid (TCA) cycle, specifically illustrating the metabolic fate of 13C4-labeled succinate. Carbon atoms are represented as spheres, with blue-filled circles indicating the 13C label. The diagram tracks the label through cycle intermediates (fumarate, malate, oxaloacetate, citrate, isocitrate, alpha-ketoglutarate) and spin-out pathways leading to lactate, pyruvate, aspartate, glutamate, and glutamine. Red rectangular outlines highlight metabolites detectable via LC-MS analysis. Labeled enzymes include LDH, ME, PEPCK, and PK. Panel B demonstrates the Experimental Setup in a rat model of cerebral ischemia. It includes a Clinical Photograph of guide cannulas implanted in the left hemisphere, a schematic of a microdialysis catheter showing substrate diffusion across a semi-permeable membrane into brain tissue, and a Diagnostic Histology image (Nissl-stained cryosection). The histology shows the striatum with markers indicating the microdialysis catheter (black arrow) and ET-1 infusion site (red arrow), used to study mitochondrial function in vivo.

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enzyme kinetics Michaelis Menten Lineweaver Burk plot

This pathophysiology diagram illustrates the life cycle of an enzyme, from primary synthesis to catalytic action. The process begins with a primary amino acid chain joined by peptide bonds, which undergoes post-translational modification to form an inactive apoenzyme. The activation phase shows a cofactor or coenzyme (blue sphere) binding to the apoenzyme to create a functional holoenzyme. The catalytic cycle follows the Michaelis-Menten and Induced Fit models in four numbered stages: (1) Formation of the active holoenzyme; (2) Binding of a two-part substrate (labeled A and B) to the active site, inducing a conformational change to form an enzyme-substrate complex; (3) Catalytic conversion of the substrate into products; and (4) Release of the products (gold structures), restoring the free holoenzyme for subsequent reactions. This schematic is designed for basic biochemistry and medical physiology education, emphasizing the structural requirements for enzymatic catalysis and the specific interactions within the active site.

Educational figure illustrating the evolutionary transition from metabolic enzyme to spindle-orientation scaffold in the guanylate kinase (GK) family. Panel A shows an enzyme kinetics plot comparing initial ADP production rates; the human enzyme and ancestral Anc-gkdup show activity, while the later Anc-GK1PID is inactive. Panel B presents a fluorescence anisotropy assay demonstrating that Anc-GK1PID acquired Pins-binding affinity, unlike its predecessor. Panels C-F display immunocytochemical images of mitotic S2 cells alongside radial histograms quantifying spindle orientation. In these panels, the mitotic spindle is visualized in red (tubulin) and the cortical Pins crescent in green (GFP-tagged Pins-Ecd). Panels D (+) control and F (Anc-GK1PID) show robust spindle alignment, evidenced by high-intensity red segments concentrated near 0 degrees on the radial histograms. Conversely, Panel C (-) control and Panel E (Anc-gkdup) exhibit randomized spindle orientation with broader, lower-intensity angular distributions. The figure demonstrates how a specific protein domain evolved to scaffold the mitotic apparatus, a critical mechanism for organized animal tissue development and asymmetric cell division.

Here are your comprehensive Medical Biochemistry Notes for MLS Year 1, drawn from Lippincott's Illustrated Biochemistry (8e), Harper's Illustrated Biochemistry (32e), and Basic Medical Biochemistry: A Clinical Approach (6e).

MEDICAL BIOCHEMISTRY - MLS YEAR 1

Comprehensive Lecture Notes

UNIT 1: CARBOHYDRATES

1.1 Classification of Carbohydrates

Carbohydrates are the most abundant organic molecules in nature. Their general formula is (CH₂O)n, where n ≥ 3.

Classification by size:

Type	Units	Examples
Monosaccharides	1	Glucose, Fructose, Galactose
Disaccharides	2	Sucrose, Lactose, Maltose
Oligosaccharides	3-10	Raffinose
Polysaccharides	>10	Starch, Glycogen, Cellulose

Classification by carbonyl group:

Aldoses - contain an aldehyde group (e.g., glucose, galactose)
Ketoses - contain a ketone group (e.g., fructose)

Isomers and Epimers:

Compounds with the same chemical formula but different structures = isomers
Glucose, fructose, mannose, and galactose all share the formula C₆H₁₂O₆
Epimers differ in configuration around only one specific carbon (e.g., glucose and galactose differ at C-4)

Clinically Important Monosaccharides:

Pentoses (C5): Ribose (in RNA), Deoxyribose (in DNA), Xylulose
Hexoses (C6): Glucose (blood sugar), Galactose (from lactose), Fructose (from sucrose/fruit)

1.2 Glycolysis (Embden-Meyerhof Pathway)

Location: Cytoplasm of all cells
Net reaction: Glucose + 2 NAD⁺ + 2 ADP + 2 Pi → 2 Pyruvate + 2 NADH + 2 ATP + 2 H₂O

Glycolysis and gluconeogenesis metabolic pathway diagram showing enzymes and intermediates

Glycolysis pathway showing all 10 steps with enzymes - Basic Medical Biochemistry

The 10 Steps of Glycolysis:

Investment Phase (uses 2 ATP):

Glucose → Glucose-6-phosphate (enzyme: Hexokinase/Glucokinase; uses 1 ATP)
Glucose-6-phosphate → Fructose-6-phosphate (enzyme: Phosphoglucose isomerase)
Fructose-6-phosphate → Fructose-1,6-bisphosphate (enzyme: Phosphofructokinase-1 [PFK-1]; uses 1 ATP) - key regulatory step
Fructose-1,6-bisphosphate → DHAP + Glyceraldehyde-3-phosphate (enzyme: Aldolase)
DHAP → Glyceraldehyde-3-phosphate (enzyme: Triose phosphate isomerase)

Payoff Phase (produces 4 ATP + 2 NADH): 6. Glyceraldehyde-3-P → 1,3-Bisphosphoglycerate (enzyme: GAPDH; produces NADH) 7. 1,3-BPG → 3-Phosphoglycerate (enzyme: Phosphoglycerate kinase; produces ATP) - substrate-level phosphorylation 8. 3-Phosphoglycerate → 2-Phosphoglycerate (enzyme: Phosphoglycerate mutase) 9. 2-Phosphoglycerate → Phosphoenolpyruvate (enzyme: Enolase) 10. PEP → Pyruvate (enzyme: Pyruvate kinase; produces ATP)

Net yield: 2 ATP + 2 NADH per glucose

Regulation of Glycolysis:

Enzyme	Activated by	Inhibited by
Hexokinase	-	Glucose-6-phosphate (product inhibition)
PFK-1 (key regulator)	AMP, ADP, Fructose-2,6-bisphosphate	ATP, citrate
Pyruvate kinase	Fructose-1,6-bisphosphate	ATP, alanine

Fate of Pyruvate:

Aerobic conditions: Pyruvate → Acetyl-CoA (via pyruvate dehydrogenase complex) → TCA cycle
Anaerobic conditions: Pyruvate → Lactate (via lactate dehydrogenase; regenerates NAD⁺)
In yeast: Pyruvate → Ethanol + CO₂ (fermentation)

1.3 Gluconeogenesis

Definition: Synthesis of glucose from non-carbohydrate precursors
Location: Primarily liver (90% in overnight fast); kidney cortex during prolonged fasting (>48 hrs, ~40%)
When it occurs: During fasting, starvation, prolonged exercise, low-carbohydrate diets

Gluconeogenesis pathway showing key precursors and bypass enzymes

Key reactions of gluconeogenesis - Basic Medical Biochemistry

Gluconeogenic Precursors:

Lactate - from anaerobic glycolysis in RBCs and exercising muscle (Cori cycle: lactate → liver → glucose → back to muscle)
Glycerol - from hydrolysis of triacylglycerols in adipose tissue → glycerol-3-phosphate → DHAP
Amino acids - most are glucogenic (except leucine and lysine which are purely ketogenic)
Odd-chain fatty acids - yield propionyl-CoA → succinyl-CoA → oxaloacetate

Three Bypass Steps (differ from glycolysis):

Glycolysis Step	Enzyme	Gluconeogenesis Bypass	Enzyme(s)
PEP → Pyruvate	Pyruvate kinase	Pyruvate → OAA → PEP	Pyruvate carboxylase (mito) + PEPCK (cyto)
Fructose-6-P → Fructose-1,6-BP	PFK-1	Fructose-1,6-BP → Fructose-6-P	Fructose-1,6-bisphosphatase
Glucose-6-P → Glucose	Hexokinase	Glucose-6-P → Glucose	Glucose-6-phosphatase (ER; liver/kidney only)

Key point: Tissues lacking glucose-6-phosphatase (brain, muscle) cannot release free glucose into blood.

1.4 Glycogen Metabolism

Glycogen = branched polymer of glucose; stored in liver (10% of weight) and muscle (1-2% of weight)

Glycogen Synthesis (Glycogenesis):

Glucose-6-P → Glucose-1-P (phosphoglucomutase)
Glucose-1-P + UTP → UDP-glucose (UDP-glucose pyrophosphorylase)
UDP-glucose added to chain: Glycogen synthase (adds α-1,4 linkages)
Branching enzyme creates α-1,6 branch points every 8-10 residues

Glycogen Breakdown (Glycogenolysis):

Glycogen phosphorylase cleaves α-1,4 bonds → glucose-1-phosphate
Debranching enzyme handles α-1,6 branch points (releases free glucose)
Glucose-1-P → Glucose-6-P → Glucose (in liver, for blood glucose maintenance)

Hormonal Regulation:

Hormone	Effect	Mechanism
Insulin (fed state)	Promotes glycogen synthesis	Activates glycogen synthase
Glucagon (fasting)	Promotes glycogenolysis	Activates phosphorylase (via cAMP)
Epinephrine (stress)	Promotes glycogenolysis (muscle & liver)	Activates phosphorylase (via cAMP)

Glycogen Storage Diseases (for MLS):

Disease	Enzyme Deficiency	Tissue	Lab Finding
Von Gierke (Type I)	Glucose-6-phosphatase	Liver, kidney	Hypoglycemia, lactic acidosis
Pompe (Type II)	Lysosomal α-1,4-glucosidase	All tissues	Cardiomegaly
McArdle (Type V)	Muscle phosphorylase	Muscle	Myoglobinuria on exercise

1.5 Pentose Phosphate Pathway (HMP Shunt)

Location: Cytoplasm (active in liver, RBCs, adrenal cortex, mammary glands)
Purpose: Produces NADPH and ribose-5-phosphate (NOT for ATP)

Two phases:

Oxidative phase (irreversible): Glucose-6-P → Ribulose-5-P + 2 NADPH + CO₂
- Key enzyme: Glucose-6-phosphate dehydrogenase (G6PD)
Non-oxidative phase (reversible): Interconverts sugars; produces ribose-5-P

Products and uses:

NADPH - used in fatty acid synthesis, steroid synthesis, glutathione regeneration, respiratory burst (neutrophils)
Ribose-5-phosphate - nucleotide and nucleic acid synthesis

G6PD Deficiency (MLS importance):

X-linked recessive; most common enzyme deficiency worldwide
RBCs cannot regenerate NADPH → cannot recycle glutathione → hemolytic anemia
Triggered by: oxidant drugs (primaquine, dapsone), fava beans, infections
Lab: Heinz bodies (denatured Hb), bite cells, low G6PD assay

UNIT 2: THE CITRIC ACID CYCLE (TCA / KREBS CYCLE)

2.1 Overview

Location: Mitochondrial matrix
Purpose: Final common pathway for oxidation of carbohydrates, fats, and proteins; generates reducing equivalents (NADH, FADH₂) for oxidative phosphorylation

Entry point: Acetyl-CoA (2 carbons) + Oxaloacetate (4 carbons) → Citrate (6 carbons)

The citric acid cycle with all intermediates and key enzymes

The citric acid cycle - Harper's Illustrated Biochemistry

2.2 The 8 Steps of the TCA Cycle

Step	Reaction	Enzyme	Cofactors/Products
1	Oxaloacetate + Acetyl-CoA → Citrate	Citrate synthase	-
2	Citrate → Isocitrate	Aconitase	-
3	Isocitrate → α-Ketoglutarate	Isocitrate dehydrogenase	NADH, CO₂
4	α-Ketoglutarate → Succinyl-CoA	α-Ketoglutarate dehydrogenase	NADH, CO₂
5	Succinyl-CoA → Succinate	Succinyl-CoA synthetase	GTP
6	Succinate → Fumarate	Succinate dehydrogenase	FADH₂
7	Fumarate → Malate	Fumarase	-
8	Malate → Oxaloacetate	Malate dehydrogenase	NADH

Per turn of TCA cycle:

3 NADH + 1 FADH₂ + 1 GTP + 2 CO₂

Total ATP yield from 1 glucose (via TCA + oxidative phosphorylation):

Glycolysis: 2 ATP + 2 NADH
Pyruvate dehydrogenase: 2 NADH
TCA (x2): 6 NADH + 2 FADH₂ + 2 GTP
Total: ~30-32 ATP

Regulation of TCA cycle:

Activated by: ADP, NAD⁺, Ca²⁺ (in muscle)
Inhibited by: ATP, NADH (product inhibition)
Rate-limiting enzymes: Isocitrate dehydrogenase, α-Ketoglutarate dehydrogenase, Citrate synthase

Anaplerosis vs Cataplerosis:

Anaplerosis = adding carbon to TCA cycle (e.g., pyruvate → oxaloacetate via pyruvate carboxylase)
Cataplerosis = withdrawing carbon (e.g., OAA → PEP for gluconeogenesis)
These must be equal to sustain the cycle

UNIT 3: LIPID METABOLISM

3.1 Fatty Acid Structure and Classification

Saturated fatty acids - no double bonds (e.g., palmitic acid C16:0, stearic acid C18:0)
Unsaturated fatty acids - one or more double bonds

Monounsaturated: one double bond (e.g., oleic acid C18:1)
Polyunsaturated: multiple double bonds (e.g., linoleic acid C18:2)

Essential fatty acids (cannot synthesize; must be in diet):

Linoleic acid (omega-6) - precursor of arachidonic acid → prostaglandins
α-Linolenic acid (omega-3) - precursor of EPA and DHA

3.2 Beta-Oxidation of Fatty Acids

Location: Mitochondrial matrix
Activation: Fatty acid + CoA → Fatty acyl-CoA (in cytoplasm; uses 2 ATP equivalents)
Transport: Long-chain fatty acids enter mitochondria via carnitine shuttle (carnitine acyltransferase I & II)

Each cycle of β-oxidation (removes 2 carbons as Acetyl-CoA):

Oxidation → FADH₂
Hydration
Oxidation → NADH
Thiolysis → Acetyl-CoA + shortened acyl-CoA

ATP yield from palmitate (C16:0):

7 cycles → 7 FADH₂ + 7 NADH + 8 Acetyl-CoA
Each Acetyl-CoA via TCA: ~10 ATP
Total: ~106 ATP (net ~104 after activation cost)

Regulation:

Carnitine transport = rate-limiting step
Malonyl-CoA (from fatty acid synthesis) inhibits carnitine acyltransferase I → prevents futile cycling of synthesis + oxidation

3.3 Ketone Body Metabolism

Where produced: Liver mitochondria (during fasting/starvation)
Ketone bodies: Acetoacetate, β-Hydroxybutyrate, Acetone

Synthesis:

Excess Acetyl-CoA (from β-oxidation when OAA is depleted) → HMG-CoA → Acetoacetate → β-Hydroxybutyrate

Uses:

Fuel for brain, heart, kidney, skeletal muscle during fasting
Brain uses ketones after 3+ days of starvation

Diabetic Ketoacidosis (DKA) - MLS relevance:

Uncontrolled Type 1 diabetes: no insulin → excessive fatty acid oxidation → ketone overproduction
Signs: acetone breath (fruity), Kussmaul respirations (deep rapid breathing to blow off CO₂), metabolic acidosis
Lab: high blood glucose, ketonemia, ketonuria, low blood pH (<7.3), low bicarbonate

3.4 Fatty Acid Synthesis

Location: Cytoplasm (liver, adipose, mammary glands)
Starting material: Acetyl-CoA (from mitochondria, transported via citrate shuttle)
Key enzyme: Fatty acid synthase (FAS) - multi-enzyme complex
Cofactors needed: NADPH (from HMP shunt), Biotin (B7), Pantothenic acid (B5)

Key steps:

Acetyl-CoA + CO₂ → Malonyl-CoA (enzyme: Acetyl-CoA carboxylase; requires biotin; rate-limiting)
Condensation + reduction + dehydration + reduction (repeat 7 times to produce palmitate C16)

Regulation:

Stimulated by: insulin, high glucose (feeds into citrate shuttle)
Inhibited by: glucagon, epinephrine, AMPK

3.5 Cholesterol Metabolism

Endogenous synthesis: Liver primarily; all nucleated cells
Key regulatory enzyme: HMG-CoA reductase (target of statins)

Synthesis pathway: Acetyl-CoA → HMG-CoA → Mevalonate → Isoprenoids → Cholesterol

Lipoproteins (critical for MLS):

Lipoprotein	Origin	Major Lipid	Function
Chylomicrons	Intestine	Triglycerides (dietary)	Transport dietary fat to tissues
VLDL	Liver	Triglycerides (endogenous)	Transport liver TG to tissues
IDL	From VLDL	TG + Cholesterol	Precursor to LDL
LDL	From IDL	Cholesterol	Delivers cholesterol to cells
HDL	Liver/intestine	Protein + cholesterol	Reverse cholesterol transport

Apolipoproteins (MLS exam favorites):

Apo B-100: LDL/VLDL receptor binding
Apo B-48: Chylomicron structural protein
Apo C-II: Activates lipoprotein lipase
Apo E: Remnant receptor binding (VLDL/IDL/chylomicron remnants)
Apo A-I: HDL structural protein; activates LCAT

UNIT 4: PROTEIN AND AMINO ACID METABOLISM

4.1 Classification of Amino Acids

20 standard amino acids - all L-configuration

By R-group:

Type	Examples
Nonpolar/hydrophobic	Glycine, Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Methionine, Tryptophan
Polar/uncharged	Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine
Positively charged (+)	Lysine, Arginine, Histidine
Negatively charged (-)	Aspartate, Glutamate

Essential amino acids (must come from diet - mnemonic: PVT TIM HaLL):
Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine*, Leucine, Lysine
(*Arginine conditionally essential)

Glucogenic vs Ketogenic:

Purely ketogenic: Leucine, Lysine
Both glucogenic & ketogenic: Isoleucine, Phenylalanine, Tyrosine, Tryptophan, Threonine
All others: Purely glucogenic

4.2 Nitrogen Metabolism and Transamination

Transamination: Transfer of amino group from amino acid to α-keto acid
Enzyme: Aminotransferases (transaminases)
Cofactor: Pyridoxal phosphate (PLP = Vitamin B6)

Key reactions:

Alanine + α-Ketoglutarate ⇌ Pyruvate + Glutamate (ALT / alanine aminotransferase)
Aspartate + α-Ketoglutarate ⇌ OAA + Glutamate (AST / aspartate aminotransferase)

MLS significance of ALT and AST:

Both elevated in liver disease (hepatitis)
ALT is more liver-specific → preferred marker for hepatocellular damage
AST:ALT ratio >2 suggests alcoholic liver disease

4.3 Oxidative Deamination and the Urea Cycle

Oxidative deamination: Glutamate → α-Ketoglutarate + NH₃
Enzyme: Glutamate dehydrogenase (mitochondria; uses NAD⁺ or NADP⁺)

Ammonia is toxic (especially to the brain) → must be converted to urea in the liver

Urea Cycle:

Step	Location	Enzyme	Reaction
1	Mitochondria	Carbamoyl phosphate synthetase I	NH₃ + CO₂ → Carbamoyl phosphate
2	Mitochondria	Ornithine transcarbamylase (OTC)	Ornithine + Carbamoyl-P → Citrulline
3	Cytoplasm	Argininosuccinate synthetase	Citrulline + Aspartate → Argininosuccinate
4	Cytoplasm	Argininosuccinate lyase	Argininosuccinate → Arginine + Fumarate
5	Cytoplasm	Arginase	Arginine → Ornithine + Urea

Net: 2 NH₃ + CO₂ → Urea + H₂O (costs 4 ATP equivalents)

Urea cycle disorders → hyperammonemia:

Symptoms: vomiting, lethargy, intellectual disability, coma
Most common: OTC deficiency (X-linked)
Lab: elevated ammonia, elevated glutamine, low BUN

4.4 Amino Acid Catabolism - Key Pathways

Branched-chain amino acids (BCAAs): Leucine, Isoleucine, Valine

Primarily catabolized in muscle (liver has limited capacity)
Defect: Maple Syrup Urine Disease (MSUD) - deficiency of branched-chain α-keto acid dehydrogenase; sweet-smelling urine, neurological damage

Phenylalanine → Tyrosine:

Enzyme: Phenylalanine hydroxylase (requires BH4 cofactor)
Deficiency: Phenylketonuria (PKU) - most common amino acid disorder; fair skin/hair, musty odor, intellectual disability; treat with low-Phe diet

Homocysteine metabolism:

Requires B12 and folate (for remethylation to methionine)
Requires B6 (for transsulfuration to cysteine)
Homocystinuria - elevated homocysteine; cardiovascular risk, lens dislocation

UNIT 5: ENZYMES

5.1 Enzyme Structure and Function

Definition: Biological catalysts (mostly proteins; some RNA = ribozymes)
Active site: Specific region where substrate binds and reaction occurs
Induced fit model: Active site changes shape to accommodate substrate

Cofactors vs Coenzymes:

Term	Definition	Example
Cofactor	Non-protein component required for activity	Metal ions (Zn²⁺, Mg²⁺, Fe²⁺)
Coenzyme (organic cofactor)	Organic molecule; usually derived from vitamins	NAD⁺ (B3), FAD (B2), CoA (B5)
Prosthetic group	Tightly bound cofactor	Heme in cytochrome P450
Apoenzyme	Enzyme without cofactor (inactive)	-
Holoenzyme	Apoenzyme + cofactor (active)	-

Isoenzymes (Isozymes):
Multiple forms of an enzyme catalyzing the same reaction but with different kinetic properties and tissue distribution.

MLS Clinically Important Isoenzymes:

Enzyme	Isoforms	Clinical Use
LDH	LDH-1 (heart), LDH-5 (liver)	Myocardial infarction, liver disease
CK	CK-MM (muscle), CK-MB (heart), CK-BB (brain)	AMI (CK-MB), muscular dystrophy (CK-MM)
ALP	Bone, liver, placenta, intestine	Bone disease, cholestasis
AST/ALT	Both elevated in liver damage	Hepatitis, cirrhosis

5.2 Enzyme Kinetics

Michaelis-Menten Equation:

$$v_0 = \frac{V_{max}[S]}{K_m + [S]}$$

Key parameters:

Vmax - maximum reaction velocity when all enzyme is saturated with substrate
Km (Michaelis constant) - substrate concentration at which v = Vmax/2; reflects enzyme-substrate affinity (low Km = high affinity)
kcat (turnover number) - number of substrate molecules converted per enzyme molecule per second

Lineweaver-Burk Plot (double-reciprocal):

x-axis: 1/[S]; y-axis: 1/v
x-intercept = -1/Km; y-intercept = 1/Vmax; slope = Km/Vmax

5.3 Enzyme Inhibition

Irreversible inhibitors: Form covalent bonds with enzyme (e.g., lead inhibits ferrochelatase; organophosphates inhibit acetylcholinesterase)

Reversible inhibitors:

Type	Mechanism	Effect on Km	Effect on Vmax	Lineweaver-Burk
Competitive	Competes with substrate at active site; overcome by increasing [S]	Increased (apparent)	Unchanged	Lines meet on y-axis
Noncompetitive	Binds allosteric site; cannot be overcome by [S]	Unchanged	Decreased	Lines meet on x-axis
Uncompetitive	Binds only E-S complex	Decreased	Decreased	Parallel lines
Mixed	Binds E or E-S with different affinities	Changes	Decreased	Lines meet in second quadrant

Mnemonics:
Competitive = Km ↑, Vmax same ("C for Changed Km")
Noncompetitive = Vmax ↓, Km same ("Non-violent = Km stays")

Examples of inhibition in pharmacology:

Statins - competitive inhibitors of HMG-CoA reductase (treat hypercholesterolemia)
Methotrexate - competitive inhibitor of dihydrofolate reductase (cancer, RA)
Aspirin - irreversible inhibitor of cyclooxygenase (COX-1 and COX-2)

5.4 Enzyme Regulation

Allosteric regulation - non-substrate molecules bind allosteric sites; change enzyme conformation
Covalent modification - phosphorylation/dephosphorylation (e.g., glycogen phosphorylase)
Proteolytic activation - zymogen (inactive precursor) activated by cleavage (e.g., trypsinogen → trypsin)
Feedback inhibition - end-product inhibits enzyme earlier in pathway
Gene expression - induction/repression of enzyme synthesis (slow response)

UNIT 6: VITAMINS

6.1 Water-Soluble Vitamins (B-complex and Vitamin C)

Vitamin	Active Form	Key Function	Deficiency Disease	Lab Coenzyme Role
B1 (Thiamine)	TPP (thiamine pyrophosphate)	Oxidative decarboxylation (PDH, α-KGD, transketolase)	Beriberi, Wernicke-Korsakoff	Carbohydrate metabolism
B2 (Riboflavin)	FAD, FMN	Electron carrier in β-oxidation, ETC	Ariboflavinosis (angular cheilitis)	β-Oxidation (FADH₂)
B3 (Niacin)	NAD⁺, NADP⁺	Electron carrier in TCA, glycolysis	Pellagra (dermatitis, diarrhea, dementia)	Redox reactions
B5 (Pantothenic acid)	Coenzyme A	Acyl group carrier (acetyl-CoA, succinyl-CoA)	Rare; burning feet syndrome	Fatty acid metabolism
B6 (Pyridoxine)	PLP (pyridoxal phosphate)	Transamination, decarboxylation of amino acids, heme synthesis	Sideroblastic anemia, peripheral neuropathy	Aminotransferases (ALT, AST)
B7 (Biotin)	Biocytin	CO₂ carrier in carboxylations (ACC, pyruvate carboxylase)	Dermatitis, alopecia (raw egg whites bind avidin)	Carboxylation reactions
B9 (Folate)	THF (tetrahydrofolate)	One-carbon transfers; nucleotide synthesis	Megaloblastic anemia, neural tube defects	DNA synthesis
B12 (Cobalamin)	Methylcobalamin, Adenosylcobalamin	Remethylation of homocysteine; odd-chain FA metabolism	Megaloblastic anemia + subacute combined degeneration of cord	Neurological function
C (Ascorbic acid)	Ascorbic acid	Collagen synthesis; antioxidant; iron absorption (Fe³⁺ → Fe²⁺)	Scurvy (bleeding gums, perifollicular hemorrhage)	Prolyl hydroxylase cofactor

Important relationships:

B12 and Folate trap: B12 deficiency traps folate as methyl-THF (methyl trap) → functional folate deficiency → megaloblastic anemia
Both B12 and folate deficiencies cause megaloblastic anemia; only B12 deficiency causes neurological symptoms
Lab distinction: MMA (methylmalonic acid) elevated in B12 deficiency only; homocysteine elevated in both

6.2 Fat-Soluble Vitamins (A, D, E, K)

Vitamin	Active Form	Key Function	Deficiency	Toxicity
A (Retinol)	Retinal (vision), Retinoic acid (gene expression)	Night vision, epithelial integrity, immune function	Night blindness, Bitot's spots, xerophthalmia	Hepatotoxicity, teratogenicity
D (Calciferol)	1,25-(OH)₂D₃ (Calcitriol)	Ca²⁺ and PO₄³⁻ absorption from gut; bone mineralization	Rickets (children), Osteomalacia (adults)	Hypercalcemia, renal stones
E (Tocopherol)	α-Tocopherol	Antioxidant (protects cell membranes from lipid peroxidation)	Hemolytic anemia, peripheral neuropathy (rare)	Anticoagulant effect
K (Phylloquinone)	Menaquinone (K₂)	Carboxylation of clotting factors II, VII, IX, X; proteins C and S	Bleeding diathesis; HDN in newborns	Hemolysis (synthetic K₃)

Vitamin D metabolism (important for MLS):

Sun → Cholecalciferol (D3) in skin (7-dehydrocholesterol + UV)
Liver → 25-hydroxyvitamin D (storage form; measured in serum)
Kidney (1α-hydroxylase) → 1,25-(OH)₂D3 (Calcitriol) (active form)
PTH stimulates renal 1α-hydroxylase
Lab: 25-OH-D3 is the best marker for Vitamin D status

UNIT 7: NUCLEOTIDES AND NUCLEIC ACIDS

7.1 Nucleotide Structure

Nucleoside = Base + Sugar
Nucleotide = Base + Sugar + Phosphate

Purines: Adenine (A), Guanine (G) - double ring
Pyrimidines: Cytosine (C), Thymine (T) [DNA only], Uracil (U) [RNA only] - single ring

Mnemonic: "Pure As Gold" = Purines - A, G; "CUT the Py" = Pyrimidines C, U, T

7.2 Purine and Pyrimidine Synthesis

Purine synthesis:

De novo: Built on ribose-5-phosphate; requires glutamine, glycine, THF, aspartate, CO₂
Salvage pathway: Recycles free purines (HGPRT enzyme; deficiency = Lesch-Nyhan syndrome)

Pyrimidine synthesis:

Ring built first (from carbamoyl phosphate + aspartate), then attached to ribose
Key enzyme: CAD (carbamoyl phosphate synthetase II, aspartate transcarbamylase, dihydroorotase)

Purine catabolism → Uric acid:

AMP → IMP → Hypoxanthine → Xanthine → Uric acid (xanthine oxidase)
GMP → Guanosine → Guanine → Xanthine → Uric acid
Hyperuricemia → Gout (urate crystals in joints); treated with allopurinol (inhibits xanthine oxidase)

7.3 DNA Structure and Replication

Double helix (Watson-Crick):

A pairs with T (2 hydrogen bonds)
G pairs with C (3 hydrogen bonds)
Antiparallel strands (5'→3' and 3'→5')
Sugar-phosphate backbone on outside; bases on inside

DNA Replication (Semiconservative):

Protein/Enzyme	Function
Helicase	Unwinds double helix
Primase	Synthesizes RNA primer
DNA Polymerase III	Synthesizes new DNA (5'→3' direction only)
DNA Polymerase I	Removes RNA primers, fills in gaps
DNA Ligase	Joins Okazaki fragments (lagging strand)
Topoisomerase	Relieves supercoiling ahead of replication fork

Leading strand - synthesized continuously (5'→3')
Lagging strand - synthesized discontinuously as Okazaki fragments (5'→3')

7.4 Protein Synthesis (Translation)

Central Dogma: DNA → RNA → Protein

Transcription:

Template strand read 3'→5'; mRNA synthesized 5'→3'
RNA polymerase (no primer needed)
mRNA processing: 5' cap + poly-A tail + splicing of introns

Translation:

Ribosomes: 80S (eukaryotes) = 60S + 40S; 70S (prokaryotes) = 50S + 30S
tRNA carries amino acids; anticodon pairs with mRNA codon
Start codon: AUG (methionine)
Stop codons: UAA, UAG, UGA ("U Are Away," "U Are Gone," "U Go Away")

UNIT 8: HEMOGLOBIN AND PORPHYRIN METABOLISM

8.1 Hemoglobin Structure

Normal adult hemoglobin:

HbA: α₂β₂ (major adult form, ~97%)
HbA₂: α₂δ₂ (~2.5%)
HbF: α₂γ₂ (fetal; higher O₂ affinity than HbA)

Heme structure: Protoporphyrin IX + Fe²⁺

O₂ binds Fe²⁺ (ferrous); if oxidized to Fe³⁺ (ferric) → methemoglobin (cannot carry O₂)

8.2 Hemoglobin-Oxygen Binding

Sigmoidal dissociation curve: Due to cooperative binding (T state vs R state)

Factors shifting curve RIGHT (decreased O₂ affinity - promotes O₂ release to tissues):

Increased CO₂ (Bohr effect)
Increased H⁺ (acidosis/lower pH)
Increased temperature
Increased 2,3-BPG (bisphosphoglycerate; made in RBCs)

Factors shifting curve LEFT (increased O₂ affinity - Hb holds on to O₂):

Decreased CO₂, decreased H⁺ (alkalosis)
HbF (fewer BPG binding sites)
CO (carbon monoxide binds Hb with 200x affinity of O₂)
Methemoglobin

8.3 Heme Synthesis and Degradation

Heme synthesis:

Begins and ends in mitochondria; middle steps in cytoplasm
Start: Glycine + Succinyl-CoA → δ-Aminolevulinic acid (ALA synthase; requires B6)
Key intermediate: Porphobilinogen → Uroporphyrin → Coproporphyrin → Protoporphyrin IX + Fe²⁺ → Heme

Clinical relevance - Porphyrias:

Porphyria	Enzyme Deficient	Key Feature
AIP (Acute Intermittent)	PBG deaminase	Attacks of abdominal pain, neuropsychiatric symptoms, port-wine urine
PCT (Porphyria Cutanea Tarda)	Uroporphyrinogen decarboxylase	Skin blistering, photosensitivity
Lead poisoning	ALA dehydratase + ferrochelatase	Microcytic anemia, neurological effects

Heme catabolism (MLS bilirubin pathway):

Heme → Biliverdin (heme oxygenase; in macrophages/spleen) → Bilirubin (fat-soluble)
Bilirubin + albumin → liver (unconjugated bilirubin = indirect)
Liver conjugates with glucuronic acid → conjugated bilirubin (direct; water-soluble)
Secreted into bile → intestine → urobilinogen → stercobilin (stool) or urobilin (urine)

Jaundice classification:

Type	Cause	Unconjugated	Conjugated	Urine bilirubin	Stool
Pre-hepatic	Hemolysis	↑↑	Normal	Absent	Normal
Hepatic	Hepatocellular damage	↑	↑	Present	Pale
Post-hepatic	Bile duct obstruction	Normal	↑↑	Present (dark)	Pale/white

UNIT 9: INTEGRATION AND ENERGY METABOLISM

9.1 Fed State vs Fasting State

Parameter	Fed (Absorptive) State	Fasting State
Key hormone	Insulin	Glucagon
Glucose metabolism	Glycolysis, glycogenesis	Glycogenolysis, gluconeogenesis
Fat metabolism	Fatty acid synthesis, TAG storage	Lipolysis, β-oxidation, ketogenesis
Protein metabolism	Protein synthesis	Protein catabolism, gluconeogenesis
Liver function	Takes up glucose	Releases glucose
Adipose	Takes up FA, stores TAG	Releases FA and glycerol
Brain	Uses glucose	Uses ketones (prolonged fast)

9.2 Metabolic Pathways Summary

Pathway	Location	Key Substrate	Key Product	Net ATP
Glycolysis	Cytoplasm	Glucose	Pyruvate	+2
TCA cycle	Mitochondria	Acetyl-CoA	CO₂ + NADH + FADH₂	+2 (GTP)
Oxidative phosphorylation	Inner mito. membrane	NADH, FADH₂	ATP	~28
β-Oxidation	Mitochondria	Fatty acyl-CoA	Acetyl-CoA + NADH + FADH₂	Variable
Gluconeogenesis	Liver/kidney	Lactate, AA, glycerol	Glucose	-6
Fatty acid synthesis	Cytoplasm	Acetyl-CoA	Palmitate	-7
HMP Shunt	Cytoplasm	Glucose-6-P	NADPH + Ribose-5-P	0

QUICK REFERENCE: KEY ENZYMES FOR MLS EXAMS

Enzyme	Pathway	Inhibited By	Clinical Relevance
Hexokinase/Glucokinase	Glycolysis	Glucose-6-P	Glucose regulation
PFK-1	Glycolysis	ATP, citrate	Rate-limiting step
Pyruvate dehydrogenase	Pyruvate → Acetyl-CoA	NADH, ATP	Thiamine deficiency (B1)
Citrate synthase	TCA	ATP, NADH	Entry to TCA
HMG-CoA reductase	Cholesterol synthesis	Statins	Target for lipid-lowering drugs
Acetyl-CoA carboxylase	FA synthesis	Malonyl-CoA, AMPK	Rate-limiting in FA synthesis
Carnitine acyltransferase I	FA transport	Malonyl-CoA	Prevents FA uptake when synthesizing
G6PD	HMP shunt	-	Deficiency causes hemolytic anemia
Phenylalanine hydroxylase	Phe → Tyr	-	Deficiency = PKU
ALA synthase	Heme synthesis	Heme (feedback)	Requires B6; first step
Xanthine oxidase	Purine catabolism	Allopurinol	Target in gout treatment

Sources:

Lippincott's Illustrated Reviews: Biochemistry, 8th ed. - Chapters on carbohydrates, gluconeogenesis, amino acid metabolism, enzyme kinetics
Harper's Illustrated Biochemistry, 32nd ed. - TCA cycle, lipid metabolism, enzyme structure
Basic Medical Biochemistry: A Clinical Approach, 6th ed. - Glycolysis, gluconeogenesis, clinical correlations

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