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SJMC Biochemistry - DNA & RNA: Complete Notes

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1. Structure of DNA / Watson and Crick Model of DNA

Background

Chemical Components of DNA

1. Phosphate group
2. Deoxyribose sugar (5-carbon, lacks -OH at 2' position)
3. Nitrogenous base - either a purine (Adenine, Guanine) or pyrimidine (Cytosine, Thymine)

Key Features of the Watson-Crick (B-form) Model

Chargaff's Rules (Base Pairing)

• Adenine (A) pairs with Thymine (T) - 2 hydrogen bonds
• Guanine (G) pairs with Cytosine (C) - 3 hydrogen bonds
• Therefore: A = T and G = C in any DNA molecule
• Purine always pairs with pyrimidine (complementary base pairing)

Stabilizing Forces

1. Hydrogen bonds between complementary bases (A-T: 2 H-bonds; G-C: 3 H-bonds)
2. Base stacking interactions (hydrophobic, between adjacent bases in the same strand)
3. Phosphodiester bonds linking nucleotides within a strand

Compaction

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2. Functions of DNA

1. Genetic information storage - DNA carries the hereditary blueprint in the sequence of bases; a gene is the segment of DNA encoding a single polypeptide chain
2. Replication - DNA replicates semi-conservatively so each daughter cell receives identical genetic information
3. Transcription template - DNA acts as a template for synthesis of RNA (mRNA, tRNA, rRNA) via RNA polymerase
4. Regulation - Promoters, enhancers, and regulatory elements in non-coding regions control gene expression
5. Mutation and evolution - Controlled variation in DNA sequence drives biological diversity

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3. Types of RNA and Their Functions

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4. Structure and Function of tRNA (Transfer RNA)

Overview

• tRNA molecules contain 70-80 nucleotides
• At least 20 types of tRNA exist in cells - one (or more) for each amino acid
• Synthesized by RNA Polymerase III

Primary Structure - Cloverleaf Pattern

The Four Arms of tRNA:

• At the 3' end: always ends in the sequence -CCA-OH
• The specific amino acid is attached here by aminoacyl-tRNA synthetase enzyme
• This is the site that "charges" tRNA

• Closest to the 5' end
• Named because it contains the modified base dihydrouridine (D)
• Involved in recognition by aminoacyl-tRNA synthetase

• Contains the trinucleotide anticodon sequence
• This is complementary to and base-pairs with the codon on mRNA
• Ensures correct amino acid is incorporated during translation
• Read in the 3'→5' direction (anticodon) matching 5'→3' on mRNA

• Contains ribothymidine (T) and pseudouridine (Ψ)
• Interacts with the ribosome (rRNA) to facilitate peptide bond formation

• Located between the anticodon loop and TΨC loop
• Varies in size - this is what makes each tRNA unique

3D Structure

• The anticodon end is at one tip of the "L"
• The amino acid acceptor end (CCA-3') is at the other tip
• This geometry allows simultaneous interaction with mRNA (at anticodon) and the ribosome peptidyl transferase center (at CCA end)

Functions of tRNA

1. Amino acid transport - physically carries specific amino acids to the ribosome
2. Codon recognition - the anticodon reads the mRNA codon by complementary base pairing (wobble base pairing at 3rd codon position)
3. Adaptor molecule - serves as the link between the nucleotide language of mRNA and the amino acid language of proteins
4. Charging - aminoacyl-tRNA synthetases attach the correct amino acid to the correct tRNA (this is the key step ensuring fidelity of translation)

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5. DNA vs RNA - Key Differences

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"Don't Anticipate Twice Variably" = D-loop, Anticodon loop, TΨC loop, Variable loopThis image shows the continuation of your SJMC Biochemistry 2nd internals PYQs - the topics are already fully covered in my previous answer! Let me give you a clean, organized summary of exactly what's asked here:

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Remaining Topics - SJMC Biochemistry 2nd Internals

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1. Difference Between DNA and RNA

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2. Structure of RNA (General)

• Single-stranded - can fold back on itself to form stem-loop / hairpin structures via intramolecular base pairing
• Sugar = Ribose - has a hydroxyl (-OH) group at the 2' position of the pentose
• Uracil replaces Thymine - uracil lacks the methyl group of thymine
• The backbone is still 3'→5' phosphodiester linkages, same as DNA
• The 2'-OH makes RNA more reactive and less chemically stable than DNA

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3. Types of RNA and Functions

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4. Structure and Function of tRNA (Detailed)

Primary Structure - Cloverleaf

The 4 Loops and 4 Stems:

• Formed by base pairing of 5' and 3' ends
• 3' end always ends in -C-C-A-OH (universal in all tRNAs)
• The amino acid is attached here (esterified to the 3'-OH of terminal adenosine)

• Named for the modified base dihydrouridine (D)
• Recognition site for aminoacyl-tRNA synthetase enzymes

• Contains the anticodon triplet (3 bases)
• Base-pairs with the complementary codon on mRNA at the ribosome A-site
• Wobble position: the 3rd base of the anticodon (5' base of anticodon) can pair with multiple codons (Crick's wobble hypothesis)

• Contains ribothymidine (T) and pseudouridine (Ψ)
• Interacts with 23S/28S rRNA of the large ribosomal subunit
• Positions tRNA correctly in the ribosome

• Between anticodon loop and TΨC loop
• Varies in size (4-21 nucleotides) - distinguishes different tRNA classes

Secondary Structure - L-Shape (3D)

• One end = anticodon (reads mRNA)
• Other end = CCA-3' (carries amino acid)
• These two functional ends are ~7.5 nm apart

Functions of tRNA

1. Amino acid transport - physically delivers the correct amino acid to the growing polypeptide chain
2. Codon decoding - anticodon reads mRNA codons by complementary antiparallel base pairing
3. Adaptor function - bridges the nucleic acid world (mRNA) with the protein world (amino acids)
4. Fidelity of translation - aminoacyl-tRNA synthetases ensure the correct amino acid is attached to the correct tRNA (this is the "second genetic code")
5. Wobble base pairing - a single tRNA can recognize multiple synonymous codons, reducing the number of tRNAs needed to 45 instead of 61

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Quick Summary Table - tRNA Loops

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All content from: Basic Medical Biochemistry - A Clinical Approach, 6th ed. and Ganong's Review of Medical Physiology, 26th ed.

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SJMC Biochemistry 2nd Internals - New Topics

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1. Nucleotides - Structure and Biological Importance

Structure of a Nucleotide

1. Nitrogenous base (purine or pyrimidine)
2. Pentose sugar (ribose in RNA; deoxyribose in DNA)
3. Phosphate group (one, two, or three)

Nitrogenous Bases

Nucleotides of Biological Importance

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2. ATP (Adenosine Triphosphate)

Structure

• Adenine (purine base)
• Ribose (pentose sugar)
• Three phosphate groups (α, β, γ) - linked by phosphoanhydride bonds

High-Energy Phosphate Bonds

• The β-γ and α-β phosphoanhydride bonds are high-energy bonds
• Hydrolysis releases ~7.3 kcal/mol (30.5 kJ/mol) of free energy
• The bond is strained because of repulsion between negatively charged oxygen atoms of adjacent phosphate groups
• The phosphate-adenosine bond (phosphoester bond) releases only ~3.4 kcal/mol - NOT a high-energy bond

ATP Reactions

• ATP → ADP + Pi : releases ~7.3 kcal/mol (most common)
• ATP → AMP + PPi : releases ~7.3 kcal/mol (used in fatty acid activation, DNA synthesis)
• AMP, ADP, ATP interconvert via adenylate kinase: 2 ADP ⇌ ATP + AMP

Functions of ATP

1. Energy currency - powers all energy-requiring cellular processes
2. Muscle contraction - myosin ATPase hydrolyzes ATP
3. Active transport - Na+/K+ ATPase, Ca2+ ATPase pumps
4. Biosynthesis - drives anabolic reactions (protein, nucleic acid, lipid synthesis)
5. Signal transduction - substrate for adenylyl cyclase → cAMP
6. Phosphorylation - protein kinases transfer phosphate from ATP to proteins

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3. Cyclic AMP (cAMP)

Structure

• cAMP = 3',5'-cyclic adenosine monophosphate
• The single phosphate group forms a cyclic ring connecting both the 3' and 5' carbons of ribose
• Formed from ATP by removal of pyrophosphate (PPi)

Metabolism of cAMP

• Phosphodiesterase is inhibited by methylxanthines (caffeine, theophylline) - this prolongs cAMP action

cAMP as a Second Messenger

1. First messenger (hormone/neurotransmitter, e.g., adrenaline, glucagon) binds to GPCR receptor
2. Activated receptor activates stimulatory G-protein (Gs) - Gα subunit exchanges GDP for GTP
3. Gα-GTP activates adenylyl cyclase
4. Adenylyl cyclase converts ATP → cAMP
5. cAMP activates Protein Kinase A (PKA)
6. PKA phosphorylates target proteins → cellular response
7. PKA catalytic subunit enters nucleus and phosphorylates CREB (cAMP Response Element Binding protein) → alters gene transcription
8. Phosphodiesterase degrades cAMP → signal terminates

Biological Effects of cAMP

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4. mRNA (Messenger RNA) - Structure

Overview

• mRNA carries the genetic message (codons) from the nucleus to ribosomes in the cytoplasm
• Constitutes ~5% of total cellular RNA
• Transcribed from DNA by RNA Polymerase II
• Has the shortest half-life among RNAs (minutes to hours)

Structure of Eukaryotic mRNA (5' → 3')

5' CAP — 5' UTR — START CODON (AUG) — CODING SEQUENCE (exons) — STOP CODON — 3' UTR — POLY-A TAIL 3'

Processing of Pre-mRNA (hnRNA → mature mRNA)

1. 5' Capping - addition of 7-methylguanosine
2. 3' Polyadenylation - addition of poly-A tail after AATAAA signal sequence
3. Splicing - removal of introns by spliceosomes; joining of exons

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5. Genetic Code

Definition

Why a Triplet Code?

• 4 bases, so: 4¹ = 4 (too few), 4² = 16 (too few for 20 amino acids), 4³ = 64 (sufficient - used)
• 64 codons specify 20 amino acids + 3 stop codons

Properties of the Genetic Code

Start and Stop Codons

Wobble Hypothesis (Crick, 1966)

• The 3rd base of the codon (3' position) can pair with more than one base in the anticodon
• This is why 45 tRNAs can decode 61 sense codons
• The 1st base of the anticodon (5' position of anticodon) shows "wobble" (flexible pairing)

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6. Chargaff's Rules

The Rules

Significance

• Chargaff's rules provided the biochemical evidence for Watson and Crick's base pairing in the double helix
• A=T: held by 2 hydrogen bonds; G=C: held by 3 hydrogen bonds
• The rules explain why DNA is double-stranded and antiparallel
• Species with high G+C content have more thermally stable DNA (more H-bonds)

Example

• T = 30% (A = T)
• G + C = 40% total → G = 20%, C = 20%

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Quick Revision Summary

Sources: Basic Medical Biochemistry - A Clinical Approach, 6th ed.; Ganong's Review of Medical Physiology, 26th ed.; Guyton & Hall Textbook of Medical Physiology

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SJMC Biochemistry - Hormone Action Topics

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1. Hormones Regulating Blood Glucose

Hypoglycemic Hormone (lowers blood glucose)

Hyperglycemic Hormones (raise blood glucose)

Memory aid: "ACTH, GH, Glucagon, Epinephrine, Cortisol, Thyroid" = all raise blood glucose. Insulin alone lowers it.

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2. Hormonal Regulation of Blood Glucose (Detailed)

Insulin - The Anabolic Hormone

• Rising blood glucose (main trigger)
• Amino acids (arginine, leucine)
• Incretins (GLP-1, GIP) from gut
• Acetylcholine (vagal stimulation)

1. Glucose enters β-cell via GLUT1/GLUT2 transporter
2. Glucose metabolism → ↑ATP
3. ATP closes K⁺-ATP channels → membrane depolarization
4. Voltage-gated Ca²⁺ channels open → Ca²⁺ influx
5. Ca²⁺ triggers exocytosis of insulin granules

Glucagon - The Catabolic Hormone

• Liver: ↑Glycogenolysis → releases glucose into blood
• Liver: ↑Gluconeogenesis (from amino acids, lactate, glycerol)
• Adipose: ↑Lipolysis → releases FFA
• Acts via cAMP → PKA pathway (receptor on liver cells)

Reciprocal Relationship

• Insulin and glucagon are reciprocally secreted: when one is high, the other is low
• Fed state (post-meal): ↑Insulin, ↓Glucagon → glucose stored
• Fasting state: ↓Insulin, ↑Glucagon → glucose mobilized
• Insulin excess → hypoglycemia → convulsions, coma
• Insulin deficiency → diabetes mellitus (chronic hyperglycemia)

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3. Glucose Tolerance Test (GTT)

Oral Glucose Tolerance Test (OGTT) - Standard Procedure

• 3 days of unrestricted diet containing ≥150 g carbohydrate/day
• 10-16 hour overnight fast
• No medications affecting glucose (steroids, thiazides, OCP - stop if possible)
• Patient must be ambulatory (bed rest impairs glucose tolerance)
• Performed 7:00-9:00 AM; patient remains seated; no smoking

1. Fasting plasma glucose measured (baseline)
2. Patient drinks 75 g glucose dissolved in 300 mL water over 5 minutes
3. Plasma glucose measured at 2 hours

• Diagnosis of gestational diabetes mellitus (GDM) - uses 75g or 100g load
• Initial postpartum screening after GDM
• When FPG is borderline (100-125 mg/dL)
• Children with suspected diabetes (dose: 1.75 g/kg, max 75 g)

• Medications (corticosteroids, thiazides, oral contraceptives)
• Intercurrent illness, trauma, stress
• Smoking or caffeine during the test
• Prolonged fasting or carbohydrate restriction before test
• Inactivity, anxiety, time of day

Normal Glucose Tolerance Curve

Blood glucose (mg/dL)

180 |        * (peak ~30-60 min)
160 |      *   *
140 |    *       *
120 |  *           *
100 | *               * (returns to fasting by 2 hrs)
 80 |____________________________
     0    30   60   90   120 min

• Peak at 30-60 minutes (~140 mg/dL max in normal)
• Returns to fasting level by 2 hours
• In diabetes: peak is higher AND fails to return to normal by 2 hours

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4. Thyroid Function Tests (TFTs) - TSH, T3, T4 Hormone Axis

Thyroid Hormone Synthesis

• The thyroid gland secretes two hormones: T4 (Thyroxine) and T3 (Triiodothyronine)
• T4 is the main secretory product (~80%); it has only mild intrinsic activity - it is a prohormone
• T3 is the biologically active hormone; ~80% of circulating T3 comes from peripheral conversion of T4 → T3 (by deiodinase enzymes in liver, kidney, muscle)
• Only about 20% of T3 is directly secreted by the thyroid

• 99.5% of thyroid hormones are protein-bound (to TBG - thyroxine binding globulin) → metabolically inactive

• Only free T3 and free T4 are clinically relevant and biologically active

The Hypothalamic-Pituitary-Thyroid (HPT) Axis

Hypothalamus
    ↓ TRH (Thyrotropin-Releasing Hormone - tripeptide)
Anterior Pituitary (thyrotroph cells)
    ↓ TSH (Thyroid-Stimulating Hormone - glycoprotein)
Thyroid Gland (follicular cells)
    ↓ T4 (80%) + T3 (20%)
Peripheral tissues (liver, kidney)
    → T4 converted to T3 (active form)
    ↓ NEGATIVE FEEDBACK
Back to Hypothalamus + Pituitary (T3/T4 suppress TRH and TSH)

Actions of Thyroid Hormones (T3/T4)

1. Increase basal metabolic rate (BMR) - main action
2. Protein synthesis - essential for growth and development
3. Increase sensitivity of β-adrenergic receptors → enhanced catecholamine response (explains tachycardia, anxiety in hyperthyroidism)
4. Carbohydrate metabolism - increase glycogenolysis, glucose absorption from gut
5. Lipid metabolism - increase lipolysis and cholesterol metabolism
6. CNS development - critical for brain maturation in fetus and infant

Thyroid Function Test Interpretation

Key Clinical Principle

• TSH is the single best screening test for thyroid dysfunction - it is the most sensitive indicator
• TSH is suppressed (<0.01 μU/mL) in hyperthyroidism
• TSH is elevated in primary hypothyroidism
• Free T4 is added for accuracy and to distinguish primary from secondary causes
• Total T3/T4 are unreliable because they vary with TBG levels (affected by pregnancy, OCP, liver disease) - always use FREE fractions

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Quick Summary Card

Sources: Ganong's Review of Medical Physiology, 26th ed.; Goodman & Gilman's Pharmacological Basis of Therapeutics; Tietz Textbook of Laboratory Medicine, 7th ed.; ROSEN's Emergency Medicine

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SJMC Biochemistry - Short Answer Topics

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1. Second Messengers

Definition

The Major Second Messenger Systems

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System 1: cAMP (Cyclic AMP) System - Adenylyl Cyclase Pathway

1. Hormone (first messenger) binds to GPCR receptor on cell surface
2. Receptor activates stimulatory G-protein (Gs) - Gα subunit releases GDP, binds GTP
3. Gα-GTP activates adenylyl cyclase (membrane-bound enzyme)
4. Adenylyl cyclase converts ATP → cAMP (cyclic AMP = 3',5'-AMP)
5. cAMP activates Protein Kinase A (PKA)
6. PKA phosphorylates enzymes/proteins → cellular response
7. Phosphodiesterase degrades cAMP → 5'-AMP (terminates signal)

• ACTH, FSH, LH, TSH, Glucagon, Adrenaline (β receptors), ADH (V2 receptor), PTH, Calcitonin

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System 2: Phospholipid / IP3-DAG System (PLC Pathway)

1. Hormone binds receptor → activates Gq protein → activates Phospholipase C (PLC)
2. PLC cleaves PIP2 (phosphatidylinositol bisphosphate) in the cell membrane into two second messengers:
   • IP3 (Inositol triphosphate) → mobilizes Ca²⁺ from endoplasmic reticulum → Ca²⁺-mediated effects (e.g., smooth muscle contraction, secretion)
   • DAG (Diacylglycerol) → activates Protein Kinase C (PKC) → phosphorylates proteins → cell response
3. DAG's lipid component is arachidonic acid - precursor for prostaglandins and leukotrienes

• Angiotensin II, Catecholamines (α1 receptors), Oxytocin, TRH, GnRH, PTH, Vasopressin (V1 receptor)

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System 3: Calcium-Calmodulin System

1. Hormone opens Ca²⁺ channels (via IP3 or membrane depolarization) → Ca²⁺ enters cell
2. Ca²⁺ binds to calmodulin (a regulatory protein with 4 Ca²⁺ binding sites)
3. Ca²⁺-calmodulin complex changes shape → activates calmodulin-dependent protein kinases
4. Kinases phosphorylate target proteins → cellular response
5. Classic example: activates myosin light chain kinase (MLCK) → smooth muscle contraction

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Summary Table of Second Messengers

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2. Diabetes Mellitus

Definition

Classification (ADA Classification)

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Type 1 Diabetes Mellitus

• Autoimmune destruction of pancreatic β-cells → absolute insulin deficiency
• Genetic susceptibility: HLA-DR/DQ genes on chromosome 6
• Triggered by: viral infection (Coxsackievirus B), toxins, environmental factors
• Gradual β-cell destruction over months to years (prediabetes period)
• Eventually: near-total β-cell loss → no insulin secretion → hyperglycemia

• Anti-GAD65 (glutamic acid decarboxylase) - highest sensitivity (91%)
• Islet Cell Antibodies (ICA)
• Insulin Autoantibodies (IAA) - more common in young children
• IA-2 (tyrosine phosphatase)
• ZnT8A

• Onset usually in childhood/adolescence (but can occur at any age)
• Lean/normal weight
• Absolute insulin deficiency → C-peptide levels very low or absent
• Prone to Diabetic Ketoacidosis (DKA)
• Requires insulin therapy (cannot be managed with oral drugs alone)

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Type 2 Diabetes Mellitus

1. Insulin resistance - cells (liver, muscle, fat) do not respond adequately to insulin
2. Relative insulin deficiency - pancreatic β-cells cannot compensate for the resistance

• Onset usually adult/middle age (but increasingly in young obese individuals)
• Often asymptomatic for years; detected incidentally
• C-peptide levels present (insulin still produced)
• NOT autoimmune
• NOT prone to DKA (but can develop HONK/HHNS)
• Managed with lifestyle modification + oral hypoglycaemics ± insulin

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Diagnostic Criteria for Diabetes (ADA)

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Classic Symptoms of Diabetes (the "3 Polys" + 1)

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Complications of Diabetes

• Diabetic retinopathy - leading cause of blindness in working-age adults
• Diabetic nephropathy - leading cause of end-stage renal disease
• Diabetic neuropathy - sensory loss, pain, autonomic dysfunction

• Coronary artery disease (MI)
• Cerebrovascular disease (stroke)
• Peripheral vascular disease (gangrene, amputation)

• Diabetic Ketoacidosis (DKA) - Type 1; absolute insulin deficiency → ketone body formation → metabolic acidosis
• Hyperosmolar Hyperglycaemic State (HHS/HONK) - Type 2; extreme hyperglycemia, dehydration, no ketoacidosis
• Hypoglycemia - from excessive insulin/OHA therapy

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Key Lab Tests in Diabetes

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3. Hormones Regulating Blood Glucose (Short Answer Version)

• Glucagon (α-cells, pancreas)
• Epinephrine/Adrenaline (adrenal medulla)
• Somatostatin (δ-cells - raises glucose by inhibiting insulin)
• Thyroid hormones (T3/T4)
• ACTH → cortisol (adrenal cortex → gluconeogenesis)
• Cortisol (glucocorticoids)
• Also: Growth Hormone (GH)

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Quick Revision Table

Sources: Guyton & Hall Textbook of Medical Physiology; Henry's Clinical Diagnosis and Management by Laboratory Methods; Tietz Textbook of Laboratory Medicine, 7th ed.