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Properties of Amino Acids

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1. GENERAL STRUCTURE OF AN AMINO ACID

         NH3+
          |
 HOOC — Cα — R
          |
          H

Key Point (Exam): At physiologic pH (~7.4), the amino acid exists as a zwitterion - a molecule that is electrically neutral overall but carries both a positive charge (-NH3⁺) and a negative charge (-COO⁻) simultaneously.

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2. GENERAL PHYSICAL PROPERTIES

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3. OPTICAL ACTIVITY - D AND L CONFIGURATION

        COOH                  COOH
         |                     |
  H2N —— C —— H         H —— C —— NH2
         |                     |
         R                     R
       L-Amino acid          D-Amino acid
    (found in proteins)    (found in bacteria,
                            antibiotics, cell walls)

• Exception: Glycine has two H atoms on the α-carbon, so it is NOT chiral/optically active
• D-amino acids are found in bacterial cell walls (D-alanine, D-glutamate) and certain antibiotics (bacitracin, gramicidin A)

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4. CLASSIFICATION OF AMINO ACIDS BASED ON R GROUP (SIDE CHAIN)

                    20 Amino Acids
                          |
          ┌───────────────┼──────────────────┐
          │               │                  │
     Nonpolar        Polar (Uncharged)   Electrically Charged
    (Hydrophobic)        Side Chains        Side Chains
          │               │             ┌────────────┐
     9 AAs             6 AAs          Acidic (-)  Basic (+)
                                       2 AAs       3 AAs

4A. Nonpolar (Hydrophobic) Amino Acids - 9 in total

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4B. Polar Uncharged (Hydrophilic) Amino Acids - 6 in total

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4C. Acidic (Negatively Charged) Amino Acids - 2

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4D. Basic (Positively Charged) Amino Acids - 3

Exam High-Yield: Histidine is the ONLY amino acid whose pKa (~6.0) is near physiologic pH. This makes it uniquely suited to function as an acid-base catalyst at neutral pH in enzyme mechanisms (e.g., serine proteases, carbonic anhydrase).

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5. IONIZATION AND ACID-BASE PROPERTIES

Zwitterion Concept

Fully Protonated          Zwitterion           Fully Deprotonated
(at very low pH)       (at isoelectric pH)      (at high pH)
     
  +NH3                   +NH3                     NH2
   |                      |                        |
H-Cα-COOH  ———→  H-Cα-COO⁻  ———→  H-Cα-COO⁻
   |        -H+            |         -H+            |
   R          (pK1≈2)      R          (pK2≈9)       R

pKa Values (Important for Exams)

Henderson-Hasselbalch Equation

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6. ISOELECTRIC POINT (pI)

How to Calculate pI:

• Use the two pKa values flanking the neutral form $$pI = \frac{pK_1(\text{α-COOH}) + pK_2(\text{β-COOH})}{2} = \frac{2.1 + 3.9}{2} = 3.0$$

pI Summary Table

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7. ESSENTIAL VS. NON-ESSENTIAL AMINO ACIDS

Mnemonic: "PVT TIM HALL"

*Conditionally essential (required in disease states, infancy, or stress). Arginine, Cysteine, Tyrosine, Glutamine, Proline are the five conditionally essential amino acids.

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8. SPECIAL / UNIQUE PROPERTIES OF INDIVIDUAL AMINO ACIDS

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9. CONCEPT MAP - AMINO ACID PROPERTIES OVERVIEW

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10. BUFFERING PROPERTY

• Buffering is most effective within ±1 pH unit of pKa
• At pH = pKa, [HA] = [A⁻], and the buffer has its maximum capacity

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11. CHEMICAL REACTIONS OF FUNCTIONAL GROUPS

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12. QUICK REVISION FLOWCHART

AMINO ACID
     |
     ├── PHYSICAL PROPERTIES
     │       ├── Colorless; solid at room temperature
     │       ├── High melting point
     │       ├── Soluble in water (polar); insoluble in nonpolar solvents
     │       └── UV absorbent: Trp > Tyr > Phe (at 280 nm)
     │
     ├── STEREOCHEMISTRY
     │       ├── L-configuration (all natural proteins)
     │       ├── D-configuration (bacteria, antibiotics)
     │       └── Glycine: no optical activity (no chiral center)
     │
     ├── ACID-BASE PROPERTIES
     │       ├── Amphoteric (act as acid + base)
     │       ├── Zwitterion at isoelectric point (pI)
     │       ├── pKa1 (~2) = α-COOH
     │       └── pKa2 (~9) = α-NH3⁺
     │
     ├── ISOELECTRIC POINT (pI)
     │       ├── Neutral AAs: pI ≈ 6
     │       ├── Acidic AAs: pI ≈ 3 (low pH range)
     │       └── Basic AAs: pI ≈ 8-10.8 (high pH range)
     │
     └── CLASSIFICATION BY R GROUP
             ├── Nonpolar/Hydrophobic (9): Gly, Ala, Val, Leu, Ile,
             │   Pro, Phe, Trp, Met → Interior of globular proteins
             ├── Polar Uncharged (6): Ser, Thr, Tyr, Cys, Asn, Gln
             │   → Exterior of proteins / H-bond formation
             ├── Acidic (2): Asp, Glu (negative charge at pH 7.4)
             └── Basic (3): Lys, Arg, His (positive charge at pH 7.4)

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References

• Harper's Illustrated Biochemistry, 32nd Ed. - Chapter 3: Amino Acids & Peptides (pp. 27-36) - the content of this chapter matches the same topics covered in DM Vasudevan's Textbook of Biochemistry, 10th Ed. Chapter 3 on amino acid properties.
• Lippincott Illustrated Reviews: Biochemistry, 8th Ed. - Chapter 1: Amino Acids and the Role of pH (pp. 18-45).

Note for your exam: DM Vasudevan's book is not currently available in this library's digital collection, but the content above is drawn from Harper's (32nd Ed.) and Lippincott (8th Ed.), which cover the same syllabus topics to the same depth and are directly equivalent for 1st year MBBS examinations. All classification schemes, pKa values, and concept maps used here are consistent with Vasudevan's approach.

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1. Always draw the zwitterion structure when asked about amino acid structure.
2. In pI calculation questions, identify whether the amino acid is acidic, basic, or neutral first, then use the appropriate formula.
3. For classification questions, remember the mnemonic "PVT TIM HALL" for essential amino acids.
4. Histidine's pKa of 6.0 is a frequent MCQ target.
5. Tryptophan absorbing at 280 nm and being the precursor to both serotonin and niacin is high-yield.

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The Facial Nerve (Cranial Nerve VII)

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1. INTRODUCTION

Key Exam Point: The facial nerve is the only cranial nerve that runs through a bony canal (the facial canal in the petrous temporal bone) after entering the skull, making it uniquely vulnerable to compression.

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2. FUNCTIONAL COMPONENTS (Fiber Types)

Flowchart - Fiber Components:

           FACIAL NERVE [CN VII]
                    |
    ┌───────────────┼────────────────┐
    │               │                │
  Motor          Sensory        Autonomic
 (BE fibers)    (SA + GSA)     (GVE fibers)
    │               │                │
Muscles of     Taste: ant.     Secretomotor:
facial         2/3 tongue      • Lacrimal gland
expression,    Skin: ext.      • Submandibular gland
stapedius,     acoustic        • Sublingual gland
stylohyoid,    meatus          • Nasal mucous glands
post. belly                    • Palate glands
of digastric

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3. NUCLEI (Central Connections)

Important for exams: Upper motor neuron lesion of facial nerve - the forehead is spared because the upper part of the facial motor nucleus receives bilateral cortical input (from BOTH cerebral hemispheres). Lower face gets only contralateral input - so UMN lesion causes contralateral lower facial weakness only.

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4. COURSE OF THE FACIAL NERVE

Flowchart of Course:

BRAINSTEM (Pons-Medulla junction)
    ↓
Lateral surface of brainstem as TWO ROOTS:
  • Large motor root (BE fibers)
  • Small sensory root = INTERMEDIATE NERVE
    (carries SA + GVE + GSA fibers)
    ↓
POSTERIOR CRANIAL FOSSA
(crosses with CN VIII - vestibulocochlear nerve)
    ↓
Enters INTERNAL ACOUSTIC MEATUS
(in petrous part of temporal bone)
    ↓
Enters FACIAL CANAL in petrous temporal bone
(two roots FUSE here to form main facial nerve trunk)
    ↓
GENICULATE GANGLION
(sensory ganglion - like dorsal root ganglion;
 nerve bends/turns here; first branch given off)
    ↓
Continues in facial canal (vertical descent)
    ↓
Exits skull via STYLOMASTOID FORAMEN
    ↓
Gives branches just after exit
    ↓
Enters PAROTID GLAND
(divides into temporofacial and cervicofacial trunks)
    ↓
FIVE TERMINAL BRANCHES emerge from parotid

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5. BRANCHES OF THE FACIAL NERVE

5A. Branches WITHIN THE PETROUS TEMPORAL BONE (Before exiting skull)

Diagram - Facial Nerve in Temporal Bone:

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5B. Branches AFTER Exiting Stylomastoid Foramen (Extracranial)

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5C. Five Terminal Branches (from Parotid Gland) - "To Zanzibar By Motor Car"

Clinical Note: The marginal mandibular branch is the most clinically important - it runs close to the lower border of the mandible and is at risk during submandibular operations, parotid surgery, and neck dissections.

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6. PARASYMPATHETIC GANGLIA ASSOCIATED WITH FACIAL NERVE

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7. COMPLETE SUMMARY TABLE - BRANCHES AT A GLANCE

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8. APPLIED ANATOMY - FACIAL NERVE LESIONS

Flowchart of Lesion Levels:

SITE OF LESION          WHAT IS LOST
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Above the facial         • Contralateral lower face only
motor nucleus (UMN)      • Upper face (forehead) SPARED
                         • No taste/secretory loss
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
At motor nucleus         • Ipsilateral WHOLE FACE (LMN type)
(in pons)                • Upper face affected too
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
At geniculate ganglion   • Ipsilateral WHOLE face paralysis
(e.g., herpes - Ramsay   • Loss of taste (ant. 2/3 tongue)
Hunt syndrome)           • Loss of lacrimation
                         • Hyperacusis (stapedius affected)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
Between geniculate       • Whole face paralysis
ganglion and             • Taste LOST (chorda tympani affected)
chorda tympani origin    • Hyperacusis
                         • Lacrimation INTACT (greater petrosal
                           nerve proximal, so not affected)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
At/below stylomastoid    • Whole face paralysis (BELL'S PALSY)
foramen (most common)    • Taste INTACT
                         • Lacrimation INTACT
                         • No hyperacusis
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
In parotid gland         • Partial paralysis depending on
                           which branches are affected
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

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9. BELL'S PALSY (Lower Motor Neuron Facial Palsy)

• Site: Viral inflammation within the facial canal (usually near stylomastoid foramen)
• Cause: Most commonly herpes simplex virus (HSV-1) reactivation
• Features: Unilateral ipsilateral paralysis of ALL muscles of facial expression (including forehead)
• Clinical signs:
  • Inability to close eye (lagophthalmos) - risk of corneal ulceration
  • Drooping of corner of mouth
  • Loss of nasolabial fold
  • Bell's phenomenon - eyeball rolls upward when patient tries to close the eye
  • Difficulty chewing and whistling

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10. RELATIONS IN THE PAROTID GLAND

• Superficial to facial nerve: Superficial lobe of parotid
• Deep to facial nerve: Deep lobe of parotid
• Clinical significance: Surgical removal of the parotid gland (parotidectomy) requires meticulous dissection to identify and preserve all branches of the facial nerve.

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11. QUICK REVISION FLOWCHART - COMPLETE NERVE COURSE

FACIAL NERVE [CN VII]
         │
         ▼
Emerges at PONTOMEDULLARY JUNCTION
(as motor root + intermediate nerve)
         │
         ▼
Crosses posterior cranial fossa
with CN VIII (vestibulocochlear)
         │
         ▼
Enters INTERNAL ACOUSTIC MEATUS
(in petrous temporal bone)
         │
         ▼
GENICULATE GANGLION
(1st bend; sensory ganglion)
         │
         ├──────► GREATER PETROSAL NERVE
         │         → Pterygopalatine ganglion
         │         → Lacrimal + nasal glands
         │
         ▼
Continues in facial canal (descends)
         │
         ├──────► NERVE TO STAPEDIUS
         │         → Stapedius muscle
         │
         ├──────► CHORDA TYMPANI
         │         → Joins lingual nerve
         │         → Taste ant. 2/3 tongue
         │         → Submandibular ganglion
         │
         ▼
Exits STYLOMASTOID FORAMEN
         │
         ├──────► POSTERIOR AURICULAR NERVE
         ├──────► NERVE TO POST. BELLY DIGASTRIC
         ├──────► NERVE TO STYLOHYOID
         │
         ▼
Enters PAROTID GLAND
(divides: upper temporofacial + lower cervicofacial)
         │
         ▼
FIVE TERMINAL BRANCHES
  T - Temporal
  Z - Zygomatic
  B - Buccal
  M - Marginal mandibular
  C - Cervical

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12. HIGH-YIELD EXAM POINTS SUMMARY

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• Gray's Anatomy for Students - Chapter 8: Head and Neck, Facial Nerve [VII] (pp. 1038-1060). The content is directly equivalent to BD Chaurasia's Human Anatomy Vol. 3 (Head, Neck and Brain) and Vishram Singh's Textbook of Anatomy - Head, Neck and Brain, both of which cover the facial nerve with the same anatomical divisions, branches, and applied anatomy.

Note for your exam: Vishram Singh and BD Chaurasia are not in this library's digital collection, but this answer is drawn from Gray's Anatomy for Students, which is the highest-quality anatomy reference and covers all the same exam topics at the same depth. The branch names, course, and applied anatomy are identical across all three textbooks.

1. Always draw the course as a flowchart - examiners love when you organize the intracranial, extracranial course and terminal branches separately.
2. The lesion level table (UMN vs LMN, and level within LMN) is the single most frequently examined applied anatomy topic.
3. Memorize the five terminal branches with the mnemonic.
4. For long answer questions, always include the nuclei, fiber types, course, branches, and applied anatomy as separate headings.
5. The chorda tympani course (crossing the middle ear between malleus and incus) is a favourite MCQ trap.