Chemical and Physical Foundations of Biological Systems Section: Content Category 5D

Structure, function, and reactivity of biologically-relevant molecules
The structure of biological molecules forms the basis of their chemical reactions including oligomerization and polymerization. Unique aspects of each type of biological molecule dictate their role in living systems, whether providing structure or information storage, or serving as fuel and catalysts.

The content in this category covers the structure, function, and reactivity of biologically-relevant molecules including the mechanistic considerations that dictate their modes of reactivity. The topics and subtopics are below.

Topic Level Key:

The abbreviations found in parentheses indicate the course(s) in which undergraduate students at many colleges and universities learn about the topics and associated subtopics. The course abbreviations are:

BC = first-semester biochemistry
BIO = two-semester sequence of introductory biology
OC = two-semester sequence of organic chemistry

Please note topics that appear on multiple content lists will be treated differently. Questions will focus on the topics as they are described in the narrative for the content category.

Nucleotides and Nucleic Acids (BC, BIO)

  • Nucleotides and nucleosides: composition
    • Sugar phosphate backbone
    • Pyrimidine, purine residues
  • Deoxyribonucleic acid: DNA; double helix
  • Chemistry (BC)
  • Other functions (BC)

Amino Acids, Peptides, Proteins (OC, BC)

  • Amino acids: description
    • Absolute configuration at the α position
    • Dipolar ions
    • Classification
      • Acidic or basic
      • Hydrophilic or hydrophobic
    • Synthesis of α-amino acids (OC)
      • Strecker Synthesis
      • Gabriel Synthesis
  • Peptides and proteins: reactions
    • Sulfur linkage for cysteine and cystine
    • Peptide linkage: polypeptides and proteins
    • Hydrolysis (BC)
  • General Principles
    • Primary structure of proteins
    • Secondary structure of proteins
    • Tertiary structure of proteins
    • Isoelectric point

The Three-Dimensional Protein Structure (BC)

  • Conformational stability
    • Hydrophobic interactions
    • Solvation layer (entropy)
  • Quaternary structure
  • Denaturing and Folding

Non-Enzymatic Protein Function (BC)

  • Binding
  • Immune system
  • Motor

Lipids (BC, OC)

  • Description, Types
    • Storage
      • Triacyl glycerols
      • Free fatty acids: saponification
    • Structural
      • Phospholipids and phosphatids
      • Sphingolipids (BC)
      • Waxes
    • Signals/cofactors
      • Fat-soluble vitamins
      • Steroids
      • Prostaglandins (BC)

Carbohydrates (OC)

  • Description
    • Nomenclature and classification, common names
    • Absolute configuration
    • Cyclic structure and conformations of hexoses
    • Epimers and anomers
  • Hydrolysis of the glycoside linkage
  • Keto-enol tautomerism of monosaccharides
  • Disaccharides (BC)
  • Polysaccharides (BC)

Aldehydes and Ketones (OC)

  • Description
    • Nomenclature
    • Physical properties
  • Important reactions
    • Nucleophilic addition reactions at C=O bond
      • Acetal, hemiacetal
      • Imine, enamine
      • Hydride reagents
      • Cyanohydrin
    • Oxidation of aldehydes
    • Reactions at adjacent positions: enolate chemistry
      • Keto-enol tautomerism (α-racemization)
      • Aldol condensation, retro-aldol
      • Kinetic versus thermodynamic enolate
  • General principles
    • Effect of substituents on reactivity of C=O; steric hindrance
    • Acidity of α-H; carbanions

Alcohols (OC)

  • Description
    • Nomenclature
    • Physical properties (acidity, hydrogen bonding)
  • Important reactions
    • Oxidation
    • Substitution reactions: SN1 or SN2
    • Protection of alcohols
    • Preparation of mesylates and tosylates

Carboxylic Acids (OC)

  • Description
    • Nomenclature
    • Physical properties
  • Important reactions
    • Carboxyl group reactions
      • Amides (and lactam), esters (and lactone), anhydride formation
      • Reduction
      • Decarboxylation
    • Reactions at 2-position, substitution

Acid Derivatives (Anhydrides, Amides, Esters) (OC)

  • Description
    • Nomenclature
    • Physical properties
  • Important reactions
    • Nucleophilic substitution
    • Transesterification
    • Hydrolysis of amides
  • General principles
    • Relative reactivity of acid derivatives
    • Steric effects
    • Electronic effects
    • Strain (e.g., β-lactams)

Phenols (OC, BC)

  • Oxidation and reduction (e.g., hydroquinones, ubiquinones): biological 2e− redox centers

Polycyclic and Heterocyclic Aromatic Compounds (OC, BC)

  • Biological aromatic heterocycles

To support your studies, see the following video tutorials below from the Khan Academy MCAT Collection. The videos and associated questions were created by the Khan Academy in collaboration with the AAMC and the Robert Wood Johnson Foundation.