Comprehensive Study Notes: Foundations of Biochemistry and Molecular Biology

Biomolecules: Structure, Classification, and Properties

Classes of Biomolecules and Their Monomers

Biomolecules are organic molecules essential for life, including carbohydrates, proteins, lipids, and nucleic acids. Each class is composed of specific monomers linked by characteristic bonds.

• Carbohydrates: Monomers are monosaccharides (e.g., glucose); linked by glycosidic bonds.

• Proteins: Monomers are amino acids; linked by peptide bonds.

• Lipids: Composed of fatty acids and glycerol; linked by ester bonds.

• Nucleic Acids: Monomers are nucleotides; linked by phosphodiester bonds.

Domains of Life: Prokaryotes vs. Eukaryotes

Cells are classified into two major domains based on structural and genetic differences.

• Prokaryotes: Lack a nucleus and membrane-bound organelles; examples include Bacteria and Archaea.

• Eukaryotes: Possess a nucleus and organelles; examples include Animals, Plants, Fungi, and Protists.

Simple Definitions of "Omics"

"Omics" refers to fields studying comprehensive sets of biological molecules.

• Genomics: Study of genomes (DNA).

• Proteomics: Study of proteins.

• Metabolomics: Study of metabolites.

Chemical Properties and Interactions

Types and Strength of Noncovalent Interactions

Noncovalent interactions are crucial for biomolecular structure and function.

• Hydrogen bonds: Attraction between a hydrogen atom and an electronegative atom (O, N).

• Ionic interactions: Attraction between oppositely charged ions.

• Van der Waals forces: Weak attractions due to transient dipoles.

• Hydrophobic interactions: Nonpolar molecules aggregate to avoid water.

Hydrogen Bonding and Water Properties

Water's unique properties arise from its ability to form hydrogen bonds.

• High specific heat and cohesion due to hydrogen bonding.

• Solvent for polar and ionic substances.

Amphipathic Molecules and Micelles

Amphipathic molecules contain both hydrophilic and hydrophobic regions, enabling formation of micelles and bilayers.

• Example: Phospholipids in cell membranes.

Acid/Base Properties, pH Scale, Buffers

Acids donate protons; bases accept protons. The pH scale measures hydrogen ion concentration.

• Henderson-Hasselbalch equation:

$pH = pK_a + \log \left( \frac{[A^-]}{[HA]} \right)$

• Buffers: Solutions that resist changes in pH.

Macromolecules: Structure and Function

Carbohydrates: Structure and Classification

Carbohydrates are classified by size and linkage.

• Monosaccharides: Simple sugars (e.g., glucose).

• Disaccharides: Two monosaccharides linked (e.g., sucrose).

• Polysaccharides: Long chains (e.g., starch, glycogen).

Carbohydrate Functions

• Energy storage: Starch in plants, glycogen in animals.

• Structural: Cellulose in plants, chitin in fungi.

Homopolysaccharides vs. Heteropolysaccharides

• Homopolysaccharides: Composed of one type of monosaccharide (e.g., cellulose).

• Heteropolysaccharides: Composed of multiple types (e.g., glycosaminoglycans).

Cyclization and Glycosidic Bonds

• Cyclization: Monosaccharides form ring structures in solution.

• Glycosidic bonds: Link monosaccharides in oligo- and polysaccharides.

Amino Acids and Proteins

Amino Acid Structure and Stereochemistry

Amino acids have a central carbon (α-carbon) bonded to an amino group, carboxyl group, hydrogen, and variable side chain (R group).

• Stereochemistry: Most amino acids are L-isomers.

Classification and Abbreviations

• Nonpolar, polar, acidic, and basic amino acids.

• Three-letter and one-letter abbreviations (e.g., Gly/G).

pKa, pI, and Zwitterions

• pKa: Acid dissociation constant for functional groups.

• pI (isoelectric point): pH at which amino acid has no net charge.

• Zwitterion: Molecule with both positive and negative charges.

Peptide Bond Formation and Cleavage

• Peptide bond: Amide linkage between amino acids.

• Formation: Condensation reaction; cleavage by hydrolysis.

Oligopeptide Properties

• Oligopeptides: Short chains of amino acids (2-20 residues).

• Properties: Sequence determines function and structure.

Nucleic Acids: DNA and RNA

Nucleotides and Nucleosides

• Nucleotide: Nitrogenous base + pentose sugar + phosphate group.

• Nucleoside: Nitrogenous base + pentose sugar.

DNA vs. RNA

• DNA: Deoxyribonucleic acid; double-stranded; stores genetic information.

• RNA: Ribonucleic acid; single-stranded; involved in protein synthesis.

Phosphodiester Bonds

• Linkage: 3' hydroxyl of one sugar to 5' phosphate of next.

Primary and Secondary Structure

• Primary: Sequence of nucleotides.

• Secondary: Double helix (DNA), stem-loop (RNA).

A-DNA vs. B-DNA

• B-DNA: Most common form; right-handed helix.

• A-DNA: More compact; forms under dehydrating conditions.

Supercoiling and Topoisomerases

• Supercoiling: Over- or under-winding of DNA.

• Topoisomerases: Enzymes that relieve supercoiling.

Genomics and Chromosome Structure

Genes, Genomes, and Chromosomes

• Gene: DNA segment coding for a functional product.

• Genome: Complete set of genetic material.

• Chromosome: DNA molecule with associated proteins.

Chromosome Structure and Terminology

• Telomeres: Protective ends of chromosomes.

• Centromeres: Region for spindle attachment during cell division.

• Histones: Proteins that package DNA into nucleosomes.

Heterochromatin vs. Euchromatin

• Heterochromatin: Densely packed, transcriptionally inactive.

• Euchromatin: Loosely packed, transcriptionally active.

DNA Replication and Repair

DNA Polymerase: Structure and Function

• DNA Polymerase: Enzyme synthesizing DNA from template.

• Klenow fragment: Large fragment of DNA Pol I with polymerase and exonuclease activity.

Leading vs. Lagging Strand

• Leading strand: Synthesized continuously.

• Lagging strand: Synthesized discontinuously as Okazaki fragments.

DNA Ligase

• Function: Seals nicks between Okazaki fragments.

Helicase and Topoisomerase

• Helicase: Unwinds DNA helix.

• Topoisomerase: Relieves supercoiling.

Nucleosome in Eukaryotic Replication

• Nucleosome: DNA wrapped around histone octamer.

Telomere Function

• Telomerase: Enzyme that extends telomeres.

DNA Proofreading and Repair

• Proofreading: DNA polymerase corrects errors via 3'→5' exonuclease activity.

• Repair mechanisms: Mismatch repair, excision repair, double-strand break repair.

Gene Expression: Transcription and Translation

Replication, Transcription, and Translation

• Replication: Copying DNA.

• Transcription: Synthesis of RNA from DNA template.

• Translation: Synthesis of protein from mRNA template.

PCR Mechanism and Uses

• Polymerase Chain Reaction (PCR): Amplifies DNA segments using cycles of denaturation, annealing, and extension.

Summary Table: Comparison of DNA and RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Strands	Double	Single
Bases	A, T, G, C	A, U, G, C
Function	Genetic storage	Protein synthesis, regulation

Additional info:

• Some topic headings were inferred and expanded for clarity.

• Definitions and examples were added for completeness.

• Table entries and some explanations were logically grouped and expanded.