Nucleic Acids

Structure and Function of Nucleic Acids

Nucleic acids are essential biological macromolecules responsible for the storage, transmission, and expression of genetic information. The two main types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

• Nucleic acids are polymers composed of nucleotide monomers.

• Each nucleotide consists of three components:

  • A phosphate group

  • A five-carbon sugar (deoxyribose in DNA, ribose in RNA)

  • A nitrogenous base (A, C, G, T in DNA; A, C, G, U in RNA)

• Purines (adenine, guanine) have a double-ring structure; pyrimidines (cytosine, thymine, uracil) have a single-ring structure.

• Nucleotides are joined by phosphodiester bonds, forming a sugar-phosphate backbone.

• The 5′ end of a nucleic acid has a phosphate group; the 3′ end has a free hydroxyl group. New nucleotides are added to the 3′ end.

• Polymerase enzymes catalyze nucleic acid polymerization.

DNA and RNA Structure

• DNA is typically double-stranded, forming a double helix stabilized by hydrogen bonds between complementary bases (A-T, C-G).

• RNA is usually single-stranded but can fold into complex three-dimensional shapes, enabling diverse functions.

• Ribozymes are RNA molecules with catalytic activity, supporting the RNA-world hypothesis (the idea that early life used RNA for both information storage and catalysis).

Example: Complementary Base Pairing

If one DNA strand has the sequence 5′-ATCG-3′, the complementary strand is 3′-TAGC-5′.

Proteins

Structure and Levels of Organization

Proteins are polymers of amino acids that perform a vast array of cellular functions, including catalysis, structure, and signaling.

• Each amino acid contains a central carbon, an amino group, a carboxyl group, a hydrogen atom, and an R group (side chain).

• Peptide bonds link amino acids via condensation reactions (water is released).

• Protein structure is organized into four levels:

  • Primary structure: Linear sequence of amino acids.

  • Secondary structure: Local folding into alpha helices and beta sheets stabilized by hydrogen bonds.

  • Tertiary structure: Overall three-dimensional shape of a single polypeptide.

  • Quaternary structure: Association of multiple polypeptide subunits.

• Protein function depends on its structure; denaturation disrupts structure and function.

Enzymes and Catalysis

• Enzymes are proteins that accelerate chemical reactions by lowering activation energy.

• The active site is where the substrate binds and the reaction occurs.

• Enzyme activity is influenced by environmental factors such as pH and temperature.

• Cofactors (inorganic ions or organic molecules) may be required for enzyme function.

Example: Effect of pH on Enzyme Activity

Extreme pH can denature enzymes, reducing their catalytic activity.

Phospholipids & Cell Membranes

Membrane Structure and Properties

The plasma membrane surrounds all cells, maintaining the internal environment and mediating interactions with the external environment.

• Phospholipids are amphipathic, containing hydrophilic (water-attracting) heads and hydrophobic (water-repelling) tails.

• In aqueous environments, phospholipids form a bilayer with hydrophobic tails inward and hydrophilic heads outward.

• The fluid-mosaic model describes the membrane as a dynamic structure with proteins embedded in or associated with the bilayer.

• Membrane fluidity and permeability are influenced by fatty acid saturation, tail length, and cholesterol content.

Membrane Transport Mechanisms

• Simple diffusion: Movement of substances down their concentration gradient without energy input.

• Facilitated diffusion: Movement down a gradient via membrane proteins (channels or carriers).

• Active transport: Movement against a gradient, requiring energy (often ATP).

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Membrane proteins include channels, carriers, and pumps.

Table: Effects of Tonicity on Cells

Example: Predicting Membrane Transport

Glucose moves into cells by facilitated diffusion, while sodium ions may be pumped out by active transport.

Cellular Organization

Prokaryotic vs. Eukaryotic Cells

Cells are classified as prokaryotic or eukaryotic based on structural differences.

• Prokaryotic cells (e.g., bacteria) lack membrane-bound organelles and have a nucleoid region for DNA.

• Eukaryotic cells (e.g., plants, animals, fungi, protists) have membrane-bound organelles and a nucleus.

• Compartmentalization in eukaryotes allows specialized functions in distinct organelles.

Major Organelles and Their Functions

• Nucleus: Stores DNA; surrounded by a nuclear envelope with pores.

• Nucleolus: Site of ribosomal RNA synthesis.

• Rough ER: Studded with ribosomes; synthesizes proteins for secretion or membranes.

• Smooth ER: Lacks ribosomes; involved in lipid synthesis and detoxification.

• Ribosomes: Sites of protein synthesis; found free in cytoplasm or on rough ER.

• Golgi apparatus: Modifies, sorts, and packages proteins and lipids.

• Lysosomes: Contain hydrolytic enzymes for digestion; optimal pH ≈ 5.0.

• Peroxisomes: Carry out specific metabolic reactions, including breakdown of fatty acids.

• Mitochondria: Produce ATP via cellular respiration; contain internal membrane folds (cristae).

• Chloroplasts (plants): Site of photosynthesis.

• Cell wall (plants, fungi, algae): Provides structural support outside the plasma membrane.

• Central vacuole (plants): Stores water and maintains cell turgor.

• Centrioles and lysosomes are characteristic of animal cells.

Endomembrane System and Protein Trafficking

• The endomembrane system includes the ER, Golgi apparatus, lysosomes, and vesicles.

• Proteins destined for secretion follow this pathway: rough ER → transport vesicle → Golgi apparatus → secretory vesicle → plasma membrane (exocytosis).

Cytoskeleton and Cell Movement

• The cytoskeleton consists of microfilaments, intermediate filaments, and microtubules.

• Motor proteins move materials along cytoskeletal tracks.

• Cilia and flagella (eukaryotic) have a 9 + 2 microtubule arrangement (axoneme).

• Prokaryotic and eukaryotic flagella differ structurally and evolved independently.

Extracellular Structures

• The extracellular matrix (ECM) is a network of proteins and polysaccharides outside animal cells, providing support and mediating cell interactions.

• Plants, fungi, and algae have rigid cell walls outside their plasma membranes.

Table: Comparison of Prokaryotic and Eukaryotic Cells

Key Terms and Concepts to Know

• Nucleic acid, nucleotide, DNA, RNA, deoxyribose, ribose, nitrogenous base

• Purine, pyrimidine, phosphodiester bond, sugar-phosphate backbone, 5′ end, 3′ end

• Double helix, complementary base pairing, polymerase, ribozyme, RNA-world hypothesis

• Amino acid, R group, peptide bond, polypeptide, primary/secondary/tertiary/quaternary structure, denaturation, enzyme, substrate, active site, activation energy, cofactor

• Phospholipid, hydrophilic, hydrophobic, amphipathic, lipid bilayer, fluid-mosaic model, membrane fluidity, membrane permeability, concentration gradient, simple diffusion, facilitated diffusion, osmosis, active transport, channel, carrier, pump, isotonic, hypotonic, hypertonic

• Prokaryotic, eukaryotic, nucleoid, plasmid, nucleus, nucleolus, rough ER, smooth ER, ribosome, Golgi apparatus, lysosome, peroxisome, mitochondrion, chloroplast, vacuole, cell wall, endomembrane system, transport vesicle, exocytosis, cytoskeleton, microfilament, intermediate filament, microtubule, motor protein, cilium, flagellum, axoneme, extracellular matrix (ECM)

Skills and Applications

• Identify nucleotide parts and distinguish DNA from RNA.

• Determine complementary DNA sequences.

• Identify 5′ and 3′ ends of nucleic acids and explain nucleotide addition.

• Recognize four levels of protein structure.

• Explain how amino acid side chains and folding affect protein function.

• Identify enzyme substrates and active sites; explain enzyme effects on activation energy.

• Predict effects of pH or temperature on enzyme activity.

• Identify hydrophilic/hydrophobic regions of phospholipids and explain bilayer formation.

• Predict how fatty acid saturation and tail length affect membrane fluidity/permeability.

• Distinguish between simple diffusion, facilitated diffusion, osmosis, and active transport.

• Predict water movement and cell volume changes in different tonicities.

• Distinguish prokaryotic and eukaryotic cells; identify organelles and their functions.

• Trace protein pathways through the endomembrane system.

• Distinguish cytoskeletal components and explain their roles.

• Explain cilia/flagella movement via the 9 + 2 axoneme.

• Describe how ECM and cytoskeleton contribute to cell structure and organization.

Exam Preparation Tips

• Practice explaining concepts from memory and comparing related structures/functions.

• Identify structures from diagrams (nucleotides, amino acids, phospholipids, organelles).

• Predict membrane transport and cell volume changes based on concentration/tonicity.

• Use specific biological terminology in explanations.

• Understand the relationship between structure and function for application questions.

Additional info: For equations, the formation of a peptide bond can be represented as:

The general structure of a nucleotide can be represented as: