Chapter 5: Carbon-Based Molecules

Introduction to Biological Macromolecules

Biological macromolecules are large, complex molecules essential for life, constructed from smaller subunits called monomers. The four major classes are carbohydrates, lipids, proteins, and nucleic acids. This guide focuses on proteins and nucleic acids, their structure, function, and significance in cellular processes.

• Polymer: A long molecule built from repeating monomer units, linked by covalent bonds.

• Proteins: Polymers of amino acids with diverse functions.

• Nucleic acids: Polymers of nucleotide monomers, responsible for genetic information storage and transfer.

Proteins

Functions of Proteins

Proteins perform a wide variety of functions in living organisms, each determined by their unique structure.

• Enzymatic proteins: Accelerate chemical reactions (e.g., digestive enzymes hydrolyze food).

• Defensive proteins: Protect against disease (e.g., antibodies).

• Storage proteins: Store amino acids (e.g., casein in milk).

• Transport proteins: Move substances across membranes (e.g., hemoglobin transports oxygen).

• Hormonal proteins: Coordinate organismal activities (e.g., insulin regulates blood sugar).

• Receptor proteins: Respond to chemical stimuli (e.g., nerve cell receptors).

• Contractile and motor proteins: Enable movement (e.g., actin and myosin in muscles).

• Structural proteins: Provide support (e.g., keratin in hair, collagen in connective tissue).

Structure of Proteins

Proteins are polymers composed of amino acids. Their structure determines their function.

• Amino acids: Monomers that combine to form polypeptides.

• Polypeptide: A polymer of amino acids in a specific sequence.

• Protein: One or more polypeptides with a specific three-dimensional conformation.

Key Concept: All proteins are constructed from the same set of 20 amino acids.

Structure of an Amino Acid

Each amino acid has a central (α) carbon atom bonded to four groups:

• Amino group (–NH2)

• Carboxyl group (–COOH)

• Hydrogen atom

• R group (side chain): Variable group that determines the properties of the amino acid

The R group can be:

• Nonpolar (hydrophobic): 9/20 amino acids

• Polar (hydrophilic): 6/20 amino acids

• Ionized (charged at cellular pH): acids and bases, hydrophilic (5/20 amino acids)

Classification of Amino Acids

Amino acids are classified into four major groups based on the properties of their R groups:

• Nonpolar (hydrophobic)

• Polar (hydrophilic)

• Acidic (negatively charged)

• Basic (positively charged)

Example: Serine (Ser, S) is a polar amino acid; Alanine (Ala, A) is nonpolar.

Formation of Polypeptides

Amino acids are joined by dehydration reactions, forming peptide bonds (covalent bonds) between the carboxyl group of one amino acid and the amino group of another.

• Polypeptide: Has an amino end (N-terminus) and a carboxyl end (C-terminus).

• Polypeptides can range from a few to thousands of amino acids.

Equation for peptide bond formation:

Levels of Protein Structure

The function of a protein depends on its conformation, which is organized into four levels:

• Primary structure: Sequence of amino acids in a polypeptide.

• Secondary structure: Local folding patterns (e.g., α-helix, β-sheet) stabilized by hydrogen bonds.

• Tertiary structure: Overall three-dimensional shape, determined by interactions among R groups.

• Quaternary structure: Association of two or more polypeptide chains (oligomeric proteins).

Example: Hemoglobin has quaternary structure, consisting of four polypeptide subunits.

Nucleic Acids

Introduction to Nucleic Acids

Nucleic acids are polymers of nucleotide monomers, essential for the storage, transmission, and expression of genetic information.

• DNA (Deoxyribonucleic acid): Stores genetic information.

• RNA (Ribonucleic acid): Involved in protein synthesis and gene regulation.

Structure of Nucleic Acids

• Nucleotide: Monomer consisting of a nitrogenous base, a pentose sugar, and a phosphate group.

• Sugar-phosphate backbone: Repeating pattern of sugar and phosphate groups, linked by phosphodiester bonds.

• Nitrogenous bases: Purines (adenine, guanine) and pyrimidines (cytosine, thymine, uracil).

Comparison of DNA and RNA

DNA and RNA differ in structure and function. The following table summarizes their main differences:

Key Terms and Concepts

• Protein

• Amino Acid

• Polypeptide

• R group

• Nonpolar

• Polar

• Hydrophobic

• Hydrophilic

• Chaperone protein

• Ubiquitin Proteasome degradation

• Nucleic Acids

• Deoxyribonucleic acid

• Ribonucleic acid

• Sugar-phosphate backbone

• Phosphodiester linkage

• Purine

• Pyrimidine

Summary Table: Protein Structure Levels

Additional info:

• Chaperone proteins assist in the proper folding of other proteins.

• Ubiquitin-proteasome degradation is a cellular process for removing damaged or unneeded proteins.

• Alterations in primary structure (e.g., single amino acid changes) can have significant effects, such as sickle cell anemia.