Chapter 5: Carbon-Based Molecules

Introduction to Biological Macromolecules

Biological macromolecules are large, complex molecules essential for life. They are typically polymers, constructed from smaller subunits called monomers, and are linked by covalent bonds. The four major classes are carbohydrates, lipids, proteins, and nucleic acids.

• Polymer: A long molecule built from repeating monomer units.

• Examples: Proteins (amino acids), Nucleic acids (nucleotides).

Proteins

Functions of Proteins

Proteins perform a wide variety of functions in living organisms, making them one of the most versatile macromolecules.

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

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

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

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

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

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

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

• Structural proteins: Provide support (e.g., collagen, keratin).

Structure of Proteins

Proteins are polymers made from amino acid monomers. The sequence and arrangement of amino acids determine the protein's structure and function.

• Amino acids: Monomers that combine to form polypeptides.

• Polypeptide: Polymer of amino acids in a specific sequence.

• Protein: One or more polypeptides with a specific 3D conformation.

Formula for peptide bond formation:

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 carbon atom (α carbon) bonded to four groups:

• Amino group ()

• Carboxyl group ()

• Hydrogen atom

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

Classification of R groups:

• Nonpolar (hydrophobic): 9/20 amino acids

• Polar (hydrophilic): 6/20 amino acids

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

Major Groups of Amino Acids

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

• Nonpolar (hydrophobic)

• Polar (hydrophilic)

• Acidic (negatively charged)

• Basic (positively charged)

Example: Serine is a polar amino acid; Alanine is nonpolar.

Formation of Polypeptides

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

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

• Can consist of a few to thousands of amino acids.

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 3D shape of a single polypeptide, 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 and are responsible for the storage and transmission of genetic information.

• Types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)

• Function: DNA stores genetic information; RNA is 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.

• Phosphodiester linkage: Covalent bond joining nucleotides in a nucleic acid chain.

• Sugar-phosphate backbone: Repeating pattern of sugar and phosphate groups in nucleic acids.

Comparison of DNA and RNA

DNA and RNA differ in structure, function, and types of nitrogenous bases.

Key Terms and Nomenclature

• 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

Learning Outcomes

• Describe structural characteristics and functions of proteins.

• Identify different types of amino acids (polar, nonpolar, charged).

• Discriminate among the different levels of protein organization.

• Predict the functional consequences of single base changes in mRNA (single AA change in protein).

• Describe the role of chaperone proteins in cells, their location and mechanism of action.

• Describe the role of proteasomes in cells, their location and function.

• Describe structural characteristics and functions of nucleic acids.

• Identify different types of nucleotides, recognize nucleotide components, compare and contrast DNA and RNA structures and functions.

Additional info:

• Proteins are synthesized by ribosomes in cells and may require chaperone proteins for proper folding.

• Proteasome degradation is a cellular process for removing damaged or unneeded proteins.

• Single amino acid changes can have significant effects on protein function, as seen in diseases like sickle cell anemia.