Essential Biological Macromolecules: Proteins and Nucleic Acids

Chapter 3: Essential Biological Macromolecules

Introduction

Biological macromolecules are large, complex molecules that are fundamental to the structure and function of living organisms. Two of the most important classes of macromolecules in biology are proteins and nucleic acids. This chapter provides an overview of their structure, function, and significance in cellular processes.

Biopolymers: Proteins

Definition and Importance

• Proteins are polymers composed of amino acid monomers linked by peptide bonds.

• The term proteios is Greek for "first" or "primary," reflecting the fundamental role of proteins in biology.

• Proteins make up approximately 20% of the human body and are present in every cell.

• They account for more than 50% of the dry mass of most cells.

High Protein Sources

• Common dietary sources of protein include: fish, soya protein, almonds, milk, cottage cheese, eggs, whey protein, brown rice, peas, and chicken breast.

Overview of Protein Functions

Proteins perform a wide variety of functions in living organisms. Major categories include:

• Enzymatic proteins: Selective acceleration of chemical reactions. Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules.

• Defensive proteins: Protection against disease. Example: Antibodies inactivate and help destroy viruses and bacteria.

• Storage proteins: Storage of amino acids. Example: Casein in milk stores amino acids for baby mammals; ovalbumin in egg white is a source for developing embryos.

• Transport proteins: Transport of substances. Example: Hemoglobin transports oxygen in blood; other proteins transport molecules across cell membranes.

• Hormonal proteins: Coordination of an organism’s activities. Example: Insulin regulates blood sugar levels.

• Receptor proteins: Response of cell to chemical stimuli. Example: Receptors in nerve cells detect signaling molecules.

• Contractile and motor proteins: Movement. Example: Actin and myosin are responsible for muscle contraction; kinesin moves cellular cargo.

• Structural proteins: Support. Example: Collagen and elastin provide support in connective tissues.

Structure of Proteins

Amino Acid Monomers

• Amino acids are organic molecules with a central carbon (α-carbon) bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).

• The properties of amino acids are determined by their R groups.

• There are 20 standard amino acids found in proteins.

• Essential amino acids are those that must be obtained from the diet because the body cannot synthesize them.

Polypeptides: Amino Acid Polymers

• A polypeptide is a polymer of amino acids linked by peptide bonds (–CO–NH–).

• Each polypeptide has a unique linear sequence of amino acids, with an amino (N-) terminus and a carboxyl (C-) terminus.

• Polypeptides can range from a few to over a thousand amino acids in length.

Making a Polypeptide Chain

• Amino acids are joined by dehydration reactions (removal of water) to form peptide bonds.

• The sequence of amino acids determines the protein’s structure and function.

• The number of possible proteins increases exponentially with length: for a 10-amino acid protein, there are $20^{10}$ possible combinations.

Four Levels of Protein Structure

• Primary structure: The unique sequence of amino acids in a polypeptide.

• Secondary structure: Coils and folds in the polypeptide chain due to hydrogen bonding (e.g., α-helix and β-pleated sheet).

• Tertiary structure: The overall 3D shape of a polypeptide, determined by interactions among R groups (side chains), including hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.

• Quaternary structure: The association of two or more polypeptide chains into a functional protein complex.

Visualizing Proteins

• Protein structures can be represented by ribbon models, space-filling models, and wireframe models to illustrate their 3D conformation.

Protein Structure and Disease

• A change in primary structure (amino acid sequence) can affect a protein’s shape and function.

• Misfolded proteins are associated with diseases such as Alzheimer’s and Parkinson’s.

• Sickle-cell disease is caused by a single amino acid substitution in hemoglobin, leading to abnormal red blood cell shape and health complications.

Denaturation and Renaturation

• Physical and chemical conditions (pH, salt concentration, temperature) can cause proteins to lose their native structure, a process called denaturation.

• Denatured proteins are biologically inactive.

• Some proteins can regain their structure through renaturation.

Protein Folding in the Cell

• Protein folding is a complex process, often requiring molecular chaperones.

• X-ray crystallography is a technique used to determine the 3D structure of proteins.

Macromolecules: Nucleic Acids

Definition and Roles

• Nucleic acids are polymers that store, transmit, and help express hereditary information.

• Two main types: Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).

• DNA encodes genetic instructions for development and functioning; RNA is involved in gene expression and regulation.

The Roles of Nucleic Acids

• The sequence of amino acids in a protein is determined by a gene, which is made of DNA.

• DNA provides directions for its own replication and directs synthesis of messenger RNA (mRNA), which controls protein synthesis (gene expression).

Components of Nucleic Acids

• Nucleic acids are polymers called polynucleotides, made of monomers called nucleotides.

• Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups.

• Nitrogenous bases are classified as pyrimidines (cytosine, thymine, uracil) and purines (adenine, guanine).

• DNA contains deoxyribose sugar; RNA contains ribose sugar.

	DNA	RNA
Number of Strands	Double	Single
Sugar	Deoxyribose	Ribose
Nitrogenous Bases	A, T, G, C	A, U, G, C

Nucleotide Polymers

• Nucleotides are joined by phosphodiester linkages (covalent bonds) between the phosphate group of one nucleotide and the sugar of the next.

• This forms a sugar-phosphate backbone with nitrogenous bases as appendages.

• The sequence of bases along a DNA or RNA polymer is unique for each gene.

Structure of DNA

• DNA consists of two polynucleotide strands forming a double helix.

• The two strands run in opposite 5' to 3' directions (antiparallel).

• Complementary base pairing occurs: Adenine (A) pairs with Thymine (T), and Guanine (G) pairs with Cytosine (C).

• Example: The complementary sequence to 5'-GGCAATT-3' is 3'-CCGTTAA-5'.

Structure of RNA

• RNA is usually single-stranded but can form complementary base pairs within or between molecules.

• In RNA, uracil (U) replaces thymine (T), so A pairs with U.

Summary Table: Proteins vs. Nucleic Acids

Property	Proteins	Nucleic Acids
Monomer	Amino acid	Nucleotide
Bond Type	Peptide bond	Phosphodiester bond
Function	Catalysis, structure, transport, defense, etc.	Genetic information storage and transfer
Examples	Hemoglobin, enzymes, antibodies	DNA, RNA