Proteins and Nucleic Acids: Structure, Function, and Biological Importance

Proteins

Overview and Functions

Proteins are essential macromolecules that account for more than 50% of the dry weight of cells. They perform a wide variety of functions necessary for life.

• Structural: Provide support and shape to cells and tissues (e.g., collagen in connective tissue).

• Contractile: Enable movement (e.g., actin and myosin in muscle contraction).

• Storage: Store nutrients and ions (e.g., ferritin stores iron).

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

• Transport: Carry substances throughout the body (e.g., hemoglobin transports oxygen).

• Signaling: Transmit signals to coordinate biological processes (e.g., insulin regulates glucose metabolism).

• Catalysts: Speed up chemical reactions as enzymes.

Amino Acids: Building Blocks of Proteins

Amino acids are organic molecules composed of carbon (C), hydrogen (H), oxygen (O), and nitrogen (N). They are the monomers that link together to form proteins.

• There are 20 different amino acids found in proteins.

• 9 amino acids are essential in humans, meaning they must be obtained from the diet because the body cannot synthesize them.

• Peptides are chains of amino acids; long peptides are called proteins.

• The function of a protein depends on its chemical structure and unique three-dimensional (3-D) shape.

General Structure of an Amino Acid

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

• Amino group ($-NH_2$)

• Carboxyl group ($-COOH$)

• Hydrogen atom

• R group (side chain): This group is unique for each amino acid and determines its identity and properties.

Example: Glycine has an R group that is a hydrogen atom, while alanine has a methyl group ($-CH_3$).

Classification of Amino Acids

Amino acids can be classified based on the properties of their R groups:

Type	Examples	Properties
Nonpolar, aliphatic	Glycine, Alanine, Valine, Leucine, Methionine, Isoleucine, Proline	Hydrophobic, found in the interior of proteins
Polar, uncharged	Serine, Threonine, Cysteine, Asparagine, Glutamine	Hydrophilic, can form hydrogen bonds
Positively charged (basic)	Lysine, Arginine, Histidine	Hydrophilic, often found on protein surfaces
Negatively charged (acidic)	Aspartate, Glutamate	Hydrophilic, often involved in active sites
Aromatic	Phenylalanine, Tyrosine, Tryptophan	Can absorb UV light, important in protein structure

Peptide Bond Formation

A peptide bond is a covalent bond that links the carboxyl group of one amino acid to the amino group of another, releasing a molecule of water (condensation reaction).

• Peptide bond structure: $\text{C-N}$ bond between amino acids.

• Equation: $\text{Amino acid}_1 + \text{Amino acid}_2 \rightarrow \text{Dipeptide} + H_2O$

Levels of Protein Structure

Proteins have four levels of structural organization:

• Primary structure: Unique sequence of amino acids in a polypeptide chain, determined by genetic information. Held together by peptide bonds.

• Secondary structure: Local folding patterns such as alpha helix and beta pleated sheet, stabilized by hydrogen bonds.

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

• Quaternary structure: Association of two or more polypeptide chains into a functional protein complex (e.g., hemoglobin). Not all proteins have this level.

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

Sickle Cell Anemia: A Protein Structure Disease

Sickle cell anemia is caused by a single amino acid substitution in the hemoglobin protein. This change alters the protein's structure and function.

• Normal hemoglobin: Glutamic acid at position 6 (coded by GAG on chromosome 11).

• Sickle cell hemoglobin: Valine at position 6 (coded by GTG).

• This single base change in DNA leads to abnormal hemoglobin that forms fibers, distorting red blood cells into a sickle shape.

Protein Folding and Chaperones

Proteins must fold into their correct 3-D shapes to function properly. Chaperones or chaperonins are specialized proteins that assist in the folding process.

• Chaperones help prevent misfolding and aggregation.

• They are especially important during the formation of tertiary structure.

Example: The "Folding@Home" project uses distributed computing to simulate protein folding.

Denaturation of Proteins

Denaturation is the process by which a protein loses its native structure and function due to external stress.

• Causes include changes in pH, chemicals, salt concentration, and heat.

• Denatured proteins cannot perform their biological functions.

Enzymes

Enzymes are proteins that act as biological catalysts, speeding up chemical reactions without being consumed or permanently altered.

• Enzymes lower the activation energy required for reactions.

• They are highly specific for their substrates.

Example: Amylase catalyzes the breakdown of starch into sugars.

Nucleic Acids

Overview and Function

Nucleic acids are macromolecules that store and transmit genetic information. They are composed of carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and phosphorus (P).

• DNA (deoxyribonucleic acid): Stores genetic information; double-stranded.

• RNA (ribonucleic acid): Involved in protein synthesis; single-stranded.

Structure of Nucleic Acids

Nucleic acids are polymers of nucleotides, each consisting of three components:

• Nitrogenous base: Adenine (A), Thymine (T, in DNA), Guanine (G), Cytosine (C), Uracil (U, in RNA)

• Pentose sugar: 5-carbon sugar (deoxyribose in DNA, ribose in RNA)

• Phosphate group

Base pairing in DNA: A pairs with T, G pairs with C.

Classification of Nitrogenous Bases

Type	Bases	Structure
Pyrimidines	Cytosine, Thymine (DNA), Uracil (RNA)	Single-ring structure
Purines	Adenine, Guanine	Double-ring structure

Functions of Nucleic Acids

• DNA: Stores hereditary information and codes for proteins.

• RNA: Transfers genetic information from DNA to ribosomes for protein synthesis.

Note: Nucleic acids are not proteins, but they are essential for protein synthesis.

Macromolecule Identification

If a molecule contains H, C, NH, COOH, and R, it is most likely an amino acid.

• Lipid: Composed mainly of C, H, and O; lacks NH and COOH groups.

• Nucleic acid: Contains C, H, O, N, and P; has phosphate groups and nitrogenous bases.

• Carbohydrate: Composed of C, H, and O; lacks NH and R groups.

• Amino acid: Contains C, H, O, N, COOH, NH2, and R group.

Additional info: The notes include questions and diagrams to reinforce understanding of protein and nucleic acid structure, classification, and function, suitable for introductory college chemistry students.