Proteins and Nucleic Acids: Structure and Function

Proteins

Overview of Proteins

Proteins are polymers whose monomers are amino acids. They are essential macromolecules in all living organisms, performing a wide variety of functions within cells.

• Enzymes: Catalyze specific chemical reactions within the cell.

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

• Cellular Linking: Link cells together and maintain tissue integrity.

• Transport: Move molecules across membranes or within the body (e.g., hemoglobin transports oxygen).

• Defense and Receptors: Involved in immune responses and cell signaling.

• Storage: Store amino acids or other substances for later use.

Amino Acid Structure

All amino acids share a common structure, consisting of:

• Amino group (-NH2)

• Carboxyl group (-COOH)

• Central carbon atom (α-carbon)

• Hydrogen atom

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

Key Point: The R group defines the specific properties of the amino acid.

• If the R group is nonpolar, the amino acid is hydrophobic (e.g., leucine, whose R group is made up of carbon and hydrogen).

• If the R group is polar, the amino acid is hydrophilic (e.g., serine, aspartic acid).

Type	Example	Structure
Hydrophobic	Leucine (Leu)	R group: CH2-CH(CH3)2
Hydrophilic	Serine (Ser)	R group: CH2OH
Hydrophilic (Acidic)	Aspartic acid (Asp)	R group: CH2COOH

How Are Proteins (Polypeptides) Made?

Proteins are formed by linking amino acids together through a dehydration reaction (also called condensation reaction), where the carboxyl group of one amino acid bonds with the amino group of another, releasing water.

• The resulting bond is called a peptide bond, a type of covalent bond.

Peptide bond formation equation:

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

Levels of Protein Structure

• Primary Structure: The linear sequence of amino acids in a polypeptide chain. No definite shape; resembles a beaded chain.

• Secondary Structure: Local folding of the polypeptide chain into structures such as α-helices and β-pleated sheets, stabilized by hydrogen bonds between backbone atoms.

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

• Quaternary Structure: The association of two or more polypeptide chains (subunits) to form a functional protein. Stabilized by the same types of interactions as tertiary structure.

Note: Hydrophobic R group amino acids are typically found on the inside of proteins, away from water.

Nucleic Acids: RNA & DNA

Overview of Nucleic Acids

Nucleic acids are polymers that store and transmit genetic information. The two main types are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

• DNA: Stores genetic material; double-stranded helix.

• RNA: Uses genetic information from DNA to direct protein synthesis; usually single-stranded.

Analogy: DNA is like the legislative branch (creates, stores, and keeps track of the "laws"), while RNA is like the executive and judicial branches (enforces and applies the law).

DNA vs. RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Strands	Double-stranded	Single-stranded
Nitrogenous Bases	Adenine (A), Thymine (T), Cytosine (C), Guanine (G)	Adenine (A), Uracil (U), Cytosine (C), Guanine (G)
Function	Stores genetic information	Transfers and translates genetic information

Nucleotides: The Building Blocks

Nucleotides are the monomers of nucleic acids. Each nucleotide consists of three parts:

• Phosphate group: Contains phosphorus and oxygen.

• Pentose sugar: Ribose in RNA, deoxyribose in DNA.

• Nitrogenous base: Adenine, Thymine (DNA only), Uracil (RNA only), Cytosine, or Guanine.

Nucleotides are joined together by dehydration reactions to form long chains. The bonds between nucleotides are called phosphodiester bonds.

Phosphodiester bond formation equation:

$\text{Nucleotide}_1 + \text{Nucleotide}_2 \rightarrow \text{Dinucleotide} + H_2O$

Summary Table: Parts of a Nucleotide

Component	Description
Phosphate group	Functional group containing phosphorus and oxygen
Pentose sugar	Ribose (RNA) or deoxyribose (DNA)
Nitrogenous base	Adenine, Thymine, Cytosine, Guanine, or Uracil

Example:

In DNA, a nucleotide might consist of a deoxyribose sugar, a phosphate group, and the nitrogenous base adenine.