UNIT 1: Review of Proteins and Nucleic Acids: Structure and Function

Proteins

Levels of Protein Structure

Proteins are complex biological macromolecules composed of amino acids. Their function is determined by their structure, which is organized into four hierarchical levels.

• Primary Structure (1°): The linear sequence of amino acids in a polypeptide chain, held together by peptide bonds. This sequence determines the protein's final 3D shape.

• Secondary Structure (2°): Local folding of the polypeptide chain into structures such as alpha helices and beta sheets, stabilized by hydrogen bonds between the backbone atoms (specifically, the carbonyl group of one amino acid and the amine group of another).

• Tertiary Structure (3°): The overall 3D shape of a single polypeptide chain, resulting from interactions among the side chains (R groups) of amino acids. These interactions include hydrogen bonding, ionic interactions, hydrophobic interactions, and disulfide bridges (covalent bonds between cysteine residues).

• Quaternary Structure (4°): The assembly of multiple folded polypeptide chains (subunits) into a functional protein complex. Not all proteins have quaternary structure; it is present in proteins composed of more than one polypeptide chain (e.g., hemoglobin).

Example: Hemoglobin is a protein with quaternary structure, consisting of four polypeptide subunits.

Key Terms and Concepts

• Amino Acid: The building block of proteins, consisting of a central carbon (alpha carbon), an amino group, a carboxyl group, a hydrogen atom, and a variable R group (side chain).

• Peptide Bond: A covalent bond formed between the carboxyl group of one amino acid and the amino group of another, releasing water (condensation reaction).

• Disulfide Bridge: A covalent bond between the sulfur atoms of two cysteine residues, stabilizing protein structure.

Equation:

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

Nucleic Acids

Structure of Nucleic Acids

Nucleic acids are polymers of nucleotides and serve as the genetic material in cells. The two main types are DNA and RNA.

• Nucleotide: The monomer of nucleic acids, consisting of a phosphate group, a pentose sugar (ribose in RNA, deoxyribose in DNA), and a nitrogenous base (adenine, thymine, cytosine, guanine, or uracil).

• Phosphodiester Bond: The covalent bond linking the phosphate group of one nucleotide to the sugar of the next, forming the backbone of the nucleic acid strand.

• 5' and 3' Ends: Nucleic acid strands have directionality, with a 5' end (phosphate group) and a 3' end (hydroxyl group).

Example: DNA consists of two antiparallel strands held together by hydrogen bonds between complementary nitrogenous bases.

RNA vs DNA

RNA and DNA differ in their sugar component and nitrogenous bases.

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Strands	Double-stranded (usually)	Single-stranded
Nitrogenous Bases	A, T, C, G	A, U, C, G
Function	Genetic information storage	Protein synthesis, gene regulation

Equation:

$\text{Nucleotide}_n + \text{Nucleotide}_{n+1} \rightarrow \text{Polynucleotide} + H_2O$

Additional info: The notes infer the importance of hydrogen bonding in secondary and tertiary protein structure, and the role of phosphodiester bonds in nucleic acid backbone formation. The comparison table between DNA and RNA is expanded for clarity.