Proteins and Nucleic Acids: Structure, Function, and Classification

Proteins (Concept 5.4)

Monomer/Subunit of Proteins

Proteins are polymers composed of monomers called amino acids. Each amino acid contains a central carbon atom (the alpha carbon) bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group).

• Amino acid: The building block of proteins, containing an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a variable R group.

• General formula: $\mathrm{NH_2{-}CHR{-}COOH}$

• Example: Glycine has R = H; Alanine has R = CH3.

Elements and Functional Groups Present

Proteins contain the elements carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and sometimes sulfur (S) (in cysteine and methionine).

• Functional groups: Amino group (-NH2), carboxyl group (-COOH), and various side chains (R groups).

Peptide Bonds

Amino acids are linked together by peptide bonds, which are covalent bonds formed between the carboxyl group of one amino acid and the amino group of another, releasing water (a dehydration reaction).

• Peptide bond formation: $\mathrm{Amino\ acid_1{-}COOH + Amino\ acid_2{-}NH_2 \rightarrow Peptide\ bond + H_2O}$

• Example: Dipeptide formation from two glycine molecules.

Recognizing Proteins by Formula or Shape

Proteins can be identified by their repeating backbone structure and the presence of peptide bonds. The general shape of a protein is determined by its sequence of amino acids and the folding of its polypeptide chain.

• Formula: Repeating units of $\mathrm{NH{-}CHR{-}CO}$

• Shape: Can be visualized as a chain with side groups projecting from the backbone.

Distinguishing the 20 Different Amino Acids

Each of the 20 standard amino acids is distinguished by its unique side chain (R group), which can be nonpolar, polar, acidic, or basic.

• Nonpolar side chains: Hydrophobic, often found in the interior of proteins.

• Polar side chains: Hydrophilic, often found on the exterior of proteins.

• Acidic/basic side chains: Can form ionic bonds and participate in active sites.

• Example: Serine (polar), Leucine (nonpolar), Aspartic acid (acidic).

Polarity of Side Chains and Protein Structure

The polarity of an amino acid's side chain influences its location in a protein's 3D structure. Hydrophobic (nonpolar) side chains tend to be buried inside the protein, while hydrophilic (polar or charged) side chains are exposed to the aqueous environment.

• Prediction: Nonpolar side chains are found in the protein core; polar/charged side chains are on the surface.

• Example: In globular proteins, valine (nonpolar) is internal, glutamine (polar) is external.

Levels of Protein Structure

Proteins have four levels of structure, each contributing to their function:

• Primary structure: Sequence of amino acids in a polypeptide chain.

• Secondary structure: Local folding into alpha helices and beta sheets, stabilized by hydrogen bonds.

• Tertiary structure: Overall 3D shape of a single polypeptide, determined by interactions among side chains.

• Quaternary structure: Association of multiple polypeptide chains into a functional protein complex.

• Example: Hemoglobin has quaternary structure with four polypeptide subunits.

Major Functions of Proteins in Living Things

Proteins perform a wide variety of functions essential for life:

• Enzymes: Catalyze biochemical reactions (e.g., amylase).

• Structural proteins: Provide support (e.g., collagen in connective tissue).

• Transport proteins: Move substances (e.g., hemoglobin transports oxygen).

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

• Signaling proteins: Coordinate cellular activities (e.g., insulin).

Nucleic Acids (Concept 5.5)

Monomer/Subunit: The Nucleotide

Nucleic acids are polymers made of monomers called nucleotides. Each nucleotide consists of three parts:

• Phosphate group

• Five-carbon sugar (ribose in RNA, deoxyribose in DNA)

• Nitrogenous base (adenine, guanine, cytosine, thymine, uracil)

• General formula: $\mathrm{Phosphate{-}Sugar{-}Base}$

• Example: ATP (adenosine triphosphate) is a nucleotide with three phosphate groups.

Purines vs Pyrimidines

Nitrogenous bases are classified as purines or pyrimidines based on their structure:

Type	Bases	Structure
Purines	Adenine (A), Guanine (G)	Double-ring
Pyrimidines	Cytosine (C), Thymine (T), Uracil (U)	Single-ring

Elements and Functional Groups Present

Nucleic acids contain carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and phosphorus (P). Functional groups include phosphate groups, hydroxyl groups, and amine groups.

• Phosphate group: -PO4

• Hydroxyl group: -OH (on the sugar)

• Amine group: -NH2 (on the base)

Recognizing Nucleic Acids by Formula or Shape

Nucleic acids are identified by their repeating backbone of sugar and phosphate groups, with nitrogenous bases projecting from the backbone.

• Formula: $\mathrm{(Phosphate{-}Sugar{-}Base)_n}$

• Shape: DNA forms a double helix; RNA is usually single-stranded.

Distinguishing DNA from RNA

DNA and RNA differ in several key ways:

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

• Example: DNA stores genetic information; RNA carries instructions for protein synthesis.