Proteins and Amino Acids: Structure, Function, and Organization

Proteins: Structure and Function

Overview of Proteins

Proteins are a major class of biomolecules essential for the structure, function, and regulation of the body's tissues and organs. They are polymers made of amino acid monomers linked by covalent bonds known as peptide bonds.

• Proteins: Polymers composed of amino acid monomers.

• Peptide Bonds: Covalent bonds that link adjacent amino acids together in a protein chain.

• Proteins have directionality, with a N-terminal (amino end) and a C-terminal (carboxyl end).

Example: Formation of proteins from amino acid monomers involves the joining of amino acids via peptide bonds, resulting in a polypeptide chain with specific terminal ends.

Amino Acids

Structure and Properties of Amino Acids

Amino acids are the building blocks of proteins. Each amino acid contains a central carbon atom bonded to four different groups: an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group).

• Amino acids: Monomers of proteins.

• Each amino acid has:

  • A central carbon atom (α-carbon)

  • An amino group (–NH2)

  • A carboxyl group (–COOH)

  • A hydrogen atom

  • A unique R group (side chain) that determines the properties of the amino acid

• Living organisms use 20 different amino acids, each with a distinct R group.

Example: The general structure of an amino acid can be represented as:

• Central carbon atom (α-carbon)

• Amino group (N-terminal)

• Carboxyl group (C-terminal)

• Hydrogen atom

• Unique R group (side chain)

Table: Components of an Amino Acid

Component	Description
Central Carbon (α-carbon)	The central atom to which all other groups are attached
Amino Group	–NH2 (N-terminal)
Carboxyl Group	–COOH (C-terminal)
Hydrogen Atom	Attached to the central carbon
R Group	Unique side chain that varies among amino acids

Protein-Related Terms

Classification by Chain Length

Terms used to describe amino acid chains depend on their length:

Term	Length of Amino Acid Chain
Amino acid	A single protein unit or monomer
Dipeptide	2 covalently linked amino acids
Peptide	2 to 50 covalently linked amino acids
Polypeptide	More than 50 covalently linked amino acids
Protein	One or more polypeptide chains in their folded, functional forms

Protein Structure

Levels of Protein Structure

Proteins have a hierarchical structure organized into four levels, each contributing to the protein's final shape and function:

1. Primary Structure: The unique sequence of amino acids in a polypeptide chain.

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

3. Tertiary Structure: The overall three-dimensional shape of a single polypeptide chain, determined by interactions among R groups.

4. Quaternary Structure: The association of two or more polypeptide chains to form a functional protein complex.

Example: The four levels of protein structure are illustrated by the progression from amino acid sequence to complex, multi-subunit protein.

Denatured Proteins & Chaperones

Protein Denaturation and Chaperone Proteins

The structure and shape of a protein are critical for its function. Denaturation is the process by which a protein loses its native shape due to changes in environmental conditions, such as pH, temperature, or salt concentration. This loss of structure results in loss of function.

• Denatured Protein: A protein that has lost its functional shape.

• Denaturation can be caused by environmental changes (e.g., heat, pH, salt concentration).

• Chaperone Proteins: Specialized proteins that help other proteins fold correctly or refold after denaturation.

Example: Chaperone proteins assist in the refolding of denatured proteins, helping them regain their functional shape.

Summary Table: Protein Structure Levels

Level	Description	Stabilizing Interactions
Primary	Sequence of amino acids	Peptide bonds
Secondary	α-helices and β-sheets	Hydrogen bonds
Tertiary	3D folding of a single polypeptide	Hydrogen bonds, ionic bonds, disulfide bridges, hydrophobic interactions
Quaternary	Association of multiple polypeptides	Same as tertiary, between subunits

Key Equations and Concepts

• Peptide Bond Formation: The formation of a peptide bond between two amino acids involves a dehydration synthesis reaction: $\text{Amino Acid}_1 + \text{Amino Acid}_2 \rightarrow \text{Dipeptide} + H_2O$

• Directionality: Proteins are synthesized from the N-terminal to the C-terminal end.

Examples and Applications

• Enzymes: Proteins that catalyze biochemical reactions.

• Structural Proteins: Such as collagen and keratin, provide support and shape to cells and tissues.

• Transport Proteins: Hemoglobin transports oxygen in the blood.

Additional info: The notes include practice questions to reinforce understanding of protein structure, amino acid components, and the role of chaperone proteins in protein folding.