Protein Structure and Function: Cell Biology Study Notes

Protein Structure and Function

Introduction to Proteins

Proteins are essential macromolecules in all living cells, responsible for a wide range of biological functions including catalysis, structural support, transport, and regulation. Their structure is determined by the sequence of amino acids, which fold into complex three-dimensional shapes.

• Definition: Proteins are polymers of amino acids linked by peptide bonds.

• Function: Enzymes, structural components, signaling molecules, and transporters.

• Example: Hemoglobin transports oxygen in blood; actin and myosin are involved in muscle contraction.

Amino Acids: Building Blocks of Proteins

Structure of Amino Acids

Amino acids are organic molecules with a central carbon atom (the alpha carbon) bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group). The properties of the side chain determine the characteristics of each amino acid.

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

• Peptide Bond Formation: Amino acids are joined by peptide bonds through a condensation reaction, releasing water ($\mathrm{H_2O}$).

• Polypeptide Backbone: Repeating sequence of $\mathrm{N{-}C{-}C}$ atoms forms the backbone of proteins.

• Example: Methionine (Met), Aspartic acid (Asp), Leucine (Leu), Tyrosine (Tyr) are shown as examples of amino acids with different side chains.

Classification of Amino Acids

Amino acids are classified based on the properties of their side chains, which affect protein folding and function.

Type	Examples	Properties
Electrically Charged (Positive)	Arginine (Arg), Histidine (His), Lysine (Lys)	Basic side chains, often found on protein surfaces, interact with negative charges.
Electrically Charged (Negative)	Aspartic acid (Asp), Glutamic acid (Glu)	Acidic side chains, often involved in ionic interactions.
Polar but Uncharged	Serine (Ser), Threonine (Thr), Asparagine (Asn), Glutamine (Gln)	Form hydrogen bonds, often found in active sites or on protein surfaces.
Special Cases	Cysteine (Cys), Glycine (Gly), Proline (Pro)	Cysteine forms disulfide bonds; Glycine is small and flexible; Proline introduces kinks in polypeptide chains.

• Hydrophobic Amino Acids: Typically found in the interior of globular proteins, stabilizing structure by avoiding water.

• Hydrophilic Amino Acids: Often located on the protein surface, interacting with the aqueous environment.

Levels of Protein Structure

Primary Structure

The primary structure of a protein is its unique sequence of amino acids, determined by genetic information.

• Peptide Bonds: Covalent bonds linking amino acids in a linear chain.

• Directionality: Proteins have an amino (N-) terminus and a carboxyl (C-) terminus.

Secondary Structure

Secondary structure refers to local folding patterns stabilized by hydrogen bonds between backbone atoms.

• Alpha Helix: Right-handed coil stabilized by hydrogen bonds; side chains project outward.

• Beta Pleated Sheet: Sheet-like arrangement; strands can be parallel or antiparallel; stabilized by hydrogen bonds.

• Example: Diagram shows hydrogen bonds (dotted lines) pulling the chain into an alpha helix or beta sheet.

Tertiary Structure

Tertiary structure is the overall three-dimensional shape of a single polypeptide, resulting from interactions among side chains (R groups).

• Hydrophobic Interactions: Nonpolar side chains cluster inside the protein.

• Hydrogen Bonding: Between polar side chains or backbone atoms.

• Ionic Interactions: Between charged side chains.

• Disulfide Bridges: Covalent bonds between cysteine residues, stabilizing structure.

Quaternary Structure

Quaternary structure arises when two or more polypeptide chains (subunits) assemble into a functional protein complex.

• Example: Hemoglobin consists of four subunits.

• Interactions: Similar to those in tertiary structure (hydrophobic, ionic, hydrogen bonds, disulfide bridges).

Summary Table: Amino Acid Properties

Group	Examples	Key Features
Nonpolar (Hydrophobic)	Leucine, Methionine, Valine	Found in protein interiors, stabilize structure
Polar (Uncharged)	Serine, Threonine	Form hydrogen bonds, often in active sites
Charged (Acidic/Basic)	Aspartic acid, Lysine	Participate in ionic interactions, often on surfaces
Special	Cysteine, Proline, Glycine	Disulfide bonds, structural kinks, flexibility

Conclusion

Understanding protein structure is fundamental to cell biology, as the shape and chemical properties of proteins determine their function in the cell. The diversity of amino acids and their interactions enable proteins to perform a vast array of biological roles.