7.4 Proteins

Amino Acids and Protein Structure

Amino acids are the building blocks of proteins, and the way they connect and fold determines what a protein can do. Understanding protein structure is essential in microbiology because nearly every cellular process, from metabolism to DNA replication, depends on proteins folding into the right shape.

Components of Amino Acid Structure

Every amino acid shares the same core framework: an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable side chain ($-R$), all attached to a central $\alpha$-carbon.

• The $\alpha$-carbon is a chiral center, meaning it can exist as two mirror-image forms: L and D stereoisomers. Biological proteins use almost exclusively the L-form, because the ribosomes and enzymes that build proteins are stereospecific.
• The side chain ($-R$) is what makes each amino acid unique. Side chains fall into a few categories:
  • Nonpolar (hydrophobic): valine, leucine, isoleucine
  • Polar (hydrophilic): asparagine, glutamine, serine
  • Acidic (negatively charged at physiological pH): aspartic acid, glutamic acid
  • Basic (positively charged at physiological pH): lysine, arginine
• Side chain properties directly shape how a protein folds. Nonpolar side chains tend to cluster together in the protein's interior, away from water. This hydrophobic effect is one of the major driving forces behind protein folding and stability. Polar and charged side chains typically face outward, interacting with the aqueous environment or with ligands and other proteins.

Peptide Bonds in Protein Formation

Amino acids link together through peptide bonds to form polypeptide chains. Here's how that bond forms:

1. The carboxyl group ($-COOH$) of one amino acid reacts with the amino group ($-NH_2$) of the next.
2. A water molecule is released (this is a condensation/dehydration reaction).
3. The result is a covalent $C-N$ bond between the two amino acids.

Two linked amino acids make a dipeptide; three make a tripeptide; longer chains are polypeptides.

The peptide bond has partial double-bond character, which makes it planar and rigid. Rotation around the $C-N$ bond is restricted. This rigidity is actually important: it constrains the backbone geometry in ways that favor the formation of regular secondary structures like $\alpha$-helices and $\beta$-sheets.

The specific sequence of amino acids in a polypeptide chain is dictated by the genetic code (the mRNA sequence read during translation). This sequence is the protein's primary structure and serves as the blueprint for all higher levels of folding.

Levels of Protein Structure

Proteins are organized into up to four structural levels, each building on the one before it:

1. Primary structure: The linear sequence of amino acids in the polypeptide chain. This sequence is encoded by genes and determines everything about how the protein will fold. Examples: the specific amino acid sequences of insulin or hemoglobin.

2. Secondary structure: Local, repeating folding patterns within the polypeptide chain. The two most common are $\alpha$-helices (coiled spirals) and $\beta$-sheets (flat, pleated arrangements of strands running side by side). Both are stabilized by hydrogen bonds between atoms of the peptide backbone (not the side chains). Keratin is rich in $\alpha$-helices; silk fibroin is dominated by $\beta$-sheets.

3. Tertiary structure: The overall three-dimensional shape of a single polypeptide chain. This level arises from interactions between the side chains, including:

   • Hydrogen bonds
   • Ionic bonds (salt bridges)
   • Van der Waals forces
   • Disulfide bridges (covalent bonds between cysteine residues)
   • Hydrophobic interactions in the protein core Tertiary structure is what gives a protein its specific function. Enzymes, for instance, depend on precise 3D folding to form their active sites.

4. Quaternary structure: The arrangement of two or more polypeptide subunits into a larger functional complex. Not all proteins have this level. Subunits can be identical (homodimer, e.g., two identical chains) or different (heterodimer). Hemoglobin is a classic example: it has four subunits (two $\alpha$ and two $\beta$ chains) that must assemble correctly for oxygen transport. DNA polymerase is another multi-subunit complex.

Proper folding is essential for function. Enzymes, transport proteins, structural proteins, and regulatory proteins all depend on their specific shapes. Denaturation (unfolding caused by heat, pH changes, or chemicals) destroys a protein's shape and typically its function. Misfolding can also cause disease: prion diseases, for example, result from proteins adopting an abnormal conformation that propagates by inducing other copies to misfold.

Protein Dynamics and Function

Proteins aren't static structures. They flex, shift, and interact in ways that are central to their roles in the cell.

• Protein folding is a complex process. A polypeptide doesn't snap instantly into its final shape; it passes through intermediate states. Chaperone proteins (such as GroEL/GroES in bacteria) assist folding by preventing the polypeptide from aggregating or getting stuck in a misfolded state.
• Enzyme catalysis depends on precise structure. The active site is a pocket formed by a specific arrangement of amino acid side chains. When a substrate binds, the enzyme often undergoes a conformational change (induced fit) that positions catalytic residues correctly and stabilizes the transition state.
• Post-translational modifications alter a protein after it's been synthesized. Common examples include:
  • Phosphorylation: addition of a phosphate group, often acting as an on/off switch for enzyme activity
  • Glycosylation: attachment of sugar chains, which can affect protein stability and cell recognition
  • Proteolytic cleavage: cutting the polypeptide to activate it (many enzymes are synthesized as inactive precursors)
• Protein-protein interactions underlie many cellular processes. Proteins form complexes for signal transduction, DNA replication, and metabolic pathways. Some interactions are stable (permanent complexes), while others are transient, assembling and disassembling as the cell's needs change.