3.3 Proteins: structure and function

Proteins are the workhorses of cells, performing a huge range of functions. From enzymes that speed up chemical reactions to structural proteins that give cells their shape, these molecular machines are essential for life. Their diverse roles stem from their unique structures, all built from amino acid building blocks.

The relationship between protein structure and function is central to understanding how cells work. A protein's 3D shape, determined by its amino acid sequence, directly controls its ability to perform specific tasks. This tight connection between form and function also matters for practical applications like drug design and treating diseases caused by misfolded proteins.

Protein Building Blocks and Structure

Building blocks of proteins

Every protein is assembled from amino acids, and there are 20 different ones commonly found in proteins. All amino acids share the same core structure: an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a distinctive side chain (also called the R group). The side chain is what makes each amino acid unique, determining its polarity, charge, and size.

Amino acids are classified by their side chain properties:

• Nonpolar (hydrophobic) amino acids have side chains that avoid water. Examples include Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan, and Methionine. These tend to cluster in the interior of a folded protein, away from the watery environment.
• Polar (hydrophilic) amino acids have side chains that form hydrogen bonds with water. Examples include Serine, Threonine, Cysteine, Asparagine, and Glutamine.
• Charged amino acids carry a positive charge (Lysine, Arginine) or negative charge (Aspartic acid, Glutamic acid) at physiological pH. These are often found on the protein's surface, interacting with the aqueous surroundings.
• Special cases: Glycine is the simplest amino acid, with just a hydrogen as its side chain, giving it unusual flexibility. Histidine can be positively charged or neutral depending on pH, making it useful in enzyme active sites. Tyrosine is both aromatic and polar.

Levels of protein structure

Proteins are organized into four levels of structure, each building on the one before it.

• Primary structure is the linear sequence of amino acids in a polypeptide chain. This sequence is encoded by the gene for that protein, and amino acids are linked together by peptide bonds. The primary structure is unique to each protein and dictates how the chain will fold.
• Secondary structure refers to local, repeating folding patterns within the polypeptide chain.
  • An $\alpha$-helix is a coiled structure stabilized by hydrogen bonds between the amino hydrogen of one amino acid and the carboxyl oxygen of the amino acid four residues ahead.
  • A $\beta$-sheet forms when multiple polypeptide strands (running parallel or antiparallel) line up side by side, held together by hydrogen bonds between the strands.
• Tertiary structure is the overall 3D shape of the entire polypeptide chain. It's stabilized by several types of interactions: hydrogen bonds, disulfide bridges (covalent bonds between cysteine residues), ionic interactions, and hydrophobic interactions (nonpolar side chains packing together in the protein's interior). This level of structure creates the specific active sites and binding pockets that give a protein its function.
• Quaternary structure is the arrangement of multiple polypeptide chains (called subunits) into a larger protein complex. The same types of interactions that stabilize tertiary structure hold subunits together. Not all proteins have quaternary structure. A protein made of a single polypeptide is monomeric, while one with multiple subunits is multimeric. Hemoglobin, for example, is a tetramer made of four subunits.

Peptide bonds in polypeptides

Peptide bonds are the covalent bonds that link amino acids together into polypeptide chains. Here's how they form:

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.

This reaction is endergonic, meaning it requires energy input (ultimately from ATP hydrolysis) to proceed in the cell.

Peptide bonds have partial double-bond character due to resonance. This restricts rotation around the bond, creating a rigid, planar structure at each peptide linkage. That rigidity is part of what allows secondary structures like $\alpha$-helices and $\beta$-sheets to form in predictable patterns.

Every polypeptide chain has a direction: it runs from the N-terminus (free amino group) to the C-terminus (free carboxyl group). By convention, amino acid sequences are always written from N-terminus to C-terminus.

Protein Function and Structure-Function Relationship

Functions of proteins

Proteins carry out nearly every job in the cell. Here are the major functional categories:

• Enzymes catalyze biochemical reactions by lowering the activation energy needed for the reaction to proceed. Each enzyme is specific to particular substrates. The lock-and-key model describes a rigid fit between enzyme and substrate, while the induced fit model (more accurate) describes the enzyme changing shape slightly to accommodate the substrate. Examples: DNA polymerase (DNA replication), pepsin (protein digestion in the stomach), catalase (breaks down $H_2O_2$ into water and oxygen).
• Hormones are chemical messengers that regulate physiological processes. Peptide hormones like insulin and growth hormone are proteins, while steroid hormones like estrogen and testosterone are lipid-derived (not proteins). Protein hormones bind to specific receptors on target cells to trigger signaling cascades.
• Structural proteins provide physical support, protection, and movement. Collagen gives connective tissue its tensile strength. Actin and myosin drive muscle contraction. Keratin forms the tough structure of hair and nails.
• Transport proteins move molecules across membranes or through the body. Hemoglobin carries oxygen in red blood cells. Ion channels control the flow of ions across membranes. Glucose transporters shuttle glucose into cells.
• Signaling proteins participate in cell communication and signal transduction. G protein-coupled receptors detect hormones and neurotransmitters. Protein kinases pass signals along by adding phosphate groups to other proteins (phosphorylation cascades).
• Antibodies (immunoglobulins) are produced by B lymphocytes and recognize specific foreign molecules called antigens. Each antibody has a variable region that binds a particular antigen with high specificity. Different classes (IgG, IgM, IgA, IgE, IgD) serve distinct roles in the immune response.
• Storage proteins store nutrients for later use. Ferritin stores iron in the liver and spleen. Casein stores amino acids in milk. Ovalbumin stores amino acids in egg whites.

Structure vs function in proteins

A protein's function depends entirely on its 3D structure. The specific folding of the polypeptide chain creates binding sites and active sites with precise shapes and chemical properties. For enzymes, even small changes to the arrangement of amino acids in the active site can destroy catalytic activity or substrate specificity.

Several things can alter or disrupt protein structure:

• Mutations in the gene can change the amino acid sequence (primary structure), which may cause the protein to fold incorrectly or become unstable. Sickle cell disease, for instance, results from a single amino acid change in hemoglobin.
• Environmental factors like extreme temperature, pH changes, or chemical denaturants can break the interactions that maintain a protein's shape. This process, called denaturation, unfolds the protein and typically destroys its function.
• Misfolding and aggregation of proteins can lead to serious diseases. In Alzheimer's disease, misfolded amyloid-beta proteins aggregate into plaques. Similar misfolding problems underlie Parkinson's disease and Huntington's disease.

Post-translational modifications can fine-tune protein structure and function after the protein is made:

• Phosphorylation (adding a phosphate group, controlled by kinases and phosphatases) can switch a protein's activity on or off.
• Glycosylation (attaching sugar chains) often affects protein folding and cell-surface recognition.
• Acetylation and methylation modify histones and other proteins, influencing gene expression and protein interactions.

These modifications can alter a protein's activity, its location within the cell, its stability, and how it interacts with other molecules.

Understanding the structure-function relationship is crucial for:

1. Designing drugs that target specific proteins involved in diseases
2. Developing therapies for protein misfolding disorders
3. Engineering proteins with new or enhanced functions for biotechnology applications