Protein Function

What are the five major functional classes of proteins?

● Metabolic enzymes are chemical catalysts that lower the activation energy of a biochemical reaction to increase the rate of product formation without altering the equilibrium constant.

● Structural proteins are often assembled into long filaments that form cytoskeletal structures involved in cell migration, chromosomal segregation, and muscle cell contraction.

● Transport proteins span membranes and function as selective pores. Passive transporters allow molecules to diffuse down a concentration gradient; active transporters act as energy-dependent pumps that transport molecules against a concentration gradient.

● Cell signaling proteins respond to changes in the extracellular environment by undergoing conformational or chemical changes that regulate cellular processes. A common mechanism to control signal transduction in cells is the phosphorylation and dephosphorylation of signaling proteins.

● Genomic caretaker proteins maintain the integrity of genetic information encoded in DNA and control gene expression. DNA metabolizing enzymes are required for DNA replication, repair, and recombination. RNA metabolizing enzymes are required for RNA transcription, processing, and stability.

How do the structure and function of hemoglobin explain oxygen transport?

● Myoglobin has a single polypeptide chain and functions as an O₂ storage protein in muscle tissues. Hemoglobin is an O₂ transport protein that contains two α-globin subunits and two β-globin subunits; together they form a heterotetramer (α₂β₂) capable of binding and transporting four O₂ molecules at a time from the lungs to the tissues.

● Each globin polypeptide contains a single heme group that reversibly binds O₂ as a ligand. Two histidine residues in the protein—His F8 (proximal histidine) and His E7 (distal histidine)—play a critical role in O₂ binding to the heme.

● Hemoglobin without bound O₂ molecules (deoxyhemoglobin) is in the T-state conformation (tense), whereas hemoglobin with bound O₂ (oxyhemoglobin) is in the R-state conformation (relaxed). The T-state conformation has a low affinity for O₂, whereas the R-state conformation has a high affinity for O₂.

● The O₂ molecule is a positive homotropic allosteric regulator that facilitates the binding of additional O₂ molecules to other globin subunits by shifting the equilibrium toward the R state (oxyhemoglobin). Conversely, CO₂, H1, and 2,3-bisphosphoglycerate (2,3-BPG) are all negative heterotropic allosteric regulators that shift the equilibrium toward the T state (deoxyhemoglobin).

● The molecular basis of the Bohr effect is the protonation of key residues at the subunit interfaces, resulting in stabilization of the T-state conformation at low pH and CO₂ binding to the N termini of the hemoglobin subunits. Elevated pH causes deprotonation of these same residues and favors the R-state conformation.

What are the mechanisms by which polar molecules are transported across hydrophobic cell membranes?

● The three major types of membrane proteins are membrane receptor proteins, membrane-bound metabolic enzymes, and membrane transport proteins. There are two classes of transporters: energy-independent passive transporters and energy-dependent active transporters.

● The K⁺ channel protein is an α-helical passive transporter found in both prokaryotic and eukaryotic cells that displays a 10,000-fold selectivity for K⁺ ions over Na⁺ ions. The molecular basis for selectivity is the specific placement of carbonyl oxygen atoms within the channel, which interact precisely with desolvated K⁺ ions but not Na⁺ ions.

● Primary active transporters require energy input, such as ATP hydrolysis, to drive protein conformational changes required for their “pumping” function. Two primary active transporters, Na⁺– K⁺ ATPase and skeletal muscle SERCA use the energy available in ATP hydrolysis to translocate ions across membranes.

● ABC transporters use ATP hydrolysis to drive the protein conformational changes required for pumping ions and small molecules across membranes. ABC transporters are homodimeric complexes containing two ATP binding half-sites that are activated by ligand-induced conformational changes.

● The human Na⁺–I^– symporter protein is a secondary active membrane symporter; however, it uses the Na⁺ gradient maintained by the Na⁺–K⁺ ATPase primary active transporter to pump I^– ions into thyroid gland cells for use in thyroid hormone synthesis.

How does the actin-myosin motor mediate ATP-dependent muscle contraction?

● According to the sliding filament model of muscle contraction, Ca²⁺– and ATP-mediated conformational changes in proteins that make up the thick and thin filaments in muscle cells lead to muscle contraction as a result of filaments physically sliding past one another.

● Thick filaments contain hundreds of myosin protein molecules arranged tail to tail within the fiber, in such a way that their globular head domains are oriented toward the two ends. Titin, the largest protein found in nature, connects the two ends of the thick filaments to anchor proteins located in regions of the sarcomere called the Z disks.

● Thin filaments consist primarily of polymerized actin proteins that serve as myosin binding sites during muscle contraction. Two other proteins in the thin filaments are tropomyosin, a dimeric α-helical protein, and troponin, a heterotrimeric protein complex that binds Ca²⁺ and regulates muscle contraction.

● Muscle contraction is initiated by neuromuscular signals that lead to the release of Ca²⁺ from the sarcoplasmic reticulum. The constant pumping of Ca²⁺ back into the sarcoplasmic reticulum by SERCA ensures that muscle relaxation occurs once the neuromuscular signals are turned off.