9.3 Protein Function and Regulation

Proteins are the workhorses of biology, performing diverse functions from structural support to enzyme catalysis. They shape our bodies, drive chemical reactions, and regulate vital processes. Understanding protein function is key to grasping how living systems operate at the molecular level.

Protein regulation fine-tunes cellular processes through post-translational modifications and intricate signaling networks. These mechanisms allow cells to respond to their environment, maintain homeostasis, and coordinate complex behaviors. Mastering protein regulation unveils the dynamic nature of cellular function.

Protein Function

Functions of proteins in biology

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• Structural proteins form supportive frameworks (collagen in connective tissue, keratin in hair and nails)
• Enzymes accelerate biochemical reactions without being consumed (amylase breaks down starch, pepsin digests proteins)
• Transport proteins move molecules across membranes or through bodily fluids (hemoglobin carries oxygen, ion channels facilitate membrane transport)
• Hormones regulate physiological processes (insulin controls glucose levels, growth hormone stimulates cell growth and division)
• Antibodies defend against foreign substances by recognizing and binding to specific antigens (IgG, IgM)
• Contractile proteins enable movement (actin and myosin facilitate muscle contraction)
• Storage proteins retain nutrients or ions for later use (ferritin stores iron, casein in milk provides amino acids)

Mechanisms of enzyme catalysis

• Enzyme catalysis follows steps:
  1. Substrate binds to active site
  2. Enzyme stabilizes transition state
  3. Chemical reaction occurs
  4. Products released
• Catalytic mechanisms lower activation energy:
  • Acid-base catalysis transfers protons
  • Covalent catalysis forms temporary bonds
  • Metal ion catalysis polarizes substrates
• Enzyme kinetics described by Michaelis-Menten equation: $v = \frac{V_{max}[S]}{K_m + [S]}$
  • $K_m$ indicates substrate affinity
  • $V_{max}$ represents maximum reaction rate
• Enzyme regulation maintains cellular homeostasis:
  • Allosteric regulation alters enzyme shape (cooperative binding, feedback inhibition)
  • Competitive inhibition blocks active site
  • Non-competitive inhibition changes enzyme conformation
  • Covalent modification alters activity (phosphorylation/dephosphorylation)
  • Zymogen activation converts inactive precursors to active enzymes

Protein Regulation

Post-translational modifications of proteins

• Phosphorylation adds phosphate groups, activating or deactivating enzymes (kinases add, phosphatases remove)
• Glycosylation attaches sugar molecules, enhancing protein stability and enabling cell-cell recognition (N-linked, O-linked)
• Ubiquitination tags proteins for degradation, signaling proteasome pathway (E1, E2, E3 enzymes)
• Acetylation modifies histones, regulating gene expression (histone acetyltransferases, deacetylases)
• Methylation influences epigenetic regulation and protein-protein interactions (DNA methyltransferases)
• Lipidation anchors proteins to membranes, affecting localization (prenylation, palmitoylation)
• Proteolytic cleavage activates zymogens and matures proteins (trypsinogen to trypsin)

Protein interactions and signaling

• Protein-protein interactions occur as transient interactions or stable complexes
• Interaction domains mediate specific binding (SH2 domains bind phosphotyrosine, PDZ domains organize signaling complexes)
• Signaling pathways transmit external stimuli:
  • G-protein coupled receptors activate G-proteins
  • Receptor tyrosine kinases autophosphorylate upon ligand binding
• Signal transduction involves second messengers (cAMP, IP3, DAG) and protein kinase cascades
• Scaffold proteins organize signaling complexes, ensuring spatial regulation
• Protein interaction networks form interactomes, analyzed through network analysis
• Cellular processes regulated by interactions include cell cycle control, apoptosis, and metabolic pathways
• Methods for studying protein interactions:
  • Yeast two-hybrid system detects binary interactions
  • Co-immunoprecipitation isolates protein complexes
  • Fluorescence resonance energy transfer (FRET) measures proximity in living cells