Organic Chemistry Unit 26 ReviewBiomolecules: Amino Acids & Proteins

Key Concepts

• Amino acids serve as the building blocks of proteins consist of an amino group, carboxyl group, hydrogen atom, and a variable side chain (R group) attached to the central α-carbon
• Peptide bonds form between the carboxyl group of one amino acid and the amino group of another amino acid through a condensation reaction releases a water molecule
• Proteins have four levels of structure: primary (amino acid sequence), secondary (local folding patterns like α-helices and β-sheets), tertiary (overall 3D shape), and quaternary (multiple polypeptide chains)
• Proteins perform diverse functions in living organisms including catalyzing reactions (enzymes), transporting molecules (hemoglobin), providing structural support (collagen), and regulating cell processes (hormones)
• Techniques used to study proteins include chromatography (separates proteins based on properties), electrophoresis (separates proteins based on size and charge), and mass spectrometry (determines the molecular mass and sequence of proteins)
  • Chromatography types include size-exclusion, ion-exchange, and affinity chromatography
  • Electrophoresis can be performed in one dimension (SDS-PAGE) or two dimensions (2D-PAGE)

Amino Acid Structure

• Amino acids have a central α-carbon bonded to an amino group ($-NH_2$), a carboxyl group ($-COOH$), a hydrogen atom, and a variable side chain (R group)
• The R group determines the unique properties of each amino acid such as polarity, charge, and hydrophobicity
• There are 20 standard amino acids classified based on the properties of their R groups: nonpolar (hydrophobic), polar (hydrophilic), acidic, and basic
• Nonpolar amino acids (glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, methionine) have hydrophobic R groups tend to be buried within the protein structure
• Polar amino acids (serine, threonine, cysteine, asparagine, glutamine) have hydrophilic R groups can form hydrogen bonds with water and other polar molecules
  • Cysteine contains a thiol group ($-SH$) can form disulfide bonds between two cysteine residues
• Acidic amino acids (aspartic acid, glutamic acid) have negatively charged R groups at physiological pH
• Basic amino acids (lysine, arginine, histidine) have positively charged R groups at physiological pH

Protein Building Blocks

• Proteins are polymers of amino acids joined together by peptide bonds
• The sequence of amino acids in a protein is determined by the genetic code each amino acid is encoded by one or more codons (triplets of nucleotides)
• During protein synthesis, the genetic information in DNA is transcribed into mRNA, which is then translated by ribosomes into a polypeptide chain
• The properties of a protein depend on its amino acid composition and sequence
• Proteins can undergo post-translational modifications (PTMs) after synthesis such as phosphorylation, glycosylation, and acetylation alter their function and regulation
• Proteins can also be degraded by proteases (enzymes that break peptide bonds) as part of cellular regulation and turnover

Peptide Bond Formation

• Peptide bonds form through a condensation reaction between the carboxyl group of one amino acid and the amino group of another amino acid
• The reaction releases a water molecule and forms a covalent bond between the carbon atom of the carboxyl group and the nitrogen atom of the amino group
• The resulting molecule is called a dipeptide has a free amino group at one end (N-terminus) and a free carboxyl group at the other end (C-terminus)
• Peptide bonds have partial double bond character due to resonance stabilization restricts rotation around the bond and gives the peptide bond a planar structure
• The peptide backbone consists of repeating units of $-N-C_α-C-$ atoms with the R groups extending from the $C_α$ atoms
  • The peptide backbone forms the main chain of the protein while the R groups form the side chains
• Multiple peptide bonds can form to create longer polypeptide chains proteins typically consist of 50-2000 amino acid residues

Protein Structure Levels

• Proteins have four levels of structure: primary, secondary, tertiary, and quaternary
• Primary structure is the linear sequence of amino acids in a polypeptide chain determined by the genetic code
• Secondary structure refers to the local folding patterns of the polypeptide chain stabilized by hydrogen bonds between the peptide backbone atoms
  • Common secondary structures include α-helices (coiled structure with 3.6 amino acids per turn) and β-sheets (extended structure with strands running parallel or antiparallel)
  • Turns and loops are also considered secondary structures connect other secondary structure elements
• Tertiary structure is the overall three-dimensional shape of a single polypeptide chain determined by interactions between the R groups (side chains) of the amino acids
  • Interactions include hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bonds
  • The tertiary structure is essential for the protein's function and stability
• Quaternary structure refers to the arrangement of multiple polypeptide chains (subunits) into a larger protein complex
  • Subunits can be identical (homooligomers) or different (heterooligomers)
  • Quaternary structure is stabilized by the same types of interactions as tertiary structure

Protein Functions

• Proteins perform a wide variety of functions in living organisms essential for life
• Enzymes are proteins that catalyze chemical reactions by lowering the activation energy
  • Enzymes have an active site where the substrate binds undergo conformational changes during catalysis
  • Examples of enzymes include DNA polymerase (DNA replication), pepsin (protein digestion), and rubisco (carbon fixation)
• Transport proteins bind and carry specific molecules or ions across membranes or throughout the body
  • Examples include hemoglobin (oxygen transport in blood), glucose transporters (glucose uptake by cells), and ion channels (movement of ions across membranes)
• Structural proteins provide mechanical support and stability to cells and tissues
  • Examples include collagen (main component of connective tissue), keratin (hair and nails), and elastin (elastic fibers in skin and blood vessels)
• Regulatory proteins help control cellular processes by binding to other proteins or DNA
  • Examples include transcription factors (regulate gene expression), hormones (signaling molecules), and antibodies (immune system proteins)
• Motor proteins generate movement by converting chemical energy into mechanical work
  • Examples include myosin (muscle contraction) and kinesin (transport along microtubules)

Lab Techniques

• Various laboratory techniques are used to study proteins' structure, function, and interactions
• Protein purification involves isolating a specific protein from a complex mixture (cell lysate) using its unique properties
  • Steps include cell lysis, centrifugation, and chromatography (size-exclusion, ion-exchange, affinity)
  • The purity of the protein is assessed by SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis)
• Protein quantification determines the concentration of a protein sample using colorimetric assays (Bradford, Lowry) or UV absorbance at 280 nm (aromatic amino acids)
• Protein structure determination reveals the three-dimensional structure of a protein at atomic resolution
  • X-ray crystallography requires growing protein crystals and measuring the diffraction of X-rays
  • Nuclear magnetic resonance (NMR) spectroscopy measures the magnetic properties of atomic nuclei in a protein sample
  • Cryo-electron microscopy (cryo-EM) uses electron beams to image frozen protein samples
• Protein-protein interactions can be studied using techniques such as co-immunoprecipitation (co-IP), yeast two-hybrid (Y2H) screening, and surface plasmon resonance (SPR)
• Protein activity assays measure the function of a protein such as enzyme kinetics (Michaelis-Menten) or binding affinity (dissociation constant, $K_d$)

Real-World Applications

• Understanding protein structure and function has numerous real-world applications in fields such as medicine, biotechnology, and agriculture
• Protein engineering involves modifying existing proteins or designing new proteins with desired properties
  • Examples include creating enzymes with improved stability or specificity, developing protein-based materials (spider silk), and designing proteins for therapeutic purposes (insulin analogs)
• Protein-based drugs (biologics) are used to treat various diseases by replacing deficient proteins or inhibiting disease-related proteins
  • Examples include monoclonal antibodies (cancer immunotherapy), enzyme replacement therapies (lysosomal storage disorders), and cytokines (inflammatory diseases)
• Protein biomarkers are used for diagnosing and monitoring diseases by detecting changes in protein levels or modifications
  • Examples include prostate-specific antigen (PSA) for prostate cancer, troponin for heart attacks, and HbA1c for diabetes
• Protein-based vaccines stimulate the immune system to produce antibodies against specific pathogens by presenting protein antigens
  • Examples include the hepatitis B vaccine (HBsAg protein) and the human papillomavirus (HPV) vaccine (L1 protein)
• Protein-based materials are used in various applications due to their unique properties such as strength, elasticity, and biocompatibility
  • Examples include collagen-based scaffolds for tissue engineering, silk-based fibers for textiles, and protein-based adhesives for wound healing