🧬Biochemistry Unit 2 – Amino Acids and Protein Structure

Key Concepts and Definitions

• Amino acids building blocks of proteins consist of an amino group, carboxyl group, hydrogen atom, and a variable side chain (R group) attached to the central alpha carbon
• 20 standard amino acids found in proteins classified based on the properties of their side chains (polar, nonpolar, charged, aromatic)
• Peptide bonds covalent linkages formed between the carboxyl group of one amino acid and the amino group of another through a condensation reaction
• Primary structure linear sequence of amino acids in a protein determined by the genetic code
• Secondary structure regular, repeating patterns of amino acid arrangement (alpha helices and beta sheets) stabilized by hydrogen bonding
  • Alpha helices coiled structures with 3.6 amino acids per turn stabilized by hydrogen bonds between the carbonyl oxygen and the amino hydrogen of every fourth residue
  • Beta sheets extended structures formed by hydrogen bonding between adjacent polypeptide chains arranged in either parallel or antiparallel orientations
• Tertiary structure three-dimensional folding of a polypeptide chain determined by interactions between amino acid side chains (hydrophobic interactions, hydrogen bonding, ionic interactions, disulfide bridges)
• Quaternary structure arrangement of multiple polypeptide subunits in a multi-subunit protein

Amino Acid Structure and Properties

• Amino acids zwitterions at physiological pH with a positively charged amino group and a negatively charged carboxyl group
• Side chains (R groups) determine the unique properties of each amino acid (size, shape, charge, hydrophobicity, reactivity)
• Nonpolar amino acids (glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophan, methionine) hydrophobic and tend to be buried in the interior of proteins
  • Glycine smallest amino acid with a single hydrogen atom as its side chain allows for flexibility in protein structures
  • Proline unique cyclic structure disrupts regular secondary structure elements like alpha helices
• Polar amino acids (serine, threonine, cysteine, asparagine, glutamine) hydrophilic and often found on the surface of proteins where they can interact with water
  • Cysteine contains a thiol group that can form disulfide bonds, contributing to protein stability
• Charged amino acids (lysine, arginine, histidine, aspartate, glutamate) play important roles in protein function, such as catalysis, binding, and regulation
  • Histidine unique properties with a pKa near physiological pH allows it to act as a proton donor or acceptor in enzymatic reactions
• Aromatic amino acids (phenylalanine, tyrosine, tryptophan) contain ring structures that can participate in stacking interactions and contribute to protein stability and function

Peptide Bond Formation

• Peptide bonds formed through a condensation reaction between the carboxyl group of one amino acid and the amino group of another, releasing a water molecule
• Peptide bonds planar and rigid due to resonance stabilization, limiting the rotational freedom of the polypeptide backbone
• Peptide bond formation is an endergonic process that requires energy input, typically in the form of ATP hydrolysis during protein synthesis
• Directionality of protein synthesis N-terminus to C-terminus determined by the genetic code and the action of ribosomes
• Peptide bonds can be cleaved by hydrolysis, a reaction catalyzed by proteolytic enzymes (proteases) in biological systems
  • Trypsin serine protease that specifically cleaves peptide bonds after lysine or arginine residues
  • Pepsin aspartic protease that functions in the acidic environment of the stomach to break down dietary proteins
• Peptide bond formation is a key step in the biosynthesis of proteins, hormones, neurotransmitters, and other biologically active peptides

Levels of Protein Structure

• Primary structure linear sequence of amino acids in a polypeptide chain determined by the genetic code
  • Amino acid sequence dictates the higher levels of protein structure and ultimately determines the function of the protein
  • Mutations in the genetic code can lead to changes in the primary structure, potentially altering protein function or stability
• Secondary structure regular, repeating patterns of amino acid arrangement stabilized by hydrogen bonding
  • Alpha helices coiled structures with 3.6 amino acids per turn and hydrogen bonds between the carbonyl oxygen and the amino hydrogen of every fourth residue
  • Beta sheets extended structures formed by hydrogen bonding between adjacent polypeptide chains arranged in either parallel or antiparallel orientations
  • Turns and loops connect secondary structure elements and allow for changes in the direction of the polypeptide chain
• Tertiary structure three-dimensional folding of a polypeptide chain determined by interactions between amino acid side chains
  • Hydrophobic interactions, hydrogen bonding, ionic interactions, and disulfide bridges contribute to the stability of the tertiary structure
  • Tertiary structure determines the overall shape and function of a protein, including the formation of active sites and binding pockets
• Quaternary structure arrangement of multiple polypeptide subunits in a multi-subunit protein
  • Subunits may be identical (homooligomers) or different (heterooligomers) and are held together by non-covalent interactions
  • Quaternary structure can provide additional levels of regulation, cooperativity, and allosteric control in protein function

Protein Folding and Stability

• Protein folding process by which a polypeptide chain acquires its native three-dimensional structure
  • Driven by the minimization of free energy and the burial of hydrophobic residues in the protein core
  • Guided by chaperone proteins that assist in the folding process and prevent aggregation
• Thermodynamic stability of proteins determined by the balance between enthalpic and entropic factors
  • Enthalpic contributions include hydrogen bonding, van der Waals interactions, and electrostatic interactions
  • Entropic contributions arise from the conformational flexibility of the polypeptide chain and the release of water molecules upon folding
• Kinetic stability of proteins related to the energy barriers between the native state and unfolded or misfolded states
  • Transition states represent the highest energy points along the folding pathway and determine the rate of folding and unfolding
• Protein misfolding can lead to aggregation and the formation of insoluble amyloid fibrils, which are associated with various diseases (Alzheimer's, Parkinson's, Huntington's)
• Protein stability can be influenced by environmental factors such as temperature, pH, and the presence of denaturants (urea, guanidinium chloride)
  • Denaturation disruption of the native structure by the breaking of non-covalent interactions, leading to the unfolding of the protein
  • Renaturation process by which a denatured protein regains its native structure under favorable conditions, demonstrating the self-assembly capabilities of polypeptide chains

Protein Function and Diversity

• Enzymes proteins that catalyze biochemical reactions by lowering the activation energy and providing a specific binding site for substrates
  • Active site region of an enzyme where the substrate binds and the catalytic reaction takes place
  • Specificity of enzymes determined by the complementarity of the active site to the substrate in terms of shape, charge, and hydrophobicity
• Transport proteins facilitate the movement of molecules across biological membranes
  • Ion channels proteins that form pores in membranes and allow the selective passage of ions down their concentration gradient
  • Carrier proteins undergo conformational changes to bind and release specific molecules, enabling their transport across membranes
• Structural proteins provide mechanical support and contribute to the organization of cells and tissues
  • Collagen most abundant protein in mammals, forming triple helical fibers that provide tensile strength to connective tissues (skin, bones, tendons)
  • Actin and tubulin globular proteins that polymerize to form cytoskeletal filaments (microfilaments and microtubules) essential for cell shape, motility, and division
• Regulatory proteins control various cellular processes by binding to specific targets and modulating their activity
  • Transcription factors proteins that bind to DNA and regulate gene expression by promoting or repressing the recruitment of RNA polymerase
  • Protein kinases enzymes that phosphorylate other proteins, often leading to changes in their activity or interactions with other molecules
• Signaling proteins mediate communication between cells and coordinate cellular responses to external stimuli
  • G protein-coupled receptors (GPCRs) largest family of membrane receptors that transduce extracellular signals into intracellular responses through the activation of G proteins
  • Cytokines small secreted proteins that bind to specific receptors on target cells and initiate signaling cascades involved in immune responses, inflammation, and cell growth

Analytical Techniques for Protein Study

• Protein purification methods used to isolate a specific protein from a complex mixture
  • Chromatography techniques that separate proteins based on differences in their size, charge, hydrophobicity, or affinity for specific ligands
  • Electrophoresis separation of proteins based on their migration in an electric field, often used in combination with SDS to denature and uniformly charge proteins
• Protein sequencing determination of the primary structure of a protein
  • Edman degradation chemical method that sequentially removes and identifies amino acids from the N-terminus of a polypeptide chain
  • Mass spectrometry analysis of peptide fragments generated by enzymatic or chemical cleavage to determine the amino acid sequence
• Protein structure determination techniques used to elucidate the three-dimensional structure of proteins
  • X-ray crystallography method that involves the diffraction of X-rays by a protein crystal to generate an electron density map, which is then used to build an atomic model of the protein
  • Nuclear magnetic resonance (NMR) spectroscopy technique that utilizes the magnetic properties of atomic nuclei to determine the structure of proteins in solution
• Protein-protein interaction studies methods used to investigate the physical associations between proteins
  • Co-immunoprecipitation technique that involves the use of an antibody to capture a target protein and its interacting partners from a cell lysate
  • Yeast two-hybrid system genetic method that detects protein-protein interactions through the reconstitution of a functional transcription factor in yeast cells
• Protein function studies techniques used to investigate the biological roles and activities of proteins
  • Enzyme kinetics measurement of the rates of enzyme-catalyzed reactions to determine kinetic parameters (Km, Vmax) and infer mechanistic details
  • Site-directed mutagenesis introduction of specific mutations into a protein sequence to probe the importance of individual amino acids in structure and function

Real-World Applications and Research

• Therapeutic proteins engineered or naturally occurring proteins used for the treatment of diseases
  • Insulin hormone used to regulate blood sugar levels in the treatment of diabetes
  • Monoclonal antibodies highly specific antibodies produced by identical immune cells, used for targeted therapies in cancer and autoimmune disorders
• Industrial enzymes proteins used in various industrial processes to catalyze specific reactions
  • Proteases enzymes used in detergents to break down protein stains and in food processing to tenderize meat
  • Cellulases enzymes used in the production of biofuels by degrading cellulose into fermentable sugars
• Protein engineering design and modification of proteins to enhance their properties or create novel functions
  • Directed evolution laboratory method that mimics natural selection to evolve proteins with desired characteristics through rounds of mutation and screening
  • Rational design approach that uses structural knowledge and computational tools to predict and introduce specific modifications into a protein sequence
• Protein biomarkers molecules used as indicators of normal or pathological biological processes, often for diagnostic or prognostic purposes
  • Prostate-specific antigen (PSA) protein biomarker used in the screening and monitoring of prostate cancer
  • Troponin I and T proteins released from damaged heart muscle, used as biomarkers for the diagnosis of myocardial infarction (heart attack)
• Protein-based biomaterials materials derived from or inspired by proteins, used in various biomedical applications
  • Spider silk proteins known for their exceptional strength and elasticity, being explored for use in tissue engineering and wound healing
  • Collagen-based scaffolds porous materials used in regenerative medicine to support cell growth and tissue repair