1: Unit 1 - Proteins
- Page ID
- 191184
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)- 1.1: Molecules of Life
- The essential elements of life, emphasizing matter and its atomic structure. It highlights the four critical classes of biological macromolecules, carbohydrates, lipids, proteins, and nucleic acids, as key components of cells that perform vital functions and constitute most cell mass. The text underscores the importance of chemical and physical foundations in understanding biological processes.
- 1.2: Chemistry of Water
- Water is vital in biochemistry, affecting solubility, pH, and molecular interactions. Its polarity enables hydrogen bonding, shaping solvent properties, ice formation, and protein folding. Weak interactions, including ionic and van der Waals forces, stabilize biomolecules. Water’s ionization regulates pH, with buffers maintaining physiological balance. The Henderson-Hasselbalch equation links pH, pKa, and acid-base dynamics, essential for biochemical reactions.
- 1.2.1: Water
- 1.2.2: The multiple roles of water
- 1.2.3: pH and Buffers
- 1.2.4: Weak Acids and Bases, pH and pKa
- 1.2.5: Buffering against pH Changes in Biological Systems
- 1.2.6: Solubility in an aqueous world - noncovalent interactions in depth
- 1.2.7: Solubility in an aqueous world - The Hydrophobic Effect
- 1.2.8: Chapter 2 Questions
- 1.3: Amino Acids and Peptides
- Amino acids serve as the building blocks of proteins, with their structure and properties determining biological function. Each amino acid contains an α-carbon, a functional side chain, and distinct stereochemistry. Side-chain interactions, including hydrogen bonding, ionic interactions, and disulfide bonds in cysteine, contribute to protein stability. Ionization states vary with pH, governed by pKa values and the Henderson-Hasselbalch equation.
- 1.4: Proteins- Structure and Folding
- Proteins drive cellular functions, with structure determining function. Primary structure consists of amino acid sequences linked by peptide bonds. Secondary structures form via hydrogen bonding, while tertiary structure results from hydrophobic forces, disulfide bonds, and salt bridges. Quaternary structure involves multimeric assemblies. Protein folding, aided by chaperonins and AI tools like AlphaFold, reveals insights into stability and disease-related misfolding.
- 1.4.1: The Structure of Proteins- An Overview
- 1.4.2: Levels of Protein Structure
- 1.4.3: Secondary Structure
- 1.4.4: Protein folding
- 1.4.5: Analyses of Protein Structure
- 1.4.6: Protein function, domains and cooperativity
- 1.4.7: The Three-Dimensional Structure of Proteins
- 1.4.7.1: Main Chain Conformations
- 1.4.7.2: Secondary Structure and Loops
- 1.4.7.3: Tertiary, Quaternary, and Symmetrical Structures
- 1.4.7.4: Secondary Structural Motifs and Domains
- 1.4.7.5: Protein with Alpha, Alpha-Beta, Beta and Little Secondary Structure
- 1.4.7.6: Intrinsically Disordered Proteins
- 1.4.7.7: Fibrillar Proteins
- 1.4.7.8: Protein Folding and Unfolding (Denaturation) - Dynamics
- 1.4.7.9: Protein Stability - Thermodynamics
- 1.4.7.10: Protein Aggregates - Amyloids, Prions and Intracellular Granules
- 1.4.7.11: Biomolecular Visualization - Conceptions and Misconceptions
- 1.4.7.12: Laboratory Determination of the Thermodynamic Parameters for Protein Denaturation
- 1.4.7.13: Predicting Structure and Function of Biomolecules Through Natural Language Processing Tools
- 1.4.7.14: Predicting Structure from Sequence and Sequence from Structure/Function (New 10/24)
- 1.4.7.15: Chapter 4 Questions
- 1.4.8: Problems - Predicting Protein Structure and Function Using Machine Learning and AI Programs
- 1.5: Protein Purification
- Protein purification isolates proteins for study using cell disruption, centrifugation, dialysis, chromatography, and electrophoresis. Centrifugation separates cellular components, while chromatography techniques: gel filtration, ion exchange, and affinity chromatography, enhance specificity. Electrophoresis sorts proteins by size and charge. Histidine tagging aids recombinant protein purification, and ELISAs quantify protein concentration.
- 1.5.1: Protein Purification
- 1.5.2: Cell Disruption
- 1.5.3: Fractionation
- 1.5.4: Electrophoresis
- 1.5.5: Electrophoresis
- 1.5.6: Gel Exclusion Chromatography
- 1.5.7: Ion Exchange Chromatography
- 1.5.8: Affinity Chromatography
- 1.5.9: High Performance Liquid Chromatography (HPLC)
- 1.5.10: Histidine Tagging
- 1.5.11: Quantification of Protein Concentration
- 1.5.12: Binding - Enzyme Linked Immunosorbant Assays (ELISAs)

