Upper-Level Introductory Biochemistry
- Page ID
- 154140
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)- Front Matter
- Biochemical processes sustain life by driving molecular interactions, enzyme activity, and metabolic pathways. Water chemistry, amino acids, and protein structure determine biological function, while enzyme catalysis and thermodynamics regulate energy flow. Metabolic pathways and allosteric control maintain cellular balance.
- 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.
- 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.
- 2.1: Water
- 2.2: The multiple roles of water
- 2.3: pH and Buffers
- 2.4: Weak Acids and Bases, pH and pKa
- 2.5: Buffering against pH Changes in Biological Systems
- 2.6: Solubility in an aqueous world - noncovalent interactions in depth
- 2.7: Solubility in an aqueous world - The Hydrophobic Effect
- 2.8: Chapter 2 Questions
- 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.
- 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.
- 4.1: The Structure of Proteins- An Overview
- 4.2: Levels of Protein Structure
- 4.3: Secondary Structure
- 4.4: Protein folding
- 4.5: Analyses of Protein Structure
- 4.6: Protein function, domains and cooperativity
- 4.7: The Three-Dimensional Structure of Proteins
- 4.8: Problems - Predicting Protein Structure and Function Using Machine Learning and AI Programs
- 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.
- 5.1: Protein Purification
- 5.2: Cell Disruption
- 5.3: Fractionation
- 5.4: Electrophoresis
- 5.5: Electrophoresis
- 5.6: Gel Exclusion Chromatography
- 5.7: Ion Exchange Chromatography
- 5.8: Affinity Chromatography
- 5.9: High Performance Liquid Chromatography (HPLC)
- 5.10: Histidine Tagging
- 5.11: Quantification of Protein Concentration
- 5.12: Binding - Enzyme Linked Immunosorbant Assays (ELISAs)
- 6: Enzyme Thermodynamics
- Living cells maintain order despite the natural tendency toward disorder, requiring continuous energy input. Thermodynamics governs biochemical reactions, distinguishing endergonic reactions, which require energy, from exergonic reactions, which occur spontaneously. Gibbs free energy (ΔG) determines reaction spontaneity, while biological systems prevent equilibrium through constant energy use. Enzymes influence reaction rates but do not alter equilibrium, enabling efficient metabolism.
- 7: Enzyme Kinetics
- Enzymes speed up biochemical reactions by lowering activation energy, making catalysis essential for life. Enzyme kinetics and reaction mechanisms explain how enzymes function, while cofactors enhance their activity. Binding interactions influence protein function, and the Michaelis-Menten equation models enzyme behavior. Ribozymes and enzyme inhibitors regulate catalytic efficiency.
- 8: Enzyme Regulation
- Enzymes catalyze reactions by creating favorable electronic environments, with serine proteases serving as key examples. A diverse range of reaction mechanisms allows enzymes to perform specific functions while maintaining regulatory control. Activation and inactivation processes enable enzymes to adjust to changing conditions, preserving homeostasis and ensuring proper cellular function.
- 12: Membranes and Membrane Proteins
- 12.1: Basic Concepts in Membranes
- 12.2: Membrane Bilayer and Monolayer Assemblies - Structures and Dynamics
- 12.3: Working with Lipids
- 12.4: Transport in Membranes
- 12.5: Problems
- 12.6: Membranes and Membrane Proteins
- 12.7: Diffusion Across a Membrane - Passive and Facilitated Diffusion
- 12.8: Diffusion Across a Membrane - Channels
- 12.9: Diffusion Across a Membrane - Pores
- 12.10: Active Transport
- 12.11: Diffusion Across a Membrane - Pores
- 13: Biochemistry of Our Senses
- 13.1: Cell Signaling
- 13.2: Ligand-gated Ion Channel Receptors
- 13.3: Nuclear Hormone Receptors
- 13.4: G-protein Coupled Receptors (GPCRs)
- 13.5: Receptor Tyrosine Kinases (RTKs)
- 13.6: Gated Ion Channels - Neural Signaling
- 13.7: Signal Transduction - Vision and Olfaction
- 13.8: Signal Transduction - Taste (Gustation)
- 13.9: Signal Transduction - Temperature
- 13.10: Signal Transduction - Pressure