5: Protein Function
- Page ID
- 14947
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Return to Fundamentals of Biochemistry Search Fundamentals of Biochemistry
- 5.1: Binding - The First Step Towards Protein Function
- This page outlines learning goals for understanding protein-ligand interactions, including binding thermodynamics, key binding constants like Kd and Ka, and the interpretation of binding curves. It compares one-site versus two-site binding models and explores cooperative and allosteric effects. It discusses experimental methods for measuring interactions and relates binding to protein functions in biological contexts.
- 5.2: Techniques to Measure Binding
- It is often essential to determine the KD for a ML complex since given that number and the concentrations of M and L in the system, we can then predict if M is bound under physiological conditions. Again, this is important since whether M is bound or free will govern its activity. To determine KD, you need to determine ML and L at equilibrium. How can we differentiate free from bound ligand? The following techniques allow such a differentiation.
- 5.03: A. Oxygen-Binding Proteins and Allosterism
- The document provides an in-depth exploration of the fundamentals of biochemistry focused on myoglobin and hemoglobin, serving as models for ligand binding. It compares their structures and functions, explains oxygen binding curves, cooperative binding, and allosteric regulation, and discusses the physiological roles and clinical implications, such as mutations leading to diseases like sickle cell anemia.
- 5.03: B. Other Allosteric Proteins
- This page covers the intricacies of allosterism in biochemistry, focusing on myoglobin, hemoglobin, and various enzymes, including lactate dehydrogenase and phosphofructokinases. It discusses structural transformations in viral enzymes and the significance of Lenacapavir as an HIV drug. The text details the kinetic behaviors of enzymes and the influence of ligand concentrations on activity.
- 5.04: A. The Immune System - Antibodies, B- cells, T-cell receptors and T-cells
- This page provides an overview of the immune system's functionality, detailing the roles of both innate and adaptive immunity, particularly focusing on the mechanisms of B cells and T cells. Key elements include the structure and diversity of antibodies, significance of immunoglobulin domains, and the dynamics of antibody-antigen interactions.
- 5.04: B. The Innate Immune System, PAMPs and DAMPs, and Inflammation
- This page discusses biochemistry learning goals, focusing on protein-ligand interactions and the immune system. Topics include immune response mechanisms, the role of signaling molecules like cGAMP, and the importance of mRNA vaccines. It explains pathogen recognition via pattern recognition receptors, inflammasome formation involving proteins like ASC, and the activation of NLRP3 by PAMPS and DAMPS.
- 5.5: Protein Interactions Modulated by Chemical Energy- Actin, Myosin, and Molecular Motors
- This page provides an in-depth exploration of the structural and functional aspects of molecular motors like myosin, kinesin, and dynein, focusing on their roles in muscle contraction and cellular motility. It covers the actomyosin cross-bridge cycle, the interaction of actin and myosin, and the regulation of muscle contraction through proteins like troponin and tropomyosin, with a detailed explanation of the biochemical underpinnings of these processes.
- 5.6: Binding - Conformational Selections and Intrinsically Disordered Proteins
- The page outlines learning goals related to protein-ligand interactions, focusing on induced fit and conformational selection, intrinsically disordered proteins (IDPs), and Molecular Recognition Features (MoRFs). It describes models of protein-ligand binding, explores mechanisms of coupling folding and binding, and discusses the role of intrinsic disorder in cellular functions.
- 5.7: Binding - Enzyme Linked Immunosorbant Assays (ELISAs)
- The page provides an educational outline for junior and senior biochemistry majors focused on understanding and applying ELISAs (Enzyme-Linked Immunosorbent Assays). It details the fundamental principles, distinguishing between formats, key steps in protocols, detection methods, interpretation of results, and advanced techniques like logit-log transformations for data analysis.
- 5.8: Problems - Predicting Protein Structure and Function Using Machine Learning and AI Programs
- The document provides exercises and instructions for using machine learning/AI algorithms to predict protein structures, functions, and interactions, as well as design proteins with specific functions. It emphasizes the use of tools such as AlphaFold, ESMFold, and iCn3D for modeling and rendering structures and interacting domains.