Principles of Physical Biochemistry
|
|
- Dustin Marshall
- 6 years ago
- Views:
Transcription
1 Principles of Physical Biochemistry Kensal E. van Hold e W. Curtis Johnso n P. Shing Ho
2
3 Preface x i PART 1 MACROMOLECULAR STRUCTURE AND DYNAMICS 1 1 Biological Macromolecules General Principles Macromolecules Configuration and Conformation Molecular Interactions in Macromolecular Structures Weak Interactions The Environment in the Cell Water Structure The Interaction of Molecules with Water Nonaqueous Environment of Biological Molecules Symmetry Relationships Between Molecules Mirror Symmetry Rotational Symmetry Multiple Symmetry Relationships and Point Groups Screw Symmetry The Structure of Proteins Amino Acids The Unique Protein Sequence Secondary Structures of Proteins Helical Symmetry Effect of the Peptide Bond on Protein Conformations The Structure of Globular Proteins 42
4 1.6 The Structure of Nucleic Acids Torsion Angles in the Polynucleotide Chain The Helical Structures of Polynucleic Acids Higher-Order Structures in Polynucleotides 60 Exercises 6 6 References 67 2 Thermodynamic Principles Heat, Work, and Energy-First Law of Thermodynamics Molecular Interpretation of Thermodynamic Quantities Entropy, Free Energy, and Equilibrium- Second Law of Thermodynamics 77 Exercises 87 References Molecular Thermodynamics Complexities in Modeling Macromolecular Structure Simplifying Assumptions Molecular Mechanics Basic Principles Molecular Potentials Bonding Potentials Nonbonding Potentials Electrostatic Interactions Dipole-Dipole Interactions van der Waals Interactions Hydrogen Bonds Stabilizing Interactions in Macromolecules Protein Structure Dipole Interactions Side Chain Interactions Electrostatic Interactions Nucleic Acid Structure Base-Pairing Base-Stacking Electrostatic Interactions Simulating Macromolecular Structure Energy Minimization Molecular Dynamics Entropy Hydration and the Hydrophobic Effect Free Energy Methods 142 Exercises 144 References 145
5 4 Statistical Thermodynamics General Principles Statistical Weights and the Partition Function Models for Structural Transitions in Biopolymers Structural Transitions in Polypeptides and Proteins Coil-Helix Transitions Statistical Methods for Predicting Protein Secondary Structures Structural Transitions in Polynucleotides and DNA Melting and Annealing of Polynucleotide Duplexes Helical Transitions in Double-Stranded DNA Supercoil Dependent DNA Transitions Predicting Helical Structures in Genomic DNA Nonregular Structures Random Walk Average Linear Dimension of a Biopolymer Simple Exact Models for Compact Structures 18 3 Exercises 18 9 References Methods for the Separation and Characterizatio n of Macromolecules General Principles Sedimentation Moving Boundary Sedimentation Zonal Sedimentation Electrophoresis and Isoelectric Focusing Electrophoresis : General Principles Electrophoresis of Nucleic Acids SDS-Gel Electrophoresis of Proteins Methods for Detecting and Analyzing Components on Gels Capillary Electrophoresis Isoelectric Focusing Mass Spectrometry General Principles : The Problem Current Techniques for Biopolymers 23 5 Exercises 236 References X-Ray Diffraction Structures at Atomic Resolution Crystals What Is a Crystal? 246
6 6.2.2 Growing Crystals Conditions for Macromolecular Crystallization Theory of X-Ray Diffraction Bragg's Law von Laue Conditions for Diffraction Determining the Crystal Morphology Solving Macromolecular Structures by X-Ray Diffraction X-Ray Scattering in Reciprocal Space: The Scatterin g Vector The Structure Factor The Phase Problem Resolution in X-Ray Diffraction Fiber Diffraction ' The Fiber Unit Cell Fiber Diffraction of Continuous Helices Fiber Diffraction of Discontinuous Helices 304 Exercises 308 References Scattering from Solutions of Macromolecules Light Scattering Fundamental Concepts Scattering from a Number of Small Particles : Rayleigh Scattering Scattering from Particles That Are Not Small Compared t o Wavelength of Radiation Dynamic Light Scattering: Measurements of Diffusion Low Angle X-Ray Scattering Neutron Scattering Raman Scattering 33 1 Exercises 337 References 33 9 PART 2 SPECTROSCOPY Quantum Mechanics and Spectroscopy Light and Transitions Postulate Approach to Quantum Mechanics Transition Energies The Quantum Mechanics of Simple Systems Approximating Solutions to Quantum Chemistry Problems The Hydrogen Molecule as the Model for a Bond 361
7 8.4 Transition Intensities Transition Dipole Directions 37 5 Exercises 37 8 References Absorption Spectroscopy Electronic Absorption Energy of Electronic Absorption Bands Transition Dipoles Proteins Nucleic Acids Applications of Electronic Absorption Spectroscopy Vibrational Absorption Energy of Vibrational Absorption Bands Transition Dipoles Instrumentation for Vibrational Spectroscopy Applications to Biological Molecules 41 2 Exercises 41 6 References Linear and Circular Dichroism Linear Dichroism of Biological Polymers Circular Dichroism of Biological Molecules Electronic CD of Nucleic Acids Electronic CD of Proteins Singular Value Decomposition and Analyzing the CD o f Proteins for Secondary Structure Vibrational CD 44 8 Exercises 449 References Emission Spectroscopy The Phenomenon Emission Lifetimes Fluorescence Spectroscopy Fluorescence Instrumentation Analytical Applications Solvent Effects Fluorescence Decay Energy Transfer Linear Polarization of Fluorescence Fluorescence Applied to Proteins 474
8 11.11 Fluorescence Applied to Nucleic Acids 47 7 Exercises 481 References Nuclear Magnetic Resonance Spectroscopy The Phenomenon The Measurable Spin-Spin Interaction Relaxation and the Nuclear Overhauser Effect Measuring the Spectrum One-Dimensional NMR of Macromolecules Two-Dimensional Fourier Transform NMR Two-Dimensional FT NMR Applied to Macromolecules 50 8 Exercises 523 References 525 PART 3 SOLUTION BEHAVIOR OF MACROMOLECULES Macromolecules in Solution : Thermodynamics and Equilibria Some Fundamentals of Solution Thermodynamics Partial Molar Quantities : Chemical Potential The Chemical Potential and Concentration : Ideal and Nonideal Solutions Applications of the Chemical Potential to Physical Equilibria Membrane Equilibria Sedimentation Equilibrium Sedimentation Equilibrium in a Density Gradient Steady-State Electrophoresis 55 6 Exercises 56 0 References Thermodynamics of Transport Processes General Principles Diffusion Transport Across Membranes Passive Transport Facilitated Transport Active Transport Selective Ion Transport and Membrane Potential- The Goldman Equation Sedimentation 582
9 Exercises 58 5 References Chemical Equilibria Involving Macromolecules Thermodynamics of Chemical Reactions in Solution : A Review Interactions Between Macromolecules Binding of Small Ligands by Macromolecules General Principles and Methods Multiple Equilibria Proton Binding: Titration Curves Binding to Nucleic Acids General Principles Special Aspects of Nonspecific Binding 62 9 Exercises 63 3 References 63 7 Solutions to Odd-Numbered Exercises 63 9 Index 647
Contents. xiii. Preface v
Contents Preface Chapter 1 Biological Macromolecules 1.1 General PrincipIes 1.1.1 Macrornolecules 1.2 1.1.2 Configuration and Conformation Molecular lnteractions in Macromolecular Structures 1.2.1 Weak
More informationBBS501 Section 1 9:00 am 10:00 am Monday thru Friday LRC 105 A & B
BBS501 Section 1 9:00 am 10:00 am Monday thru Friday LRC 105 A & B Lecturers: Dr. Yie-Hwa Chang Room M130 Phone: #79263 E-mail:changy@slu.edu Dr. Tomasz Heyduk Room M99 Phone: #79238 E-mail: heydukt@slu.edu
More informationProtein Structure Analysis and Verification. Course S Basics for Biosystems of the Cell exercise work. Maija Nevala, BIO, 67485U 16.1.
Protein Structure Analysis and Verification Course S-114.2500 Basics for Biosystems of the Cell exercise work Maija Nevala, BIO, 67485U 16.1.2008 1. Preface When faced with an unknown protein, scientists
More informationSpectroscopy Chapter 13
Spectroscopy Chapter 13 Electromagnetic Spectrum Electromagnetic spectrum in terms of wavelength, frequency and Energy c=λν c= speed of light in a vacuum 3x108 m/s v= frequency in Hertz (Hz s-1 ) λ= wavelength
More informationXV 74. Flouorescence-Polarization-Circular-Dichroism- Jablonski diagram Where does the energy go?
XV 74 Flouorescence-Polarization-Circular-Dichroism- Jablonski diagram Where does the energy go? 1) Excite system through A Absorbance S 0 S n Excite from ground excited singlet S = 0 could be any of them
More informationCode Course name CFU Year G6403B Info not available 3 1
Basic aims The aim of the course is an in-depth discussion of the structureactivity relationships of the main classes of biological molecules. Strategies for synthesis, isolation and structural characterization
More informationNPTEL VIDEO LECTURE TOPICS FOR BIO-TECHNOLOGY
NPTEL VIDEO LECTURE TOPICS FOR BIO-TECHNOLOGY New No.1, Vembuliamman Koil Street, Pazhavanthangal, Chennai 600 114 Phone: 98841 65649 / 98847 36552 E-mail: nptel@linuxpert.in NPTEL Video Course - Biotechnology
More informationBasics of protein structure
Today: 1. Projects a. Requirements: i. Critical review of one paper ii. At least one computational result b. Noon, Dec. 3 rd written report and oral presentation are due; submit via email to bphys101@fas.harvard.edu
More informationIntroduction to" Protein Structure
Introduction to" Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Learning Objectives Outline the basic levels of protein structure.
More informationHomework Due by 5PM September 20 (next class) Does everyone have a topic that has been approved by the faculty?
Howdy Folks. Homework Due by 5PM September 20 (next class) 5-Problems Every Week due 1 week later. Does everyone have a topic that has been approved by the faculty? Practice your presentation as I will
More informationScattering Lecture. February 24, 2014
Scattering Lecture February 24, 2014 Structure Determination by Scattering Waves of radiation scattered by different objects interfere to give rise to an observable pattern! The wavelength needs to close
More informationTHE UNIVERSITY OF MANITOBA. PAPER NO: 409 LOCATION: Fr. Kennedy Gold Gym PAGE NO: 1 of 6 DEPARTMENT & COURSE NO: CHEM 4630 TIME: 3 HOURS
PAPER NO: 409 LOCATION: Fr. Kennedy Gold Gym PAGE NO: 1 of 6 DEPARTMENT & COURSE NO: CHEM 4630 TIME: 3 HOURS EXAMINATION: Biochemistry of Proteins EXAMINER: J. O'Neil Section 1: You must answer all of
More informationEXAM I COURSE TFY4310 MOLECULAR BIOPHYSICS December Suggested resolution
page 1 of 7 EXAM I COURSE TFY4310 MOLECULAR BIOPHYSICS December 2013 Suggested resolution Exercise 1. [total: 25 p] a) [t: 5 p] Describe the bonding [1.5 p] and the molecular orbitals [1.5 p] of the ethylene
More information4. Circular Dichroism - Spectroscopy
4. Circular Dichroism - Spectroscopy The optical rotatory dispersion (ORD) and the circular dichroism (CD) are special variations of absorption spectroscopy in the UV and VIS region of the spectrum. The
More informationModern Optical Spectroscopy
Modern Optical Spectroscopy With Exercises and Examples from Biophysics and Biochemistry von William W Parson 1. Auflage Springer-Verlag Berlin Heidelberg 2006 Verlag C.H. Beck im Internet: www.beck.de
More informationI690/B680 Structural Bioinformatics Spring Protein Structure Determination by NMR Spectroscopy
I690/B680 Structural Bioinformatics Spring 2006 Protein Structure Determination by NMR Spectroscopy Suggested Reading (1) Van Holde, Johnson, Ho. Principles of Physical Biochemistry, 2 nd Ed., Prentice
More informationBIBC 100. Structural Biochemistry
BIBC 100 Structural Biochemistry http://classes.biology.ucsd.edu/bibc100.wi14 Papers- Dialogue with Scientists Questions: Why? How? What? So What? Dialogue Structure to explain function Knowledge Food
More informationCHEMISTRY (CHEM) CHEM 5800 Principles Of Materials Chemistry. Tutorial in selected topics in materials chemistry. S/U grading only.
Chemistry (CHEM) 1 CHEMISTRY (CHEM) CHEM 5100 Principles of Organic and Inorganic Chemistry Study of coordination compounds with a focus on ligand bonding, electron counting, molecular orbital theory,
More informationCircular Dichroism & Optical Rotatory Dispersion. Proteins (KCsa) Polysaccharides (agarose) DNA CHEM 305. Many biomolecules are α-helical!
Circular Dichroism & Optical Rotatory Dispersion Polysaccharides (agarose) DNA Proteins (KCsa) Many biomolecules are α-helical! How can we measure the amount and changes in amount of helical structure
More informationIntroduction to Polymer Physics
Introduction to Polymer Physics Enrico Carlon, KU Leuven, Belgium February-May, 2016 Enrico Carlon, KU Leuven, Belgium Introduction to Polymer Physics February-May, 2016 1 / 28 Polymers in Chemistry and
More informationSpectroscopy of Polymers
Spectroscopy of Polymers Jack L. Koenig Case Western Reserve University WOMACS Professional Reference Book American Chemical Society, Washington, DC 1992 Contents Preface m xiii Theory of Polymer Characterization
More informationStructural Bioinformatics (C3210) Molecular Mechanics
Structural Bioinformatics (C3210) Molecular Mechanics How to Calculate Energies Calculation of molecular energies is of key importance in protein folding, molecular modelling etc. There are two main computational
More informationNMR, X-ray Diffraction, Protein Structure, and RasMol
NMR, X-ray Diffraction, Protein Structure, and RasMol Introduction So far we have been mostly concerned with the proteins themselves. The techniques (NMR or X-ray diffraction) used to determine a structure
More informationMedical Biophysics II. Final exam theoretical questions 2013.
Medical Biophysics II. Final exam theoretical questions 2013. 1. Early atomic models. Rutherford-experiment. Franck-Hertz experiment. Bohr model of atom. 2. Quantum mechanical atomic model. Quantum numbers.
More informationCD Basis Set of Spectra that is used is that derived from comparing the spectra of globular proteins whose secondary structures are known from X-ray
CD Basis Set of Spectra that is used is that derived from comparing the spectra of globular proteins whose secondary structures are known from X-ray crystallography An example of the use of CD Modeling
More informationLecture 3: Light absorbance
Lecture 3: Light absorbance Perturbation Response 1 Light in Chemistry Light Response 0-3 Absorbance spectrum of benzene 2 Absorption Visible Light in Chemistry S 2 S 1 Fluorescence http://www.microscopyu.com
More informationPhET Interactive Chemistry Simulations Aligned to an Example General Chemistry Curriculum
PhET Interactive Chemistry Simulations Aligned to an Example General Chemistry Curriculum Alignment is based on the topics and subtopics addressed by each sim. Sims that directly address the topic area
More informationPresenter: She Zhang
Presenter: She Zhang Introduction Dr. David Baker Introduction Why design proteins de novo? It is not clear how non-covalent interactions favor one specific native structure over many other non-native
More informationDetermining Protein Structure BIBC 100
Determining Protein Structure BIBC 100 Determining Protein Structure X-Ray Diffraction Interactions of x-rays with electrons in molecules in a crystal NMR- Nuclear Magnetic Resonance Interactions of magnetic
More informationCHEMISTRY (CHEM) CHEM 1200 Problem Solving In General Chemistry
Chemistry (CHEM) 1 CHEMISTRY (CHEM) CHEM 1090 Elementary Chemistry [0-3 credit hours (0-2, 0, 0-1)] For students who major in science, engineering or other fields which require chemistry as a prerequisite
More informationProtein Dynamics. The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron.
Protein Dynamics The space-filling structures of myoglobin and hemoglobin show that there are no pathways for O 2 to reach the heme iron. Below is myoglobin hydrated with 350 water molecules. Only a small
More informationMolecular Modelling. part of Bioinformatik von RNA- und Proteinstrukturen. Sonja Prohaska. Leipzig, SS Computational EvoDevo University Leipzig
part of Bioinformatik von RNA- und Proteinstrukturen Computational EvoDevo University Leipzig Leipzig, SS 2011 Protein Structure levels or organization Primary structure: sequence of amino acids (from
More information1) NMR is a method of chemical analysis. (Who uses NMR in this way?) 2) NMR is used as a method for medical imaging. (called MRI )
Uses of NMR: 1) NMR is a method of chemical analysis. (Who uses NMR in this way?) 2) NMR is used as a method for medical imaging. (called MRI ) 3) NMR is used as a method for determining of protein, DNA,
More informationDEPARTMENT OF PHYSICS UNIVERSITY OF PUNE PUNE SYLLABUS for the M.Phil. (Physics ) Course
DEPARTMENT OF PHYSICS UNIVERSITY OF PUNE PUNE - 411007 SYLLABUS for the M.Phil. (Physics ) Course Each Student will be required to do 3 courses, out of which two are common courses. The third course syllabus
More informationFluorescence 2009 update
XV 74 Fluorescence 2009 update Jablonski diagram Where does the energy go? Can be viewed like multistep kinetic pathway 1) Excite system through A Absorbance S 0 S n Excite from ground excited singlet
More informationIntroductory Physical Chemistry Final Exam Points of Focus
Introductory Physical Chemistry Final Exam Points of Focus Gas Laws: Understand the foundations of the basic SI units of Pressure and Temperature. Know and be able to use the ideal gas law. Know and be
More informationChapter 1. Topic: Overview of basic principles
Chapter 1 Topic: Overview of basic principles Four major themes of biochemistry I. What are living organism made from? II. How do organism acquire and use energy? III. How does an organism maintain its
More informationProtein-Ligand Interactions: hydrodynamics and calorimetry
Protein-Ligand Interactions: hydrodynamics and calorimetry Approach Stephen E. Harding Babur Z. Chowdhry OXFORD UNIVERSITY PRESS , New York Oxford University Press, 2001 978-0-19-963746-1 List of protocols
More informationChristopher Pavlik Bioanalytical Chemistry March 2, 2011
Nuclear Magnetic Resonance of Proteins Christopher Pavlik Bioanalytical Chemistry March 2, 2011 Nuclear Magnetic Resonance NMR Application of a magnetic field causes absorption of EM energy that induces
More informationProteins polymer molecules, folded in complex structures. Konstantin Popov Department of Biochemistry and Biophysics
Proteins polymer molecules, folded in complex structures Konstantin Popov Department of Biochemistry and Biophysics Outline General aspects of polymer theory Size and persistent length of ideal linear
More informationT 1, T 2, NOE (reminder)
T 1, T 2, NOE (reminder) T 1 is the time constant for longitudinal relaxation - the process of re-establishing the Boltzmann distribution of the energy level populations of the system following perturbation
More informationCORE MOLIT ACTIVITIES at a glance
CORE MOLIT ACTIVITIES at a glance 1. Amplification of Biochemical Signals: The ELISA Test http://molit.concord.org/database/activities/248.html The shape of molecules affects the way they function. A test
More informationBIMS 503 Exam I. Sign Pledge Here: Questions from Robert Nakamoto (40 pts. Total)
BIMS 503 Exam I September 24, 2007 _ /email: Sign Pledge Here: Questions from Robert Nakamoto (40 pts. Total) Questions 1-6 refer to this situation: You are able to partially purify an enzyme activity
More informationBIOCHEMISTRY GUIDED NOTES - AP BIOLOGY-
BIOCHEMISTRY GUIDED NOTES - AP BIOLOGY- ELEMENTS AND COMPOUNDS - anything that has mass and takes up space. - cannot be broken down to other substances. - substance containing two or more different elements
More informationEVPP 110 Lecture Exam #1 Study Questions Fall 2003 Dr. Largen
EVPP 110 Lecture Exam #1 Study Questions Fall 2003 Dr. Largen These study questions are meant to focus your study of the material for the first exam. The absence here of a topic or point covered in lecture
More informationWhat happens when light falls on a material? Transmission Reflection Absorption Luminescence. Elastic Scattering Inelastic Scattering
Raman Spectroscopy What happens when light falls on a material? Transmission Reflection Absorption Luminescence Elastic Scattering Inelastic Scattering Raman, Fluorescence and IR Scattering Absorption
More informationNanobiotechnology. Place: IOP 1 st Meeting Room Time: 9:30-12:00. Reference: Review Papers. Grade: 40% midterm, 60% final report (oral + written)
Nanobiotechnology Place: IOP 1 st Meeting Room Time: 9:30-12:00 Reference: Review Papers Grade: 40% midterm, 60% final report (oral + written) Midterm: 5/18 Oral Presentation 1. 20 minutes each person
More informationMULTIPLE CHOICE. Circle the one alternative that best completes the statement or answers the question.
Summer Work Quiz - Molecules and Chemistry Name MULTIPLE CHOICE. Circle the one alternative that best completes the statement or answers the question. 1) The four most common elements in living organisms
More informationHarald Ibach Hans Lüth SOLID-STATE PHYSICS. An Introduction to Theory and Experiment
Harald Ibach Hans Lüth SOLID-STATE PHYSICS An Introduction to Theory and Experiment With 230 Figures Springer-Verlag Berlin Heidelberg New York London Paris Tokyo Hong Kong Barcelona Budapest Contents
More informationProteins are not rigid structures: Protein dynamics, conformational variability, and thermodynamic stability
Proteins are not rigid structures: Protein dynamics, conformational variability, and thermodynamic stability Dr. Andrew Lee UNC School of Pharmacy (Div. Chemical Biology and Medicinal Chemistry) UNC Med
More informationSkoog Chapter 6 Introduction to Spectrometric Methods
Skoog Chapter 6 Introduction to Spectrometric Methods General Properties of Electromagnetic Radiation (EM) Wave Properties of EM Quantum Mechanical Properties of EM Quantitative Aspects of Spectrochemical
More informationDetails of Protein Structure
Details of Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Anne Mølgaard, Kemisk Institut, Københavns Universitet Learning Objectives
More informationAn Introduction to Polymer Physics
An Introduction to Polymer Physics David I. Bower Formerly at the University of Leeds (CAMBRIDGE UNIVERSITY PRESS Preface Acknowledgements xii xv 1 Introduction 1 1.1 Polymers and the scope of the book
More informationCAP 5510 Lecture 3 Protein Structures
CAP 5510 Lecture 3 Protein Structures Su-Shing Chen Bioinformatics CISE 8/19/2005 Su-Shing Chen, CISE 1 Protein Conformation 8/19/2005 Su-Shing Chen, CISE 2 Protein Conformational Structures Hydrophobicity
More informationAn Introduction to Diffraction and Scattering. School of Chemistry The University of Sydney
An Introduction to Diffraction and Scattering Brendan J. Kennedy School of Chemistry The University of Sydney 1) Strong forces 2) Weak forces Types of Forces 3) Electromagnetic forces 4) Gravity Types
More informationPhysical Background Of Nuclear Magnetic Resonance Spectroscopy
Physical Background Of Nuclear Magnetic Resonance Spectroscopy Michael McClellan Spring 2009 Department of Physics and Physical Oceanography University of North Carolina Wilmington What is Spectroscopy?
More informationThe Oxford Solid State Basics
The Oxford Solid State Basics Steven H. Simon University of Oxford OXFORD UNIVERSITY PRESS Contents 1 About Condensed Matter Physics 1 1.1 What Is Condensed Matter Physics 1 1.2 Why Do We Study Condensed
More information(DPHY 21) 1) a) Discuss the propagation of light in conducting surface. b) Discuss about the metallic reflection at oblique incidence.
(DPHY 21) ASSIGNMENT - 1, MAY - 2015. PAPER- V : ELECTROMAGNETIC THEORY AND MODERN OPTICS 1) a) Discuss the propagation of light in conducting surface. b) Discuss about the metallic reflection at oblique
More informationINTRODUCTION TO MODERN VIBRATIONAL SPECTROSCOPY
INTRODUCTION TO MODERN VIBRATIONAL SPECTROSCOPY MAX DIEM Department of Chemistry City University of New York Hunter College A Wiley-Interscience Publication JOHN WILEY & SONS New York Chichester Brisbane
More informationCHEMISTRY (CHEM) CHEM 208. Introduction to Chemical Analysis II - SL
Chemistry (CHEM) 1 CHEMISTRY (CHEM) CHEM 100. Elements of General Chemistry Prerequisite(s): Completion of general education requirement in mathematics recommended. Description: The basic concepts of general
More informationBiochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015,
Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015, Course,Informa5on, BIOC%530% GraduateAlevel,discussion,of,the,structure,,func5on,,and,chemistry,of,proteins,and, nucleic,acids,,control,of,enzyma5c,reac5ons.,please,see,the,course,syllabus,and,
More informationFundamentals of Nanoscale Film Analysis
Fundamentals of Nanoscale Film Analysis Terry L. Alford Arizona State University Tempe, AZ, USA Leonard C. Feldman Vanderbilt University Nashville, TN, USA James W. Mayer Arizona State University Tempe,
More informationBIOCHEMISTRY Course Outline (Fall, 2011)
BIOCHEMISTRY 402 - Course Outline (Fall, 2011) Number OVERVIEW OF LECTURE TOPICS: of Lectures INSTRUCTOR 1. Structural Components of Proteins G. Brayer (a) Amino Acids and the Polypeptide Chain Backbone...2
More informationLecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability
Lecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions Van der Waals Interactions
More informationLecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability
Lecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions: Van der Waals Interactions
More informationEffects of Chemical Exchange on NMR Spectra
Effects of Chemical Exchange on NMR Spectra Chemical exchange refers to any process in which a nucleus exchanges between two or more environments in which its NMR parameters (e.g. chemical shift, scalar
More informationSpin Relaxation and NOEs BCMB/CHEM 8190
Spin Relaxation and NOEs BCMB/CHEM 8190 T 1, T 2 (reminder), NOE T 1 is the time constant for longitudinal relaxation - the process of re-establishing the Boltzmann distribution of the energy level populations
More informationK ex. Conformational equilibrium. equilibrium K B
Effects of Chemical Exchange on NMR Spectra Chemical exchange refers to any yprocess in which a nucleus exchanges between two or more environments in which its NMR parameters (e.g. chemical shift, scalar
More informationTypical examination questions (with answer notes)
Chemistry with Medicinal Chemistry (CMC)-3 Biophysical Chemistry Module Biomolecular Interactions (Professor Alan Cooper) Typical examination questions (with answer notes) The following questions are adapted
More informationChemistry 460/395. Biophysical Chemistry. Fall Dr. Duarte Mota de Freitas. FH125, Exts or 87045,
Chemistry 460/395 Biophysical Chemistry Fall 2012 Dr. Duarte Mota de Freitas FH125, Exts. 83091 or 87045, E-mail dfreita@luc.edu Lecture Date Topic 1 8/27 Introduction; Amino Acids 2 8/29 Non-covalent
More informationElectronic Spectra of Complexes
Electronic Spectra of Complexes Interpret electronic spectra of coordination compounds Correlate with bonding Orbital filling and electronic transitions Electron-electron repulsion Application of MO theory
More informationMolecular Driving Forces
Molecular Driving Forces Statistical Thermodynamics in Chemistry and Biology SUBGfittingen 7 At 216 513 073 / / Ken A. Dill Sarina Bromberg With the assistance of Dirk Stigter on the Electrostatics chapters
More informationCore Level Spectroscopies
Core Level Spectroscopies Spectroscopies involving core levels are element-sensitive, and that makes them very useful for understanding chemical bonding, as well as for the study of complex materials.
More informationChemistry. Atomic and Molecular Structure
Chemistry Atomic and Molecular Structure 1. The periodic table displays the elements in increasing atomic number and shows how periodicity of the physical and chemical properties of the elements relates
More informationMOLECULAR LIGHT SCATTERING AND OPTICAL ACTIVITY
MOLECULAR LIGHT SCATTERING AND OPTICAL ACTIVITY Second edition, revised and enlarged LAURENCE D. BARRON, F.R.S.E. Gardiner Professor of Chemistry, University of Glasgow 122. CAMBRIDGE UNIVERSITY PRESS
More informationBiomolecules. Energetics in biology. Biomolecules inside the cell
Biomolecules Energetics in biology Biomolecules inside the cell Energetics in biology The production of energy, its storage, and its use are central to the economy of the cell. Energy may be defined as
More informationBiochemistry 530 NMR Theory and Practice
Biochemistry 530 NMR Theory and Practice Gabriele Varani Department of Biochemistry and Department of Chemistry University of Washington 1D spectra contain structural information.. but is hard to extract:
More informationPatrick: An Introduction to Medicinal Chemistry 5e Chapter 01
Questions Patrick: An Introduction to Medicinal Chemistry 5e 01) Which of the following molecules is a phospholipid? a. i b. ii c. iii d. iv 02) Which of the following statements is false regarding the
More informationFoundations in Microbiology Seventh Edition
Lecture PowerPoint to accompany Foundations in Microbiology Seventh Edition Talaro Chapter 2 The Chemistry of Biology Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
More informationIntroduction to Computational Structural Biology
Introduction to Computational Structural Biology Part I 1. Introduction The disciplinary character of Computational Structural Biology The mathematical background required and the topics covered Bibliography
More informationLecture 2. Fundamentals and Theories of Self-Assembly
10.524 Lecture 2. Fundamentals and Theories of Self-Assembly Instructor: Prof. Zhiyong Gu (Chemical Engineering & UML CHN/NCOE Nanomanufacturing Center) Lecture 2: Fundamentals and Theories of Self-Assembly
More informationNMR BMB 173 Lecture 16, February
NMR The Structural Biology Continuum Today s lecture: NMR Lots of slides adapted from Levitt, Spin Dynamics; Creighton, Proteins; And Andy Rawlinson There are three types of particles in the universe Quarks
More informationProtein folding. Today s Outline
Protein folding Today s Outline Review of previous sessions Thermodynamics of folding and unfolding Determinants of folding Techniques for measuring folding The folding process The folding problem: Prediction
More informationF. Piazza Center for Molecular Biophysics and University of Orléans, France. Selected topic in Physical Biology. Lecture 1
Zhou Pei-Yuan Centre for Applied Mathematics, Tsinghua University November 2013 F. Piazza Center for Molecular Biophysics and University of Orléans, France Selected topic in Physical Biology Lecture 1
More informationThe Chemistry department approved by the American Chemical Society offers a Chemistry degree in the following concentrations:
Chemistry 1 Chemistry 203-C Materials Science Building Telephone: 256.824.6153 Email: chem.admin@uah.edu (chem@uah.edu) The Chemistry department approved by the American Chemical Society offers a Chemistry
More informationReflection = EM strikes a boundary between two media differing in η and bounces back
Reflection = EM strikes a boundary between two media differing in η and bounces back Incident ray θ 1 θ 2 Reflected ray Medium 1 (air) η = 1.00 Medium 2 (glass) η = 1.50 Specular reflection = situation
More informationZAHID IQBAL WARRAICH
Q1 Chromatography is an important analytical technique in chemistry. There is a number of techniques under the general heading of chromatography. (a) Paper and gas chromatography rely on partition to separate
More information2015 AP Biology Unit 2 PRETEST- Introduction to the Cell and Biochemistry
Name: Class: _ Date: _ 2015 AP Biology Unit 2 PRETEST- Introduction to the Cell and Biochemistry Multiple Choice Identify the choice that best completes the statement or answers the question. 1) In what
More informationComprehensive Handbook of Calorimetry and Thermal Analysis
Comprehensive Handbook of Calorimetry and Thermal Analysis Michio Sorai Editor-in-Chief The Japan Society of Calorimetry and Thermal Analysis John Wiley & Sons, Ltd Contents Preface xi Acknowledgements
More informationChemistry in Biology. Section 1. Atoms, Elements, and Compounds
Section 1 Atoms, Elements, and Compounds Atoms! Chemistry is the study of matter.! Atoms are the building blocks of matter.! Neutrons and protons are located at the center of the atom.! Protons are positively
More informationBiochemistry Quiz Review 1I. 1. Of the 20 standard amino acids, only is not optically active. The reason is that its side chain.
Biochemistry Quiz Review 1I A general note: Short answer questions are just that, short. Writing a paragraph filled with every term you can remember from class won t improve your answer just answer clearly,
More informationDental Biochemistry EXAM I
Dental Biochemistry EXAM I August 29, 2005 In the reaction below: CH 3 -CH 2 OH -~ ethanol CH 3 -CHO acetaldehyde A. acetoacetate is being produced B. ethanol is being oxidized to acetaldehyde C. acetaldehyde
More informationBiomolecules: lecture 10
Biomolecules: lecture 10 - understanding in detail how protein 3D structures form - realize that protein molecules are not static wire models but instead dynamic, where in principle every atom moves (yet
More informationBMB/Bi/Ch 173 Winter 2018
BMB/Bi/Ch 173 Winter 2018 Homework Set 8.1 (100 Points) Assigned 2-27-18, due 3-6-18 by 10:30 a.m. TA: Rachael Kuintzle. Office hours: SFL 220, Friday 3/2 4:00-5:00pm and SFL 229, Monday 3/5 4:00-5:30pm.
More informationCh 313 FINAL EXAM OUTLINE Spring 2010
Ch 313 FINAL EXAM OUTLINE Spring 2010 NOTE: Use this outline at your own risk sometimes a topic is omitted that you are still responsible for. It is meant to be a study aid and is not meant to be a replacement
More informationCHM1001, 1002, 1051, <PHY1101, 1102, 1001, 1002> or <BIO1101, 1102, 1105, 1106> Total 16 cr.
Major: (1) credits: - Multiple majors: minimum of 4 credits - Single major: minimum of 48 credits - Teacher training program: minimum of 51 credits () Required courses: 0 credits Required: CHM101, 151,
More informationProtein Dynamics, Allostery and Function
Protein Dynamics, Allostery and Function Lecture 3. Protein Dynamics Xiaolin Cheng UT/ORNL Center for Molecular Biophysics SJTU Summer School 2017 1 Obtaining Dynamic Information Experimental Approaches
More informationLight scattering Small and large particles
Scattering by macromolecules E B Incident light Scattered Light particle Oscillating E field from light makes electronic cloud oscillate surrounding the particle Intensity: I E Accelerating charges means
More information2: CHEMICAL COMPOSITION OF THE BODY
1 2: CHEMICAL COMPOSITION OF THE BODY Although most students of human physiology have had at least some chemistry, this chapter serves very well as a review and as a glossary of chemical terms. In particular,
More informationCHEMISTRY PHYSICAL. of FOODS INTRODUCTION TO THE. CRC Press. Translated by Jonathan Rhoades. Taylor & Francis Croup
Christos Ritzoulis Translated by Jonathan Rhoades INTRODUCTION TO THE PHYSICAL CHEMISTRY of FOODS CRC Press Taylor & Francis Croup Boca Raton London NewYork CRC Press is an imprint of the Taylor & Francis
More information