Discussion topic for week 5 : Enzyme reactions
|
|
- Kelley Butler
- 6 years ago
- Views:
Transcription
1 Discussion topic for wee 5 : Enzyme reactions The loc in ey hypothesis (Emil Fischer) asserts that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another. What are the problems associated with this hypothesis?
2 Enzymes and Molecular Machines (Nelson, chap. 10) Enzymes are biological catalysts that enhance the rate of chem. reactions. Machines use free energy from an external source (e.g. ATP, concentration or potential difference) to do useful wor. Examples: Motors: transduce free energy into linear or rotary motion myosin on actin in muscles, inesin on microtubules in cells. Pumps: create concentration differences across membranes sodium-potassium pump transports 3 Na + ions out of the cell and 2 K + ions into the cell in one cycle. Synthases: drive chemical reactions to synthesize biomolecules ATP synthase synthesizes the ATP molecules that are used by most of the molecular machines in the cells.
3 Enzymes An extreme example: catalese Consider the decomposition of hydrogen peroxide: H 2 O 2 H 2 O + ½ O 2 DG 0 = -41 so the reaction is highly favoured but due to a high activation barrier it proceeds very slowly: for 1 M solution the rate is 10-8 M/s (reaction velocity) Adding 1 mm catalese into the solution increases the rate by 10 12! 10-3 N A catalese molecules perform 10 4 N A hydrolisis reactions per sec. So 1 catalese molecule catalyses 10 7 reactions per sec. (rate: 10-7 s) H 2 O 2 is produced in cells while eliminating free radicals. Because it is toxic, its rapid breadown is important. More typical rates for enzymes are around 10 3 s -1
4 Simple model of enzyme reactions: Chemical reactions involving biomolecules are extremely complex. Free energy surface typically involves thousands of coordinates. Nevertheless a reaction usually proceeds along the path of least resistance (called reaction coordinate) which allows a simple description. transition state A simple reaction: H + H 2 H 2 + H
5 An enzyme facilitates a chemical reaction by binding to the transition state and thereby reducing the activation energy, DG (but not DG) rate e -DG e -( DE -ST) e S e -DE e -DE Free energy surface along the reaction coordinate DG DG DG DG Substrate Enzyme + substrate
6 Direction of the reaction is controlled by DG. By changing DG, we can reverse the direction. The reverse reaction does not necessarily follow the same reaction coordinate. L - malate fumarase fumarate reverse reaction
7 A schematic picture of an enzyme E binding to a substrate S: E + S ES EP E + P E+S: The enzyme has a binding site that is a good match for the subst. S ES: In order to bind, S must deform which stretches a bond to breaing pt. EP: Thermal fluctuations brea the bond producing an EP complex E+P: The P state is not a good match to the binding site, hence it unbinds, leaving the enzyme free for binding of the next substrate.
8 Corresponding free energy surface
9 Enzyme Kinetics: Consider an enzyme reaction with rate constants 1, 2 and 3 Assume: E S c S 1 ES EP { ce, cp}, 2-2, 3-3, 3 { 1, 2} For a single enzyme, the reaction simplifies to 2 E P Let probability of E unoccupied be P E and occupied P ES = (1- P E ) The rate of change of P E is E S 1c S -1 ES 2 E P dp dt E -1c S P E -1 2 P ES
10 Assuming quasi-steady state, the time derivative vanishes, yielding Rate of production of P per enzyme: Reaction velocity for a concentration c E of enzymes max max , K c v c K c v v c c c P c v M E S M S S S E ES E - - S S ES ES Es S c c P P P c ) ( P ES Michaelis-Menten (MM) rule
11 Experimental data for pancreatic carboxypeptidase v max =0.085 mm/s K M =6.4 mm cs 1 1 v vmax 1 KM cs v vmax K c M S
12 MM rule displays saturation inetics, which has very general validity The ey idea is the processing time for S P At low substrate concentrations, there are more enzymes than S so that there is no waiting and hence v is proportional to c S As c S is increased beyond K M, there is competition among S for access to an enzyme, and they have to queue for processing. Maximum velocity of the reaction is determined by the number of enzymes available and the processing rate (the rate limiting step) Modulation of enzyme activity: 2 e -DG Regulate the rate of enzyme production Competitive inhibition: direct binding of another molecule Noncompetitive inhibition: binding of a molecule to a second site
13 Recent developments (Adenylate inase) We now very little about the actual dynamical processes occurring in enzymes. There are only a few simple cases where the physical mechanism is understood, e.g. oxygen binding in myoglobin. Adenylate inase catalyzes: ADP + ADP ATP + AMP Recent wor indicates that the rate limiting step is the enzyme conformation, and not the chemistry.
14 Molecular motors in muscles: myosin and actin For structure of the myosin and actin filaments in a myofibril, see Experiment with optical tweezers demonstrates how myosin pulls an actin filament when 1 mm of ATP is added to the system. From Finer et al. Single myosin molecule mechanics Nature, 1994.
15 Translocation of proteins across membrane: Proteins produced in the cell are exported outside through proteins in the membrane that form pores. To pass through the pore, the protein has to unfold. The reverse motion is suppressed because the chemical asymmetries between inside and outside of the cell leads to a more stable protein structure outside. Factors contributing to asymmetry: ph ion concentration disulfide bonding binding of sugars protein catalyzes translocation
16 Macroscopic machines are deterministic, there are no random fluctuations But molecular machines operate in a noisy environment with lots of random fluctuations. Consider the ratchets below as possible models for molecular machines. In G-ratchet the spring retracts during the passage but pops bac after In S-ratchet a latch releases the spring after the passage, which stays up Can either ratchet pull a load f towards right doing useful wor?
17 Unloaded G-ratchet maes no net motion, the loaded one moves to the left S-ratchet moves to the right if e f.l, and to the left if e < f.l (no net motion if e f.l)
18 Simple model for a perfect Brownian ratchet: (e ) In the absence of any forces, the ratchet diffuses freely until it travels a distance L. From 2 x 2Dt tstep L 2D 2 Thus the average speed is: v L tstep 2D L Next we introduce a load f that pulls the ratchet to the left. The potential energy increases as U fx in the interval [0, L] From Boltzmann distribution, the equilibrium probability will be lie - fx P( x) e 0
19 We need an equation to describe the nonequilibrium probability distribution of the ratchet s position (cf. Fic s law and Nerst-Planc Eq.) x Dx L a-dx/2 a a+dx/2 a+dx The net flux from a a+dx depends on (1) the probabilities at those points and (2) the external forces. If there are N ratchets in our ensemble, the bins at a and a+dx have NP( a) D x and NP( a Dx) Dx ratchets. Assuming they move randomly, the net migration from left to right is DN (1) LR 1 2 N P( a) - P( a Dx) Dx NDx 2 dp( x) dx xa dp( x) -NDDt dx xa
20 Next consider the flux due to an external force, Drift velocity due to this force: v d f Df - D du dx ( D ) The number of ratchets moving from left to right: (2) LR D N NP( a) v d Dt - NDP du dx Adding the two contributions and dividing by Dt, we obtain for the flux j dp -ND dx P du dx Steady state: flux is constant, and from continuity eq. it is also uniform Dt du f - dx xa dj dx d dp P du 0 0 dx dx dx (Smoluchowsi eq.)
21 Since the potential is periodic, periodic too. U( x L) U( x) the solutions must be First consider the equilibrium case: dp P du j 0 0 P( x) dx dx A possible nonequilibrium solution for the perfect ratchet is 1. vanishes at x = L 2. yields a constant flux P( x) C e -( x-l) f -1 Ce -U (Boltzmann dist.) ( U fx) - NDC - f e -( x-l) f f e -( x-l) f -1 NDCf 3. hence solves the Smoluchowsi eq.
22 Average speed of the perfect ratchet: The average number of ratchets in the interval [0, L] N L 0 NP( x) dx NC L 0 e -( x-l) f -1 dx NC- f e ( L-x) f - x L 0 NC f e fl -1- fl The time it taes for these ratchets move is and the speed is L v Dt Lj N L NCDf f NC Dt e fl N j -1- fl -1 D L fl 2 e fl -1- fl -1
23 Too complicated to mae sense, so consider the limits: z e fl << 1 fl v D L v z 2 D L 1 fl z 2 z 2 e 2 - fl -1- z -1 2D L activation barrier Plot of the ratchet speed / (2D/L) as a function of z = fl/ Activation barrier ics in around fl = 5
24 Estimate the speed for a typical molecular machine For small molecules, ions etc.: R 1-3 Å, D 10-9 m 2 /s For macromolecules, proteins: R 1-3 nm, D m 2 /s Typical length scale: L = 1 nm Average speed: v = 2D/L = 0.2 m/s, (e.g. to move 200 steps taes 1 ms) The perfect ratchet assumption is that bacward rate vanishes When e net motion is possible. In summary: fl D 6R ( e fl) the forward and bacward rates become equal and no 1. Molecular machines move by random wal over free energy surface 2. Their speed is determined by the activation energy barrier (but not e)
25 Molecular Recognition Cells contain thousands of different proteins. Each protein performs a specific tas that may require its interaction with a specific biomolecule, e.g. DNA, another protein or a ligand. How does a protein distinguish that biomolecule from the thousands of others that are floating around the cell? The loc and ey hypothesis of Fischer (1894), namely, shape complementarity of the interacting parts, provided the first clues. Going beyond the descriptive accounts of protein interactions using cartoons to a quantitative accounts that can mae predictions has only become possible in the last decade thans to the advances in Structure determination of complexes and single molecule exp s Computer power and simulation methods
26 Molecular recognition covers a vast area of research Enzyme function Protein-ligand interactions: binding of a ligand changes the conformation of a protein enabling its function, e.g. ligand-gated ion channels, oxygen binding to hemoglobin. Protein-protein interactions: e.g. formation of protein complexes (tertiary structure), signal transduction across membrane, protein transport and modification Protein-DNA (or RNA) interactions: reading and duplication of DNA, protein manufacturing Protein interactions with non-native peptides: e.g. toxins from the venomous animals (spiders, snaes, scorpions, snails) Protein interactions with chemical compounds: e.g. drugs
27 Experimental methods: Structure determination of complexes using x-ray diffraction or NMR Measurement of dissociation (or binding) constants. (mm range: wea binding, μm range: intermediate, nm range: strong) High-throughput screening (automated testing of large number of compounds to discover new drugs) Theoretical methods: Docing methods (popular in in silico drug design) Monte Carlo methods: search for the free energy minimum using the Metropolis algorithm Brownian dynamics simulations: water is treated as continuum and protein is rigid, but simulations are fast enough to observe docing Molecular dynamics simulations: realistic representation but too slow to observe docing
28 Crystal structure of the barnase (blue) - barstar (green) complex The unbound conformations are superimposed in light blue and orange.
29 Close up view showing the side chain pairs in the hot spot. In the complex: barnase (blue) - barstar (green) Comparison of the two structures shows the importance of side chain flexibility
30 Docing methods There are various docing methods that search for the free energy minimum of a protein-macromolecule system. The basic ingredients are: A phenomenological energy functional. Typically consists of: electrostatic, Lennard-Jones, hydrogen bond, solvation and entropic terms. It is parametrized using a training set. A search algorithm. Two common methods employed: 1. Random search using the Monte Carlo method 2. Systematic search using a grid over the active site In the current docing methods, ligand flexibility (mainly torsion angles) is also taen into account (target protein is still rigid). Here genetic algorithms provide a very efficient tool (different conformations correspond to mutations). AutoDoc is the most popular method at present.
31 Computer simulation of protein interactions Protein association can be broadly divided into two stages: 1. Diffusional motion until they form an encounter complex 2. Non-diffusional rearrangement process leading to the final bound complex. The first stage could tae quite a long time (ms), so it is neither possible nor desirable to use molecular dynamics. Brownian dynamics (BD) is the natural tool for this stage. The second stage involves conformational changes in the protein, and also dehydration and rehydration of water molecules. Thus a microscopic description that treats all the atoms in the system is necessary at this stage, which is provided by molecular dynamics (MD). The focus is, however, on the binding. Can we avoid the BD stage?
32 Molecular dynamics combined with docing Test study in gramicidin channel: 1. Find the initial gramicidin channelorganic cation configuration from AutoDoc 2. Then employ this in MD simulations
33 Organic cations that bind to the gramicidin channel
34 Methylammonium Formamidinum TMA Ethylammonium Guanidinum TEA
35 Calculation of free energy profiles for ions Potential of Mean Force (PMF) of a molecule is calculated using the channel axis (z) as the reaction coordinate The PMF is obtained from the Boltzmann factor by measuring the z coordinates of the molecule W ( z) W ( z0) - ln ρ(z) ρ(z 0 ) Umbrella sampling A harmonic potential is used to constrain the molecule at various points on the channel axis (typical interval, fraction of an Å), and its z coordinate is sampled during MD simulations The z distributions are unbiased and combined to obtain the PMF profile along the z axis.
36 Free energy profiles (potential of mean force, PMF) of cations determined from umbrella sampling calculations
37 Binding constants Binding constant is obtained by integrating the free energy of the ligand in a volume around the binding site K V e -[ W ( r) -W 0 ]/ d 3 r R z e -W ( z) / where we have approximated the volume with a cylinder of radius R. Using the PMF s, we can estimate the binding constants: Methylammonium: K = 4.1 M -1 (exp: 4.4 M -1 ) Ethylammonium : K = 0.2 M -1 (exp: ~ 0) dz Formamidinium: K = 0.6 M -1 (exp: 23 M -1 ) (there is a deeper site)
38 Drugs from toxins Development of new drugs is at an all time low. Major problem: finding new compounds with high specificity and affinity. High hopes from in silico drug design methods. Example: Conotoxins as drug leads Conotoxins are small peptides found in the venom of cone snails that selectively bind to specific ion channels with high affinity. It is estimated that there are over 50,000 different conotoxins. Already a few new drugs have been developed from conotoxins. The potential for development of further drugs is enormous. -conotoxin bound to K + channel
39 Exp. structure of the KcsA*- charybdotoxin complex (NMR) Important pairs: Y78 (ABCD) K27 D80 (D) R34 D64, D80 (C) - R25 D64 (B) - K11 K11 R34 K27 is the pore inserting lysine a common thread in scorpion and other toxins.
40 NMR structure of ShK toxin Developing drugs from ShK toxin for autoimmune diseases ShK toxin binds to Kv1.3 channels with picomolar affinity, hence a good candidate for treatment of autoimmune diseases. ShK toxin has three disulfide bonds and three other bonds: D5 K30 K18 R24 T6 F27 These bonds confer ShK toxin an extraordinary stability not seen in other toxins
41 Kv1.3-ShK complex (Docing + MD) Monomers A and C Monomers B and D
42 Pair distances in the Kv1.3-ShK complex (in A) Kv1.3 ShK HADDOCK MD aver. Exp. D376 O1(C) R1 N S378 O(B) H19 N ** Y400 O(ABD) K22 N ** G401 O(B) S20 OH ** G401 O(A) Y23 OH ** D402 O(A) R11 N * H404-C(C) F27-C" * V406 C1(B) M21 C" * D376 O1(C) R29 N * ** strong, * intermediate ints. (from alanine scanning Raucher, 1998) R24 (**) and T13 and L25 (*) are not seen in the complex (allosteric)
43 Convergence of the PMF for the Kv1.3-ShK complex
44 PMF of ShK for Kv1.1, Kv1.2, and Kv1.3
45 Comparison of binding free energies of ShK to Kv1.x Binding free energies are obtained from the PMF by integrating it along the z-axis. Complex DG well DG b (PMF) DG b (exp) Kv1.1 ShK ± ± 0.1 Kv1.2 ShK ± ± 0.1 Kv1.3 ShK ± ± 0.1 Excellent agreement with experiment for all three channels, which provides an independent test for the accuracy of the complex models.
46 Average pair distance as a function of window position ** denotes strong coupling and * intermediate coupling * * ** * ** ** **
Lecture 27. Transition States and Enzyme Catalysis
Lecture 27 Transition States and Enzyme Catalysis Reading for Today: Chapter 15 sections B and C Chapter 16 next two lectures 4/8/16 1 Pop Question 9 Binding data for your thesis protein (YTP), binding
More informationFor slowly varying probabilities, the continuum form of these equations is. = (r + d)p T (x) (u + l)p D (x) ar x p T(x, t) + a2 r
3.2 Molecular Motors A variety of cellular processes requiring mechanical work, such as movement, transport and packaging material, are performed with the aid of protein motors. These molecules consume
More informationSECOND PUBLIC EXAMINATION. Honour School of Physics Part C: 4 Year Course. Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS
2757 SECOND PUBLIC EXAMINATION Honour School of Physics Part C: 4 Year Course Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS TRINITY TERM 2011 Monday, 27 June, 9.30 am 12.30 pm Answer
More informationAnatoly B. Kolomeisky. Department of Chemistry CAN WE UNDERSTAND THE COMPLEX DYNAMICS OF MOTOR PROTEINS USING SIMPLE STOCHASTIC MODELS?
Anatoly B. Kolomeisky Department of Chemistry CAN WE UNDERSTAND THE COMPLEX DYNAMICS OF MOTOR PROTEINS USING SIMPLE STOCHASTIC MODELS? Motor Proteins Enzymes that convert the chemical energy into mechanical
More information2013 W. H. Freeman and Company. 6 Enzymes
2013 W. H. Freeman and Company 6 Enzymes CHAPTER 6 Enzymes Key topics about enzyme function: Physiological significance of enzymes Origin of catalytic power of enzymes Chemical mechanisms of catalysis
More informationMolecular Machines and Enzymes
Molecular Machines and Enzymes Principles of functioning of molecular machines Enzymes and catalysis Molecular motors: kinesin 1 NB Queste diapositive sono state preparate per il corso di Biofisica tenuto
More informationChemical Kinetics. Topic 7
Chemical Kinetics Topic 7 Corrosion of Titanic wrec Casón shipwrec 2Fe(s) + 3/2O 2 (g) + H 2 O --> Fe 2 O 3.H 2 O(s) 2Na(s) + 2H 2 O --> 2NaOH(aq) + H 2 (g) Two examples of the time needed for a chemical
More informationChapter 6: Outline-2. Chapter 6: Outline Properties of Enzymes. Introduction. Activation Energy, E act. Activation Energy-2
Chapter 6: Outline- Properties of Enzymes Classification of Enzymes Enzyme inetics Michaelis-Menten inetics Lineweaver-Burke Plots Enzyme Inhibition Catalysis Catalytic Mechanisms Cofactors Chapter 6:
More informationLecture 7 : Molecular Motors. Dr Eileen Nugent
Lecture 7 : Molecular Motors Dr Eileen Nugent Molecular Motors Energy Sources: Protonmotive Force, ATP Single Molecule Biophysical Techniques : Optical Tweezers, Atomic Force Microscopy, Single Molecule
More informationSample Questions for the Chemistry of Life Topic Test
Sample Questions for the Chemistry of Life Topic Test 1. Enzymes play a crucial role in biology by serving as biological catalysts, increasing the rates of biochemical reactions by decreasing their activation
More informationAnatoly B. Kolomeisky Department of Chemistry Center for Theoretical Biological Physics How to Understand Molecular Transport through Channels: The
Anatoly B. Kolomeisy Department of Chemistry Center for Theoretical Biological Physics How to Understand Molecular Transport through Channels: The Role of Interactions Transport Through Channels Oil pumping
More informationComputational Biology 1
Computational Biology 1 Protein Function & nzyme inetics Guna Rajagopal, Bioinformatics Institute, guna@bii.a-star.edu.sg References : Molecular Biology of the Cell, 4 th d. Alberts et. al. Pg. 129 190
More informationSample Question Solutions for the Chemistry of Life Topic Test
Sample Question Solutions for the Chemistry of Life Topic Test 1. Enzymes play a crucial role in biology by serving as biological catalysts, increasing the rates of biochemical reactions by decreasing
More informationPrevious Class. Today. Cosubstrates (cofactors)
Previous Class Cosubstrates (cofactors) Today Proximity effect Basic equations of Kinetics Steady state kinetics Michaelis Menten equations and parameters Enzyme Kinetics Enzyme kinetics implies characterizing
More informationActo-myosin: from muscles to single molecules. Justin Molloy MRC National Institute for Medical Research LONDON
Acto-myosin: from muscles to single molecules. Justin Molloy MRC National Institute for Medical Research LONDON Energy in Biological systems: 1 Photon = 400 pn.nm 1 ATP = 100 pn.nm 1 Ion moving across
More informationLecture 11: Enzymes: Kinetics [PDF] Reading: Berg, Tymoczko & Stryer, Chapter 8, pp
Lecture 11: Enzymes: Kinetics [PDF] Reading: Berg, Tymoczko & Stryer, Chapter 8, pp. 216-225 Updated on: 2/4/07 at 9:00 pm Key Concepts Kinetics is the study of reaction rates. Study of enzyme kinetics
More informationf) Adding an enzyme does not change the Gibbs free energy. It only increases the rate of the reaction by lowering the activation energy.
Problem Set 2-Answer Key BILD1 SP16 1) How does an enzyme catalyze a chemical reaction? Define the terms and substrate and active site. An enzyme lowers the energy of activation so the reaction proceeds
More informationProgram for the rest of the course
Program for the rest of the course 16.4 Enzyme kinetics 17.4 Metabolic Control Analysis 19.4. Exercise session 5 23.4. Metabolic Control Analysis, cont. 24.4 Recap 27.4 Exercise session 6 etabolic Modelling
More informationChapter 6- An Introduction to Metabolism*
Chapter 6- An Introduction to Metabolism* *Lecture notes are to be used as a study guide only and do not represent the comprehensive information you will need to know for the exams. The Energy of Life
More informationReceptor Based Drug Design (1)
Induced Fit Model For more than 100 years, the behaviour of enzymes had been explained by the "lock-and-key" mechanism developed by pioneering German chemist Emil Fischer. Fischer thought that the chemicals
More informationMembrane Proteins: 1. Integral proteins: 2. Peripheral proteins: 3. Amphitropic proteins:
Membrane Proteins: 1. Integral proteins: proteins that insert into/span the membrane bilayer; or covalently linked to membrane lipids. (Interact with the hydrophobic part of the membrane) 2. Peripheral
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 informationChemical kinetics and catalysis
Chemical kinetics and catalysis Outline Classification of chemical reactions Definition of chemical kinetics Rate of chemical reaction The law of chemical raction rate Collision theory of reactions, transition
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 informationChem 204. Mid-Term Exam I. July 21, There are 3 sections to this exam: Answer ALL questions
Chem 204 Mid-Term Exam I July 21, 2009 Name: Answer Key Student ID: There are 3 sections to this exam: Answer ALL questions Section I: Multiple-Choice 20 questions, 2 pts each Section II: Fill-in-the-Blank
More informationReaction Kinetics. An Introduction
Reaction Kinetics An Introduction A condition of equilibrium is reached in a system when opposing changes occur simultaneously at the same rate. The rate of a chemical reaction may be defined as the #
More informationFree Energy. because H is negative doesn't mean that G will be negative and just because S is positive doesn't mean that G will be negative.
Biochemistry 462a Bioenergetics Reading - Lehninger Principles, Chapter 14, pp. 485-512 Practice problems - Chapter 14: 2-8, 10, 12, 13; Physical Chemistry extra problems, free energy problems Free Energy
More informationIt is generally believed that the catalytic reactions occur in at least two steps.
Lecture 16 MECHANISM OF ENZYME ACTION A chemical reaction such as A ----> P takes place because a certain fraction of the substrate possesses enough energy to attain an activated condition called the transition
More informationCHEMISTRY. 2 Types of Properties Associated with Matter. Composition of Matter. Physical: properties that do not change the identity of the substance
CHEMISTRY Composition of Matter Matter Mass Anything that occupies space and has mass Quantity of matter an object has Weight Pull of gravity on an object 2 Types of Properties Associated with Matter Physical:
More informationAn Introduction to Metabolism
An Introduction to Metabolism I. All of an organism=s chemical reactions taken together is called metabolism. A. Metabolic pathways begin with a specific molecule, which is then altered in a series of
More informationEnzyme Kinetics: The study of reaction rates. For each very short segment dt of the reaction: V k 1 [S]
Enzyme Kinetics: The study of reaction rates. For the one-way st -order reaction: S the rate of reaction (V) is: V P [ P] moles / L t sec For each very short segment dt of the reaction: d[ P] d[ S] V dt
More informationMetabolism and enzymes
Metabolism and enzymes 4-11-16 What is a chemical reaction? A chemical reaction is a process that forms or breaks the chemical bonds that hold atoms together Chemical reactions convert one set of chemical
More informationEnzyme reaction example of Catalysis, simplest form: E + P at end of reaction No consumption of E (ES): enzyme-substrate complex Intermediate
V 41 Enzyme Kinetics Enzyme reaction example of Catalysis, simplest form: k 1 E + S k -1 ES E at beginning and ES k 2 k -2 E + P at end of reaction No consumption of E (ES): enzyme-substrate complex Intermediate
More informationMolecular Interactions F14NMI. Lecture 4: worked answers to practice questions
Molecular Interactions F14NMI Lecture 4: worked answers to practice questions http://comp.chem.nottingham.ac.uk/teaching/f14nmi jonathan.hirst@nottingham.ac.uk (1) (a) Describe the Monte Carlo algorithm
More informationThe Potassium Ion Channel: Rahmat Muhammad
The Potassium Ion Channel: 1952-1998 1998 Rahmat Muhammad Ions: Cell volume regulation Electrical impulse formation (e.g. sodium, potassium) Lipid membrane: the dielectric barrier Pro: compartmentalization
More informationRegulation of metabolism
Regulation of metabolism So far in this course we have assumed that the metabolic system is in steady state For the rest of the course, we will abandon this assumption, and look at techniques for analyzing
More informationEnergy, Enzymes, and Metabolism. Energy, Enzymes, and Metabolism. A. Energy and Energy Conversions. A. Energy and Energy Conversions
Energy, Enzymes, and Metabolism Lecture Series 6 Energy, Enzymes, and Metabolism B. ATP: Transferring Energy in Cells D. Molecular Structure Determines Enzyme Fxn Energy is the capacity to do work (cause
More informationEnzyme Kinetics. Michaelis-Menten Theory Dehaloperoxidase: Multi-functional Enzyme. NC State University
Enzyme Kinetics Michaelis-Menten Theory Dehaloperoxidase: Multi-functional Enzyme NC State University Michaelis-Menton kinetics The rate of an enzyme catalyzed reaction in which substrate S is converted
More informationMetabolism and Enzymes
Energy Basics Metabolism and Enzymes Chapter 5 Pgs. 77 86 Chapter 8 Pgs. 142 162 Energy is the capacity to cause change, and is required to do work. Very difficult to define quantity. Two types of energy:
More informationSoftwares for Molecular Docking. Lokesh P. Tripathi NCBS 17 December 2007
Softwares for Molecular Docking Lokesh P. Tripathi NCBS 17 December 2007 Molecular Docking Attempt to predict structures of an intermolecular complex between two or more molecules Receptor-ligand (or drug)
More informationLecture # 3, 4 Selecting a Catalyst (Non-Kinetic Parameters), Review of Enzyme Kinetics, Selectivity, ph and Temperature Effects
1.492 - Integrated Chemical Engineering (ICE Topics: Biocatalysis MIT Chemical Engineering Department Instructor: Professor Kristala Prather Fall 24 Lecture # 3, 4 Selecting a Catalyst (Non-Kinetic Parameters,
More informationFrom Friday s material
5.111 Lecture 35 35.1 Kinetics Topic: Catalysis Chapter 13 (Section 13.14-13.15) From Friday s material Le Chatelier's Principle - when a stress is applied to a system in equilibrium, the equilibrium tends
More informationEnergy Transformation and Metabolism (Outline)
Energy Transformation and Metabolism (Outline) - Definitions & Laws of Thermodynamics - Overview of energy flow ecosystem - Biochemical processes: Anabolic/endergonic & Catabolic/exergonic - Chemical reactions
More informationBiochemistry. Lecture 8 Enzyme Kinetics
Biochemistry Lecture 8 Enzyme Kinetics Why Enzymes? igher reaction rates Greater reaction specificity Milder reaction conditions Capacity for regulation C - - C N 2 - C N 2 - C - C Chorismate mutase -
More informationIntroduction to Physiology II: Control of Cell Volume and Membrane Potential
Introduction to Physiology II: Control of Cell Volume and Membrane Potential J. P. Keener Mathematics Department Math Physiology p.1/23 Basic Problem The cell is full of stuff: Proteins, ions, fats, etc.
More informationENZYME KINETICS. Medical Biochemistry, Lecture 24
ENZYME KINETICS Medical Biochemistry, Lecture 24 Lecture 24, Outline Michaelis-Menten kinetics Interpretations and uses of the Michaelis- Menten equation Enzyme inhibitors: types and kinetics Enzyme Kinetics
More informationEnzyme Reactions. Lecture 13: Kinetics II Michaelis-Menten Kinetics. Margaret A. Daugherty Fall v = k 1 [A] E + S ES ES* EP E + P
Lecture 13: Kinetics II Michaelis-Menten Kinetics Margaret A. Daugherty Fall 2003 Enzyme Reactions E + S ES ES* EP E + P E = enzyme ES = enzyme-substrate complex ES* = enzyme/transition state complex EP
More informationMichaelis-Menten Kinetics. Lecture 13: Kinetics II. Enzyme Reactions. Margaret A. Daugherty. Fall Substrates bind to the enzyme s active site
Lecture 13: Kinetics II Michaelis-Menten Kinetics Margaret A. Daugherty Fall 2003 Enzyme Reactions E + S ES ES* EP E + P E = enzyme ES = enzyme-substrate complex ES* = enzyme/transition state complex EP
More informationMetabolism: Energy and Enzymes. February 24 th, 2012
Metabolism: Energy and Enzymes February 24 th, 2012 1 Outline Forms of Energy Laws of Thermodynamics Metabolic Reactions ATP Metabolic Pathways Energy of Activation Enzymes Photosynthesis Cellular Respiration
More informationOverview of Kinetics
Overview of Kinetics [P] t = ν = k[s] Velocity of reaction Conc. of reactant(s) Rate of reaction M/sec Rate constant sec -1, M -1 sec -1 1 st order reaction-rate depends on concentration of one reactant
More informationChemical Kinetics. Kinetics is the study of how fast chemical reactions occur. There are 4 important factors which affect rates of reactions:
Chemical Kinetics Kinetics is the study of how fast chemical reactions occur. There are 4 important factors which affect rates of reactions: reactant concentration temperature action of catalysts surface
More informationMicroteaching topics solutions Department of Biological Engineering TA Training
Microteaching topics solutions Department of Biological Engineering TA Training Here we include brief solution outlines, so you can focus your efforts on how best to teach the topic at hand, and not on
More informationObjectives INTRODUCTION TO METABOLISM. Metabolism. Catabolic Pathways. Anabolic Pathways 3/6/2011. How to Read a Chemical Equation
Objectives INTRODUCTION TO METABOLISM. Chapter 8 Metabolism, Energy, and Life Explain the role of catabolic and anabolic pathways in cell metabolism Distinguish between kinetic and potential energy Distinguish
More informationREVIEW 1: BIOCHEMISTRY UNIT. A. Top 10 If you learned anything from this unit, you should have learned:
Period Date REVIEW 1: BIOCHEMISTRY UNIT A. Top 10 If you learned anything from this unit, you should have learned: 1. All living matter made up of CHONPS 2. Bonds a. covalent bonds are strong b. hydrogen
More informationGround Rules of Metabolism CHAPTER 6
Ground Rules of Metabolism CHAPTER 6 Antioxidants You ve heard the term. What s the big deal? Found naturally in many fruits and vegetables Added to many products What do they actually do? Antioxidants
More informationIn silico pharmacology for drug discovery
In silico pharmacology for drug discovery In silico drug design In silico methods can contribute to drug targets identification through application of bionformatics tools. Currently, the application of
More informationPETER PAZMANY CATHOLIC UNIVERSITY Consortium members SEMMELWEIS UNIVERSITY, DIALOG CAMPUS PUBLISHER
PETER PAZMANY SEMMELWEIS CATHOLIC UNIVERSITY UNIVERSITY Development of Complex Curricula for Molecular Bionics and Infobionics Programs within a consortial* framework** Consortium leader PETER PAZMANY
More informationEnzyme Catalysis & Biotechnology
L28-1 Enzyme Catalysis & Biotechnology Bovine Pancreatic RNase A Biochemistry, Life, and all that L28-2 A brief word about biochemistry traditionally, chemical engineers used organic and inorganic chemistry
More informationEnergy Transformation, Cellular Energy & Enzymes (Outline)
Energy Transformation, Cellular Energy & Enzymes (Outline) Energy conversions and recycling of matter in the ecosystem. Forms of energy: potential and kinetic energy The two laws of thermodynamic and definitions
More informationCHEM 251 (4 credits): Description
CHEM 251 (4 credits): Intermediate Reactions of Nucleophiles and Electrophiles (Reactivity 2) Description: An understanding of chemical reactivity, initiated in Reactivity 1, is further developed based
More informationThe Molecular Dynamics Method
The Molecular Dynamics Method Thermal motion of a lipid bilayer Water permeation through channels Selective sugar transport Potential Energy (hyper)surface What is Force? Energy U(x) F = d dx U(x) Conformation
More informationBiochemistry 462a - Enzyme Kinetics Reading - Chapter 8 Practice problems - Chapter 8: (not yet assigned); Enzymes extra problems
Biochemistry 462a - Enzyme Kinetics Reading - Chapter 8 Practice problems - Chapter 8: (not yet assigned); Enzymes extra problems Introduction Enzymes are Biological Catalysis A catalyst is a substance
More informationPolymerization and force generation
Polymerization and force generation by Eric Cytrynbaum April 8, 2008 Equilibrium polymer in a box An equilibrium polymer is a polymer has no source of extraneous energy available to it. This does not mean
More informationPhys498BIO; Prof. Paul Selvin Hw #9 Assigned Wed. 4/18/12: Due 4/25/08
1. Ionic Movements Across a Permeable Membrane: The Nernst Potential. In class we showed that if a non-permeable membrane separates a solution with high [KCl] from a solution with low [KCl], the net charge
More informationSECOND PUBLIC EXAMINATION. Honour School of Physics Part C: 4 Year Course. Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS
2757 SECOND PUBLIC EXAMINATION Honour School of Physics Part C: 4 Year Course Honour School of Physics and Philosophy Part C C7: BIOLOGICAL PHYSICS TRINITY TERM 2013 Monday, 17 June, 2.30 pm 5.45 pm 15
More informationATP ATP. The energy needs of life. Living economy. Where do we get the energy from? 9/11/2015. Making energy! Organisms are endergonic systems
Making energy! ATP The energy needs of life rganisms are endergonic systems What do we need energy for? synthesis building biomolecules reproduction movement active transport temperature regulation 2007-2008
More informationLecture 15 (10/20/17) Lecture 15 (10/20/17)
Reading: Ch6; 98-203 Ch6; Box 6- Lecture 5 (0/20/7) Problems: Ch6 (text); 8, 9, 0,, 2, 3, 4, 5, 6 Ch6 (study guide-facts); 6, 7, 8, 9, 20, 2 8, 0, 2 Ch6 (study guide-applying); NEXT Reading: Ch6; 207-20
More informationTOPIC 6: Chemical kinetics
TOPIC 6: Chemical kinetics Reaction rates Reaction rate laws Integrated reaction rate laws Reaction mechanism Kinetic theories Arrhenius law Catalysis Enzimatic catalysis Fuente: Cedre http://loincognito.-iles.wordpress.com/202/04/titanic-
More informationA) at equilibrium B) endergonic C) endothermic D) exergonic E) exothermic.
CHEM 2770: Elements of Biochemistry Mid Term EXAMINATION VERSION A Date: October 29, 2014 Instructor: H. Perreault Location: 172 Schultz Time: 4 or 6 pm. Duration: 1 hour Instructions Please mark the Answer
More informationCellular Automata Approaches to Enzymatic Reaction Networks
Cellular Automata Approaches to Enzymatic Reaction Networks Jörg R. Weimar Institute of Scientific Computing, Technical University Braunschweig, D-38092 Braunschweig, Germany J.Weimar@tu-bs.de, http://www.jweimar.de
More informationBiochemistry Enzyme kinetics
1 Description of Module Subject Name Paper Name Module Name/Title Enzyme Kinetics Dr. Vijaya Khader Dr. MC Varadaraj 2 1. Objectives 2. Enzymes as biological catalyst 3. Enzyme Catalysis 4. Understanding
More informationMembranes 2: Transportation
Membranes 2: Transportation Steven E. Massey, Ph.D. Associate Professor Bioinformatics Department of Biology University of Puerto Rico Río Piedras Office & Lab: NCN#343B Tel: 787-764-0000 ext. 7798 E-mail:
More informationStatistical mechanics of biological processes
Statistical mechanics of biological processes 1 Modeling biological processes Describing biological processes requires models. If reaction occurs on timescales much faster than that of connected processes
More informationStructural Bioinformatics (C3210) Molecular Docking
Structural Bioinformatics (C3210) Molecular Docking Molecular Recognition, Molecular Docking Molecular recognition is the ability of biomolecules to recognize other biomolecules and selectively interact
More informationAdvanced Higher Biology. Unit 1- Cells and Proteins 2c) Membrane Proteins
Advanced Higher Biology Unit 1- Cells and Proteins 2c) Membrane Proteins Membrane Structure Phospholipid bilayer Transmembrane protein Integral protein Movement of Molecules Across Membranes Phospholipid
More informationDiscussion Exercise 5: Analyzing Graphical Data
Discussion Exercise 5: Analyzing Graphical Data Skill 1: Use axis labels to describe a phenomenon as a function of a variable Some value y may be described as a function of some variable x and used to
More informationNon equilibrium thermodynamics: foundations, scope, and extension to the meso scale. Miguel Rubi
Non equilibrium thermodynamics: foundations, scope, and extension to the meso scale Miguel Rubi References S.R. de Groot and P. Mazur, Non equilibrium Thermodynamics, Dover, New York, 1984 J.M. Vilar and
More informationChapter 5. Energy Flow in the Life of a Cell
Chapter 5 Energy Flow in the Life of a Cell Including some materials from lectures by Gregory Ahearn University of North Florida Ammended by John Crocker Copyright 2009 Pearson Education, Inc.. Review
More information4 Examples of enzymes
Catalysis 1 4 Examples of enzymes Adding water to a substrate: Serine proteases. Carbonic anhydrase. Restrictions Endonuclease. Transfer of a Phosphoryl group from ATP to a nucleotide. Nucleoside monophosphate
More informationChapter 8: An Introduction to Metabolism. 1. Energy & Chemical Reactions 2. ATP 3. Enzymes & Metabolic Pathways
Chapter 8: An Introduction to Metabolism 1. Energy & Chemical Reactions 2. ATP 3. Enzymes & Metabolic Pathways 1. Energy & Chemical Reactions 2 Basic Forms of Energy Kinetic Energy (KE) energy in motion
More informationControlled healing of graphene nanopore
Controlled healing of graphene nanopore Konstantin Zakharchenko Alexander Balatsky Zakharchenko K.V., Balatsky A.V. Controlled healing of graphene nanopore. Carbon (80), December 2014, pp. 12 18. http://dx.doi.org/10.1016/j.carbon.2014.07.085
More information9/25/2011. Outline. Overview: The Energy of Life. I. Forms of Energy II. Laws of Thermodynamics III. Energy and metabolism IV. ATP V.
Chapter 8 Introduction to Metabolism Outline I. Forms of Energy II. Laws of Thermodynamics III. Energy and metabolism IV. ATP V. Enzymes Overview: The Energy of Life Figure 8.1 The living cell is a miniature
More informationCHAPTER 1: ENZYME KINETICS AND APPLICATIONS
CHAPTER 1: ENZYME KINETICS AND APPLICATIONS EM 1 2012/13 ERT 317 BIOCHEMICAL ENGINEERING Course details Credit hours/units : 4 Contact hours : 3 hr (L), 3 hr (P) and 1 hr (T) per week Evaluations Final
More informationLecture #8 9/21/01 Dr. Hirsh
Lecture #8 9/21/01 Dr. Hirsh Types of Energy Kinetic = energy of motion - force x distance Potential = stored energy In bonds, concentration gradients, electrical potential gradients, torsional tension
More information!n[a] =!n[a] o. " kt. Half lives. Half Life of a First Order Reaction! Pressure of methyl isonitrile as a function of time!
Half lives Half life: t 1/2 t 1/2 is the time it takes for the concentration of a reactant to drop to half of its initial value. For the reaction A! products Half Life of a First Order Reaction! Pressure
More information2 4 Chemical Reactions and Enzymes Slide 1 of 34
2 4 Chemical Reactions and Enzymes 1 of 34 Chemical Reactions Chemical Reactions A chemical reaction is a process that changes one set of chemicals into another set of chemicals. Some chemical reactions
More informationthe spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together Chemical structure Covalent bond Ionic bond
Chemical structure the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together Covalent bond bond formed by the sharing of valence electrons between atoms Ionic bond
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 information2 4 Chemical Reactions and Enzymes Chemical Reactions
Chemical Reactions A chemical reaction occurs when chemical bonds are broken and reformed. Rust forms very slowly, while rocket fuel combustion is explosive! The significance of this comparison is that
More informationKinetics. Chapter 14. Chemical Kinetics
Lecture Presentation Chapter 14 Yonsei University In kinetics we study the rate at which a chemical process occurs. Besides information about the speed at which reactions occur, kinetics also sheds light
More informationC a h p a t p e t r e r 6 E z n y z m y e m s
Chapter 6 Enzymes 1. An Introduction to Enzymes Enzymes are catalytically active biological macromolecules Enzymes are catalysts of biological systems Almost every biochemical reaction is catalyzed by
More informationAn Introduction to Metabolism
CAMPBELL BIOLOGY IN FOCUS Urry Cain Wasserman Minorsky Jackson Reece 6 An Introduction to Metabolism Lecture Presentations by Kathleen Fitzpatrick and Nicole Tunbridge Overview: The Energy of Life The
More informationPhysical Biochemistry. Kwan Hee Lee, Ph.D. Handong Global University
Physical Biochemistry Kwan Hee Lee, Ph.D. Handong Global University Week 9 CHAPTER 4 Physical Equilibria Basic Concepts Biological organisms are highly inhomogeneous. Different regions of each cell have
More informationThermodynamics and Kinetics
Thermodynamics and Kinetics Lecture 12 Free Energy Applications NC State University Isolated system requires DS > 0 DS sys > 0 Isolated system: Entropy increases for any spontaneous process System and
More informationTransporters and Membrane Motors Nov 15, 2007
BtuB OM vitamin B12 transporter F O F 1 ATP synthase Human multiple drug resistance transporter P-glycoprotein Transporters and Membrane Motors Nov 15, 2007 Transport and membrane motors Concentrations
More informationBIOLOGICAL SCIENCE. Lecture Presentation by Cindy S. Malone, PhD, California State University Northridge. FIFTH EDITION Freeman Quillin Allison
BIOLOGICAL SCIENCE FIFTH EDITION Freeman Quillin Allison 8 Lecture Presentation by Cindy S. Malone, PhD, California State University Northridge Roadmap 8 In this chapter you will learn how Enzymes use
More informationBCH 3023 Fall 2008 Exam 2, Form C Name: ANSWER KEY
Name: ANSWER KEY In class, we discussed one method to linearize the Michaelis-Menton equation. There are other methods to do this, one being an Eadie-Hofstee plot. Given the Eadie-Hofstee plot below, answer
More informationCELL BIOLOGY - CLUTCH CH. 9 - TRANSPORT ACROSS MEMBRANES.
!! www.clutchprep.com K + K + K + K + CELL BIOLOGY - CLUTCH CONCEPT: PRINCIPLES OF TRANSMEMBRANE TRANSPORT Membranes and Gradients Cells must be able to communicate across their membrane barriers to materials
More informationMichaelis-Menton kinetics
Michaelis-Menton kinetics The rate of an enzyme catalyzed reaction in which substrate S is converted into products P depends on the concentration of the enzyme E even though the enzyme does not undergo
More informationGeneral Biology. The Energy of Life The living cell is a miniature factory where thousands of reactions occur; it converts energy in many ways
Course No: BNG2003 Credits: 3.00 General Biology 5. An Introduction into Cell Metabolism The Energy of Life The living cell is a miniature factory where thousands of reactions occur; it converts energy
More information