A. Reaction Mechanisms and Catalysis (1) proximity effect (2) acid-base catalysts (3) electrostatic (4) functional groups (5) structural flexibility

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "A. Reaction Mechanisms and Catalysis (1) proximity effect (2) acid-base catalysts (3) electrostatic (4) functional groups (5) structural flexibility"

Transcription

1 (P&S Ch 5; Fer Ch 2, 9; Palm Ch 10,11; Zub Ch 9) A. Reaction Mechanisms and Catalysis (1) proximity effect (2) acid-base catalysts (3) electrostatic (4) functional groups (5) structural flexibility B. Active Site Investigations (1) kinetic studies (2) detection of intermediates (3) x-ray crystallographic studies (4) chemical modification of amino acid side chains (5) site-directed mutagenesis studies C. Specific enzymes (1) lactate dehydrogenase and alcohol dehydrogenase (2) ribonuclease A (3) triose phosphate isomerase (4) amino acyl trna synthetases (5) carbonic anhydrase 77

2 (1) Proximity effect--enzymes bring reacting species close together -an enzyme can accelerate a rxn between two species simply by holding the two reactants close together in an appropriate orientation -intramolecular rxns between groups that are tied together in a single molecule are faster than the corresponding intermolecular rxns between two independent molecule, eg., cyclization of succinic acid to form succinyl anhydride c.f. formation of acetic anhydride from two molecules of acetic acid -difference in rates are 3-4 orders of magnitude (intramolecular> intermolecular) -effect is due mostly to the differences between the entropy changes that accompany the inter- and intramolecular rxns -formation of P involves a much larger loss of translational and rotational entropy in the intermolecular rxn 78

3 -a negative change in entropy increases both the overall free energy change in the rxn (ΔG = ΔH -TΔS) and the activation free energy (ΔG = ΔH - TΔS ) for the formation of the transition state -in the intramolecular rxn much of this entropy decrease has already occurred during the preparation of the reagent -enzymes that take catalyze intermolecular rxns take advantage of the proximity effect by binding the reactants close together in the active site, so that the reactive groups are oriented appropriately for the rxn -once the substrates are fixed this way the rxn behaves kinetically like an intramolecular process -the entropy decrease associated with the formation of the transition state has been moved to an earlier step, the binding of the substrates to form the E-S complex (2) Acid-Base Catalysis -task of a catalyst is to make a potentially reactive group more reactive by increasing its intrinsic electrophilic or nucleophilic 79

4 character -simplest way is to add or remove a proton eg., hydrolysis of an ester -hydrolysis of an ester in neutral aqueous solution can occur if the O atom of H 2 O, acting as a nucleophile, attacks the positively charged carbon -initial product is an intermediate where the carbon atom has four substituents in a tetrahedral arrangement -rxn is completed by the rapid breakdown of the tetrahedral intermediate to release the alcohol -H 2 O is intrinsically a comparatively weak nucleophile, and its rxn with esters in the absence of a catalyst is very slow -hydrolysis of esters occurs much more rapidly at high ph, when the negatively charged OH - replaces H 2 O as the reactive nucleophile -the nucleophilic character of H 2 O itself can be increased by 80

5 interaction with a basic group other than OH - where the base offers a pair of electrons to one of the protons of the H 2 O and increases the electron density of the oxygen -general base--used to describe any substance that is capable of binding a proton in aqueous soln -enzymes use a number of functional groups to fill this role (necessary since the [OH - ] at physiological ph limits its availability] -only requirement is that the base start out in the unprotonated form, which means that the ambient ph must be above the pk a of the conjugate acid -candidates include: basic groups from the ionizable or polar amino acid side chains, an amino-terminal NH 2 group, a carboxyl-terminal carboxylate ion, or from the oxygen or nitrogen atom of a peptide bond -the pk a of these groups can vary over a considerable range environment 81

6 -using a general base rather than OH - has the advantage that the basic group that is provided by the protein can be positioned precisely with respect to the substrate in the active site, allowing the proximity effect to come into play -hydrolysis of an ester can also be catalyzed by an acid where the acid donates a proton to the oxygen of the ester's carbonyl group, increasing the positive charge on the carbon and increasing the susceptibility of the ester to attack by a nucleophile -general acid--any substance that is capable of releasing a proton, and enzymes almost always use such proton donors in preference to H + or OH - because a general acid can operate at moderate ph and is easy to fix in position -requirement is that the ph be below the pk a (3) Electrostatic interactions --enzymes act by stabilizing the distribution of electrical charge in transition states -suppose the active site of an enzyme included a positively charged amino acid side chain, such as Lys or Arg, located near the oxygen atom of a carbonyl group. A fixed positive charge 82

7 in this region would favor the formation of the tetrahedral intermediate, even if there were no transfer of a proton from the charged species to the oxygen. A fixed negative charge in the region of the nucleophile would have a similar effect. The interactions of such fixed charges are termed electrostatic effects. -as a reacting substrate is transformed into a transition state, the changing charges on its atoms interact with the charges on all of the other atoms in the surrounding protein, and also with the charges on any nearby water molecules -the energy difference between the initial state and the transition state thus depends critically on the details of the protein structure -modern computational techniques, when taken with the wealth of structural information from X-ray crystallography and other biophysical studies, have made it possible to calculate the contributions that various components of an enzyme's active site make to the activation free energy (ΔG ), and to predict quantitatively how ΔG might be altered by modifications of the protein 83

8 -can be tested experimentally by modifying the gene that encodes the protein (site-directed mutagenesis) (4) Nucleophilic/Electrophilic Catalysis (a) Nucleophilic Catalysis--strategy is to use stronger nucleophilic groups (than water) as part of the enzyme's active site -HOCH 2 group of a serine residue often used as a nucleophile -instead of immediately yielding the free COOH, the breakdown of the tetrahedral intermediate yields an intermediate ester that is covalently attached to the enzyme -the acyl-enzyme intermediate must be hydrolyzed by a second rxn in which H 2 O is the nucelophile -proteolytic enzymes (serine proteases) work in this way -two step pathway requires that the intermediate be more susceptible to nucleophilic attack by H 2 O than by the original ester or amide 84

9 -nucleophilic groups on enzymes participate in a variety of other types of rxn in addition to hydrolytic rxns, eg., acetoacetic acid decarboxylase -rxn proceeds by the formation of a Schiff base intermediate, in which the substrate is covalently attached to the ε-amino group of a lysine residue at the enzyme's active site -this intermediate is formed by a nucleophilic attack of the amino group on the carbonyl carbon, followed by the splitting out of H 2 O -protonation of the nitrogen atom of the Schiff base introduces a positive charge that pulls electrons from the nearby carboncarbon bond, causing decarboxylation -this is an extreme example of an electrostatic effect where the enzyme introduces a charged group into the substrate itself -basic feature of this mechanism is the formation of an intermediate state in which the substrate is covalently attached 85

10 to a nucleophilic group on the enzyme -the -CH 2 SH of cysteine is often used as a nucleophile also -the COOH of Asp and Glu participate in rxns involving the hydrolysis of ATP and -the imidazole ring of His can play a similar role -some enzymes use coenzymes: thiamine, biotin, pyridoxamine, or tetrahydrofolate as additional nucleophilic reagents (b) Electrophilic Catalysis--numerous enzymes use bound metal ions to form complexes with substrates -metal ion functions as an electrophilic group -eg., carbonic anhydrase--contains a Zn 2+ ion in the active site and forms a complex with the carbonyl oxygen atom of the aldehyde or peptide substrate -withdrawal of electrons by the Zn 2+ increases the partial positive charge on the carbonyl carbon atom and promotes the rxn of carbon with a nucleophile 86

11 (5) Structural Flexibility--some enzymes undergo major structural rearrangements when they bind substrates or inhibitors -eg., hexokinase ATP + glucose ADP + glucose-6-phosphate -hexokinase binds glucose, it undergoes a structural organization that brings together the elements of the active site -the enzyme literally closes like a set of jaws around the substrate referred to as an induced fit -carboxypeptidase A undergoes a major structural change when it binds its substrate -rearrangement of the protein pulls the hydrophobic part of the substrate out of the aqueous soln by surrounding it with nonpolar portions of the protein -advantages: (1) maximizes the favorable entropy change associated with removing a hydrophobic molecule from H 2 O (2) allows enzyme to intensify the electrostatic effects that promote the formation of the transition state (the substrate is 87

12 forced to respond to the directed electrostatic fields from the enzyme's functional groups, instead of the disordered fields from the solvent -structural change can help to explain the high specificity of some enzymatic rxns; eg., hexokinase undergoes a structural change upon binding glucose which promotes the binding of the other substrate (ATP) -ATP doesn't bind unless glucose is already present in the catalytic site -if ATP were to bind in the absence of glucose, the enzyme might have a tendency to catalyze the transfer of phosphate from ATP to water, resulting in a wasteful loss of ATP: ATP + H 2 O ADP + Pi -X-ray crystal structure of an enzyme give only static snapshots of the molecules, which can be very flexible -vibrations and rotations involving only a few atoms to s 88

13 -larger motions, i.e., flipping of aromatic rings 10-9 to 10-8 s -major reorganizations 10-6 to 10-3 s -all these can be important for catalysis 89

Key Concepts.

Key Concepts. Lectures 13-14: Enzyme Catalytic Mechanisms [PDF] Reading: Berg, Tymoczko & Stryer, Chapter 9, pp. 241-254 Updated on: 2/7/07 at 9:15 pm movie of chemical mechanism of serine proteases (from Voet & Voet,

More information

Enzymes Enzyme Mechanism

Enzymes Enzyme Mechanism Mechanisms of Enzymes BCMB 3100 Chapters 6, 7, 8 Enzymes Enzyme Mechanism 1 Energy diagrams Binding modes of enzyme catalysis Chemical modes of enzyme catalysis Acid-Base catalysis Covalent catalysis Binding

More information

Enzymes Enzyme Mechanism

Enzymes Enzyme Mechanism BCMB 3100 Chapters 6, 7, 8 Enzymes Enzyme Mechanism 1 Mechanisms of Enzymes Energy diagrams Binding modes of enzyme catalysis Chemical modes of enzyme catalysis Acid-Base catalysis Covalent catalysis Binding

More information

10/26/2010. An Example of a Polar Reaction: Addition of H 2 O to Ethylene. to Ethylene

10/26/2010. An Example of a Polar Reaction: Addition of H 2 O to Ethylene. to Ethylene 6.5 An Example of a Polar Reaction: Addition of H 2 O to Ethylene Addition of water to ethylene Typical polar process Acid catalyzed addition reaction (Electophilic addition reaction) Polar Reaction All

More information

Biochemistry 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 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 information

What is an enzyme? Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics. Margaret A. Daugherty Fall 2004 KEY FEATURES OF ENZYMES

What is an enzyme? Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics. Margaret A. Daugherty Fall 2004 KEY FEATURES OF ENZYMES Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics Margaret A. Daugherty Fall 2004 What is an enzyme? General Properties Mostly proteins, but some are actually RNAs Biological catalysts

More information

Biologic catalysts 1. Shared properties with chemical catalysts a. Enzymes are neither consumed nor produced during the course of a reaction. b.

Biologic catalysts 1. Shared properties with chemical catalysts a. Enzymes are neither consumed nor produced during the course of a reaction. b. Enzyme definition Enzymes are protein catalysts that increase the velocity of a chemical reaction and are not consumed during the reaction they catalyze. [Note: Some types of RNA can act like enzymes,

More information

MITOCW watch?v=gboyppj9ok4

MITOCW watch?v=gboyppj9ok4 MITOCW watch?v=gboyppj9ok4 The following content is provided under a Creative Commons license. Your support will help MIT OpenCourseWare continue to offer high quality educational resources for free. To

More information

Lecture 14 (10/18/17) Lecture 14 (10/18/17)

Lecture 14 (10/18/17) Lecture 14 (10/18/17) Lecture 14 (10/18/17) Reading: Ch6; 190-191, 194-195, 197-198 Problems: Ch6 (text); 7, 24 Ch6 (study guide-facts); 4, 13 NEXT Reading: Ch6; 198-203 Ch6; Box 6-1 Problems: Ch6 (text); 8, 9, 10, 11, 12,

More information

C a h p a t p e t r e r 6 E z n y z m y e m s

C 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 information

Chapter 25: The Chemistry of Life: Organic and Biological Chemistry

Chapter 25: The Chemistry of Life: Organic and Biological Chemistry Chemistry: The Central Science Chapter 25: The Chemistry of Life: Organic and Biological Chemistry The study of carbon compounds constitutes a separate branch of chemistry known as organic chemistry The

More information

Chapter 8 Metabolism: Energy, Enzymes, and Regulation

Chapter 8 Metabolism: Energy, Enzymes, and Regulation Chapter 8 Metabolism: Energy, Enzymes, and Regulation Energy: Capacity to do work or cause a particular change. Thus, all physical and chemical processes are the result of the application or movement of

More information

Energy, Enzymes, and Metabolism. Energy, Enzymes, and Metabolism. A. Energy and Energy Conversions. A. Energy and Energy Conversions

Energy, 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 information

Enzymes and Enzyme Kinetics I. Dr. Kevin Ahern

Enzymes and Enzyme Kinetics I. Dr. Kevin Ahern Enzymes and Enzyme Kinetics I Dr. Kevin Ahern Enzymatic Reactions Enzymatic Reactions Enzymatically Catalyzed Reactions Background Substrates Bound at Active Site of the Methylene Tetrahydrofolate Reductase

More information

Synthesis of Nitriles a. dehydration of 1 amides using POCl 3 : b. SN2 reaction of cyanide ion on halides:

Synthesis of Nitriles a. dehydration of 1 amides using POCl 3 : b. SN2 reaction of cyanide ion on halides: I. Nitriles Nitriles consist of the CN functional group, and are linear with sp hybridization on C and N. Nitriles are non-basic at nitrogen, since the lone pair exists in an sp orbital (50% s character

More information

Chapter 8: An Introduction to Metabolism

Chapter 8: An Introduction to Metabolism Chapter 8: An Introduction to Metabolism Key Concepts 8.1 An organism s metabolism transforms matter and energy, subject to the laws of thermodynamics 8.2 The free-energy change of a reaction tells us

More information

Study Guide: Basic Chemistry, Water, Life Compounds and Enzymes

Study Guide: Basic Chemistry, Water, Life Compounds and Enzymes Study Guide: Basic Chemistry, Water, Life Compounds and Enzymes 1. Lipids are good energy-storage molecules because a) the can absorb a large amount of energy while maintaining a constant temperature b)

More information

NAME. EXAM I I. / 36 September 25, 2000 Biochemistry I II. / 26 BICH421/621 III. / 38 TOTAL /100

NAME. EXAM I I. / 36 September 25, 2000 Biochemistry I II. / 26 BICH421/621 III. / 38 TOTAL /100 EXAM I I. / 6 September 25, 2000 Biochemistry I II. / 26 BIH421/621 III. / 8 TOTAL /100 I. MULTIPLE HOIE (6 points) hoose the BEST answer to the question by circling the appropriate letter. 1. An amino

More information

Enzyme Catalysis & Biotechnology

Enzyme 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 information

Chapter 6- An Introduction to Metabolism*

Chapter 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 information

Chapter 19. Synthesis and Reactions of b-dicarbonyl Compounds: More Chemistry of Enolate Anions. ß-dicarbonyl compounds. Why are ß-dicarbonyls useful?

Chapter 19. Synthesis and Reactions of b-dicarbonyl Compounds: More Chemistry of Enolate Anions. ß-dicarbonyl compounds. Why are ß-dicarbonyls useful? Chapter 19 Synthesis and Reactions of b-dicarbonyl Compounds: More Chemistry of Enolate Anions ß-dicarbonyl compounds Two carbonyl groups separated by a carbon Three common types ß-diketone ß-ketoester

More information

Courtesy of Elsevier. Used with permission.

Courtesy of Elsevier. Used with permission. Chemistry 5.07 2013 Problem Set 5 Answers Problem 1 Succinate dehydrogenase (SDH) is a heterotetramer enzyme complex that catalyzes the oxidation of succinate to fumarate with concomitant reduction of

More information

CHEM 3653 Exam # 1 (03/07/13)

CHEM 3653 Exam # 1 (03/07/13) 1. Using phylogeny all living organisms can be divided into the following domains: A. Bacteria, Eukarya, and Vertebrate B. Archaea and Eukarya C. Bacteria, Eukarya, and Archaea D. Eukarya and Bacteria

More information

Chapter 8 Notes. An Introduction to Metabolism

Chapter 8 Notes. An Introduction to Metabolism Chapter 8 Notes An Introduction to Metabolism Describe how allosteric regulators may inhibit or stimulate the activity of an enzyme. Objectives Distinguish between the following pairs of terms: catabolic

More information

Chemistry 5.07SC Biological Chemistry I Fall Semester, 2013

Chemistry 5.07SC Biological Chemistry I Fall Semester, 2013 Chemistry 5.07SC Biological Chemistry I Fall Semester, 2013 Lecture 10. Biochemical Transformations II. Phosphoryl transfer and the kinetics and thermodynamics of energy currency in the cell: ATP and GTP.

More information

CHAPTER 6--- CHEMISTRY IN BIOLOGY. Miss Queen

CHAPTER 6--- CHEMISTRY IN BIOLOGY. Miss Queen CHAPTER 6--- CHEMISTRY IN BIOLOGY Miss Queen SECTION 6.1 Atoms, Elements, Compounds COMPOSITION OF MATTER Matter - Everything in universe is composed of matter Matter is anything that occupies space or

More information

CHAPTER 29 HW: AMINO ACIDS + PROTEINS

CHAPTER 29 HW: AMINO ACIDS + PROTEINS CAPTER 29 W: AMI ACIDS + PRTEIS For all problems, consult the table of 20 Amino Acids provided in lecture if an amino acid structure is needed; these will be given on exams. Use natural amino acids (L)

More information

A. Two of the common amino acids are analyzed. Amino acid X and amino acid Y both have an isoionic point in the range of

A. Two of the common amino acids are analyzed. Amino acid X and amino acid Y both have an isoionic point in the range of Questions with Answers- Amino Acids & Peptides A. Two of the common amino acids are analyzed. Amino acid X and amino acid Y both have an isoionic point in the range of 5.0-6.5 (Questions 1-4) 1. Which

More information

Carboxylic Acids O R C + H + O - Chemistry 618B

Carboxylic Acids O R C + H + O - Chemistry 618B arboxylic Acids R H R + H + - R - Nomenclature - IUPA IUPA names: drop the -e from the parent alkane and add the suffix -oic acid If the compound contains a carbon-carbon double bond, change the infix

More information

Exam II. Thursday in class Review Session Tuesday

Exam II. Thursday in class Review Session Tuesday Exam II Thursday 10.30.08 in class Review Session Tuesday 10.28.08 Be able to draw a free energy diagram for an enzymatic reaction Know Michaelis-Menten Kinetics Understand the various types of inhibition

More information

Chapter 5. Directions and Rates of Biochemical Processes

Chapter 5. Directions and Rates of Biochemical Processes Chapter 5 Directions and Rates of Biochemical Processes Key Questions What factors determine which way a reaction will go? What factors determine the rate of a chemical reaction? How do enzymes work? How

More information

BIOLOGY. An Introduction to Metabolism CAMPBELL. Reece Urry Cain Wasserman Minorsky Jackson

BIOLOGY. An Introduction to Metabolism CAMPBELL. Reece Urry Cain Wasserman Minorsky Jackson CAMPBELL BIOLOGY TENTH EDITION Reece Urry Cain Wasserman Minorsky Jackson 8 An Introduction to Metabolism Lecture Presentation by Nicole Tunbridge and Kathleen Fitzpatrick The Energy of Life The living

More information

Making Sugars. Carbon Dioxide. Properties of Carbon Dioxide

Making Sugars. Carbon Dioxide. Properties of Carbon Dioxide Making Sugars The reactions that take carbon dioxide to sugar involve nucleophilic attack at the carbon of carbon dioxide and reduction. The reducing equivalents come from NADPH. Energy is transmitted

More information

BIOCHEMISTRY. František Vácha. JKU, Linz.

BIOCHEMISTRY. František Vácha. JKU, Linz. BIOCHEMISTRY František Vácha http://www.prf.jcu.cz/~vacha/ JKU, Linz Recommended reading: D.L. Nelson, M.M. Cox Lehninger Principles of Biochemistry D.J. Voet, J.G. Voet, C.W. Pratt Principles of Biochemistry

More information

Lecture 11: Enzymes: Kinetics [PDF] Reading: Berg, Tymoczko & Stryer, Chapter 8, pp

Lecture 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 information

1. Amino Acids and Peptides Structures and Properties

1. Amino Acids and Peptides Structures and Properties 1. Amino Acids and Peptides Structures and Properties Chemical nature of amino acids The!-amino acids in peptides and proteins (excluding proline) consist of a carboxylic acid ( COOH) and an amino ( NH

More information

Metabolism: Energy and Enzymes. February 24 th, 2012

Metabolism: 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 information

Synthesis and Structure of Alcohols Alcohols can be considered organic analogues of water.

Synthesis and Structure of Alcohols Alcohols can be considered organic analogues of water. Synthesis and Structure of Alcohols Alcohols can be considered organic analogues of water. Alcohols are usually classified as primary, secondary and tertiary. Alcohols with the hydroxyl bound directly

More information

Properties of Amines

Properties of Amines Properties of Amines 1. Boiling Point and Water Solubility It is instructive to compare the boiling points and water solubility of amines with those of corresponding alcohols and ethers. The dominant factor

More information

CHEMISTRY 1A Fall 2010 Final Exam Key

CHEMISTRY 1A Fall 2010 Final Exam Key CHEMISTRY 1A Fall 2010 Final Exam Key YOU MIGHT FIND THE FOLLOWING USEFUL; 0.008314 kj H E ( n)rt R = K mol 0.00418 kj q C cal m w T g C H rxn = H f (products) H f (reactants) Electronegativities H 2.2

More information

Metabolism and Enzymes

Metabolism 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 information

ALE 4. Effect of Temperature and Catalysts on the Rate of a Chemical Reaction

ALE 4. Effect of Temperature and Catalysts on the Rate of a Chemical Reaction Name Chem 163 Section: Team Number: ALE 4. Effect of Temperature and Catalysts on the Rate of a Chemical Reaction (Reference: 16.5 16.6 & 16.8 Silberberg 5 th edition) Why do reaction rates increase as

More information

2 4 Chemical Reactions and Enzymes

2 4 Chemical Reactions and Enzymes 2 4 Chemical Reactions and Enzymes THINK ABOUT IT Living things are made up of chemical compounds, but chemistry isn t just what life is made of chemistry is also what life does. Everything that happens

More information

12U Biochemistry Unit Test

12U Biochemistry Unit Test 1 12U Biology: Biochemistry Test 12U Biochemistry Unit Test Modified True/False Indicate whether the statement is true or false. If false, change the identified word or phrase to make the statement true.

More information

BCMB 3100 Chapters 6,7,8 Enzyme Basics. Six Classes (IUBMB) Kinetics Michaelis-Menten Equation Vo, Km, Vmax, Kcat Lineweaver-Burk Plot

BCMB 3100 Chapters 6,7,8 Enzyme Basics. Six Classes (IUBMB) Kinetics Michaelis-Menten Equation Vo, Km, Vmax, Kcat Lineweaver-Burk Plot BCMB 3100 Chapters 6,7,8 Enzyme Basics Six Classes (IUBMB) Kinetics Michaelis-Menten Equation Vo, Km, Vmax, Kcat Lineweaver-Burk Plot Enzymes are biological macromolecules that increase the rate of the

More information

Enzyme Enzymes are proteins that act as biological catalysts. Enzymes accelerate, or catalyze, chemical reactions. The molecules at the beginning of

Enzyme Enzymes are proteins that act as biological catalysts. Enzymes accelerate, or catalyze, chemical reactions. The molecules at the beginning of Enzyme Enzyme Enzymes are proteins that act as biological catalysts. Enzymes accelerate, or catalyze, chemical reactions. The molecules at the beginning of the process are called substrates and the enzyme

More information

Organic Chemistry, 7 L. G. Wade, Jr. Chapter , Prentice Hall

Organic Chemistry, 7 L. G. Wade, Jr. Chapter , Prentice Hall Organic Chemistry, 7 th Edition L. G. Wade, Jr. Chapter 17 Reactions of Aromatic Compounds 2010, Prentice Hall Electrophilic Aromatic Substitution Although h benzene s pi electrons are in a stable aromatic

More information

Lecture 2: Biological Thermodynamics [PDF] Key Concepts

Lecture 2: Biological Thermodynamics [PDF] Key Concepts Lecture 2: Biological Thermodynamics [PDF] Reading: Berg, Tymoczko & Stryer: pp. 11-14; pp. 208-210 problems in textbook: chapter 1, pp. 23-24, #4; and thermodynamics practice problems [PDF] Updated on:

More information

Reaction Thermodynamics

Reaction Thermodynamics Reaction Thermodynamics Thermodynamics reflects the degree to which a reaction is favored or disfavored Recall: G = Gibbs free energy = the energy available to do work ΔG = change in G of the system as

More information

It is generally believed that the catalytic reactions occur in at least two steps.

It 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 information

Thermodynamics is the study of energy and its effects on matter

Thermodynamics is the study of energy and its effects on matter 00Note Set 3 1 THE ENERGETICS OF LIFE Thermodynamics and Bioenergetics: Thermodynamics is the study of energy and its effects on matter Bioenergetics is the quantitative analysis of how organisms gain

More information

Chapter 11, Part 1: Polar substitution reactions involving alkyl halides

Chapter 11, Part 1: Polar substitution reactions involving alkyl halides hapter 11, Part 1: Polar substitution reactions involving alkyl halides Overview: The nature of alkyl halides and other groups with electrophilic sp 3 hybridized leads them to react with nucleophiles and

More information

Cellular Respiration: Harvesting Chemical Energy. 9.1 Catabolic pathways yield energy by oxidizing organic fuels

Cellular Respiration: Harvesting Chemical Energy. 9.1 Catabolic pathways yield energy by oxidizing organic fuels Cellular Respiration: Harvesting Chemical Energy 9.1 Catabolic pathways yield energy by oxidizing organic fuels 9.2 Glycolysis harvests chemical energy by oxidizing glucose to pyruvate 9.3 The citric acid

More information

Chapter 6: Energy and Metabolism

Chapter 6: Energy and Metabolism Chapter 6: Energy and Metabolism Student: 1. Oxidation and reduction reactions are chemical processes that result in a gain or loss in A) atoms. B) neutrons. C) electrons. D) molecules. E) protons. 2.

More information

Answers to Chapter 6 (in-text & asterisked problems)

Answers to Chapter 6 (in-text & asterisked problems) Introduction to Bioorganic Chemistry and Chemical Biology 1 Answers to Chapter 6 (intext & asterisked problems) Answer 6.1 olve the equation. Convert temperature in C to K by adding 273. Plug the numbers

More information

Chem 263 March 28, 2006

Chem 263 March 28, 2006 Chem 263 March 28, 2006 Properties of Carboxylic Acids Since carboxylic acids are structurally related to both ketones and aldehydes, we would expect to see some similar structural properties. The carbonyl

More information

Alcohols. Alcohol any organic compound containing a hydroxyl (R-OH) group. Alcohols are an extremely important organic source

Alcohols. Alcohol any organic compound containing a hydroxyl (R-OH) group. Alcohols are an extremely important organic source Alcohols Alcohol any organic compound containing a hydroxyl (R-OH) group Uses: synthetic intermediate, cleanser, cosmetics, fuel, alcoholic beverages, etc. Alcohols are an extremely important organic source

More information

Lecture # 3, 4 Selecting a Catalyst (Non-Kinetic Parameters), Review of Enzyme Kinetics, Selectivity, ph and Temperature Effects

Lecture # 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 information

NH 2. Biochemistry I, Fall Term Sept 9, Lecture 5: Amino Acids & Peptides Assigned reading in Campbell: Chapter

NH 2. Biochemistry I, Fall Term Sept 9, Lecture 5: Amino Acids & Peptides Assigned reading in Campbell: Chapter Biochemistry I, Fall Term Sept 9, 2005 Lecture 5: Amino Acids & Peptides Assigned reading in Campbell: Chapter 3.1-3.4. Key Terms: ptical Activity, Chirality Peptide bond Condensation reaction ydrolysis

More information

Chapter 5 Metabolism: Energy & Enzymes

Chapter 5 Metabolism: Energy & Enzymes Energy Energy is the capacity to do work Kinetic energy Energy of motion Potential energy Stored energy What do you use for energy? Where do you think the energy is stored these molecules? The BONDS! Every

More information

Objective 14. Develop synthesis strategies for organic synthesis.

Objective 14. Develop synthesis strategies for organic synthesis. Objective 14. Develop synthesis strategies for organic synthesis. Skills: Draw structure ID structural features and reactive sites (alpha C, beta C, LG, etc.) ID Nu - and E + use curved arrows to show

More information

Chem 263 Nov 24, Properties of Carboxylic Acids

Chem 263 Nov 24, Properties of Carboxylic Acids Chem 263 ov 24, 2009 Properties of Carboxylic Acids Since carboxylic acids are structurally related to both ketones and aldehydes, we would expect to see some similar structural properties. The carbonyl

More information

Introduction to Enzymes

Introduction to Enzymes Introduction to Enzymes Lysozyme active site Chapter 8 Part 1 HIV-1 Protease with bound Inhibitor Dr. Ray How Enzymes Function What structural features allow an enzyme to have its unique biochemical function?

More information

Chapter 5 Volume 2 Operation of enzymes- The nutcracker mechanism *

Chapter 5 Volume 2 Operation of enzymes- The nutcracker mechanism * Chapter 5, Vol. 2, Operation of enzymes 2-5-1 Chapter 5 Volume 2 Operation of enzymes- The nutcracker mechanism * Fortunately Dorovska-Taran and Martnek with their respective coworkers measured the steady-state

More information

Energy Transformation, Cellular Energy & Enzymes (Outline)

Energy 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 information

Lecture Notes Chem 51C S. King Chapter 24 Carbonyl Condensation Reactions

Lecture Notes Chem 51C S. King Chapter 24 Carbonyl Condensation Reactions Lecture Notes Chem 51C S. King Chapter 24 Carbonyl Condensation Reactions I. Reaction of Enols & Enolates with ther Carbonyls Enols and enolates are electron rich nucleophiles that react with a number

More information

Problems from Previous Class

Problems from Previous Class 1 Problems from Previous lass 1. What is K m? What are the units of K m? 2. What is V max? What are the units of V max? 3. Write down the Michaelis-Menten equation. 4. What order of reaction is the reaction

More information

Chapter 17 Aldehydes and Ketones

Chapter 17 Aldehydes and Ketones hapter 17 Aldehydes and Ketones arbonyl Groups polarized (1) Aldehydes and Ketones ' aldehydes ketones : and : are poor leaving groups (2) arboxylic Acid Derivatives l ' ' 2 carboxylic acid substituent

More information

Chapter 20: Aldehydes and Ketones

Chapter 20: Aldehydes and Ketones hem A225 Notes Page 67 I. Introduction hapter 20: Aldehydes and Ketones Aldehydes and ketones contain a carbonyl group (=) with no other heteroatoms attached. An aldehyde has at least one hydrogen attached;

More information

I. Flow of Energy in Living Things II. Laws of Thermodynamics & Free Energy III. Activation Energy IV. Enzymes V. Reaction Coupling VI.

I. Flow of Energy in Living Things II. Laws of Thermodynamics & Free Energy III. Activation Energy IV. Enzymes V. Reaction Coupling VI. Chapter 6 Energy & Metabolism I. Flow of Energy in Living Things II. Laws of Thermodynamics & Free Energy III. Activation Energy IV. Enzymes V. Reaction Coupling VI. Metabolism I. Flow of Energy in Living

More information

Aldehydes and Ketones : Aldol Reactions

Aldehydes and Ketones : Aldol Reactions Aldehydes and Ketones : Aldol Reactions The Acidity of the a Hydrogens of Carbonyl Compounds: Enolate Anions Hydrogens on carbons a to carbonyls are unusually acidic The resulting anion is stabilized by

More information

CARBOXYLIC ACIDS and their Derivatives Nucleophilic Acyl substitution - Review the nomenclature for these compounds in your textbook

CARBOXYLIC ACIDS and their Derivatives Nucleophilic Acyl substitution - Review the nomenclature for these compounds in your textbook CARBXYLIC ACIDS and their Derivatives Nucleophilic Acyl substitution - Review the nomenclature for these compounds in your textbook R Z R Z R Z - the basicity of Z determines the relative stability of

More information

Chapter 16. Aldehydes and Ketones I. Nucleophilic Addition to the Carbonyl Group. Physical Properties of Aldehydes and Ketones. Synthesis of Aldehydes

Chapter 16. Aldehydes and Ketones I. Nucleophilic Addition to the Carbonyl Group. Physical Properties of Aldehydes and Ketones. Synthesis of Aldehydes Nomenclature of Aldehydes and Ketones Chapter 16 Aldehydes and Ketones I. Aldehydes replace the -e of the parent alkane with -al The functional group needs no number Nucleophilic Addition to the Carbonyl

More information

4. The Michaelis-Menten combined rate constant Km, is defined for the following kinetic mechanism as k 1 k 2 E + S ES E + P k -1

4. The Michaelis-Menten combined rate constant Km, is defined for the following kinetic mechanism as k 1 k 2 E + S ES E + P k -1 Fall 2000 CH 595C Exam 1 Answer Key Multiple Choice 1. One of the reasons that enzymes are such efficient catalysts is that a) the energy level of the enzyme-transition state complex is much higher than

More information

Glendale Community College, AZ

Glendale Community College, AZ Glendale Community College, AZ Mrs. Sandy Gruin n BS in chemistry from Bowling Green State University n MS in Biochemistry from Montana State University n NIH research grant University of Pennsylvania

More information

Dr. Mohamed El-Newehy

Dr. Mohamed El-Newehy By Dr. Mohamed El-Newehy Chemistry Department, College of Science, King Saud University http://fac.ksu.edu.sa/melnewehy Carboxylic acids and Their Derivatives 1 Structure of Carboxylic Acids -The functional

More information

Applications of Free Energy. NC State University

Applications of Free Energy. NC State University Chemistry 433 Lecture 15 Applications of Free Energy NC State University Thermodynamics of glycolysis Reaction kj/mol D-glucose + ATP D-glucose-6-phosphate + ADP ΔG o = -16.7 D-glucose-6-phosphate p D-fructose-6-phosphate

More information

Aldol Reactions pka of a-h ~ 20

Aldol Reactions pka of a-h ~ 20 Enolate Anions Chapter 17 Hydrogen on a carbons a to a carbonyl is unusually acidic The resulting anion is stabilized by resonance to the carbonyl Aldehydes and Ketones II Aldol Reactions pka of a-h ~

More information

When we deprotonate we generate enolates or enols. Mechanism for deprotonation: Resonance form of the anion:

When we deprotonate we generate enolates or enols. Mechanism for deprotonation: Resonance form of the anion: Lecture 5 Carbonyl Chemistry III September 26, 2013 Ketone substrates form tertiary alcohol products, and aldehyde substrates form secondary alcohol products. The second step (treatment with aqueous acid)

More information

Aldehydes and Ketones: Nucleophilic Addition Reactions

Aldehydes and Ketones: Nucleophilic Addition Reactions Aldehydes and Ketones: Nucleophilic Addition Reactions Why this Chapter? Much of organic chemistry involves the chemistry of carbonyl compounds Aldehydes/ketones are intermediates in synthesis of pharmaceutical

More information

Ch. 2 BASIC CHEMISTRY. Copyright 2010 Pearson Education, Inc.

Ch. 2 BASIC CHEMISTRY. Copyright 2010 Pearson Education, Inc. Ch. 2 BASIC CHEMISTRY Matter and Composition of Matter Definition: Anything that has mass and occupies space Matter is made up of elements An element cannot be broken down by ordinary chemical means Atoms

More information

Amines. Introduction Organic derivatives of ammonia. Many are biologically active.

Amines. Introduction Organic derivatives of ammonia. Many are biologically active. Amines Introduction Organic derivatives of ammonia. Many are biologically active. 1 Biological Activity Neurotransmitters: dopamine Bioregulators: epinephrine Vitamins: niacin, B 6 Alkaloids: nicotine,

More information

A. Review of Acidity and pk a Common way to examine acidity is to use the Bronsted-Lowry acid-base equation:

A. Review of Acidity and pk a Common way to examine acidity is to use the Bronsted-Lowry acid-base equation: 1 Chapter 22: Reactions of Enols and Enolates I. Alpha Substitution verview: A. Review of Acidity and pk a Common way to examine acidity is to use the Bronsted-Lowry acid-base equation: Recall that the

More information

An Introduction to Metabolism

An Introduction to Metabolism Chapter 8 1 An Introduction to Metabolism PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley with contributions from

More information

Loudon Chapter 20 & 21 Review: Carboxylic Acids & Derivatives CHEM 3331, Jacquie Richardson, Fall Page 1

Loudon Chapter 20 & 21 Review: Carboxylic Acids & Derivatives CHEM 3331, Jacquie Richardson, Fall Page 1 Loudon Chapter 20 & 21 eview: Carboxylic Acids & Derivatives CEM 3331, Jacquie ichardson, Fall 2010 - Page 1 These two chapters cover compounds which are all at the three bonds to more electronegative

More information

Covalent bonds can have ionic character These are polar covalent bonds

Covalent bonds can have ionic character These are polar covalent bonds Polar Covalent Bonds: Electronegativity Covalent bonds can have ionic character These are polar covalent bonds Bonding electrons attracted more strongly by one atom than by the other Electron distribution

More information

Carbon and. Molecular Diversity. Organic Molecules. The Carbon Atom. Carbon s Compatibility. Variations in Carbon Skeletons 10/13/2015

Carbon and. Molecular Diversity. Organic Molecules. The Carbon Atom. Carbon s Compatibility. Variations in Carbon Skeletons 10/13/2015 Organic Molecules Carbon and Molecular Diversity What is an organic molecule? Molecule that contains carbon What are the major elements of life? C, H, N, O, P, and S The Carbon Atom What makes the carbon

More information

Buffer solutions المحاليل المنظمة

Buffer solutions المحاليل المنظمة Buffer solutions المحاليل المنظمة Presented by Dr. Mohammad Saadeh The requirements for the Pharmaceutical Biochemistry I Philadelphia University Faculty of pharmacy Understanding ph balance The human

More information

Energy Transformation and Metabolism (Outline)

Energy 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 information

Protein synthesis II Biochemistry 302. Bob Kelm February 25, 2004

Protein synthesis II Biochemistry 302. Bob Kelm February 25, 2004 Protein synthesis II Biochemistry 302 Bob Kelm February 25, 2004 Two idealized views of the 70S ribosomal complex during translation 70S cavity Fig. 27.25 50S tunnel View with 30S subunit in front, 50S

More information

Electrophilic Aromatic Substitution. Dr. Mishu Singh Department of chemistry Maharana Pratap Govt.P.G.College Hardoi

Electrophilic Aromatic Substitution. Dr. Mishu Singh Department of chemistry Maharana Pratap Govt.P.G.College Hardoi Electrophilic Aromatic Substitution Dr. Mishu Singh Department of chemistry Maharana Pratap Govt.P.G.College Hardoi 1 Recall the electophilic addition of HBr (or Br2) to alkenes H + nu cleophile H Br H

More information

4. Single > Double > Triple [bond length]

4. Single > Double > Triple [bond length] 1. Sigma bonds are significantly stronger than pi bonds. This is because sigma bonds allow for electron density to be concentrated to a much larger degree between the two nuclei. The lowest energy state

More information

1-How can we distinguish between D-amino acid and L-amino acid?

1-How can we distinguish between D-amino acid and L-amino acid? AMINO ACIDS (2) Questions from the previous lecture : 1-How can we distinguish between D-amino acid and L-amino acid? According to the location of the amino group in the amino acid, the R group is above,

More information

Biology: The Core (Simon) Chapter 2 The Chemistry of Life. Multiple-Choice Questions

Biology: The Core (Simon) Chapter 2 The Chemistry of Life. Multiple-Choice Questions Biology: The Core (Simon) Chapter 2 The Chemistry of Life Multiple-Choice Questions 1) The chemical name for table salt is sodium chloride, or simply NaCl. What type of chemical is NaCl? A) Compound B)

More information

Chapter 6 Chemistry in Biology

Chapter 6 Chemistry in Biology Section 1: Atoms, Elements, and Compounds Section 2: Chemical Reactions Section 3: Water and Solutions Section 4: The Building Blocks of Life Click on a lesson name to select. 6.1 Atoms, Elements, and

More information

18: Reactions of Enolate Ions and Enols

18: Reactions of Enolate Ions and Enols 18: Reactions of Enolate Ions and Enols 18.1 Enolate Ions and Enols 18-3 Halogenation, Alkylation, and Condensation Reactions (18.1A) 18-3 Acidity of α-c-h's (18.1B) 18-4 Resonance Stabilization Enol Form

More information

1. Which of the following has the lowest vapor pressure? A) H 2 O B) NaCl C) NH 3 D) O 2 E) CH 4

1. Which of the following has the lowest vapor pressure? A) H 2 O B) NaCl C) NH 3 D) O 2 E) CH 4 Name: Date: 1. Which of the following has the lowest vapor pressure? A) H O B) NaCl C) NH 3 D) O E) CH 4. Which of the following species exhibit hydrogen bonding? (Check all that apply.) A) HBr B) NO 3

More information

Enzyme 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 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 information

LS1a Fall 2014 Practice Problem Set #1. 1. Consider a hypothetical reaction carried out at constant temperature and pressure:

LS1a Fall 2014 Practice Problem Set #1. 1. Consider a hypothetical reaction carried out at constant temperature and pressure: LS1a Fall 2014 Practice Problem Set #1 I. Basic Concept Questions 1. Consider a hypothetical reaction carried out at constant temperature and pressure: The Gibbs free energy curve of this reaction is depicted

More information

Amino Acids and Peptides

Amino Acids and Peptides Amino Acids Amino Acids and Peptides Amino acid a compound that contains both an amino group and a carboxyl group α-amino acid an amino acid in which the amino group is on the carbon adjacent to the carboxyl

More information