4 Examples of enzymes

Size: px
Start display at page:

Download "4 Examples of enzymes"

Transcription

1 Catalysis 1

2 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 (NMP) kinase. 2

3 4 different challenges Serine proteases - chymotrypsin: promoting a reaction that is immeasurably slow at neutral ph. Carbonic anhydrase: Making a fast reaction even faster. Restrictions Endonucleases - EcoRV: attaining a high level of specificity. NMP kinase: Transfer of a Phosphoryl group from ATP to a nucleotide and not to water. 3

4 4 strategies for catalysis 1. Covalent catalysis. 2. General acid-base catalysis. 3. Metal ion catalysis. 4. Catalysis by approximation. They are not mutually exclusive! 4

5 1. Covalent catalysis The active site usually contains a powerful nucleophile. The nucleophile is temporarily covalently bound to the substrate. Chymotrypsin is a good example. 5

6 2. General acid-base catalysis An acid or a base plays the role of a proton donor or acceptor. Not water. Again chymotrypsin s active site is a good example 6

7 3. Metal ion catalysis Metals are good electrophilic catalysts stabilizing negative charges. They can also generate a nucleophile by increasing the acidity of an adjacent molecule (e.g. Carbonic anhydrase). The metal may bind the substrate to increase the binding energy (e.g. NMP kinase). 7

8 4. Catalysis by approximation Bringing two substrates close together. NMP kinase brings two nucleotides close together so that the transfer of the Phosphoryl group is from one to the other. 8

9 1. Proteases Proteases Proteins must have a certain turnover rate. Many regulatory steps are achieved by the concerted breakdown of proteins (e.g. cell cycle). Unfolded proteins are also degraded, so as not to cause any problems. In the gut proteins are broken down to their amino acid components. 9

10 1. Proteases The proteolytic reaction Addition of water to the peptide bond. R O C N H R' O + H 2 O + R C O R' NH 3 + The reaction is thermodynamically favored. In the absence of a catalysis at neutral ph however, t 1/2 may be as long as hundreds of years. 10

11 1. Proteases Chymotrypsin Chymotrypsin cleaves peptide bonds on the C- terminal side of large hydrophobics. It is a good example of covalent modification as a catalytic strategy. 11

12 1. Proteases What is the nucleophile? Reactions with organofluorophosphates (e.g. DIPF) selectively labels Ser

13 1. Proteases Monitoring kinetics 13

14 1. Proteases Kinetic analysis 14

15 1. Proteases A reaction in two stages A. Acyl enzyme intermediate formation releasing the amine. B. Hydrolysis of the acyl enzyme releasing the COO -. 15

16 1. Proteases 16

17 1. Proteases 17

18 1. Proteases The catalytic triad Asp 102 increases the catalytic power of H57. His 57 serves as a general base catalyst. Thus an alkoxide is formed which is a much stronger nucleophile than a hydroxyl. 18

19 1. Proteases The reaction as a whole 19

20 1. Proteases Step 1 Substrate binds. Nucleophilic attack of the alkoxide on the peptide carbonyl carbon. 20

21 1. Proteases Step 2 A change in the geometry of the peptide bond from trigonal planer to tetrahedral. 21

22 1. Proteases Step 2 cont. The formal negative charge on the carbonyl oxygen is stabilized by the oxyanion hole. 22

23 1. Proteases Step 3 Collapse to an acyl enzyme intermediate. 23

24 1. Proteases Step 4 The amine group leaves the enzyme. Thus half of the substrate remains bound to the enzyme. 24

25 1. Proteases Step 5 A water molecules replaces the amine. His 57 acts as a general base catalyst again activating the water molecule. It now undertakes a nucleophilic attack on the acyl carbon. 25

26 1. Proteases Step 6 Formation of an unstable tetrahedral intermediate. 26

27 1. Proteases Step 7 The tetrahedral intermediate breaks down. 27

28 1. Proteases Step 8 Release of the carboxylic acid. The cycle is now complete. 28

29 1. Proteases Specificity cause A hydrophobic pocket selectively binds large hydrophobic amino acids. Trypsin and elastase contain other pockets defining their specificity. 29

30 1. Proteases 30

31 1. Proteases 31

32 1. Proteases Different serine proteases: 1. Subtilisin 32

33 1. Proteases Different serine proteases: 2. Carboxypeptidase II Thus, the catalytic triad has appeared at least 3 times during the course of evolution! 33

34 2. Carbonic anhydrase Carbonic anhydrase (CA) CA catalyses the hydration and dehydration of CO 2. 34

35 2. Carbonic anhydrase CA s importance The natural rate of the reactions is fast: k 1 = 0.15 s -1, however it is not fast enough. In the presence of the enzyme k cat = 10 6 s -1. The need for the enzyme arises from the fact that at times we need CO 2 (e.g. in the lungs) and at time bicarbonate. 35

36 2. Carbonic anhydrase CA and Zinc CA was the first enzyme known to contain Zinc. Now as much as 1/3 of all enzymes are known to contain bound metal ions. Zinc is found in biology only as Zn 2+. It is normally coordinated by four ligands. Remember that coordination is when one of the partners in the bond donates the pair of electrons entirely. 36

37 2. Carbonic anhydrase Due to the coordination the net charge due to the Zn 2+ is

38 2. Carbonic anhydrase Catalysis and ph The midpoint in the transition is around ph 7. Thus a group with a pk A of 7 is critical to the enzyme s activity. It is not a Histidine but rather a water molecule k cat (10 6 s -1 ) 38

39 2. Carbonic anhydrase Thus the binding of water to Zn 2+ lowers the water s pk A from 15.4 to 7. 39

40 2. Carbonic anhydrase The mechanism 40

41 2. Carbonic anhydrase Step 1 Zn 2+ facilitates the release of a H + from the bound water molecule. 41

42 2. Carbonic anhydrase Step 2 The CO 2 binds in the enzyme s active site. It is positioned accordingly for the attack. 42

43 2. Carbonic anhydrase Step 3 Nucleophilic attack by the hydroxide ion. The CO 2 is converted to bicarbonate ion. 43

44 2. Carbonic anhydrase Step 4 Regeneration of the catalytic site though the exchange of water and the release of bicarbonate. 44

45 2. Carbonic anhydrase The proton paradox One of the steps in the reaction involves the deprotonation of the water to form a hydroxide ion. When the enzyme is working in the opposite direction (dehydration of bicarbonate) the hydroxide ion protonates to form water. 45

46 2. Carbonic anhydrase The proton paradox cont. Proton diffusion in water is very rapid, with second order rate constants of M -1 s -1. Thus k -1 must be lower than M -1 s -1. The equilibrium constant for H + release, K = k 1 /k -1 =10-7 M. Thus k 1 must be equal to 10 4 s -1. In other words, the rate of H + diffusion limits the rate of H + release to less than 10 4 s -1 for a group with a pka= 7. 46

47 2. Carbonic anhydrase The proton paradox cont. However if CO 2 is hydrated at a rate constant of 10 6 s -1 then every step in the reaction must proceed at least as fast. How can this be if the rate of proton release is only 10 4 s -1? How can this apparent paradox be resolved? 47

48 2. Carbonic anhydrase The proton shuffle The resolution of the paradox was possible upon noticing that maximal acceleration of the hydration reaction was only possible in the presence of buffer. The reason is that the [H + ] is only 10-7 M, but the concentration of the buffer can be much higher. 48

49 2. Carbonic anhydrase The proton shuffle cont. If the buffer (BH + ) has a pk A of 7 (similar to the water molecule bound to the Zn 2+ ) then the following equilibrium constant is obtained: 49

50 2. Carbonic anhydrase The proton shuffle cont. Now the rate of deprotonation k 1 (or the rate of H + abstraction by the buffer) will be equal to: k 1 [B]. The second order rate constants k 1 and k -1 will be limited by buffer diffusion to values less than 10 9 M -1 s -1. Thus, [B] higher than 10-3 M will be able to support rate constant for hydration of CO 2 of 10 6 s -1. This is because: k 1 [B] = (10 9 M -1 s -1 ) (10-3 M) = 10 6 s

51 2. Carbonic anhydrase The proton shuffle cont. Experimental date supports this prediction. 51

52 2. Carbonic anhydrase So what is the buffer? Most buffers are too big to reach the active site of the enzyme. For this reason the enzyme has positioned a His residue to act as the buffer in close proximity: a built-in H + shuffle. 52

53 2. Carbonic anhydrase A built-in proton shuffle So the enzyme has evolved a mechanism to control H + release and uptake to dramatically accelerate the rate of the reaction. This is seen in many other instances in which enzymes use acid-base catalysis. It also explains the prominence of such catalytic mechanisms. 53

54 2. Carbonic anhydrase Evolution of Zn 2+ active sites The enzymes referred to so far are called α- carbonic anhydrases (α-cas). Bacteria and pants contain β-cas that are distinct from α-cas, although they contain Zn 2+ in their active site. The ligands for Zn 2+ are 1 His and 2 Cys residues, as opposed to 3 His in α-cas. 54

55 4. NMP kinases Nucleotide monophosphate kinases Nucleotide monophosphate (NMP) kinases catalyze the reversible transfer of a Phosphoryl from an NTP to an NMP. They can also be used to generate some NTP from two NDPs when NTP concentrations is being exhausted. Remember that: [ATP] > [ADP] > [AMP] 55

56 4. NMP kinases 56

57 4. NMP kinases Adenylate kinase We will concentrate on adenylate kinase. Its biggest challenge is to transfer the Phosphoryl group to an AMP and avoid the competing reaction - hydrolysis. It provides an example for: Induced fit. Metal ion catalysis which is different than the one used by the other enzymes previously discussed. 57

58 4. NMP kinases NMP kinases form a family 58

59 4. NMP kinases A core domain of an NMP kinase 59

60 4. NMP kinases The P-loop: G-XXXX-G-K 60

61 4. NMP kinases What is the real substrate? The affinity of NTPs for Mg 2+ (or Mn 2+ ) is 10-4 M. Since [Mg 2+ ]~10-3 in the cell all NTPs are found as: NTP-Mg 2+ 61

62 4. NMP kinases How does it affect catalysis? Mg 2+ neutralizes the charge on the NTP to minimize non-specific interactions. The interactions between the Mg 2+ and the NTP hold it in a stable conformation ready for catalysis. It provides for additional possibilities for interaction with the enzyme thereby increasing the binding energy. 62

63 4. NMP kinases In some enzymes the Mg 2+ is bound directly to the side chains (often E or D). In other there are bridging water molecules. 63

64 4. NMP kinases Binding induces a big conformational change The binding of ATP causes a large conformational change in the protein. The P-loop closes down on the ATP interacting with the β- phosphate. The movement of the P-loop enables the top domain of the protein to move closing down on the substrate further. 64

65 4. NMP kinases Catalysis Once the ATP is bound its γ-phosphate ions are positioned exactly near the AMP ready for catalysis. Binding of the AMP causes additional conformational change in the protein. Without the binding of both substrates the reaction will not take place. This is how hydrolysis is prevented. 65

66 4. NMP kinases P-loop conservation 66

67 4. NMP kinases P-loop conservation cont. 67

Lecture 15: Enzymes & Kinetics. Mechanisms ROLE OF THE TRANSITION STATE. H-O-H + Cl - H-O δ- H Cl δ- HO - + H-Cl. Margaret A. Daugherty.

Lecture 15: Enzymes & Kinetics. Mechanisms ROLE OF THE TRANSITION STATE. H-O-H + Cl - H-O δ- H Cl δ- HO - + H-Cl. Margaret A. Daugherty. Lecture 15: Enzymes & Kinetics Mechanisms Margaret A. Daugherty Fall 2004 ROLE OF THE TRANSITION STATE Consider the reaction: H-O-H + Cl - H-O δ- H Cl δ- HO - + H-Cl Reactants Transition state Products

More information

Enzyme function: the transition state. Enzymes & Kinetics V: Mechanisms. Catalytic Reactions. Margaret A. Daugherty A B. Lecture 16: Fall 2003

Enzyme function: the transition state. Enzymes & Kinetics V: Mechanisms. Catalytic Reactions. Margaret A. Daugherty A B. Lecture 16: Fall 2003 Lecture 16: Enzymes & Kinetics V: Mechanisms Margaret A. Daugherty Fall 2003 Enzyme function: the transition state Catalytic Reactions A B Catalysts (e.g. enzymes) act by lowering the transition state

More information

Catalytic Reactions. Intermediate State in Catalysis. Lecture 16: Catalyzed reaction. Uncatalyzed reaction. Enzymes & Kinetics V: Mechanisms

Catalytic Reactions. Intermediate State in Catalysis. Lecture 16: Catalyzed reaction. Uncatalyzed reaction. Enzymes & Kinetics V: Mechanisms Enzyme function: the transition state Catalytic Reactions Lecture 16: Enzymes & Kinetics V: Mechanisms Margaret A. Daugherty Fall 2003 A B Catalysts (e.g. enzymes) act by lowering the transition state

More information

Chapter 15: Enyzmatic Catalysis

Chapter 15: Enyzmatic Catalysis Chapter 15: Enyzmatic Catalysis Voet & Voet: Pages 496-508 Slide 1 Catalytic Mechanisms Catalysis is a process that increases the rate at which a reaction approaches equilibrium Rate enhancement depends

More information

It s the amino acids!

It s the amino acids! Catalytic Mechanisms HOW do enzymes do their job? Reducing activation energy sure, but HOW does an enzyme catalysis reduce the energy barrier ΔG? Remember: The rate of a chemical reaction of substrate

More information

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

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

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

More information

[Urea] (M) k (s -1 )

[Urea] (M) k (s -1 ) BMB178 Fall 2018 Problem Set 1 Due: 10/26/2018, noon Office hour: 10/25/2018, SFL GSR218 7 9 pm Problem 1. Transition state theory (20 points): Consider a unimolecular reaction where a substrate S is converted

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

[Urea] (M) k (s -1 )

[Urea] (M) k (s -1 ) BMB178 Fall 2018 Problem Set 1 Due: 10/26/2018, noon Office hour: 10/25/2018, SFL GSR218 7 9 pm Problem 1. Transition state theory (20 points): Consider a unimolecular reaction where a substrate S is converted

More information

Membrane Proteins: 1. Integral proteins: 2. Peripheral proteins: 3. Amphitropic proteins:

Membrane 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 information

Chemistry Problem Set #9 Due on Thursday 11/15/18 in class.

Chemistry Problem Set #9 Due on Thursday 11/15/18 in class. Chemistry 391 - Problem Set #9 Due on Thursday 11/15/18 in class. Name 1. There is a real enzyme called cocaine esterase that is produced in bacteria that live at the base of the coca plant. The enzyme

More information

G. GENERAL ACID-BASE CATALYSIS

G. GENERAL ACID-BASE CATALYSIS G. GENERAL ACID-BASE CATALYSIS Towards a Better Chemical Mechanism via Catalysis There are two types of mechanisms we ll be discussing this semester. Kinetic mechanisms are concerned with rate constants

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 4. Examples of enzymatic reactions acid-base catalysis: give and take protons covalent catalysis: a transient covalent bond is formed between the enzyme and the substrate metal ion catalysis:

More information

2. Which of the following are nucleophiles and which are electrophiles?

2. Which of the following are nucleophiles and which are electrophiles? Life Sciences 1a ractice roblems 7 1. a) ow many intermediates are there in the reaction? b) ow many transition states are there? c) What is the fastest step in the reaction? d) Which is more stable, A

More information

Reading for today: Chapter 16 (selections from Sections A, B and C) Friday and Monday: Chapter 17 (Diffusion)

Reading for today: Chapter 16 (selections from Sections A, B and C) Friday and Monday: Chapter 17 (Diffusion) Lecture 29 Enzymes Reading for today: Chapter 6 (selections from Sections, B and C) Friday and Monday: Chapter 7 (Diffusion) 4/3/6 Today s Goals Michaelis-Menten mechanism for simple enzyme reactions:

More information

Enzymes I. Dr. Mamoun Ahram Summer semester,

Enzymes I. Dr. Mamoun Ahram Summer semester, Enzymes I Dr. Mamoun Ahram Summer semester, 2017-2018 Resources Mark's Basic Medical Biochemistry Other resources NCBI Bookshelf: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=books The Medical Biochemistry

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

Chapters 5-6 Enzymes. Catalyst: A substance that speeds up the rate of a chemical reaction but is not itself consumed.

Chapters 5-6 Enzymes. Catalyst: A substance that speeds up the rate of a chemical reaction but is not itself consumed. hapters 56 Enzymes atalyst: A substance that speeds up the rate of a chemical reaction but is not itself consumed. Most biological catalysts are proteins but some RA are catalysts too. e.g. Peptide bonds

More information

Mechanisms of catalysis

Mechanisms of catalysis Mechanisms of catalysis Proximity and orientation effects Proximity: Reaction between bound molecules doesn't require an improbable collision of 2 molecules -- they're already in "contact" (increases the

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

Two requirements for life: Self-replication and appropriate catalysis. A. Most enzymes (def.: biological catalysts) are proteins

Two requirements for life: Self-replication and appropriate catalysis. A. Most enzymes (def.: biological catalysts) are proteins Enzymes We must be able to enhance the rates of many physical and chemical processes to remain alive and healthy. Support for that assertion: Maladies of genetic origin. Examples: Sickle-cell anemia (physical)

More information

BSc and MSc Degree Examinations

BSc and MSc Degree Examinations Examination Candidate Number: Desk Number: BSc and MSc Degree Examinations 2018-9 Department : BIOLOGY Title of Exam: Molecular Biology and Biochemistry Part I Time Allowed: 1 hour and 30 minutes Marking

More information

Pyruvate is reduced to lactate in anaerobic metabolism in muscle cells

Pyruvate is reduced to lactate in anaerobic metabolism in muscle cells Pyruvate is reduced to lactate in anaerobic metabolism in muscle cells Transferases and hydrolases catalyze group transfer reactions Acyl transfer: Hexokinase catalyzes a phosphoryl transfer from ATP to

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

2013 W. H. Freeman and Company. 6 Enzymes

2013 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 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

Enzyme Kinetics 2014

Enzyme Kinetics 2014 V 41 Enzyme Kinetics 2014 Atkins Ch.23, Tinoco 4 th -Ch.8 Enzyme rxn example Catalysis/Mechanism: E + S k -1 ES k 1 ES E is at beginning and k 2 k -2 E + P at end of reaction Catalyst: No consumption of

More information

Principles of Enzyme Catalysis Arthur L. Haas, Ph.D. Department of Biochemistry and Molecular Biology

Principles of Enzyme Catalysis Arthur L. Haas, Ph.D. Department of Biochemistry and Molecular Biology Principles of Enzyme Catalysis Arthur L. Haas, Ph.D. Department of Biochemistry and Molecular Biology Review: Garrett and Grisham, Enzyme Specificity and Regulation (Chapt. 13) and Mechanisms of Enzyme

More information

BMB Lecture 2

BMB Lecture 2 BMB 178 2018 Lecture 2 How to map transition state Covalent Catalysis How to Map Transition States 1. Linear Free Energy Relationship 2. Kinetic Isotope Effects 3. Transition state analogues Linear Free

More information

Enzymes! Accelerate reactions by x 10 6 (and up to x ) Specific with respect to reaction catalized.

Enzymes! Accelerate reactions by x 10 6 (and up to x ) Specific with respect to reaction catalized. Enzymes! Accelerate reactions by x 10 6 (and up to x 10 19 ) Specific with respect to reaction catalized. Selective with respect to reagent recognized. Cartoon Guide to Genetics Gonick & Wheelis 1 Microreview

More information

Acid/Base catalysis Covalent catalysis Metal ion catalysis Electrostatic catalysis Proximity and orientation Preferential binding of the transition

Acid/Base catalysis Covalent catalysis Metal ion catalysis Electrostatic catalysis Proximity and orientation Preferential binding of the transition Enzyme catalysis Factors that contribute to catalytic power of enzymes Acid/Base catalysis Covalent catalysis Metal ion catalysis Electrostatic catalysis Proximity and orientation Preferential binding

More information

BMB Lecture Covalent Catalysis 2. General Acid-base catalysis

BMB Lecture Covalent Catalysis 2. General Acid-base catalysis BMB 178 2017 Lecture 3 1. Covalent Catalysis 2. General Acid-base catalysis Evidences for A Covalent Intermediate Direct Evidences: Direct observation of formation and disappearance of an intermediate

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 9 Biochemical Transformations I. Carbon-carbon bond forming and cleaving reactions in Biology (see the Lexicon). Enzymes catalyze a limited

More information

Catalytic power of enzymes

Catalytic power of enzymes Enzyme catalysis Catalytic power of enzymes Enzymatic reactions are involved in most biological processes. There is a major practical and fundamental interest in finding out what makes enzymes so efficient

More information

Catalysis. Instructor: Dr. Tsung-Lin Li Genomics Research Center Academia Sinica

Catalysis. Instructor: Dr. Tsung-Lin Li Genomics Research Center Academia Sinica Catalysis Instructor: Dr. Tsung-Lin Li Genomics Research Center Academia Sinica References: Biochemistry" by Donald Voet and Judith G. Voet Biochemistry" by Christopher K. Mathews, K. E. Van Hold and Kevin

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

Biochemistry 3100 Sample Problems Binding proteins, Kinetics & Catalysis

Biochemistry 3100 Sample Problems Binding proteins, Kinetics & Catalysis (1) Draw an approximate denaturation curve for a typical blood protein (eg myoglobin) as a function of ph. (2) Myoglobin is a simple, single subunit binding protein that has an oxygen storage function

More information

Chapter 14. Outline. How Much Enzyme-Induced Rate Accelerations?

Chapter 14. Outline.   How Much Enzyme-Induced Rate Accelerations? Chapter 14 Reginald H. Garrett Charles M. Grisham Mechanisms of Enzyme Action http://lms.ls.ntou.edu.tw/course/106 hanjia@mail.ntou.edu.tw il t Essential Questions Before this class, ask your self the

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

BIOLOGICAL SCIENCE. Lecture Presentation by Cindy S. Malone, PhD, California State University Northridge. FIFTH EDITION Freeman Quillin Allison

BIOLOGICAL 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 information

Exam 3 11/10/2014 Last Name (PRINT): First Name: Pg Topic Pts Total possible 3 Multiple. 12 choice 4 Multiple. 9 choice 5 Multiple

Exam 3 11/10/2014 Last Name (PRINT): First Name: Pg Topic Pts Total possible 3 Multiple. 12 choice 4 Multiple. 9 choice 5 Multiple Last Name (PRINT): First Name: Pg Topic Pts Total possible 3 Multiple 12 choice 4 Multiple 9 choice 5 Multiple 12 choice 6 Multiple 16 choice, start T/F 7 T/F and Fill in Blank 22 8 Binding problems 12

More information

Lec.1 Chemistry Of Water

Lec.1 Chemistry Of Water Lec.1 Chemistry Of Water Biochemistry & Medicine Biochemistry can be defined as the science concerned with the chemical basis of life. Biochemistry can be described as the science concerned with the chemical

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

Lecture 12. Metalloproteins - II

Lecture 12. Metalloproteins - II Lecture 12 Metalloproteins - II Metalloenzymes Metalloproteins with one labile coordination site around the metal centre are known as metalloenzyme. As with all enzymes, the shape of the active site is

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

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

L. LEWIS ACID CATALYSIS

L. LEWIS ACID CATALYSIS L. LEWIS ACID CATALYSIS Background Twenty amino acids is not enough. The breadth of chemistry handled by enzymes requires that additional chemical species be employed in catalysis. So-called cofactors

More information

Metabolism and enzymes

Metabolism 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 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

Overview of Kinetics

Overview 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 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

What is an enzyme? Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics. Margaret A. Daugherty Fall General Properties

What is an enzyme? Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics. Margaret A. Daugherty Fall General Properties Lecture 12: Enzymes & Kinetics I Introduction to Enzymes and Kinetics Margaret A. Daugherty Fall 2003 ENZYMES: Why, what, when, where, how? All but the who! What: proteins that exert kinetic control over

More information

Final Chem 4511/6501 Spring 2011 May 5, 2011 b Name

Final Chem 4511/6501 Spring 2011 May 5, 2011 b Name Key 1) [10 points] In RNA, G commonly forms a wobble pair with U. a) Draw a G-U wobble base pair, include riboses and 5 phosphates. b) Label the major groove and the minor groove. c) Label the atoms of

More information

4. What is the general expression Keq (the equilibrium constant) in terms of product and reactant concentration? tell us about the enzyme.

4. What is the general expression Keq (the equilibrium constant) in terms of product and reactant concentration? tell us about the enzyme. Section 8 Enzyme Kinetics Pre-Activity Assignment 1. Produce a reading log for the sections in your text that discuss the Michaelis-Menten equation and including kcat. 2. Focus on the derivation of the

More information

Biochemistry Enzyme kinetics

Biochemistry 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 information

Exam 4 April 15, 2005 CHEM 3511 Print Name: KEY Signature

Exam 4 April 15, 2005 CHEM 3511 Print Name: KEY Signature 1) (8 pts) General Properties of Enzymes. Give four properties of enzymaticallycatalyzed reactions. The answers should indicate how enzymatic reactions differ from non-enzymatic reactions. Write four only

More information

Unit 3. Enzymes. Catalysis and enzyme kinetics.

Unit 3. Enzymes. Catalysis and enzyme kinetics. Unit 3 Enzymes. Catalysis and enzyme kinetics. OUTLINE 3.1. Characteristics of biological catalysts. Coenzymes, cofactors, vitamins Enzyme nomenclature and classification 3.2. Enzyme catalysis. Transition

More information

Chapter 8. Enzymes: basic concept and kinetics

Chapter 8. Enzymes: basic concept and kinetics Chapter 8 Enzymes: basic concept and kinetics Learning objectives: mechanism of enzymatic catalysis Michaelis -Menton Model Inhibition Single Molecule of Enzymatic Reaction Enzymes: catalysis chemical

More information

Biological Chemistry and Metabolic Pathways

Biological Chemistry and Metabolic Pathways Biological Chemistry and Metabolic Pathways 1. Reaction a. Thermodynamics b. Kinetics 2. Enzyme a. Structure and Function b. Regulation of Activity c. Kinetics d. Inhibition 3. Metabolic Pathways a. REDOX

More information

2017 Ebneshahidi. Dr. Ali Ebneshahidi

2017 Ebneshahidi. Dr. Ali Ebneshahidi Dr. Ali Ebneshahidi A. Introduction Chemistry science that deals with the composition of substances and the changes that take place in their composition. Organic chemistry chemistry that deals with organic

More information

An Introduction to Metabolism. Chapter 8

An Introduction to Metabolism. Chapter 8 An Introduction to Metabolism Chapter 8 METABOLISM I. Introduction All of an organism s chemical reactions Thousands of reactions in a cell Example: digest starch use sugar for energy and to build new

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

Henderson - Hasselbalch equation

Henderson - Hasselbalch equation Structure & Properties of Water Bent geometry, O- bond length of 0.958Å Can form ydrogen bonds Comprehensive Exam eview 12/03/2009 enderson - asselbalch equation From [ ][ ] K = [ ] The 6 step approach

More information

CHEM 251 (4 credits): Description

CHEM 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 information

PETER PAZMANY CATHOLIC UNIVERSITY Consortium members SEMMELWEIS UNIVERSITY, DIALOG CAMPUS PUBLISHER

PETER 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 information

ATP ATP. The energy needs of life. Living economy. Where do we get the energy from? 9/11/2015. Making energy! Organisms are endergonic systems

ATP 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 information

Enzyme reactions mechanisms and Immobilization of enzymes

Enzyme reactions mechanisms and Immobilization of enzymes Enzyme reactions mechanisms and Immobilization of enzymes Lecture 18.11.2016 CHEM-E3140 Bioprocess Technology II Aalto University School of Chemical Technology Ossi Turunen 1 Reaction mechanisms 1) General

More information

Course Goals for CHEM 202

Course Goals for CHEM 202 Course Goals for CHEM 202 Students will use their understanding of chemical bonding and energetics to predict and explain changes in enthalpy, entropy, and free energy for a variety of processes and reactions.

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

Lecture 12: Burst Substrates and the V vs [S] Experiment

Lecture 12: Burst Substrates and the V vs [S] Experiment Biological Chemistry Laboratory Biology 3515/Chemistry 3515 Spring 2019 Lecture 12: Burst Substrates and the V vs [S] Experiment 14 February 2019 c David P. Goldenberg University of Utah goldenberg@biology.utah.edu

More information

An Introduction to Metabolism

An Introduction to Metabolism Chapter 8 An Introduction to Metabolism Edited by Shawn Lester PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by Erin Barley

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

Chapter 6 Overview. Enzymes. Catalysis most important function of proteins. Globular protein Increase rate of metabolic processes

Chapter 6 Overview. Enzymes. Catalysis most important function of proteins. Globular protein Increase rate of metabolic processes Chapter 6 Overview Enzymes Catalysis most important function of proteins n Enzymes protein catalysts Globular protein Increase rate of metabolic processes Enzymes kinetics info on reaction rates & measure

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

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

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

Department of Chemistry and Biochemistry University of Lethbridge. Biochemistry II. Bioenergetics

Department of Chemistry and Biochemistry University of Lethbridge. Biochemistry II. Bioenergetics Department of Chemistry and Biochemistry University of Lethbridge II. Bioenergetics Slide 1 Bioenergetics Bioenergetics is the quantitative study of energy relationships and energy conversion in biological

More information

An Introduction to Metabolism

An Introduction to Metabolism An Introduction to Metabolism Chapter 8 Objectives Distinguish between the following pairs of terms: catabolic and anabolic pathways; kinetic and potential energy; open and closed systems; exergonic and

More information

Chapter 6. Ground Rules Of Metabolism

Chapter 6. Ground Rules Of Metabolism Chapter 6 Ground Rules Of Metabolism Alcohol Dehydrogenase An enzyme Breaks down ethanol and other toxic alcohols Allows humans to drink Metabolism Is the totality of an organism s chemical reactions Arises

More information

Lecture 16 (10/23/17) Lecture 16 (10/23/17)

Lecture 16 (10/23/17) Lecture 16 (10/23/17) Lecture 16 (10/23/17) Reading: Ch6; 207-210 Ch6; 192-193, 195-196, 205-206 Problems: Ch6 (text); 18, 19, 20, 21, 22 Ch6 (study guide-facts); 9, 11 Ch6 (study guide-applying); 2 NEXT Reading: Ch6; 213-218

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

Enzymes as machines: how they work

Enzymes as machines: how they work Enzymes as machines: how they work Biophysical Society Summer Course 26 June 2014 Charlie Carter They are Just as Scared of You, As You are of Them Adapted from: Steve Cote, Chapel Hill artist Readings

More information

An Introduction to Metabolism

An Introduction to Metabolism LECTURE PRESENTATIONS For CAMPBELL BIOLOGY, NINTH EDITION Jane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson Chapter 8 An Introduction to Metabolism

More information

Ch 4: Cellular Metabolism, Part 1

Ch 4: Cellular Metabolism, Part 1 Developed by John Gallagher, MS, DVM Ch 4: Cellular Metabolism, Part 1 Energy as it relates to Biology Energy for synthesis and movement Energy transformation Enzymes and how they speed reactions Metabolism

More information

Brønsted Acid Proton donor Base Proton acceptor O CH 3 COH + H H 3 O + + CH 3 CO -

Brønsted Acid Proton donor Base Proton acceptor O CH 3 COH + H H 3 O + + CH 3 CO - hap 7. Acid and Bases Brønsted Acid Proton donor Base Proton acceptor 3 3 3-2 acid base conj. acid conj. base 3 2 S 4 3 - S 4 base acid conj. acid conj. base 6 5 N 2 N 2 6 5 N - N 3 acid base conj. base

More information

Chapter 5. Energy Flow in the Life of a Cell

Chapter 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 information

Chapter 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 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 information

489--Lectures 3 and 4. Fundamentals of Inorganic Chemistry

489--Lectures 3 and 4. Fundamentals of Inorganic Chemistry 489--Lectures 3 and 4 Fundamentals of Inorganic Chemistry (with special relevance to biological systems) Some slides courtesy of Prof. Xuan Zhao (U. Memphis) and Prof. Yi Lu (U. Illinois) Fundamentals

More information

2. In regards to the fluid mosaic model, which of the following is TRUE?

2. In regards to the fluid mosaic model, which of the following is TRUE? General Biology: Exam I Sample Questions 1. How many electrons are required to fill the valence shell of a neutral atom with an atomic number of 24? a. 0 the atom is inert b. 1 c. 2 d. 4 e. 6 2. In regards

More information

Lecture Series 9 Cellular Pathways That Harvest Chemical Energy

Lecture Series 9 Cellular Pathways That Harvest Chemical Energy Lecture Series 9 Cellular Pathways That Harvest Chemical Energy Reading Assignments Review Chapter 3 Energy, Catalysis, & Biosynthesis Read Chapter 13 How Cells obtain Energy from Food Read Chapter 14

More information

Enzymes are macromolecules (proteins) that act as a catalyst

Enzymes are macromolecules (proteins) that act as a catalyst Chapter 8.4 Enzymes Enzymes speed up metabolic reactions by lowering energy barriers Even though a reaction is spontaneous (exergonic) it may be incredibly slow Enzymes cause hydrolysis to occur at a faster

More information

9/25/2011. Outline. Overview: The Energy of Life. I. Forms of Energy II. Laws of Thermodynamics III. Energy and metabolism IV. ATP V.

9/25/2011. 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 information

An Introduction to Metabolism

An Introduction to Metabolism Chapter 8 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

An Introduction to Metabolism

An Introduction to Metabolism Chapter 8 An Introduction to Metabolism Dr. Wendy Sera Houston Community College Biology 1406 Key Concepts in Chapter 8 1. An organism s metabolism transforms matter and energy, subject to the laws of

More information

BIOLOGY 10/11/2014. An Introduction to Metabolism. Outline. Overview: The Energy of Life

BIOLOGY 10/11/2014. An Introduction to Metabolism. Outline. Overview: The Energy of Life 8 An Introduction to Metabolism CAMPBELL BIOLOGY TENTH EDITION Reece Urry Cain Wasserman Minorsky Jackson Outline I. Forms of Energy II. Laws of Thermodynamics III. Energy and metabolism IV. ATP V. Enzymes

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

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 Enzymes are biological macromolecules that increase the rate of the reaction. Six major groups of enzymes (pgs. 94-95/98-99) Oxidoreductases:

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