Biologisch-chemisches Praktikum, Teil B Peptide and protein chemistry

Size: px
Start display at page:

Download "Biologisch-chemisches Praktikum, Teil B Peptide and protein chemistry"

Transcription

1 Biologisch-chemisches Praktikum, Teil B Peptide and protein chemistry Part 2: Peptide synthesis (protease inhibitor) Protein labeling Protease inhibition assay Riboflavin analog: pk a change upon binding to protein Phytocyanin: folding, stability, non-covalent bonds 1

2 Solid-phase Peptide Synthesis Robert B. Merrifield 2

3 SPPS: Fmoc- and Boc-Strategy F TFA Fmoc Boc: 3

4 SPPS: Activators Carbodiimides: Triazoles: C DCC ATU PyBP C DIC BTU CTU CMU 4

5 ATU: eighbouring Group Effect 5

6 Proteases 6

7 Protease Inhibitors Reversible: BPTI Atazanavir Saquinavir Irreversible: PMSF E-64 7

8 Why Antipain Analog? Antipain Antipain analog Lysine is easier to couple and easier to deprotect. Methyl ester difficult to remove on resine and impossible in solution. iether of the modifications affects activity! 8

9 Urea Linker Formation Boc Boc Boc Boc Boc Boc Boc Boc C C C C C C 2 9

10 Two Compounds with the Same Mass Exact Mass: Molecular Weight: Exact Mass: Molecular Weight:

11 Trypsin Inhibition by Methyl-Antipain 0.5 D 410, AU VV = VV mmmmmm MMMMMMMM MMMMMMMM + KK ii Time, sec 11

12 Trypsin Inhibition by Methyl-Antipain: Fitting to Correct Equation 16 Trypsin inhibition by methyl-antipain R2K 0.5 mm L-BAPA, p 8.1, RT, µm trypsin 14 Rate, M/min Vo ± 0.22 E 0.56 ± Ki ± R2 = A K R2= [Me-AP R2K], M 12

13 Important!!! Please give unused synthesized inhibitor to me for purification! 13

14 Protein Labeling Purposes: Protein structure and dynamics Protein-protein and protein-ligand interactions Protein distribution, transport and fate in vivo Drug delivery Protein visualization Methods: Modification of native amino acids (mostly lysine and cysteine) Incorporation of modifieable unnatural amino acids Incorporation of pre-labeled peptides using native chemical ligation (CL) 14

15 Protein Labeling: Examples -ydroxysuccinimid (S) ester: Maleimide: Click reaction: 15

16 Thermodynamics of Protein Folding U F K ffffffffffffff = F U GG ffffffffffffff = RRRR ln KK ffffffffffffff = UU FF TT SS UU FF Bond breaking and formation Folding of peptide chain Release of structured water molecules For most globular proteins G folding = kcal/mol 16

17 Entropic Contributions to Protein Folding 17

18 Energetics and Kinetics of Folding Easy and fast Difficult and slow (or not) A.orwich. J. Clin Invest. 2002;110(9):

19 on-covalent Bonds in Protein Structure ydrophobic interactions Van der Waals interactions Ionic interactions ydrogen bonds Disruption of non-covalent bonds can: Provide information of their relative contribution to the structure Give estimate of protein s thermodynamic stabilty Allow study of protein folding kinetics/pathways 19

20 Protein Structure Disruptors (Denaturants) Chaotropic Agents a + - S C Denaturing Detergent a + S - Sodium dodecyl sulfate (SDS) 20

21 Phytocyanin Light-harvesting Antenna 21

22 Chromophore: Phycocyanobilin 22

23 Phycocyanobilin Bound to Phycocyanin C C 3 C C S Cys 23

24 Phycocyanobilin Free in Solution 24

25 Interior of Folded Proteins Provide Enviroment Very Different from Solution 25

26 pk a s of Amino Acids Differ on Protein Surface and in Protein Interior AA/Group Summary of measured amino acid pk a values in folded proteins pk a value in alanine pentapeptides Low pk a value Folded proteins igh pk a value Asp Glu is Cys Tyr Lys C-term term Grimsley, G. R., et al. (2009). Protein Sci 18(1):

27 Effects of Ligand (Substrate) Binding to Proteins Change in pk a Spectral properties Redox potentials Bond strength ucleo-/electrophilic properties Stereoselectivity 27

28 Riboflavin-binding Protein (RBP) from Chicken Egg Whites 220 amino acids Glycosilated (pos. 36 and 147) eavily phosphorilated (loop ) K d (Riboflavin) = 1.3 nm (p 6-9) Monaco,. L. (1997). EMB J 16(7):

29 Structures of Riboflavin and Its Derivatives Riboflavin Adenine Dinucleotide (FAD) Riboflavin Mononucleotide (FM) Riboflavin (vitamin B 2 ) P P

30 Spectra of Free and RBP-bound Riboflavin at Various p free bound Chenprakhon, P., et al. (2012). Journal of Chemical Education 89(6):

31 pk a Determination of Free and RBP-bound Riboflavin Fit to equation: AA oooooo = AA 1111 pppp + AA AA 1111 pppp aa 1111 pppp aa pppp Derived from: pppp = ppkk aa + log AA enderson-asselbalch equation Chenprakhon, P., et al. (2012). Journal of Chemical Education 89(6):

32 Using SciDAVis to fit pk a data AA oooooo = AA 1111 pppp + AA AA 1111 pppp aa 1111 pppp aa pppp a = 0,0899 +/- 0,00069 b = 0,127 +/- 0,00075 K = 10,01 +/- 0,045 R^2 = 0,

33 Using SciDAVis to fit pk a data Change! 33

34 eutral Red Riboflavin Analog

35 Why analog? Advantages: igher analytical wavelengths (no protein interference) Lower pk a Stronger signal Beautiful color Disadvatages: Weaker binding (2.2 µm at p 9.0) More expensive 35

36 Protein Folding in the GroEL/ES Chaperone Cage M. ayer-artl,, A. Bracher, F. U. artl. Trends in Biochem. Sciences Vol. 41, p

Nafith Abu Tarboush DDS, MSc, PhD

Nafith Abu Tarboush DDS, MSc, PhD Nafith Abu Tarboush DDS, MSc, PhD natarboush@ju.edu.jo www.facebook.com/natarboush Protein conformation Many conformations are possible for proteins due to flexibility of amino acids linked by peptide

More information

Exams written in pencil or erasable ink will not be re-graded under any circumstances.

Exams written in pencil or erasable ink will not be re-graded under any circumstances. Biochemistry 461, Section I May 21, 1998 Final Exam Prof. Jason D. Kahn Your Printed ame: Your SS#: Your Signature: You have 120 minutes for this exam. The exam has 7 questions, worth 200 points. Do all

More information

Name. The following exam contains 44 questions, valued at 2.6 points/question. 2. Which of the following is not a principal use of proteins?

Name. The following exam contains 44 questions, valued at 2.6 points/question. 2. Which of the following is not a principal use of proteins? Chemistry 131 Exam 3 Practice Proteins, Enzymes, and Carbohydrates Spring 2018 Name The following exam contains 44 questions, valued at 2.6 points/question 1. Which of the following is a protein? a. Amylase

More information

Midterm 1 Last, First

Midterm 1 Last, First Midterm 1 BIS 105 Prof. T. Murphy April 23, 2014 There should be 6 pages in this exam. Exam instructions (1) Please write your name on the top of every page of the exam (2) Show all work for full credit

More information

Objective: You will be able to explain how the subcomponents of

Objective: You will be able to explain how the subcomponents of Objective: You will be able to explain how the subcomponents of nucleic acids determine the properties of that polymer. Do Now: Read the first two paragraphs from enduring understanding 4.A Essential knowledge:

More information

Chapter 3. Structure of Enzymes. Enzyme Engineering

Chapter 3. Structure of Enzymes. Enzyme Engineering Chapter 3. Structure of Enzymes Enzyme Engineering 3.1 Introduction With purified protein, Determining M r of the protein Determining composition of amino acids and the primary structure Determining the

More information

Reading from the NCBI

Reading from the NCBI Reading from the NCBI http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=thermodyn amics&rid=stryer.section.156#167 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=stability,pr otein&rid=stryer.section.365#371

More information

Properties of amino acids in proteins

Properties of amino acids in proteins Properties of amino acids in proteins one of the primary roles of DNA (but far from the only one!!!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids

More information

Chapter 23 Enzymes 1

Chapter 23 Enzymes 1 Chapter 23 Enzymes 1 Enzymes Ribbon diagram of cytochrome c oxidase, the enzyme that directly uses oxygen during respiration. 2 Enzyme Catalysis Enzyme: A biological catalyst. With the exception of some

More information

Practice Problems 3. a. What is the name of the bond formed between two amino acids? Are these bonds free to rotate?

Practice Problems 3. a. What is the name of the bond formed between two amino acids? Are these bonds free to rotate? Life Sciences 1a Practice Problems 3 1. Draw the oligopeptide for Ala-Phe-Gly-Thr-Asp. You do not need to indicate the stereochemistry of the sidechains. Denote with arrows the bonds formed between the

More information

An Introduction to Enzyme and Coenzyme Chemistry, 2nd Ed. T. D. H. Bugg, Blackwell Science, Oxford, 2004

An Introduction to Enzyme and Coenzyme Chemistry, 2nd Ed. T. D. H. Bugg, Blackwell Science, Oxford, 2004 Combinatorial synthesis of linchpin β-turn mimic 1 2 DCC, BT 1 2 n -tbu 1 n -tbu 1) 2 FMC DCC, BT 2) piperidine 1 2 2 n -tbu 3 DCC, BT 1 2 n -tbu 3 1) Ph 3 P 2) cyclization 3) CF 3 C 2 2 1 n 3 2 Evaluated

More information

BIOCHEMISTRY 460 FIRST HOUR EXAMINATION FORM A (yellow) ANSWER KEY February 11, 2008

BIOCHEMISTRY 460 FIRST HOUR EXAMINATION FORM A (yellow) ANSWER KEY February 11, 2008 WRITE YOUR AND I.D. NUMBER LEGIBLY ON EVERY PAGE PAGES WILL BE SEPARATED FOR GRADING! CHECK TO BE SURE YOU HAVE 6 PAGES, (print): ANSWERS INCLUDING COVER PAGE. I swear/affirm that I have neither given

More information

Chemical Mechanism of Enzymes

Chemical Mechanism of Enzymes Chemical Mechanism of Enzymes Enzyme Engineering 5.2 Definition of the mechanism 1. The sequence from substrate(s) to product(s) : Reaction steps 2. The rates at which the complex are interconverted 3.

More information

AP Bio. Protiens Chapter 5 1

AP Bio. Protiens Chapter 5 1 Concept.4: Proteins have many structures, resulting in a wide range of functions Proteins account for more than 0% of the dry mass of most cells Protein functions include structural support, storage, transport,

More information

Proteins. Amino acids, structure and function. The Nobel Prize in Chemistry 2012 Robert J. Lefkowitz Brian K. Kobilka

Proteins. Amino acids, structure and function. The Nobel Prize in Chemistry 2012 Robert J. Lefkowitz Brian K. Kobilka Proteins Amino acids, structure and function The Nobel Prize in Chemistry 2012 Robert J. Lefkowitz Brian K. Kobilka O O HO N N HN OH Ser65-Tyr66-Gly67 The Nobel prize in chemistry 2008 Osamu Shimomura,

More information

PROTEINS. Amino acids are the building blocks of proteins. Acid L-form * * Lecture 6 Macromolecules #2 O = N -C -C-O.

PROTEINS. Amino acids are the building blocks of proteins. Acid L-form * * Lecture 6 Macromolecules #2 O = N -C -C-O. Proteins: Linear polymers of amino acids workhorses of the cell tools, machines & scaffolds Lecture 6 Macromolecules #2 PRTEINS 1 Enzymes catalysts that mediate reactions, increase reaction rate Structural

More information

The MOLECULES of LIFE

The MOLECULES of LIFE The MOLECULES of LIFE Physical and Chemical Principles Solutions Manual Prepared by James Fraser and Samuel Leachman Chapter 16 Principles of Enzyme Catalysis Problems True/False and Multiple Choice 1.

More information

Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A

Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A Biological systems interact, and these systems and their interactions possess complex properties. STOP at enduring understanding 4A Homework Watch the Bozeman video called, Biological Molecules Objective:

More information

ENZYMES: CLASSIFICATION, STRUCTURE

ENZYMES: CLASSIFICATION, STRUCTURE ENZYMES: CLASSIFICATION, STRUCTURE Enzymes - catalysts of biological reactions Accelerate reactions by a millions fold Common features for enzymes and inorganic catalysts: 1. Catalyze only thermodynamically

More information

Lecture 18 (10/27/17) Lecture 18 (10/27/17)

Lecture 18 (10/27/17) Lecture 18 (10/27/17) Reading: Ch6; 225-232 Lecture 18 (10/27/17) Problems: Ch5 (text); 2 Ch6 (study guide-facts); 5, 6, 7, 14 NEXT Reading: Ch5; 164, 166-169 Problems: none Remember Monday at 6:30 in PHO-206 is the first MB

More information

Proteins are sometimes only produced in one cell type or cell compartment (brain has 15,000 expressed proteins, gut has 2,000).

Proteins are sometimes only produced in one cell type or cell compartment (brain has 15,000 expressed proteins, gut has 2,000). Lecture 2: Principles of Protein Structure: Amino Acids Why study proteins? Proteins underpin every aspect of biological activity and therefore are targets for drug design and medicinal therapy, and in

More information

AA s are the building blocks of proteins

AA s are the building blocks of proteins Chamras Chemistry 106 Lecture otes Chapter 24: Amino Acids, Peptides, and Proteins General Formula: () n (') α-amino Acids: (n = 1) Example: Amino Acids and Proteins: Glycine Alanine Valine AA s are the

More information

Biomolecules: amino acids

Biomolecules: amino acids Biomolecules: amino acids Amino acids Amino acids are the building blocks of proteins They are also part of hormones, neurotransmitters and metabolic intermediates There are 20 different amino acids in

More information

9/11/18. Cell Function & Chemistry. Molecular and Cellular Biology. 2. Bio-Chemical Foundations & Key Molecules of a Cell

9/11/18. Cell Function & Chemistry. Molecular and Cellular Biology. 2. Bio-Chemical Foundations & Key Molecules of a Cell Molecular and Cellular Biology Cell Function & Chemistry 2. Bio-Chemical Foundations & Key Molecules of a Cell Prof. Dr. Klaus Heese Interaction Molecular Bonds Define Cellular Functions Water H 2 O Interactions

More information

Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Concept 5.4: Proteins have many structures, resulting in a wide range of functions Proteins account for more than 50% of the dry mass of most cells Protein functions include structural support, storage,

More information

Chapter 6. Flow of energy through life. Chemical reactions of life. Examples. Examples. Chemical reactions & energy 9/7/2012. Enzymes & Metabolism

Chapter 6. Flow of energy through life. Chemical reactions of life. Examples. Examples. Chemical reactions & energy 9/7/2012. Enzymes & Metabolism Flow of energy through life Chapter 6 Life is built on chemical reactions Enzymes & Metabolism Chemical reactions of life Examples Metabolism Forming bonds between molecules Dehydration synthesis Anabolic

More information

Electronic Supplementary Information. Table of Contents

Electronic Supplementary Information. Table of Contents Electronic Supplementary Information Examination of native chemical ligation using peptidyl prolyl thioester Takahiro Nakamura, Akira Shigenaga, Kohei Sato, Yusuke Tsuda, Ken Sakamoto, and Akira Otaka*

More information

2. Which of the following amino acids is most likely to be found on the outer surface of a properly folded protein?

2. Which of the following amino acids is most likely to be found on the outer surface of a properly folded protein? Name: WHITE Student Number: Answer the following questions on the computer scoring sheet. 1 mark each 1. Which of the following amino acids would have the highest relative mobility R f in normal thin layer

More information

Chapter 6. Metabolism & Enzymes. AP Biology

Chapter 6. Metabolism & Enzymes. AP Biology Chapter 6. Metabolism & Enzymes Flow of energy through life Life is built on chemical reactions Chemical reactions of life Metabolism forming bonds between molecules dehydration synthesis anabolic reactions

More information

Examples. Chapter 8. Metabolism & Enzymes. Flow of energy through life. Examples. Chemical reactions of life. Chemical reactions & energy

Examples. Chapter 8. Metabolism & Enzymes. Flow of energy through life. Examples. Chemical reactions of life. Chemical reactions & energy WH Examples dehydration synthesis Chapter 8 Metabolism & Enzymes + H 2 O hydrolysis + H 2 O Flow of energy through life Life is built on chemical reactions Examples dehydration synthesis hydrolysis 2005-2006

More information

The Structure and Function of Large Biological Molecules Part 4: Proteins Chapter 5

The Structure and Function of Large Biological Molecules Part 4: Proteins Chapter 5 Key Concepts: The Structure and Function of Large Biological Molecules Part 4: Proteins Chapter 5 Proteins include a diversity of structures, resulting in a wide range of functions Proteins Enzymatic s

More information

Supplementary Materials for

Supplementary Materials for advances.sciencemag.org/cgi/content/full/2/1/e1500678/dc1 Supplementary Materials for Chemical synthesis of erythropoietin glycoforms for insights into the relationship between glycosylation pattern and

More information

Metabolism & Enzymes. From food webs to the life of a cell. Flow of energy through life. Life is built on chemical reactions

Metabolism & Enzymes. From food webs to the life of a cell. Flow of energy through life. Life is built on chemical reactions Metabolism & Enzymes 2007-2008 From food webs to the life of a cell energy energy energy Flow of energy through life Life is built on chemical reactions transforming energy from one form to another organic

More information

Biological Sciences 4087 Exam I 9/20/11

Biological Sciences 4087 Exam I 9/20/11 Name: Biological Sciences 4087 Exam I 9/20/11 Total: 100 points Be sure to include units where appropriate. Show all calculations. There are 5 pages and 11 questions. 1.(20pts)A. If ph = 4.6, [H + ] =

More information

Chapter 5. Macromolecules

Chapter 5. Macromolecules Chapter 5. Macromolecules Macromolecules Smaller organic molecules join together to form larger molecules macromolecules 4 major classes of macromolecules: carbohydrates lipids proteins nucleic acids Polymers

More information

UNIVERSITY OF GUELPH CHEM 4540 ENZYMOLOGY Winter 2005 Quiz #2: March 24, 2005, 11:30 12:50 Instructor: Prof R. Merrill ANSWERS

UNIVERSITY OF GUELPH CHEM 4540 ENZYMOLOGY Winter 2005 Quiz #2: March 24, 2005, 11:30 12:50 Instructor: Prof R. Merrill ANSWERS UNIVERSITY F GUELPH CHEM 4540 ENZYMLGY Winter 2005 Quiz #2: March 24, 2005, 11:30 12:50 Instructor: Prof R. Merrill ANSWERS Instructions: Time allowed = 80 minutes. Total marks = 30. This quiz represents

More information

Short polymer. Dehydration removes a water molecule, forming a new bond. Longer polymer (a) Dehydration reaction in the synthesis of a polymer

Short polymer. Dehydration removes a water molecule, forming a new bond. Longer polymer (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3 H HO H Short polymer Dehydration removes a water molecule, forming a new bond Unlinked monomer H 2 O HO 1 2 3 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3

More information

Macromolecules of Life -3 Amino Acids & Proteins

Macromolecules of Life -3 Amino Acids & Proteins Macromolecules of Life -3 Amino Acids & Proteins Shu-Ping Lin, Ph.D. Institute of Biomedical Engineering E-mail: splin@dragon.nchu.edu.tw Website: http://web.nchu.edu.tw/pweb/users/splin/ Amino Acids Proteins

More information

GRU3L1 Metabolism & Enzymes. AP Biology

GRU3L1 Metabolism & Enzymes. AP Biology GRU3L1 Metabolism & Enzymes From food webs to the life of a cell energy energy energy Flow of energy through life Life is built on chemical reactions u transforming energy from one form to organic molecules

More information

Chapter 11: Enzyme Catalysis

Chapter 11: Enzyme Catalysis Chapter 11: Enzyme Catalysis Matching A) high B) deprotonated C) protonated D) least resistance E) motion F) rate-determining G) leaving group H) short peptides I) amino acid J) low K) coenzymes L) concerted

More information

Distribution of the amino acids in Nature Frequency in proteins (%)

Distribution of the amino acids in Nature Frequency in proteins (%) Distribution of the amino acids in ature Amino Acid Frequency in proteins (%) Leucine Alanine Glycine erine Valine Glutamic acid Threonine Arginine Lysine Aspartic acid Isoleucine Proline Asparagine Glutamine

More information

Enzymes: The Catalysts of Life

Enzymes: The Catalysts of Life Chapter 6 Enzymes: The Catalysts of Life Lectures by Kathleen Fitzpatrick Simon Fraser University Activation Energy and the Metastable State Many thermodynamically feasible reactions in a cell that could

More information

For questions 1-4, match the carbohydrate with its size/functional group name:

For questions 1-4, match the carbohydrate with its size/functional group name: Chemistry 11 Fall 2013 Examination #5 PRACTICE 1 For the first portion of this exam, select the best answer choice for the questions below and mark the answers on your scantron. Then answer the free response

More information

Enzyme Catalytic Mechanisms. Dr. Kevin Ahern

Enzyme Catalytic Mechanisms. Dr. Kevin Ahern Enzyme Catalytic Mechanisms Dr. Kevin Ahern Cleave Peptide Bonds Specificity of Cutting Common Active Site Composition/Structure Mechanistically Well Studied Chymotrypsin Chymotrypsin Catalysis H2O Chymotrypsin

More information

Enzymes. Ms. Paxson. From food webs to the life of a cell. Enzymes. Metabolism. Flow of energy through life. Examples. Examples

Enzymes. Ms. Paxson. From food webs to the life of a cell. Enzymes. Metabolism. Flow of energy through life. Examples. Examples From food webs to the life of a cell energy energy energy Flow of energy through life Life is built on chemical reactions sun transforming energy from one form to another solar energy ATP & organic molecules

More information

Macromolecules Structure and Function

Macromolecules Structure and Function Macromolecules Structure and Function Within cells, small organic molecules (monomers) are joined together to form larger molecules (polymers). Macromolecules are large molecules composed of thousands

More information

Methionine (Met or M)

Methionine (Met or M) Fig. 5-17 Nonpolar Fig. 5-17a Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Polar Trypotphan (Trp

More information

Previous Class. Today. Detection of enzymatic intermediates: Protein tyrosine phosphatase mechanism. Protein Kinase Catalytic Properties

Previous Class. Today. Detection of enzymatic intermediates: Protein tyrosine phosphatase mechanism. Protein Kinase Catalytic Properties Previous Class Detection of enzymatic intermediates: Protein tyrosine phosphatase mechanism Today Protein Kinase Catalytic Properties Protein Phosphorylation Phosphorylation: key protein modification

More information

Biological Molecules Ch 2: Chemistry Comes to Life

Biological Molecules Ch 2: Chemistry Comes to Life Outline Biological Molecules Ch 2: Chemistry Comes to Life Biol 105 Lecture 3 Reading Chapter 2 (pages 31 39) Biological Molecules Carbohydrates Lipids Amino acids and Proteins Nucleotides and Nucleic

More information

Lipids: diverse group of hydrophobic molecules

Lipids: diverse group of hydrophobic molecules Lipids: diverse group of hydrophobic molecules Lipids only macromolecules that do not form polymers li3le or no affinity for water hydrophobic consist mostly of hydrocarbons nonpolar covalent bonds fats

More information

Introduction to Peptide Sequencing

Introduction to Peptide Sequencing Introduction to Peptide equencing Quadrupole Ion Traps tructural Biophysics Course December 3, 2014 12/8/14 Introduction to Peptide equencing - athan Yates 1 Why are ion traps used to sequence peptides?

More information

Previous Class. Today. Term test I discussions. Detection of enzymatic intermediates: chymotrypsin mechanism

Previous Class. Today. Term test I discussions. Detection of enzymatic intermediates: chymotrypsin mechanism Term test I discussions Previous Class Today Detection of enzymatic intermediates: chymotrypsin mechanism Mechanistic Understanding of Enzymemediated Reactions Ultimate goals: Identification of the intermediates,

More information

Qualitative test of protein-lab2

Qualitative test of protein-lab2 1- Qualitative chemical reactions of amino acid protein functional groups: Certain functional groups in proteins can react to produce characteristically colored products. The color intensity of the product

More information

Beta Amyloid Peptides

Beta Amyloid Peptides Beta Amyloid Peptides The Most Comprehensive Collection for Alzheimer s Disease Academic Services Pharmaceutical Services Beta Amyloid Peptides The Most Comprehensive Collection for Alzheimer s Disease

More information

Organic Molecules: Proteins

Organic Molecules: Proteins Organic Molecules: Proteins Proteins Most structurally & functionally diverse group Function: involved in almost everything enzymes (pepsin, DNA polymerase) structure (keratin, collagen) carriers & transport

More information

AP Biology. Metabolism & Enzymes

AP Biology. Metabolism & Enzymes Metabolism & Enzymes From food webs to the life of a cell energy energy energy Flow of energy through life Life is built on chemical reactions transforming energy from one form to another organic molecules

More information

A Chemical Look at Proteins: Workhorses of the Cell

A Chemical Look at Proteins: Workhorses of the Cell A Chemical Look at Proteins: Workhorses of the Cell A A Life ciences 1a Lecture otes et 4 pring 2006 Prof. Daniel Kahne Life requires chemistry 2 amino acid monomer and it is proteins that make the chemistry

More information

Multiple-Choice Questions Answer ALL 20 multiple-choice questions on the Scantron Card in PENCIL

Multiple-Choice Questions Answer ALL 20 multiple-choice questions on the Scantron Card in PENCIL Multiple-Choice Questions Answer ALL 20 multiple-choice questions on the Scantron Card in PENCIL For Questions 1-10 choose ONE INCORRECT answer. 1. Which ONE of the following statements concerning the

More information

An efficient methodology to introduce o-(aminomethyl) phenyl-boronic acids into peptides: alkylation of secondary amines

An efficient methodology to introduce o-(aminomethyl) phenyl-boronic acids into peptides: alkylation of secondary amines Electronic Supplementary Material (ESI) for ew Journal of Chemistry. This journal is The Royal Society of Chemistry and the Centre ational de la Recherche Scientifique 2016 An efficient methodology to

More information

Proteins. (b) Protein Structure and Conformational Change

Proteins. (b) Protein Structure and Conformational Change Proteins (b) Protein Structure and Conformational Change Protein Structure and Conformational Change Proteins contain the elements carbon (C), hydrogen (H), oxygen (O2) and nitrogen (N2) Some may also

More information

For questions 1-4, match the carbohydrate with its size/functional group name:

For questions 1-4, match the carbohydrate with its size/functional group name: Chemistry 11 Fall 2013 Examination #5 PRACTICE 1 ANSWERS For the first portion of this exam, select the best answer choice for the questions below and mark the answers on your scantron. Then answer the

More information

CHAPTER 9: CATALYTIC STRATEGIES. Chess vs Enzymes King vs Substrate

CHAPTER 9: CATALYTIC STRATEGIES. Chess vs Enzymes King vs Substrate CHAPTER 9: CATALYTIC STRATEGIES Chess vs Enzymes King vs Substrate INTRODUCTION CHAPTER 9 What are the sources of the catalytic power and specificity of enzymes? Problems in reactions in cells Neutral

More information

increase rate of reaction without being consumed reduce activation energy don t change free energy ( G) released or required

increase rate of reaction without being consumed reduce activation energy don t change free energy ( G) released or required Enzymes Enzymes Biological catalysts proteins (& RNA) facilitate chemical reactions increase rate of reaction without being consumed reduce activation energy don t change free energy ( G) released or required

More information

Review of Energetics Intro

Review of Energetics Intro Review of Energetics Intro Learning Check The First Law of Thermodynamics states that energy can be Created Destroyed Converted All of the above Learning Check The second law of thermodynamics essentially

More information

Amino acids. Side chain. -Carbon atom. Carboxyl group. Amino group

Amino acids. Side chain. -Carbon atom. Carboxyl group. Amino group PROTEINS Amino acids Side chain -Carbon atom Amino group Carboxyl group Amino acids Primary structure Amino acid monomers Peptide bond Peptide bond Amino group Carboxyl group Peptide bond N-terminal (

More information

PAPER No. : 16, Bioorganic and biophysical chemistry MODULE No. : 22, Mechanism of enzyme catalyst reaction (I) Chymotrypsin

PAPER No. : 16, Bioorganic and biophysical chemistry MODULE No. : 22, Mechanism of enzyme catalyst reaction (I) Chymotrypsin Subject Paper No and Title 16 Bio-organic and Biophysical Module No and Title 22 Mechanism of Enzyme Catalyzed reactions I Module Tag CHE_P16_M22 Chymotrypsin TABLE OF CONTENTS 1. Learning outcomes 2.

More information

Oxidative Phosphorylation

Oxidative Phosphorylation Oxidative Phosphorylation Energy from Reduced Fuels Is Used to Synthesize ATP in Animals Carbohydrates, lipids, and amino acids are the main reduced fuels for the cell. Electrons from reduced fuels are

More information

Proteins. Bởi: OpenStaxCollege

Proteins. Bởi: OpenStaxCollege Proteins Bởi: OpenStaxCollege Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory,

More information

Molecular and Cellular Biology. 2. Bio-Chemical Foundations & Key Molecules of a Cell

Molecular and Cellular Biology. 2. Bio-Chemical Foundations & Key Molecules of a Cell Molecular and Cellular Biology 2. Bio-Chemical Foundations & Key Molecules of a Cell Prof. Dr. Klaus Heese Cell Function & Chemistry Interaction 1 Molecular Bonds Define Cellular Functions Interactions

More information

CS612 - Algorithms in Bioinformatics

CS612 - Algorithms in Bioinformatics Spring 2016 Protein Structure February 7, 2016 Introduction to Protein Structure A protein is a linear chain of organic molecular building blocks called amino acids. Introduction to Protein Structure Amine

More information

This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is worth 2 points.

This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is worth 2 points. MBB 407/511 Molecular Biology and Biochemistry First Examination - October 1, 2002 Name Social Security Number This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is

More information

Protein. An Introduction to Protein Structure and Denaturation by Acidification and Temperature Acid. By Noel Ways

Protein. An Introduction to Protein Structure and Denaturation by Acidification and Temperature Acid. By Noel Ways Protein An Introduction to Protein Structure and Denaturation by Acidification and Temperature Acid By oel Ways Amino Acids and Protein Structure A protein is a polymer of amino acids that obtains a unique

More information

Third Exam Practice Test

Third Exam Practice Test Third Exam Practice Test 1. A mixture of aspartic acid, methionine and arginine can be separated by electrophoresis. Explain how this would be done and what exactly happens during the separation. What

More information

The building blocks of life.

The building blocks of life. The building blocks of life. All the functions of the cell are based on chemical reactions. the building blocks of organisms BIOMOLECULE MONOMER POLYMER carbohydrate monosaccharide polysaccharide lipid

More information

University of Nevada, Reno. Active Insulin Analogs That Do Not Require Refrigeration

University of Nevada, Reno. Active Insulin Analogs That Do Not Require Refrigeration University of Nevada, Reno Active Insulin Analogs That Do Not Require Refrigeration A thesis submitted in partial fulfillment of the requirements for the degree of BACHELORS OF SCIENCE IN BIOLOGY/MOLECULAR

More information

Supplementary Information

Supplementary Information Supplementary Information Efficient use of the Dmab Protecting Group: Applications for the Solid-Phase Synthesis of N- Linked Glycopeptides Trent Conroy, Katrina A. Jolliffe and Richard J. Payne* School

More information

Lecture 5- DNA Arrays and Introduction to Protein Structure and Function. Light directed synthesis of oligonucleotides NVTR O O O O O BPG BPG BPG BPG

Lecture 5- DNA Arrays and Introduction to Protein Structure and Function. Light directed synthesis of oligonucleotides NVTR O O O O O BPG BPG BPG BPG Lecture 5- D rrays and Introduction to Protein tructure and Function Light directed synthesis of oligonucleotides 2 itroveratryloxy group PG >300nm light PG PG C 2 PG C VT P PG Can now undergo another

More information

Hydrogen Bonds and Biological Activities

Hydrogen Bonds and Biological Activities ugo Kubinyi, www.kubinyi.de ydrogen Bonds and Biological Activities ugo Kubinyi Germany EMail kubinyi@tonline.de omepage www.kubinyi.de ugo Kubinyi, www.kubinyi.de ature of the ydrogen Bond C=... a hydrogen

More information

The three important structural features of proteins:

The three important structural features of proteins: The three important structural features of proteins: a. Primary (1 o ) The amino acid sequence (coded by genes) b. Secondary (2 o ) The interaction of amino acids that are close together or far apart in

More information

CHAPTER 21: Amino Acids, Proteins, & Enzymes. General, Organic, & Biological Chemistry Janice Gorzynski Smith

CHAPTER 21: Amino Acids, Proteins, & Enzymes. General, Organic, & Biological Chemistry Janice Gorzynski Smith CHAPTER 21: Amino Acids, Proteins, & Enzymes General, Organic, & Biological Chemistry Janice Gorzynski Smith CHAPTER 21: Amino Acids, Proteins, Enzymes Learning Objectives: q The 20 common, naturally occurring

More information

Protein structure. Dr. Mamoun Ahram Summer semester,

Protein structure. Dr. Mamoun Ahram Summer semester, Protein structure Dr. Mamoun Ahram Summer semester, 2017-2018 Overview of proteins Proteins have different structures and some have repeating inner structures, other do not. A protein may have gazillion

More information

Molecular Graphics Perspective of Protein Structure and Function

Molecular Graphics Perspective of Protein Structure and Function Molecular Graphics Perspective of Protein Structure and Function VMD Highlights > 20,000 registered Users Platforms: Unix (16 builds) Windows MacOS X Display of large biomolecules and simulation trajectories

More information

3150:112 SAMPLE TEST 2. Print out a copy Answer the questions on your own. Check the answers at GOBC Ans.pdf. Good Luck!

3150:112 SAMPLE TEST 2. Print out a copy Answer the questions on your own. Check the answers at GOBC Ans.pdf. Good Luck! SAMPLE TEST 2 3150:112 Print out a copy Answer the questions on your own. Check the answers at GOBC Ans.pdf. Good Luck! QUESTIONS 1-3 REFER TO TE FOLLOWING: A. C 2 O O B. C 2 O O O C 2 O C. O C 2 O 1.

More information

Development of a Cell-penetrating Peptide that Exhibits Responsive. Changes in its Secondary Structure in the Cellular Environment

Development of a Cell-penetrating Peptide that Exhibits Responsive. Changes in its Secondary Structure in the Cellular Environment Development of a Cell-penetrating Peptide that Exhibits Responsive Changes in its Secondary Structure in the Cellular Environment iroko Yamashita, 1 Takuma Kato, 2 Makoto ba, 2 Takashi Misawa, 1 Takayuki

More information

Chapter 8. Metabolism. Topics in lectures 15 and 16. Chemical foundations Catabolism Biosynthesis

Chapter 8. Metabolism. Topics in lectures 15 and 16. Chemical foundations Catabolism Biosynthesis Chapter 8 Topics in lectures 15 and 16 Metabolism Chemical foundations Catabolism Biosynthesis 1 Metabolism Chemical Foundations Enzymes REDOX Catabolism Pathways Anabolism Principles and pathways 2 Chemical

More information

7/11/17. Cell Function & Chemistry. Molecular and Cellular Biology. 2. Bio-Chemical Foundations & Key Molecules of a Cell

7/11/17. Cell Function & Chemistry. Molecular and Cellular Biology. 2. Bio-Chemical Foundations & Key Molecules of a Cell Molecular and Cellular Biology Cell Function & Chemistry 2. Bio-Chemical Foundations & Key Molecules of a Cell Prof. Dr. Klaus Heese Interaction Molecular Bonds Define Cellular Functions Water H 2 O Interactions

More information

LAB#23: Biochemical Evidence of Evolution Name: Period Date :

LAB#23: Biochemical Evidence of Evolution Name: Period Date : LAB#23: Biochemical Evidence of Name: Period Date : Laboratory Experience #23 Bridge Worth 80 Lab Minutes If two organisms have similar portions of DNA (genes), these organisms will probably make similar

More information

Lecture 15. Membrane Proteins I

Lecture 15. Membrane Proteins I Lecture 15 Membrane Proteins I Introduction What are membrane proteins and where do they exist? Proteins consist of three main classes which are classified as globular, fibrous and membrane proteins. A

More information

Bioinformatics for molecular biology

Bioinformatics for molecular biology Bioinformatics for molecular biology Structural bioinformatics tools, predictors, and 3D modeling Structural Biology Review Dr Research Scientist Department of Microbiology, Oslo University Hospital -

More information

Reading Assignments. A. Energy and Energy Conversions. Lecture Series 9 Cellular Pathways That Harvest Chemical Energy. gasoline) or elevated mass.

Reading Assignments. A. Energy and Energy Conversions. Lecture Series 9 Cellular Pathways That Harvest Chemical Energy. gasoline) or elevated mass. 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

BIO th September, 1997

BIO th September, 1997 BIO 451 26th September, 1997 EXAM I This exam will be taken apart for grading. Please PRINT your name on each page. If you do not have sufficient room for your answer in the space provided, please continue

More information

Bielkoviny, enzýmy. Július Cirák. Protein Structure Timothy G. Standish

Bielkoviny, enzýmy. Július Cirák. Protein Structure Timothy G. Standish Bielkoviny, enzýmy Július irák Alanine Acid Different Amino Acid lasses 2 on-polar Aspartic acid 2 Amine Generic 2? R Acid Basic Polar istidine 2 S 2 + ysteine Levels f Protein rganization Primary Structure

More information

BIO 311C Spring Lecture 15 Friday 26 Feb. 1

BIO 311C Spring Lecture 15 Friday 26 Feb. 1 BIO 311C Spring 2010 Lecture 15 Friday 26 Feb. 1 Illustration of a Polypeptide amino acids peptide bonds Review Polypeptide (chain) See textbook, Fig 5.21, p. 82 for a more clear illustration Folding and

More information

Supporting Information. Recyclable hypervalent-iodine-mediated solid-phase peptide

Supporting Information. Recyclable hypervalent-iodine-mediated solid-phase peptide Supporting Information Recyclable hypervalent-iodine-mediated solid-phase peptide synthesis and cyclic peptide synthesis Dan Liu, Ya-Li Guo, Jin Qu and Chi Zhang* for Address: State Key Laboratory of Elemento-Organic

More information

Enzymes and Metabolism

Enzymes and Metabolism PowerPoint Lecture Slides prepared by Vince Austin, University of Kentucky Enzymes and Metabolism Human Anatomy & Physiology, Sixth Edition Elaine N. Marieb 1 Protein Macromolecules composed of combinations

More information

MBioS 303 Recitation Introductory Biochemistry, Summer 2008 Practice Problem Set #7: General Metabolism Concepts, Glycolysis and the TCA Cycle

MBioS 303 Recitation Introductory Biochemistry, Summer 2008 Practice Problem Set #7: General Metabolism Concepts, Glycolysis and the TCA Cycle MBioS 303 Recitation Introductory Biochemistry, Summer 2008 Practice Problem Set #7: General Metabolism Concepts, Glycolysis and the TCA Cycle (1) Glucose 1-pohsphate is converted to fructose 6-phosphate

More information

Supplemental Information

Supplemental Information Electronic upplementary Material (EI) for rganic & Biomolecular Chemistry. This journal is The Royal ociety of Chemistry 2014 upplemental Information olid-phase ynthesis of Peptoid-like ligomers Containing

More information

Gentilucci, Amino Acids, Peptides, and Proteins. Peptides and proteins are polymers of amino acids linked together by amide bonds CH 3

Gentilucci, Amino Acids, Peptides, and Proteins. Peptides and proteins are polymers of amino acids linked together by amide bonds CH 3 Amino Acids Peptides and proteins are polymers of amino acids linked together by amide bonds Aliphatic Side-Chain Amino Acids - - H CH glycine alanine 3 proline valine CH CH 3 - leucine - isoleucine CH

More information

Amylase: a sample enzyme

Amylase: a sample enzyme Amylase: a sample enzyme Objectives: After completion of this laboratory exercise you will be able to: 1. Explain the importance of enzymes in biology. 2. Explain the basic properties of an enzyme as a

More information

Page 8/6: The cell. Where to start: Proteins (control a cell) (start/end products)

Page 8/6: The cell. Where to start: Proteins (control a cell) (start/end products) Page 8/6: The cell Where to start: Proteins (control a cell) (start/end products) Page 11/10: Structural hierarchy Proteins Phenotype of organism 3 Dimensional structure Function by interaction THE PROTEIN

More information